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Bug #7942
openlocal GCTF fails with a matplotlib error
Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
08/15/2019
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 3.4
Show in known bugs:
No
Workaround:
Description
I think this is a matplotlib version
... writing JPEG: 19may24g_b_032gr_08sq_010hl_04ex-a-pow.jpg
/gpfs/research/stagg/software/myami_pythonconda/lib/python2.7/site-packages/numpy/ma/core.py:6461: MaskedArrayFutureWarning: In the future the default for ma.maximum.reduce will be axis=0, not the current None, to match np.maximum.reduce. Explicitly pass 0 or None to silence this warning.
return self.reduce(a)
/gpfs/research/stagg/software/myami_pythonconda/lib/python2.7/site-packages/numpy/ma/core.py:6461: MaskedArrayFutureWarning: In the future the default for ma.minimum.reduce will be axis=0, not the current None, to match np.minimum.reduce. Explicitly pass 0 or None to silence this warning.
return self.reduce(a)
/gpfs/research/stagg/software/myami_pythonconda/lib/python2.7/site-packages/matplotlib/collections.py:608: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
if self._edgecolors_original != 'face':
Traceback (most recent call last):
File "/gpfs/research/stagg/software/myamidev/appion/bin/gctf.py", line 707, in <module>
imgLoop.run()
File "/gpfs/research/stagg/software/myamidev/appion/appionlib/appionLoop2.py", line 89, in run
results = self.loopProcessImage(imgdata)
File "/gpfs/research/stagg/software/myamidev/appion/appionlib/appionLoop2.py", line 147, in loopProcessImage
return self.processImage(imgdata)
File "/gpfs/research/stagg/software/myamidev/appion/bin/gctf.py", line 452, in processImage
self.generateLocalCTFmap(apDisplay.short(imgdata['filename']),dimx,dimy)
File "/gpfs/research/stagg/software/myamidev/appion/bin/gctf.py", line 468, in generateLocalCTFmap
self.plotGridContour(map_array,fbase)
File "/gpfs/research/stagg/software/myamidev/appion/bin/gctf.py", line 581, in plotGridContour
plt.clabel(CS, fontsize=9, inline=1)
File "/gpfs/research/stagg/software/myami_pythonconda/lib/python2.7/site-packages/matplotlib/pyplot.py", line 2614, in clabel
ret = ax.clabel(CS, *args, **kwargs)
File "/gpfs/research/stagg/software/myami_pythonconda/lib/python2.7/site-packages/matplotlib/axes.py", line 7987, in clabel
return CS.clabel(*args, **kwargs)
File "/gpfs/research/stagg/software/myami_pythonconda/lib/python2.7/site-packages/matplotlib/contour.py", line 220, in clabel
self.labels(inline, inline_spacing)
File "/gpfs/research/stagg/software/myami_pythonconda/lib/python2.7/site-packages/matplotlib/contour.py", line 668, in labels
inline_spacing)
File "/gpfs/research/stagg/software/myami_pythonconda/lib/python2.7/site-packages/matplotlib/contour.py", line 483, in calc_label_rot_and_inline
nlc.append(np.r_[lc[:I[0] + 1], xy1])
TypeError: slice indices must be integers or None or have an __index__ method
I think this is a problem with the matplotlib version. I'm on:
import numpy
numpy.__version__
'1.16.4'
import matplotlib
matplotlib.__version__
'1.3.1'
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