Is there a simple way to plot an image in a notebook? I.e. the output of the imshow function in matplotlib...

asked 2011-12-01 15:36:21 +0200

Anonymous

I have been wondering how to do something seemingly really simple, but seem to be missing something - sage allows users to do all kinds of fancy plotting in the notebook but I can't get it to display a 2d matrix as an image (matplotlib's imshow function).

I see that it is possible to call imshow and save the result to file, but I want to display the result in the notebook instead - did I miss something?

Cheers

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answered 2011-12-01 16:13:36 +0200

kcrisman
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I've modified the examples you're alluding to in the Sage plotting reference, under "NUMERICAL PLOTTING" (caps in original).

from pylab import * 
imshow([[(0,0,0)]])
savefig('')

This works. Because I don't know much about how matplotlib works, unfortunately when I do another figure it just adds to this one (or if I do another one first, this adds to it). Hopefully someone else - or you - can answer that for me!

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And once that's resolved, we should probably add this to the doc, right?

kcrisman ( 2011-12-01 16:13:56 +0200 )edit

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use clf() to "clear" the figure and stop adding to it.

Jason Grout ( 2011-12-01 21:52:39 +0200 )edit

Jason (G.), let's add that to the documentation, shall we? This is now http://trac.sagemath.org/sage_trac/ticket/12114. More and more SD 35.5 fodder...

kcrisman ( 2011-12-03 10:49:51 +0200 )edit

I'm doing imshow(img) and I get this AxesImage(60,48;372x384) AxesImage(60,48;372x384) What does it mean?

roi.holtzman ( 2017-06-08 19:16:13 +0200 )edit

It means it generates an image. Sage doesn't actually show the image onscreen without further commands, such as savefig; see @benjaminfjones answer below.

kcrisman ( 2017-06-08 19:37:49 +0200 )edit

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answered 2011-12-01 21:54:25 +0200

Jason Grout
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matrix_plotuses matplotlib's imshow to plot a matrix. matrix_plot should be called automatically if you try to plot a matrix. See, for example, http://sagenb.org/home/pub/1685/

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Oh, I thought he was asking about wanting to do it in the context of some other mpl stuff in the notebook, not just to plot a matrix.

kcrisman ( 2011-12-03 10:47:07 +0200 )edit

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answered 2011-12-01 16:26:02 +0200

benjaminfjones
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(referencing @kcrisman 's answer) I think it is maybe better not to import pylab into the global namespace, so just import pylab. To reset the plot, so to speak, you should call pylab.close() (or just close() if you import *) like this:

import pylab
pylab.imshow([[1,0],[0,1]])
pylab.savefig('plot1.png')
pylab.close()
pylab.imshow([[1,2],[0,1]])
pylab.savefig('plot2.png')

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Do these saved files ever get deleted once they are created?

Jason ( 2011-12-01 18:13:30 +0200 )edit

Only if you do it yourself. If you're working in the Sage notebook, they exist in the DATA directory associated to the worksheet. For example when I ran the above in the Sage notebook I get files created called $HOME/.sage/sage_notebook.sagenb/home/admin/0/cells/1/plot1.png

benjaminfjones ( 2011-12-01 19:30:29 +0200 )edit

1

They aren't stored in the DATA directory, but in a cell-specific output directory. They are supposed to be deleted when the cell is deleted, or even when the output of the cell is deleted (but apparently this didn't actually happen, but a patch was recently merged that actually does delete such files).

Jason Grout ( 2011-12-01 21:51:49 +0200 )edit

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Is there a simple way to plot an image in a notebook? I.e. the output of the imshow function in matplotlib...

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