Actions
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'
Updated by Anchi Cheng about 5 years ago
A test script is written to test this.
Works on numpy 1.7.1 and matplotlib 1.2.1
Updated by Scott Stagg about 5 years ago
Works now. Here is a dump of my python packages:
[sstagg@hpc-login-vm3 test]$ conda list # packages in environment at /gpfs/research/stagg/software/myami_pythonconda2: # # Name Version Build Channel _libgcc_mutex 0.1 main asn1crypto 0.24.0 py27_0 backports 1.0 py_2 backports.functools_lru_cache 1.5 py_2 backports_abc 0.5 py27_0 blas 1.0 mkl bzip2 1.0.8 h7b6447c_0 ca-certificates 2019.5.15 1 certifi 2019.6.16 py27_1 cffi 1.12.3 py27h2e261b9_0 chardet 3.0.4 py27_1 conda 4.7.11 py27_0 conda-package-handling 1.3.11 py27_0 cryptography 2.7 py27h1ba5d50_0 cycler 0.10.0 py27_0 dbus 1.13.6 h746ee38_0 enum34 1.1.6 py27_1 expat 2.2.6 he6710b0_0 fontconfig 2.13.0 h9420a91_0 freetype 2.9.1 h8a8886c_1 functools32 3.2.3.2 py27_1 futures 3.3.0 py27_0 glib 2.56.2 hd408876_0 gst-plugins-base 1.14.0 hbbd80ab_1 gstreamer 1.14.0 hb453b48_1 icu 58.2 h9c2bf20_1 idna 2.8 py27_0 intel-openmp 2019.4 243 ipaddress 1.0.22 py27_0 joblib 0.13.2 py27_0 jpeg 9b h024ee3a_2 kiwisolver 1.1.0 py27he6710b0_0 libarchive 3.3.3 h5d8350f_5 libedit 3.1.20181209 hc058e9b_0 libffi 3.2.1 hd88cf55_4 libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 libpng 1.6.37 hbc83047_0 libstdcxx-ng 9.1.0 hdf63c60_0 libtiff 4.0.10 h2733197_2 libuuid 1.0.3 h1bed415_2 libxcb 1.13 h1bed415_1 libxml2 2.9.9 hea5a465_1 lz4-c 1.8.1.2 h14c3975_0 lzo 2.10 h49e0be7_2 matplotlib 2.2.3 py27hb69df0a_0 mkl 2019.4 243 mkl_fft 1.0.12 py27ha843d7b_0 mkl_random 1.0.2 py27hd81dba3_0 mysql-connector-c 6.1.11 h597af5e_0 mysql-python 1.2.5 py27h7b6447c_0 ncurses 6.1 he6710b0_1 numpy 1.16.4 py27h7e9f1db_0 numpy-base 1.16.4 py27hde5b4d6_0 olefile 0.46 py27_0 openssl 1.1.1c h7b6447c_1 pandas 0.24.2 py27he6710b0_0 pcre 8.43 he6710b0_0 pillow 6.1.0 py27h34e0f95_0 pip 19.1.1 py27_0 pycosat 0.6.3 py27h14c3975_0 pycparser 2.19 py27_0 pyopenssl 19.0.0 py27_0 pyparsing 2.4.0 py_0 pyqt 5.9.2 py27h05f1152_2 pysocks 1.7.0 py27_0 python 2.7.16 h9bab390_0 python-dateutil 2.8.0 py27_0 python-libarchive-c 2.8 py27_11 pytz 2019.1 py_0 qt 5.9.7 h5867ecd_1 readline 7.0 h7b6447c_5 requests 2.22.0 py27_0 ruamel_yaml 0.15.46 py27h14c3975_0 scipy 1.2.1 py27h7c811a0_0 setuptools 41.0.1 py27_0 singledispatch 3.4.0.3 py27_0 sip 4.19.8 py27hf484d3e_0 six 1.12.0 py27_0 sqlite 3.29.0 h7b6447c_0 subprocess32 3.5.4 py27h7b6447c_0 tk 8.6.8 hbc83047_0 tornado 5.1.1 py27h7b6447c_0 tqdm 4.32.1 py_0 urllib3 1.24.2 py27_0 wheel 0.33.4 py27_0 xz 5.2.4 h14c3975_4 yaml 0.1.7 had09818_2 zlib 1.2.11 h7b6447c_3 zstd 1.3.7 h0b5b093_0
Actions