Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

VTK reading errors #12

Open
jrhomburger opened this issue Oct 29, 2021 · 3 comments
Open

VTK reading errors #12

jrhomburger opened this issue Oct 29, 2021 · 3 comments

Comments

@jrhomburger
Copy link

Receiving the following error when running:

vtkPolyDataReader (0x55a6391564c0): Error reading ascii cell data! for file: /data/mri/ukb-cardiac-mri/1000948/cine_motion/myo_contour_ED_z02.vtk

Resulting in:

Traceback (most recent call last):
  File "/opt/ukbb_cardiac/short_axis/eval_strain_sax.py", line 55, in <module>
    data_dir, args.par_dir, motion_dir, "{0}/strain_sa".format(data_dir)
  File "/opt/ukbb_cardiac/common/cardiac_utils.py", line 1143, in cine_2d_sa_motion_and_strain_analysis
    "{0}/myo_contour_fr".format(output_dir), T, dt, output_name_stem
  File "/opt/ukbb_cardiac/common/cardiac_utils.py", line 816, in evaluate_strain_by_length
    p1 = np.array(points.GetPoint(ids.GetId(0)))
ValueError: expects 0 <= i && i < GetNumberOfIds()

I have MIRTK installed and VTK package linked - not sure what is causing this error.
@iimog
Copy link

iimog commented Aug 8, 2022

This happens when your python vtk version is more recent than the vtk version used for compiling mirtk. You probably have vtk version 9 in python and vtk 7 in mirtk. Two possible solutions are:

  1. use the most recent mirtk version from github and compile it with vtk version 9 (only works since July 2022)
  2. add a line instructing vtk to write the old file format version in python
writer.SetFileVersion(42)

You might still get a warning but it should work.

iimog added a commit to BioMeDS/ukbb_cardiac that referenced this issue Sep 1, 2022
@iimog
Remove manual re-write of vtk file version
ab54466 
this is no longer required with recent versions of mirtk and vtk
if there is a mismatch between vtk version used by python and mirtk
the writer should be instructed to output the old file version using
writer.SetFileVersion(42)

Related baiwenjia#12
@jrhomburger
Copy link
Author

Thanks - this is helpful. Saw many of your changes - have you considered merging that back into the main repository? I think many of those are much needed for this to work with current data.

also, were you able to get this work with current version TF or did you have to use a past version of TF? It may be worth including a requirements.txt with versions of the packages you are using. In the past, we had to downgrade TF to 2.1 for the models to work.

@iimog
Copy link

iimog commented Sep 10, 2022

I'd be happy to merge my changes into the main repository. I was hesitant to create a pull request because many of these changes just make the code work with current library versions while breaking backwards compatibility. If @baiwenjia is interested, in merging anyway, I'll gladly create a pull request.

It is a good idea to document working library versions. For me, the code works with tensorflow version 2.9.1.

my full conda environment 
# packages in environment at /home/markus/miniconda3/envs/ukbb_cardiac:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
abseil-cpp                20211102.0           h27087fc_1    conda-forge
absl-py                   1.2.0              pyhd8ed1ab_0    conda-forge
aiohttp                   3.8.1            py39hb9d737c_1    conda-forge
aiosignal                 1.2.0              pyhd8ed1ab_0    conda-forge
alsa-lib                  1.2.6.1              h7f98852_0    conda-forge
aom                       3.4.0                h27087fc_1    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge
attr                      2.5.1                h166bdaf_0    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
blinker                   1.4                        py_1    conda-forge
blosc                     1.21.1               h83bc5f7_3    conda-forge
brotli                    1.0.9                h166bdaf_7    conda-forge
brotli-bin                1.0.9                h166bdaf_7    conda-forge
brotlipy                  0.7.0           py39hb9d737c_1004    conda-forge
brunsli                   0.1                  h9c3ff4c_0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
c-blosc2                  2.2.0                h7a311fb_0    conda-forge
ca-certificates           2022.6.15            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.0.0              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            ha61ee94_1011    conda-forge
certifi                   2022.6.15        py39hf3d152e_0    conda-forge
cffi                      1.15.1           py39he91dace_0    conda-forge
cfitsio                   4.1.0                hd9d235c_0    conda-forge
charls                    2.3.4                h9c3ff4c_0    conda-forge
charset-normalizer        2.1.0              pyhd8ed1ab_0    conda-forge
click                     8.1.3            py39hf3d152e_0    conda-forge
cloudpickle               2.1.0              pyhd8ed1ab_0    conda-forge
cmake                     3.23.3               h5432695_0    conda-forge
cryptography              37.0.4           py39hd97740a_0    conda-forge
curl                      7.83.1               h7bff187_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.0           py39hb9d737c_0    conda-forge
dask-core                 2022.7.1           pyhd8ed1ab_0    conda-forge
dav1d                     1.0.0                h166bdaf_1    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
double-conversion         3.2.0                h9c3ff4c_0    conda-forge
eigen                     3.2                           3    bioconda
expat                     2.4.8                h27087fc_0    conda-forge
ffmpeg                    4.4.2           gpl_h2b602b6_106    conda-forge
fftw                      3.3.10          nompi_h77c792f_102    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.0               h8e229c2_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.34.4           py39hb9d737c_0    conda-forge
freeglut                  3.2.2                h9c3ff4c_1    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
frozenlist                1.3.1            py39hb9d737c_0    conda-forge
fsspec                    2022.7.1           pyhd8ed1ab_0    conda-forge
gast                      0.4.0              pyh9f0ad1d_0    conda-forge
gettext                   0.19.8.1          h73d1719_1008    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
gl2ps                     1.4.2                h0708190_0    conda-forge
glew                      2.1.0                h9c3ff4c_2    conda-forge
glib                      2.72.1               h6239696_0    conda-forge
glib-tools                2.72.1               h6239696_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gnutls                    3.7.6                hf3e180e_5    conda-forge
google-auth               2.9.1              pyh6c4a22f_0    conda-forge
google-auth-oauthlib      0.4.6              pyhd8ed1ab_0    conda-forge
google-pasta              0.2.0              pyh8c360ce_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
grpc-cpp                  1.46.3               hbd84cd8_2    conda-forge
grpcio                    1.46.3           py39h7ad10b3_2    conda-forge
gst-plugins-base          1.20.3               hf6a322e_0    conda-forge
gstreamer                 1.20.3               hd4edc92_0    conda-forge
h5py                      3.7.0           nompi_py39h63b1161_100    conda-forge
harfbuzz                  5.1.0                hf9f4e7c_0    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.12.1          nompi_h2386368_104    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
imagecodecs               2022.7.31        py39he992b3b_0    conda-forge
imageio                   2.21.0             pyhfa7a67d_0    conda-forge
importlib-metadata        4.11.4           py39hf3d152e_0    conda-forge
jack                      1.9.18            h8c3723f_1002    conda-forge
jasper                    2.0.33               ha77e612_0    conda-forge
jpeg                      9e                   h166bdaf_2    conda-forge
jsoncpp                   1.9.5                h4bd325d_1    conda-forge
jxrlib                    1.1                  h7f98852_2    conda-forge
keras                     2.9.0              pyhd8ed1ab_0    conda-forge
keras-preprocessing       1.1.2              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4            py39hf939315_0    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
lame                      3.100             h7f98852_1001    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.0.6                h9c3ff4c_0    conda-forge
libavif                   0.10.1               h166bdaf_1    conda-forge
libblas                   3.9.0           15_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_7    conda-forge
libbrotlidec              1.0.9                h166bdaf_7    conda-forge
libbrotlienc              1.0.9                h166bdaf_7    conda-forge
libcap                    2.64                 ha37c62d_0    conda-forge
libcblas                  3.9.0           15_linux64_openblas    conda-forge
libclang                  14.0.6          default_h2e3cab8_0    conda-forge
libclang13                14.0.6          default_h3a83d3e_0    conda-forge
libcups                   2.3.3                hf5a7f15_1    conda-forge
libcurl                   7.83.1               h7bff187_0    conda-forge
libdb                     6.2.32               h9c3ff4c_0    conda-forge
libdeflate                1.12                 h166bdaf_0    conda-forge
libdrm                    2.4.112              h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.3.4                h27087fc_0    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libglib                   2.72.1               h2d90d5f_0    conda-forge
libglu                    9.0.0             he1b5a44_1001    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libidn2                   2.3.3                h166bdaf_0    conda-forge
liblapack                 3.9.0           15_linux64_openblas    conda-forge
liblapacke                3.9.0           15_linux64_openblas    conda-forge
libllvm14                 14.0.6               he0ac6c6_0    conda-forge
libnetcdf                 4.8.1           nompi_h329d8a1_102    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.20          pthreads_h78a6416_1    conda-forge
libopencv                 4.6.0            py39he08f5c2_2    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpciaccess              0.16                 h516909a_0    conda-forge
libpng                    1.6.37               h753d276_3    conda-forge
libpq                     14.4                 hd77ab85_0    conda-forge
libprotobuf               3.20.1               h6239696_0    conda-forge
libsndfile                1.0.31               h9c3ff4c_1    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libtasn1                  4.18.0               h166bdaf_1    conda-forge
libtheora                 1.1.1             h7f98852_1005    conda-forge
libtiff                   4.4.0                h0d92c0b_2    conda-forge
libtool                   2.4.6             h9c3ff4c_1008    conda-forge
libudev1                  249                  h166bdaf_4    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.44.2               h166bdaf_0    conda-forge
libva                     2.15.0               h166bdaf_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libvpx                    1.11.0               h9c3ff4c_3    conda-forge
libwebp                   1.2.3                h522a892_1    conda-forge
libwebp-base              1.2.3                h166bdaf_2    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.14               h22db469_3    conda-forge
libzip                    1.9.2                hc869a4a_0    conda-forge
libzlib                   1.2.12               h166bdaf_2    conda-forge
libzopfli                 1.0.3                h9c3ff4c_0    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
loguru                    0.6.0            py39hf3d152e_1    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
markdown                  3.4.1              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.1            py39hb9d737c_1    conda-forge
matplotlib                3.5.2            py39hf3d152e_1    conda-forge
matplotlib-base           3.5.2            py39h700656a_1    conda-forge
multidict                 6.0.2            py39hb9d737c_1    conda-forge
munkres                   1.0.7                      py_1    bioconda
mysql-common              8.0.30               haf5c9bc_0    conda-forge
mysql-libs                8.0.30               h28c427c_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nettle                    3.8.1                hc379101_1    conda-forge
networkx                  2.8.5              pyhd8ed1ab_0    conda-forge
nibabel                   4.0.1              pyhd8ed1ab_0    conda-forge
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.78                 h2350873_0    conda-forge
numpy                     1.23.1           py39hba7629e_0    conda-forge
oauthlib                  3.2.0              pyhd8ed1ab_0    conda-forge
opencv                    4.6.0            py39hf3d152e_2    conda-forge
openh264                  2.2.0                h27087fc_2    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1q               h166bdaf_0    conda-forge
opt_einsum                3.3.0              pyhd8ed1ab_1    conda-forge
p11-kit                   0.24.1               hc5aa10d_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.3            py39h1832856_0    conda-forge
partd                     1.2.0              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pillow                    9.2.0            py39hae2aec6_0    conda-forge
pip                       22.2.2             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
ply                       3.11                       py_1    conda-forge
portaudio                 19.6.0               h57a0ea0_5    conda-forge
proj                      9.0.1                h93bde94_1    conda-forge
protobuf                  3.20.1           py39h5a03fae_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pugixml                   1.11.4               h9c3ff4c_0    conda-forge
pulseaudio                14.0                 h7f54b18_8    conda-forge
py-opencv                 4.6.0            py39hef51801_2    conda-forge
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.7                      py_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydicom                   2.3.0              pyh6c4a22f_0    conda-forge
pyjwt                     2.4.0              pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.7           py39h18e9c17_0    conda-forge
pyqt5-sip                 12.11.0          py39h5a03fae_0    conda-forge
pysocks                   1.7.1            py39hf3d152e_5    conda-forge
python                    3.9.13          h9a8a25e_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-flatbuffers        1.12               pyhd8ed1ab_1    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pywavelets                1.3.0            py39hd257fcd_1    conda-forge
pyyaml                    6.0              py39hb9d737c_4    conda-forge
qt-main                   5.15.4               ha5833f6_2    conda-forge
re2                       2022.06.01           h27087fc_0    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.1              pyhd8ed1ab_0    conda-forge
rhash                     1.4.3                h166bdaf_0    conda-forge
rsa                       4.9                pyhd8ed1ab_0    conda-forge
scikit-image              0.19.3           py39h1832856_0    conda-forge
scipy                     1.9.0            py39h8ba3f38_0    conda-forge
setuptools                63.3.0           py39hf3d152e_0    conda-forge
sip                       6.6.2            py39h5a03fae_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.9                hbd366e4_1    conda-forge
sqlite                    3.39.2               h4ff8645_0    conda-forge
svt-av1                   1.1.0                h27087fc_1    conda-forge
tbb                       2021.5.0             h924138e_1    conda-forge
tbb-devel                 2021.5.0             h924138e_1    conda-forge
tensorboard               2.9.0              pyhd8ed1ab_0    conda-forge
tensorboard-data-server   0.6.0            py39hd97740a_2    conda-forge
tensorboard-plugin-wit    1.8.1              pyhd8ed1ab_0    conda-forge
tensorflow                2.9.1           cpu_py39h4655687_0    conda-forge
tensorflow-base           2.9.1           cpu_py39hfe2e05e_0    conda-forge
tensorflow-estimator      2.9.1           cpu_py39heaff504_0    conda-forge
termcolor                 1.1.0              pyhd8ed1ab_3    conda-forge
tifffile                  2022.7.31          pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2              py39hb9d737c_0    conda-forge
typing-extensions         4.3.0                hd8ed1ab_0    conda-forge
typing_extensions         4.3.0              pyha770c72_0    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
unicodedata2              14.0.0           py39hb9d737c_1    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
utfcpp                    3.2.1                ha770c72_0    conda-forge
vtk                       9.1.0           qt_py39h105b9e9_211    conda-forge
werkzeug                  2.2.1              pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
wrapt                     1.14.1           py39hb9d737c_0    conda-forge
x264                      1!161.3030           h7f98852_1    conda-forge
x265                      3.5                  h924138e_3    conda-forge
xcb-util                  0.4.0                h516909a_0    conda-forge
xcb-util-image            0.4.0                h166bdaf_0    conda-forge
xcb-util-keysyms          0.4.0                h516909a_0    conda-forge
xcb-util-renderutil       0.3.9                h166bdaf_0    conda-forge
xcb-util-wm               0.4.1                h516909a_0    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-inputproto           2.3.2             h7f98852_1002    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxi                1.7.10               h7f98852_0    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yarl                      1.7.2            py39hb9d737c_2    conda-forge
zfp                       0.5.5                h9c3ff4c_8    conda-forge
zipp                      3.8.1              pyhd8ed1ab_0    conda-forge
zlib                      1.2.12               h166bdaf_2    conda-forge
zlib-ng                   2.0.6                h166bdaf_0    conda-forge
zstd                      1.5.2                h8a70e8d_2    conda-forge

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@jrhomburger @iimog