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MathOnco / valis

Virtual Alignment of pathoLogy Image Series
https://valis.readthedocs.io/en/latest/
MIT License
119 stars 29 forks source link

dependencies issue #18

Closed NicolasNerr closed 2 years ago

NicolasNerr commented 2 years ago

Hello,

Thank you for your work and the open-source method, it is greatly appreciated.

I have some troubles running the repo, specifically when trying to instanciate a Valis object. The error is ExecutableNotFound: mvn not found on path. I don't really know what 'mvn' relates to and I have not seen any mention of this dependancy in the installation doc. Do you have an idea on what is the issue here ?

Thank you so much. Kind regards, Nicolas

cdgatenbee commented 2 years ago

Hi @NicolasNerr, Sorry about this. I believe this is referring to the need to have Maven installed (https://maven.apache.org/download.cgi), which is now required by the scyjava package (https://github.com/scijava/scyjava), which in turn is used to read some of the specialized slide formats. Please try installing Maven and let me know how it goes. Also, thank you for bringing this to my attention, I'll be sure to update the installation instructions in the readme.

Best, Chandler

NicolasNerr commented 2 years ago

Dear @cdgatenbee,

Thank you for your feedback. This was indeed the issue, after installing it and adding the binaries to the path variable the problem is solved ! Thank you,I didn't know about Maven.

If you have a bit more time to spare, I then attempted a registration. When trying to register a set of various IHC slides to an HE reference slide, I have an error during the "calculating transformations" step : "affine does not support optional argument premultiplied". It seems the error is thrown by pyvips.

The slides I used are in .tiff format and the code is the base example provided in the doc : registrar = registration.Valis(slide_src_dir, results_dst_dir, reference_img_f=reference_slide, align_to_reference=True) rigid_registrar, non_rigid_registrar, error_df = registrar.register() registrar.register_micro(max_non_rigid_registartion_dim_px=2000, align_to_reference=True) Have you encountered this error before ?

Thank you so much, Best regards.

cdgatenbee commented 2 years ago

Hi @NicolasNerr, Glad to hear that solved the first issue :) About this second one, this issue has come up before (issue number #16) . The problem was that an older version of pyvips was being used, but I believe was resolved by creating a new conda environment and installing pyvips via conda. As long as you're not on windows, this is ideal because pyvips will also install the most recent version of libvips, which does support the "premultiplied" argument for the "affine" function. Please try installing the most recent version of libvips and pyvips and hopefully that will resolve the issue, but if not let me know.

Best, Chandler

NicolasNerr commented 2 years ago

Hi @cdgatenbee ,

Indeed, I did not see this previous issue. However after installing every required package inside a conda environment, I am now unable to import valis due to some error, that I am not sure to fully understand.

"OSError: cannot load library '/home/anaconda3/envs/valis_env/lib/libvips.so.42': /home/anaconda3/envs/valis_env/lib/./libMagickCore-7.Q16HDRI.so.10: undefined symbol: xmlNanoFTPInit, version LIBXML2_2.4.30"

packages versions are : 

_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
asttokens                 2.0.8                    pypi_0    pypi
atk-1.0                   2.36.0               h3371d22_4    conda-forge
backcall                  0.2.0                    pypi_0    pypi
beautifulsoup4            4.11.1                   pypi_0    pypi
bioformats-jar            2020.5.27                pypi_0    pypi
boost-cpp                 1.78.0               h75c5d50_1    conda-forge
bottleneck                1.3.5           py310hde88566_0    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.9.24            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0            ha61ee94_1014    conda-forge
certifi                   2022.9.24          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_0    conda-forge
cfitsio                   4.1.0                hd9d235c_0    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.5              pyhd8ed1ab_0    conda-forge
colour-science            0.4.1                    pypi_0    pypi
conda                     4.14.0          py310hff52083_0    conda-forge
conda-package-handling    1.9.0           py310h5764c6d_0    conda-forge
contourpy                 1.0.5                    pypi_0    pypi
cryptography              37.0.4          py310h597c629_0    conda-forge
cycler                    0.11.0                   pypi_0    pypi
debugpy                   1.6.3                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
dnspython                 2.2.1                    pypi_0    pypi
elementpath               2.5.3                    pypi_0    pypi
email-validator           1.3.0                    pypi_0    pypi
entrypoints               0.4                      pypi_0    pypi
executing                 1.1.0                    pypi_0    pypi
expat                     2.4.9                h27087fc_0    conda-forge
fastcluster               1.2.6                    pypi_0    pypi
fftw                      3.3.10          nompi_hf0379b8_105    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               hc2a2eb6_1    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.37.3                   pypi_0    pypi
freetype                  2.12.1               hca18f0e_0    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gdk-pixbuf                2.42.8               hff1cb4f_1    conda-forge
gettext                   0.19.8.1          h27087fc_1009    conda-forge
ghostscript               9.54.0               h27087fc_2    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
glib                      2.74.0               h6239696_0    conda-forge
glib-tools                2.74.0               h6239696_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
graphviz                  6.0.1                h5abf519_0    conda-forge
gstreamer-orc             0.4.32               h7f98852_1    conda-forge
gtk2                      2.24.33              h90689f9_2    conda-forge
gts                       0.7.6                h64030ff_2    conda-forge
h5py                      3.7.0           nompi_py310h416281c_101    conda-forge
harfbuzz                  5.2.0                hf9f4e7c_0    conda-forge
hdf5                      1.12.2          nompi_h2386368_100    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imageio                   2.22.0                   pypi_0    pypi
imagemagick               7.1.0_48        pl5321h2a53dc9_1    conda-forge
interpolation             2.2.4                    pypi_0    pypi
ipykernel                 6.16.0                   pypi_0    pypi
ipython                   8.5.0                    pypi_0    pypi
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.1                   pypi_0    pypi
jgo                       1.0.4                    pypi_0    pypi
joblib                    1.2.0                    pypi_0    pypi
jpeg                      9e                   h166bdaf_2    conda-forge
jpype1                    1.4.0                    pypi_0    pypi
jupyter-client            7.3.5                    pypi_0    pypi
jupyter-core              4.11.1                   pypi_0    pypi
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4                    pypi_0    pypi
krb5                      1.19.3               h3790be6_0    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
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libcurl                   7.83.1               h7bff187_0    conda-forge
libdeflate                1.14                 h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libexif                   0.6.21               h7f98852_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgd                     2.3.3                h18fbbfe_3    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libglib                   2.74.0               h7a41b64_0    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
libgsf                    1.14.50              he99f2b3_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libmatio                  1.5.23               h63e3022_1    conda-forge
libnghttp2                1.47.0               hdcd2b5c_1    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libpng                    1.6.38               h753d276_0    conda-forge
librsvg                   2.54.4               h7abd40a_0    conda-forge
libsqlite                 3.39.3               h753d276_0    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libtiff                   4.4.0                h55922b4_4    conda-forge
libtool                   2.4.6             h9c3ff4c_1008    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
**libvips**                   8.13.1               h90b0b56_1    conda-forge
libwebp                   1.2.4                h522a892_0    conda-forge
libwebp-base              1.2.4                h166bdaf_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.10.2               h4c7fe37_1    conda-forge
libzlib                   1.2.12               h166bdaf_3    conda-forge
llvmlite                  0.39.1                   pypi_0    pypi
lxml                      4.9.1                    pypi_0    pypi
matplotlib                3.6.0                    pypi_0    pypi
matplotlib-inline         0.1.6                    pypi_0    pypi
ncurses                   6.3                  h27087fc_1    conda-forge
nest-asyncio              1.5.5                    pypi_0    pypi
networkx                  2.8.6                    pypi_0    pypi
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.78                 h2350873_0    conda-forge
numba                     0.56.2                   pypi_0    pypi
numpy                     1.23.3          py310h53a5b5f_0    conda-forge
ome-types                 0.3.1                    pypi_0    pypi
opencv-contrib-python     4.6.0.66                 pypi_0    pypi
openjpeg                  2.5.0                h7d73246_1    conda-forge
openslide                 3.4.1                h71beb9a_5    conda-forge
openssl                   1.1.1q               h166bdaf_0    conda-forge
packaging                 21.3                     pypi_0    pypi
pandas                    1.5.0                    pypi_0    pypi
pango                     1.50.10              hc4f8a73_0    conda-forge
parso                     0.8.3                    pypi_0    pypi
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.37                hc3806b6_1    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pexpect                   4.8.0                    pypi_0    pypi
physics-tenpy             0.9.0           py310h91b1402_1    conda-forge
pickleshare               0.7.5                    pypi_0    pypi
pillow                    9.2.0           py310hbd86126_2    conda-forge
pint                      0.19.2                   pypi_0    pypi
pip                       22.2.2             pyhd8ed1ab_0    conda-forge
**pixman**                    0.40.0               h36c2ea0_0    conda-forge
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
pkgconfig                 1.5.5           py310hff52083_2    conda-forge
poppler                   22.04.0              h0733791_3    conda-forge
poppler-data              0.4.11               hd8ed1ab_0    conda-forge
prompt-toolkit            3.0.31                   pypi_0    pypi
psutil                    5.9.2                    pypi_0    pypi
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.2                    pypi_0    pypi
pycosat                   0.6.3           py310h5764c6d_1010    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.2                   pypi_0    pypi
pygments                  2.13.0                   pypi_0    pypi
pyopenssl                 22.0.0             pyhd8ed1ab_1    conda-forge
pyparsing                 3.0.9                    pypi_0    pypi
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.6          h582c2e5_0_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python_abi                3.10                    2_cp310    conda-forge
pytz                      2022.2.1                 pypi_0    pypi
**pyvips**                    2.2.1           py310h39a615a_0    conda-forge
pywavelets                1.4.1                    pypi_0    pypi
pyyaml                    6.0             py310h5764c6d_4    conda-forge
pyzmq                     24.0.1                   pypi_0    pypi
readline                  8.1.2                h0f457ee_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
ruamel_yaml               0.15.80         py310h5764c6d_1007    conda-forge
scikit-image              0.19.3                   pypi_0    pypi
scikit-learn              1.1.2                    pypi_0    pypi
scipy                     1.9.1           py310hdfbd76f_0    conda-forge
scyjava                   1.6.0                    pypi_0    pypi
setuptools                59.8.0                   pypi_0    pypi
shapely                   1.8.4                    pypi_0    pypi
simpleitk                 2.2.0                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
soupsieve                 2.3.2.post1              pypi_0    pypi
sqlite                    3.39.3               h4ff8645_0    conda-forge
stack-data                0.5.1                    pypi_0    pypi
tempita                   0.5.2                    pypi_0    pypi
threadpoolctl             3.1.0                    pypi_0    pypi
tifffile                  2022.8.12                pypi_0    pypi
tk                        8.6.12               h27826a3_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2                      pypi_0    pypi
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.4.0                    pypi_0    pypi
typing-extensions         4.3.0                    pypi_0    pypi
tzdata                    2022d                h191b570_0    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
**valis-wsi**                 1.0.0rc11                pypi_0    pypi
wcwidth                   0.2.5                    pypi_0    pypi
weightedstats             0.4.1                    pypi_0    pypi
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xmlschema                 1.11.3                   pypi_0    pypi
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-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                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zlib                      1.2.12               h166bdaf_3    conda-forge
zstd                      1.5.2                h6239696_4    conda-forge

I don't know if someone encountered something similar, but I am kind of struggling with these dependencies issues.

Kind regards, Nicolas

NicolasNerr commented 2 years ago

Hi @cdgatenbee ,

False alert. I finally managed to make it work with a proper conda environment. Thank you for the work and congratulations for your ranking in the leaderboard for the ACROBAT challenge.

Best regards, Nicolas