ukbb_cardiac
ukbb_cardiac copied to clipboard
Published
20 hours ago •
baiwenjia
baiwenjia
VTK reading errors
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.
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:
- use the most recent
mirtkversion from github and compile it withvtkversion 9 (only works since July 2022) - add a line instructing
vtkto write the old file format version in python
writer.SetFileVersion(42)
You might still get a warning but it should work.
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.
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