Closed NicolasNerr closed 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
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.
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
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
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
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