matplotlib

Antoine De Pauw wrote:
> Thanks Jeff,
> 
> In fact my points are arranged in three unsorted arrays, with a simple scheme (thats why I couldn't plot them with imshow and others)
> 
> arrays:
> 
> [lat][lon][val]
> [-10][ 17][0.3]
> [ 37][ 23][3.7]
>  ...  ...  ...
> 
> and so for many rows...
> 
> what I have to do is looping through my arrays like that
> 
> while i < rowcount:
>     plot_to_map(lat[i],lon[i],val[i])
> 
> it is evidently an idea of how it could be done easily but my knowledge of these libraries is too weak for me to figure out how to do it
> 
> my data comes from huge binary files but is extremely simple, so it would be really easy for anyone to help me as the problem itself is how to put unsorted points on the map with latitude and longitude coordinates
> 

Antoine:  You haven't said if your data forms a rectangular array.  If 
so, you can build a 2-d array from the input file and plot it with 
imshow.  If not, you can still plug the elements into a 2-d masked 
array, leaving the missing pixels masked.  You say the points are 
'unsorted', does that mean they are randomly distributed and do not form 
a rectangular grid?

It would really be much easier to help if you gave us more information, 
such as how the data is structured, what the pixel footprint is, etc. 
Perhaps you could post the binary file on an ftp site somewhere with 
code to read it.

Also, please hit 'reply all' when replying, so the matplotlib users 
mailing list is CC'ed.

-Jeff
>> Antoine De Pauw wrote:
>>> Sir,
>>>
>>> I'm sorry, as english is not my mothertongue and it is sometimes difficult to be understandable.
>>>
>>> All is in the script I gave to you initially, except the point drawing code which would be useless as it is proven not to work (I dont know the method to do it).
>>>
>>> What I have is a map, and a set of pixels I have to put on it with geographic coordinates.
>>>
>>> I cannot find the right method to put colour pixels on the map, that's the problem.
>>>
>>> I have that map in miller projection, and three arrays containing respectively latitude, longitude and satellite measured value.
>>>
>>> What I need to obtain is something approximately like this: http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703_00_lr.gif but with the basemap toolkit.
>>>
>>> So, my question is: how could I do to plot a coloured pixel at coordinates lat:lon on that map? If I have just the method to project a geographic coordinate on the map and put a coloured pixel at the right place, all is done and I just have to loop my arrays... Also, I would have to implement some antialiasing on the map.
>>>   
>> Antoine:
>>
>> Are the pixels arranged on a regular grid - or are they randomly 
>> distributed?  If they are on a grid, it's easy (using pcolor or imshow). 
>>
>> If you could send me your data I may be able to get you started.
>>
>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>
>>
>> -Jeff
>>> If this is not possible to do it in a simple and explainable way, please tell me and I'll continue using matlab or searching for the bit of code which will save me
>>>
>>> Anyway, I have to thank you for your interest to help me..
>>>
>>> Many thanks,
>>>
>>> Antoine De Pauw
>>>
>>>   
>>>> Antoine De Pauw wrote:
>>>>     
>>>>> Hi, and thanks for the answer
>>>>>
>>>>> In fact, what I do is reading a binary file to obtain 3 arrays (Lat,Lon,Val) describing geographic points which are associated by index (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>>>>
>>>>> What I need to do is to plot some points on the map (miller projection for most) based on latitude and longitude, to obtain a colour map (points are unordered, it is from IASI satellite computations)
>>>>>
>>>>> I'm able to create a map, draw simple things on it, etc but the problem I have is any method I try for plotting points is failing, either pcolor, pcolormesh, imshow, etc.
>>>>>
>>>>> When I found your post on that mailing list, I figured out that you might have the experience and skills to easily explain to me how to manipulate these points and plot them on the map, as there's like no help on the web except standard examples...
>>>>>
>>>>> Please tell me if this is possible for you to give me some tips, or if it takes too much of your time just advice me some lectures
>>>>>
>>>>> Best regards,
>>>>>
>>>>> De Pauw Antoine
>>>>>   
>>>>>       
>>>> Antoine:  It would really help to have a script demonstrating your 
>>>> problem.  It sounds to me like you want to plot markers representing a 
>>>> set of points - for that you should use the scatter method.  pcolor, 
>>>> pcolormesh and friends are for plotting gridded data.
>>>>
>>>> -Jeff
>>>>     
>>>>>   
>>>>>       
>>>>>> De Pauw Antoine wrote:
>>>>>>     
>>>>>>         
>>>>>>> Dear sir,
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> I&#8217;m currently trying to improve our plotting tools here at the &#8220;Quantum 
>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre de 
>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>> solution, on an explanation from you here: 
>>>>>>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> It seems that you could help me find a solution, as I cannot plot any 
>>>>>>> points on maps.
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> Could you please tell me what I could do to plot data in a simple way, 
>>>>>>> assuming I have 3 unordered arrays containing respectively latitude, 
>>>>>>> longitude and values to plot?
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> Some tips would be very nice from you as any method I have tried so far 
>>>>>>> give me some errors&#8230;
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> Thank you very much in advance,
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> PS: I give you the code I&#8217;m using currently, missing the plotting part
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>
>>>>>>> from numpy import *
>>>>>>>
>>>>>>> from scipy.io.numpyio import fread
>>>>>>>
>>>>>>> import matplotlib.pyplot as plt
>>>>>>>
>>>>>>> import numpy as np
>>>>>>>
>>>>>>> import os
>>>>>>>
>>>>>>> import sys
>>>>>>>
>>>>>>> import array
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> fileName="c:/20080821.b56"
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> print('preparing map')   
>>>>>>>
>>>>>>> map = 
>>>>>>> Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>>>>>>>
>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>
>>>>>>> map.drawmapboundary()
>>>>>>>
>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>
>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>
>>>>>>> print('reading binary data')
>>>>>>>
>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>
>>>>>>> Lat=zeros(nbreligne)
>>>>>>>
>>>>>>> Lon=zeros(nbreligne)
>>>>>>>
>>>>>>> Val=zeros(nbreligne)
>>>>>>>
>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>
>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>
>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>
>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>
>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>
>>>>>>> i=0
>>>>>>>
>>>>>>> while i < nbreligne:
>>>>>>>
>>>>>>>     if(Lon[i]>180):
>>>>>>>
>>>>>>>         print(Lon[i])
>>>>>>>
>>>>>>>         Lon[i]-=360
>>>>>>>
>>>>>>>         print(Lon[i])
>>>>>>>
>>>>>>>     i+=1
>>>>>>>
>>>>>>> print('plotting data')
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> #plotting code comes here
>>>>>>>       
>>>>>>>           
>>>>>> Antoine:  If you send me a self-contained script that produces the 
>>>>>> problem you see, I can help you debug it.  As it stands now, I have very 
>>>>>> little to work with - it could be your plotting commands, or it could be 
>>>>>> your data.
>>>>>>
>>>>>> -Jeff
>>>>>>     
>>>>>>         
>>>>>>>  
>>>>>>>
>>>>>>> print('saving map')       
>>>>>>>
>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>
>>>>>>> print('done')
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> *Antoine De Pauw*
>>>>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and 
>>>>>>> photophysics laboratory
>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>>       
>>>>>>>           
>>>>>> -- 
>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>
>>>>>>
>>>>>>     
>>>>>>         
>>>>>   
>>>>>       
>>>> -- 
>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>
>>>>
>>>>
>>>>     
>>>
>>>   
>>
>> -- 
>> Jeffrey S. Whitaker         Phone : (303)497-6313
>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>> 325 Broadway                Boulder, CO, USA 80305-3328
>>
>>
>>
> 
> 


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

in fact the points are not in a rectangular array and pixels are missing, like you said

I'll put the code and binary file online tomorrow as I have not access to it today, but reading it is not the problem

when read, the values are in three arrays of same size, which I will have to convert to a 2D masked array... we'll see tomorrow if I have succeeded

many thanks

>Antoine De Pauw wrote:
>> Thanks Jeff,
>> 
>> In fact my points are arranged in three unsorted arrays, with a simple scheme (thats why I couldn't plot them with imshow and others)
>> 
>> arrays:
>> 
>> [lat][lon][val]
>> [-10][ 17][0.3]
>> [ 37][ 23][3.7]
>>  ...  ...  ...
>> 
>> and so for many rows...
>> 
>> what I have to do is looping through my arrays like that
>> 
>> while i < rowcount:
>>     plot_to_map(lat[i],lon[i],val[i])
>> 
>> it is evidently an idea of how it could be done easily but my knowledge of these libraries is too weak for me to figure out how to do it
>> 
>> my data comes from huge binary files but is extremely simple, so it would be really easy for anyone to help me as the problem itself is how to put unsorted points on the map with latitude and longitude coordinates
>> 
>
>Antoine:  You haven't said if your data forms a rectangular array.  If 
>so, you can build a 2-d array from the input file and plot it with 
>imshow.  If not, you can still plug the elements into a 2-d masked 
>array, leaving the missing pixels masked.  You say the points are 
>'unsorted', does that mean they are randomly distributed and do not form 
>a rectangular grid?
>
>It would really be much easier to help if you gave us more information, 
>such as how the data is structured, what the pixel footprint is, etc. 
>Perhaps you could post the binary file on an ftp site somewhere with 
>code to read it.
>
>Also, please hit 'reply all' when replying, so the matplotlib users 
>mailing list is CC'ed.
>
>-Jeff
>>> Antoine De Pauw wrote:
>>>> Sir,
>>>>
>>>> I'm sorry, as english is not my mothertongue and it is sometimes difficult to be understandable.
>>>>
>>>> All is in the script I gave to you initially, except the point drawing code which would be useless as it is proven not to work (I dont know the method to do it).
>>>>
>>>> What I have is a map, and a set of pixels I have to put on it with geographic coordinates.
>>>>
>>>> I cannot find the right method to put colour pixels on the map, that's the problem.
>>>>
>>>> I have that map in miller projection, and three arrays containing respectively latitude, longitude and satellite measured value.
>>>>
>>>> What I need to obtain is something approximately like this: http://wwwoma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703_00_lr.gif but with the basemap toolkit.
>>>>
>>>> So, my question is: how could I do to plot a coloured pixel at coordinates lat:lon on that map? If I have just the method to project a geographic coordinate on the map and put a coloured pixel at the right place, all is done and I just have to loop my arrays... Also, I would have to implement some antialiasing on the map.
>>>>   
>>> Antoine:
>>>
>>> Are the pixels arranged on a regular grid - or are they randomly 
>>> distributed?  If they are on a grid, it's easy (using pcolor or imshow) 
>>>
>>> If you could send me your data I may be able to get you started.
>>>
>>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>>
>>>
>>> -Jeff
>>>> If this is not possible to do it in a simple and explainable way, please tell me and I'll continue using matlab or searching for the bit of code which will save me
>>>>
>>>> Anyway, I have to thank you for your interest to help me..
>>>>
>>>> Many thanks,
>>>>
>>>> Antoine De Pauw
>>>>
>>>>   
>>>>> Antoine De Pauw wrote:
>>>>>     
>>>>>> Hi, and thanks for the answer
>>>>>>
>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays (Lat,Lon,Val) describing geographic points which are associated by index (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>>>>>
>>>>>> What I need to do is to plot some points on the map (miller projection for most) based on latitude and longitude, to obtain a colour map (points are unordered, it is from IASI satellite computations)
>>>>>>
>>>>>> I'm able to create a map, draw simple things on it, etc but the problem I have is any method I try for plotting points is failing, either pcolor, pcolormesh, imshow, etc.
>>>>>>
>>>>>> When I found your post on that mailing list, I figured out that you might have the experience and skills to easily explain to me how to manipulate these points and plot them on the map, as there's like no help on the web except standard examples...
>>>>>>
>>>>>> Please tell me if this is possible for you to give me some tips, or if it takes too much of your time just advice me some lectures
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> De Pauw Antoine
>>>>>>   
>>>>>>       
>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>> problem.  It sounds to me like you want to plot markers representing a 
>>>>> set of points - for that you should use the scatter method.  pcolor, 
>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>
>>>>> -Jeff
>>>>>     
>>>>>>   
>>>>>>       
>>>>>>> De Pauw Antoine wrote:
>>>>>>>     
>>>>>>>         
>>>>>>>> Dear sir,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at the &#8220;Quantum 
>>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre de 
>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>> solution, on an explanation from you here: 
>>>>>>>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> It seems that you could help me find a solution, as I cannot plot any 
>>>>>>>> points on maps.
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Could you please tell me what I could do to plot data in a simple way, 
>>>>>>>> assuming I have 3 unordered arrays containing respectively latitude, 
>>>>>>>> longitude and values to plot?
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Some tips would be very nice from you as any method I have tried so far 
>>>>>>>> give me some errors&#8230;
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Thank you very much in advance,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the plotting part
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>
>>>>>>>> from numpy import *
>>>>>>>>
>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>
>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>
>>>>>>>> import numpy as np
>>>>>>>>
>>>>>>>> import os
>>>>>>>>
>>>>>>>> import sys
>>>>>>>>
>>>>>>>> import array
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> print('preparing map')   
>>>>>>>>
>>>>>>>> map = 
>>>>>>>> Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>>>>>>>>
>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>
>>>>>>>> map.drawmapboundary()
>>>>>>>>
>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>
>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>
>>>>>>>> print('reading binary data')
>>>>>>>>
>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>
>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>
>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>
>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>
>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>
>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>
>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>
>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>
>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>
>>>>>>>> i=0
>>>>>>>>
>>>>>>>> while i < nbreligne:
>>>>>>>>
>>>>>>>>     if(Lon[i]>180):
>>>>>>>>
>>>>>>>>         print(Lon[i])
>>>>>>>>
>>>>>>>>         Lon[i]-=360
>>>>>>>>
>>>>>>>>         print(Lon[i])
>>>>>>>>
>>>>>>>>     i+=1
>>>>>>>>
>>>>>>>> print('plotting data')
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> #plotting code comes here
>>>>>>>>       
>>>>>>>>           
>>>>>>> Antoine:  If you send me a self-contained script that produces the 
>>>>>>> problem you see, I can help you debug it.  As it stands now, I have very 
>>>>>>> little to work with - it could be your plotting commands, or it could be 
>>>>>>> your data.
>>>>>>>
>>>>>>> -Jeff
>>>>>>>     
>>>>>>>         
>>>>>>>>  
>>>>>>>>
>>>>>>>> print('saving map')       
>>>>>>>>
>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>
>>>>>>>> print('done')
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> *Antoine De Pauw*
>>>>>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and 
>>>>>>>> photophysics laboratory
>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>>       
>>>>>>>>           
>>>>>>> -- 
>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>         
>>>>>>   
>>>>>>       
>>>>> -- 
>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>
>>>>>
>>>>>
>>>>>     
>>>>
>>>>   
>>>
>>> -- 
>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>
>>>
>>>
>> 
>> 
>
>
>-- 
>Jeffrey S. Whitaker         Phone  : (303)497-6313
>Meteorologist               FAX    : (303)497-6449
>NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>325 Broadway                Office : Skaggs Research Cntr 1D-113
>Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>
>

Hi Jeff,

I have put the code online with a sample of the data here:

http://snipplr.com/view/8307/map-plotting-python-code-temporary/

I hope you'll be able to give me some advice as it is quite difficult for
someone new in python and scientific computation

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB

-----Original Message-----
From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
Sent: mercredi 10 septembre 2008 16:45
To: Antoine De Pauw
Cc: Matplotlib Users
Subject: Re: Information request

Antoine De Pauw wrote:
> Thanks Jeff,
> 
> In fact my points are arranged in three unsorted arrays, with a simple
scheme (thats why I couldn't plot them with imshow and others)
> 
> arrays:
> 
> [lat][lon][val]
> [-10][ 17][0.3]
> [ 37][ 23][3.7]
>  ...  ...  ...
> 
> and so for many rows...
> 
> what I have to do is looping through my arrays like that
> 
> while i < rowcount:
>     plot_to_map(lat[i],lon[i],val[i])
> 
> it is evidently an idea of how it could be done easily but my knowledge of
these libraries is too weak for me to figure out how to do it
> 
> my data comes from huge binary files but is extremely simple, so it would
be really easy for anyone to help me as the problem itself is how to put
unsorted points on the map with latitude and longitude coordinates
> 

Antoine:  You haven't said if your data forms a rectangular array.  If 
so, you can build a 2-d array from the input file and plot it with 
imshow.  If not, you can still plug the elements into a 2-d masked 
array, leaving the missing pixels masked.  You say the points are 
'unsorted', does that mean they are randomly distributed and do not form 
a rectangular grid?

It would really be much easier to help if you gave us more information, 
such as how the data is structured, what the pixel footprint is, etc. 
Perhaps you could post the binary file on an ftp site somewhere with 
code to read it.

Also, please hit 'reply all' when replying, so the matplotlib users 
mailing list is CC'ed.

-Jeff
>> Antoine De Pauw wrote:
>>> Sir,
>>>
>>> I'm sorry, as english is not my mothertongue and it is sometimes
difficult to be understandable.
>>>
>>> All is in the script I gave to you initially, except the point drawing
code which would be useless as it is proven not to work (I dont know the
method to do it).
>>>
>>> What I have is a map, and a set of pixels I have to put on it with
geographic coordinates.
>>>
>>> I cannot find the right method to put colour pixels on the map, that's
the problem.
>>>
>>> I have that map in miller projection, and three arrays containing
respectively latitude, longitude and satellite measured value.
>>>
>>> What I need to obtain is something approximately like this:
http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
_00_lr.gif but with the basemap toolkit.
>>>
>>> So, my question is: how could I do to plot a coloured pixel at
coordinates lat:lon on that map? If I have just the method to project a
geographic coordinate on the map and put a coloured pixel at the right
place, all is done and I just have to loop my arrays... Also, I would have
to implement some antialiasing on the map.
>>>   
>> Antoine:
>>
>> Are the pixels arranged on a regular grid - or are they randomly 
>> distributed?  If they are on a grid, it's easy (using pcolor or imshow). 
>>
>> If you could send me your data I may be able to get you started.
>>
>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>
>>
>> -Jeff
>>> If this is not possible to do it in a simple and explainable way, please
tell me and I'll continue using matlab or searching for the bit of code
which will save me
>>>
>>> Anyway, I have to thank you for your interest to help me..
>>>
>>> Many thanks,
>>>
>>> Antoine De Pauw
>>>
>>>   
>>>> Antoine De Pauw wrote:
>>>>     
>>>>> Hi, and thanks for the answer
>>>>>
>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
(Lat,Lon,Val) describing geographic points which are associated by index
(like point 1 is Lat[0]:Lon[0] with value Val[0])
>>>>>
>>>>> What I need to do is to plot some points on the map (miller projection
for most) based on latitude and longitude, to obtain a colour map (points
are unordered, it is from IASI satellite computations)
>>>>>
>>>>> I'm able to create a map, draw simple things on it, etc but the
problem I have is any method I try for plotting points is failing, either
pcolor, pcolormesh, imshow, etc.
>>>>>
>>>>> When I found your post on that mailing list, I figured out that you
might have the experience and skills to easily explain to me how to
manipulate these points and plot them on the map, as there's like no help on
the web except standard examples...
>>>>>
>>>>> Please tell me if this is possible for you to give me some tips, or if
it takes too much of your time just advice me some lectures
>>>>>
>>>>> Best regards,
>>>>>
>>>>> De Pauw Antoine
>>>>>   
>>>>>       
>>>> Antoine:  It would really help to have a script demonstrating your 
>>>> problem.  It sounds to me like you want to plot markers representing a 
>>>> set of points - for that you should use the scatter method.  pcolor, 
>>>> pcolormesh and friends are for plotting gridded data.
>>>>
>>>> -Jeff
>>>>     
>>>>>   
>>>>>       
>>>>>> De Pauw Antoine wrote:
>>>>>>     
>>>>>>         
>>>>>>> Dear sir,
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> I&#8217;m currently trying to improve our plotting tools here at the
&#8220;Quantum 
>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre de

>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>> solution, on an explanation from you here: 
>>>>>>>
http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> It seems that you could help me find a solution, as I cannot plot
any 
>>>>>>> points on maps.
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> Could you please tell me what I could do to plot data in a simple
way, 
>>>>>>> assuming I have 3 unordered arrays containing respectively latitude,

>>>>>>> longitude and values to plot?
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> Some tips would be very nice from you as any method I have tried so
far 
>>>>>>> give me some errors&#8230;
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> Thank you very much in advance,
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
plotting part
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>
>>>>>>> from numpy import *
>>>>>>>
>>>>>>> from scipy.io.numpyio import fread
>>>>>>>
>>>>>>> import matplotlib.pyplot as plt
>>>>>>>
>>>>>>> import numpy as np
>>>>>>>
>>>>>>> import os
>>>>>>>
>>>>>>> import sys
>>>>>>>
>>>>>>> import array
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> fileName="c:/20080821.b56"
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> print('preparing map')   
>>>>>>>
>>>>>>> map = 
>>>>>>>
Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>>>>>>>
>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>
>>>>>>> map.drawmapboundary()
>>>>>>>
>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>
>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>
>>>>>>> print('reading binary data')
>>>>>>>
>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>
>>>>>>> Lat=zeros(nbreligne)
>>>>>>>
>>>>>>> Lon=zeros(nbreligne)
>>>>>>>
>>>>>>> Val=zeros(nbreligne)
>>>>>>>
>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>
>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>
>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>
>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>
>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>
>>>>>>> i=0
>>>>>>>
>>>>>>> while i < nbreligne:
>>>>>>>
>>>>>>>     if(Lon[i]>180):
>>>>>>>
>>>>>>>         print(Lon[i])
>>>>>>>
>>>>>>>         Lon[i]-=360
>>>>>>>
>>>>>>>         print(Lon[i])
>>>>>>>
>>>>>>>     i+=1
>>>>>>>
>>>>>>> print('plotting data')
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> #plotting code comes here
>>>>>>>       
>>>>>>>           
>>>>>> Antoine:  If you send me a self-contained script that produces the 
>>>>>> problem you see, I can help you debug it.  As it stands now, I have
very 
>>>>>> little to work with - it could be your plotting commands, or it could
be 
>>>>>> your data.
>>>>>>
>>>>>> -Jeff
>>>>>>     
>>>>>>         
>>>>>>>  
>>>>>>>
>>>>>>> print('saving map')       
>>>>>>>
>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>
>>>>>>> print('done')
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>> *Antoine De Pauw*
>>>>>>> Collaborateur de recherches, Informatique - Research collaborator,
IT
>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
and 
>>>>>>> photophysics laboratory
>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>
>>>>>>>  
>>>>>>>
>>>>>>>       
>>>>>>>           
>>>>>> -- 
>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>
>>>>>>
>>>>>>     
>>>>>>         
>>>>>   
>>>>>       
>>>> -- 
>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>
>>>>
>>>>
>>>>     
>>>
>>>   
>>
>> -- 
>> Jeffrey S. Whitaker         Phone : (303)497-6313
>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>> 325 Broadway                Boulder, CO, USA 80305-3328
>>
>>
>>
> 
> 


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

De Pauw Antoine wrote:
> Hi Jeff,
>
> I have put the code online with a sample of the data here:
>
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> I hope you'll be able to give me some advice as it is quite difficult for
> someone new in python and scientific computation
>   

Antoine:  How big are the pixels?  Is the text file lon,lat,data or 
lat,lon,data?

-Jeff
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
> Sent: mercredi 10 septembre 2008 16:45
> To: Antoine De Pauw
> Cc: Matplotlib Users
> Subject: Re: Information request
>
> Antoine De Pauw wrote:
>   
>> Thanks Jeff,
>>
>> In fact my points are arranged in three unsorted arrays, with a simple
>>     
> scheme (thats why I couldn't plot them with imshow and others)
>   
>> arrays:
>>
>> [lat][lon][val]
>> [-10][ 17][0.3]
>> [ 37][ 23][3.7]
>>  ...  ...  ...
>>
>> and so for many rows...
>>
>> what I have to do is looping through my arrays like that
>>
>> while i < rowcount:
>>     plot_to_map(lat[i],lon[i],val[i])
>>
>> it is evidently an idea of how it could be done easily but my knowledge of
>>     
> these libraries is too weak for me to figure out how to do it
>   
>> my data comes from huge binary files but is extremely simple, so it would
>>     
> be really easy for anyone to help me as the problem itself is how to put
> unsorted points on the map with latitude and longitude coordinates
>   
>
> Antoine:  You haven't said if your data forms a rectangular array.  If 
> so, you can build a 2-d array from the input file and plot it with 
> imshow.  If not, you can still plug the elements into a 2-d masked 
> array, leaving the missing pixels masked.  You say the points are 
> 'unsorted', does that mean they are randomly distributed and do not form 
> a rectangular grid?
>
> It would really be much easier to help if you gave us more information, 
> such as how the data is structured, what the pixel footprint is, etc. 
> Perhaps you could post the binary file on an ftp site somewhere with 
> code to read it.
>
> Also, please hit 'reply all' when replying, so the matplotlib users 
> mailing list is CC'ed.
>
> -Jeff
>   
>>> Antoine De Pauw wrote:
>>>       
>>>> Sir,
>>>>
>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>         
> difficult to be understandable.
>   
>>>> All is in the script I gave to you initially, except the point drawing
>>>>         
> code which would be useless as it is proven not to work (I dont know the
> method to do it).
>   
>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>         
> geographic coordinates.
>   
>>>> I cannot find the right method to put colour pixels on the map, that's
>>>>         
> the problem.
>   
>>>> I have that map in miller projection, and three arrays containing
>>>>         
> respectively latitude, longitude and satellite measured value.
>   
>>>> What I need to obtain is something approximately like this:
>>>>         
> http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
> _00_lr.gif but with the basemap toolkit.
>   
>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>         
> coordinates lat:lon on that map? If I have just the method to project a
> geographic coordinate on the map and put a coloured pixel at the right
> place, all is done and I just have to loop my arrays... Also, I would have
> to implement some antialiasing on the map.
>   
>>>>   
>>>>         
>>> Antoine:
>>>
>>> Are the pixels arranged on a regular grid - or are they randomly 
>>> distributed?  If they are on a grid, it's easy (using pcolor or imshow). 
>>>
>>> If you could send me your data I may be able to get you started.
>>>
>>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>>
>>>
>>> -Jeff
>>>       
>>>> If this is not possible to do it in a simple and explainable way, please
>>>>         
> tell me and I'll continue using matlab or searching for the bit of code
> which will save me
>   
>>>> Anyway, I have to thank you for your interest to help me..
>>>>
>>>> Many thanks,
>>>>
>>>> Antoine De Pauw
>>>>
>>>>   
>>>>         
>>>>> Antoine De Pauw wrote:
>>>>>     
>>>>>           
>>>>>> Hi, and thanks for the answer
>>>>>>
>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>             
> (Lat,Lon,Val) describing geographic points which are associated by index
> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>   
>>>>>> What I need to do is to plot some points on the map (miller projection
>>>>>>             
> for most) based on latitude and longitude, to obtain a colour map (points
> are unordered, it is from IASI satellite computations)
>   
>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>             
> problem I have is any method I try for plotting points is failing, either
> pcolor, pcolormesh, imshow, etc.
>   
>>>>>> When I found your post on that mailing list, I figured out that you
>>>>>>             
> might have the experience and skills to easily explain to me how to
> manipulate these points and plot them on the map, as there's like no help on
> the web except standard examples...
>   
>>>>>> Please tell me if this is possible for you to give me some tips, or if
>>>>>>             
> it takes too much of your time just advice me some lectures
>   
>>>>>> Best regards,
>>>>>>
>>>>>> De Pauw Antoine
>>>>>>   
>>>>>>       
>>>>>>             
>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>> problem.  It sounds to me like you want to plot markers representing a 
>>>>> set of points - for that you should use the scatter method.  pcolor, 
>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>
>>>>> -Jeff
>>>>>     
>>>>>           
>>>>>>   
>>>>>>       
>>>>>>             
>>>>>>> De Pauw Antoine wrote:
>>>>>>>     
>>>>>>>         
>>>>>>>               
>>>>>>>> Dear sir,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at the
>>>>>>>>                 
> &#8220;Quantum 
>   
>>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre de
>>>>>>>>                 
>
>   
>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>
>>>>>>>>                 
> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>   
>>>>>>>>  
>>>>>>>>
>>>>>>>> It seems that you could help me find a solution, as I cannot plot
>>>>>>>>                 
> any 
>   
>>>>>>>> points on maps.
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Could you please tell me what I could do to plot data in a simple
>>>>>>>>                 
> way, 
>   
>>>>>>>> assuming I have 3 unordered arrays containing respectively latitude,
>>>>>>>>                 
>
>   
>>>>>>>> longitude and values to plot?
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Some tips would be very nice from you as any method I have tried so
>>>>>>>>                 
> far 
>   
>>>>>>>> give me some errors&#8230;
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Thank you very much in advance,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>                 
> plotting part
>   
>>>>>>>>  
>>>>>>>>
>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>
>>>>>>>> from numpy import *
>>>>>>>>
>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>
>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>
>>>>>>>> import numpy as np
>>>>>>>>
>>>>>>>> import os
>>>>>>>>
>>>>>>>> import sys
>>>>>>>>
>>>>>>>> import array
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> print('preparing map')   
>>>>>>>>
>>>>>>>> map = 
>>>>>>>>
>>>>>>>>                 
> Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>
>>>>>>>> map.drawmapboundary()
>>>>>>>>
>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>
>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>
>>>>>>>> print('reading binary data')
>>>>>>>>
>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>
>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>
>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>
>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>
>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>
>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>
>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>
>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>
>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>
>>>>>>>> i=0
>>>>>>>>
>>>>>>>> while i < nbreligne:
>>>>>>>>
>>>>>>>>     if(Lon[i]>180):
>>>>>>>>
>>>>>>>>         print(Lon[i])
>>>>>>>>
>>>>>>>>         Lon[i]-=360
>>>>>>>>
>>>>>>>>         print(Lon[i])
>>>>>>>>
>>>>>>>>     i+=1
>>>>>>>>
>>>>>>>> print('plotting data')
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> #plotting code comes here
>>>>>>>>       
>>>>>>>>           
>>>>>>>>                 
>>>>>>> Antoine:  If you send me a self-contained script that produces the 
>>>>>>> problem you see, I can help you debug it.  As it stands now, I have
>>>>>>>               
> very 
>   
>>>>>>> little to work with - it could be your plotting commands, or it could
>>>>>>>               
> be 
>   
>>>>>>> your data.
>>>>>>>
>>>>>>> -Jeff
>>>>>>>     
>>>>>>>         
>>>>>>>               
>>>>>>>>  
>>>>>>>>
>>>>>>>> print('saving map')       
>>>>>>>>
>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>
>>>>>>>> print('done')
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> *Antoine De Pauw*
>>>>>>>> Collaborateur de recherches, Informatique - Research collaborator,
>>>>>>>>                 
> IT
>   
>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
>>>>>>>>                 
> and 
>   
>>>>>>>> photophysics laboratory
>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>>       
>>>>>>>>           
>>>>>>>>                 
>>>>>>> -- 
>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>         
>>>>>>>               
>>>>>>   
>>>>>>       
>>>>>>             
>>>>> -- 
>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>
>>>>>
>>>>>
>>>>>     
>>>>>           
>>>>   
>>>>         
>>> -- 
>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>
>>>
>>>
>>>       
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

De Pauw Antoine wrote:
> Hi Jeff,
>
> I have put the code online with a sample of the data here:
>
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> I hope you'll be able to give me some advice as it is quite difficult for
> someone new in python and scientific computation
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine: I may have the size of the pixels wrong, and lat/lon 
transposed, but this is the general idea:

from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import numpy as np
lats = []; lons = []; data = []
for line in open('pixels.dat'):
    linesplit = line.split(',')
    lons.append(float(linesplit[1]))
    lats.append(float(linesplit[0]))
    data.append(float(linesplit[2]))
map = 
Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
                          
urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
x,y = map(lons,lats)
plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
plt.colorbar(shrink=0.6)
map.drawcoastlines()
plt.show()

-Jeff

> -----Original Message-----
> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
> Sent: mercredi 10 septembre 2008 16:45
> To: Antoine De Pauw
> Cc: Matplotlib Users
> Subject: Re: Information request
>
> Antoine De Pauw wrote:
>   
>> Thanks Jeff,
>>
>> In fact my points are arranged in three unsorted arrays, with a simple
>>     
> scheme (thats why I couldn't plot them with imshow and others)
>   
>> arrays:
>>
>> [lat][lon][val]
>> [-10][ 17][0.3]
>> [ 37][ 23][3.7]
>>  ...  ...  ...
>>
>> and so for many rows...
>>
>> what I have to do is looping through my arrays like that
>>
>> while i < rowcount:
>>     plot_to_map(lat[i],lon[i],val[i])
>>
>> it is evidently an idea of how it could be done easily but my knowledge of
>>     
> these libraries is too weak for me to figure out how to do it
>   
>> my data comes from huge binary files but is extremely simple, so it would
>>     
> be really easy for anyone to help me as the problem itself is how to put
> unsorted points on the map with latitude and longitude coordinates
>   
>
> Antoine:  You haven't said if your data forms a rectangular array.  If 
> so, you can build a 2-d array from the input file and plot it with 
> imshow.  If not, you can still plug the elements into a 2-d masked 
> array, leaving the missing pixels masked.  You say the points are 
> 'unsorted', does that mean they are randomly distributed and do not form 
> a rectangular grid?
>
> It would really be much easier to help if you gave us more information, 
> such as how the data is structured, what the pixel footprint is, etc. 
> Perhaps you could post the binary file on an ftp site somewhere with 
> code to read it.
>
> Also, please hit 'reply all' when replying, so the matplotlib users 
> mailing list is CC'ed.
>
> -Jeff
>   
>>> Antoine De Pauw wrote:
>>>       
>>>> Sir,
>>>>
>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>         
> difficult to be understandable.
>   
>>>> All is in the script I gave to you initially, except the point drawing
>>>>         
> code which would be useless as it is proven not to work (I dont know the
> method to do it).
>   
>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>         
> geographic coordinates.
>   
>>>> I cannot find the right method to put colour pixels on the map, that's
>>>>         
> the problem.
>   
>>>> I have that map in miller projection, and three arrays containing
>>>>         
> respectively latitude, longitude and satellite measured value.
>   
>>>> What I need to obtain is something approximately like this:
>>>>         
> http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
> _00_lr.gif but with the basemap toolkit.
>   
>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>         
> coordinates lat:lon on that map? If I have just the method to project a
> geographic coordinate on the map and put a coloured pixel at the right
> place, all is done and I just have to loop my arrays... Also, I would have
> to implement some antialiasing on the map.
>   
>>>>   
>>>>         
>>> Antoine:
>>>
>>> Are the pixels arranged on a regular grid - or are they randomly 
>>> distributed?  If they are on a grid, it's easy (using pcolor or imshow). 
>>>
>>> If you could send me your data I may be able to get you started.
>>>
>>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>>
>>>
>>> -Jeff
>>>       
>>>> If this is not possible to do it in a simple and explainable way, please
>>>>         
> tell me and I'll continue using matlab or searching for the bit of code
> which will save me
>   
>>>> Anyway, I have to thank you for your interest to help me..
>>>>
>>>> Many thanks,
>>>>
>>>> Antoine De Pauw
>>>>
>>>>   
>>>>         
>>>>> Antoine De Pauw wrote:
>>>>>     
>>>>>           
>>>>>> Hi, and thanks for the answer
>>>>>>
>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>             
> (Lat,Lon,Val) describing geographic points which are associated by index
> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>   
>>>>>> What I need to do is to plot some points on the map (miller projection
>>>>>>             
> for most) based on latitude and longitude, to obtain a colour map (points
> are unordered, it is from IASI satellite computations)
>   
>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>             
> problem I have is any method I try for plotting points is failing, either
> pcolor, pcolormesh, imshow, etc.
>   
>>>>>> When I found your post on that mailing list, I figured out that you
>>>>>>             
> might have the experience and skills to easily explain to me how to
> manipulate these points and plot them on the map, as there's like no help on
> the web except standard examples...
>   
>>>>>> Please tell me if this is possible for you to give me some tips, or if
>>>>>>             
> it takes too much of your time just advice me some lectures
>   
>>>>>> Best regards,
>>>>>>
>>>>>> De Pauw Antoine
>>>>>>   
>>>>>>       
>>>>>>             
>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>> problem.  It sounds to me like you want to plot markers representing a 
>>>>> set of points - for that you should use the scatter method.  pcolor, 
>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>
>>>>> -Jeff
>>>>>     
>>>>>           
>>>>>>   
>>>>>>       
>>>>>>             
>>>>>>> De Pauw Antoine wrote:
>>>>>>>     
>>>>>>>         
>>>>>>>               
>>>>>>>> Dear sir,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at the
>>>>>>>>                 
> &#8220;Quantum 
>   
>>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre de
>>>>>>>>                 
>
>   
>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>
>>>>>>>>                 
> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>   
>>>>>>>>  
>>>>>>>>
>>>>>>>> It seems that you could help me find a solution, as I cannot plot
>>>>>>>>                 
> any 
>   
>>>>>>>> points on maps.
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Could you please tell me what I could do to plot data in a simple
>>>>>>>>                 
> way, 
>   
>>>>>>>> assuming I have 3 unordered arrays containing respectively latitude,
>>>>>>>>                 
>
>   
>>>>>>>> longitude and values to plot?
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Some tips would be very nice from you as any method I have tried so
>>>>>>>>                 
> far 
>   
>>>>>>>> give me some errors&#8230;
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Thank you very much in advance,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>                 
> plotting part
>   
>>>>>>>>  
>>>>>>>>
>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>
>>>>>>>> from numpy import *
>>>>>>>>
>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>
>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>
>>>>>>>> import numpy as np
>>>>>>>>
>>>>>>>> import os
>>>>>>>>
>>>>>>>> import sys
>>>>>>>>
>>>>>>>> import array
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> print('preparing map')   
>>>>>>>>
>>>>>>>> map = 
>>>>>>>>
>>>>>>>>                 
> Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>
>>>>>>>> map.drawmapboundary()
>>>>>>>>
>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>
>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>
>>>>>>>> print('reading binary data')
>>>>>>>>
>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>
>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>
>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>
>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>
>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>
>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>
>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>
>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>
>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>
>>>>>>>> i=0
>>>>>>>>
>>>>>>>> while i < nbreligne:
>>>>>>>>
>>>>>>>>     if(Lon[i]>180):
>>>>>>>>
>>>>>>>>         print(Lon[i])
>>>>>>>>
>>>>>>>>         Lon[i]-=360
>>>>>>>>
>>>>>>>>         print(Lon[i])
>>>>>>>>
>>>>>>>>     i+=1
>>>>>>>>
>>>>>>>> print('plotting data')
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> #plotting code comes here
>>>>>>>>       
>>>>>>>>           
>>>>>>>>                 
>>>>>>> Antoine:  If you send me a self-contained script that produces the 
>>>>>>> problem you see, I can help you debug it.  As it stands now, I have
>>>>>>>               
> very 
>   
>>>>>>> little to work with - it could be your plotting commands, or it could
>>>>>>>               
> be 
>   
>>>>>>> your data.
>>>>>>>
>>>>>>> -Jeff
>>>>>>>     
>>>>>>>         
>>>>>>>               
>>>>>>>>  
>>>>>>>>
>>>>>>>> print('saving map')       
>>>>>>>>
>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>
>>>>>>>> print('done')
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> *Antoine De Pauw*
>>>>>>>> Collaborateur de recherches, Informatique - Research collaborator,
>>>>>>>>                 
> IT
>   
>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
>>>>>>>>                 
> and 
>   
>>>>>>>> photophysics laboratory
>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>>       
>>>>>>>>           
>>>>>>>>                 
>>>>>>> -- 
>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>         
>>>>>>>               
>>>>>>   
>>>>>>       
>>>>>>             
>>>>> -- 
>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>
>>>>>
>>>>>
>>>>>     
>>>>>           
>>>>   
>>>>         
>>> -- 
>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>
>>>
>>>
>>>       
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Thanks Jeff,

This seems to work with csv file types, and I've been experimenting a bit
with it

However, when I try to implement this with my original code (with binary
files), I get an error like that one:

Traceback (most recent call last):
  File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module>
    x,y = map(Lon,Lat)
TypeError: 'numpy.ndarray' object is not callable

I think this is coming from the fact I use array objects to store values...
could you confirm it?

Also, I'll see if it is possible to invert color scale and mask everything
under a certain value

Thanks very much for your help!

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: jeudi 11 septembre 2008 14:10
To: De Pauw Antoine
Cc: 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Hi Jeff,
>
> I have put the code online with a sample of the data here:
>
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> I hope you'll be able to give me some advice as it is quite difficult for
> someone new in python and scientific computation
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine: I may have the size of the pixels wrong, and lat/lon 
transposed, but this is the general idea:

from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import numpy as np
lats = []; lons = []; data = []
for line in open('pixels.dat'):
    linesplit = line.split(',')
    lons.append(float(linesplit[1]))
    lats.append(float(linesplit[0]))
    data.append(float(linesplit[2]))
map = 
Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
                          
urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
x,y = map(lons,lats)
plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
plt.colorbar(shrink=0.6)
map.drawcoastlines()
plt.show()

-Jeff

> -----Original Message-----
> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
> Sent: mercredi 10 septembre 2008 16:45
> To: Antoine De Pauw
> Cc: Matplotlib Users
> Subject: Re: Information request
>
> Antoine De Pauw wrote:
>   
>> Thanks Jeff,
>>
>> In fact my points are arranged in three unsorted arrays, with a simple
>>     
> scheme (thats why I couldn't plot them with imshow and others)
>   
>> arrays:
>>
>> [lat][lon][val]
>> [-10][ 17][0.3]
>> [ 37][ 23][3.7]
>>  ...  ...  ...
>>
>> and so for many rows...
>>
>> what I have to do is looping through my arrays like that
>>
>> while i < rowcount:
>>     plot_to_map(lat[i],lon[i],val[i])
>>
>> it is evidently an idea of how it could be done easily but my knowledge
of
>>     
> these libraries is too weak for me to figure out how to do it
>   
>> my data comes from huge binary files but is extremely simple, so it would
>>     
> be really easy for anyone to help me as the problem itself is how to put
> unsorted points on the map with latitude and longitude coordinates
>   
>
> Antoine:  You haven't said if your data forms a rectangular array.  If 
> so, you can build a 2-d array from the input file and plot it with 
> imshow.  If not, you can still plug the elements into a 2-d masked 
> array, leaving the missing pixels masked.  You say the points are 
> 'unsorted', does that mean they are randomly distributed and do not form 
> a rectangular grid?
>
> It would really be much easier to help if you gave us more information, 
> such as how the data is structured, what the pixel footprint is, etc. 
> Perhaps you could post the binary file on an ftp site somewhere with 
> code to read it.
>
> Also, please hit 'reply all' when replying, so the matplotlib users 
> mailing list is CC'ed.
>
> -Jeff
>   
>>> Antoine De Pauw wrote:
>>>       
>>>> Sir,
>>>>
>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>         
> difficult to be understandable.
>   
>>>> All is in the script I gave to you initially, except the point drawing
>>>>         
> code which would be useless as it is proven not to work (I dont know the
> method to do it).
>   
>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>         
> geographic coordinates.
>   
>>>> I cannot find the right method to put colour pixels on the map, that's
>>>>         
> the problem.
>   
>>>> I have that map in miller projection, and three arrays containing
>>>>         
> respectively latitude, longitude and satellite measured value.
>   
>>>> What I need to obtain is something approximately like this:
>>>>         
>
http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
> _00_lr.gif but with the basemap toolkit.
>   
>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>         
> coordinates lat:lon on that map? If I have just the method to project a
> geographic coordinate on the map and put a coloured pixel at the right
> place, all is done and I just have to loop my arrays... Also, I would have
> to implement some antialiasing on the map.
>   
>>>>   
>>>>         
>>> Antoine:
>>>
>>> Are the pixels arranged on a regular grid - or are they randomly 
>>> distributed?  If they are on a grid, it's easy (using pcolor or imshow).

>>>
>>> If you could send me your data I may be able to get you started.
>>>
>>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>>
>>>
>>> -Jeff
>>>       
>>>> If this is not possible to do it in a simple and explainable way,
please
>>>>         
> tell me and I'll continue using matlab or searching for the bit of code
> which will save me
>   
>>>> Anyway, I have to thank you for your interest to help me..
>>>>
>>>> Many thanks,
>>>>
>>>> Antoine De Pauw
>>>>
>>>>   
>>>>         
>>>>> Antoine De Pauw wrote:
>>>>>     
>>>>>           
>>>>>> Hi, and thanks for the answer
>>>>>>
>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>             
> (Lat,Lon,Val) describing geographic points which are associated by index
> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>   
>>>>>> What I need to do is to plot some points on the map (miller
projection
>>>>>>             
> for most) based on latitude and longitude, to obtain a colour map (points
> are unordered, it is from IASI satellite computations)
>   
>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>             
> problem I have is any method I try for plotting points is failing, either
> pcolor, pcolormesh, imshow, etc.
>   
>>>>>> When I found your post on that mailing list, I figured out that you
>>>>>>             
> might have the experience and skills to easily explain to me how to
> manipulate these points and plot them on the map, as there's like no help
on
> the web except standard examples...
>   
>>>>>> Please tell me if this is possible for you to give me some tips, or
if
>>>>>>             
> it takes too much of your time just advice me some lectures
>   
>>>>>> Best regards,
>>>>>>
>>>>>> De Pauw Antoine
>>>>>>   
>>>>>>       
>>>>>>             
>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>> problem.  It sounds to me like you want to plot markers representing a

>>>>> set of points - for that you should use the scatter method.  pcolor, 
>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>
>>>>> -Jeff
>>>>>     
>>>>>           
>>>>>>   
>>>>>>       
>>>>>>             
>>>>>>> De Pauw Antoine wrote:
>>>>>>>     
>>>>>>>         
>>>>>>>               
>>>>>>>> Dear sir,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at
the
>>>>>>>>                 
> &#8220;Quantum 
>   
>>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre
de
>>>>>>>>                 
>
>   
>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>
>>>>>>>>                 
> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>   
>>>>>>>>  
>>>>>>>>
>>>>>>>> It seems that you could help me find a solution, as I cannot plot
>>>>>>>>                 
> any 
>   
>>>>>>>> points on maps.
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Could you please tell me what I could do to plot data in a simple
>>>>>>>>                 
> way, 
>   
>>>>>>>> assuming I have 3 unordered arrays containing respectively
latitude,
>>>>>>>>                 
>
>   
>>>>>>>> longitude and values to plot?
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Some tips would be very nice from you as any method I have tried so
>>>>>>>>                 
> far 
>   
>>>>>>>> give me some errors&#8230;
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Thank you very much in advance,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>                 
> plotting part
>   
>>>>>>>>  
>>>>>>>>
>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>
>>>>>>>> from numpy import *
>>>>>>>>
>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>
>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>
>>>>>>>> import numpy as np
>>>>>>>>
>>>>>>>> import os
>>>>>>>>
>>>>>>>> import sys
>>>>>>>>
>>>>>>>> import array
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> print('preparing map')   
>>>>>>>>
>>>>>>>> map = 
>>>>>>>>
>>>>>>>>                 
>
Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>
>>>>>>>> map.drawmapboundary()
>>>>>>>>
>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>
>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>
>>>>>>>> print('reading binary data')
>>>>>>>>
>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>
>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>
>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>
>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>
>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>
>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>
>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>
>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>
>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>
>>>>>>>> i=0
>>>>>>>>
>>>>>>>> while i < nbreligne:
>>>>>>>>
>>>>>>>>     if(Lon[i]>180):
>>>>>>>>
>>>>>>>>         print(Lon[i])
>>>>>>>>
>>>>>>>>         Lon[i]-=360
>>>>>>>>
>>>>>>>>         print(Lon[i])
>>>>>>>>
>>>>>>>>     i+=1
>>>>>>>>
>>>>>>>> print('plotting data')
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> #plotting code comes here
>>>>>>>>       
>>>>>>>>           
>>>>>>>>                 
>>>>>>> Antoine:  If you send me a self-contained script that produces the 
>>>>>>> problem you see, I can help you debug it.  As it stands now, I have
>>>>>>>               
> very 
>   
>>>>>>> little to work with - it could be your plotting commands, or it
could
>>>>>>>               
> be 
>   
>>>>>>> your data.
>>>>>>>
>>>>>>> -Jeff
>>>>>>>     
>>>>>>>         
>>>>>>>               
>>>>>>>>  
>>>>>>>>
>>>>>>>> print('saving map')       
>>>>>>>>
>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>
>>>>>>>> print('done')
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>> *Antoine De Pauw*
>>>>>>>> Collaborateur de recherches, Informatique - Research collaborator,
>>>>>>>>                 
> IT
>   
>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum
chemistry
>>>>>>>>                 
> and 
>   
>>>>>>>> photophysics laboratory
>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>
>>>>>>>>  
>>>>>>>>
>>>>>>>>       
>>>>>>>>           
>>>>>>>>                 
>>>>>>> -- 
>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>         
>>>>>>>               
>>>>>>   
>>>>>>       
>>>>>>             
>>>>> -- 
>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>
>>>>>
>>>>>
>>>>>     
>>>>>           
>>>>   
>>>>         
>>> -- 
>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>
>>>
>>>
>>>       
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

De Pauw Antoine wrote:
> Thanks Jeff,
>
> This seems to work with csv file types, and I've been experimenting a bit
> with it
>
> However, when I try to implement this with my original code (with binary
> files), I get an error like that one:
>
> Traceback (most recent call last):
>   File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module>
>     x,y = map(Lon,Lat)
> TypeError: 'numpy.ndarray' object is not callable
>
> I think this is coming from the fact I use array objects to store values...
> could you confirm it?
>   

Antoine:  It looks like you the object map is not a Basemap instance, 
but a numpy array.  Try putting 'print type(map)' just ahead of this 
statement to verify this. I suspect your re-using the name 'map' in your 
code,  overwriting the Basemap class instance.

-Jeff
> Also, I'll see if it is possible to invert color scale and mask everything
> under a certain value
>
> Thanks very much for your help!
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: jeudi 11 septembre 2008 14:10
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Hi Jeff,
>>
>> I have put the code online with a sample of the data here:
>>
>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>
>> I hope you'll be able to give me some advice as it is quite difficult for
>> someone new in python and scientific computation
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine: I may have the size of the pixels wrong, and lat/lon 
> transposed, but this is the general idea:
>
> from mpl_toolkits.basemap import Basemap
> import matplotlib.pyplot as plt
> import numpy as np
> lats = []; lons = []; data = []
> for line in open('pixels.dat'):
>     linesplit = line.split(',')
>     lons.append(float(linesplit[1]))
>     lats.append(float(linesplit[0]))
>     data.append(float(linesplit[2]))
> map = 
> Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
>                           
> urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
> x,y = map(lons,lats)
> plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
> plt.colorbar(shrink=0.6)
> map.drawcoastlines()
> plt.show()
>
> -Jeff
>
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
>> Sent: mercredi 10 septembre 2008 16:45
>> To: Antoine De Pauw
>> Cc: Matplotlib Users
>> Subject: Re: Information request
>>
>> Antoine De Pauw wrote:
>>   
>>     
>>> Thanks Jeff,
>>>
>>> In fact my points are arranged in three unsorted arrays, with a simple
>>>     
>>>       
>> scheme (thats why I couldn't plot them with imshow and others)
>>   
>>     
>>> arrays:
>>>
>>> [lat][lon][val]
>>> [-10][ 17][0.3]
>>> [ 37][ 23][3.7]
>>>  ...  ...  ...
>>>
>>> and so for many rows...
>>>
>>> what I have to do is looping through my arrays like that
>>>
>>> while i < rowcount:
>>>     plot_to_map(lat[i],lon[i],val[i])
>>>
>>> it is evidently an idea of how it could be done easily but my knowledge
>>>       
> of
>   
>>>     
>>>       
>> these libraries is too weak for me to figure out how to do it
>>   
>>     
>>> my data comes from huge binary files but is extremely simple, so it would
>>>     
>>>       
>> be really easy for anyone to help me as the problem itself is how to put
>> unsorted points on the map with latitude and longitude coordinates
>>   
>>
>> Antoine:  You haven't said if your data forms a rectangular array.  If 
>> so, you can build a 2-d array from the input file and plot it with 
>> imshow.  If not, you can still plug the elements into a 2-d masked 
>> array, leaving the missing pixels masked.  You say the points are 
>> 'unsorted', does that mean they are randomly distributed and do not form 
>> a rectangular grid?
>>
>> It would really be much easier to help if you gave us more information, 
>> such as how the data is structured, what the pixel footprint is, etc. 
>> Perhaps you could post the binary file on an ftp site somewhere with 
>> code to read it.
>>
>> Also, please hit 'reply all' when replying, so the matplotlib users 
>> mailing list is CC'ed.
>>
>> -Jeff
>>   
>>     
>>>> Antoine De Pauw wrote:
>>>>       
>>>>         
>>>>> Sir,
>>>>>
>>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>>         
>>>>>           
>> difficult to be understandable.
>>   
>>     
>>>>> All is in the script I gave to you initially, except the point drawing
>>>>>         
>>>>>           
>> code which would be useless as it is proven not to work (I dont know the
>> method to do it).
>>   
>>     
>>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>>         
>>>>>           
>> geographic coordinates.
>>   
>>     
>>>>> I cannot find the right method to put colour pixels on the map, that's
>>>>>         
>>>>>           
>> the problem.
>>   
>>     
>>>>> I have that map in miller projection, and three arrays containing
>>>>>         
>>>>>           
>> respectively latitude, longitude and satellite measured value.
>>   
>>     
>>>>> What I need to obtain is something approximately like this:
>>>>>         
>>>>>           
> http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
>   
>> _00_lr.gif but with the basemap toolkit.
>>   
>>     
>>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>>         
>>>>>           
>> coordinates lat:lon on that map? If I have just the method to project a
>> geographic coordinate on the map and put a coloured pixel at the right
>> place, all is done and I just have to loop my arrays... Also, I would have
>> to implement some antialiasing on the map.
>>   
>>     
>>>>>   
>>>>>         
>>>>>           
>>>> Antoine:
>>>>
>>>> Are the pixels arranged on a regular grid - or are they randomly 
>>>> distributed?  If they are on a grid, it's easy (using pcolor or imshow).
>>>>         
>
>   
>>>> If you could send me your data I may be able to get you started.
>>>>
>>>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>>>
>>>>
>>>> -Jeff
>>>>       
>>>>         
>>>>> If this is not possible to do it in a simple and explainable way,
>>>>>           
> please
>   
>>>>>         
>>>>>           
>> tell me and I'll continue using matlab or searching for the bit of code
>> which will save me
>>   
>>     
>>>>> Anyway, I have to thank you for your interest to help me..
>>>>>
>>>>> Many thanks,
>>>>>
>>>>> Antoine De Pauw
>>>>>
>>>>>   
>>>>>         
>>>>>           
>>>>>> Antoine De Pauw wrote:
>>>>>>     
>>>>>>           
>>>>>>             
>>>>>>> Hi, and thanks for the answer
>>>>>>>
>>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>>             
>>>>>>>               
>> (Lat,Lon,Val) describing geographic points which are associated by index
>> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>   
>>     
>>>>>>> What I need to do is to plot some points on the map (miller
>>>>>>>               
> projection
>   
>>>>>>>             
>>>>>>>               
>> for most) based on latitude and longitude, to obtain a colour map (points
>> are unordered, it is from IASI satellite computations)
>>   
>>     
>>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>>             
>>>>>>>               
>> problem I have is any method I try for plotting points is failing, either
>> pcolor, pcolormesh, imshow, etc.
>>   
>>     
>>>>>>> When I found your post on that mailing list, I figured out that you
>>>>>>>             
>>>>>>>               
>> might have the experience and skills to easily explain to me how to
>> manipulate these points and plot them on the map, as there's like no help
>>     
> on
>   
>> the web except standard examples...
>>   
>>     
>>>>>>> Please tell me if this is possible for you to give me some tips, or
>>>>>>>               
> if
>   
>>>>>>>             
>>>>>>>               
>> it takes too much of your time just advice me some lectures
>>   
>>     
>>>>>>> Best regards,
>>>>>>>
>>>>>>> De Pauw Antoine
>>>>>>>   
>>>>>>>       
>>>>>>>             
>>>>>>>               
>>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>>> problem.  It sounds to me like you want to plot markers representing a
>>>>>>             
>
>   
>>>>>> set of points - for that you should use the scatter method.  pcolor, 
>>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>>
>>>>>> -Jeff
>>>>>>     
>>>>>>           
>>>>>>             
>>>>>>>   
>>>>>>>       
>>>>>>>             
>>>>>>>               
>>>>>>>> De Pauw Antoine wrote:
>>>>>>>>     
>>>>>>>>         
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>> Dear sir,
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at
>>>>>>>>>                   
> the
>   
>>>>>>>>>                 
>>>>>>>>>                   
>> &#8220;Quantum 
>>   
>>     
>>>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre
>>>>>>>>>                   
> de
>   
>>>>>>>>>                 
>>>>>>>>>                   
>>   
>>     
>>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>>
>>>>>>>>>                 
>>>>>>>>>                   
>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>   
>>     
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> It seems that you could help me find a solution, as I cannot plot
>>>>>>>>>                 
>>>>>>>>>                   
>> any 
>>   
>>     
>>>>>>>>> points on maps.
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> Could you please tell me what I could do to plot data in a simple
>>>>>>>>>                 
>>>>>>>>>                   
>> way, 
>>   
>>     
>>>>>>>>> assuming I have 3 unordered arrays containing respectively
>>>>>>>>>                   
> latitude,
>   
>>>>>>>>>                 
>>>>>>>>>                   
>>   
>>     
>>>>>>>>> longitude and values to plot?
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> Some tips would be very nice from you as any method I have tried so
>>>>>>>>>                 
>>>>>>>>>                   
>> far 
>>   
>>     
>>>>>>>>> give me some errors&#8230;
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> Thank you very much in advance,
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> Best regards,
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>>                 
>>>>>>>>>                   
>> plotting part
>>   
>>     
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>>
>>>>>>>>> from numpy import *
>>>>>>>>>
>>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>>
>>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>>
>>>>>>>>> import numpy as np
>>>>>>>>>
>>>>>>>>> import os
>>>>>>>>>
>>>>>>>>> import sys
>>>>>>>>>
>>>>>>>>> import array
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> print('preparing map')   
>>>>>>>>>
>>>>>>>>> map = 
>>>>>>>>>
>>>>>>>>>                 
>>>>>>>>>                   
> Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>   
>>     
>>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>>
>>>>>>>>> map.drawmapboundary()
>>>>>>>>>
>>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>>
>>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>>
>>>>>>>>> print('reading binary data')
>>>>>>>>>
>>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>>
>>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>>
>>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>>
>>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>>
>>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>>
>>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>>
>>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>>
>>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>>
>>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>>
>>>>>>>>> i=0
>>>>>>>>>
>>>>>>>>> while i < nbreligne:
>>>>>>>>>
>>>>>>>>>     if(Lon[i]>180):
>>>>>>>>>
>>>>>>>>>         print(Lon[i])
>>>>>>>>>
>>>>>>>>>         Lon[i]-=360
>>>>>>>>>
>>>>>>>>>         print(Lon[i])
>>>>>>>>>
>>>>>>>>>     i+=1
>>>>>>>>>
>>>>>>>>> print('plotting data')
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> #plotting code comes here
>>>>>>>>>       
>>>>>>>>>           
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> Antoine:  If you send me a self-contained script that produces the 
>>>>>>>> problem you see, I can help you debug it.  As it stands now, I have
>>>>>>>>               
>>>>>>>>                 
>> very 
>>   
>>     
>>>>>>>> little to work with - it could be your plotting commands, or it
>>>>>>>>                 
> could
>   
>>>>>>>>               
>>>>>>>>                 
>> be 
>>   
>>     
>>>>>>>> your data.
>>>>>>>>
>>>>>>>> -Jeff
>>>>>>>>     
>>>>>>>>         
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> print('saving map')       
>>>>>>>>>
>>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>>
>>>>>>>>> print('done')
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> *Antoine De Pauw*
>>>>>>>>> Collaborateur de recherches, Informatique - Research collaborator,
>>>>>>>>>                 
>>>>>>>>>                   
>> IT
>>   
>>     
>>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum
>>>>>>>>>                   
> chemistry
>   
>>>>>>>>>                 
>>>>>>>>>                   
>> and 
>>   
>>     
>>>>>>>>> photophysics laboratory
>>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>>       
>>>>>>>>>           
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> -- 
>>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>>
>>>>>>>>
>>>>>>>>     
>>>>>>>>         
>>>>>>>>               
>>>>>>>>                 
>>>>>>>   
>>>>>>>       
>>>>>>>             
>>>>>>>               
>>>>>> -- 
>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>
>>>>>>
>>>>>>
>>>>>>     
>>>>>>           
>>>>>>             
>>>>>   
>>>>>         
>>>>>           
>>>> -- 
>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>
>>>>
>>>>
>>>>       
>>>>         
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Jeff,

The map object is from the Basemap type, the only different thing is the
Lon,Lat and Val objects which are from the type array instead of lists

Anyway, solutions are slowly showing themselves and I thank you all

Have a nice day

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: jeudi 11 septembre 2008 15:29
To: De Pauw Antoine
Cc: 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Thanks Jeff,
>
> This seems to work with csv file types, and I've been experimenting a bit
> with it
>
> However, when I try to implement this with my original code (with binary
> files), I get an error like that one:
>
> Traceback (most recent call last):
>   File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module>
>     x,y = map(Lon,Lat)
> TypeError: 'numpy.ndarray' object is not callable
>
> I think this is coming from the fact I use array objects to store
values...
> could you confirm it?
>   

Antoine:  It looks like you the object map is not a Basemap instance, 
but a numpy array.  Try putting 'print type(map)' just ahead of this 
statement to verify this. I suspect your re-using the name 'map' in your 
code,  overwriting the Basemap class instance.

-Jeff
> Also, I'll see if it is possible to invert color scale and mask everything
> under a certain value
>
> Thanks very much for your help!
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: jeudi 11 septembre 2008 14:10
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Hi Jeff,
>>
>> I have put the code online with a sample of the data here:
>>
>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>
>> I hope you'll be able to give me some advice as it is quite difficult for
>> someone new in python and scientific computation
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine: I may have the size of the pixels wrong, and lat/lon 
> transposed, but this is the general idea:
>
> from mpl_toolkits.basemap import Basemap
> import matplotlib.pyplot as plt
> import numpy as np
> lats = []; lons = []; data = []
> for line in open('pixels.dat'):
>     linesplit = line.split(',')
>     lons.append(float(linesplit[1]))
>     lats.append(float(linesplit[0]))
>     data.append(float(linesplit[2]))
> map = 
> Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
>                           
> urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
> x,y = map(lons,lats)
> plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
> plt.colorbar(shrink=0.6)
> map.drawcoastlines()
> plt.show()
>
> -Jeff
>
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
>> Sent: mercredi 10 septembre 2008 16:45
>> To: Antoine De Pauw
>> Cc: Matplotlib Users
>> Subject: Re: Information request
>>
>> Antoine De Pauw wrote:
>>   
>>     
>>> Thanks Jeff,
>>>
>>> In fact my points are arranged in three unsorted arrays, with a simple
>>>     
>>>       
>> scheme (thats why I couldn't plot them with imshow and others)
>>   
>>     
>>> arrays:
>>>
>>> [lat][lon][val]
>>> [-10][ 17][0.3]
>>> [ 37][ 23][3.7]
>>>  ...  ...  ...
>>>
>>> and so for many rows...
>>>
>>> what I have to do is looping through my arrays like that
>>>
>>> while i < rowcount:
>>>     plot_to_map(lat[i],lon[i],val[i])
>>>
>>> it is evidently an idea of how it could be done easily but my knowledge
>>>       
> of
>   
>>>     
>>>       
>> these libraries is too weak for me to figure out how to do it
>>   
>>     
>>> my data comes from huge binary files but is extremely simple, so it
would
>>>     
>>>       
>> be really easy for anyone to help me as the problem itself is how to put
>> unsorted points on the map with latitude and longitude coordinates
>>   
>>
>> Antoine:  You haven't said if your data forms a rectangular array.  If 
>> so, you can build a 2-d array from the input file and plot it with 
>> imshow.  If not, you can still plug the elements into a 2-d masked 
>> array, leaving the missing pixels masked.  You say the points are 
>> 'unsorted', does that mean they are randomly distributed and do not form 
>> a rectangular grid?
>>
>> It would really be much easier to help if you gave us more information, 
>> such as how the data is structured, what the pixel footprint is, etc. 
>> Perhaps you could post the binary file on an ftp site somewhere with 
>> code to read it.
>>
>> Also, please hit 'reply all' when replying, so the matplotlib users 
>> mailing list is CC'ed.
>>
>> -Jeff
>>   
>>     
>>>> Antoine De Pauw wrote:
>>>>       
>>>>         
>>>>> Sir,
>>>>>
>>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>>         
>>>>>           
>> difficult to be understandable.
>>   
>>     
>>>>> All is in the script I gave to you initially, except the point drawing
>>>>>         
>>>>>           
>> code which would be useless as it is proven not to work (I dont know the
>> method to do it).
>>   
>>     
>>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>>         
>>>>>           
>> geographic coordinates.
>>   
>>     
>>>>> I cannot find the right method to put colour pixels on the map, that's
>>>>>         
>>>>>           
>> the problem.
>>   
>>     
>>>>> I have that map in miller projection, and three arrays containing
>>>>>         
>>>>>           
>> respectively latitude, longitude and satellite measured value.
>>   
>>     
>>>>> What I need to obtain is something approximately like this:
>>>>>         
>>>>>           
>
http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
>   
>> _00_lr.gif but with the basemap toolkit.
>>   
>>     
>>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>>         
>>>>>           
>> coordinates lat:lon on that map? If I have just the method to project a
>> geographic coordinate on the map and put a coloured pixel at the right
>> place, all is done and I just have to loop my arrays... Also, I would
have
>> to implement some antialiasing on the map.
>>   
>>     
>>>>>   
>>>>>         
>>>>>           
>>>> Antoine:
>>>>
>>>> Are the pixels arranged on a regular grid - or are they randomly 
>>>> distributed?  If they are on a grid, it's easy (using pcolor or
imshow).
>>>>         
>
>   
>>>> If you could send me your data I may be able to get you started.
>>>>
>>>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>>>
>>>>
>>>> -Jeff
>>>>       
>>>>         
>>>>> If this is not possible to do it in a simple and explainable way,
>>>>>           
> please
>   
>>>>>         
>>>>>           
>> tell me and I'll continue using matlab or searching for the bit of code
>> which will save me
>>   
>>     
>>>>> Anyway, I have to thank you for your interest to help me..
>>>>>
>>>>> Many thanks,
>>>>>
>>>>> Antoine De Pauw
>>>>>
>>>>>   
>>>>>         
>>>>>           
>>>>>> Antoine De Pauw wrote:
>>>>>>     
>>>>>>           
>>>>>>             
>>>>>>> Hi, and thanks for the answer
>>>>>>>
>>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>>             
>>>>>>>               
>> (Lat,Lon,Val) describing geographic points which are associated by index
>> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>   
>>     
>>>>>>> What I need to do is to plot some points on the map (miller
>>>>>>>               
> projection
>   
>>>>>>>             
>>>>>>>               
>> for most) based on latitude and longitude, to obtain a colour map (points
>> are unordered, it is from IASI satellite computations)
>>   
>>     
>>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>>             
>>>>>>>               
>> problem I have is any method I try for plotting points is failing, either
>> pcolor, pcolormesh, imshow, etc.
>>   
>>     
>>>>>>> When I found your post on that mailing list, I figured out that you
>>>>>>>             
>>>>>>>               
>> might have the experience and skills to easily explain to me how to
>> manipulate these points and plot them on the map, as there's like no help
>>     
> on
>   
>> the web except standard examples...
>>   
>>     
>>>>>>> Please tell me if this is possible for you to give me some tips, or
>>>>>>>               
> if
>   
>>>>>>>             
>>>>>>>               
>> it takes too much of your time just advice me some lectures
>>   
>>     
>>>>>>> Best regards,
>>>>>>>
>>>>>>> De Pauw Antoine
>>>>>>>   
>>>>>>>       
>>>>>>>             
>>>>>>>               
>>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>>> problem.  It sounds to me like you want to plot markers representing
a
>>>>>>             
>
>   
>>>>>> set of points - for that you should use the scatter method.  pcolor, 
>>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>>
>>>>>> -Jeff
>>>>>>     
>>>>>>           
>>>>>>             
>>>>>>>   
>>>>>>>       
>>>>>>>             
>>>>>>>               
>>>>>>>> De Pauw Antoine wrote:
>>>>>>>>     
>>>>>>>>         
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>> Dear sir,
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at
>>>>>>>>>                   
> the
>   
>>>>>>>>>                 
>>>>>>>>>                   
>> &#8220;Quantum 
>>   
>>     
>>>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre
>>>>>>>>>                   
> de
>   
>>>>>>>>>                 
>>>>>>>>>                   
>>   
>>     
>>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>>
>>>>>>>>>                 
>>>>>>>>>                   
>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>   
>>     
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> It seems that you could help me find a solution, as I cannot plot
>>>>>>>>>                 
>>>>>>>>>                   
>> any 
>>   
>>     
>>>>>>>>> points on maps.
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> Could you please tell me what I could do to plot data in a simple
>>>>>>>>>                 
>>>>>>>>>                   
>> way, 
>>   
>>     
>>>>>>>>> assuming I have 3 unordered arrays containing respectively
>>>>>>>>>                   
> latitude,
>   
>>>>>>>>>                 
>>>>>>>>>                   
>>   
>>     
>>>>>>>>> longitude and values to plot?
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> Some tips would be very nice from you as any method I have tried
so
>>>>>>>>>                 
>>>>>>>>>                   
>> far 
>>   
>>     
>>>>>>>>> give me some errors&#8230;
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> Thank you very much in advance,
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> Best regards,
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>>                 
>>>>>>>>>                   
>> plotting part
>>   
>>     
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>>
>>>>>>>>> from numpy import *
>>>>>>>>>
>>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>>
>>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>>
>>>>>>>>> import numpy as np
>>>>>>>>>
>>>>>>>>> import os
>>>>>>>>>
>>>>>>>>> import sys
>>>>>>>>>
>>>>>>>>> import array
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> print('preparing map')   
>>>>>>>>>
>>>>>>>>> map = 
>>>>>>>>>
>>>>>>>>>                 
>>>>>>>>>                   
>
Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>   
>>     
>>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>>
>>>>>>>>> map.drawmapboundary()
>>>>>>>>>
>>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>>
>>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>>
>>>>>>>>> print('reading binary data')
>>>>>>>>>
>>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>>
>>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>>
>>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>>
>>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>>
>>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>>
>>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>>
>>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>>
>>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>>
>>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>>
>>>>>>>>> i=0
>>>>>>>>>
>>>>>>>>> while i < nbreligne:
>>>>>>>>>
>>>>>>>>>     if(Lon[i]>180):
>>>>>>>>>
>>>>>>>>>         print(Lon[i])
>>>>>>>>>
>>>>>>>>>         Lon[i]-=360
>>>>>>>>>
>>>>>>>>>         print(Lon[i])
>>>>>>>>>
>>>>>>>>>     i+=1
>>>>>>>>>
>>>>>>>>> print('plotting data')
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> #plotting code comes here
>>>>>>>>>       
>>>>>>>>>           
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> Antoine:  If you send me a self-contained script that produces the 
>>>>>>>> problem you see, I can help you debug it.  As it stands now, I have
>>>>>>>>               
>>>>>>>>                 
>> very 
>>   
>>     
>>>>>>>> little to work with - it could be your plotting commands, or it
>>>>>>>>                 
> could
>   
>>>>>>>>               
>>>>>>>>                 
>> be 
>>   
>>     
>>>>>>>> your data.
>>>>>>>>
>>>>>>>> -Jeff
>>>>>>>>     
>>>>>>>>         
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> print('saving map')       
>>>>>>>>>
>>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>>
>>>>>>>>> print('done')
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>> *Antoine De Pauw*
>>>>>>>>> Collaborateur de recherches, Informatique - Research collaborator,
>>>>>>>>>                 
>>>>>>>>>                   
>> IT
>>   
>>     
>>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum
>>>>>>>>>                   
> chemistry
>   
>>>>>>>>>                 
>>>>>>>>>                   
>> and 
>>   
>>     
>>>>>>>>> photophysics laboratory
>>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>>
>>>>>>>>>  
>>>>>>>>>
>>>>>>>>>       
>>>>>>>>>           
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> -- 
>>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>>
>>>>>>>>
>>>>>>>>     
>>>>>>>>         
>>>>>>>>               
>>>>>>>>                 
>>>>>>>   
>>>>>>>       
>>>>>>>             
>>>>>>>               
>>>>>> -- 
>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>
>>>>>>
>>>>>>
>>>>>>     
>>>>>>           
>>>>>>             
>>>>>   
>>>>>         
>>>>>           
>>>> -- 
>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>
>>>>
>>>>
>>>>       
>>>>         
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

De Pauw Antoine wrote:
> Jeff,
>
> The map object is from the Basemap type, the only different thing is the
> Lon,Lat and Val objects which are from the type array instead of lists
>
> Anyway, solutions are slowly showing themselves and I thank you all
>
> Have a nice day
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  It should not matter if Lon and Lat are python arrays, lists 
or numpy arrays.  The Basemap instance __call__ method handles them all. 
There must be something else going on.  It is always better to post 
actual code so we can see what is happening and test it ourselves.

-Jeff
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: jeudi 11 septembre 2008 15:29
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Thanks Jeff,
>>
>> This seems to work with csv file types, and I've been experimenting a bit
>> with it
>>
>> However, when I try to implement this with my original code (with binary
>> files), I get an error like that one:
>>
>> Traceback (most recent call last):
>>   File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module>
>>     x,y = map(Lon,Lat)
>> TypeError: 'numpy.ndarray' object is not callable
>>
>> I think this is coming from the fact I use array objects to store
>>     
> values...
>   
>> could you confirm it?
>>   
>>     
>
> Antoine:  It looks like you the object map is not a Basemap instance, 
> but a numpy array.  Try putting 'print type(map)' just ahead of this 
> statement to verify this. I suspect your re-using the name 'map' in your 
> code,  overwriting the Basemap class instance.
>
> -Jeff
>   
>> Also, I'll see if it is possible to invert color scale and mask everything
>> under a certain value
>>
>> Thanks very much for your help!
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>
>>
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: jeudi 11 septembre 2008 14:10
>> To: De Pauw Antoine
>> Cc: 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Hi Jeff,
>>>
>>> I have put the code online with a sample of the data here:
>>>
>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>
>>> I hope you'll be able to give me some advice as it is quite difficult for
>>> someone new in python and scientific computation
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>   
>>>     
>>>       
>> Antoine: I may have the size of the pixels wrong, and lat/lon 
>> transposed, but this is the general idea:
>>
>> from mpl_toolkits.basemap import Basemap
>> import matplotlib.pyplot as plt
>> import numpy as np
>> lats = []; lons = []; data = []
>> for line in open('pixels.dat'):
>>     linesplit = line.split(',')
>>     lons.append(float(linesplit[1]))
>>     lats.append(float(linesplit[0]))
>>     data.append(float(linesplit[2]))
>> map = 
>> Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
>>                           
>> urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
>> x,y = map(lons,lats)
>> plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
>> plt.colorbar(shrink=0.6)
>> map.drawcoastlines()
>> plt.show()
>>
>> -Jeff
>>
>>   
>>     
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
>>> Sent: mercredi 10 septembre 2008 16:45
>>> To: Antoine De Pauw
>>> Cc: Matplotlib Users
>>> Subject: Re: Information request
>>>
>>> Antoine De Pauw wrote:
>>>   
>>>     
>>>       
>>>> Thanks Jeff,
>>>>
>>>> In fact my points are arranged in three unsorted arrays, with a simple
>>>>     
>>>>       
>>>>         
>>> scheme (thats why I couldn't plot them with imshow and others)
>>>   
>>>     
>>>       
>>>> arrays:
>>>>
>>>> [lat][lon][val]
>>>> [-10][ 17][0.3]
>>>> [ 37][ 23][3.7]
>>>>  ...  ...  ...
>>>>
>>>> and so for many rows...
>>>>
>>>> what I have to do is looping through my arrays like that
>>>>
>>>> while i < rowcount:
>>>>     plot_to_map(lat[i],lon[i],val[i])
>>>>
>>>> it is evidently an idea of how it could be done easily but my knowledge
>>>>       
>>>>         
>> of
>>   
>>     
>>>>     
>>>>       
>>>>         
>>> these libraries is too weak for me to figure out how to do it
>>>   
>>>     
>>>       
>>>> my data comes from huge binary files but is extremely simple, so it
>>>>         
> would
>   
>>>>     
>>>>       
>>>>         
>>> be really easy for anyone to help me as the problem itself is how to put
>>> unsorted points on the map with latitude and longitude coordinates
>>>   
>>>
>>> Antoine:  You haven't said if your data forms a rectangular array.  If 
>>> so, you can build a 2-d array from the input file and plot it with 
>>> imshow.  If not, you can still plug the elements into a 2-d masked 
>>> array, leaving the missing pixels masked.  You say the points are 
>>> 'unsorted', does that mean they are randomly distributed and do not form 
>>> a rectangular grid?
>>>
>>> It would really be much easier to help if you gave us more information, 
>>> such as how the data is structured, what the pixel footprint is, etc. 
>>> Perhaps you could post the binary file on an ftp site somewhere with 
>>> code to read it.
>>>
>>> Also, please hit 'reply all' when replying, so the matplotlib users 
>>> mailing list is CC'ed.
>>>
>>> -Jeff
>>>   
>>>     
>>>       
>>>>> Antoine De Pauw wrote:
>>>>>       
>>>>>         
>>>>>           
>>>>>> Sir,
>>>>>>
>>>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>>>         
>>>>>>           
>>>>>>             
>>> difficult to be understandable.
>>>   
>>>     
>>>       
>>>>>> All is in the script I gave to you initially, except the point drawing
>>>>>>         
>>>>>>           
>>>>>>             
>>> code which would be useless as it is proven not to work (I dont know the
>>> method to do it).
>>>   
>>>     
>>>       
>>>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>>>         
>>>>>>           
>>>>>>             
>>> geographic coordinates.
>>>   
>>>     
>>>       
>>>>>> I cannot find the right method to put colour pixels on the map, that's
>>>>>>         
>>>>>>           
>>>>>>             
>>> the problem.
>>>   
>>>     
>>>       
>>>>>> I have that map in miller projection, and three arrays containing
>>>>>>         
>>>>>>           
>>>>>>             
>>> respectively latitude, longitude and satellite measured value.
>>>   
>>>     
>>>       
>>>>>> What I need to obtain is something approximately like this:
>>>>>>         
>>>>>>           
>>>>>>             
> http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
>   
>>   
>>     
>>> _00_lr.gif but with the basemap toolkit.
>>>   
>>>     
>>>       
>>>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>>>         
>>>>>>           
>>>>>>             
>>> coordinates lat:lon on that map? If I have just the method to project a
>>> geographic coordinate on the map and put a coloured pixel at the right
>>> place, all is done and I just have to loop my arrays... Also, I would
>>>       
> have
>   
>>> to implement some antialiasing on the map.
>>>   
>>>     
>>>       
>>>>>>   
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> Antoine:
>>>>>
>>>>> Are the pixels arranged on a regular grid - or are they randomly 
>>>>> distributed?  If they are on a grid, it's easy (using pcolor or
>>>>>           
> imshow).
>   
>>>>>         
>>>>>           
>>   
>>     
>>>>> If you could send me your data I may be able to get you started.
>>>>>
>>>>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>>>>
>>>>>
>>>>> -Jeff
>>>>>       
>>>>>         
>>>>>           
>>>>>> If this is not possible to do it in a simple and explainable way,
>>>>>>           
>>>>>>             
>> please
>>   
>>     
>>>>>>         
>>>>>>           
>>>>>>             
>>> tell me and I'll continue using matlab or searching for the bit of code
>>> which will save me
>>>   
>>>     
>>>       
>>>>>> Anyway, I have to thank you for your interest to help me..
>>>>>>
>>>>>> Many thanks,
>>>>>>
>>>>>> Antoine De Pauw
>>>>>>
>>>>>>   
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> Antoine De Pauw wrote:
>>>>>>>     
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> Hi, and thanks for the answer
>>>>>>>>
>>>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>> (Lat,Lon,Val) describing geographic points which are associated by index
>>> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>>   
>>>     
>>>       
>>>>>>>> What I need to do is to plot some points on the map (miller
>>>>>>>>               
>>>>>>>>                 
>> projection
>>   
>>     
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>> for most) based on latitude and longitude, to obtain a colour map (points
>>> are unordered, it is from IASI satellite computations)
>>>   
>>>     
>>>       
>>>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>> problem I have is any method I try for plotting points is failing, either
>>> pcolor, pcolormesh, imshow, etc.
>>>   
>>>     
>>>       
>>>>>>>> When I found your post on that mailing list, I figured out that you
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>> might have the experience and skills to easily explain to me how to
>>> manipulate these points and plot them on the map, as there's like no help
>>>     
>>>       
>> on
>>   
>>     
>>> the web except standard examples...
>>>   
>>>     
>>>       
>>>>>>>> Please tell me if this is possible for you to give me some tips, or
>>>>>>>>               
>>>>>>>>                 
>> if
>>   
>>     
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>> it takes too much of your time just advice me some lectures
>>>   
>>>     
>>>       
>>>>>>>> Best regards,
>>>>>>>>
>>>>>>>> De Pauw Antoine
>>>>>>>>   
>>>>>>>>       
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>>>> problem.  It sounds to me like you want to plot markers representing
>>>>>>>               
> a
>   
>>>>>>>             
>>>>>>>               
>>   
>>     
>>>>>>> set of points - for that you should use the scatter method.  pcolor, 
>>>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>>>
>>>>>>> -Jeff
>>>>>>>     
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>>   
>>>>>>>>       
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>> De Pauw Antoine wrote:
>>>>>>>>>     
>>>>>>>>>         
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>> Dear sir,
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at
>>>>>>>>>>                   
>>>>>>>>>>                     
>> the
>>   
>>     
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> &#8220;Quantum 
>>>   
>>>     
>>>       
>>>>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre
>>>>>>>>>>                   
>>>>>>>>>>                     
>> de
>>   
>>     
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>   
>>>     
>>>       
>>>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>>>
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>>   
>>>     
>>>       
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> It seems that you could help me find a solution, as I cannot plot
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> any 
>>>   
>>>     
>>>       
>>>>>>>>>> points on maps.
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> Could you please tell me what I could do to plot data in a simple
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> way, 
>>>   
>>>     
>>>       
>>>>>>>>>> assuming I have 3 unordered arrays containing respectively
>>>>>>>>>>                   
>>>>>>>>>>                     
>> latitude,
>>   
>>     
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>   
>>>     
>>>       
>>>>>>>>>> longitude and values to plot?
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> Some tips would be very nice from you as any method I have tried
>>>>>>>>>>                     
> so
>   
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> far 
>>>   
>>>     
>>>       
>>>>>>>>>> give me some errors&#8230;
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> Thank you very much in advance,
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> Best regards,
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> plotting part
>>>   
>>>     
>>>       
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>>>
>>>>>>>>>> from numpy import *
>>>>>>>>>>
>>>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>>>
>>>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>>>
>>>>>>>>>> import numpy as np
>>>>>>>>>>
>>>>>>>>>> import os
>>>>>>>>>>
>>>>>>>>>> import sys
>>>>>>>>>>
>>>>>>>>>> import array
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> print('preparing map')   
>>>>>>>>>>
>>>>>>>>>> map = 
>>>>>>>>>>
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
> Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>>>
>>>>>>>>>> map.drawmapboundary()
>>>>>>>>>>
>>>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>>>
>>>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>>>
>>>>>>>>>> print('reading binary data')
>>>>>>>>>>
>>>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>>>
>>>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>>>
>>>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>>>
>>>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>>>
>>>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>>>
>>>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>>>
>>>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>>>
>>>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>>>
>>>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>>>
>>>>>>>>>> i=0
>>>>>>>>>>
>>>>>>>>>> while i < nbreligne:
>>>>>>>>>>
>>>>>>>>>>     if(Lon[i]>180):
>>>>>>>>>>
>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>
>>>>>>>>>>         Lon[i]-=360
>>>>>>>>>>
>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>
>>>>>>>>>>     i+=1
>>>>>>>>>>
>>>>>>>>>> print('plotting data')
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> #plotting code comes here
>>>>>>>>>>       
>>>>>>>>>>           
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>> Antoine:  If you send me a self-contained script that produces the 
>>>>>>>>> problem you see, I can help you debug it.  As it stands now, I have
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> very 
>>>   
>>>     
>>>       
>>>>>>>>> little to work with - it could be your plotting commands, or it
>>>>>>>>>                 
>>>>>>>>>                   
>> could
>>   
>>     
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> be 
>>>   
>>>     
>>>       
>>>>>>>>> your data.
>>>>>>>>>
>>>>>>>>> -Jeff
>>>>>>>>>     
>>>>>>>>>         
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> print('saving map')       
>>>>>>>>>>
>>>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>>>
>>>>>>>>>> print('done')
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> *Antoine De Pauw*
>>>>>>>>>> Collaborateur de recherches, Informatique - Research collaborator,
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> IT
>>>   
>>>     
>>>       
>>>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum
>>>>>>>>>>                   
>>>>>>>>>>                     
>> chemistry
>>   
>>     
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> and 
>>>   
>>>     
>>>       
>>>>>>>>>> photophysics laboratory
>>>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>>       
>>>>>>>>>>           
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>> -- 
>>>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>     
>>>>>>>>>         
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>   
>>>>>>>>       
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> -- 
>>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>   
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> -- 
>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>
>>>>>
>>>>>
>>>>>       
>>>>>         
>>>>>           
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Hi Jeff,

I updated my code snippet and uploaded the image I created with a complete
set of data:

http://snipplr.com/view/8307/map-plotting-python-code-temporary/

And here's the picture generated:

http://www.kirikoo.net/images/5shrad-20080912-105759.png

I now understand the process and I'm able to reproduce it for other
datasets, but I need to implement some antialiasing for it..

Is it possible to do?

Many thanks for your precious help!

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: jeudi 11 septembre 2008 16:48
To: De Pauw Antoine
Cc: 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Jeff,
>
> The map object is from the Basemap type, the only different thing is the
> Lon,Lat and Val objects which are from the type array instead of lists
>
> Anyway, solutions are slowly showing themselves and I thank you all
>
> Have a nice day
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  It should not matter if Lon and Lat are python arrays, lists 
or numpy arrays.  The Basemap instance __call__ method handles them all. 
There must be something else going on.  It is always better to post 
actual code so we can see what is happening and test it ourselves.

-Jeff
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: jeudi 11 septembre 2008 15:29
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Thanks Jeff,
>>
>> This seems to work with csv file types, and I've been experimenting a bit
>> with it
>>
>> However, when I try to implement this with my original code (with binary
>> files), I get an error like that one:
>>
>> Traceback (most recent call last):
>>   File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module>
>>     x,y = map(Lon,Lat)
>> TypeError: 'numpy.ndarray' object is not callable
>>
>> I think this is coming from the fact I use array objects to store
>>     
> values...
>   
>> could you confirm it?
>>   
>>     
>
> Antoine:  It looks like you the object map is not a Basemap instance, 
> but a numpy array.  Try putting 'print type(map)' just ahead of this 
> statement to verify this. I suspect your re-using the name 'map' in your 
> code,  overwriting the Basemap class instance.
>
> -Jeff
>   
>> Also, I'll see if it is possible to invert color scale and mask
everything
>> under a certain value
>>
>> Thanks very much for your help!
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>
>>
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: jeudi 11 septembre 2008 14:10
>> To: De Pauw Antoine
>> Cc: 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Hi Jeff,
>>>
>>> I have put the code online with a sample of the data here:
>>>
>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>
>>> I hope you'll be able to give me some advice as it is quite difficult
for
>>> someone new in python and scientific computation
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>   
>>>     
>>>       
>> Antoine: I may have the size of the pixels wrong, and lat/lon 
>> transposed, but this is the general idea:
>>
>> from mpl_toolkits.basemap import Basemap
>> import matplotlib.pyplot as plt
>> import numpy as np
>> lats = []; lons = []; data = []
>> for line in open('pixels.dat'):
>>     linesplit = line.split(',')
>>     lons.append(float(linesplit[1]))
>>     lats.append(float(linesplit[0]))
>>     data.append(float(linesplit[2]))
>> map = 
>> Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
>>                           
>> urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
>> x,y = map(lons,lats)
>> plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
>> plt.colorbar(shrink=0.6)
>> map.drawcoastlines()
>> plt.show()
>>
>> -Jeff
>>
>>   
>>     
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
>>> Sent: mercredi 10 septembre 2008 16:45
>>> To: Antoine De Pauw
>>> Cc: Matplotlib Users
>>> Subject: Re: Information request
>>>
>>> Antoine De Pauw wrote:
>>>   
>>>     
>>>       
>>>> Thanks Jeff,
>>>>
>>>> In fact my points are arranged in three unsorted arrays, with a simple
>>>>     
>>>>       
>>>>         
>>> scheme (thats why I couldn't plot them with imshow and others)
>>>   
>>>     
>>>       
>>>> arrays:
>>>>
>>>> [lat][lon][val]
>>>> [-10][ 17][0.3]
>>>> [ 37][ 23][3.7]
>>>>  ...  ...  ...
>>>>
>>>> and so for many rows...
>>>>
>>>> what I have to do is looping through my arrays like that
>>>>
>>>> while i < rowcount:
>>>>     plot_to_map(lat[i],lon[i],val[i])
>>>>
>>>> it is evidently an idea of how it could be done easily but my knowledge
>>>>       
>>>>         
>> of
>>   
>>     
>>>>     
>>>>       
>>>>         
>>> these libraries is too weak for me to figure out how to do it
>>>   
>>>     
>>>       
>>>> my data comes from huge binary files but is extremely simple, so it
>>>>         
> would
>   
>>>>     
>>>>       
>>>>         
>>> be really easy for anyone to help me as the problem itself is how to put
>>> unsorted points on the map with latitude and longitude coordinates
>>>   
>>>
>>> Antoine:  You haven't said if your data forms a rectangular array.  If 
>>> so, you can build a 2-d array from the input file and plot it with 
>>> imshow.  If not, you can still plug the elements into a 2-d masked 
>>> array, leaving the missing pixels masked.  You say the points are 
>>> 'unsorted', does that mean they are randomly distributed and do not form

>>> a rectangular grid?
>>>
>>> It would really be much easier to help if you gave us more information, 
>>> such as how the data is structured, what the pixel footprint is, etc. 
>>> Perhaps you could post the binary file on an ftp site somewhere with 
>>> code to read it.
>>>
>>> Also, please hit 'reply all' when replying, so the matplotlib users 
>>> mailing list is CC'ed.
>>>
>>> -Jeff
>>>   
>>>     
>>>       
>>>>> Antoine De Pauw wrote:
>>>>>       
>>>>>         
>>>>>           
>>>>>> Sir,
>>>>>>
>>>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>>>         
>>>>>>           
>>>>>>             
>>> difficult to be understandable.
>>>   
>>>     
>>>       
>>>>>> All is in the script I gave to you initially, except the point
drawing
>>>>>>         
>>>>>>           
>>>>>>             
>>> code which would be useless as it is proven not to work (I dont know the
>>> method to do it).
>>>   
>>>     
>>>       
>>>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>>>         
>>>>>>           
>>>>>>             
>>> geographic coordinates.
>>>   
>>>     
>>>       
>>>>>> I cannot find the right method to put colour pixels on the map,
that's
>>>>>>         
>>>>>>           
>>>>>>             
>>> the problem.
>>>   
>>>     
>>>       
>>>>>> I have that map in miller projection, and three arrays containing
>>>>>>         
>>>>>>           
>>>>>>             
>>> respectively latitude, longitude and satellite measured value.
>>>   
>>>     
>>>       
>>>>>> What I need to obtain is something approximately like this:
>>>>>>         
>>>>>>           
>>>>>>             
>
http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
>   
>>   
>>     
>>> _00_lr.gif but with the basemap toolkit.
>>>   
>>>     
>>>       
>>>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>>>         
>>>>>>           
>>>>>>             
>>> coordinates lat:lon on that map? If I have just the method to project a
>>> geographic coordinate on the map and put a coloured pixel at the right
>>> place, all is done and I just have to loop my arrays... Also, I would
>>>       
> have
>   
>>> to implement some antialiasing on the map.
>>>   
>>>     
>>>       
>>>>>>   
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> Antoine:
>>>>>
>>>>> Are the pixels arranged on a regular grid - or are they randomly 
>>>>> distributed?  If they are on a grid, it's easy (using pcolor or
>>>>>           
> imshow).
>   
>>>>>         
>>>>>           
>>   
>>     
>>>>> If you could send me your data I may be able to get you started.
>>>>>
>>>>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>>>>
>>>>>
>>>>> -Jeff
>>>>>       
>>>>>         
>>>>>           
>>>>>> If this is not possible to do it in a simple and explainable way,
>>>>>>           
>>>>>>             
>> please
>>   
>>     
>>>>>>         
>>>>>>           
>>>>>>             
>>> tell me and I'll continue using matlab or searching for the bit of code
>>> which will save me
>>>   
>>>     
>>>       
>>>>>> Anyway, I have to thank you for your interest to help me..
>>>>>>
>>>>>> Many thanks,
>>>>>>
>>>>>> Antoine De Pauw
>>>>>>
>>>>>>   
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> Antoine De Pauw wrote:
>>>>>>>     
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> Hi, and thanks for the answer
>>>>>>>>
>>>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>> (Lat,Lon,Val) describing geographic points which are associated by index
>>> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>>   
>>>     
>>>       
>>>>>>>> What I need to do is to plot some points on the map (miller
>>>>>>>>               
>>>>>>>>                 
>> projection
>>   
>>     
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>> for most) based on latitude and longitude, to obtain a colour map
(points
>>> are unordered, it is from IASI satellite computations)
>>>   
>>>     
>>>       
>>>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>> problem I have is any method I try for plotting points is failing,
either
>>> pcolor, pcolormesh, imshow, etc.
>>>   
>>>     
>>>       
>>>>>>>> When I found your post on that mailing list, I figured out that you
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>> might have the experience and skills to easily explain to me how to
>>> manipulate these points and plot them on the map, as there's like no
help
>>>     
>>>       
>> on
>>   
>>     
>>> the web except standard examples...
>>>   
>>>     
>>>       
>>>>>>>> Please tell me if this is possible for you to give me some tips, or
>>>>>>>>               
>>>>>>>>                 
>> if
>>   
>>     
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>> it takes too much of your time just advice me some lectures
>>>   
>>>     
>>>       
>>>>>>>> Best regards,
>>>>>>>>
>>>>>>>> De Pauw Antoine
>>>>>>>>   
>>>>>>>>       
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>>>> problem.  It sounds to me like you want to plot markers representing
>>>>>>>               
> a
>   
>>>>>>>             
>>>>>>>               
>>   
>>     
>>>>>>> set of points - for that you should use the scatter method.  pcolor,

>>>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>>>
>>>>>>> -Jeff
>>>>>>>     
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>>   
>>>>>>>>       
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>> De Pauw Antoine wrote:
>>>>>>>>>     
>>>>>>>>>         
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>> Dear sir,
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at
>>>>>>>>>>                   
>>>>>>>>>>                     
>> the
>>   
>>     
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> &#8220;Quantum 
>>>   
>>>     
>>>       
>>>>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre
>>>>>>>>>>                   
>>>>>>>>>>                     
>> de
>>   
>>     
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>   
>>>     
>>>       
>>>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>>>
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>>   
>>>     
>>>       
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> It seems that you could help me find a solution, as I cannot plot
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> any 
>>>   
>>>     
>>>       
>>>>>>>>>> points on maps.
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> Could you please tell me what I could do to plot data in a simple
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> way, 
>>>   
>>>     
>>>       
>>>>>>>>>> assuming I have 3 unordered arrays containing respectively
>>>>>>>>>>                   
>>>>>>>>>>                     
>> latitude,
>>   
>>     
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>   
>>>     
>>>       
>>>>>>>>>> longitude and values to plot?
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> Some tips would be very nice from you as any method I have tried
>>>>>>>>>>                     
> so
>   
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> far 
>>>   
>>>     
>>>       
>>>>>>>>>> give me some errors&#8230;
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> Thank you very much in advance,
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> Best regards,
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> plotting part
>>>   
>>>     
>>>       
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>>>
>>>>>>>>>> from numpy import *
>>>>>>>>>>
>>>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>>>
>>>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>>>
>>>>>>>>>> import numpy as np
>>>>>>>>>>
>>>>>>>>>> import os
>>>>>>>>>>
>>>>>>>>>> import sys
>>>>>>>>>>
>>>>>>>>>> import array
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> print('preparing map')   
>>>>>>>>>>
>>>>>>>>>> map = 
>>>>>>>>>>
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>
Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>>>
>>>>>>>>>> map.drawmapboundary()
>>>>>>>>>>
>>>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>>>
>>>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>>>
>>>>>>>>>> print('reading binary data')
>>>>>>>>>>
>>>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>>>
>>>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>>>
>>>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>>>
>>>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>>>
>>>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>>>
>>>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>>>
>>>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>>>
>>>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>>>
>>>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>>>
>>>>>>>>>> i=0
>>>>>>>>>>
>>>>>>>>>> while i < nbreligne:
>>>>>>>>>>
>>>>>>>>>>     if(Lon[i]>180):
>>>>>>>>>>
>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>
>>>>>>>>>>         Lon[i]-=360
>>>>>>>>>>
>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>
>>>>>>>>>>     i+=1
>>>>>>>>>>
>>>>>>>>>> print('plotting data')
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> #plotting code comes here
>>>>>>>>>>       
>>>>>>>>>>           
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>> Antoine:  If you send me a self-contained script that produces the

>>>>>>>>> problem you see, I can help you debug it.  As it stands now, I
have
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> very 
>>>   
>>>     
>>>       
>>>>>>>>> little to work with - it could be your plotting commands, or it
>>>>>>>>>                 
>>>>>>>>>                   
>> could
>>   
>>     
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> be 
>>>   
>>>     
>>>       
>>>>>>>>> your data.
>>>>>>>>>
>>>>>>>>> -Jeff
>>>>>>>>>     
>>>>>>>>>         
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> print('saving map')       
>>>>>>>>>>
>>>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>>>
>>>>>>>>>> print('done')
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>> *Antoine De Pauw*
>>>>>>>>>> Collaborateur de recherches, Informatique - Research
collaborator,
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> IT
>>>   
>>>     
>>>       
>>>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum
>>>>>>>>>>                   
>>>>>>>>>>                     
>> chemistry
>>   
>>     
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> and 
>>>   
>>>     
>>>       
>>>>>>>>>> photophysics laboratory
>>>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>>>
>>>>>>>>>>  
>>>>>>>>>>
>>>>>>>>>>       
>>>>>>>>>>           
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>> -- 
>>>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>     
>>>>>>>>>         
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>   
>>>>>>>>       
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> -- 
>>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>   
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> -- 
>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>
>>>>>
>>>>>
>>>>>       
>>>>>         
>>>>>           
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

De Pauw Antoine wrote:
> Hi Jeff,
>
> I updated my code snippet and uploaded the image I created with a complete
> set of data:
>
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> And here's the picture generated:
>
> http://www.kirikoo.net/images/5shrad-20080912-105759.png
>
> I now understand the process and I'm able to reproduce it for other
> datasets, but I need to implement some antialiasing for it..
>
> Is it possible to do?
>
> Many thanks for your precious help!
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  If you do

 >>> from pylab import scatter
 >>> help(scatter)

you will see that scatter takes an antialised keyword

     antialiased    Boolean or sequence of booleans    

-Jeff

>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: jeudi 11 septembre 2008 16:48
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Jeff,
>>
>> The map object is from the Basemap type, the only different thing is the
>> Lon,Lat and Val objects which are from the type array instead of lists
>>
>> Anyway, solutions are slowly showing themselves and I thank you all
>>
>> Have a nice day
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine:  It should not matter if Lon and Lat are python arrays, lists 
> or numpy arrays.  The Basemap instance __call__ method handles them all. 
> There must be something else going on.  It is always better to post 
> actual code so we can see what is happening and test it ourselves.
>
> -Jeff
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: jeudi 11 septembre 2008 15:29
>> To: De Pauw Antoine
>> Cc: 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Thanks Jeff,
>>>
>>> This seems to work with csv file types, and I've been experimenting a bit
>>> with it
>>>
>>> However, when I try to implement this with my original code (with binary
>>> files), I get an error like that one:
>>>
>>> Traceback (most recent call last):
>>>   File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module>
>>>     x,y = map(Lon,Lat)
>>> TypeError: 'numpy.ndarray' object is not callable
>>>
>>> I think this is coming from the fact I use array objects to store
>>>     
>>>       
>> values...
>>   
>>     
>>> could you confirm it?
>>>   
>>>     
>>>       
>> Antoine:  It looks like you the object map is not a Basemap instance, 
>> but a numpy array.  Try putting 'print type(map)' just ahead of this 
>> statement to verify this. I suspect your re-using the name 'map' in your 
>> code,  overwriting the Basemap class instance.
>>
>> -Jeff
>>   
>>     
>>> Also, I'll see if it is possible to invert color scale and mask
>>>       
> everything
>   
>>> under a certain value
>>>
>>> Thanks very much for your help!
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>
>>>
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: jeudi 11 septembre 2008 14:10
>>> To: De Pauw Antoine
>>> Cc: 'Matplotlib Users'
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> De Pauw Antoine wrote:
>>>   
>>>     
>>>       
>>>> Hi Jeff,
>>>>
>>>> I have put the code online with a sample of the data here:
>>>>
>>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>>
>>>> I hope you'll be able to give me some advice as it is quite difficult
>>>>         
> for
>   
>>>> someone new in python and scientific computation
>>>>
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>   
>>>>     
>>>>       
>>>>         
>>> Antoine: I may have the size of the pixels wrong, and lat/lon 
>>> transposed, but this is the general idea:
>>>
>>> from mpl_toolkits.basemap import Basemap
>>> import matplotlib.pyplot as plt
>>> import numpy as np
>>> lats = []; lons = []; data = []
>>> for line in open('pixels.dat'):
>>>     linesplit = line.split(',')
>>>     lons.append(float(linesplit[1]))
>>>     lats.append(float(linesplit[0]))
>>>     data.append(float(linesplit[2]))
>>> map = 
>>> Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
>>>                           
>>> urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
>>> x,y = map(lons,lats)
>>> plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
>>> plt.colorbar(shrink=0.6)
>>> map.drawcoastlines()
>>> plt.show()
>>>
>>> -Jeff
>>>
>>>   
>>>     
>>>       
>>>> -----Original Message-----
>>>> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
>>>> Sent: mercredi 10 septembre 2008 16:45
>>>> To: Antoine De Pauw
>>>> Cc: Matplotlib Users
>>>> Subject: Re: Information request
>>>>
>>>> Antoine De Pauw wrote:
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> Thanks Jeff,
>>>>>
>>>>> In fact my points are arranged in three unsorted arrays, with a simple
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> scheme (thats why I couldn't plot them with imshow and others)
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> arrays:
>>>>>
>>>>> [lat][lon][val]
>>>>> [-10][ 17][0.3]
>>>>> [ 37][ 23][3.7]
>>>>>  ...  ...  ...
>>>>>
>>>>> and so for many rows...
>>>>>
>>>>> what I have to do is looping through my arrays like that
>>>>>
>>>>> while i < rowcount:
>>>>>     plot_to_map(lat[i],lon[i],val[i])
>>>>>
>>>>> it is evidently an idea of how it could be done easily but my knowledge
>>>>>       
>>>>>         
>>>>>           
>>> of
>>>   
>>>     
>>>       
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> these libraries is too weak for me to figure out how to do it
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> my data comes from huge binary files but is extremely simple, so it
>>>>>         
>>>>>           
>> would
>>   
>>     
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> be really easy for anyone to help me as the problem itself is how to put
>>>> unsorted points on the map with latitude and longitude coordinates
>>>>   
>>>>
>>>> Antoine:  You haven't said if your data forms a rectangular array.  If 
>>>> so, you can build a 2-d array from the input file and plot it with 
>>>> imshow.  If not, you can still plug the elements into a 2-d masked 
>>>> array, leaving the missing pixels masked.  You say the points are 
>>>> 'unsorted', does that mean they are randomly distributed and do not form
>>>>         
>
>   
>>>> a rectangular grid?
>>>>
>>>> It would really be much easier to help if you gave us more information, 
>>>> such as how the data is structured, what the pixel footprint is, etc. 
>>>> Perhaps you could post the binary file on an ftp site somewhere with 
>>>> code to read it.
>>>>
>>>> Also, please hit 'reply all' when replying, so the matplotlib users 
>>>> mailing list is CC'ed.
>>>>
>>>> -Jeff
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>> Antoine De Pauw wrote:
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> Sir,
>>>>>>>
>>>>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> difficult to be understandable.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> All is in the script I gave to you initially, except the point
>>>>>>>               
> drawing
>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> code which would be useless as it is proven not to work (I dont know the
>>>> method to do it).
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> geographic coordinates.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> I cannot find the right method to put colour pixels on the map,
>>>>>>>               
> that's
>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> the problem.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> I have that map in miller projection, and three arrays containing
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> respectively latitude, longitude and satellite measured value.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> What I need to obtain is something approximately like this:
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
> http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>> _00_lr.gif but with the basemap toolkit.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> coordinates lat:lon on that map? If I have just the method to project a
>>>> geographic coordinate on the map and put a coloured pixel at the right
>>>> place, all is done and I just have to loop my arrays... Also, I would
>>>>       
>>>>         
>> have
>>   
>>     
>>>> to implement some antialiasing on the map.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> Antoine:
>>>>>>
>>>>>> Are the pixels arranged on a regular grid - or are they randomly 
>>>>>> distributed?  If they are on a grid, it's easy (using pcolor or
>>>>>>           
>>>>>>             
>> imshow).
>>   
>>     
>>>>>>         
>>>>>>           
>>>>>>             
>>>   
>>>     
>>>       
>>>>>> If you could send me your data I may be able to get you started.
>>>>>>
>>>>>> (I'm cc'ing the matplotlib list so others can join in the discussion).
>>>>>>
>>>>>>
>>>>>> -Jeff
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> If this is not possible to do it in a simple and explainable way,
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>> please
>>>   
>>>     
>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> tell me and I'll continue using matlab or searching for the bit of code
>>>> which will save me
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> Anyway, I have to thank you for your interest to help me..
>>>>>>>
>>>>>>> Many thanks,
>>>>>>>
>>>>>>> Antoine De Pauw
>>>>>>>
>>>>>>>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> Antoine De Pauw wrote:
>>>>>>>>     
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>> Hi, and thanks for the answer
>>>>>>>>>
>>>>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> (Lat,Lon,Val) describing geographic points which are associated by index
>>>> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> What I need to do is to plot some points on the map (miller
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> projection
>>>   
>>>     
>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> for most) based on latitude and longitude, to obtain a colour map
>>>>         
> (points
>   
>>>> are unordered, it is from IASI satellite computations)
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> problem I have is any method I try for plotting points is failing,
>>>>         
> either
>   
>>>> pcolor, pcolormesh, imshow, etc.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> When I found your post on that mailing list, I figured out that you
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> might have the experience and skills to easily explain to me how to
>>>> manipulate these points and plot them on the map, as there's like no
>>>>         
> help
>   
>>>>     
>>>>       
>>>>         
>>> on
>>>   
>>>     
>>>       
>>>> the web except standard examples...
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> Please tell me if this is possible for you to give me some tips, or
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> if
>>>   
>>>     
>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> it takes too much of your time just advice me some lectures
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> Best regards,
>>>>>>>>>
>>>>>>>>> De Pauw Antoine
>>>>>>>>>   
>>>>>>>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>>>>> problem.  It sounds to me like you want to plot markers representing
>>>>>>>>               
>>>>>>>>                 
>> a
>>   
>>     
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>   
>>>     
>>>       
>>>>>>>> set of points - for that you should use the scatter method.  pcolor,
>>>>>>>>                 
>
>   
>>>>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>>>>
>>>>>>>> -Jeff
>>>>>>>>     
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>>   
>>>>>>>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>> De Pauw Antoine wrote:
>>>>>>>>>>     
>>>>>>>>>>         
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>>> Dear sir,
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> the
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> &#8220;Quantum 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> Chemistry and Photophysics&#8221; section of the Université Libre
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> de
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>>>>
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> It seems that you could help me find a solution, as I cannot plot
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> any 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> points on maps.
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Could you please tell me what I could do to plot data in a simple
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> way, 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> assuming I have 3 unordered arrays containing respectively
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> latitude,
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> longitude and values to plot?
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Some tips would be very nice from you as any method I have tried
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>> so
>>   
>>     
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> far 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> give me some errors&#8230;
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Thank you very much in advance,
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Best regards,
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> plotting part
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>>>>
>>>>>>>>>>> from numpy import *
>>>>>>>>>>>
>>>>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>>>>
>>>>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>>>>
>>>>>>>>>>> import numpy as np
>>>>>>>>>>>
>>>>>>>>>>> import os
>>>>>>>>>>>
>>>>>>>>>>> import sys
>>>>>>>>>>>
>>>>>>>>>>> import array
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> print('preparing map')   
>>>>>>>>>>>
>>>>>>>>>>> map = 
>>>>>>>>>>>
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
> Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>>>>
>>>>>>>>>>> map.drawmapboundary()
>>>>>>>>>>>
>>>>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>>>>
>>>>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>>>>
>>>>>>>>>>> print('reading binary data')
>>>>>>>>>>>
>>>>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>>>>
>>>>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>>>>
>>>>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>>>>
>>>>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>>>>
>>>>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>>>>
>>>>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>>>>
>>>>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>>>>
>>>>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>>>>
>>>>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>>>>
>>>>>>>>>>> i=0
>>>>>>>>>>>
>>>>>>>>>>> while i < nbreligne:
>>>>>>>>>>>
>>>>>>>>>>>     if(Lon[i]>180):
>>>>>>>>>>>
>>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>>
>>>>>>>>>>>         Lon[i]-=360
>>>>>>>>>>>
>>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>>
>>>>>>>>>>>     i+=1
>>>>>>>>>>>
>>>>>>>>>>> print('plotting data')
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> #plotting code comes here
>>>>>>>>>>>       
>>>>>>>>>>>           
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>> Antoine:  If you send me a self-contained script that produces the
>>>>>>>>>>                     
>
>   
>>>>>>>>>> problem you see, I can help you debug it.  As it stands now, I
>>>>>>>>>>                     
> have
>   
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>> very 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>> little to work with - it could be your plotting commands, or it
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> could
>>>   
>>>     
>>>       
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>> be 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>> your data.
>>>>>>>>>>
>>>>>>>>>> -Jeff
>>>>>>>>>>     
>>>>>>>>>>         
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> print('saving map')       
>>>>>>>>>>>
>>>>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>>>>
>>>>>>>>>>> print('done')
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> *Antoine De Pauw*
>>>>>>>>>>> Collaborateur de recherches, Informatique - Research
>>>>>>>>>>>                       
> collaborator,
>   
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> IT
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> chemistry
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> and 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> photophysics laboratory
>>>>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>>       
>>>>>>>>>>>           
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>> -- 
>>>>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>     
>>>>>>>>>>         
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>   
>>>>>>>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> -- 
>>>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>     
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> -- 
>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>
>>>>>>
>>>>>>
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>   
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Thanks Jeff,

Antialiasing is not very useful as my pixel size is small... also, I used
octagon shapes to have a smoother picture

Now I'm looking for suppressing pixels under (or over) a certain value, but
a couple hours of searching and testing didn't help...

I'll see Monday if I find some tips

Have a nice weekend

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: vendredi 12 septembre 2008 13:26
To: De Pauw Antoine
Cc: 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Hi Jeff,
>
> I updated my code snippet and uploaded the image I created with a complete
> set of data:
>
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> And here's the picture generated:
>
> http://www.kirikoo.net/images/5shrad-20080912-105759.png
>
> I now understand the process and I'm able to reproduce it for other
> datasets, but I need to implement some antialiasing for it..
>
> Is it possible to do?
>
> Many thanks for your precious help!
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  If you do

 >>> from pylab import scatter
 >>> help(scatter)

you will see that scatter takes an antialised keyword

     antialiased    Boolean or sequence of booleans    

-Jeff

>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: jeudi 11 septembre 2008 16:48
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Jeff,
>>
>> The map object is from the Basemap type, the only different thing is the
>> Lon,Lat and Val objects which are from the type array instead of lists
>>
>> Anyway, solutions are slowly showing themselves and I thank you all
>>
>> Have a nice day
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine:  It should not matter if Lon and Lat are python arrays, lists 
> or numpy arrays.  The Basemap instance __call__ method handles them all. 
> There must be something else going on.  It is always better to post 
> actual code so we can see what is happening and test it ourselves.
>
> -Jeff
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: jeudi 11 septembre 2008 15:29
>> To: De Pauw Antoine
>> Cc: 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Thanks Jeff,
>>>
>>> This seems to work with csv file types, and I've been experimenting a
bit
>>> with it
>>>
>>> However, when I try to implement this with my original code (with binary
>>> files), I get an error like that one:
>>>
>>> Traceback (most recent call last):
>>>   File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module>
>>>     x,y = map(Lon,Lat)
>>> TypeError: 'numpy.ndarray' object is not callable
>>>
>>> I think this is coming from the fact I use array objects to store
>>>     
>>>       
>> values...
>>   
>>     
>>> could you confirm it?
>>>   
>>>     
>>>       
>> Antoine:  It looks like you the object map is not a Basemap instance, 
>> but a numpy array.  Try putting 'print type(map)' just ahead of this 
>> statement to verify this. I suspect your re-using the name 'map' in your 
>> code,  overwriting the Basemap class instance.
>>
>> -Jeff
>>   
>>     
>>> Also, I'll see if it is possible to invert color scale and mask
>>>       
> everything
>   
>>> under a certain value
>>>
>>> Thanks very much for your help!
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>
>>>
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: jeudi 11 septembre 2008 14:10
>>> To: De Pauw Antoine
>>> Cc: 'Matplotlib Users'
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> De Pauw Antoine wrote:
>>>   
>>>     
>>>       
>>>> Hi Jeff,
>>>>
>>>> I have put the code online with a sample of the data here:
>>>>
>>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>>
>>>> I hope you'll be able to give me some advice as it is quite difficult
>>>>         
> for
>   
>>>> someone new in python and scientific computation
>>>>
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>   
>>>>     
>>>>       
>>>>         
>>> Antoine: I may have the size of the pixels wrong, and lat/lon 
>>> transposed, but this is the general idea:
>>>
>>> from mpl_toolkits.basemap import Basemap
>>> import matplotlib.pyplot as plt
>>> import numpy as np
>>> lats = []; lons = []; data = []
>>> for line in open('pixels.dat'):
>>>     linesplit = line.split(',')
>>>     lons.append(float(linesplit[1]))
>>>     lats.append(float(linesplit[0]))
>>>     data.append(float(linesplit[2]))
>>> map = 
>>> Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
>>>                           
>>> urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
>>> x,y = map(lons,lats)
>>> plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
>>> plt.colorbar(shrink=0.6)
>>> map.drawcoastlines()
>>> plt.show()
>>>
>>> -Jeff
>>>
>>>   
>>>     
>>>       
>>>> -----Original Message-----
>>>> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
>>>> Sent: mercredi 10 septembre 2008 16:45
>>>> To: Antoine De Pauw
>>>> Cc: Matplotlib Users
>>>> Subject: Re: Information request
>>>>
>>>> Antoine De Pauw wrote:
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> Thanks Jeff,
>>>>>
>>>>> In fact my points are arranged in three unsorted arrays, with a simple
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> scheme (thats why I couldn't plot them with imshow and others)
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> arrays:
>>>>>
>>>>> [lat][lon][val]
>>>>> [-10][ 17][0.3]
>>>>> [ 37][ 23][3.7]
>>>>>  ...  ...  ...
>>>>>
>>>>> and so for many rows...
>>>>>
>>>>> what I have to do is looping through my arrays like that
>>>>>
>>>>> while i < rowcount:
>>>>>     plot_to_map(lat[i],lon[i],val[i])
>>>>>
>>>>> it is evidently an idea of how it could be done easily but my
knowledge
>>>>>       
>>>>>         
>>>>>           
>>> of
>>>   
>>>     
>>>       
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> these libraries is too weak for me to figure out how to do it
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> my data comes from huge binary files but is extremely simple, so it
>>>>>         
>>>>>           
>> would
>>   
>>     
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> be really easy for anyone to help me as the problem itself is how to
put
>>>> unsorted points on the map with latitude and longitude coordinates
>>>>   
>>>>
>>>> Antoine:  You haven't said if your data forms a rectangular array.  If 
>>>> so, you can build a 2-d array from the input file and plot it with 
>>>> imshow.  If not, you can still plug the elements into a 2-d masked 
>>>> array, leaving the missing pixels masked.  You say the points are 
>>>> 'unsorted', does that mean they are randomly distributed and do not
form
>>>>         
>
>   
>>>> a rectangular grid?
>>>>
>>>> It would really be much easier to help if you gave us more information,

>>>> such as how the data is structured, what the pixel footprint is, etc. 
>>>> Perhaps you could post the binary file on an ftp site somewhere with 
>>>> code to read it.
>>>>
>>>> Also, please hit 'reply all' when replying, so the matplotlib users 
>>>> mailing list is CC'ed.
>>>>
>>>> -Jeff
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>> Antoine De Pauw wrote:
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> Sir,
>>>>>>>
>>>>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> difficult to be understandable.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> All is in the script I gave to you initially, except the point
>>>>>>>               
> drawing
>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> code which would be useless as it is proven not to work (I dont know
the
>>>> method to do it).
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> geographic coordinates.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> I cannot find the right method to put colour pixels on the map,
>>>>>>>               
> that's
>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> the problem.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> I have that map in miller projection, and three arrays containing
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> respectively latitude, longitude and satellite measured value.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> What I need to obtain is something approximately like this:
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>
http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>> _00_lr.gif but with the basemap toolkit.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> coordinates lat:lon on that map? If I have just the method to project a
>>>> geographic coordinate on the map and put a coloured pixel at the right
>>>> place, all is done and I just have to loop my arrays... Also, I would
>>>>       
>>>>         
>> have
>>   
>>     
>>>> to implement some antialiasing on the map.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> Antoine:
>>>>>>
>>>>>> Are the pixels arranged on a regular grid - or are they randomly 
>>>>>> distributed?  If they are on a grid, it's easy (using pcolor or
>>>>>>           
>>>>>>             
>> imshow).
>>   
>>     
>>>>>>         
>>>>>>           
>>>>>>             
>>>   
>>>     
>>>       
>>>>>> If you could send me your data I may be able to get you started.
>>>>>>
>>>>>> (I'm cc'ing the matplotlib list so others can join in the
discussion).
>>>>>>
>>>>>>
>>>>>> -Jeff
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> If this is not possible to do it in a simple and explainable way,
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>> please
>>>   
>>>     
>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> tell me and I'll continue using matlab or searching for the bit of code
>>>> which will save me
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> Anyway, I have to thank you for your interest to help me..
>>>>>>>
>>>>>>> Many thanks,
>>>>>>>
>>>>>>> Antoine De Pauw
>>>>>>>
>>>>>>>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> Antoine De Pauw wrote:
>>>>>>>>     
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>> Hi, and thanks for the answer
>>>>>>>>>
>>>>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> (Lat,Lon,Val) describing geographic points which are associated by
index
>>>> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> What I need to do is to plot some points on the map (miller
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> projection
>>>   
>>>     
>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> for most) based on latitude and longitude, to obtain a colour map
>>>>         
> (points
>   
>>>> are unordered, it is from IASI satellite computations)
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> problem I have is any method I try for plotting points is failing,
>>>>         
> either
>   
>>>> pcolor, pcolormesh, imshow, etc.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> When I found your post on that mailing list, I figured out that
you
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> might have the experience and skills to easily explain to me how to
>>>> manipulate these points and plot them on the map, as there's like no
>>>>         
> help
>   
>>>>     
>>>>       
>>>>         
>>> on
>>>   
>>>     
>>>       
>>>> the web except standard examples...
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> Please tell me if this is possible for you to give me some tips,
or
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> if
>>>   
>>>     
>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> it takes too much of your time just advice me some lectures
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> Best regards,
>>>>>>>>>
>>>>>>>>> De Pauw Antoine
>>>>>>>>>   
>>>>>>>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>>>>> problem.  It sounds to me like you want to plot markers
representing
>>>>>>>>               
>>>>>>>>                 
>> a
>>   
>>     
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>   
>>>     
>>>       
>>>>>>>> set of points - for that you should use the scatter method.
pcolor,
>>>>>>>>                 
>
>   
>>>>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>>>>
>>>>>>>> -Jeff
>>>>>>>>     
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>>   
>>>>>>>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>> De Pauw Antoine wrote:
>>>>>>>>>>     
>>>>>>>>>>         
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>>> Dear sir,
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> the
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> &#8220;Quantum 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> Chemistry and Photophysics&#8221; section of the Université
Libre
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> de
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>>>>
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> It seems that you could help me find a solution, as I cannot
plot
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> any 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> points on maps.
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Could you please tell me what I could do to plot data in a
simple
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> way, 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> assuming I have 3 unordered arrays containing respectively
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> latitude,
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> longitude and values to plot?
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Some tips would be very nice from you as any method I have tried
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>> so
>>   
>>     
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> far 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> give me some errors&#8230;
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Thank you very much in advance,
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Best regards,
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> plotting part
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>>>>
>>>>>>>>>>> from numpy import *
>>>>>>>>>>>
>>>>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>>>>
>>>>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>>>>
>>>>>>>>>>> import numpy as np
>>>>>>>>>>>
>>>>>>>>>>> import os
>>>>>>>>>>>
>>>>>>>>>>> import sys
>>>>>>>>>>>
>>>>>>>>>>> import array
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> print('preparing map')   
>>>>>>>>>>>
>>>>>>>>>>> map = 
>>>>>>>>>>>
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>
Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>>>>
>>>>>>>>>>> map.drawmapboundary()
>>>>>>>>>>>
>>>>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>>>>
>>>>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>>>>
>>>>>>>>>>> print('reading binary data')
>>>>>>>>>>>
>>>>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>>>>
>>>>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>>>>
>>>>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>>>>
>>>>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>>>>
>>>>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>>>>
>>>>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>>>>
>>>>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>>>>
>>>>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>>>>
>>>>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>>>>
>>>>>>>>>>> i=0
>>>>>>>>>>>
>>>>>>>>>>> while i < nbreligne:
>>>>>>>>>>>
>>>>>>>>>>>     if(Lon[i]>180):
>>>>>>>>>>>
>>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>>
>>>>>>>>>>>         Lon[i]-=360
>>>>>>>>>>>
>>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>>
>>>>>>>>>>>     i+=1
>>>>>>>>>>>
>>>>>>>>>>> print('plotting data')
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> #plotting code comes here
>>>>>>>>>>>       
>>>>>>>>>>>           
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>> Antoine:  If you send me a self-contained script that produces
the
>>>>>>>>>>                     
>
>   
>>>>>>>>>> problem you see, I can help you debug it.  As it stands now, I
>>>>>>>>>>                     
> have
>   
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>> very 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>> little to work with - it could be your plotting commands, or it
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> could
>>>   
>>>     
>>>       
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>> be 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>> your data.
>>>>>>>>>>
>>>>>>>>>> -Jeff
>>>>>>>>>>     
>>>>>>>>>>         
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> print('saving map')       
>>>>>>>>>>>
>>>>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>>>>
>>>>>>>>>>> print('done')
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> *Antoine De Pauw*
>>>>>>>>>>> Collaborateur de recherches, Informatique - Research
>>>>>>>>>>>                       
> collaborator,
>   
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> IT
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> chemistry
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> and 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> photophysics laboratory
>>>>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>>       
>>>>>>>>>>>           
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>> -- 
>>>>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>     
>>>>>>>>>>         
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>   
>>>>>>>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> -- 
>>>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>     
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> -- 
>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>
>>>>>>
>>>>>>
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>   
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Hi Jeff,

I have played a bit with Matplotlib since last week, and I may still have
some questions for you

I have masked my value array so it doesn't draw points under a certain
value, but doing this causes the colormap to rescale for the new values

I have tried to set a custom colormap but it isn't the thing to do as data
is varying in time

So is it possible to avoid the colormap to rescale itself?

Also, I had a look at imshow and the interpolation process is really
interesting for smooth maps.. does a way to interpolate scattered data
exist?

The code I use didn't change since last time, all I did is adding a bit,
testing and deleting..

Best regards,

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB

-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: vendredi 12 septembre 2008 13:26
To: De Pauw Antoine
Cc: 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Hi Jeff,
>
> I updated my code snippet and uploaded the image I created with a complete
> set of data:
>
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> And here's the picture generated:
>
> http://www.kirikoo.net/images/5shrad-20080912-105759.png
>
> I now understand the process and I'm able to reproduce it for other
> datasets, but I need to implement some antialiasing for it..
>
> Is it possible to do?
>
> Many thanks for your precious help!
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  If you do

 >>> from pylab import scatter
 >>> help(scatter)

you will see that scatter takes an antialised keyword

     antialiased    Boolean or sequence of booleans    

-Jeff

>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: jeudi 11 septembre 2008 16:48
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Jeff,
>>
>> The map object is from the Basemap type, the only different thing is the
>> Lon,Lat and Val objects which are from the type array instead of lists
>>
>> Anyway, solutions are slowly showing themselves and I thank you all
>>
>> Have a nice day
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine:  It should not matter if Lon and Lat are python arrays, lists 
> or numpy arrays.  The Basemap instance __call__ method handles them all. 
> There must be something else going on.  It is always better to post 
> actual code so we can see what is happening and test it ourselves.
>
> -Jeff
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: jeudi 11 septembre 2008 15:29
>> To: De Pauw Antoine
>> Cc: 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Thanks Jeff,
>>>
>>> This seems to work with csv file types, and I've been experimenting a
bit
>>> with it
>>>
>>> However, when I try to implement this with my original code (with binary
>>> files), I get an error like that one:
>>>
>>> Traceback (most recent call last):
>>>   File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module>
>>>     x,y = map(Lon,Lat)
>>> TypeError: 'numpy.ndarray' object is not callable
>>>
>>> I think this is coming from the fact I use array objects to store
>>>     
>>>       
>> values...
>>   
>>     
>>> could you confirm it?
>>>   
>>>     
>>>       
>> Antoine:  It looks like you the object map is not a Basemap instance, 
>> but a numpy array.  Try putting 'print type(map)' just ahead of this 
>> statement to verify this. I suspect your re-using the name 'map' in your 
>> code,  overwriting the Basemap class instance.
>>
>> -Jeff
>>   
>>     
>>> Also, I'll see if it is possible to invert color scale and mask
>>>       
> everything
>   
>>> under a certain value
>>>
>>> Thanks very much for your help!
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>
>>>
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: jeudi 11 septembre 2008 14:10
>>> To: De Pauw Antoine
>>> Cc: 'Matplotlib Users'
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> De Pauw Antoine wrote:
>>>   
>>>     
>>>       
>>>> Hi Jeff,
>>>>
>>>> I have put the code online with a sample of the data here:
>>>>
>>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>>
>>>> I hope you'll be able to give me some advice as it is quite difficult
>>>>         
> for
>   
>>>> someone new in python and scientific computation
>>>>
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>   
>>>>     
>>>>       
>>>>         
>>> Antoine: I may have the size of the pixels wrong, and lat/lon 
>>> transposed, but this is the general idea:
>>>
>>> from mpl_toolkits.basemap import Basemap
>>> import matplotlib.pyplot as plt
>>> import numpy as np
>>> lats = []; lons = []; data = []
>>> for line in open('pixels.dat'):
>>>     linesplit = line.split(',')
>>>     lons.append(float(linesplit[1]))
>>>     lats.append(float(linesplit[0]))
>>>     data.append(float(linesplit[2]))
>>> map = 
>>> Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
>>>                           
>>> urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
>>> x,y = map(lons,lats)
>>> plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
>>> plt.colorbar(shrink=0.6)
>>> map.drawcoastlines()
>>> plt.show()
>>>
>>> -Jeff
>>>
>>>   
>>>     
>>>       
>>>> -----Original Message-----
>>>> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
>>>> Sent: mercredi 10 septembre 2008 16:45
>>>> To: Antoine De Pauw
>>>> Cc: Matplotlib Users
>>>> Subject: Re: Information request
>>>>
>>>> Antoine De Pauw wrote:
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> Thanks Jeff,
>>>>>
>>>>> In fact my points are arranged in three unsorted arrays, with a simple
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> scheme (thats why I couldn't plot them with imshow and others)
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> arrays:
>>>>>
>>>>> [lat][lon][val]
>>>>> [-10][ 17][0.3]
>>>>> [ 37][ 23][3.7]
>>>>>  ...  ...  ...
>>>>>
>>>>> and so for many rows...
>>>>>
>>>>> what I have to do is looping through my arrays like that
>>>>>
>>>>> while i < rowcount:
>>>>>     plot_to_map(lat[i],lon[i],val[i])
>>>>>
>>>>> it is evidently an idea of how it could be done easily but my
knowledge
>>>>>       
>>>>>         
>>>>>           
>>> of
>>>   
>>>     
>>>       
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> these libraries is too weak for me to figure out how to do it
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> my data comes from huge binary files but is extremely simple, so it
>>>>>         
>>>>>           
>> would
>>   
>>     
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> be really easy for anyone to help me as the problem itself is how to
put
>>>> unsorted points on the map with latitude and longitude coordinates
>>>>   
>>>>
>>>> Antoine:  You haven't said if your data forms a rectangular array.  If 
>>>> so, you can build a 2-d array from the input file and plot it with 
>>>> imshow.  If not, you can still plug the elements into a 2-d masked 
>>>> array, leaving the missing pixels masked.  You say the points are 
>>>> 'unsorted', does that mean they are randomly distributed and do not
form
>>>>         
>
>   
>>>> a rectangular grid?
>>>>
>>>> It would really be much easier to help if you gave us more information,

>>>> such as how the data is structured, what the pixel footprint is, etc. 
>>>> Perhaps you could post the binary file on an ftp site somewhere with 
>>>> code to read it.
>>>>
>>>> Also, please hit 'reply all' when replying, so the matplotlib users 
>>>> mailing list is CC'ed.
>>>>
>>>> -Jeff
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>> Antoine De Pauw wrote:
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> Sir,
>>>>>>>
>>>>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> difficult to be understandable.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> All is in the script I gave to you initially, except the point
>>>>>>>               
> drawing
>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> code which would be useless as it is proven not to work (I dont know
the
>>>> method to do it).
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> geographic coordinates.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> I cannot find the right method to put colour pixels on the map,
>>>>>>>               
> that's
>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> the problem.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> I have that map in miller projection, and three arrays containing
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> respectively latitude, longitude and satellite measured value.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> What I need to obtain is something approximately like this:
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>
http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>> _00_lr.gif but with the basemap toolkit.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> coordinates lat:lon on that map? If I have just the method to project a
>>>> geographic coordinate on the map and put a coloured pixel at the right
>>>> place, all is done and I just have to loop my arrays... Also, I would
>>>>       
>>>>         
>> have
>>   
>>     
>>>> to implement some antialiasing on the map.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> Antoine:
>>>>>>
>>>>>> Are the pixels arranged on a regular grid - or are they randomly 
>>>>>> distributed?  If they are on a grid, it's easy (using pcolor or
>>>>>>           
>>>>>>             
>> imshow).
>>   
>>     
>>>>>>         
>>>>>>           
>>>>>>             
>>>   
>>>     
>>>       
>>>>>> If you could send me your data I may be able to get you started.
>>>>>>
>>>>>> (I'm cc'ing the matplotlib list so others can join in the
discussion).
>>>>>>
>>>>>>
>>>>>> -Jeff
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> If this is not possible to do it in a simple and explainable way,
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>> please
>>>   
>>>     
>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> tell me and I'll continue using matlab or searching for the bit of code
>>>> which will save me
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> Anyway, I have to thank you for your interest to help me..
>>>>>>>
>>>>>>> Many thanks,
>>>>>>>
>>>>>>> Antoine De Pauw
>>>>>>>
>>>>>>>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> Antoine De Pauw wrote:
>>>>>>>>     
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>> Hi, and thanks for the answer
>>>>>>>>>
>>>>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> (Lat,Lon,Val) describing geographic points which are associated by
index
>>>> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> What I need to do is to plot some points on the map (miller
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> projection
>>>   
>>>     
>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> for most) based on latitude and longitude, to obtain a colour map
>>>>         
> (points
>   
>>>> are unordered, it is from IASI satellite computations)
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> problem I have is any method I try for plotting points is failing,
>>>>         
> either
>   
>>>> pcolor, pcolormesh, imshow, etc.
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> When I found your post on that mailing list, I figured out that
you
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> might have the experience and skills to easily explain to me how to
>>>> manipulate these points and plot them on the map, as there's like no
>>>>         
> help
>   
>>>>     
>>>>       
>>>>         
>>> on
>>>   
>>>     
>>>       
>>>> the web except standard examples...
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> Please tell me if this is possible for you to give me some tips,
or
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> if
>>>   
>>>     
>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>> it takes too much of your time just advice me some lectures
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> Best regards,
>>>>>>>>>
>>>>>>>>> De Pauw Antoine
>>>>>>>>>   
>>>>>>>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>>>>> problem.  It sounds to me like you want to plot markers
representing
>>>>>>>>               
>>>>>>>>                 
>> a
>>   
>>     
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>   
>>>     
>>>       
>>>>>>>> set of points - for that you should use the scatter method.
pcolor,
>>>>>>>>                 
>
>   
>>>>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>>>>
>>>>>>>> -Jeff
>>>>>>>>     
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>>   
>>>>>>>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>> De Pauw Antoine wrote:
>>>>>>>>>>     
>>>>>>>>>>         
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>>> Dear sir,
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> the
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> &#8220;Quantum 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> Chemistry and Photophysics&#8221; section of the Université
Libre
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> de
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>>>>
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> It seems that you could help me find a solution, as I cannot
plot
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> any 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> points on maps.
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Could you please tell me what I could do to plot data in a
simple
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> way, 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> assuming I have 3 unordered arrays containing respectively
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> latitude,
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> longitude and values to plot?
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Some tips would be very nice from you as any method I have tried
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>> so
>>   
>>     
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> far 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> give me some errors&#8230;
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Thank you very much in advance,
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> Best regards,
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> plotting part
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>>>>
>>>>>>>>>>> from numpy import *
>>>>>>>>>>>
>>>>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>>>>
>>>>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>>>>
>>>>>>>>>>> import numpy as np
>>>>>>>>>>>
>>>>>>>>>>> import os
>>>>>>>>>>>
>>>>>>>>>>> import sys
>>>>>>>>>>>
>>>>>>>>>>> import array
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> print('preparing map')   
>>>>>>>>>>>
>>>>>>>>>>> map = 
>>>>>>>>>>>
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>
Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>>>>
>>>>>>>>>>> map.drawmapboundary()
>>>>>>>>>>>
>>>>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>>>>
>>>>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>>>>
>>>>>>>>>>> print('reading binary data')
>>>>>>>>>>>
>>>>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>>>>
>>>>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>>>>
>>>>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>>>>
>>>>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>>>>
>>>>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>>>>
>>>>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>>>>
>>>>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>>>>
>>>>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>>>>
>>>>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>>>>
>>>>>>>>>>> i=0
>>>>>>>>>>>
>>>>>>>>>>> while i < nbreligne:
>>>>>>>>>>>
>>>>>>>>>>>     if(Lon[i]>180):
>>>>>>>>>>>
>>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>>
>>>>>>>>>>>         Lon[i]-=360
>>>>>>>>>>>
>>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>>
>>>>>>>>>>>     i+=1
>>>>>>>>>>>
>>>>>>>>>>> print('plotting data')
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> #plotting code comes here
>>>>>>>>>>>       
>>>>>>>>>>>           
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>> Antoine:  If you send me a self-contained script that produces
the
>>>>>>>>>>                     
>
>   
>>>>>>>>>> problem you see, I can help you debug it.  As it stands now, I
>>>>>>>>>>                     
> have
>   
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>> very 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>> little to work with - it could be your plotting commands, or it
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>> could
>>>   
>>>     
>>>       
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>> be 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>> your data.
>>>>>>>>>>
>>>>>>>>>> -Jeff
>>>>>>>>>>     
>>>>>>>>>>         
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> print('saving map')       
>>>>>>>>>>>
>>>>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>>>>
>>>>>>>>>>> print('done')
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>> *Antoine De Pauw*
>>>>>>>>>>> Collaborateur de recherches, Informatique - Research
>>>>>>>>>>>                       
> collaborator,
>   
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> IT
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>> chemistry
>>>   
>>>     
>>>       
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> and 
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>> photophysics laboratory
>>>>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>>>>
>>>>>>>>>>>  
>>>>>>>>>>>
>>>>>>>>>>>       
>>>>>>>>>>>           
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>> -- 
>>>>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>     
>>>>>>>>>>         
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>   
>>>>>>>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> -- 
>>>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>     
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> -- 
>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>
>>>>>>
>>>>>>
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>   
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

De Pauw Antoine wrote:
> Hi Jeff,
>
> I have played a bit with Matplotlib since last week, and I may still have
> some questions for you
>
> I have masked my value array so it doesn't draw points under a certain
> value, but doing this causes the colormap to rescale for the new values
>   

Antoine:  Don't quite know what you're trying to accomplish, but you can 
use the vmin/vmax keywords to imshow, pcolor or scatter to scale the 
colormap to a certain range.  Also, take a look at the image_masked.py 
example to see how to set the 'over/under' color in a colormap.
> I have tried to set a custom colormap but it isn't the thing to do as data
> is varying in time
>
> So is it possible to avoid the colormap to rescale itself?
>
> Also, I had a look at imshow and the interpolation process is really
> interesting for smooth maps.. does a way to interpolate scattered data
> exist?
>   
If you have the most recent version of matplotlib you can use the 
griddata function to interpolate scattered data to a regular grid.

-Jeff
> The code I use didn't change since last time, all I did is adding a bit,
> testing and deleting..
>
> Best regards,
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: vendredi 12 septembre 2008 13:26
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Hi Jeff,
>>
>> I updated my code snippet and uploaded the image I created with a complete
>> set of data:
>>
>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>
>> And here's the picture generated:
>>
>> http://www.kirikoo.net/images/5shrad-20080912-105759.png
>>
>> I now understand the process and I'm able to reproduce it for other
>> datasets, but I need to implement some antialiasing for it..
>>
>> Is it possible to do?
>>
>> Many thanks for your precious help!
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine:  If you do
>
>  >>> from pylab import scatter
>  >>> help(scatter)
>
> you will see that scatter takes an antialised keyword
>
>      antialiased    Boolean or sequence of booleans    
>
> -Jeff
>
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: jeudi 11 septembre 2008 16:48
>> To: De Pauw Antoine
>> Cc: 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Jeff,
>>>
>>> The map object is from the Basemap type, the only different thing is the
>>> Lon,Lat and Val objects which are from the type array instead of lists
>>>
>>> Anyway, solutions are slowly showing themselves and I thank you all
>>>
>>> Have a nice day
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>   
>>>     
>>>       
>> Antoine:  It should not matter if Lon and Lat are python arrays, lists 
>> or numpy arrays.  The Basemap instance __call__ method handles them all. 
>> There must be something else going on.  It is always better to post 
>> actual code so we can see what is happening and test it ourselves.
>>
>> -Jeff
>>   
>>     
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: jeudi 11 septembre 2008 15:29
>>> To: De Pauw Antoine
>>> Cc: 'Matplotlib Users'
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> De Pauw Antoine wrote:
>>>   
>>>     
>>>       
>>>> Thanks Jeff,
>>>>
>>>> This seems to work with csv file types, and I've been experimenting a
>>>>         
> bit
>   
>>>> with it
>>>>
>>>> However, when I try to implement this with my original code (with binary
>>>> files), I get an error like that one:
>>>>
>>>> Traceback (most recent call last):
>>>>   File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module>
>>>>     x,y = map(Lon,Lat)
>>>> TypeError: 'numpy.ndarray' object is not callable
>>>>
>>>> I think this is coming from the fact I use array objects to store
>>>>     
>>>>       
>>>>         
>>> values...
>>>   
>>>     
>>>       
>>>> could you confirm it?
>>>>   
>>>>     
>>>>       
>>>>         
>>> Antoine:  It looks like you the object map is not a Basemap instance, 
>>> but a numpy array.  Try putting 'print type(map)' just ahead of this 
>>> statement to verify this. I suspect your re-using the name 'map' in your 
>>> code,  overwriting the Basemap class instance.
>>>
>>> -Jeff
>>>   
>>>     
>>>       
>>>> Also, I'll see if it is possible to invert color scale and mask
>>>>       
>>>>         
>> everything
>>   
>>     
>>>> under a certain value
>>>>
>>>> Thanks very much for your help!
>>>>
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>> Sent: jeudi 11 septembre 2008 14:10
>>>> To: De Pauw Antoine
>>>> Cc: 'Matplotlib Users'
>>>> Subject: Re: [Matplotlib-users] Information request
>>>>
>>>> De Pauw Antoine wrote:
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> Hi Jeff,
>>>>>
>>>>> I have put the code online with a sample of the data here:
>>>>>
>>>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>>>
>>>>> I hope you'll be able to give me some advice as it is quite difficult
>>>>>         
>>>>>           
>> for
>>   
>>     
>>>>> someone new in python and scientific computation
>>>>>
>>>>> Antoine De Pauw
>>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
>>>>>           
> and
>   
>>>>> photophysics laboratory
>>>>> Université Libre de Bruxelles - ULB
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> Antoine: I may have the size of the pixels wrong, and lat/lon 
>>>> transposed, but this is the general idea:
>>>>
>>>> from mpl_toolkits.basemap import Basemap
>>>> import matplotlib.pyplot as plt
>>>> import numpy as np
>>>> lats = []; lons = []; data = []
>>>> for line in open('pixels.dat'):
>>>>     linesplit = line.split(',')
>>>>     lons.append(float(linesplit[1]))
>>>>     lats.append(float(linesplit[0]))
>>>>     data.append(float(linesplit[2]))
>>>> map = 
>>>> Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
>>>>                           
>>>> urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
>>>> x,y = map(lons,lats)
>>>> plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
>>>> plt.colorbar(shrink=0.6)
>>>> map.drawcoastlines()
>>>> plt.show()
>>>>
>>>> -Jeff
>>>>
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> -----Original Message-----
>>>>> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
>>>>> Sent: mercredi 10 septembre 2008 16:45
>>>>> To: Antoine De Pauw
>>>>> Cc: Matplotlib Users
>>>>> Subject: Re: Information request
>>>>>
>>>>> Antoine De Pauw wrote:
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> Thanks Jeff,
>>>>>>
>>>>>> In fact my points are arranged in three unsorted arrays, with a simple
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> scheme (thats why I couldn't plot them with imshow and others)
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> arrays:
>>>>>>
>>>>>> [lat][lon][val]
>>>>>> [-10][ 17][0.3]
>>>>>> [ 37][ 23][3.7]
>>>>>>  ...  ...  ...
>>>>>>
>>>>>> and so for many rows...
>>>>>>
>>>>>> what I have to do is looping through my arrays like that
>>>>>>
>>>>>> while i < rowcount:
>>>>>>     plot_to_map(lat[i],lon[i],val[i])
>>>>>>
>>>>>> it is evidently an idea of how it could be done easily but my
>>>>>>             
> knowledge
>   
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>> of
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> these libraries is too weak for me to figure out how to do it
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> my data comes from huge binary files but is extremely simple, so it
>>>>>>         
>>>>>>           
>>>>>>             
>>> would
>>>   
>>>     
>>>       
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> be really easy for anyone to help me as the problem itself is how to
>>>>>           
> put
>   
>>>>> unsorted points on the map with latitude and longitude coordinates
>>>>>   
>>>>>
>>>>> Antoine:  You haven't said if your data forms a rectangular array.  If 
>>>>> so, you can build a 2-d array from the input file and plot it with 
>>>>> imshow.  If not, you can still plug the elements into a 2-d masked 
>>>>> array, leaving the missing pixels masked.  You say the points are 
>>>>> 'unsorted', does that mean they are randomly distributed and do not
>>>>>           
> form
>   
>>>>>         
>>>>>           
>>   
>>     
>>>>> a rectangular grid?
>>>>>
>>>>> It would really be much easier to help if you gave us more information,
>>>>>           
>
>   
>>>>> such as how the data is structured, what the pixel footprint is, etc. 
>>>>> Perhaps you could post the binary file on an ftp site somewhere with 
>>>>> code to read it.
>>>>>
>>>>> Also, please hit 'reply all' when replying, so the matplotlib users 
>>>>> mailing list is CC'ed.
>>>>>
>>>>> -Jeff
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>> Antoine De Pauw wrote:
>>>>>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> Sir,
>>>>>>>>
>>>>>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> difficult to be understandable.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> All is in the script I gave to you initially, except the point
>>>>>>>>               
>>>>>>>>                 
>> drawing
>>   
>>     
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> code which would be useless as it is proven not to work (I dont know
>>>>>           
> the
>   
>>>>> method to do it).
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> geographic coordinates.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> I cannot find the right method to put colour pixels on the map,
>>>>>>>>               
>>>>>>>>                 
>> that's
>>   
>>     
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> the problem.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> I have that map in miller projection, and three arrays containing
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> respectively latitude, longitude and satellite measured value.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> What I need to obtain is something approximately like this:
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
> http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> _00_lr.gif but with the basemap toolkit.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> coordinates lat:lon on that map? If I have just the method to project a
>>>>> geographic coordinate on the map and put a coloured pixel at the right
>>>>> place, all is done and I just have to loop my arrays... Also, I would
>>>>>       
>>>>>         
>>>>>           
>>> have
>>>   
>>>     
>>>       
>>>>> to implement some antialiasing on the map.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>   
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> Antoine:
>>>>>>>
>>>>>>> Are the pixels arranged on a regular grid - or are they randomly 
>>>>>>> distributed?  If they are on a grid, it's easy (using pcolor or
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>> imshow).
>>>   
>>>     
>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> If you could send me your data I may be able to get you started.
>>>>>>>
>>>>>>> (I'm cc'ing the matplotlib list so others can join in the
>>>>>>>               
> discussion).
>   
>>>>>>> -Jeff
>>>>>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> If this is not possible to do it in a simple and explainable way,
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>> please
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> tell me and I'll continue using matlab or searching for the bit of code
>>>>> which will save me
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> Anyway, I have to thank you for your interest to help me..
>>>>>>>>
>>>>>>>> Many thanks,
>>>>>>>>
>>>>>>>> Antoine De Pauw
>>>>>>>>
>>>>>>>>   
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>> Antoine De Pauw wrote:
>>>>>>>>>     
>>>>>>>>>           
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>> Hi, and thanks for the answer
>>>>>>>>>>
>>>>>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>> (Lat,Lon,Val) describing geographic points which are associated by
>>>>>           
> index
>   
>>>>> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>> What I need to do is to plot some points on the map (miller
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>> projection
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>> for most) based on latitude and longitude, to obtain a colour map
>>>>>         
>>>>>           
>> (points
>>   
>>     
>>>>> are unordered, it is from IASI satellite computations)
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>> problem I have is any method I try for plotting points is failing,
>>>>>         
>>>>>           
>> either
>>   
>>     
>>>>> pcolor, pcolormesh, imshow, etc.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>> When I found your post on that mailing list, I figured out that
>>>>>>>>>>                     
> you
>   
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>> might have the experience and skills to easily explain to me how to
>>>>> manipulate these points and plot them on the map, as there's like no
>>>>>         
>>>>>           
>> help
>>   
>>     
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> on
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> the web except standard examples...
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>> Please tell me if this is possible for you to give me some tips,
>>>>>>>>>>                     
> or
>   
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>> if
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>> it takes too much of your time just advice me some lectures
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>> Best regards,
>>>>>>>>>>
>>>>>>>>>> De Pauw Antoine
>>>>>>>>>>   
>>>>>>>>>>       
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>> Antoine:  It would really help to have a script demonstrating your 
>>>>>>>>> problem.  It sounds to me like you want to plot markers
>>>>>>>>>                   
> representing
>   
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> a
>>>   
>>>     
>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> set of points - for that you should use the scatter method.
>>>>>>>>>                   
> pcolor,
>   
>>>>>>>>>                 
>>>>>>>>>                   
>>   
>>     
>>>>>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>>>>>
>>>>>>>>> -Jeff
>>>>>>>>>     
>>>>>>>>>           
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>>   
>>>>>>>>>>       
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>>> De Pauw Antoine wrote:
>>>>>>>>>>>     
>>>>>>>>>>>         
>>>>>>>>>>>               
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>>>> Dear sir,
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> I&#8217;m currently trying to improve our plotting tools here at
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>> the
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> &#8220;Quantum 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> Chemistry and Photophysics&#8221; section of the Université
>>>>>>>>>>>>                         
> Libre
>   
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>> de
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a 
>>>>>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>>>>>
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> It seems that you could help me find a solution, as I cannot
>>>>>>>>>>>>                         
> plot
>   
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> any 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> points on maps.
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> Could you please tell me what I could do to plot data in a
>>>>>>>>>>>>                         
> simple
>   
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> way, 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> assuming I have 3 unordered arrays containing respectively
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>> latitude,
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> longitude and values to plot?
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> Some tips would be very nice from you as any method I have tried
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>> so
>>>   
>>>     
>>>       
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> far 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> give me some errors&#8230;
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you very much in advance,
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> Best regards,
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> plotting part
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>>>>>
>>>>>>>>>>>> from numpy import *
>>>>>>>>>>>>
>>>>>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>>>>>
>>>>>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>>>>>
>>>>>>>>>>>> import numpy as np
>>>>>>>>>>>>
>>>>>>>>>>>> import os
>>>>>>>>>>>>
>>>>>>>>>>>> import sys
>>>>>>>>>>>>
>>>>>>>>>>>> import array
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> print('preparing map')   
>>>>>>>>>>>>
>>>>>>>>>>>> map = 
>>>>>>>>>>>>
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
> Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>>>>>
>>>>>>>>>>>> map.drawmapboundary()
>>>>>>>>>>>>
>>>>>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>>>>>
>>>>>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>>>>>
>>>>>>>>>>>> print('reading binary data')
>>>>>>>>>>>>
>>>>>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>>>>>
>>>>>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>>>>>
>>>>>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>>>>>
>>>>>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>>>>>
>>>>>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>>>>>
>>>>>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>>>>>
>>>>>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>>>>>
>>>>>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>>>>>
>>>>>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>>>>>
>>>>>>>>>>>> i=0
>>>>>>>>>>>>
>>>>>>>>>>>> while i < nbreligne:
>>>>>>>>>>>>
>>>>>>>>>>>>     if(Lon[i]>180):
>>>>>>>>>>>>
>>>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>>>
>>>>>>>>>>>>         Lon[i]-=360
>>>>>>>>>>>>
>>>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>>>
>>>>>>>>>>>>     i+=1
>>>>>>>>>>>>
>>>>>>>>>>>> print('plotting data')
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> #plotting code comes here
>>>>>>>>>>>>       
>>>>>>>>>>>>           
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>>>>>>>> Antoine:  If you send me a self-contained script that produces
>>>>>>>>>>>                       
> the
>   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>   
>>     
>>>>>>>>>>> problem you see, I can help you debug it.  As it stands now, I
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>> have
>>   
>>     
>>>>>>>>>>>               
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>> very 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>> little to work with - it could be your plotting commands, or it
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> could
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>               
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>> be 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>> your data.
>>>>>>>>>>>
>>>>>>>>>>> -Jeff
>>>>>>>>>>>     
>>>>>>>>>>>         
>>>>>>>>>>>               
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> print('saving map')       
>>>>>>>>>>>>
>>>>>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>>>>>
>>>>>>>>>>>> print('done')
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> *Antoine De Pauw*
>>>>>>>>>>>> Collaborateur de recherches, Informatique - Research
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>> collaborator,
>>   
>>     
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> IT
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>> chemistry
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> and 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> photophysics laboratory
>>>>>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>>       
>>>>>>>>>>>>           
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>>>>>>>> -- 
>>>>>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>     
>>>>>>>>>>>         
>>>>>>>>>>>               
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>>   
>>>>>>>>>>       
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>> -- 
>>>>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>     
>>>>>>>>>           
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>   
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> -- 
>>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>   
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Jeff,

In fact my satellite data is displaying clouds of various gases, and I don’t
like the fact that "empty" places are left dark blue (I use jet reversed
cmap)

By masking data under a certain value, I isolate the clouds and then they
are in evidence

When I use vmin and vmax I'm able to avoid the colormap rescaling and I keep
the cloud's original colour, but then it is the colorbar which poses
problems, as there's a part of the bar that is useless

I guess what I should do is setting a new colorbar myself, but there again,
it is not very easy to understand... that kind of libraries are really
occult for a non-scientific IT graduate like me

Now for the antialiasing and interpolation, the thing I try to do is making
it look less pixeled, I don't need all the points to be interpolated, but
just make the existing points smoother to have a smooth, quality figure

You have helped me a lot, and I know my questions were beginners ones, so
I'll understand if you prefer giving some time to something more interesting

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: mardi 16 septembre 2008 13:16
To: De Pauw Antoine
Cc: 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Hi Jeff,
>
> I have played a bit with Matplotlib since last week, and I may still have
> some questions for you
>
> I have masked my value array so it doesn't draw points under a certain
> value, but doing this causes the colormap to rescale for the new values
>   

Antoine:  Don't quite know what you're trying to accomplish, but you can 
use the vmin/vmax keywords to imshow, pcolor or scatter to scale the 
colormap to a certain range.  Also, take a look at the image_masked.py 
example to see how to set the 'over/under' color in a colormap.
> I have tried to set a custom colormap but it isn't the thing to do as data
> is varying in time
>
> So is it possible to avoid the colormap to rescale itself?
>
> Also, I had a look at imshow and the interpolation process is really
> interesting for smooth maps.. does a way to interpolate scattered data
> exist?
>   
If you have the most recent version of matplotlib you can use the 
griddata function to interpolate scattered data to a regular grid.

-Jeff
> The code I use didn't change since last time, all I did is adding a bit,
> testing and deleting..
>
> Best regards,
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: vendredi 12 septembre 2008 13:26
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Hi Jeff,
>>
>> I updated my code snippet and uploaded the image I created with a
complete
>> set of data:
>>
>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>
>> And here's the picture generated:
>>
>> http://www.kirikoo.net/images/5shrad-20080912-105759.png
>>
>> I now understand the process and I'm able to reproduce it for other
>> datasets, but I need to implement some antialiasing for it..
>>
>> Is it possible to do?
>>
>> Many thanks for your precious help!
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine:  If you do
>
>  >>> from pylab import scatter
>  >>> help(scatter)
>
> you will see that scatter takes an antialised keyword
>
>      antialiased    Boolean or sequence of booleans    
>
> -Jeff
>
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: jeudi 11 septembre 2008 16:48
>> To: De Pauw Antoine
>> Cc: 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Jeff,
>>>
>>> The map object is from the Basemap type, the only different thing is the
>>> Lon,Lat and Val objects which are from the type array instead of lists
>>>
>>> Anyway, solutions are slowly showing themselves and I thank you all
>>>
>>> Have a nice day
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>   
>>>     
>>>       
>> Antoine:  It should not matter if Lon and Lat are python arrays, lists 
>> or numpy arrays.  The Basemap instance __call__ method handles them all. 
>> There must be something else going on.  It is always better to post 
>> actual code so we can see what is happening and test it ourselves.
>>
>> -Jeff
>>   
>>     
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: jeudi 11 septembre 2008 15:29
>>> To: De Pauw Antoine
>>> Cc: 'Matplotlib Users'
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> De Pauw Antoine wrote:
>>>   
>>>     
>>>       
>>>> Thanks Jeff,
>>>>
>>>> This seems to work with csv file types, and I've been experimenting a
>>>>         
> bit
>   
>>>> with it
>>>>
>>>> However, when I try to implement this with my original code (with
binary
>>>> files), I get an error like that one:
>>>>
>>>> Traceback (most recent call last):
>>>>   File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module>
>>>>     x,y = map(Lon,Lat)
>>>> TypeError: 'numpy.ndarray' object is not callable
>>>>
>>>> I think this is coming from the fact I use array objects to store
>>>>     
>>>>       
>>>>         
>>> values...
>>>   
>>>     
>>>       
>>>> could you confirm it?
>>>>   
>>>>     
>>>>       
>>>>         
>>> Antoine:  It looks like you the object map is not a Basemap instance, 
>>> but a numpy array.  Try putting 'print type(map)' just ahead of this 
>>> statement to verify this. I suspect your re-using the name 'map' in your

>>> code,  overwriting the Basemap class instance.
>>>
>>> -Jeff
>>>   
>>>     
>>>       
>>>> Also, I'll see if it is possible to invert color scale and mask
>>>>       
>>>>         
>> everything
>>   
>>     
>>>> under a certain value
>>>>
>>>> Thanks very much for your help!
>>>>
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>> Sent: jeudi 11 septembre 2008 14:10
>>>> To: De Pauw Antoine
>>>> Cc: 'Matplotlib Users'
>>>> Subject: Re: [Matplotlib-users] Information request
>>>>
>>>> De Pauw Antoine wrote:
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> Hi Jeff,
>>>>>
>>>>> I have put the code online with a sample of the data here:
>>>>>
>>>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>>>
>>>>> I hope you'll be able to give me some advice as it is quite difficult
>>>>>         
>>>>>           
>> for
>>   
>>     
>>>>> someone new in python and scientific computation
>>>>>
>>>>> Antoine De Pauw
>>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
>>>>>           
> and
>   
>>>>> photophysics laboratory
>>>>> Université Libre de Bruxelles - ULB
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> Antoine: I may have the size of the pixels wrong, and lat/lon 
>>>> transposed, but this is the general idea:
>>>>
>>>> from mpl_toolkits.basemap import Basemap
>>>> import matplotlib.pyplot as plt
>>>> import numpy as np
>>>> lats = []; lons = []; data = []
>>>> for line in open('pixels.dat'):
>>>>     linesplit = line.split(',')
>>>>     lons.append(float(linesplit[1]))
>>>>     lats.append(float(linesplit[0]))
>>>>     data.append(float(linesplit[2]))
>>>> map = 
>>>> Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\
>>>>                           
>>>> urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l')
>>>> x,y = map(lons,lats)
>>>>
plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet)
>>>> plt.colorbar(shrink=0.6)
>>>> map.drawcoastlines()
>>>> plt.show()
>>>>
>>>> -Jeff
>>>>
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> -----Original Message-----
>>>>> From: Jeff Whitaker [mailto:Jeffrey.S.Whitaker@...] 
>>>>> Sent: mercredi 10 septembre 2008 16:45
>>>>> To: Antoine De Pauw
>>>>> Cc: Matplotlib Users
>>>>> Subject: Re: Information request
>>>>>
>>>>> Antoine De Pauw wrote:
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> Thanks Jeff,
>>>>>>
>>>>>> In fact my points are arranged in three unsorted arrays, with a
simple
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> scheme (thats why I couldn't plot them with imshow and others)
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> arrays:
>>>>>>
>>>>>> [lat][lon][val]
>>>>>> [-10][ 17][0.3]
>>>>>> [ 37][ 23][3.7]
>>>>>>  ...  ...  ...
>>>>>>
>>>>>> and so for many rows...
>>>>>>
>>>>>> what I have to do is looping through my arrays like that
>>>>>>
>>>>>> while i < rowcount:
>>>>>>     plot_to_map(lat[i],lon[i],val[i])
>>>>>>
>>>>>> it is evidently an idea of how it could be done easily but my
>>>>>>             
> knowledge
>   
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>> of
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> these libraries is too weak for me to figure out how to do it
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> my data comes from huge binary files but is extremely simple, so it
>>>>>>         
>>>>>>           
>>>>>>             
>>> would
>>>   
>>>     
>>>       
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> be really easy for anyone to help me as the problem itself is how to
>>>>>           
> put
>   
>>>>> unsorted points on the map with latitude and longitude coordinates
>>>>>   
>>>>>
>>>>> Antoine:  You haven't said if your data forms a rectangular array.  If

>>>>> so, you can build a 2-d array from the input file and plot it with 
>>>>> imshow.  If not, you can still plug the elements into a 2-d masked 
>>>>> array, leaving the missing pixels masked.  You say the points are 
>>>>> 'unsorted', does that mean they are randomly distributed and do not
>>>>>           
> form
>   
>>>>>         
>>>>>           
>>   
>>     
>>>>> a rectangular grid?
>>>>>
>>>>> It would really be much easier to help if you gave us more
information,
>>>>>           
>
>   
>>>>> such as how the data is structured, what the pixel footprint is, etc. 
>>>>> Perhaps you could post the binary file on an ftp site somewhere with 
>>>>> code to read it.
>>>>>
>>>>> Also, please hit 'reply all' when replying, so the matplotlib users 
>>>>> mailing list is CC'ed.
>>>>>
>>>>> -Jeff
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>> Antoine De Pauw wrote:
>>>>>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> Sir,
>>>>>>>>
>>>>>>>> I'm sorry, as english is not my mothertongue and it is sometimes
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> difficult to be understandable.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> All is in the script I gave to you initially, except the point
>>>>>>>>               
>>>>>>>>                 
>> drawing
>>   
>>     
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> code which would be useless as it is proven not to work (I dont know
>>>>>           
> the
>   
>>>>> method to do it).
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> What I have is a map, and a set of pixels I have to put on it with
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> geographic coordinates.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> I cannot find the right method to put colour pixels on the map,
>>>>>>>>               
>>>>>>>>                 
>> that's
>>   
>>     
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> the problem.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> I have that map in miller projection, and three arrays containing
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> respectively latitude, longitude and satellite measured value.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> What I need to obtain is something approximately like this:
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>
http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> _00_lr.gif but with the basemap toolkit.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> So, my question is: how could I do to plot a coloured pixel at
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> coordinates lat:lon on that map? If I have just the method to project
a
>>>>> geographic coordinate on the map and put a coloured pixel at the right
>>>>> place, all is done and I just have to loop my arrays... Also, I would
>>>>>       
>>>>>         
>>>>>           
>>> have
>>>   
>>>     
>>>       
>>>>> to implement some antialiasing on the map.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>   
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> Antoine:
>>>>>>>
>>>>>>> Are the pixels arranged on a regular grid - or are they randomly 
>>>>>>> distributed?  If they are on a grid, it's easy (using pcolor or
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>> imshow).
>>>   
>>>     
>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> If you could send me your data I may be able to get you started.
>>>>>>>
>>>>>>> (I'm cc'ing the matplotlib list so others can join in the
>>>>>>>               
> discussion).
>   
>>>>>>> -Jeff
>>>>>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> If this is not possible to do it in a simple and explainable way,
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>> please
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>> tell me and I'll continue using matlab or searching for the bit of
code
>>>>> which will save me
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>> Anyway, I have to thank you for your interest to help me..
>>>>>>>>
>>>>>>>> Many thanks,
>>>>>>>>
>>>>>>>> Antoine De Pauw
>>>>>>>>
>>>>>>>>   
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>> Antoine De Pauw wrote:
>>>>>>>>>     
>>>>>>>>>           
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>> Hi, and thanks for the answer
>>>>>>>>>>
>>>>>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>> (Lat,Lon,Val) describing geographic points which are associated by
>>>>>           
> index
>   
>>>>> (like point 1 is Lat[0]:Lon[0] with value Val[0])
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>> What I need to do is to plot some points on the map (miller
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>> projection
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>> for most) based on latitude and longitude, to obtain a colour map
>>>>>         
>>>>>           
>> (points
>>   
>>     
>>>>> are unordered, it is from IASI satellite computations)
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>> I'm able to create a map, draw simple things on it, etc but the
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>> problem I have is any method I try for plotting points is failing,
>>>>>         
>>>>>           
>> either
>>   
>>     
>>>>> pcolor, pcolormesh, imshow, etc.
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>> When I found your post on that mailing list, I figured out that
>>>>>>>>>>                     
> you
>   
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>> might have the experience and skills to easily explain to me how to
>>>>> manipulate these points and plot them on the map, as there's like no
>>>>>         
>>>>>           
>> help
>>   
>>     
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> on
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> the web except standard examples...
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>> Please tell me if this is possible for you to give me some tips,
>>>>>>>>>>                     
> or
>   
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>> if
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>> it takes too much of your time just advice me some lectures
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>> Best regards,
>>>>>>>>>>
>>>>>>>>>> De Pauw Antoine
>>>>>>>>>>   
>>>>>>>>>>       
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>> Antoine:  It would really help to have a script demonstrating your

>>>>>>>>> problem.  It sounds to me like you want to plot markers
>>>>>>>>>                   
> representing
>   
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>> a
>>>   
>>>     
>>>       
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>> set of points - for that you should use the scatter method.
>>>>>>>>>                   
> pcolor,
>   
>>>>>>>>>                 
>>>>>>>>>                   
>>   
>>     
>>>>>>>>> pcolormesh and friends are for plotting gridded data.
>>>>>>>>>
>>>>>>>>> -Jeff
>>>>>>>>>     
>>>>>>>>>           
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>>>   
>>>>>>>>>>       
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>>>> De Pauw Antoine wrote:
>>>>>>>>>>>     
>>>>>>>>>>>         
>>>>>>>>>>>               
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>>>> Dear sir,
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> I&#8217;m currently trying to improve our plotting tools here
at
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>> the
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> &#8220;Quantum 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> Chemistry and Photophysics&#8221; section of the Université
>>>>>>>>>>>>                         
> Libre
>   
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>> de
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a

>>>>>>>>>>>> solution, on an explanation from you here: 
>>>>>>>>>>>>
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> It seems that you could help me find a solution, as I cannot
>>>>>>>>>>>>                         
> plot
>   
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> any 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> points on maps.
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> Could you please tell me what I could do to plot data in a
>>>>>>>>>>>>                         
> simple
>   
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> way, 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> assuming I have 3 unordered arrays containing respectively
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>> latitude,
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> longitude and values to plot?
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> Some tips would be very nice from you as any method I have
tried
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>> so
>>>   
>>>     
>>>       
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> far 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> give me some errors&#8230;
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you very much in advance,
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> Best regards,
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> PS: I give you the code I&#8217;m using currently, missing the
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> plotting part
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> from mpl_toolkits.basemap import Basemap
>>>>>>>>>>>>
>>>>>>>>>>>> from numpy import *
>>>>>>>>>>>>
>>>>>>>>>>>> from scipy.io.numpyio import fread
>>>>>>>>>>>>
>>>>>>>>>>>> import matplotlib.pyplot as plt
>>>>>>>>>>>>
>>>>>>>>>>>> import numpy as np
>>>>>>>>>>>>
>>>>>>>>>>>> import os
>>>>>>>>>>>>
>>>>>>>>>>>> import sys
>>>>>>>>>>>>
>>>>>>>>>>>> import array
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> fileName="c:/20080821.b56"
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> print('preparing map')   
>>>>>>>>>>>>
>>>>>>>>>>>> map = 
>>>>>>>>>>>>
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>
Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.)
>   
>>   
>>     
>>>   
>>>     
>>>       
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> map.drawcoastlines(0.5,antialiased=1)
>>>>>>>>>>>>
>>>>>>>>>>>> map.drawmapboundary()
>>>>>>>>>>>>
>>>>>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, 
>>>>>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-")
>>>>>>>>>>>>
>>>>>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, 
>>>>>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-")
>>>>>>>>>>>>
>>>>>>>>>>>> print('reading binary data')
>>>>>>>>>>>>
>>>>>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>>>>>>>>>>>
>>>>>>>>>>>> Lat=zeros(nbreligne)
>>>>>>>>>>>>
>>>>>>>>>>>> Lon=zeros(nbreligne)
>>>>>>>>>>>>
>>>>>>>>>>>> Val=zeros(nbreligne)
>>>>>>>>>>>>
>>>>>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1)       
>>>>>>>>>>>>
>>>>>>>>>>>> Lat=rawfile[0:nbreligne]
>>>>>>>>>>>>
>>>>>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2]
>>>>>>>>>>>>
>>>>>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>>>>>>>>>>>
>>>>>>>>>>>> print('shifting latitudes and projecting to map')
>>>>>>>>>>>>
>>>>>>>>>>>> i=0
>>>>>>>>>>>>
>>>>>>>>>>>> while i < nbreligne:
>>>>>>>>>>>>
>>>>>>>>>>>>     if(Lon[i]>180):
>>>>>>>>>>>>
>>>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>>>
>>>>>>>>>>>>         Lon[i]-=360
>>>>>>>>>>>>
>>>>>>>>>>>>         print(Lon[i])
>>>>>>>>>>>>
>>>>>>>>>>>>     i+=1
>>>>>>>>>>>>
>>>>>>>>>>>> print('plotting data')
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> #plotting code comes here
>>>>>>>>>>>>       
>>>>>>>>>>>>           
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>>>>>>>> Antoine:  If you send me a self-contained script that produces
>>>>>>>>>>>                       
> the
>   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>   
>>     
>>>>>>>>>>> problem you see, I can help you debug it.  As it stands now, I
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>> have
>>   
>>     
>>>>>>>>>>>               
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>> very 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>> little to work with - it could be your plotting commands, or it
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>> could
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>               
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>> be 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>> your data.
>>>>>>>>>>>
>>>>>>>>>>> -Jeff
>>>>>>>>>>>     
>>>>>>>>>>>         
>>>>>>>>>>>               
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> print('saving map')       
>>>>>>>>>>>>
>>>>>>>>>>>> plt.savefig("testfig.png",dpi=600)
>>>>>>>>>>>>
>>>>>>>>>>>> print('done')
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>> *Antoine De Pauw*
>>>>>>>>>>>> Collaborateur de recherches, Informatique - Research
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>> collaborator,
>>   
>>     
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> IT
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>> chemistry
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>> and 
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>>>>>>> photophysics laboratory
>>>>>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>*
>>>>>>>>>>>>
>>>>>>>>>>>>  
>>>>>>>>>>>>
>>>>>>>>>>>>       
>>>>>>>>>>>>           
>>>>>>>>>>>>                 
>>>>>>>>>>>>                   
>>>>>>>>>>>>                     
>>>>>>>>>>>>                       
>>>>>>>>>>>>                         
>>>>>>>>>>> -- 
>>>>>>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>     
>>>>>>>>>>>         
>>>>>>>>>>>               
>>>>>>>>>>>                 
>>>>>>>>>>>                   
>>>>>>>>>>>                     
>>>>>>>>>>>                       
>>>>>>>>>>   
>>>>>>>>>>       
>>>>>>>>>>             
>>>>>>>>>>               
>>>>>>>>>>                 
>>>>>>>>>>                   
>>>>>>>>>>                     
>>>>>>>>> -- 
>>>>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>     
>>>>>>>>>           
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>>   
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> -- 
>>>>>>> Jeffrey S. Whitaker         Phone : (303)497-6313
>>>>>>> NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
>>>>>>> 325 Broadway                Boulder, CO, USA 80305-3328
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>   
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

De Pauw Antoine wrote:
> Jeff,
> 
> In fact my satellite data is displaying clouds of various gases, and I don’t
> like the fact that "empty" places are left dark blue (I use jet reversed
> cmap)
> 
> By masking data under a certain value, I isolate the clouds and then they
> are in evidence
> 
> When I use vmin and vmax I'm able to avoid the colormap rescaling and I keep
> the cloud's original colour, but then it is the colorbar which poses
> problems, as there's a part of the bar that is useless

Can you provide a compact example script, completely self-contained, 
that illustrates the problem with the colorbar?  Perhaps by modifying 
one of the standard mpl examples, such as image_masked.py? From what you 
have said, I would expect that some combination of masking, using vmin 
and vmax, and using the special value colors, would work adequately with 
the present colorbar.

Eric

Eric,

I solved the problem by using vmin/vmax, masking and the heat colorbar
That choice is then "self-masking" for undesired pixels left after masking
and vmin/vmax

Now the thing I still have to do is smoothing scattered data, after that
I'll implement it with GTK or any other windowing system and when it is
finished I'll provide it to the community for example purpose

In fact I'm not demanding for code or so, but for method names which could
help me do what I need, with code examples for instance

The source code is the same as the one posted initially in that mail, except
the masked array which is, I think, straightforward for most of you

Now I have scattered data on my map, antialiased and so, but it still needs
some smoothing as it still looks very pixelated (that is due to the
satellite coverage)

The image generated is here:
http://www.kirikoo.net/images/5shrad-20080917-102544.png

Also, I couldn't find any way to reduce the colorbar font size

Do you know of any ways to achieve these goals?

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Eric Firing [mailto:efiring@...] 
Sent: mardi 16 septembre 2008 21:58
To: De Pauw Antoine
Cc: 'Jeff Whitaker'; 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Jeff,
> 
> In fact my satellite data is displaying clouds of various gases, and I
don’t
> like the fact that "empty" places are left dark blue (I use jet reversed
> cmap)
> 
> By masking data under a certain value, I isolate the clouds and then they
> are in evidence
> 
> When I use vmin and vmax I'm able to avoid the colormap rescaling and I
keep
> the cloud's original colour, but then it is the colorbar which poses
> problems, as there's a part of the bar that is useless

Can you provide a compact example script, completely self-contained, 
that illustrates the problem with the colorbar?  Perhaps by modifying 
one of the standard mpl examples, such as image_masked.py? From what you 
have said, I would expect that some combination of masking, using vmin 
and vmax, and using the special value colors, would work adequately with 
the present colorbar.

Eric

On Wed, Sep 17, 2008 at 3:28 AM, De Pauw Antoine <andepauw@...> wrote:

> The image generated is here:
> http://www.kirikoo.net/images/5shrad-20080917-102544.png
>
> Also, I couldn't find any way to reduce the colorbar font size

The colorbar method returns a matplotlib.colorbar.Colorbar instance,
which has matplotlib.axes.Axes instance stored as an attribute.  Thus
you can do:

cb = colorbar(something....)

for t in cb.get_yticklabels():
    t.set_fontsize(10)

Eric: when you get some time, could you add docstrings to colorbar
which document the publicly accessible attributes?

JDH

Hi John,

I used your example with the missing .ax to modify these font sizes and it
works nicely

Anyway, by investigation, I found that there is no way of interpolation
using scattered data

I tried to figure out how to grid my values and use imshow or pcolor, but
with no success yet..

Could you explain me how I could do to grid, for example, that data:

Lat[] (double array containing latitudes)
Lon[] (double array containing longitudes)
Val[] (double array containing values)

Each of the arrays having the same size, and Val[1] has latitude Lat[1] and
longitude Lon[1], and so on, and the coordinates are completely unordered

When I try to use griddata and use imshow or pcolor with the output array,
my figure is blank

A simple example or guideline would do, I guess, as I've already gained a
good knowledge of the language

Thanks in advance

PS: Here's the code snippet:
http://snipplr.com/view/8307/map-plotting-python-code-temporary/


Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: John Hunter [mailto:jdh2358@...] 
Sent: mercredi 17 septembre 2008 13:00
To: De Pauw Antoine
Cc: Eric Firing; Jeff Whitaker; Matplotlib Users
Subject: Re: [Matplotlib-users] Information request

On Wed, Sep 17, 2008 at 3:28 AM, De Pauw Antoine <andepauw@...> wrote:

> The image generated is here:
> http://www.kirikoo.net/images/5shrad-20080917-102544.png
>
> Also, I couldn't find any way to reduce the colorbar font size

The colorbar method returns a matplotlib.colorbar.Colorbar instance,
which has matplotlib.axes.Axes instance stored as an attribute.  Thus
you can do:

cb = colorbar(something....)

for t in cb.get_yticklabels():
    t.set_fontsize(10)

Eric: when you get some time, could you add docstrings to colorbar
which document the publicly accessible attributes?

JDH

De Pauw Antoine wrote:
> Hi John,
>
> I used your example with the missing .ax to modify these font sizes and it
> works nicely
>
> Anyway, by investigation, I found that there is no way of interpolation
> using scattered data
>
> I tried to figure out how to grid my values and use imshow or pcolor, but
> with no success yet..
>
> Could you explain me how I could do to grid, for example, that data:
>
> Lat[] (double array containing latitudes)
> Lon[] (double array containing longitudes)
> Val[] (double array containing values)
>
> Each of the arrays having the same size, and Val[1] has latitude Lat[1] and
> longitude Lon[1], and so on, and the coordinates are completely unordered
>
> When I try to use griddata and use imshow or pcolor with the output array,
> my figure is blank
>
> A simple example or guideline would do, I guess, as I've already gained a
> good knowledge of the language
>
> Thanks in advance
>
> PS: Here's the code snippet:
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  Griddata should work fine.  Your code snippet does not try to 
use griddata, so I can't guess what is wrong.  Let me suggest again  - 
please post complete, self-contained examples that demonstrate your 
problem. 

Did you look at the griddata_demo.py example?

-Jeff

>
> -----Original Message-----
> From: John Hunter [mailto:jdh2358@...] 
> Sent: mercredi 17 septembre 2008 13:00
> To: De Pauw Antoine
> Cc: Eric Firing; Jeff Whitaker; Matplotlib Users
> Subject: Re: [Matplotlib-users] Information request
>
> On Wed, Sep 17, 2008 at 3:28 AM, De Pauw Antoine <andepauw@...> wrote:
>
>   
>> The image generated is here:
>> http://www.kirikoo.net/images/5shrad-20080917-102544.png
>>
>> Also, I couldn't find any way to reduce the colorbar font size
>>     
>
> The colorbar method returns a matplotlib.colorbar.Colorbar instance,
> which has matplotlib.axes.Axes instance stored as an attribute.  Thus
> you can do:
>
> cb = colorbar(something....)
>
> for t in cb.get_yticklabels():
>     t.set_fontsize(10)
>
> Eric: when you get some time, could you add docstrings to colorbar
> which document the publicly accessible attributes?
>
> JDH
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Jeff,

Sorry, I have forgotten to add this piece of code since I'm continually
adding/removing bits

This code comes instead of the scatter method and colorbar things:

xi=np.linspace(-180,180,360)
yi=np.linspace(-90,90,180)
zi=griddata(Lon,Lat,Val_masked,xi,yi)

Is it done the good way?
If it is, what's the best method to display it with interpolation?

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: mercredi 17 septembre 2008 13:40
To: De Pauw Antoine
Cc: 'John Hunter'; 'Eric Firing'; 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Hi John,
>
> I used your example with the missing .ax to modify these font sizes and it
> works nicely
>
> Anyway, by investigation, I found that there is no way of interpolation
> using scattered data
>
> I tried to figure out how to grid my values and use imshow or pcolor, but
> with no success yet..
>
> Could you explain me how I could do to grid, for example, that data:
>
> Lat[] (double array containing latitudes)
> Lon[] (double array containing longitudes)
> Val[] (double array containing values)
>
> Each of the arrays having the same size, and Val[1] has latitude Lat[1]
and
> longitude Lon[1], and so on, and the coordinates are completely unordered
>
> When I try to use griddata and use imshow or pcolor with the output array,
> my figure is blank
>
> A simple example or guideline would do, I guess, as I've already gained a
> good knowledge of the language
>
> Thanks in advance
>
> PS: Here's the code snippet:
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  Griddata should work fine.  Your code snippet does not try to 
use griddata, so I can't guess what is wrong.  Let me suggest again  - 
please post complete, self-contained examples that demonstrate your 
problem. 

Did you look at the griddata_demo.py example?

-Jeff

>
> -----Original Message-----
> From: John Hunter [mailto:jdh2358@...] 
> Sent: mercredi 17 septembre 2008 13:00
> To: De Pauw Antoine
> Cc: Eric Firing; Jeff Whitaker; Matplotlib Users
> Subject: Re: [Matplotlib-users] Information request
>
> On Wed, Sep 17, 2008 at 3:28 AM, De Pauw Antoine <andepauw@...>
wrote:
>
>   
>> The image generated is here:
>> http://www.kirikoo.net/images/5shrad-20080917-102544.png
>>
>> Also, I couldn't find any way to reduce the colorbar font size
>>     
>
> The colorbar method returns a matplotlib.colorbar.Colorbar instance,
> which has matplotlib.axes.Axes instance stored as an attribute.  Thus
> you can do:
>
> cb = colorbar(something....)
>
> for t in cb.get_yticklabels():
>     t.set_fontsize(10)
>
> Eric: when you get some time, could you add docstrings to colorbar
> which document the publicly accessible attributes?
>
> JDH
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Jeff,

I finally managed to obtain a neat image with imshow and griddata

The code snippet is here:
http://snipplr.com/view/8307/map-plotting-python-code-temporary/

The only problem I have is now a grey line surrounding the plot, as you can
see in this low-res sample:
http://www.kirikoo.net/images/5shrad-20080917-151205.png

I have added zero-value points at the corners of the map, thinking that
interpolation simply didn't do its job between the points because of a lack
of data, but it's still the same

The masked array has been replaced with a "replace by zero if superior to
-1.2" thing as the border was surrounding masked zone as well

Is there a border to imshow? If yes, how to remove it?

Also, I tried with aspect='auto' as it seemed to be there for that, but
still no progress

Thanks for the tips and have a nice evening!

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: mercredi 17 septembre 2008 13:40
To: De Pauw Antoine
Cc: 'John Hunter'; 'Eric Firing'; 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Hi John,
>
> I used your example with the missing .ax to modify these font sizes and it
> works nicely
>
> Anyway, by investigation, I found that there is no way of interpolation
> using scattered data
>
> I tried to figure out how to grid my values and use imshow or pcolor, but
> with no success yet..
>
> Could you explain me how I could do to grid, for example, that data:
>
> Lat[] (double array containing latitudes)
> Lon[] (double array containing longitudes)
> Val[] (double array containing values)
>
> Each of the arrays having the same size, and Val[1] has latitude Lat[1]
and
> longitude Lon[1], and so on, and the coordinates are completely unordered
>
> When I try to use griddata and use imshow or pcolor with the output array,
> my figure is blank
>
> A simple example or guideline would do, I guess, as I've already gained a
> good knowledge of the language
>
> Thanks in advance
>
> PS: Here's the code snippet:
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  Griddata should work fine.  Your code snippet does not try to 
use griddata, so I can't guess what is wrong.  Let me suggest again  - 
please post complete, self-contained examples that demonstrate your 
problem. 

Did you look at the griddata_demo.py example?

-Jeff

>
> -----Original Message-----
> From: John Hunter [mailto:jdh2358@...] 
> Sent: mercredi 17 septembre 2008 13:00
> To: De Pauw Antoine
> Cc: Eric Firing; Jeff Whitaker; Matplotlib Users
> Subject: Re: [Matplotlib-users] Information request
>
> On Wed, Sep 17, 2008 at 3:28 AM, De Pauw Antoine <andepauw@...>
wrote:
>
>   
>> The image generated is here:
>> http://www.kirikoo.net/images/5shrad-20080917-102544.png
>>
>> Also, I couldn't find any way to reduce the colorbar font size
>>     
>
> The colorbar method returns a matplotlib.colorbar.Colorbar instance,
> which has matplotlib.axes.Axes instance stored as an attribute.  Thus
> you can do:
>
> cb = colorbar(something....)
>
> for t in cb.get_yticklabels():
>     t.set_fontsize(10)
>
> Eric: when you get some time, could you add docstrings to colorbar
> which document the publicly accessible attributes?
>
> JDH
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

De Pauw Antoine wrote:
> Jeff,
>
> I finally managed to obtain a neat image with imshow and griddata
>
> The code snippet is here:
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> The only problem I have is now a grey line surrounding the plot, as you can
> see in this low-res sample:
> http://www.kirikoo.net/images/5shrad-20080917-151205.png
>   

Antoine:  Sorry, but I don't see it.
> I have added zero-value points at the corners of the map, thinking that
> interpolation simply didn't do its job between the points because of a lack
> of data, but it's still the same
>
> The masked array has been replaced with a "replace by zero if superior to
> -1.2" thing as the border was surrounding masked zone as well
>
> Is there a border to imshow?
No.

-Jeff
>  If yes, how to remove it?
>
> Also, I tried with aspect='auto' as it seemed to be there for that, but
> still no progress
>   
> Thanks for the tips and have a nice evening!
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: mercredi 17 septembre 2008 13:40
> To: De Pauw Antoine
> Cc: 'John Hunter'; 'Eric Firing'; 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Hi John,
>>
>> I used your example with the missing .ax to modify these font sizes and it
>> works nicely
>>
>> Anyway, by investigation, I found that there is no way of interpolation
>> using scattered data
>>
>> I tried to figure out how to grid my values and use imshow or pcolor, but
>> with no success yet..
>>
>> Could you explain me how I could do to grid, for example, that data:
>>
>> Lat[] (double array containing latitudes)
>> Lon[] (double array containing longitudes)
>> Val[] (double array containing values)
>>
>> Each of the arrays having the same size, and Val[1] has latitude Lat[1]
>>     
> and
>   
>> longitude Lon[1], and so on, and the coordinates are completely unordered
>>
>> When I try to use griddata and use imshow or pcolor with the output array,
>> my figure is blank
>>
>> A simple example or guideline would do, I guess, as I've already gained a
>> good knowledge of the language
>>
>> Thanks in advance
>>
>> PS: Here's the code snippet:
>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine:  Griddata should work fine.  Your code snippet does not try to 
> use griddata, so I can't guess what is wrong.  Let me suggest again  - 
> please post complete, self-contained examples that demonstrate your 
> problem. 
>
> Did you look at the griddata_demo.py example?
>
> -Jeff
>
>   
>> -----Original Message-----
>> From: John Hunter [mailto:jdh2358@...] 
>> Sent: mercredi 17 septembre 2008 13:00
>> To: De Pauw Antoine
>> Cc: Eric Firing; Jeff Whitaker; Matplotlib Users
>> Subject: Re: [Matplotlib-users] Information request
>>
>> On Wed, Sep 17, 2008 at 3:28 AM, De Pauw Antoine <andepauw@...>
>>     
> wrote:
>   
>>   
>>     
>>> The image generated is here:
>>> http://www.kirikoo.net/images/5shrad-20080917-102544.png
>>>
>>> Also, I couldn't find any way to reduce the colorbar font size
>>>     
>>>       
>> The colorbar method returns a matplotlib.colorbar.Colorbar instance,
>> which has matplotlib.axes.Axes instance stored as an attribute.  Thus
>> you can do:
>>
>> cb = colorbar(something....)
>>
>> for t in cb.get_yticklabels():
>>     t.set_fontsize(10)
>>
>> Eric: when you get some time, could you add docstrings to colorbar
>> which document the publicly accessible attributes?
>>
>> JDH
>>
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

On Wed, Sep 17, 2008 at 11:08 AM, Jeff Whitaker <jswhit@...> wrote:
> De Pauw Antoine wrote:
>> Jeff,
>>
>> I finally managed to obtain a neat image with imshow and griddata
>>
>> The code snippet is here:
>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>
>> The only problem I have is now a grey line surrounding the plot, as you can
>> see in this low-res sample:
>> http://www.kirikoo.net/images/5shrad-20080917-151205.png
>>
>
> Antoine:  Sorry, but I don't see it.

There is a very faint horizontal grey line at the top and bottom of
the plot, just inside the axes border.  I think this is what he is
referring to.

JDH

John Hunter wrote:
> On Wed, Sep 17, 2008 at 11:08 AM, Jeff Whitaker <jswhit@...> wrote:
>   
>> De Pauw Antoine wrote:
>>     
>>> Jeff,
>>>
>>> I finally managed to obtain a neat image with imshow and griddata
>>>
>>> The code snippet is here:
>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>
>>> The only problem I have is now a grey line surrounding the plot, as you can
>>> see in this low-res sample:
>>> http://www.kirikoo.net/images/5shrad-20080917-151205.png
>>>
>>>       
>> Antoine:  Sorry, but I don't see it.
>>     
>
> There is a very faint horizontal grey line at the top and bottom of
> the plot, just inside the axes border.  I think this is what he is
> referring to.
>
> JDH
>   
John:  Well, you're eyes are better than mine.  I still can't see it.  
No idea why it might be there either.

-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

On Wed, Sep 17, 2008 at 11:48 AM, Jeff Whitaker <jswhit@...> wrote:


> John:  Well, you're eyes are better than mine.  I still can't see it.  No
> idea why it might be there either.

Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
axes border.  The black horizontal line is the top axes border, the
horizontal grey line is the artifact, the vertical dashed line is a
grid line.  I don't know if this offers a clue, but if you look at a
zoom in the upper right corner, the grey  line seems to break up and
curve down and to the right (corner.png)

On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...> wrote:

> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
> axes border.  The black horizontal line is the top axes border, the
> horizontal grey line is the artifact, the vertical dashed line is a
> grid line.  I don't know if this offers a clue, but if you look at a
> zoom in the upper right corner, the grey  line seems to break up and
> curve down and to the right (corner.png)

Sorry, screwed up corner.png (I attached the original and not the
screenshot).  The correct screenshot is attached

John Hunter wrote:
> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...> wrote:
>
>   
>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>> axes border.  The black horizontal line is the top axes border, the
>> horizontal grey line is the artifact, the vertical dashed line is a
>> grid line.  I don't know if this offers a clue, but if you look at a
>> zoom in the upper right corner, the grey  line seems to break up and
>> curve down and to the right (corner.png)
>>     
>
> Sorry, screwed up corner.png (I attached the original and not the
> screenshot).  The correct screenshot is attached
>   
>
>

John:   OK, now I finally see it.  Antoine:  Do these artifacts 
disappear if you comment out the imshow call?

-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Jeff,

Yes they disappear, and they fluctuate with the interpolation method used

For example, nearest interpolation don't show the line

Also, if I reduce the grid resolution, the line is thicker, and if I use a
masked array to get rid of undesired values, the border shows really
strongly

Here's an example everyone will see:

http://img225.imageshack.us/img225/2671/testfigep2.png

(everything except the clouds is noise)

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: mercredi 17 septembre 2008 19:05
To: John Hunter
Cc: De Pauw Antoine; Matplotlib Users
Subject: Re: [Matplotlib-users] Information request

John Hunter wrote:
> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...> wrote:
>
>   
>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>> axes border.  The black horizontal line is the top axes border, the
>> horizontal grey line is the artifact, the vertical dashed line is a
>> grid line.  I don't know if this offers a clue, but if you look at a
>> zoom in the upper right corner, the grey  line seems to break up and
>> curve down and to the right (corner.png)
>>     
>
> Sorry, screwed up corner.png (I attached the original and not the
> screenshot).  The correct screenshot is attached
>   
>
>

John:   OK, now I finally see it.  Antoine:  Do these artifacts 
disappear if you comment out the imshow call?

-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

De Pauw Antoine wrote:
> Jeff,
>
> Yes they disappear, and they fluctuate with the interpolation method used
>
> For example, nearest interpolation don't show the line
>
> Also, if I reduce the grid resolution, the line is thicker, and if I use a
> masked array to get rid of undesired values, the border shows really
> strongly
>
> Here's an example everyone will see:
>
> http://img225.imageshack.us/img225/2671/testfigep2.png
>
> (everything except the clouds is noise)
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
plot. I see a white border along the north and south pole, but I 
intrepret that to be missing values.  However, my eyes are notoriously 
bad.  I'd like to be to run a script that generates the artifacts 
myself, so I can zoom in and see the problem myself.  Does the 
griddata_demo.py script show the same problem for you?

-Jeff
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: mercredi 17 septembre 2008 19:05
> To: John Hunter
> Cc: De Pauw Antoine; Matplotlib Users
> Subject: Re: [Matplotlib-users] Information request
>
> John Hunter wrote:
>   
>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...> wrote:
>>
>>   
>>     
>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>> axes border.  The black horizontal line is the top axes border, the
>>> horizontal grey line is the artifact, the vertical dashed line is a
>>> grid line.  I don't know if this offers a clue, but if you look at a
>>> zoom in the upper right corner, the grey  line seems to break up and
>>> curve down and to the right (corner.png)
>>>     
>>>       
>> Sorry, screwed up corner.png (I attached the original and not the
>> screenshot).  The correct screenshot is attached
>>   
>>
>>
>>     
>
> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
> disappear if you comment out the imshow call?
>
> -Jeff
>
>   


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Jeff,

No the example doesn't show that line

If I reduce the amount of data, the border will be on every side of the plot

I'll show you an orthographic plot with no maskinf tomorrow and you will see the problem easily, it wraps in a white line along the 0° meridian and a white circle in the pole

I think it's the imshow layer that is not totally transparent on the map background.. I tried every trick I could for example to put some zero-valued points on each corner to make imshow interpolate correctly the sides, but that doesn't make any difference

>De Pauw Antoine wrote:
>> Jeff,
>>
>> Yes they disappear, and they fluctuate with the interpolation method used
>>
>> For example, nearest interpolation don't show the line
>>
>> Also, if I reduce the grid resolution, the line is thicker, and if I use a
>> masked array to get rid of undesired values, the border shows really
>> strongly
>>
>> Here's an example everyone will see:
>>
>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>
>> (everything except the clouds is noise)
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>
>Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
>plot. I see a white border along the north and south pole, but I 
>intrepret that to be missing values.  However, my eyes are notoriously 
>bad.  I'd like to be to run a script that generates the artifacts 
>myself, so I can zoom in and see the problem myself.  Does the 
>griddata_demo.py script show the same problem for you?
>
>-Jeff
>>
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: mercredi 17 septembre 2008 19:05
>> To: John Hunter
>> Cc: De Pauw Antoine; Matplotlib Users
>> Subject: Re: [Matplotlib-users] Information request
>>
>> John Hunter wrote:
>>   
>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...> wrote:
>>>
>>>   
>>>     
>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>> axes border.  The black horizontal line is the top axes border, the
>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>> curve down and to the right (corner.png)
>>>>     
>>>>       
>>> Sorry, screwed up corner.png (I attached the original and not the
>>> screenshot).  The correct screenshot is attached
>>>   
>>>
>>>
>>>     
>>
>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>> disappear if you comment out the imshow call?
>>
>> -Jeff
>>
>>   
>
>
>-- 
>Jeffrey S. Whitaker         Phone  : (303)497-6313
>Meteorologist               FAX    : (303)497-6449
>NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>325 Broadway                Office : Skaggs Research Cntr 1D-113
>Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>
>
>

Jeff,

I included here a figure where you'll see the border problem for imshow in
my case

http://img217.imageshack.us/img217/5240/testfigzp3.png

The border wraps at -180 and 180 to form the white line

PS: it is atmospheric ice and not SO2, I just omitted to change the title ^^

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Antoine De Pauw [mailto:andepauw@...] 
Sent: jeudi 18 septembre 2008 17:23
To: Jeff Whitaker; andepauw@...
Cc: 'John Hunter'; 'Matplotlib Users'
Subject: re:Re: [Matplotlib-users] Information request

Jeff,

No the example doesn't show that line

If I reduce the amount of data, the border will be on every side of the plot

I'll show you an orthographic plot with no maskinf tomorrow and you will see
the problem easily, it wraps in a white line along the 0° meridian and a
white circle in the pole

I think it's the imshow layer that is not totally transparent on the map
background.. I tried every trick I could for example to put some zero-valued
points on each corner to make imshow interpolate correctly the sides, but
that doesn't make any difference

>De Pauw Antoine wrote:
>> Jeff,
>>
>> Yes they disappear, and they fluctuate with the interpolation method used
>>
>> For example, nearest interpolation don't show the line
>>
>> Also, if I reduce the grid resolution, the line is thicker, and if I use
a
>> masked array to get rid of undesired values, the border shows really
>> strongly
>>
>> Here's an example everyone will see:
>>
>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>
>> (everything except the clouds is noise)
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>
>Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
>plot. I see a white border along the north and south pole, but I 
>intrepret that to be missing values.  However, my eyes are notoriously 
>bad.  I'd like to be to run a script that generates the artifacts 
>myself, so I can zoom in and see the problem myself.  Does the 
>griddata_demo.py script show the same problem for you?
>
>-Jeff
>>
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: mercredi 17 septembre 2008 19:05
>> To: John Hunter
>> Cc: De Pauw Antoine; Matplotlib Users
>> Subject: Re: [Matplotlib-users] Information request
>>
>> John Hunter wrote:
>>   
>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...> wrote:
>>>
>>>   
>>>     
>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>> axes border.  The black horizontal line is the top axes border, the
>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>> curve down and to the right (corner.png)
>>>>     
>>>>       
>>> Sorry, screwed up corner.png (I attached the original and not the
>>> screenshot).  The correct screenshot is attached
>>>   
>>>
>>>
>>>     
>>
>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>> disappear if you comment out the imshow call?
>>
>> -Jeff
>>
>>   
>
>
>-- 
>Jeffrey S. Whitaker         Phone  : (303)497-6313
>Meteorologist               FAX    : (303)497-6449
>NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>325 Broadway                Office : Skaggs Research Cntr 1D-113
>Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>
>
>

Jeff,

The code snippet has been provided, if you run it with the csv reading code
instead of my binary file reading code you'll see it works

I have added some points at each corner of the map (-180:90 180:90 -180:-90
180:-90) with zero values and the white gap persists

If you cannot help me, that's not a problem, I just cannot give you a better
explanation...

Empty data is something normal in my files, sometimes the satellite has gaps
on its measurements and empty zones on the map are normal

The only problem is that it surrounds all the plot with a grayish border or
shadow when I plot it (a mickey-shaped data plot with white zeroed values
would give a mickey-shaped grey border), and all I want to know is if it is
normal that imshow has such a border, and if it is possible that it comes
from the library

I'll keep searching till I have a solution

Is there another plotting method than imshow which also has interpolation?

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: lundi 22 septembre 2008 13:59
To: De Pauw Antoine
Cc: 'John Hunter'; 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Jeff,
>
> I included here a figure where you'll see the border problem for imshow in
> my case
>
> http://img217.imageshack.us/img217/5240/testfigzp3.png
>
> The border wraps at -180 and 180 to form the white line
>
> PS: it is atmospheric ice and not SO2, I just omitted to change the title
^^
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  I hate to keep repeating myself - but we can't do much if you 
don't provide a self-contained script, that I can run, which reproduces 
the problem.  My guess is that the line along the dateline, and the 
point at the South Pole are missing values (which griddata set to 
missing because they are outside the extent of the data) - but that's 
just a guess until I can reproduce it.

-Jeff
>
> -----Original Message-----
> From: Antoine De Pauw [mailto:andepauw@...] 
> Sent: jeudi 18 septembre 2008 17:23
> To: Jeff Whitaker; andepauw@...
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: re:Re: [Matplotlib-users] Information request
>
> Jeff,
>
> No the example doesn't show that line
>
> If I reduce the amount of data, the border will be on every side of the
plot
>
> I'll show you an orthographic plot with no maskinf tomorrow and you will
see
> the problem easily, it wraps in a white line along the 0° meridian and a
> white circle in the pole
>
> I think it's the imshow layer that is not totally transparent on the map
> background.. I tried every trick I could for example to put some
zero-valued
> points on each corner to make imshow interpolate correctly the sides, but
> that doesn't make any difference
>
>   
>> De Pauw Antoine wrote:
>>     
>>> Jeff,
>>>
>>> Yes they disappear, and they fluctuate with the interpolation method
used
>>>
>>> For example, nearest interpolation don't show the line
>>>
>>> Also, if I reduce the grid resolution, the line is thicker, and if I use
>>>       
> a
>   
>>> masked array to get rid of undesired values, the border shows really
>>> strongly
>>>
>>> Here's an example everyone will see:
>>>
>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>
>>> (everything except the clouds is noise)
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>   
>>>       
>> Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
>> plot. I see a white border along the north and south pole, but I 
>> intrepret that to be missing values.  However, my eyes are notoriously 
>> bad.  I'd like to be to run a script that generates the artifacts 
>> myself, so I can zoom in and see the problem myself.  Does the 
>> griddata_demo.py script show the same problem for you?
>>
>> -Jeff
>>     
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: mercredi 17 septembre 2008 19:05
>>> To: John Hunter
>>> Cc: De Pauw Antoine; Matplotlib Users
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> John Hunter wrote:
>>>   
>>>       
>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
wrote:
>>>>
>>>>   
>>>>     
>>>>         
>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>>> curve down and to the right (corner.png)
>>>>>     
>>>>>       
>>>>>           
>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>> screenshot).  The correct screenshot is attached
>>>>   
>>>>
>>>>
>>>>     
>>>>         
>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>> disappear if you comment out the imshow call?
>>>
>>> -Jeff
>>>
>>>   
>>>       
>> -- 
>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>> Meteorologist               FAX    : (303)497-6449
>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>
>>
>>
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

De Pauw Antoine wrote:
> Jeff,
>
> I included here a figure where you'll see the border problem for imshow in
> my case
>
> http://img217.imageshack.us/img217/5240/testfigzp3.png
>
> The border wraps at -180 and 180 to form the white line
>
> PS: it is atmospheric ice and not SO2, I just omitted to change the title ^^
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  I hate to keep repeating myself - but we can't do much if you 
don't provide a self-contained script, that I can run, which reproduces 
the problem.  My guess is that the line along the dateline, and the 
point at the South Pole are missing values (which griddata set to 
missing because they are outside the extent of the data) - but that's 
just a guess until I can reproduce it.

-Jeff
>
> -----Original Message-----
> From: Antoine De Pauw [mailto:andepauw@...] 
> Sent: jeudi 18 septembre 2008 17:23
> To: Jeff Whitaker; andepauw@...
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: re:Re: [Matplotlib-users] Information request
>
> Jeff,
>
> No the example doesn't show that line
>
> If I reduce the amount of data, the border will be on every side of the plot
>
> I'll show you an orthographic plot with no maskinf tomorrow and you will see
> the problem easily, it wraps in a white line along the 0° meridian and a
> white circle in the pole
>
> I think it's the imshow layer that is not totally transparent on the map
> background.. I tried every trick I could for example to put some zero-valued
> points on each corner to make imshow interpolate correctly the sides, but
> that doesn't make any difference
>
>   
>> De Pauw Antoine wrote:
>>     
>>> Jeff,
>>>
>>> Yes they disappear, and they fluctuate with the interpolation method used
>>>
>>> For example, nearest interpolation don't show the line
>>>
>>> Also, if I reduce the grid resolution, the line is thicker, and if I use
>>>       
> a
>   
>>> masked array to get rid of undesired values, the border shows really
>>> strongly
>>>
>>> Here's an example everyone will see:
>>>
>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>
>>> (everything except the clouds is noise)
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>   
>>>       
>> Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
>> plot. I see a white border along the north and south pole, but I 
>> intrepret that to be missing values.  However, my eyes are notoriously 
>> bad.  I'd like to be to run a script that generates the artifacts 
>> myself, so I can zoom in and see the problem myself.  Does the 
>> griddata_demo.py script show the same problem for you?
>>
>> -Jeff
>>     
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: mercredi 17 septembre 2008 19:05
>>> To: John Hunter
>>> Cc: De Pauw Antoine; Matplotlib Users
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> John Hunter wrote:
>>>   
>>>       
>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...> wrote:
>>>>
>>>>   
>>>>     
>>>>         
>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>>> curve down and to the right (corner.png)
>>>>>     
>>>>>       
>>>>>           
>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>> screenshot).  The correct screenshot is attached
>>>>   
>>>>
>>>>
>>>>     
>>>>         
>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>> disappear if you comment out the imshow call?
>>>
>>> -Jeff
>>>
>>>   
>>>       
>> -- 
>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>> Meteorologist               FAX    : (303)497-6449
>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>
>>
>>
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Jeff,

I still don't know how to either remove this artifact or fill my arrays with
values to remove empty regions, and I'll make a last attempt to resolve it

I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56

The actual code snippet is here:
http://snipplr.com/view/8307/map-plotting-python-code-temporary/

I hope you'll be able to reproduce it, I set the cmap to winter for you to
see the gap... setting it to hot will make the grayish border visible in
high resolution by zooming it... I think the border (not the empty zone)
could be an artifact with the hot colormap


Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: lundi 22 septembre 2008 13:59
To: De Pauw Antoine
Cc: 'John Hunter'; 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Jeff,
>
> I included here a figure where you'll see the border problem for imshow in
> my case
>
> http://img217.imageshack.us/img217/5240/testfigzp3.png
>
> The border wraps at -180 and 180 to form the white line
>
> PS: it is atmospheric ice and not SO2, I just omitted to change the title
^^
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine:  I hate to keep repeating myself - but we can't do much if you 
don't provide a self-contained script, that I can run, which reproduces 
the problem.  My guess is that the line along the dateline, and the 
point at the South Pole are missing values (which griddata set to 
missing because they are outside the extent of the data) - but that's 
just a guess until I can reproduce it.

-Jeff
>
> -----Original Message-----
> From: Antoine De Pauw [mailto:andepauw@...] 
> Sent: jeudi 18 septembre 2008 17:23
> To: Jeff Whitaker; andepauw@...
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: re:Re: [Matplotlib-users] Information request
>
> Jeff,
>
> No the example doesn't show that line
>
> If I reduce the amount of data, the border will be on every side of the
plot
>
> I'll show you an orthographic plot with no maskinf tomorrow and you will
see
> the problem easily, it wraps in a white line along the 0° meridian and a
> white circle in the pole
>
> I think it's the imshow layer that is not totally transparent on the map
> background.. I tried every trick I could for example to put some
zero-valued
> points on each corner to make imshow interpolate correctly the sides, but
> that doesn't make any difference
>
>   
>> De Pauw Antoine wrote:
>>     
>>> Jeff,
>>>
>>> Yes they disappear, and they fluctuate with the interpolation method
used
>>>
>>> For example, nearest interpolation don't show the line
>>>
>>> Also, if I reduce the grid resolution, the line is thicker, and if I use
>>>       
> a
>   
>>> masked array to get rid of undesired values, the border shows really
>>> strongly
>>>
>>> Here's an example everyone will see:
>>>
>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>
>>> (everything except the clouds is noise)
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>   
>>>       
>> Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
>> plot. I see a white border along the north and south pole, but I 
>> intrepret that to be missing values.  However, my eyes are notoriously 
>> bad.  I'd like to be to run a script that generates the artifacts 
>> myself, so I can zoom in and see the problem myself.  Does the 
>> griddata_demo.py script show the same problem for you?
>>
>> -Jeff
>>     
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: mercredi 17 septembre 2008 19:05
>>> To: John Hunter
>>> Cc: De Pauw Antoine; Matplotlib Users
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> John Hunter wrote:
>>>   
>>>       
>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
wrote:
>>>>
>>>>   
>>>>     
>>>>         
>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>>> curve down and to the right (corner.png)
>>>>>     
>>>>>       
>>>>>           
>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>> screenshot).  The correct screenshot is attached
>>>>   
>>>>
>>>>
>>>>     
>>>>         
>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>> disappear if you comment out the imshow call?
>>>
>>> -Jeff
>>>
>>>   
>>>       
>> -- 
>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>> Meteorologist               FAX    : (303)497-6449
>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>
>>
>>
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

De Pauw Antoine wrote:
> Jeff,
>
> I still don't know how to either remove this artifact or fill my arrays with
> values to remove empty regions, and I'll make a last attempt to resolve it
>
> I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56
>
> The actual code snippet is here:
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> I hope you'll be able to reproduce it, I set the cmap to winter for you to
> see the gap... setting it to hot will make the grayish border visible in
> high resolution by zooming it... I think the border (not the empty zone)
> could be an artifact with the hot colormap
>
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>
>
>   

Antoine:  As I suspected, that gap around the edges of the plot is a 
consequence of the gridding procedure.  griddata doesn't do 
extrapolation, so there are missing values on the grid outside the 
convex hull of the input observations.  You can either just live with 
it, or set the plotting region so that it fits entirely within the 
convex hull of the data.  This is what I've done in the modified version 
of your script below.  I've also eliminated the transform_scalar call by 
gridding directly on the projection grid (instead of gridding to a 
lat/lon grid, then interpolating to the projection grid).  Hope this helps.

-Jeff

from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import numpy as np
import os
fileName = '20080821.b56'
nx = 360; ny = 180
titre='SO2'
legende='Delta Brightness Temperature (K)'
nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
rawfile=np.fromfile(open(fileName,'rb'),'<d',-1)
Lat=rawfile[0:nbreligne]
Lon=rawfile[nbreligne:nbreligne*2]
Val=rawfile[nbreligne*21:nbreligne*22]
map=Basemap(projection='mill',llcrnrlat=-89,urcrnrlat=89,\
            urcrnrlon=179,llcrnrlon=-179,resolution='l')
xi=np.linspace(map.xmin,map.xmax,nx)
yi=np.linspace(map.ymin,map.ymax,ny)
x, y = map(Lon, Lat)
zi=mlab.griddata(x,y,Val,xi,yi)
map.imshow(zi,plt.cm.winter,vmin=-5,vmax=-1.2)
cb=plt.colorbar(shrink=0.6)
cb.ax.set_ylabel(legende,fontsize=11)
for t in cb.ax.get_yticklabels():
    t.set_fontsize(7)
meridians = np.arange(-180,180,60)
parallels = np.arange(-90,90,30)
map.drawparallels(parallels,labels=[1,0,0,0],fontsize=7,linewidth=0.25)
map.drawmeridians(meridians,labels=[0,0,0,1],fontsize=7,linewidth=0.25)
map.drawcoastlines(0.25,antialiased=1)
plt.title(titre)
plt.show()
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: lundi 22 septembre 2008 13:59
> To: De Pauw Antoine
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Jeff,
>>
>> I included here a figure where you'll see the border problem for imshow in
>> my case
>>
>> http://img217.imageshack.us/img217/5240/testfigzp3.png
>>
>> The border wraps at -180 and 180 to form the white line
>>
>> PS: it is atmospheric ice and not SO2, I just omitted to change the title
>>     
> ^^
>   
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine:  I hate to keep repeating myself - but we can't do much if you 
> don't provide a self-contained script, that I can run, which reproduces 
> the problem.  My guess is that the line along the dateline, and the 
> point at the South Pole are missing values (which griddata set to 
> missing because they are outside the extent of the data) - but that's 
> just a guess until I can reproduce it.
>
> -Jeff
>   
>> -----Original Message-----
>> From: Antoine De Pauw [mailto:andepauw@...] 
>> Sent: jeudi 18 septembre 2008 17:23
>> To: Jeff Whitaker; andepauw@...
>> Cc: 'John Hunter'; 'Matplotlib Users'
>> Subject: re:Re: [Matplotlib-users] Information request
>>
>> Jeff,
>>
>> No the example doesn't show that line
>>
>> If I reduce the amount of data, the border will be on every side of the
>>     
> plot
>   
>> I'll show you an orthographic plot with no maskinf tomorrow and you will
>>     
> see
>   
>> the problem easily, it wraps in a white line along the 0° meridian and a
>> white circle in the pole
>>
>> I think it's the imshow layer that is not totally transparent on the map
>> background.. I tried every trick I could for example to put some
>>     
> zero-valued
>   
>> points on each corner to make imshow interpolate correctly the sides, but
>> that doesn't make any difference
>>
>>   
>>     
>>> De Pauw Antoine wrote:
>>>     
>>>       
>>>> Jeff,
>>>>
>>>> Yes they disappear, and they fluctuate with the interpolation method
>>>>         
> used
>   
>>>> For example, nearest interpolation don't show the line
>>>>
>>>> Also, if I reduce the grid resolution, the line is thicker, and if I use
>>>>       
>>>>         
>> a
>>   
>>     
>>>> masked array to get rid of undesired values, the border shows really
>>>> strongly
>>>>
>>>> Here's an example everyone will see:
>>>>
>>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>>
>>>> (everything except the clouds is noise)
>>>>
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>   
>>>>       
>>>>         
>>> Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
>>> plot. I see a white border along the north and south pole, but I 
>>> intrepret that to be missing values.  However, my eyes are notoriously 
>>> bad.  I'd like to be to run a script that generates the artifacts 
>>> myself, so I can zoom in and see the problem myself.  Does the 
>>> griddata_demo.py script show the same problem for you?
>>>
>>> -Jeff
>>>     
>>>       
>>>> -----Original Message-----
>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>> Sent: mercredi 17 septembre 2008 19:05
>>>> To: John Hunter
>>>> Cc: De Pauw Antoine; Matplotlib Users
>>>> Subject: Re: [Matplotlib-users] Information request
>>>>
>>>> John Hunter wrote:
>>>>   
>>>>       
>>>>         
>>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
>>>>>           
> wrote:
>   
>>>>>   
>>>>>     
>>>>>         
>>>>>           
>>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>>>> curve down and to the right (corner.png)
>>>>>>     
>>>>>>       
>>>>>>           
>>>>>>             
>>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>>> screenshot).  The correct screenshot is attached
>>>>>   
>>>>>
>>>>>
>>>>>     
>>>>>         
>>>>>           
>>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>>> disappear if you comment out the imshow call?
>>>>
>>>> -Jeff
>>>>
>>>>   
>>>>       
>>>>         
>>> -- 
>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>> Meteorologist               FAX    : (303)497-6449
>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>
>>>
>>>
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

De Pauw Antoine wrote:
> Jeff,
>
> I still don't know how to either remove this artifact or fill my arrays with
> values to remove empty regions, and I'll make a last attempt to resolve it
>
> I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56
>
> The actual code snippet is here:
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> I hope you'll be able to reproduce it, I set the cmap to winter for you to
> see the gap... setting it to hot will make the grayish border visible in
> high resolution by zooming it... I think the border (not the empty zone)
> could be an artifact with the hot colormap
>
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>
>   

Antoine:  Here is a version that just plots the pixels directly, without 
interpolating to a grid.  I personally like this better, since you can 
easily see where you actually have data.

HTH,

-Jeff

from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import numpy as np
import os
fileName = '20080821.b56'
titre='SO2'
legende='Delta Brightness Temperature (K)'
nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
rawfile=np.fromfile(open(fileName,'rb'),'<d',-1)
Lat=rawfile[0:nbreligne]
Lon=rawfile[nbreligne:nbreligne*2]
Val=rawfile[nbreligne*21:nbreligne*22]
map=Basemap(projection='mill',llcrnrlat=-90,urcrnrlat=90,\
            urcrnrlon=180,llcrnrlon=-180,resolution='l')
x, y = map(Lon, Lat)
plt.scatter(x,y,s=25,c=Val,marker='s',edgecolor="None",cmap=plt.cm.winter,vmin=-5,vmax=-1.2, 
alpha=0.5)
cb=plt.colorbar(shrink=0.6)
cb.ax.set_ylabel(legende,fontsize=11)
for t in cb.ax.get_yticklabels():
    t.set_fontsize(7)
meridians = np.arange(-180,180,60)
parallels = np.arange(-90,90,30)
map.drawparallels(parallels,labels=[1,0,0,0],fontsize=7,linewidth=0.25)
map.drawmeridians(meridians,labels=[0,0,0,1],fontsize=7,linewidth=0.25)
map.drawcoastlines(0.25,antialiased=1)
plt.title(titre)
plt.show()
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: lundi 22 septembre 2008 13:59
> To: De Pauw Antoine
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Jeff,
>>
>> I included here a figure where you'll see the border problem for imshow in
>> my case
>>
>> http://img217.imageshack.us/img217/5240/testfigzp3.png
>>
>> The border wraps at -180 and 180 to form the white line
>>
>> PS: it is atmospheric ice and not SO2, I just omitted to change the title
>>     
> ^^
>   
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine:  I hate to keep repeating myself - but we can't do much if you 
> don't provide a self-contained script, that I can run, which reproduces 
> the problem.  My guess is that the line along the dateline, and the 
> point at the South Pole are missing values (which griddata set to 
> missing because they are outside the extent of the data) - but that's 
> just a guess until I can reproduce it.
>
> -Jeff
>   
>> -----Original Message-----
>> From: Antoine De Pauw [mailto:andepauw@...] 
>> Sent: jeudi 18 septembre 2008 17:23
>> To: Jeff Whitaker; andepauw@...
>> Cc: 'John Hunter'; 'Matplotlib Users'
>> Subject: re:Re: [Matplotlib-users] Information request
>>
>> Jeff,
>>
>> No the example doesn't show that line
>>
>> If I reduce the amount of data, the border will be on every side of the
>>     
> plot
>   
>> I'll show you an orthographic plot with no maskinf tomorrow and you will
>>     
> see
>   
>> the problem easily, it wraps in a white line along the 0° meridian and a
>> white circle in the pole
>>
>> I think it's the imshow layer that is not totally transparent on the map
>> background.. I tried every trick I could for example to put some
>>     
> zero-valued
>   
>> points on each corner to make imshow interpolate correctly the sides, but
>> that doesn't make any difference
>>
>>   
>>     
>>> De Pauw Antoine wrote:
>>>     
>>>       
>>>> Jeff,
>>>>
>>>> Yes they disappear, and they fluctuate with the interpolation method
>>>>         
> used
>   
>>>> For example, nearest interpolation don't show the line
>>>>
>>>> Also, if I reduce the grid resolution, the line is thicker, and if I use
>>>>       
>>>>         
>> a
>>   
>>     
>>>> masked array to get rid of undesired values, the border shows really
>>>> strongly
>>>>
>>>> Here's an example everyone will see:
>>>>
>>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>>
>>>> (everything except the clouds is noise)
>>>>
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>   
>>>>       
>>>>         
>>> Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
>>> plot. I see a white border along the north and south pole, but I 
>>> intrepret that to be missing values.  However, my eyes are notoriously 
>>> bad.  I'd like to be to run a script that generates the artifacts 
>>> myself, so I can zoom in and see the problem myself.  Does the 
>>> griddata_demo.py script show the same problem for you?
>>>
>>> -Jeff
>>>     
>>>       
>>>> -----Original Message-----
>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>> Sent: mercredi 17 septembre 2008 19:05
>>>> To: John Hunter
>>>> Cc: De Pauw Antoine; Matplotlib Users
>>>> Subject: Re: [Matplotlib-users] Information request
>>>>
>>>> John Hunter wrote:
>>>>   
>>>>       
>>>>         
>>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
>>>>>           
> wrote:
>   
>>>>>   
>>>>>     
>>>>>         
>>>>>           
>>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>>>> curve down and to the right (corner.png)
>>>>>>     
>>>>>>       
>>>>>>           
>>>>>>             
>>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>>> screenshot).  The correct screenshot is attached
>>>>>   
>>>>>
>>>>>
>>>>>     
>>>>>         
>>>>>           
>>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>>> disappear if you comment out the imshow call?
>>>>
>>>> -Jeff
>>>>
>>>>   
>>>>       
>>>>         
>>> -- 
>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>> Meteorologist               FAX    : (303)497-6449
>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>
>>>
>>>
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Jeff,

Thanks for your help, I now know that it's a missing data problem

However, I need to make, for example, orthographic maps of ozone centered on
the polar region, and there is no possibility to cut the unaesthetic regions
of the plot in that case

I'll try to plot a data grid containing the weaker value for all points
before the actual data I'm plotting, to see if I can set the background
color and avoid these gaps

If you know of any method to do that instead of plotting a whole grid before
anything else, please tell

I have to thank you for your help and I wonder how you find the time
required to work on that mailing list

Have a nice day,

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: mardi 23 septembre 2008 20:38
To: De Pauw Antoine
Cc: 'John Hunter'; 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Jeff,
>
> I still don't know how to either remove this artifact or fill my arrays
with
> values to remove empty regions, and I'll make a last attempt to resolve it
>
> I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56
>
> The actual code snippet is here:
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> I hope you'll be able to reproduce it, I set the cmap to winter for you to
> see the gap... setting it to hot will make the grayish border visible in
> high resolution by zooming it... I think the border (not the empty zone)
> could be an artifact with the hot colormap
>
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>
>   

Antoine:  Here is a version that just plots the pixels directly, without 
interpolating to a grid.  I personally like this better, since you can 
easily see where you actually have data.

HTH,

-Jeff

from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import numpy as np
import os
fileName = '20080821.b56'
titre='SO2'
legende='Delta Brightness Temperature (K)'
nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
rawfile=np.fromfile(open(fileName,'rb'),'<d',-1)
Lat=rawfile[0:nbreligne]
Lon=rawfile[nbreligne:nbreligne*2]
Val=rawfile[nbreligne*21:nbreligne*22]
map=Basemap(projection='mill',llcrnrlat=-90,urcrnrlat=90,\
            urcrnrlon=180,llcrnrlon=-180,resolution='l')
x, y = map(Lon, Lat)
plt.scatter(x,y,s=25,c=Val,marker='s',edgecolor="None",cmap=plt.cm.winter,vm
in=-5,vmax=-1.2, 
alpha=0.5)
cb=plt.colorbar(shrink=0.6)
cb.ax.set_ylabel(legende,fontsize=11)
for t in cb.ax.get_yticklabels():
    t.set_fontsize(7)
meridians = np.arange(-180,180,60)
parallels = np.arange(-90,90,30)
map.drawparallels(parallels,labels=[1,0,0,0],fontsize=7,linewidth=0.25)
map.drawmeridians(meridians,labels=[0,0,0,1],fontsize=7,linewidth=0.25)
map.drawcoastlines(0.25,antialiased=1)
plt.title(titre)
plt.show()
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: lundi 22 septembre 2008 13:59
> To: De Pauw Antoine
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Jeff,
>>
>> I included here a figure where you'll see the border problem for imshow
in
>> my case
>>
>> http://img217.imageshack.us/img217/5240/testfigzp3.png
>>
>> The border wraps at -180 and 180 to form the white line
>>
>> PS: it is atmospheric ice and not SO2, I just omitted to change the title
>>     
> ^^
>   
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine:  I hate to keep repeating myself - but we can't do much if you 
> don't provide a self-contained script, that I can run, which reproduces 
> the problem.  My guess is that the line along the dateline, and the 
> point at the South Pole are missing values (which griddata set to 
> missing because they are outside the extent of the data) - but that's 
> just a guess until I can reproduce it.
>
> -Jeff
>   
>> -----Original Message-----
>> From: Antoine De Pauw [mailto:andepauw@...] 
>> Sent: jeudi 18 septembre 2008 17:23
>> To: Jeff Whitaker; andepauw@...
>> Cc: 'John Hunter'; 'Matplotlib Users'
>> Subject: re:Re: [Matplotlib-users] Information request
>>
>> Jeff,
>>
>> No the example doesn't show that line
>>
>> If I reduce the amount of data, the border will be on every side of the
>>     
> plot
>   
>> I'll show you an orthographic plot with no maskinf tomorrow and you will
>>     
> see
>   
>> the problem easily, it wraps in a white line along the 0° meridian and a
>> white circle in the pole
>>
>> I think it's the imshow layer that is not totally transparent on the map
>> background.. I tried every trick I could for example to put some
>>     
> zero-valued
>   
>> points on each corner to make imshow interpolate correctly the sides, but
>> that doesn't make any difference
>>
>>   
>>     
>>> De Pauw Antoine wrote:
>>>     
>>>       
>>>> Jeff,
>>>>
>>>> Yes they disappear, and they fluctuate with the interpolation method
>>>>         
> used
>   
>>>> For example, nearest interpolation don't show the line
>>>>
>>>> Also, if I reduce the grid resolution, the line is thicker, and if I
use
>>>>       
>>>>         
>> a
>>   
>>     
>>>> masked array to get rid of undesired values, the border shows really
>>>> strongly
>>>>
>>>> Here's an example everyone will see:
>>>>
>>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>>
>>>> (everything except the clouds is noise)
>>>>
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>   
>>>>       
>>>>         
>>> Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
>>> plot. I see a white border along the north and south pole, but I 
>>> intrepret that to be missing values.  However, my eyes are notoriously 
>>> bad.  I'd like to be to run a script that generates the artifacts 
>>> myself, so I can zoom in and see the problem myself.  Does the 
>>> griddata_demo.py script show the same problem for you?
>>>
>>> -Jeff
>>>     
>>>       
>>>> -----Original Message-----
>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>> Sent: mercredi 17 septembre 2008 19:05
>>>> To: John Hunter
>>>> Cc: De Pauw Antoine; Matplotlib Users
>>>> Subject: Re: [Matplotlib-users] Information request
>>>>
>>>> John Hunter wrote:
>>>>   
>>>>       
>>>>         
>>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
>>>>>           
> wrote:
>   
>>>>>   
>>>>>     
>>>>>         
>>>>>           
>>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>>>> curve down and to the right (corner.png)
>>>>>>     
>>>>>>       
>>>>>>           
>>>>>>             
>>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>>> screenshot).  The correct screenshot is attached
>>>>>   
>>>>>
>>>>>
>>>>>     
>>>>>         
>>>>>           
>>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>>> disappear if you comment out the imshow call?
>>>>
>>>> -Jeff
>>>>
>>>>   
>>>>       
>>>>         
>>> -- 
>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>> Meteorologist               FAX    : (303)497-6449
>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>
>>>
>>>
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Hi Jeff,

I finally found out how to fill my figure with a background color using
axes.set_axis_bgcolor(color), but I'm facing the following problem now:

How could I get the lower color of a colormap? This is quite undocumented
and I don’t know the colormap properties I could use for that

I know there must be an accessible value somewhere, like for the
ax.get_yticklabels() you gave me

If someone had the clue, my problems would then be completely solved

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB


-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: mardi 23 septembre 2008 20:38
To: De Pauw Antoine
Cc: 'John Hunter'; 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Jeff,
>
> I still don't know how to either remove this artifact or fill my arrays
with
> values to remove empty regions, and I'll make a last attempt to resolve it
>
> I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56
>
> The actual code snippet is here:
> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>
> I hope you'll be able to reproduce it, I set the cmap to winter for you to
> see the gap... setting it to hot will make the grayish border visible in
> high resolution by zooming it... I think the border (not the empty zone)
> could be an artifact with the hot colormap
>
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>
>   

Antoine:  Here is a version that just plots the pixels directly, without 
interpolating to a grid.  I personally like this better, since you can 
easily see where you actually have data.

HTH,

-Jeff

from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import numpy as np
import os
fileName = '20080821.b56'
titre='SO2'
legende='Delta Brightness Temperature (K)'
nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
rawfile=np.fromfile(open(fileName,'rb'),'<d',-1)
Lat=rawfile[0:nbreligne]
Lon=rawfile[nbreligne:nbreligne*2]
Val=rawfile[nbreligne*21:nbreligne*22]
map=Basemap(projection='mill',llcrnrlat=-90,urcrnrlat=90,\
            urcrnrlon=180,llcrnrlon=-180,resolution='l')
x, y = map(Lon, Lat)
plt.scatter(x,y,s=25,c=Val,marker='s',edgecolor="None",cmap=plt.cm.winter,vm
in=-5,vmax=-1.2, 
alpha=0.5)
cb=plt.colorbar(shrink=0.6)
cb.ax.set_ylabel(legende,fontsize=11)
for t in cb.ax.get_yticklabels():
    t.set_fontsize(7)
meridians = np.arange(-180,180,60)
parallels = np.arange(-90,90,30)
map.drawparallels(parallels,labels=[1,0,0,0],fontsize=7,linewidth=0.25)
map.drawmeridians(meridians,labels=[0,0,0,1],fontsize=7,linewidth=0.25)
map.drawcoastlines(0.25,antialiased=1)
plt.title(titre)
plt.show()
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: lundi 22 septembre 2008 13:59
> To: De Pauw Antoine
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Jeff,
>>
>> I included here a figure where you'll see the border problem for imshow
in
>> my case
>>
>> http://img217.imageshack.us/img217/5240/testfigzp3.png
>>
>> The border wraps at -180 and 180 to form the white line
>>
>> PS: it is atmospheric ice and not SO2, I just omitted to change the title
>>     
> ^^
>   
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine:  I hate to keep repeating myself - but we can't do much if you 
> don't provide a self-contained script, that I can run, which reproduces 
> the problem.  My guess is that the line along the dateline, and the 
> point at the South Pole are missing values (which griddata set to 
> missing because they are outside the extent of the data) - but that's 
> just a guess until I can reproduce it.
>
> -Jeff
>   
>> -----Original Message-----
>> From: Antoine De Pauw [mailto:andepauw@...] 
>> Sent: jeudi 18 septembre 2008 17:23
>> To: Jeff Whitaker; andepauw@...
>> Cc: 'John Hunter'; 'Matplotlib Users'
>> Subject: re:Re: [Matplotlib-users] Information request
>>
>> Jeff,
>>
>> No the example doesn't show that line
>>
>> If I reduce the amount of data, the border will be on every side of the
>>     
> plot
>   
>> I'll show you an orthographic plot with no maskinf tomorrow and you will
>>     
> see
>   
>> the problem easily, it wraps in a white line along the 0° meridian and a
>> white circle in the pole
>>
>> I think it's the imshow layer that is not totally transparent on the map
>> background.. I tried every trick I could for example to put some
>>     
> zero-valued
>   
>> points on each corner to make imshow interpolate correctly the sides, but
>> that doesn't make any difference
>>
>>   
>>     
>>> De Pauw Antoine wrote:
>>>     
>>>       
>>>> Jeff,
>>>>
>>>> Yes they disappear, and they fluctuate with the interpolation method
>>>>         
> used
>   
>>>> For example, nearest interpolation don't show the line
>>>>
>>>> Also, if I reduce the grid resolution, the line is thicker, and if I
use
>>>>       
>>>>         
>> a
>>   
>>     
>>>> masked array to get rid of undesired values, the border shows really
>>>> strongly
>>>>
>>>> Here's an example everyone will see:
>>>>
>>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>>
>>>> (everything except the clouds is noise)
>>>>
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>   
>>>>       
>>>>         
>>> Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
>>> plot. I see a white border along the north and south pole, but I 
>>> intrepret that to be missing values.  However, my eyes are notoriously 
>>> bad.  I'd like to be to run a script that generates the artifacts 
>>> myself, so I can zoom in and see the problem myself.  Does the 
>>> griddata_demo.py script show the same problem for you?
>>>
>>> -Jeff
>>>     
>>>       
>>>> -----Original Message-----
>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>> Sent: mercredi 17 septembre 2008 19:05
>>>> To: John Hunter
>>>> Cc: De Pauw Antoine; Matplotlib Users
>>>> Subject: Re: [Matplotlib-users] Information request
>>>>
>>>> John Hunter wrote:
>>>>   
>>>>       
>>>>         
>>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
>>>>>           
> wrote:
>   
>>>>>   
>>>>>     
>>>>>         
>>>>>           
>>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>>>> curve down and to the right (corner.png)
>>>>>>     
>>>>>>       
>>>>>>           
>>>>>>             
>>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>>> screenshot).  The correct screenshot is attached
>>>>>   
>>>>>
>>>>>
>>>>>     
>>>>>         
>>>>>           
>>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>>> disappear if you comment out the imshow call?
>>>>
>>>> -Jeff
>>>>
>>>>   
>>>>       
>>>>         
>>> -- 
>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>> Meteorologist               FAX    : (303)497-6449
>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>
>>>
>>>
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

De Pauw Antoine wrote:
> Hi Jeff,
>
> I finally found out how to fill my figure with a background color using
> axes.set_axis_bgcolor(color), but I'm facing the following problem now:
>
> How could I get the lower color of a colormap? This is quite undocumented
> and I don’t know the colormap properties I could use for that
>
> I know there must be an accessible value somewhere, like for the
> ax.get_yticklabels() you gave me
>
> If someone had the clue, my problems would then be completely solved
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine: To get the RGBA value associated with a particular data value, 
just call the colormap as a function as pass it that value. For example

 >>> import matplotlib.pyplot as plt
 >>> plt.cm.jet(1)
(0.0, 0.0, 0.517825311942959, 1.0)

BTW: the 'fill_color' kwarg of drawmapboundary basemap method allows you 
to set the background color of the map.

http://matplotlib.sourceforge.net/basemap/doc/html/api/basemap_api.html

It fills only the map region (which for some projections, like the 
orthographic, is not the same as the axes region).


-Jeff
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: mardi 23 septembre 2008 20:38
> To: De Pauw Antoine
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Jeff,
>>
>> I still don't know how to either remove this artifact or fill my arrays
>>     
> with
>   
>> values to remove empty regions, and I'll make a last attempt to resolve it
>>
>> I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56
>>
>> The actual code snippet is here:
>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>
>> I hope you'll be able to reproduce it, I set the cmap to winter for you to
>> see the gap... setting it to hot will make the grayish border visible in
>> high resolution by zooming it... I think the border (not the empty zone)
>> could be an artifact with the hot colormap
>>
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>
>>   
>>     
>
> Antoine:  Here is a version that just plots the pixels directly, without 
> interpolating to a grid.  I personally like this better, since you can 
> easily see where you actually have data.
>
> HTH,
>
> -Jeff
>
> from mpl_toolkits.basemap import Basemap
> import matplotlib.pyplot as plt
> import matplotlib.mlab as mlab
> import numpy as np
> import os
> fileName = '20080821.b56'
> titre='SO2'
> legende='Delta Brightness Temperature (K)'
> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
> rawfile=np.fromfile(open(fileName,'rb'),'<d',-1)
> Lat=rawfile[0:nbreligne]
> Lon=rawfile[nbreligne:nbreligne*2]
> Val=rawfile[nbreligne*21:nbreligne*22]
> map=Basemap(projection='mill',llcrnrlat=-90,urcrnrlat=90,\
>             urcrnrlon=180,llcrnrlon=-180,resolution='l')
> x, y = map(Lon, Lat)
> plt.scatter(x,y,s=25,c=Val,marker='s',edgecolor="None",cmap=plt.cm.winter,vm
> in=-5,vmax=-1.2, 
> alpha=0.5)
> cb=plt.colorbar(shrink=0.6)
> cb.ax.set_ylabel(legende,fontsize=11)
> for t in cb.ax.get_yticklabels():
>     t.set_fontsize(7)
> meridians = np.arange(-180,180,60)
> parallels = np.arange(-90,90,30)
> map.drawparallels(parallels,labels=[1,0,0,0],fontsize=7,linewidth=0.25)
> map.drawmeridians(meridians,labels=[0,0,0,1],fontsize=7,linewidth=0.25)
> map.drawcoastlines(0.25,antialiased=1)
> plt.title(titre)
> plt.show()
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: lundi 22 septembre 2008 13:59
>> To: De Pauw Antoine
>> Cc: 'John Hunter'; 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Jeff,
>>>
>>> I included here a figure where you'll see the border problem for imshow
>>>       
> in
>   
>>> my case
>>>
>>> http://img217.imageshack.us/img217/5240/testfigzp3.png
>>>
>>> The border wraps at -180 and 180 to form the white line
>>>
>>> PS: it is atmospheric ice and not SO2, I just omitted to change the title
>>>     
>>>       
>> ^^
>>   
>>     
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>   
>>>     
>>>       
>> Antoine:  I hate to keep repeating myself - but we can't do much if you 
>> don't provide a self-contained script, that I can run, which reproduces 
>> the problem.  My guess is that the line along the dateline, and the 
>> point at the South Pole are missing values (which griddata set to 
>> missing because they are outside the extent of the data) - but that's 
>> just a guess until I can reproduce it.
>>
>> -Jeff
>>   
>>     
>>> -----Original Message-----
>>> From: Antoine De Pauw [mailto:andepauw@...] 
>>> Sent: jeudi 18 septembre 2008 17:23
>>> To: Jeff Whitaker; andepauw@...
>>> Cc: 'John Hunter'; 'Matplotlib Users'
>>> Subject: re:Re: [Matplotlib-users] Information request
>>>
>>> Jeff,
>>>
>>> No the example doesn't show that line
>>>
>>> If I reduce the amount of data, the border will be on every side of the
>>>     
>>>       
>> plot
>>   
>>     
>>> I'll show you an orthographic plot with no maskinf tomorrow and you will
>>>     
>>>       
>> see
>>   
>>     
>>> the problem easily, it wraps in a white line along the 0° meridian and a
>>> white circle in the pole
>>>
>>> I think it's the imshow layer that is not totally transparent on the map
>>> background.. I tried every trick I could for example to put some
>>>     
>>>       
>> zero-valued
>>   
>>     
>>> points on each corner to make imshow interpolate correctly the sides, but
>>> that doesn't make any difference
>>>
>>>   
>>>     
>>>       
>>>> De Pauw Antoine wrote:
>>>>     
>>>>       
>>>>         
>>>>> Jeff,
>>>>>
>>>>> Yes they disappear, and they fluctuate with the interpolation method
>>>>>         
>>>>>           
>> used
>>   
>>     
>>>>> For example, nearest interpolation don't show the line
>>>>>
>>>>> Also, if I reduce the grid resolution, the line is thicker, and if I
>>>>>           
> use
>   
>>>>>       
>>>>>         
>>>>>           
>>> a
>>>   
>>>     
>>>       
>>>>> masked array to get rid of undesired values, the border shows really
>>>>> strongly
>>>>>
>>>>> Here's an example everyone will see:
>>>>>
>>>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>>>
>>>>> (everything except the clouds is noise)
>>>>>
>>>>> Antoine De Pauw
>>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
>>>>>           
> and
>   
>>>>> photophysics laboratory
>>>>> Université Libre de Bruxelles - ULB
>>>>>   
>>>>>       
>>>>>         
>>>>>           
>>>> Antoine:  Sorry to seem dense, but I don't see anything wrong with that 
>>>> plot. I see a white border along the north and south pole, but I 
>>>> intrepret that to be missing values.  However, my eyes are notoriously 
>>>> bad.  I'd like to be to run a script that generates the artifacts 
>>>> myself, so I can zoom in and see the problem myself.  Does the 
>>>> griddata_demo.py script show the same problem for you?
>>>>
>>>> -Jeff
>>>>     
>>>>       
>>>>         
>>>>> -----Original Message-----
>>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>>> Sent: mercredi 17 septembre 2008 19:05
>>>>> To: John Hunter
>>>>> Cc: De Pauw Antoine; Matplotlib Users
>>>>> Subject: Re: [Matplotlib-users] Information request
>>>>>
>>>>> John Hunter wrote:
>>>>>   
>>>>>       
>>>>>         
>>>>>           
>>>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
>>>>>>           
>>>>>>             
>> wrote:
>>   
>>     
>>>>>>   
>>>>>>     
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near the
>>>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>>>>> curve down and to the right (corner.png)
>>>>>>>     
>>>>>>>       
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>>>> screenshot).  The correct screenshot is attached
>>>>>>   
>>>>>>
>>>>>>
>>>>>>     
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>>>> disappear if you comment out the imshow call?
>>>>>
>>>>> -Jeff
>>>>>
>>>>>   
>>>>>       
>>>>>         
>>>>>           
>>>> -- 
>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>> Meteorologist               FAX    : (303)497-6449
>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>
>>>>
>>>>
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

On Thu, Sep 25, 2008 at 7:15 AM, Jeff Whitaker <jswhit@...> wrote:
> De Pauw Antoine wrote:
>> Hi Jeff,
>>
>> I finally found out how to fill my figure with a background color using
>> axes.set_axis_bgcolor(color), but I'm facing the following problem now:
>>
>> How could I get the lower color of a colormap? This is quite undocumented
>> and I don't know the colormap properties I could use for that
>>
>> I know there must be an accessible value somewhere, like for the
>> ax.get_yticklabels() you gave me
>>
>> If someone had the clue, my problems would then be completely solved

You can get the lowest color of a colormap by evaluating it at zero, eg


In [1]: import matplotlib.cm as cm

In [2]: cm.jet(0)
Out[2]: (0.0, 0.0, 0.5, 1.0)

Jeff,

Thanks for the tip, it's now working perfectly

However, there's still that border with the imshow plot, and I think it
would be good to have it transparent

There's a zoomed picture I made:
http://img218.imageshack.us/img218/5833/imshowborderxz9.png

You see the shadow around the data...

It would be nice for next releases of Matplotlib to get rid of that, but I'm
not able to patch it myself or so... I know there's still a lot of work with
the lib but keep the good work, it is really fantastic

Thanks for your help!

Antoine De Pauw
Collaborateur de recherches, Informatique - Research collaborator, IT
Laboratoire de chimie quantique et photophysique - Quantum chemistry and
photophysics laboratory
Université Libre de Bruxelles - ULB

-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: jeudi 25 septembre 2008 14:15
To: De Pauw Antoine
Cc: 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Hi Jeff,
>
> I finally found out how to fill my figure with a background color using
> axes.set_axis_bgcolor(color), but I'm facing the following problem now:
>
> How could I get the lower color of a colormap? This is quite undocumented
> and I don’t know the colormap properties I could use for that
>
> I know there must be an accessible value somewhere, like for the
> ax.get_yticklabels() you gave me
>
> If someone had the clue, my problems would then be completely solved
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine: To get the RGBA value associated with a particular data value, 
just call the colormap as a function as pass it that value. For example

 >>> import matplotlib.pyplot as plt
 >>> plt.cm.jet(1)
(0.0, 0.0, 0.517825311942959, 1.0)

BTW: the 'fill_color' kwarg of drawmapboundary basemap method allows you 
to set the background color of the map.

http://matplotlib.sourceforge.net/basemap/doc/html/api/basemap_api.html

It fills only the map region (which for some projections, like the 
orthographic, is not the same as the axes region).


-Jeff
>
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: mardi 23 septembre 2008 20:38
> To: De Pauw Antoine
> Cc: 'John Hunter'; 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Jeff,
>>
>> I still don't know how to either remove this artifact or fill my arrays
>>     
> with
>   
>> values to remove empty regions, and I'll make a last attempt to resolve
it
>>
>> I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56
>>
>> The actual code snippet is here:
>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>
>> I hope you'll be able to reproduce it, I set the cmap to winter for you
to
>> see the gap... setting it to hot will make the grayish border visible in
>> high resolution by zooming it... I think the border (not the empty zone)
>> could be an artifact with the hot colormap
>>
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>
>>   
>>     
>
> Antoine:  Here is a version that just plots the pixels directly, without 
> interpolating to a grid.  I personally like this better, since you can 
> easily see where you actually have data.
>
> HTH,
>
> -Jeff
>
> from mpl_toolkits.basemap import Basemap
> import matplotlib.pyplot as plt
> import matplotlib.mlab as mlab
> import numpy as np
> import os
> fileName = '20080821.b56'
> titre='SO2'
> legende='Delta Brightness Temperature (K)'
> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
> rawfile=np.fromfile(open(fileName,'rb'),'<d',-1)
> Lat=rawfile[0:nbreligne]
> Lon=rawfile[nbreligne:nbreligne*2]
> Val=rawfile[nbreligne*21:nbreligne*22]
> map=Basemap(projection='mill',llcrnrlat=-90,urcrnrlat=90,\
>             urcrnrlon=180,llcrnrlon=-180,resolution='l')
> x, y = map(Lon, Lat)
>
plt.scatter(x,y,s=25,c=Val,marker='s',edgecolor="None",cmap=plt.cm.winter,vm
> in=-5,vmax=-1.2, 
> alpha=0.5)
> cb=plt.colorbar(shrink=0.6)
> cb.ax.set_ylabel(legende,fontsize=11)
> for t in cb.ax.get_yticklabels():
>     t.set_fontsize(7)
> meridians = np.arange(-180,180,60)
> parallels = np.arange(-90,90,30)
> map.drawparallels(parallels,labels=[1,0,0,0],fontsize=7,linewidth=0.25)
> map.drawmeridians(meridians,labels=[0,0,0,1],fontsize=7,linewidth=0.25)
> map.drawcoastlines(0.25,antialiased=1)
> plt.title(titre)
> plt.show()
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: lundi 22 septembre 2008 13:59
>> To: De Pauw Antoine
>> Cc: 'John Hunter'; 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Jeff,
>>>
>>> I included here a figure where you'll see the border problem for imshow
>>>       
> in
>   
>>> my case
>>>
>>> http://img217.imageshack.us/img217/5240/testfigzp3.png
>>>
>>> The border wraps at -180 and 180 to form the white line
>>>
>>> PS: it is atmospheric ice and not SO2, I just omitted to change the
title
>>>     
>>>       
>> ^^
>>   
>>     
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>   
>>>     
>>>       
>> Antoine:  I hate to keep repeating myself - but we can't do much if you 
>> don't provide a self-contained script, that I can run, which reproduces 
>> the problem.  My guess is that the line along the dateline, and the 
>> point at the South Pole are missing values (which griddata set to 
>> missing because they are outside the extent of the data) - but that's 
>> just a guess until I can reproduce it.
>>
>> -Jeff
>>   
>>     
>>> -----Original Message-----
>>> From: Antoine De Pauw [mailto:andepauw@...] 
>>> Sent: jeudi 18 septembre 2008 17:23
>>> To: Jeff Whitaker; andepauw@...
>>> Cc: 'John Hunter'; 'Matplotlib Users'
>>> Subject: re:Re: [Matplotlib-users] Information request
>>>
>>> Jeff,
>>>
>>> No the example doesn't show that line
>>>
>>> If I reduce the amount of data, the border will be on every side of the
>>>     
>>>       
>> plot
>>   
>>     
>>> I'll show you an orthographic plot with no maskinf tomorrow and you will
>>>     
>>>       
>> see
>>   
>>     
>>> the problem easily, it wraps in a white line along the 0° meridian and a
>>> white circle in the pole
>>>
>>> I think it's the imshow layer that is not totally transparent on the map
>>> background.. I tried every trick I could for example to put some
>>>     
>>>       
>> zero-valued
>>   
>>     
>>> points on each corner to make imshow interpolate correctly the sides,
but
>>> that doesn't make any difference
>>>
>>>   
>>>     
>>>       
>>>> De Pauw Antoine wrote:
>>>>     
>>>>       
>>>>         
>>>>> Jeff,
>>>>>
>>>>> Yes they disappear, and they fluctuate with the interpolation method
>>>>>         
>>>>>           
>> used
>>   
>>     
>>>>> For example, nearest interpolation don't show the line
>>>>>
>>>>> Also, if I reduce the grid resolution, the line is thicker, and if I
>>>>>           
> use
>   
>>>>>       
>>>>>         
>>>>>           
>>> a
>>>   
>>>     
>>>       
>>>>> masked array to get rid of undesired values, the border shows really
>>>>> strongly
>>>>>
>>>>> Here's an example everyone will see:
>>>>>
>>>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>>>
>>>>> (everything except the clouds is noise)
>>>>>
>>>>> Antoine De Pauw
>>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
>>>>>           
> and
>   
>>>>> photophysics laboratory
>>>>> Université Libre de Bruxelles - ULB
>>>>>   
>>>>>       
>>>>>         
>>>>>           
>>>> Antoine:  Sorry to seem dense, but I don't see anything wrong with that

>>>> plot. I see a white border along the north and south pole, but I 
>>>> intrepret that to be missing values.  However, my eyes are notoriously 
>>>> bad.  I'd like to be to run a script that generates the artifacts 
>>>> myself, so I can zoom in and see the problem myself.  Does the 
>>>> griddata_demo.py script show the same problem for you?
>>>>
>>>> -Jeff
>>>>     
>>>>       
>>>>         
>>>>> -----Original Message-----
>>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>>> Sent: mercredi 17 septembre 2008 19:05
>>>>> To: John Hunter
>>>>> Cc: De Pauw Antoine; Matplotlib Users
>>>>> Subject: Re: [Matplotlib-users] Information request
>>>>>
>>>>> John Hunter wrote:
>>>>>   
>>>>>       
>>>>>         
>>>>>           
>>>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
>>>>>>           
>>>>>>             
>> wrote:
>>   
>>     
>>>>>>   
>>>>>>     
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near
the
>>>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>>>>> curve down and to the right (corner.png)
>>>>>>>     
>>>>>>>       
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>>>> screenshot).  The correct screenshot is attached
>>>>>>   
>>>>>>
>>>>>>
>>>>>>     
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>>>> disappear if you comment out the imshow call?
>>>>>
>>>>> -Jeff
>>>>>
>>>>>   
>>>>>       
>>>>>         
>>>>>           
>>>> -- 
>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>> Meteorologist               FAX    : (303)497-6449
>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>
>>>>
>>>>
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

De Pauw Antoine wrote:
> Jeff,
>
> Thanks for the tip, it's now working perfectly
>
> However, there's still that border with the imshow plot, and I think it
> would be good to have it transparent
>
> There's a zoomed picture I made:
> http://img218.imageshack.us/img218/5833/imshowborderxz9.png
>
> You see the shadow around the data...
>
> It would be nice for next releases of Matplotlib to get rid of that, but I'm
> not able to patch it myself or so... I know there's still a lot of work with
> the lib but keep the good work, it is really fantastic
>
> Thanks for your help!
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine: I thought we agreed that it's not an imshow bug - but rather 
due to the griddata gridding procedure returning missing values outside 
the convex hull of the input data. Do you disagree? I see no such border 
around an imshow plot that contains no missing values. If you shrink the 
size of the map plotting region so it's fully within the convex hull of 
the data, the border disappears.

-Jeff
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: jeudi 25 septembre 2008 14:15
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Hi Jeff,
>>
>> I finally found out how to fill my figure with a background color using
>> axes.set_axis_bgcolor(color), but I'm facing the following problem now:
>>
>> How could I get the lower color of a colormap? This is quite undocumented
>> and I don’t know the colormap properties I could use for that
>>
>> I know there must be an accessible value somewhere, like for the
>> ax.get_yticklabels() you gave me
>>
>> If someone had the clue, my problems would then be completely solved
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine: To get the RGBA value associated with a particular data value, 
> just call the colormap as a function as pass it that value. For example
>
>  >>> import matplotlib.pyplot as plt
>  >>> plt.cm.jet(1)
> (0.0, 0.0, 0.517825311942959, 1.0)
>
> BTW: the 'fill_color' kwarg of drawmapboundary basemap method allows you 
> to set the background color of the map.
>
> http://matplotlib.sourceforge.net/basemap/doc/html/api/basemap_api.html
>
> It fills only the map region (which for some projections, like the 
> orthographic, is not the same as the axes region).
>
>
> -Jeff
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: mardi 23 septembre 2008 20:38
>> To: De Pauw Antoine
>> Cc: 'John Hunter'; 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Jeff,
>>>
>>> I still don't know how to either remove this artifact or fill my arrays
>>>     
>>>       
>> with
>>   
>>     
>>> values to remove empty regions, and I'll make a last attempt to resolve
>>>       
> it
>   
>>> I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56
>>>
>>> The actual code snippet is here:
>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>
>>> I hope you'll be able to reproduce it, I set the cmap to winter for you
>>>       
> to
>   
>>> see the gap... setting it to hot will make the grayish border visible in
>>> high resolution by zooming it... I think the border (not the empty zone)
>>> could be an artifact with the hot colormap
>>>
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>
>>>   
>>>     
>>>       
>> Antoine:  Here is a version that just plots the pixels directly, without 
>> interpolating to a grid.  I personally like this better, since you can 
>> easily see where you actually have data.
>>
>> HTH,
>>
>> -Jeff
>>
>> from mpl_toolkits.basemap import Basemap
>> import matplotlib.pyplot as plt
>> import matplotlib.mlab as mlab
>> import numpy as np
>> import os
>> fileName = '20080821.b56'
>> titre='SO2'
>> legende='Delta Brightness Temperature (K)'
>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>> rawfile=np.fromfile(open(fileName,'rb'),'<d',-1)
>> Lat=rawfile[0:nbreligne]
>> Lon=rawfile[nbreligne:nbreligne*2]
>> Val=rawfile[nbreligne*21:nbreligne*22]
>> map=Basemap(projection='mill',llcrnrlat=-90,urcrnrlat=90,\
>>             urcrnrlon=180,llcrnrlon=-180,resolution='l')
>> x, y = map(Lon, Lat)
>>
>>     
> plt.scatter(x,y,s=25,c=Val,marker='s',edgecolor="None",cmap=plt.cm.winter,vm
>   
>> in=-5,vmax=-1.2, 
>> alpha=0.5)
>> cb=plt.colorbar(shrink=0.6)
>> cb.ax.set_ylabel(legende,fontsize=11)
>> for t in cb.ax.get_yticklabels():
>>     t.set_fontsize(7)
>> meridians = np.arange(-180,180,60)
>> parallels = np.arange(-90,90,30)
>> map.drawparallels(parallels,labels=[1,0,0,0],fontsize=7,linewidth=0.25)
>> map.drawmeridians(meridians,labels=[0,0,0,1],fontsize=7,linewidth=0.25)
>> map.drawcoastlines(0.25,antialiased=1)
>> plt.title(titre)
>> plt.show()
>>   
>>     
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: lundi 22 septembre 2008 13:59
>>> To: De Pauw Antoine
>>> Cc: 'John Hunter'; 'Matplotlib Users'
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> De Pauw Antoine wrote:
>>>   
>>>     
>>>       
>>>> Jeff,
>>>>
>>>> I included here a figure where you'll see the border problem for imshow
>>>>       
>>>>         
>> in
>>   
>>     
>>>> my case
>>>>
>>>> http://img217.imageshack.us/img217/5240/testfigzp3.png
>>>>
>>>> The border wraps at -180 and 180 to form the white line
>>>>
>>>> PS: it is atmospheric ice and not SO2, I just omitted to change the
>>>>         
> title
>   
>>>>     
>>>>       
>>>>         
>>> ^^
>>>   
>>>     
>>>       
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>   
>>>>     
>>>>       
>>>>         
>>> Antoine:  I hate to keep repeating myself - but we can't do much if you 
>>> don't provide a self-contained script, that I can run, which reproduces 
>>> the problem.  My guess is that the line along the dateline, and the 
>>> point at the South Pole are missing values (which griddata set to 
>>> missing because they are outside the extent of the data) - but that's 
>>> just a guess until I can reproduce it.
>>>
>>> -Jeff
>>>   
>>>     
>>>       
>>>> -----Original Message-----
>>>> From: Antoine De Pauw [mailto:andepauw@...] 
>>>> Sent: jeudi 18 septembre 2008 17:23
>>>> To: Jeff Whitaker; andepauw@...
>>>> Cc: 'John Hunter'; 'Matplotlib Users'
>>>> Subject: re:Re: [Matplotlib-users] Information request
>>>>
>>>> Jeff,
>>>>
>>>> No the example doesn't show that line
>>>>
>>>> If I reduce the amount of data, the border will be on every side of the
>>>>     
>>>>       
>>>>         
>>> plot
>>>   
>>>     
>>>       
>>>> I'll show you an orthographic plot with no maskinf tomorrow and you will
>>>>     
>>>>       
>>>>         
>>> see
>>>   
>>>     
>>>       
>>>> the problem easily, it wraps in a white line along the 0° meridian and a
>>>> white circle in the pole
>>>>
>>>> I think it's the imshow layer that is not totally transparent on the map
>>>> background.. I tried every trick I could for example to put some
>>>>     
>>>>       
>>>>         
>>> zero-valued
>>>   
>>>     
>>>       
>>>> points on each corner to make imshow interpolate correctly the sides,
>>>>         
> but
>   
>>>> that doesn't make any difference
>>>>
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> De Pauw Antoine wrote:
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> Jeff,
>>>>>>
>>>>>> Yes they disappear, and they fluctuate with the interpolation method
>>>>>>         
>>>>>>           
>>>>>>             
>>> used
>>>   
>>>     
>>>       
>>>>>> For example, nearest interpolation don't show the line
>>>>>>
>>>>>> Also, if I reduce the grid resolution, the line is thicker, and if I
>>>>>>           
>>>>>>             
>> use
>>   
>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>> a
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>> masked array to get rid of undesired values, the border shows really
>>>>>> strongly
>>>>>>
>>>>>> Here's an example everyone will see:
>>>>>>
>>>>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>>>>
>>>>>> (everything except the clouds is noise)
>>>>>>
>>>>>> Antoine De Pauw
>>>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
>>>>>>           
>>>>>>             
>> and
>>   
>>     
>>>>>> photophysics laboratory
>>>>>> Université Libre de Bruxelles - ULB
>>>>>>   
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> Antoine:  Sorry to seem dense, but I don't see anything wrong with that
>>>>>           
>
>   
>>>>> plot. I see a white border along the north and south pole, but I 
>>>>> intrepret that to be missing values.  However, my eyes are notoriously 
>>>>> bad.  I'd like to be to run a script that generates the artifacts 
>>>>> myself, so I can zoom in and see the problem myself.  Does the 
>>>>> griddata_demo.py script show the same problem for you?
>>>>>
>>>>> -Jeff
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> -----Original Message-----
>>>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>>>> Sent: mercredi 17 septembre 2008 19:05
>>>>>> To: John Hunter
>>>>>> Cc: De Pauw Antoine; Matplotlib Users
>>>>>> Subject: Re: [Matplotlib-users] Information request
>>>>>>
>>>>>> John Hunter wrote:
>>>>>>   
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>> wrote:
>>>   
>>>     
>>>       
>>>>>>>   
>>>>>>>     
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near
>>>>>>>>                 
> the
>   
>>>>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>>>>> grid line.  I don't know if this offers a clue, but if you look at a
>>>>>>>> zoom in the upper right corner, the grey  line seems to break up and
>>>>>>>> curve down and to the right (corner.png)
>>>>>>>>     
>>>>>>>>       
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>>>>> screenshot).  The correct screenshot is attached
>>>>>>>   
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>>>>> disappear if you comment out the imshow call?
>>>>>>
>>>>>> -Jeff
>>>>>>
>>>>>>   
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> -- 
>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>> Meteorologist               FAX    : (303)497-6449
>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>
>>>>>
>>>>>
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>   
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Jeff,

I totally agree this is due to missing values

Again I've got difficulties to find good words so forgive me, what I tried
to say is that the ability to have that border transparent would be a good
feature in next releases, for people who need to interpolate and plot such
data and have an aesthetic result

Imshow is the ideal candidate for satellite data as it has some nice
interpolation features and it is fast, so it can be batch-run on the server
every time we receive data, without too much computation time

The alternative I'm using now is a double or quadruple size grid to reduce
the width of that border, with background color set to the lower colormap
color

That way, the border is really hard to see and it makes (almost) quality
plots for publications

-----Original Message-----
From: Jeff Whitaker [mailto:jswhit@...] 
Sent: Thursday, 25 September, 2008 15:34
To: De Pauw Antoine
Cc: 'Matplotlib Users'
Subject: Re: [Matplotlib-users] Information request

De Pauw Antoine wrote:
> Jeff,
>
> Thanks for the tip, it's now working perfectly
>
> However, there's still that border with the imshow plot, and I think it
> would be good to have it transparent
>
> There's a zoomed picture I made:
> http://img218.imageshack.us/img218/5833/imshowborderxz9.png
>
> You see the shadow around the data...
>
> It would be nice for next releases of Matplotlib to get rid of that, but
I'm
> not able to patch it myself or so... I know there's still a lot of work
with
> the lib but keep the good work, it is really fantastic
>
> Thanks for your help!
>
> Antoine De Pauw
> Collaborateur de recherches, Informatique - Research collaborator, IT
> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
> photophysics laboratory
> Université Libre de Bruxelles - ULB
>   

Antoine: I thought we agreed that it's not an imshow bug - but rather 
due to the griddata gridding procedure returning missing values outside 
the convex hull of the input data. Do you disagree? I see no such border 
around an imshow plot that contains no missing values. If you shrink the 
size of the map plotting region so it's fully within the convex hull of 
the data, the border disappears.

-Jeff
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: jeudi 25 septembre 2008 14:15
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Hi Jeff,
>>
>> I finally found out how to fill my figure with a background color using
>> axes.set_axis_bgcolor(color), but I'm facing the following problem now:
>>
>> How could I get the lower color of a colormap? This is quite undocumented
>> and I don’t know the colormap properties I could use for that
>>
>> I know there must be an accessible value somewhere, like for the
>> ax.get_yticklabels() you gave me
>>
>> If someone had the clue, my problems would then be completely solved
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine: To get the RGBA value associated with a particular data value, 
> just call the colormap as a function as pass it that value. For example
>
>  >>> import matplotlib.pyplot as plt
>  >>> plt.cm.jet(1)
> (0.0, 0.0, 0.517825311942959, 1.0)
>
> BTW: the 'fill_color' kwarg of drawmapboundary basemap method allows you 
> to set the background color of the map.
>
> http://matplotlib.sourceforge.net/basemap/doc/html/api/basemap_api.html
>
> It fills only the map region (which for some projections, like the 
> orthographic, is not the same as the axes region).
>
>
> -Jeff
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: mardi 23 septembre 2008 20:38
>> To: De Pauw Antoine
>> Cc: 'John Hunter'; 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Jeff,
>>>
>>> I still don't know how to either remove this artifact or fill my arrays
>>>     
>>>       
>> with
>>   
>>     
>>> values to remove empty regions, and I'll make a last attempt to resolve
>>>       
> it
>   
>>> I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56
>>>
>>> The actual code snippet is here:
>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>
>>> I hope you'll be able to reproduce it, I set the cmap to winter for you
>>>       
> to
>   
>>> see the gap... setting it to hot will make the grayish border visible in
>>> high resolution by zooming it... I think the border (not the empty zone)
>>> could be an artifact with the hot colormap
>>>
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>
>>>   
>>>     
>>>       
>> Antoine:  Here is a version that just plots the pixels directly, without 
>> interpolating to a grid.  I personally like this better, since you can 
>> easily see where you actually have data.
>>
>> HTH,
>>
>> -Jeff
>>
>> from mpl_toolkits.basemap import Basemap
>> import matplotlib.pyplot as plt
>> import matplotlib.mlab as mlab
>> import numpy as np
>> import os
>> fileName = '20080821.b56'
>> titre='SO2'
>> legende='Delta Brightness Temperature (K)'
>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>> rawfile=np.fromfile(open(fileName,'rb'),'<d',-1)
>> Lat=rawfile[0:nbreligne]
>> Lon=rawfile[nbreligne:nbreligne*2]
>> Val=rawfile[nbreligne*21:nbreligne*22]
>> map=Basemap(projection='mill',llcrnrlat=-90,urcrnrlat=90,\
>>             urcrnrlon=180,llcrnrlon=-180,resolution='l')
>> x, y = map(Lon, Lat)
>>
>>     
>
plt.scatter(x,y,s=25,c=Val,marker='s',edgecolor="None",cmap=plt.cm.winter,vm
>   
>> in=-5,vmax=-1.2, 
>> alpha=0.5)
>> cb=plt.colorbar(shrink=0.6)
>> cb.ax.set_ylabel(legende,fontsize=11)
>> for t in cb.ax.get_yticklabels():
>>     t.set_fontsize(7)
>> meridians = np.arange(-180,180,60)
>> parallels = np.arange(-90,90,30)
>> map.drawparallels(parallels,labels=[1,0,0,0],fontsize=7,linewidth=0.25)
>> map.drawmeridians(meridians,labels=[0,0,0,1],fontsize=7,linewidth=0.25)
>> map.drawcoastlines(0.25,antialiased=1)
>> plt.title(titre)
>> plt.show()
>>   
>>     
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: lundi 22 septembre 2008 13:59
>>> To: De Pauw Antoine
>>> Cc: 'John Hunter'; 'Matplotlib Users'
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> De Pauw Antoine wrote:
>>>   
>>>     
>>>       
>>>> Jeff,
>>>>
>>>> I included here a figure where you'll see the border problem for imshow
>>>>       
>>>>         
>> in
>>   
>>     
>>>> my case
>>>>
>>>> http://img217.imageshack.us/img217/5240/testfigzp3.png
>>>>
>>>> The border wraps at -180 and 180 to form the white line
>>>>
>>>> PS: it is atmospheric ice and not SO2, I just omitted to change the
>>>>         
> title
>   
>>>>     
>>>>       
>>>>         
>>> ^^
>>>   
>>>     
>>>       
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>   
>>>>     
>>>>       
>>>>         
>>> Antoine:  I hate to keep repeating myself - but we can't do much if you 
>>> don't provide a self-contained script, that I can run, which reproduces 
>>> the problem.  My guess is that the line along the dateline, and the 
>>> point at the South Pole are missing values (which griddata set to 
>>> missing because they are outside the extent of the data) - but that's 
>>> just a guess until I can reproduce it.
>>>
>>> -Jeff
>>>   
>>>     
>>>       
>>>> -----Original Message-----
>>>> From: Antoine De Pauw [mailto:andepauw@...] 
>>>> Sent: jeudi 18 septembre 2008 17:23
>>>> To: Jeff Whitaker; andepauw@...
>>>> Cc: 'John Hunter'; 'Matplotlib Users'
>>>> Subject: re:Re: [Matplotlib-users] Information request
>>>>
>>>> Jeff,
>>>>
>>>> No the example doesn't show that line
>>>>
>>>> If I reduce the amount of data, the border will be on every side of the
>>>>     
>>>>       
>>>>         
>>> plot
>>>   
>>>     
>>>       
>>>> I'll show you an orthographic plot with no maskinf tomorrow and you
will
>>>>     
>>>>       
>>>>         
>>> see
>>>   
>>>     
>>>       
>>>> the problem easily, it wraps in a white line along the 0° meridian and
a
>>>> white circle in the pole
>>>>
>>>> I think it's the imshow layer that is not totally transparent on the
map
>>>> background.. I tried every trick I could for example to put some
>>>>     
>>>>       
>>>>         
>>> zero-valued
>>>   
>>>     
>>>       
>>>> points on each corner to make imshow interpolate correctly the sides,
>>>>         
> but
>   
>>>> that doesn't make any difference
>>>>
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> De Pauw Antoine wrote:
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> Jeff,
>>>>>>
>>>>>> Yes they disappear, and they fluctuate with the interpolation method
>>>>>>         
>>>>>>           
>>>>>>             
>>> used
>>>   
>>>     
>>>       
>>>>>> For example, nearest interpolation don't show the line
>>>>>>
>>>>>> Also, if I reduce the grid resolution, the line is thicker, and if I
>>>>>>           
>>>>>>             
>> use
>>   
>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>> a
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>> masked array to get rid of undesired values, the border shows really
>>>>>> strongly
>>>>>>
>>>>>> Here's an example everyone will see:
>>>>>>
>>>>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>>>>
>>>>>> (everything except the clouds is noise)
>>>>>>
>>>>>> Antoine De Pauw
>>>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
>>>>>>           
>>>>>>             
>> and
>>   
>>     
>>>>>> photophysics laboratory
>>>>>> Université Libre de Bruxelles - ULB
>>>>>>   
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> Antoine:  Sorry to seem dense, but I don't see anything wrong with
that
>>>>>           
>
>   
>>>>> plot. I see a white border along the north and south pole, but I 
>>>>> intrepret that to be missing values.  However, my eyes are notoriously

>>>>> bad.  I'd like to be to run a script that generates the artifacts 
>>>>> myself, so I can zoom in and see the problem myself.  Does the 
>>>>> griddata_demo.py script show the same problem for you?
>>>>>
>>>>> -Jeff
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> -----Original Message-----
>>>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>>>> Sent: mercredi 17 septembre 2008 19:05
>>>>>> To: John Hunter
>>>>>> Cc: De Pauw Antoine; Matplotlib Users
>>>>>> Subject: Re: [Matplotlib-users] Information request
>>>>>>
>>>>>> John Hunter wrote:
>>>>>>   
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>> wrote:
>>>   
>>>     
>>>       
>>>>>>>   
>>>>>>>     
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near
>>>>>>>>                 
> the
>   
>>>>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>>>>> grid line.  I don't know if this offers a clue, but if you look at
a
>>>>>>>> zoom in the upper right corner, the grey  line seems to break up
and
>>>>>>>> curve down and to the right (corner.png)
>>>>>>>>     
>>>>>>>>       
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>>>>> screenshot).  The correct screenshot is attached
>>>>>>>   
>>>>>>>
>>>>>>>
>>>>>>>     
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>>>>> disappear if you comment out the imshow call?
>>>>>>
>>>>>> -Jeff
>>>>>>
>>>>>>   
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> -- 
>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>> Meteorologist               FAX    : (303)497-6449
>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>
>>>>>
>>>>>
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>   
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Antoine De Pauw wrote:
> Jeff,
>
> I totally agree this is due to missing values
>
> Again I've got difficulties to find good words so forgive me, what I tried
> to say is that the ability to have that border transparent would be a good
> feature in next releases, for people who need to interpolate and plot such
> data and have an aesthetic result
>   

Antoine: First of all, let's not call it a 'border' - it happens to show 
up around the border of the image in your case, but fundamentally it's 
just missing pixels in the image. The missing pixels are already 
transparent - what you're seeing is the axes background showing through 
the missing values.
> Imshow is the ideal candidate for satellite data as it has some nice
> interpolation features and it is fast, so it can be batch-run on the server
> every time we receive data, without too much computation time
>
> The alternative I'm using now is a double or quadruple size grid to reduce
> the width of that border, with background color set to the lower colormap
> color
>
> That way, the border is really hard to see and it makes (almost) quality
> plots for publications
>   
I think you're already doing everything that can be done - aside from 
making the plot region smaller so it's inside the convex hull of the 
data and there are no missing values. I don't see how changing the 
behavior of imshow would help you any further.

-Jeff
> -----Original Message-----
> From: Jeff Whitaker [mailto:jswhit@...] 
> Sent: Thursday, 25 September, 2008 15:34
> To: De Pauw Antoine
> Cc: 'Matplotlib Users'
> Subject: Re: [Matplotlib-users] Information request
>
> De Pauw Antoine wrote:
>   
>> Jeff,
>>
>> Thanks for the tip, it's now working perfectly
>>
>> However, there's still that border with the imshow plot, and I think it
>> would be good to have it transparent
>>
>> There's a zoomed picture I made:
>> http://img218.imageshack.us/img218/5833/imshowborderxz9.png
>>
>> You see the shadow around the data...
>>
>> It would be nice for next releases of Matplotlib to get rid of that, but
>>     
> I'm
>   
>> not able to patch it myself or so... I know there's still a lot of work
>>     
> with
>   
>> the lib but keep the good work, it is really fantastic
>>
>> Thanks for your help!
>>
>> Antoine De Pauw
>> Collaborateur de recherches, Informatique - Research collaborator, IT
>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>> photophysics laboratory
>> Université Libre de Bruxelles - ULB
>>   
>>     
>
> Antoine: I thought we agreed that it's not an imshow bug - but rather 
> due to the griddata gridding procedure returning missing values outside 
> the convex hull of the input data. Do you disagree? I see no such border 
> around an imshow plot that contains no missing values. If you shrink the 
> size of the map plotting region so it's fully within the convex hull of 
> the data, the border disappears.
>
> -Jeff
>   
>> -----Original Message-----
>> From: Jeff Whitaker [mailto:jswhit@...] 
>> Sent: jeudi 25 septembre 2008 14:15
>> To: De Pauw Antoine
>> Cc: 'Matplotlib Users'
>> Subject: Re: [Matplotlib-users] Information request
>>
>> De Pauw Antoine wrote:
>>   
>>     
>>> Hi Jeff,
>>>
>>> I finally found out how to fill my figure with a background color using
>>> axes.set_axis_bgcolor(color), but I'm facing the following problem now:
>>>
>>> How could I get the lower color of a colormap? This is quite undocumented
>>> and I don’t know the colormap properties I could use for that
>>>
>>> I know there must be an accessible value somewhere, like for the
>>> ax.get_yticklabels() you gave me
>>>
>>> If someone had the clue, my problems would then be completely solved
>>>
>>> Antoine De Pauw
>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>> photophysics laboratory
>>> Université Libre de Bruxelles - ULB
>>>   
>>>     
>>>       
>> Antoine: To get the RGBA value associated with a particular data value, 
>> just call the colormap as a function as pass it that value. For example
>>
>>  >>> import matplotlib.pyplot as plt
>>  >>> plt.cm.jet(1)
>> (0.0, 0.0, 0.517825311942959, 1.0)
>>
>> BTW: the 'fill_color' kwarg of drawmapboundary basemap method allows you 
>> to set the background color of the map.
>>
>> http://matplotlib.sourceforge.net/basemap/doc/html/api/basemap_api.html
>>
>> It fills only the map region (which for some projections, like the 
>> orthographic, is not the same as the axes region).
>>
>>
>> -Jeff
>>   
>>     
>>> -----Original Message-----
>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>> Sent: mardi 23 septembre 2008 20:38
>>> To: De Pauw Antoine
>>> Cc: 'John Hunter'; 'Matplotlib Users'
>>> Subject: Re: [Matplotlib-users] Information request
>>>
>>> De Pauw Antoine wrote:
>>>   
>>>     
>>>       
>>>> Jeff,
>>>>
>>>> I still don't know how to either remove this artifact or fill my arrays
>>>>     
>>>>       
>>>>         
>>> with
>>>   
>>>     
>>>       
>>>> values to remove empty regions, and I'll make a last attempt to resolve
>>>>       
>>>>         
>> it
>>   
>>     
>>>> I uploaded a data file here: http://scqp.ulb.ac.be/20080821.b56
>>>>
>>>> The actual code snippet is here:
>>>> http://snipplr.com/view/8307/map-plotting-python-code-temporary/
>>>>
>>>> I hope you'll be able to reproduce it, I set the cmap to winter for you
>>>>       
>>>>         
>> to
>>   
>>     
>>>> see the gap... setting it to hot will make the grayish border visible in
>>>> high resolution by zooming it... I think the border (not the empty zone)
>>>> could be an artifact with the hot colormap
>>>>
>>>>
>>>> Antoine De Pauw
>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry and
>>>> photophysics laboratory
>>>> Université Libre de Bruxelles - ULB
>>>>
>>>>   
>>>>     
>>>>       
>>>>         
>>> Antoine:  Here is a version that just plots the pixels directly, without 
>>> interpolating to a grid.  I personally like this better, since you can 
>>> easily see where you actually have data.
>>>
>>> HTH,
>>>
>>> -Jeff
>>>
>>> from mpl_toolkits.basemap import Basemap
>>> import matplotlib.pyplot as plt
>>> import matplotlib.mlab as mlab
>>> import numpy as np
>>> import os
>>> fileName = '20080821.b56'
>>> titre='SO2'
>>> legende='Delta Brightness Temperature (K)'
>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:]))
>>> rawfile=np.fromfile(open(fileName,'rb'),'<d',-1)
>>> Lat=rawfile[0:nbreligne]
>>> Lon=rawfile[nbreligne:nbreligne*2]
>>> Val=rawfile[nbreligne*21:nbreligne*22]
>>> map=Basemap(projection='mill',llcrnrlat=-90,urcrnrlat=90,\
>>>             urcrnrlon=180,llcrnrlon=-180,resolution='l')
>>> x, y = map(Lon, Lat)
>>>
>>>     
>>>       
> plt.scatter(x,y,s=25,c=Val,marker='s',edgecolor="None",cmap=plt.cm.winter,vm
>   
>>   
>>     
>>> in=-5,vmax=-1.2, 
>>> alpha=0.5)
>>> cb=plt.colorbar(shrink=0.6)
>>> cb.ax.set_ylabel(legende,fontsize=11)
>>> for t in cb.ax.get_yticklabels():
>>>     t.set_fontsize(7)
>>> meridians = np.arange(-180,180,60)
>>> parallels = np.arange(-90,90,30)
>>> map.drawparallels(parallels,labels=[1,0,0,0],fontsize=7,linewidth=0.25)
>>> map.drawmeridians(meridians,labels=[0,0,0,1],fontsize=7,linewidth=0.25)
>>> map.drawcoastlines(0.25,antialiased=1)
>>> plt.title(titre)
>>> plt.show()
>>>   
>>>     
>>>       
>>>> -----Original Message-----
>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>> Sent: lundi 22 septembre 2008 13:59
>>>> To: De Pauw Antoine
>>>> Cc: 'John Hunter'; 'Matplotlib Users'
>>>> Subject: Re: [Matplotlib-users] Information request
>>>>
>>>> De Pauw Antoine wrote:
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> Jeff,
>>>>>
>>>>> I included here a figure where you'll see the border problem for imshow
>>>>>       
>>>>>         
>>>>>           
>>> in
>>>   
>>>     
>>>       
>>>>> my case
>>>>>
>>>>> http://img217.imageshack.us/img217/5240/testfigzp3.png
>>>>>
>>>>> The border wraps at -180 and 180 to form the white line
>>>>>
>>>>> PS: it is atmospheric ice and not SO2, I just omitted to change the
>>>>>         
>>>>>           
>> title
>>   
>>     
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> ^^
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> Antoine De Pauw
>>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
>>>>>           
> and
>   
>>>>> photophysics laboratory
>>>>> Université Libre de Bruxelles - ULB
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> Antoine:  I hate to keep repeating myself - but we can't do much if you 
>>>> don't provide a self-contained script, that I can run, which reproduces 
>>>> the problem.  My guess is that the line along the dateline, and the 
>>>> point at the South Pole are missing values (which griddata set to 
>>>> missing because they are outside the extent of the data) - but that's 
>>>> just a guess until I can reproduce it.
>>>>
>>>> -Jeff
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> -----Original Message-----
>>>>> From: Antoine De Pauw [mailto:andepauw@...] 
>>>>> Sent: jeudi 18 septembre 2008 17:23
>>>>> To: Jeff Whitaker; andepauw@...
>>>>> Cc: 'John Hunter'; 'Matplotlib Users'
>>>>> Subject: re:Re: [Matplotlib-users] Information request
>>>>>
>>>>> Jeff,
>>>>>
>>>>> No the example doesn't show that line
>>>>>
>>>>> If I reduce the amount of data, the border will be on every side of the
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> plot
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> I'll show you an orthographic plot with no maskinf tomorrow and you
>>>>>           
> will
>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> see
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> the problem easily, it wraps in a white line along the 0° meridian and
>>>>>           
> a
>   
>>>>> white circle in the pole
>>>>>
>>>>> I think it's the imshow layer that is not totally transparent on the
>>>>>           
> map
>   
>>>>> background.. I tried every trick I could for example to put some
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>> zero-valued
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> points on each corner to make imshow interpolate correctly the sides,
>>>>>         
>>>>>           
>> but
>>   
>>     
>>>>> that doesn't make any difference
>>>>>
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>> De Pauw Antoine wrote:
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> Jeff,
>>>>>>>
>>>>>>> Yes they disappear, and they fluctuate with the interpolation method
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>> used
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>> For example, nearest interpolation don't show the line
>>>>>>>
>>>>>>> Also, if I reduce the grid resolution, the line is thicker, and if I
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>> use
>>>   
>>>     
>>>       
>>>>>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>> a
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>>>> masked array to get rid of undesired values, the border shows really
>>>>>>> strongly
>>>>>>>
>>>>>>> Here's an example everyone will see:
>>>>>>>
>>>>>>> http://img225.imageshack.us/img225/2671/testfigep2.png
>>>>>>>
>>>>>>> (everything except the clouds is noise)
>>>>>>>
>>>>>>> Antoine De Pauw
>>>>>>> Collaborateur de recherches, Informatique - Research collaborator, IT
>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum chemistry
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>> and
>>>   
>>>     
>>>       
>>>>>>> photophysics laboratory
>>>>>>> Université Libre de Bruxelles - ULB
>>>>>>>   
>>>>>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> Antoine:  Sorry to seem dense, but I don't see anything wrong with
>>>>>>             
> that
>   
>>>>>>           
>>>>>>             
>>   
>>     
>>>>>> plot. I see a white border along the north and south pole, but I 
>>>>>> intrepret that to be missing values.  However, my eyes are notoriously
>>>>>>             
>
>   
>>>>>> bad.  I'd like to be to run a script that generates the artifacts 
>>>>>> myself, so I can zoom in and see the problem myself.  Does the 
>>>>>> griddata_demo.py script show the same problem for you?
>>>>>>
>>>>>> -Jeff
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>>> -----Original Message-----
>>>>>>> From: Jeff Whitaker [mailto:jswhit@...] 
>>>>>>> Sent: mercredi 17 septembre 2008 19:05
>>>>>>> To: John Hunter
>>>>>>> Cc: De Pauw Antoine; Matplotlib Users
>>>>>>> Subject: Re: [Matplotlib-users] Information request
>>>>>>>
>>>>>>> John Hunter wrote:
>>>>>>>   
>>>>>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>>> On Wed, Sep 17, 2008 at 11:54 AM, John Hunter <jdh2358@...>
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>> wrote:
>>>>   
>>>>     
>>>>       
>>>>         
>>>>>>>>   
>>>>>>>>     
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>>>> Attached is a screenshot (zoom.png) from the gimp, zoomed in near
>>>>>>>>>                 
>>>>>>>>>                   
>> the
>>   
>>     
>>>>>>>>> axes border.  The black horizontal line is the top axes border, the
>>>>>>>>> horizontal grey line is the artifact, the vertical dashed line is a
>>>>>>>>> grid line.  I don't know if this offers a clue, but if you look at
>>>>>>>>>                   
> a
>   
>>>>>>>>> zoom in the upper right corner, the grey  line seems to break up
>>>>>>>>>                   
> and
>   
>>>>>>>>> curve down and to the right (corner.png)
>>>>>>>>>     
>>>>>>>>>       
>>>>>>>>>           
>>>>>>>>>             
>>>>>>>>>               
>>>>>>>>>                 
>>>>>>>>>                   
>>>>>>>> Sorry, screwed up corner.png (I attached the original and not the
>>>>>>>> screenshot).  The correct screenshot is attached
>>>>>>>>   
>>>>>>>>
>>>>>>>>
>>>>>>>>     
>>>>>>>>         
>>>>>>>>           
>>>>>>>>             
>>>>>>>>               
>>>>>>>>                 
>>>>>>> John:   OK, now I finally see it.  Antoine:  Do these artifacts 
>>>>>>> disappear if you comment out the imshow call?
>>>>>>>
>>>>>>> -Jeff
>>>>>>>
>>>>>>>   
>>>>>>>       
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>> -- 
>>>>>> Jeffrey S. Whitaker         Phone  : (303)497-6313
>>>>>> Meteorologist               FAX    : (303)497-6449
>>>>>> NOAA/OAR/PSD  R/PSD1        Email  : Jeffrey.S.Whitaker@...
>>>>>> 325 Broadway                Office : Skaggs Research Cntr 1D-113
>>>>>> Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg
>>>>>>
>>>>>>
>>>>>>
>>>>>>     
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>>           
>>>>   
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
>>   
>>     
>
>
>   


-- 
Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328