## Re: [Matplotlib-users] images from data

 Re: [Matplotlib-users] images from data From: Robert Kern - 2006-04-29 18:12:32 ```Michael V. De Palatis wrote: > On Sat, Apr 29, 2006 at 09:59:14AM -0700, Andrew Straw wrote: > >>If you data is regularly spaced, you can just use imshow or pcolor. If >>it's not regularaly spaced, see >>http://www.scipy.org/Wiki/Cookbook/Matplotlib/Gridding_irregularly_spaced_data > > Perhaps I'm missing something or did not explain my problem > properly. I am well aware that what I want to use is imshow (or, > apparently, pcolor). However, my problem is that I have all THREE > values in data form, not just x and y (that is, I do not have a > function to get z(x, y), but rather I have data points for z). > > I do not see a straightforward way to use imshow or pcolor to be able > to plot this data as they want a matrix that I have no idea how to > generate. Okay, so your x,y data is regularly spaced. What you have to do is create an array of the appropriate size to put all of your z values in. Then go through your list of points and populate the z array in the appropriate places. You will have to convert your x,y coordinates into i,j indices. If you know the spacing, this should not be difficult. Alternatively, you can sort the (x,y,z) tuples, turn it into an array, extract the z column, reshape the z column into the appropriate matrix, and transpose it (presuming you want y to be vertical): In [18]: xyz = [(1, 0, 10), (0, 1, 20), (0, 0, 30), (1, 1, 40)] In [19]: xyz.sort() In [20]: xyz Out[20]: [(0, 0, 30), (0, 1, 20), (1, 0, 10), (1, 1, 40)] In [21]: xyza = array(xyz) In [22]: z = xyza[:,-1] In [23]: z Out[23]: array([30, 20, 10, 40]) In [24]: z = transpose(reshape(z, (2,2))) In [25]: z Out[25]: array([[30, 10], [20, 40]]) -- Robert Kern robert.kern@... "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco ```

 [Matplotlib-users] images from data From: Michael V. De Palatis - 2006-04-29 15:53:12 ```Hi all, I am trying to use imshow to plot an image from some data. Basically, I have a list of x, y, and z values, and I want to plot z as a function of x and y. Unfortunately, most of the examples do this as far as I can tell. Instead, they (at most) take a list of x and y then make a *function* z out of that, and plot z, rather than having actual data from a file for all three. The only one that does seem to do something like this seems to be dependent on a binary file, which unfortunately is not the format I have the data in. Sure, I could convert the very large files I already have into binary, but in the long run, I think it would be better for me to be able to simply use the ASCII data that I am provided with since that can't be changed. Is there an easy way to do this, or will I just have to convert the files? Thanks, Mike ```
 Re: [Matplotlib-users] images from data From: Andrew Straw - 2006-04-29 16:59:17 ```If you data is regularly spaced, you can just use imshow or pcolor. If it's not regularaly spaced, see http://www.scipy.org/Wiki/Cookbook/Matplotlib/Gridding_irregularly_spaced_data Michael V. De Palatis wrote: >Hi all, > >I am trying to use imshow to plot an image from some data. Basically, >I have a list of x, y, and z values, and I want to plot z as a >function of x and y. > >Unfortunately, most of the examples do this as far as I can >tell. Instead, they (at most) take a list of x and y then make a >*function* z out of that, and plot z, rather than having actual data >from a file for all three. > >The only one that does seem to do something like this seems to be >dependent on a binary file, which unfortunately is not the format I >have the data in. Sure, I could convert the very large files I already >have into binary, but in the long run, I think it would be better for >me to be able to simply use the ASCII data that I am provided with >since that can't be changed. > >Is there an easy way to do this, or will I just have to convert the >files? > >Thanks, > >Mike > > >------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Matplotlib-users mailing list >Matplotlib-users@... >https://lists.sourceforge.net/lists/listinfo/matplotlib-users > > ```
 Re: [Matplotlib-users] images from data From: Michael V. De Palatis - 2006-04-29 17:53:05 ```On Sat, Apr 29, 2006 at 09:59:14AM -0700, Andrew Straw wrote: > If you data is regularly spaced, you can just use imshow or pcolor. If > it's not regularaly spaced, see > http://www.scipy.org/Wiki/Cookbook/Matplotlib/Gridding_irregularly_spaced_data Perhaps I'm missing something or did not explain my problem properly. I am well aware that what I want to use is imshow (or, apparently, pcolor). However, my problem is that I have all THREE values in data form, not just x and y (that is, I do not have a function to get z(x, y), but rather I have data points for z). I do not see a straightforward way to use imshow or pcolor to be able to plot this data as they want a matrix that I have no idea how to generate. Thanks, Mike > > Michael V. De Palatis wrote: > > >Hi all, > > > >I am trying to use imshow to plot an image from some data. Basically, > >I have a list of x, y, and z values, and I want to plot z as a > >function of x and y. > > > >Unfortunately, most of the examples do this as far as I can > >tell. Instead, they (at most) take a list of x and y then make a > >*function* z out of that, and plot z, rather than having actual data > >from a file for all three. > > > >The only one that does seem to do something like this seems to be > >dependent on a binary file, which unfortunately is not the format I > >have the data in. Sure, I could convert the very large files I already > >have into binary, but in the long run, I think it would be better for > >me to be able to simply use the ASCII data that I am provided with > >since that can't be changed. > > > >Is there an easy way to do this, or will I just have to convert the > >files? > > > >Thanks, > > > >Mike > > > > > >------------------------------------------------------- > >Using Tomcat but need to do more? Need to support web services, security? > >Get stuff done quickly with pre-integrated technology to make your job easier > >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > >_______________________________________________ > >Matplotlib-users mailing list > >Matplotlib-users@... > >https://lists.sourceforge.net/lists/listinfo/matplotlib-users > > > > ```
 Re: [Matplotlib-users] images from data From: Robert Kern - 2006-04-29 18:12:32 ```Michael V. De Palatis wrote: > On Sat, Apr 29, 2006 at 09:59:14AM -0700, Andrew Straw wrote: > >>If you data is regularly spaced, you can just use imshow or pcolor. If >>it's not regularaly spaced, see >>http://www.scipy.org/Wiki/Cookbook/Matplotlib/Gridding_irregularly_spaced_data > > Perhaps I'm missing something or did not explain my problem > properly. I am well aware that what I want to use is imshow (or, > apparently, pcolor). However, my problem is that I have all THREE > values in data form, not just x and y (that is, I do not have a > function to get z(x, y), but rather I have data points for z). > > I do not see a straightforward way to use imshow or pcolor to be able > to plot this data as they want a matrix that I have no idea how to > generate. Okay, so your x,y data is regularly spaced. What you have to do is create an array of the appropriate size to put all of your z values in. Then go through your list of points and populate the z array in the appropriate places. You will have to convert your x,y coordinates into i,j indices. If you know the spacing, this should not be difficult. Alternatively, you can sort the (x,y,z) tuples, turn it into an array, extract the z column, reshape the z column into the appropriate matrix, and transpose it (presuming you want y to be vertical): In [18]: xyz = [(1, 0, 10), (0, 1, 20), (0, 0, 30), (1, 1, 40)] In [19]: xyz.sort() In [20]: xyz Out[20]: [(0, 0, 30), (0, 1, 20), (1, 0, 10), (1, 1, 40)] In [21]: xyza = array(xyz) In [22]: z = xyza[:,-1] In [23]: z Out[23]: array([30, 20, 10, 40]) In [24]: z = transpose(reshape(z, (2,2))) In [25]: z Out[25]: array([[30, 10], [20, 40]]) -- Robert Kern robert.kern@... "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco ```
 Re: [Matplotlib-users] images from data From: Eric Firing - 2006-04-29 18:42:31 ```Michael, How easy it is to do this depends on your ascii file format, and how the data are organized in it. Are the points in order? e.g. x0, y0, z00 x0, y1, z01 x0, y2, z02 x1, y0, z10 x1, y1, z11 x1, y2, z12 Are the values space-delimited, or comma-delimited, or in some other format? Is the grid uniform in the sense that all the x-intervals are the same and all the y-intervals are the same? Eric Michael V. De Palatis wrote: > Hi all, > > I am trying to use imshow to plot an image from some data. Basically, > I have a list of x, y, and z values, and I want to plot z as a > function of x and y. > > Unfortunately, most of the examples do this as far as I can > tell. Instead, they (at most) take a list of x and y then make a > *function* z out of that, and plot z, rather than having actual data > from a file for all three. > > The only one that does seem to do something like this seems to be > dependent on a binary file, which unfortunately is not the format I > have the data in. Sure, I could convert the very large files I already > have into binary, but in the long run, I think it would be better for > me to be able to simply use the ASCII data that I am provided with > since that can't be changed. > > Is there an easy way to do this, or will I just have to convert the > files? > > Thanks, > > Mike > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users@... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users ```
 Re: [Matplotlib-users] images from data From: Michael V. De Palatis - 2006-04-29 18:57:52 ```On Sat, Apr 29, 2006 at 08:41:48AM -1000, Eric Firing wrote: > How easy it is to do this depends on your ascii file format, and how the > data are organized in it. Are the points in order? e.g. > > x0, y0, z00 > x0, y1, z01 > x0, y2, z02 > x1, y0, z10 > x1, y1, z11 > x1, y2, z12 This is precisely the ordering. > Are the values space-delimited, or comma-delimited, or in some other > format? The values are space-delimited. The way I am reading them in is with readline, then splitting the resulting string and appending to a list of x, y, and z values. > Is the grid uniform in the sense that all the x-intervals are the same > and all the y-intervals are the same? Unfortunately, the grid is not uniform. From the responses I have been getting thus far, it's looking like this is going to be far more complicated than I had hoped... Would it in principle be difficult to write a function similar to imshow that can take 3 arrays and plot z (in color, say) as a function of x and y? To me, it would seem that it would essentially be the same as the plot function, except that it takes an extra array... Mike ```
 Re: [Matplotlib-users] images from data From: Robert Kern - 2006-04-29 19:33:49 ```Michael V. De Palatis wrote: > Unfortunately, the grid is not uniform. From the responses I have been > getting thus far, it's looking like this is going to be far more > complicated than I had hoped... Look in examples/quadmesh_demo.py . Or pretend like it's not a grid at all and just use the information Andrew gave you the first time: http://www.scipy.org/Wiki/Cookbook/Matplotlib/Gridding_irregularly_spaced_data -- Robert Kern robert.kern@... "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco ```
 Re: [Matplotlib-users] images from data From: Eric Firing - 2006-04-30 18:48:22 Attachments: xyz.asc pc_xyz.py ```Michael V. De Palatis wrote: > On Sat, Apr 29, 2006 at 08:41:48AM -1000, Eric Firing wrote: > >>How easy it is to do this depends on your ascii file format, and how the >>data are organized in it. Are the points in order? e.g. >> >>x0, y0, z00 >>x0, y1, z01 >>x0, y2, z02 >>x1, y0, z10 >>x1, y1, z11 >>x1, y2, z12 > > > This is precisely the ordering. > > >>Are the values space-delimited, or comma-delimited, or in some other >>format? > > > The values are space-delimited. The way I am reading them in is with > readline, then splitting the resulting string and appending to a list > of x, y, and z values. > > >>Is the grid uniform in the sense that all the x-intervals are the same >>and all the y-intervals are the same? > > > Unfortunately, the grid is not uniform. From the responses I have been > getting thus far, it's looking like this is going to be far more > complicated than I had hoped... It might not be complicated, but forget about using imshow--it is for image data, which are inherently evenly spaced. Pcolor and pcolormesh don't have this limitation. Note that Zij will give the color of the box with diagonal corners (Xij, Yij) and (Xi+1,j+1, Yi+1,j+1), so if Z has the same dimensions as X and Y, the last row and column will not be shown. If your input data are intended to give the (x,y) positions of the centers of regions rather than the corners, then you will need to do some sort of regridding of Z, or shifting of your X and Y points, in order to get everything exactly right with pcolor and pcolormesh. The attached script and sample data file show how you can put the data from your ascii file into X, Y, and Z arrays, and plot them using pcolor or pcolormesh. This is for the simple case in which treating x and y as corners is good enough. Note that the grid does not have to form rectangular cells; they can be quadrilaterals. I illustrated this in the sample file by shifting one point. Eric ```
 Re: [Matplotlib-users] images from data From: Michael V. De Palatis - 2006-04-30 21:07:40 ```On Sun, Apr 30, 2006 at 08:48:06AM -1000, Eric Firing wrote: > It might not be complicated, but forget about using imshow--it is for > image data, which are inherently evenly spaced. Pcolor and pcolormesh > don't have this limitation. Note that Zij will give the color of the > box with diagonal corners (Xij, Yij) and (Xi+1,j+1, Yi+1,j+1), so if Z > has the same dimensions as X and Y, the last row and column will not be > shown. If your input data are intended to give the (x,y) positions of > the centers of regions rather than the corners, then you will need to do > some sort of regridding of Z, or shifting of your X and Y points, in > order to get everything exactly right with pcolor and pcolormesh. > > The attached script and sample data file show how you can put the data > from your ascii file into X, Y, and Z arrays, and plot them using pcolor > or pcolormesh. This is for the simple case in which treating x and y as > corners is good enough. Note that the grid does not have to form > rectangular cells; they can be quadrilaterals. I illustrated this in > the sample file by shifting one point. > > Eric > > > > 1.0 1.0 1.1 > 1.0 1.5 1.2 > 1.0 2.5 1.1 > 1.0 4.0 1.0 > 1.0 4.5 1.0 > 2.0 1.0 1.2 > 2.0 1.5 1.3 > 2.5 2.9 1.4 > 2.0 4.0 1.1 > 2.0 4.5 1.1 > 3.0 1.0 1.0 > 3.0 1.5 1.3 > 3.0 2.5 1.5 > 3.0 4.0 1.2 > 3.0 4.5 1.2 > 4.0 1.0 1.0 > 4.0 1.5 1.3 > 4.0 2.5 1.5 > 4.0 4.0 1.2 > 4.0 4.5 1.2 > #!/usr/bin/env python > > from pylab import subplot, show > from pylab import nx as N > > fname = 'xyz.asc' > nx, ny = (4,5) > > lines = open(fname).readlines() > a_list = [[float(field) for field in line.split()] for line in lines] > a = N.array(a_list) > > X = N.reshape(a[:,0], (nx, ny)) > Y = N.reshape(a[:,1], (nx, ny)) > Z = N.reshape(a[:,2], (nx, ny)) > > ax = subplot(1,2,1) > ax.pcolor(X,Y,Z, shading='flat') > > ax = subplot(1,2,2) > ax.pcolormesh(X,Y,Z, shading='flat') > > show() Unfortunately, I couldn't even get this example to work. It was some sort of error related to pcolor not being a method of subplot, or something like that (sorry, I don't have the exact error message with me right now). Essentially, it seems to me that the above example *would* in principle work, though it's still going to take me a while to get things working. I have a thesis to turn in on Friday, or else I would keep playing with it until I got it to work. As it is, I'm going to have to do without it (luckily, I can use the program that's exporting the data to make my plots, I just think they're ugly). Perhaps in the next few weeks I'll play with it some more and write up the results if I get it working well. Thanks for all the responses, Mike ```