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From: Karl Young <karl.young@uc...>  20090604 23:39:09

I have 2 float arrays of the same dimension which I use to generate a 3rd array, again of the same dimension, containing integers from a small set (I obtain the 3rd array via clustering in the 2 dimensional space of points obtained as values from the same location in the initial 2 arrays). I'd like to do a scatter plot using scatter, with xaxis values as values from the first array, yvalues as values from the second array and color of the points corresponding to the integer in the 3rd array (so far so good; I can do that much). Then I'd like to plot an image using imshow of the 3rd array with colors corresponding to those in the scatter plot. I can generate the image with imshow ok but can't the colors to match those in the scatter plot. Here's a snippet (assume array1,array2, and array3 are 2D arrays): hot() scatter(array1.ravel(), array2.ravel(), c = numpy.array(array3.ravel(),float)) imshow(array3) show() The main problem is that I can't figure out how to force the plot colors for imshow to correspond to those in scatter. Thanks for any thought or suggestions. Cheers,  KY 
From: Karl Young <karl.young@uc...>  20090604 23:39:09

I have 2 float arrays of the same dimension which I use to generate a 3rd array, again of the same dimension, containing integers from a small set (I obtain the 3rd array via clustering in the 2 dimensional space of points obtained as values from the same location in the initial 2 arrays). I'd like to do a scatter plot using scatter, with xaxis values as values from the first array, yvalues as values from the second array and color of the points corresponding to the integer in the 3rd array (so far so good; I can do that much). Then I'd like to plot an image using imshow of the 3rd array with colors corresponding to those in the scatter plot. I can generate the image with imshow ok but can't the colors to match those in the scatter plot. Here's a snippet (assume array1,array2, and array3 are 2D arrays): hot() scatter(array1.ravel(), array2.ravel(), c = numpy.array(array3.ravel(),float)) imshow(array3) show() The main problem is that I can't figure out how to force the plot colors for imshow to correspond to those in scatter. Thanks for any thought or suggestions. Cheers,  KY 
From: John Hunter <jdh2358@gm...>  20090605 12:52:02

On Thu, Jun 4, 2009 at 6:38 PM, Karl Young<karl.young@...> wrote: > > I have 2 float arrays of the same dimension which I use to generate a > 3rd array, again of the same dimension, containing integers from a small > set (I obtain the 3rd array via clustering in the 2 dimensional space of > points obtained as values from the same location in the initial 2 > arrays). I'd like to do a scatter plot using scatter, with xaxis values > as values from the first array, yvalues as values from the second array > and color of the points corresponding to the integer in the 3rd array > (so far so good; I can do that much). Then I'd like to plot an image > using imshow of the 3rd array with colors corresponding to those in the > scatter plot. I can generate the image with imshow ok but can't the > colors to match those in the scatter plot. Here's a snippet (assume > array1,array2, and array3 are 2D arrays): > > hot() > scatter(array1.ravel(), array2.ravel(), c = > numpy.array(array3.ravel(),float)) > imshow(array3) > show() > > The main problem is that I can't figure out how to force the plot colors > for imshow to correspond to those in scatter. Thanks for any thought or > suggestions. Cheers, w/o a complete, self contained code sample that we can run and play with on our machines, it is harder to help. Have you tried forcing the clim to be set to the interval you want? http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.clim JDH 
From: Young, Karl <karl.young@uc...>  20090605 15:38:31

Thanks for the tip and sorry I didn't include a complete code snippet; the current code involves images (scipy.ndimage) and clustering code and I thought that was a little too much too include; I'll try to extract something simpler. I guess the main question is how to use a set of integers to index a color space consistently for both scatter and imshow but I'll try to come up with a simple example. Thanks agan. ________________________________________ From: John Hunter [jdh2358@...] Sent: Friday, June 05, 2009 5:43 AM To: Young, Karl Cc: matplotlibusers@... Subject: Re: [Matplotlibusers] consistent colors between imshow and scatter On Thu, Jun 4, 2009 at 6:38 PM, Karl Young<karl.young@...> wrote: > > I have 2 float arrays of the same dimension which I use to generate a > 3rd array, again of the same dimension, containing integers from a small > set (I obtain the 3rd array via clustering in the 2 dimensional space of > points obtained as values from the same location in the initial 2 > arrays). I'd like to do a scatter plot using scatter, with xaxis values > as values from the first array, yvalues as values from the second array > and color of the points corresponding to the integer in the 3rd array > (so far so good; I can do that much). Then I'd like to plot an image > using imshow of the 3rd array with colors corresponding to those in the > scatter plot. I can generate the image with imshow ok but can't the > colors to match those in the scatter plot. Here's a snippet (assume > array1,array2, and array3 are 2D arrays): > > hot() > scatter(array1.ravel(), array2.ravel(), c = > numpy.array(array3.ravel(),float)) > imshow(array3) > show() > > The main problem is that I can't figure out how to force the plot colors > for imshow to correspond to those in scatter. Thanks for any thought or > suggestions. Cheers, w/o a complete, self contained code sample that we can run and play with on our machines, it is harder to help. Have you tried forcing the clim to be set to the interval you want? http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.clim JDH 
From: Eric Firing <efiring@ha...>  20090605 17:44:00

Young, Karl wrote: > Thanks for the tip and sorry I didn't include a complete code > snippet; the current code involves images (scipy.ndimage) and > clustering code and I thought that was a little too much too include; > I'll try to extract something simpler. I guess the main question is > how to use a set of integers to index a color space consistently for > both scatter and imshow but I'll try to come up with a simple > example. Thanks agan. > Karl, It sounds like you need to specify the norm=colors.NoNorm() argument. http://matplotlib.sourceforge.net/api/colors_api.html?highlight=nonorm#matplotlib.colors.NoNorm Then if your data are integers (typed as integers, not just taking integer values), they will be interpreted as indices into the color table. You will probably also want to generate that table yourself and specify it via the cmap=my_cmap kwarg. If you have only a few values, then you may want to generate it as a colors.ListedColormap: http://matplotlib.sourceforge.net/api/colors_api.html?highlight=listedcolormap#matplotlib.colors.ListedColormap http://matplotlib.sourceforge.net/examples/api/colorbar_only.html?highlight=listedcolormap It looks like we don't have any good examples sitting around showing the use of NoNorm; but try it anyway. Eric 
From: Young, Karl <karl.young@uc...>  20090605 18:06:47

Hi Eric, Thanks much  I'll try that. ________________________________________ From: Eric Firing [efiring@...] Sent: Friday, June 05, 2009 10:43 AM To: Young, Karl Cc: John Hunter; matplotlibusers@... Subject: Re: [Matplotlibusers] consistent colors between imshow and scatter Young, Karl wrote: > Thanks for the tip and sorry I didn't include a complete code > snippet; the current code involves images (scipy.ndimage) and > clustering code and I thought that was a little too much too include; > I'll try to extract something simpler. I guess the main question is > how to use a set of integers to index a color space consistently for > both scatter and imshow but I'll try to come up with a simple > example. Thanks agan. > Karl, It sounds like you need to specify the norm=colors.NoNorm() argument. http://matplotlib.sourceforge.net/api/colors_api.html?highlight=nonorm#matplotlib.colors.NoNorm Then if your data are integers (typed as integers, not just taking integer values), they will be interpreted as indices into the color table. You will probably also want to generate that table yourself and specify it via the cmap=my_cmap kwarg. If you have only a few values, then you may want to generate it as a colors.ListedColormap: http://matplotlib.sourceforge.net/api/colors_api.html?highlight=listedcolormap#matplotlib.colors.ListedColormap http://matplotlib.sourceforge.net/examples/api/colorbar_only.html?highlight=listedcolormap It looks like we don't have any good examples sitting around showing the use of NoNorm; but try it anyway. Eric 
From: Karl Young <karl.young@uc...>  20090605 21:02:32

hmmm... in response to John's earlier request I cobbled a simple example but that seems to work; either there's a strange error in the more complex version or my misunderstanding of color maps is messing with me. Anyway, for the record, here's an example of what I want to do (that actually seems to work)  #!/usr/bin/env python # Example to try and use same color maps for scatter and imshow import numpy as np from pylab import * # size of array dimensions size = 10 # cluster centers acenter1 = 3.0 asigma1 = 1.0 bcenter1 = 6.0 bsigma1 = 0.5 acenter2 = 8.0 asigma2 = 2.0 bcenter2 = 3.0 bsigma2 = 1.0 acenter3 = 13.0 asigma3 = 2.0 bcenter3 = 10.0 bsigma3 = 1.0 # populate arrays with random values distrubted about 2 locations # (i.e. 2 clusters) a = np.zeros([size,size],float) b = np.zeros([size,size],float) c = np.zeros([size,size],int) # populate arrays for i in range(size): for j in range(size): switcher = np.random.randint(3) if switcher == 0: # cluster 1 a[i,j] = np.random.normal(acenter1,asigma1) b[i,j] = np.random.normal(bcenter1,bsigma1) c[i,j] = 0 elif switcher == 1 : # cluster 2 a[i,j] = np.random.normal(acenter2,asigma2) b[i,j] = np.random.normal(bcenter2,bsigma2) c[i,j] = 1 else: a[i,j] = np.random.normal(acenter3,asigma3) b[i,j] = np.random.normal(bcenter3,bsigma3) c[i,j] = 2 hot() subplot(1,2,1) scatter(np.ravel(a),np.ravel(b),c=np.ravel(c)) subplot(1,2,2) imshow(c) show()  > Young, Karl wrote: > >> Thanks for the tip and sorry I didn't include a complete code >> snippet; the current code involves images (scipy.ndimage) and >> clustering code and I thought that was a little too much too include; >> I'll try to extract something simpler. I guess the main question is >> how to use a set of integers to index a color space consistently for >> both scatter and imshow but I'll try to come up with a simple >> example. Thanks agan. >> >> > > Karl, > > It sounds like you need to specify the norm=colors.NoNorm() argument. > http://matplotlib.sourceforge.net/api/colors_api.html?highlight=nonorm#matplotlib.colors.NoNorm > Then if your data are integers (typed as integers, not just taking > integer values), they will be interpreted as indices into the color > table. You will probably also want to generate that table yourself and > specify it via the cmap=my_cmap kwarg. If you have only a few values, > then you may want to generate it as a colors.ListedColormap: > http://matplotlib.sourceforge.net/api/colors_api.html?highlight=listedcolormap#matplotlib.colors.ListedColormap > http://matplotlib.sourceforge.net/examples/api/colorbar_only.html?highlight=listedcolormap > > It looks like we don't have any good examples sitting around showing the > use of NoNorm; but try it anyway. > > Eric > > . > > 
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