SIRF-SuperBuild
SIRF-SuperBuild copied to clipboard
SyneRBI
Windows: Build success but python cannot load SIRF
I built locally on Windows10 with VS community edition and NVIDIA SDK.
conda create --name sirf_b2 python numpy openblas matplotlib=3.4 docopt cmake deprecation -c conda-forge
conda activate sirf_b2
cmake ../SIRF-SuperBuild -DSIRF_TAG=origin/master -DSTIR_TAG=origin/master -DCIL_TAG=origin/master -DBUILD_Gadgetron=OFF -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_Boost=ON -DBoost_ROOT=C:\Apps\boost_1_72_0 -DUSE_SYSTEM_FFTW=OFF
After sourcing the env_sirf.PS1 environment file on PowerShell, I can run SIRF C++ unit tests (excluding the MR tests as I haven't built Gadgetron)
cd builds\SIRF\build
ctest -v --output-on-failure -R CPLUS -E MR -C Release
which outputs:
Test project C:/Users/ofn77899/Dev/buildVC/builds/SIRF/build
Start 6: REG_TEST_CPLUSPLUS
1/7 Test #6: REG_TEST_CPLUSPLUS ...................... Passed 4.40 sec
Start 9: PET_TESTS_CPLUSPLUS_1
2/7 Test #9: PET_TESTS_CPLUSPLUS_1 ................... Passed 66.29 sec
Start 10: PET_TESTS_CPLUSPLUS_4
3/7 Test #10: PET_TESTS_CPLUSPLUS_4 ................... Passed 65.26 sec
Start 14: SYN_TEST_STIR_TO_NIFTI_CPLUSPLUS
4/7 Test #14: SYN_TEST_STIR_TO_NIFTI_CPLUSPLUS ........ Passed 1.05 sec
Start 15: SYN_TEST_GADGETRON_TO_NIFTI_CPLUSPLUS
5/7 Test #15: SYN_TEST_GADGETRON_TO_NIFTI_CPLUSPLUS ... Passed 0.53 sec
Start 18: SYN_TEST_CPLUSPLUS
6/7 Test #18: SYN_TEST_CPLUSPLUS ......................***Failed 12.42 sec
// ----------------------------------------------------------------------- //
// Starting STIRImageData->NiftiImageData test...
//------------------------------------------------------------------------ //
INFO: Reading C:/Users/ofn77899/Dev/buildVC/sources/SIRF/data/examples/MR/zenodo/dicom_as_nifti.nii via ITK non-DICOM IO
WARNING: Unable to determine patient position. Internally this will generally be handled by assuming HFS
Saving image to file (results/stir_to_nifti.nii)...done.
Image comparison: metadata do not match, doing resampling...
No transformations set, using identity.
// ----------------------------------------------------------------------- //
// Finished STIRImageData->NiftiImageData test.
//------------------------------------------------------------------------ //
// ----------------------------------------------------------------------- //
// Starting GadgetronImageData->NiftiImageData test...
//------------------------------------------------------------------------ //
group 2019-12-11 16:38:14
variable image_1
number of images: 31
image data type: 5
variable xml
GadgetronImagesVector::set_up_geom_info(). Warning, you set up geometry for slices whose width is not their distance.This setup does probably not account for overlaps or gaps between slices.
Image comparison: metadata do not match, doing resampling...
No transformations set, using identity.
// ----------------------------------------------------------------------- //
// Finished GadgetronImageData->NiftiImageData test.
//------------------------------------------------------------------------ //
// ----------------------------------------------------------------------- //
// Starting complex resampler test...
//------------------------------------------------------------------------ //
Started reading acquisitions from C:/Users/ofn77899/Dev/buildVC/sources/SIRF/data/examples/MR/grappa2_1rep.h5
0%..10%..20%..30%..40%..49%..59%..69%..79%..89%..98%..
Finished reading acquisitions from C:/Users/ofn77899/Dev/buildVC/sources/SIRF/data/examples/MR/grappa2_1rep.h5
connection to gadgetron server failed, trying again...
connection to gadgetron server failed, trying again...
connection to gadgetron server failed, trying again...
connection to gadgetron server failed, trying again...
connection to gadgetron server failed
Here's the error:
Server running Gadgetron not accessible
Start 20: SIRF_TEST_COMMON_CPLUSPLUS
7/7 Test #20: SIRF_TEST_COMMON_CPLUSPLUS .............. Passed 0.10 sec
86% tests passed, 1 tests failed out of 7
Total Test time (real) = 150.22 sec
The following tests FAILED:
18 - SYN_TEST_CPLUSPLUS (Failed)
Errors while running CTest
All unit tests involving python ctest -v --output-on-failure -R PYTHON -E MR -C Release fail with
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\pysirf.py", line 13, in <module>
from . import _pysirf
ImportError: DLL load failed while importing _pysirf: The specified module could not be found.
All output here
Test project C:/Users/ofn77899/Dev/buildVC/builds/SIRF/build
Start 7: REG_TESTS_PYTHON
1/8 Test #7: REG_TESTS_PYTHON .....................***Failed 0.09 sec
C:\Apps\miniconda3\envs\sirf_b2\python.exe: No module named nose
Start 8: REG_PYTHON_ALGEBRA
2/8 Test #8: REG_PYTHON_ALGEBRA ...................***Failed 1.55 sec
E
======================================================================
ERROR: test_algebra (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: test_algebra
Traceback (most recent call last):
File "C:\Apps\miniconda3\envs\sirf_b2\lib\unittest\loader.py", line 154, in loadTestsFromName
module = __import__(module_name)
File "C:\Users\ofn77899\Dev\buildVC\sources\SIRF\src\Registration\pReg\tests\test_algebra.py", line 22, in <module>
import sirf.Reg as reg
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\Reg.py", line 28, in <module>
from sirf import SIRF
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\SIRF.py", line 36, in <module>
import sirf.pysirf as pysirf
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\pysirf.py", line 13, in <module>
from . import _pysirf
ImportError: DLL load failed while importing _pysirf: The specified module could not be found.
----------------------------------------------------------------------
Ran 1 test in 0.000s
FAILED (errors=1)
Start 11: PET_TESTS_PYTHON
3/8 Test #11: PET_TESTS_PYTHON .....................***Failed 0.10 sec
C:\Apps\miniconda3\envs\sirf_b2\python.exe: No module named nose
Start 12: PET_PYTHON_ALGEBRA
4/8 Test #12: PET_PYTHON_ALGEBRA ...................***Failed 1.62 sec
E
======================================================================
ERROR: test_algebra (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: test_algebra
Traceback (most recent call last):
File "C:\Apps\miniconda3\envs\sirf_b2\lib\unittest\loader.py", line 154, in loadTestsFromName
module = __import__(module_name)
File "C:\Users\ofn77899\Dev\buildVC\sources\SIRF\src\xSTIR\pSTIR\tests\test_algebra.py", line 22, in <module>
import sirf.STIR as pet
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\STIR.py", line 39, in <module>
from sirf import SIRF
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\SIRF.py", line 36, in <module>
import sirf.pysirf as pysirf
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\pysirf.py", line 13, in <module>
from . import _pysirf
ImportError: DLL load failed while importing _pysirf: The specified module could not be found.
----------------------------------------------------------------------
Ran 1 test in 0.000s
FAILED (errors=1)
Start 13: PET_PYTHON_OBJFUN
5/8 Test #13: PET_PYTHON_OBJFUN ....................***Failed 1.48 sec
E
======================================================================
ERROR: test_ObjectiveFunction (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: test_ObjectiveFunction
Traceback (most recent call last):
File "C:\Apps\miniconda3\envs\sirf_b2\lib\unittest\loader.py", line 154, in loadTestsFromName
module = __import__(module_name)
File "C:\Users\ofn77899\Dev\buildVC\sources\SIRF\src\xSTIR\pSTIR\tests\test_ObjectiveFunction.py", line 22, in <module>
import sirf.STIR as pet
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\STIR.py", line 39, in <module>
from sirf import SIRF
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\SIRF.py", line 36, in <module>
import sirf.pysirf as pysirf
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\pysirf.py", line 13, in <module>
from . import _pysirf
ImportError: DLL load failed while importing _pysirf: The specified module could not be found.
----------------------------------------------------------------------
Ran 1 test in 0.000s
FAILED (errors=1)
Start 16: SYN_TEST_GADGETRON_TO_NIFTI_PYTHON
6/8 Test #16: SYN_TEST_GADGETRON_TO_NIFTI_PYTHON ...***Failed 1.49 sec
Traceback (most recent call last):
File "C:\Users\ofn77899\Dev\buildVC\sources\SIRF\src\Synergistic\pSyn\tests\tests_syn.py", line 3, in <module>
from sirf.SIRF import ImageData
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\SIRF.py", line 36, in <module>
import sirf.pysirf as pysirf
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\pysirf.py", line 13, in <module>
from . import _pysirf
ImportError: DLL load failed while importing _pysirf: The specified module could not be found.
Start 17: SYN_TEST_STIR_TO_NIFTI_PYTHON
7/8 Test #17: SYN_TEST_STIR_TO_NIFTI_PYTHON ........***Failed 1.48 sec
Traceback (most recent call last):
File "C:\Users\ofn77899\Dev\buildVC\sources\SIRF\src\Synergistic\pSyn\tests\tests_syn.py", line 3, in <module>
from sirf.SIRF import ImageData
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\SIRF.py", line 36, in <module>
import sirf.pysirf as pysirf
File "C:\Users\ofn77899\Dev\buildVC\INSTALL\python\sirf\pysirf.py", line 13, in <module>
from . import _pysirf
ImportError: DLL load failed while importing _pysirf: The specified module could not be found.
Start 19: SYN_TEST_PYTHON
8/8 Test #19: SYN_TEST_PYTHON ......................***Failed 0.12 sec
C:\Apps\miniconda3\envs\sirf_b2\python.exe: No module named nose
0% tests passed, 8 tests failed out of 8
Total Test time (real) = 8.16 sec
The following tests FAILED:
7 - REG_TESTS_PYTHON (Failed)
8 - REG_PYTHON_ALGEBRA (Failed)
11 - PET_TESTS_PYTHON (Failed)
12 - PET_PYTHON_ALGEBRA (Failed)
13 - PET_PYTHON_OBJFUN (Failed)
16 - SYN_TEST_GADGETRON_TO_NIFTI_PYTHON (Failed)
17 - SYN_TEST_STIR_TO_NIFTI_PYTHON (Failed)
19 - SYN_TEST_PYTHON (Failed)
Errors while running CTest
The environment variables PATH and PYTHONPATH seem to be correct.
PATH
My $Env:Path is
C:\Users\ofn77899\Dev\buildVC\INSTALL\bin;C:\Users\ofn77899\Dev\buildVC\INSTALL\bin;C:\Users\ofn77899\Dev\buildVC\INSTALL\bin;C:\Apps\miniconda3\envs\sirf_b2;C:\Apps\miniconda3\envs\sirf_b2\Library\mingw-w64\bin;C:\Apps\miniconda3\envs\sirf_b2\Library\usr\bin;C:\Apps\miniconda3\envs\sirf_b2\Library\bin;C:\Apps\miniconda3\envs\sirf_b2\Scripts;C:\Apps\miniconda3\envs\sirf_b2\bin;C:\Apps\miniconda3\condabin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\libnvvp;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\ProgramData\chocolatey\bin;C:\WINDOWS\System32\OpenSSH;C:\Program Files\Docker\Docker\resources\bin;C:\ProgramData\DockerDesktop\version-bin;C:\Apps\Vagrant\bin;C:\Users\ofn77899\AppData\Local\Microsoft\WindowsApps;C:\Users\ofn77899\AppData\Local\Programs\Microsoft VS Code\bin;C:\Users\ofn77899\AppData\Local\Programs\Git\cmd;C:\Apps\GitHub CLI;C:\Users\ofn77899\Dev\buildVC\INSTALL\FFTW;C:\Apps\boost_1_72_0\lib64-msvc-14.2;C:\Users\ofn77899\Dev\buildVC\INSTALL\FFTW;C:\Apps\boost_1_72_0\lib64-msvc-14.2;C:\Program Files (x86)\PowerShell Community Extensions\Pscx3\Pscx\Apps;C:\Users\ofn77899\Dev\buildVC\INSTALL\FFTW;C:\Apps\boost_1_72_0\lib64-msvc-14.2
PYTHONPATH
C:\Users\ofn77899\Dev\buildVC\INSTALL\python;C:\Users\ofn77899\Dev\buildVC\INSTALL\python;C:\Users\ofn77899\Dev\buildVC\INSTALL\python;
@paskino You probably need to add C:\Users\ofn77899\Dev\buildVC\INSTALL\python to PATH to help Python find _pysirf.pyd and other SIRF Python dll's.
@paskino regarding MR (and some SYN) tests: can you not run Gadgetron on SIRF VM?
Thanks @evgueni-ovtchinnikov , I tried to add to PATH with
$Env:Path="C:\Users\ofn77899\Dev\buildVC\INSTALL\python;$Env:Path"
(sirf_b2) PS C:\Users\ofn77899\Dev\buildVC\builds\SIRF\build> $Env:Path C:\Users\ofn77899\Dev\buildVC\INSTALL\python;
C:\Users\ofn77899\Dev\buildVC\INSTALL\bin;
C:\Users\ofn77899\Dev\buildVC\INSTALL\bin;
C:\Users\ofn77899\Dev\buildVC\INSTALL\bin;
C:\Apps\miniconda3\envs\sirf_b2;
C:\Apps\miniconda3\envs\sirf_b2\Library\mingw-w64\bin;
C:\Apps\miniconda3\envs\sirf_b2\Library\usr\bin;
C:\Apps\miniconda3\envs\sirf_b2\Library\bin;
C:\Apps\miniconda3\envs\sirf_b2\Scripts;
C:\Apps\miniconda3\envs\sirf_b2\bin;
C:\Apps\miniconda3\condabin;
C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\bin;
C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\libnvvp;
C:\WINDOWS\system32;C:\WINDOWS;
C:\WINDOWS\System32\Wbem;
C:\WINDOWS\System32\WindowsPowerShell\v1.0;
C:\ProgramData\chocolatey\bin;
C:\WINDOWS\System32\OpenSSH;
C:\Program Files\Docker\Docker\resources\bin;
C:\ProgramData\DockerDesktop\version-bin;
C:\Apps\Vagrant\bin;
C:\Users\ofn77899\AppData\Local\Microsoft\WindowsApps;
C:\Users\ofn77899\AppData\Local\Programs\Microsoft VS Code\bin;
C:\Users\ofn77899\AppData\Local\Programs\Git\cmd;
C:\Apps\GitHub CLI;C:\Users\ofn77899\Dev\buildVC\INSTALL\FFTW;
C:\Apps\boost_1_72_0\lib64-msvc-14.2;
C:\Users\ofn77899\Dev\buildVC\INSTALL\FFTW;
C:\Apps\boost_1_72_0\lib64-msvc-14.2;
C:\Program Files (x86)\PowerShell Community Extensions\Pscx3\Pscx\Apps;
C:\Users\ofn77899\Dev\buildVC\INSTALL\FFTW;
C:\Apps\boost_1_72_0\lib64-msvc-14.2
but still get the same error.
I think you have to compare your 2 paths from within python, as it'll change where it finds DLLs compare to where the executable finds them. I still think it's a conflict between the HDF5/FFTW/Boost library used by SIRF and the ones installed by conda and hence used by conda's python.
See also https://bugs.python.org/issue43173 for some info on where it finds DLLs
Just to be clear, I did not install HDF5, FFTW or Boost with conda
conda list
# packages in environment at C:\Apps\miniconda3\envs\sirf_b2:
#
# Name Version Build Channel
bzip2 1.0.8 h8ffe710_4 conda-forge
ca-certificates 2022.6.15 h5b45459_0 conda-forge
certifi 2022.6.15 py310h5588dad_0 conda-forge
cmake 3.23.2 h39d44d4_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
deprecation 2.1.0 pyh9f0ad1d_0 conda-forge
docopt 0.6.2 py_1 conda-forge
freetype 2.10.4 h546665d_1 conda-forge
gettext 0.19.8.1 ha2e2712_1008 conda-forge
glib 2.70.2 h7755175_4 conda-forge
glib-tools 2.70.2 h7755175_4 conda-forge
gst-plugins-base 1.20.3 he07aa86_0 conda-forge
gstreamer 1.20.3 hdff456e_0 conda-forge
icu 70.1 h0e60522_0 conda-forge
intel-openmp 2022.1.0 h57928b3_3787 conda-forge
jpeg 9e h8ffe710_1 conda-forge
kiwisolver 1.4.3 py310h476a331_0 conda-forge
krb5 1.19.3 h1176d77_0 conda-forge
lcms2 2.12 h2a16943_0 conda-forge
lerc 3.0 h0e60522_0 conda-forge
libblas 3.9.0 15_win64_mkl conda-forge
libcblas 3.9.0 15_win64_mkl conda-forge
libclang 14.0.5 default_h77d9078_0 conda-forge
libclang13 14.0.5 default_h77d9078_0 conda-forge
libdeflate 1.12 h8ffe710_0 conda-forge
libffi 3.4.2 h8ffe710_5 conda-forge
libflang 5.0.0 h6538335_20180525 conda-forge
libglib 2.70.2 h3be07f2_4 conda-forge
libiconv 1.16 he774522_0 conda-forge
liblapack 3.9.0 15_win64_mkl conda-forge
libogg 1.3.4 h8ffe710_1 conda-forge
libopenblas 0.3.20 pthreads_hc469a61_0 conda-forge
libpng 1.6.37 h1d00b33_2 conda-forge
libtiff 4.4.0 h2ed3b44_1 conda-forge
libvorbis 1.3.7 h0e60522_0 conda-forge
libwebp 1.2.2 h57928b3_0 conda-forge
libwebp-base 1.2.2 h8ffe710_1 conda-forge
libxcb 1.13 hcd874cb_1004 conda-forge
libzlib 1.2.12 h8ffe710_1 conda-forge
llvm-meta 5.0.0 0 conda-forge
lz4-c 1.9.3 h8ffe710_1 conda-forge
m2w64-gcc-libgfortran 5.3.0 6 conda-forge
m2w64-gcc-libs 5.3.0 7 conda-forge
m2w64-gcc-libs-core 5.3.0 7 conda-forge
m2w64-gmp 6.1.0 2 conda-forge
m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge
matplotlib 3.4.3 py310h5588dad_2 conda-forge
matplotlib-base 3.4.3 py310h79a7439_2 conda-forge
mkl 2022.1.0 h6a75c08_874 conda-forge
msys2-conda-epoch 20160418 1 conda-forge
nose 1.3.7 py_1006 conda-forge
numpy 1.22.4 py310hed7ac4c_0 conda-forge
openblas 0.3.20 pthreads_h543f93c_0 conda-forge
openjpeg 2.4.0 hb211442_1 conda-forge
openmp 5.0.0 vc14_1 conda-forge
openssl 1.1.1p h8ffe710_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pcre 8.45 h0e60522_0 conda-forge
pillow 9.1.1 py310h767b3fd_1 conda-forge
pip 22.1.2 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 hcd874cb_1001 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyqt 5.15.4 py310hbabf5d4_1 conda-forge
pyqt5-sip 12.9.0 py310h8a704f9_1 conda-forge
python 3.10.5 h9a09f29_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 2_cp310 conda-forge
qt-main 5.15.4 h467ea89_2 conda-forge
setuptools 62.6.0 py310h5588dad_0 conda-forge
sip 6.5.1 py310h8a704f9_2 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.38.5 h8ffe710_0 conda-forge
tbb 2021.5.0 h2d74725_1 conda-forge
tk 8.6.12 h8ffe710_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tornado 6.1 py310he2412df_3 conda-forge
tzdata 2022a h191b570_0 conda-forge
ucrt 10.0.20348.0 h57928b3_0 conda-forge
vc 14.2 hb210afc_6 conda-forge
vs2015_runtime 14.29.30037 h902a5da_6 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.9 hcd874cb_0 conda-forge
xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge
xz 5.2.5 h62dcd97_1 conda-forge
zlib 1.2.12 h8ffe710_1 conda-forge
zstd 1.5.2 h6255e5f_1 conda-forge
>>> import os
>>> for el in os.environ['PATH'].split(';'):
... print (el)
...
C:\Users\ofn77899\Dev\buildVC\INSTALL\python
C:\Users\ofn77899\Dev\buildVC\INSTALL\bin
C:\Users\ofn77899\Dev\buildVC\INSTALL\bin
C:\Users\ofn77899\Dev\buildVC\INSTALL\bin
C:\Apps\miniconda3\envs\sirf_b2
C:\Apps\miniconda3\envs\sirf_b2\Library\mingw-w64\bin
C:\Apps\miniconda3\envs\sirf_b2\Library\usr\bin
C:\Apps\miniconda3\envs\sirf_b2\Library\bin
C:\Apps\miniconda3\envs\sirf_b2\Scripts
C:\Apps\miniconda3\envs\sirf_b2\bin
C:\Apps\miniconda3\condabin
C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\bin
C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v9.2\libnvvp
C:\WINDOWS\system32
C:\WINDOWS
C:\WINDOWS\System32\Wbem
C:\WINDOWS\System32\WindowsPowerShell\v1.0
C:\ProgramData\chocolatey\bin
C:\WINDOWS\System32\OpenSSH
C:\Program Files\Docker\Docker\resources\bin
C:\ProgramData\DockerDesktop\version-bin
C:\Apps\Vagrant\bin
C:\Users\ofn77899\AppData\Local\Microsoft\WindowsApps
C:\Users\ofn77899\AppData\Local\Programs\Microsoft VS Code\bin
C:\Users\ofn77899\AppData\Local\Programs\Git\cmd
C:\Apps\GitHub CLI
C:\Users\ofn77899\Dev\buildVC\INSTALL\FFTW
C:\Apps\boost_1_72_0\lib64-msvc-14.2
C:\Users\ofn77899\Dev\buildVC\INSTALL\FFTW
C:\Apps\boost_1_72_0\lib64-msvc-14.2
C:\Program Files (x86)\PowerShell Community Extensions\Pscx3\Pscx\Apps
C:\Users\ofn77899\Dev\buildVC\INSTALL\FFTW
C:\Apps\boost_1_72_0\lib64-msvc-14.2
I made some progress, installing SIRF directly in the conda environment!
conda create --name sirf_b2 python numpy openblas matplotlib=3.4 docopt cmake deprecation nose -c conda-forge
cmake ../SIRF-SuperBuild -DSIRF_TAG=origin/master -DSTIR_TAG=origin/master \
-DCIL_TAG=origin/master -DBUILD_Gadgetron=OFF -DUSE_SYSTEM_HDF5=OFF \
-DUSE_SYSTEM_Boost=ON -DBoost_ROOT=C:\Apps\boost_1_72_0 \
-DUSE_SYSTEM_FFTW=OFF \
-DPYTHON_DEST_DIR=%CONDA_PREFIX%\lib\site-packages \
-DCMAKE_INSTALL_PREFIX=%CONDA_PREFIX%
Now the unittest fail trying to load a file, although the file in question exists in the appropriate directory.
sirf.Utilities.error: ??? '\'Error opening file "C:\\\\Apps\\\\miniconda3\\\\envs\\\\sirf_b3"\\\\share\\\\SIRF-3.3\\\\data\\\\examples\\\\PET\\\\thorax_single_slice\\\\emission.hv\\n\' exception caught at line 327 of C:\\Users\\ofn77899\\Dev\\buildVC3\\sources\\SIRF\\src\\xSTIR\\cSTIR\\cstir.cpp; the reconstruction engine output may provide more information'
for el in os.environ['PATH'].split(';'): ... print (el)
and sys.path? (in your previous set-up)
I made some progress, installing SIRF directly in the conda environment!
great. Are these lines the only difference?
-DPYTHON_DEST_DIR=%CONDA_PREFIX%\lib\site-packages \
-DCMAKE_INSTALL_PREFIX=%CONDA_PREFIX%
The file-not-found seems to be due to backslash issues (unless it's really not there). Likely the file-ath is the output of the following
os.path.join(examples_data_path('PET'),'thorax_single_slice','emission.hv')
What's the return value of examples_data_path('PET')? and of your SIRF_PATH environment variable? Content of my env_sirf.PS1 is
# need to be forward slashes, as otherwise cannot find files
$Env:SIRF_PATH = "C:/Users/krisf/Documents/devel/buildVC/SIRF-SuperBuild/sources/SIRF"
configured at https://github.com/SyneRBI/SIRF-SuperBuild/blob/c19d1340dfc623518c3594538cc4a7121a14b670/env_sirf.PS1.in#L7
Looks like that installing in the conda environment works.
. C:\Apps\miniconda3\envs\sirf_b3\bin\env_sirf.PS1
ctest -C Release -R PET_ --output-on-failure Test project C:/Users/ofn77899/Dev/buildVC3/builds/SIRF/build
Start 9: PET_TESTS_CPLUSPLUS_1
1/5 Test #9: PET_TESTS_CPLUSPLUS_1 ............ Passed 53.46 sec
Start 10: PET_TESTS_CPLUSPLUS_4
2/5 Test #10: PET_TESTS_CPLUSPLUS_4 ............ Passed 54.96 sec
Start 11: PET_TESTS_PYTHON
3/5 Test #11: PET_TESTS_PYTHON ................. Passed 123.90 sec
Start 12: PET_PYTHON_ALGEBRA
4/5 Test #12: PET_PYTHON_ALGEBRA ............... Passed 8.65 sec
Start 13: PET_PYTHON_OBJFUN
5/5 Test #13: PET_PYTHON_OBJFUN ................ Passed 1.67 sec
100% tests passed, 0 tests failed out of 5
Total Test time (real) = 242.76 sec
No, I did not use PowerShell, rather command prompt. So I had added the environment variables by hand.
ok, but what were there values then? Is there a difference in what they should be between PS and CMD?
Also, is the same cause for your original problems (i.e. do yo really have to install in the conda dirs?)
Yes, outside of conda dirs neither PowerShell, nor CMD worked.
I had an issue with setting the path with " on CMD, but now, without double quotes, it seems to be working fine.
set SIRF_PATH=C:/Users/ofn77899/Dev/buildVC3/sources/SIRF
set SIRF_INSTALL_PATH=C:\Apps\miniconda3\envs\sirf_b3
ctest -C Release -R PET_ --output-on-failure
Test project C:/Users/ofn77899/Dev/buildVC3/builds/SIRF/build
Start 9: PET_TESTS_CPLUSPLUS_1
1/5 Test #9: PET_TESTS_CPLUSPLUS_1 ............ Passed 56.74 sec
Start 10: PET_TESTS_CPLUSPLUS_4
2/5 Test #10: PET_TESTS_CPLUSPLUS_4 ............ Passed 63.69 sec
Start 11: PET_TESTS_PYTHON
3/5 Test #11: PET_TESTS_PYTHON ................. Passed 105.89 sec
Start 12: PET_PYTHON_ALGEBRA
4/5 Test #12: PET_PYTHON_ALGEBRA ............... Passed 9.77 sec
Start 13: PET_PYTHON_OBJFUN
5/5 Test #13: PET_PYTHON_OBJFUN ................ Passed 1.84 sec
100% tests passed, 0 tests failed out of 5
Total Test time (real) = 760.05 sec
ok. could make a env_sirf.cmd.in then.
I think this indicates we do miss something in our env_sirf.PS1 though. Just not sure what it is. The only way I now to track it down is what I have suggested already.
Aside from that, if you go the conda way, I would highly recommend using conda for fftw, boost and itk. Ideally HDF5 as well but that might fail.
I've just read here that
Note that on Windows, from Python 3.9 onwards, DLL paths must be added by calling os.add_dll_directory() within Python rather than by setting PATH.
Indeed, in my tests I'm using python 3.10. This would explain all my failed attempts in using environment variables.
https://docs.python.org/3/library/os.html#os.add_dll_directory https://stackoverflow.com/questions/67805339/is-the-function-os-add-dll-directory-adding-directories-permanently
Some more discussion on Python add_dll_directory here https://discourse.vtk.org/t/how-to-write-a-custom-function-that-uses-vtk-c-and-then-use-it-in-python/9030/7?u=edoardo_pasca
that cookie stuff referenced there is just ridiculously complicated. sigh. I guess you'd have to make a persistent cookie somehow (no idea how to do that in Python), as we surely don't want to tell people to call add_dll_directory explicitly like that whenever they want to import sirf.