Closed larsoner closed 6 years ago
nfoti
commented
6 years ago @larsoner Unfortunately now I can only draw a single label and the resulting color is wrong. When i specify the color of the label to 'steelblue' the label is drawn as a violet color. If I specify the color to be 'darkred' the label ends up being gray.
larsoner
commented
6 years ago Yes CircleCI agrees this is an incorrect fix :)
Clearly some work still to do, but if you're on a time crunch, this gives you some indication of the lines of code you could try tweaking.
mwaskom
commented
6 years ago Is there an issue describing the problem to link?
larsoner
commented
6 years ago No, this can serve as the issue. All labels are blue, here is plot_label.py on my system with master:
This happens independent of Mayavi version (at least back to the commit where PyQt5 support was added) and VTK version (at least 7.1 and 8), likely due to an update in NumPy breaking some Mayavi assumption or check. I haven't isolated the problem so haven't opened an upstream bug or tried to fix it. We might need both an upstream fix and a workaround here.
mwaskom
commented
6 years ago Huh, those labels look black and gold to me :)
nfoti
commented
6 years ago Thank @larsoner. I will take a look at the link you sent later today. I realized that I may have been getting weird results from changing which version of mayavi I was using.
Also, I am using the mne conda environment, but I had to make the default channel conda-forge rather that defaults because of a problem with the mkl numpy that the environment wants to load and another package wanting openblas. Thus, I'm getting numpy 1.14 instead of 1.13 which could also be causing the weirdness.
larsoner
commented
6 years ago @nfoti I recommend this one actually, it uses VTK from pip which is version 8 (works for HiDPI screens):
mwaskom
commented
6 years ago FWIW i set up a new environment with mayavi over the weekend and am not seeing this problem. Here's what I am working with:
apptools 4.4.0 py36_0 conda-forge attrs 17.4.0 py_0 conda-forge backports 1.0 py36_1 conda-forge backports.functools_lru_cache 1.5 py36_0 conda-forge blas 1.1 openblas conda-forge bleach 2.1.3 py_0 conda-forge bzip2 1.0.6 1 conda-forge ca-certificates 2018.1.18 0 conda-forge cairo 1.14.6 5 conda-forge certifi 2018.1.18 py36_0 conda-forge click 6.7 py_1 conda-forge configobj 5.0.6 py36_0 curl 7.59.0 0 conda-forge cycler 0.10.0 py36_0 conda-forge dask-core 0.17.1 py_0 conda-forge dbus 1.10.22 0 conda-forge decorator 4.2.1 py36_0 conda-forge entrypoints 0.2.3 py36_1 conda-forge envisage 4.5.1 py36_0 conda-forge expat 2.2.5 0 conda-forge fontconfig 2.12.1 6 conda-forge freetype 2.7 2 conda-forge funcsigs 1.0.2 py_2 conda-forge future 0.16.0 py36_0 conda-forge gettext 0.19.8.1 0 conda-forge glib 2.51.4 0 conda-forge gmp 6.1.2 0 conda-forge graphite2 1.3.11 0 conda-forge gsl 2.4 blas_openblas_0 [blas_openblas] conda-forge gst-plugins-base 1.8.0 0 conda-forge gstreamer 1.8.0 1 conda-forge h5py 2.7.1 py36_1 conda-forge harfbuzz 1.4.3 0 conda-forge hdf5 1.8.18 3 conda-forge html5lib 1.0.1 py_0 conda-forge icu 58.2 0 conda-forge imageio 2.2.0 py36_0 conda-forge ipykernel 4.8.2 py36_0 conda-forge ipython 6.2.1 py36_1 conda-forge ipython_genutils 0.2.0 py36_0 conda-forge ipywidgets 7.1.2 py36_0 conda-forge isodate 0.6.0 py_0 conda-forge jedi 0.11.1 py36_0 conda-forge jinja2 2.10 py36_0 conda-forge jpeg 9b 2 conda-forge jsoncpp 0.10.6 1 conda-forge jsonschema 2.6.0 py36_1 conda-forge jupyter 1.0.0 py36_0 conda-forge jupyter_client 5.2.3 py36_0 conda-forge jupyter_console 5.2.0 py36_0 conda-forge jupyter_core 4.4.0 py_0 conda-forge keepalive 0.5 py36_0 conda-forge kiwisolver 1.0.1 py36_1 conda-forge krb5 1.14.2 0 conda-forge libffi 3.2.1 3 conda-forge libgcc 7.2.0 h69d50b8_2 libgcc-ng 7.2.0 hdf63c60_3 libgfortran 3.0.0 1 libiconv 1.15 0 conda-forge libpng 1.6.28 2 conda-forge libsodium 1.0.15 1 conda-forge libssh2 1.8.0 2 conda-forge libstdcxx-ng 7.2.0 hdf63c60_3 libtiff 4.0.7 1 conda-forge libxcb 1.13 0 conda-forge libxml2 2.9.8 0 conda-forge libxslt 1.1.32 0 conda-forge lxml 4.2.0 py36_0 conda-forge lyman 1.0markupsafe 1.0 py36_0 conda-forge matplotlib 2.0.0 np112py36_2 conda-forge mayavi 4.5.0 py36_3 conda-forge mistune 0.8.3 py_0 conda-forge mock 2.0.0 py36_0 conda-forge moss 0.5 nbconvert 5.3.1 py_1 conda-forge nbformat 4.4.0 py36_0 conda-forge ncurses 5.9 10 conda-forge networkx 2.1 py36_0 conda-forge nibabel 2.2.1 py36_0 conda-forge nibabel 2.2.1 nipype 1.0.1 py36_0 conda-forge notebook 5.4.1 py36_0 conda-forge numpy 1.12.1 py36_blas_openblas_201 [blas_openblas] conda-forge olefile 0.45.1 py36_0 conda-forge openblas 0.2.20 7 conda-forge openssl 1.0.2n 0 conda-forge packaging 17.1 py_0 conda-forge pandas 0.22.0 py36_0 conda-forge pandoc 2.1.2 0 conda-forge pandocfilters 1.4.1 py36_0 conda-forge pango 1.40.4 0 conda-forge parso 0.1.1 py_0 conda-forge patsy 0.5.0 py36_0 conda-forge pbr 3.1.1 py36_0 conda-forge pcre 8.39 0 conda-forge pexpect 4.4.0 py36_0 conda-forge pickleshare 0.7.4 py36_0 conda-forge pillow 4.3.0 py36_1 conda-forge pip 9.0.2 py36_0 conda-forge pixman 0.34.0 1 conda-forge pluggy 0.6.0 py_0 conda-forge prompt_toolkit 1.0.15 py36_0 conda-forge prov 1.5.0 py36_0 conda-forge psutil 5.4.3 py36_0 conda-forge ptyprocess 0.5.2 py36_0 conda-forge py 1.5.2 py_0 conda-forge pydicom 1.0.2 py_0 conda-forge pydotplus 2.0.2 py36_0 conda-forge pyface 5.1.0 py36_1 conda-forge pygments 2.2.0 py36_0 conda-forge pyparsing 2.2.0 py36_0 conda-forge pyqt 4.11.4 py36_3 conda-forge pysurfer 0.8.0 pytest 3.4.2 py36_0 conda-forge python 3.6.3 1 conda-forge python-dateutil 2.7.0 py_0 conda-forge pytz 2018.3 py_0 conda-forge pywavelets 0.5.2 py36_1 conda-forge pyzmq 17.0.0 py36_3 conda-forge qt 4.8.7 7 conda-forge qtconsole 4.3.1 py36_0 conda-forge r-assertthat 0.2.0 r3.4.1_0 conda-forge r-base 3.4.1 2 conda-forge r-bh 1.66.0_1 r3.4.1_0 conda-forge r-bindr 0.1.1 r3.4.1_0 conda-forge r-bindrcpp 0.2 r3.4.1_0 conda-forge r-bit 1.1_12 r3.4.1_0 conda-forge r-bit64 0.9_5 r3.4.1_0 conda-forge r-blob 1.1.0 r3.4.1_0 conda-forge r-cli 1.0.0 r3.4.1_0 conda-forge r-crayon 1.3.4 r3.4.1_0 conda-forge r-dbi 0.8 r3.4.1_0 conda-forge r-dbplyr 1.1.0 r3.4.1_0 conda-forge r-digest 0.6.12 r3.4.1_0 conda-forge r-dplyr 0.7.4 r3.4.1_0 conda-forge r-glue 1.2.0 r3.4.1_0 conda-forge r-magrittr 1.5 r3.4.1_0 conda-forge r-memoise 1.1.0 r3.4.1_0 conda-forge r-pillar 1.2.1 r3.4.1_0 conda-forge r-pkgconfig 2.0.1 r3.4.1_0 conda-forge r-plogr 0.1_1 r3.4.1_0 conda-forge r-purrr 0.2.4 r3.4.1_0 conda-forge r-r6 2.2.2 r3.4.1_0 conda-forge r-rcpp 0.12.15 r3.4.1_0 conda-forge r-rlang 0.2.0 r3.4.1_0 conda-forge r-rsqlite 2.0 r3.4.1_0 conda-forge r-tibble 1.4.2 r3.4.1_0 conda-forge r-utf8 1.1.3 r3.4.1_0 conda-forge rdflib 4.2.2 py36_0 conda-forge readline 6.2 0 conda-forge rpy2 2.8.5 py36r3.4.1_0 conda-forge scikit-image 0.13.1 py36_0 conda-forge scikit-learn 0.19.1 py36_blas_openblas_201 [blas_openblas] conda-forge scipy 1.0.0 py36_blas_openblas_201 [blas_openblas] conda-forge seaborn 0.8.1 py36_0 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 39.0.0 py36_0 conda-forge simplegeneric 0.8.1 py36_0 conda-forge simplejson 3.13.2 py36_0 conda-forge singledispatch 3.4.0.3 py36_0 conda-forge sip 4.18 py36_1 conda-forge six 1.11.0 py36_1 conda-forge sparqlwrapper 1.8.0 py36_0 conda-forge sqlite 3.13.0 1 conda-forge statsmodels 0.8.0 py36_0 conda-forge tbb 2018_20171205 0 conda-forge terminado 0.8.1 py36_0 conda-forge testpath 0.3.1 py36_0 conda-forge tk 8.5.19 2 conda-forge toolz 0.9.0 py_0 conda-forge tornado 4.5.3 py36_0 conda-forge traitlets 4.3.2 py36_0 conda-forge traits 4.6.0 py36_1 conda-forge traitsui 5.1.0 py36_0 conda-forge vtk 7.1.1 py36_202 conda-forge wcwidth 0.1.7 py36_0 conda-forge webencodings 0.5 py36_0 conda-forge wheel 0.30.0 py36_2 conda-forge widgetsnbextension 3.1.4 py36_0 conda-forge xorg-libxau 1.0.8 3 conda-forge xorg-libxdmcp 1.1.2 3 conda-forge xvfbwrapper 0.2.9 py36_0 conda-forge xz 5.2.3 0 conda-forge zeromq 4.2.3 2 conda-forge zlib 1.2.11 0 conda-forge
larsoner
commented
6 years ago NumPy 1.12 adds evidence of a NumPy-related Mayavi bug
nfoti
commented
6 years ago I didn't end up fixing the problem, but I did end up finding out that surf.module_manager.scalar_lut_manager.lut.table stores values in [0, 255] rather than [0., 1.], so I udpated like 3260 in surfer/viz.py to l_m.lut.table.from_array((cmap * 255).astype(np.uint8)). That lets me draw labels in different colors, but not the colors I specify. I also read that updating the lookup table directly may not register with VTK so I explicitly called surf.update_pipeline() right after line 3260 however, that didn't seem to help.
I'm happy to keep trying out potential fixes, but I don't think I know VTK or mayavi well enough to figure out the bug on my own right now.
EDIT: I don't think the [0, 255] thing is entirely true as I also got similar results form sending [0., 1.] values into the lut too. I ended up playing with this for a while after posting this and I'm wondering if the problem is that the array in the VTK object is storing floating point values which are then used as indices which I don't think numpy supports anymore. I didn't have time to figure out how to put ints in the VTK array, but that may be a good thing to try.
larsoner
commented
6 years ago Okay @nfoti I have another iteration for you to try
larsoner
commented
6 years ago Fixed for real this time on CircleCI
codecov-io
commented
6 years ago Merging #229 into master will increase coverage by
0.04%. The diff coverage is100%.
@@ Coverage Diff @@
## master #229 +/- ##
==========================================
+ Coverage 74.25% 74.29% +0.04%
==========================================
Files 7 7
Lines 2435 2439 +4
Branches 485 487 +2
==========================================
+ Hits 1808 1812 +4
Misses 454 454
Partials 173 173This PR fixes the issue for me.
Thanks.
larsoner
commented
6 years ago Upstream bug:
larsoner
commented
6 years ago Updated to latest vtk and skipped the image-saving tests that were failing on Travis OSX, probably due to an updated image (?). Ready for review/merge from my end.
larsoner
commented
6 years ago Since this fixes things for @nfoti and there are no other complaints, I'll go ahead and merge. If people look and find other problems let me know
@nfoti can you see if this fixes your label problem?
On my system, all labels were blue. There is probably an upstream bug that needs to be fixed, but this is a workaround in the meantime.