Comments (10)
adamltyson
commented on May 30, 2024
Hi,
Thanks for raising this issue.
I’m not officially supporting cellfinder on macOS, chiefly because:
- macOS doesn’t support CUDA, so cell classification will be slow
- Most macs that people have are not powerful enough to run cellfinder properly
That being said, I’ll see if I can find a Mac to look into this problem.
If there is demand for Mac support (and people have sufficiently powerful machines for this) I can revisit proper support.
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vigji
commented on May 30, 2024
I have to say, it's not a machine that can support the heavy lifting for this, so it's entirely reasonable.
Anyway, it mysteriously managed to install from the same environment when installing from a local cloned folder.
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adamltyson
commented on May 30, 2024
Reopening just to see if it's an easy fix
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vigji
commented on May 30, 2024
If you are having a look at this, I am getting this error when trying to pip install on a Windows (from ether pip or a local repo with the latest version):
ERROR: Command errored out with exit status 1:
command: 'C:\Users\lpetrucco\anaconda3\envs\amap_env\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\LPETRU~1\\AppData\\Local\\Temp\\pip-install-0_weoiei\\cellfinder\\setup.py'"'"'; __file__='"'"'C:\\Users\\LPETRU~1\\AppData\\Local\\Temp\\pip-install-0_weoiei\\cellfinder\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\LPETRU~1\AppData\Local\Temp\pip-record-iqkxei9h\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\lpetrucco\anaconda3\envs\amap_env\Include\cellfinder'
cwd: C:\Users\LPETRU~1\AppData\Local\Temp\pip-install-0_weoiei\cellfinder\
Complete output (128 lines):
running install
running build
running build_py
creating build
creating build\lib.win-amd64-3.7
creating build\lib.win-amd64-3.7\cellfinder
copying cellfinder\main.py -> build\lib.win-amd64-3.7\cellfinder
copying cellfinder\__init__.py -> build\lib.win-amd64-3.7\cellfinder
package init file 'pip-egg-info\__init__.py' not found (or not a regular file)
creating build\lib.win-amd64-3.7\cellfinder\analyse
copying cellfinder\analyse\__init__.py -> build\lib.win-amd64-3.7\cellfinder\analyse
creating build\lib.win-amd64-3.7\cellfinder\classify
copying cellfinder\classify\augment.py -> build\lib.win-amd64-3.7\cellfinder\classify
copying cellfinder\classify\classify.py -> build\lib.win-amd64-3.7\cellfinder\classify
copying cellfinder\classify\cube_generator.py -> build\lib.win-amd64-3.7\cellfinder\classify
copying cellfinder\classify\resnet.py -> build\lib.win-amd64-3.7\cellfinder\classify
copying cellfinder\classify\tools.py -> build\lib.win-amd64-3.7\cellfinder\classify
copying cellfinder\classify\__init__.py -> build\lib.win-amd64-3.7\cellfinder\classify
creating build\lib.win-amd64-3.7\cellfinder\config
copying cellfinder\config\__init__.py -> build\lib.win-amd64-3.7\cellfinder\config
creating build\lib.win-amd64-3.7\cellfinder\detect
copying cellfinder\detect\detect.py -> build\lib.win-amd64-3.7\cellfinder\detect
copying cellfinder\detect\__init__.py -> build\lib.win-amd64-3.7\cellfinder\detect
creating build\lib.win-amd64-3.7\cellfinder\download
copying cellfinder\download\cli.py -> build\lib.win-amd64-3.7\cellfinder\download
copying cellfinder\download\download.py -> build\lib.win-amd64-3.7\cellfinder\download
copying cellfinder\download\models.py -> build\lib.win-amd64-3.7\cellfinder\download
copying cellfinder\download\__init__.py -> build\lib.win-amd64-3.7\cellfinder\download
creating build\lib.win-amd64-3.7\cellfinder\extract
copying cellfinder\extract\extract_cubes.py -> build\lib.win-amd64-3.7\cellfinder\extract
copying cellfinder\extract\__init__.py -> build\lib.win-amd64-3.7\cellfinder\extract
creating build\lib.win-amd64-3.7\cellfinder\figures
copying cellfinder\figures\cli.py -> build\lib.win-amd64-3.7\cellfinder\figures
copying cellfinder\figures\figures.py -> build\lib.win-amd64-3.7\cellfinder\figures
copying cellfinder\figures\__init__.py -> build\lib.win-amd64-3.7\cellfinder\figures
creating build\lib.win-amd64-3.7\cellfinder\standard_space
copying cellfinder\standard_space\cells_to_standard_space.py -> build\lib.win-amd64-3.7\cellfinder\standard_space
copying cellfinder\standard_space\__init__.py -> build\lib.win-amd64-3.7\cellfinder\standard_space
creating build\lib.win-amd64-3.7\cellfinder\summarise
copying cellfinder\summarise\count_summary.py -> build\lib.win-amd64-3.7\cellfinder\summarise
copying cellfinder\summarise\__init__.py -> build\lib.win-amd64-3.7\cellfinder\summarise
creating build\lib.win-amd64-3.7\cellfinder\tools
copying cellfinder\tools\array_operations.py -> build\lib.win-amd64-3.7\cellfinder\tools
copying cellfinder\tools\geometry.py -> build\lib.win-amd64-3.7\cellfinder\tools
copying cellfinder\tools\image_processing.py -> build\lib.win-amd64-3.7\cellfinder\tools
copying cellfinder\tools\parser.py -> build\lib.win-amd64-3.7\cellfinder\tools
copying cellfinder\tools\prep.py -> build\lib.win-amd64-3.7\cellfinder\tools
copying cellfinder\tools\system.py -> build\lib.win-amd64-3.7\cellfinder\tools
copying cellfinder\tools\tf.py -> build\lib.win-amd64-3.7\cellfinder\tools
copying cellfinder\tools\tiff.py -> build\lib.win-amd64-3.7\cellfinder\tools
copying cellfinder\tools\tools.py -> build\lib.win-amd64-3.7\cellfinder\tools
copying cellfinder\tools\__init__.py -> build\lib.win-amd64-3.7\cellfinder\tools
creating build\lib.win-amd64-3.7\cellfinder\train
copying cellfinder\train\curation.py -> build\lib.win-amd64-3.7\cellfinder\train
copying cellfinder\train\train_yml.py -> build\lib.win-amd64-3.7\cellfinder\train
copying cellfinder\train\__init__.py -> build\lib.win-amd64-3.7\cellfinder\train
creating build\lib.win-amd64-3.7\cellfinder\utils
copying cellfinder\utils\xml_crop.py -> build\lib.win-amd64-3.7\cellfinder\utils
copying cellfinder\utils\xml_scale.py -> build\lib.win-amd64-3.7\cellfinder\utils
copying cellfinder\utils\__init__.py -> build\lib.win-amd64-3.7\cellfinder\utils
creating build\lib.win-amd64-3.7\cellfinder\viewer
copying cellfinder\viewer\three_dimensional.py -> build\lib.win-amd64-3.7\cellfinder\viewer
copying cellfinder\viewer\two_dimensional.py -> build\lib.win-amd64-3.7\cellfinder\viewer
copying cellfinder\viewer\__init__.py -> build\lib.win-amd64-3.7\cellfinder\viewer
creating build\lib.win-amd64-3.7\cellfinder\analyse\group
copying cellfinder\analyse\group\region_summary.py -> build\lib.win-amd64-3.7\cellfinder\analyse\group
copying cellfinder\analyse\group\__init__.py -> build\lib.win-amd64-3.7\cellfinder\analyse\group
creating build\lib.win-amd64-3.7\cellfinder\detect\filters
copying cellfinder\detect\filters\setup_filters.py -> build\lib.win-amd64-3.7\cellfinder\detect\filters
copying cellfinder\detect\filters\__init__.py -> build\lib.win-amd64-3.7\cellfinder\detect\filters
creating build\lib.win-amd64-3.7\cellfinder\detect\filters\plane_filters
copying cellfinder\detect\filters\plane_filters\classical_filter.py -> build\lib.win-amd64-3.7\cellfinder\detect\filters\plane_filters
copying cellfinder\detect\filters\plane_filters\multiprocessing.py -> build\lib.win-amd64-3.7\cellfinder\detect\filters\plane_filters
copying cellfinder\detect\filters\plane_filters\tile_walker.py -> build\lib.win-amd64-3.7\cellfinder\detect\filters\plane_filters
copying cellfinder\detect\filters\plane_filters\__init__.py -> build\lib.win-amd64-3.7\cellfinder\detect\filters\plane_filters
creating build\lib.win-amd64-3.7\cellfinder\detect\filters\volume_filters
copying cellfinder\detect\filters\volume_filters\multiprocessing.py -> build\lib.win-amd64-3.7\cellfinder\detect\filters\volume_filters
copying cellfinder\detect\filters\volume_filters\structure_splitting.py -> build\lib.win-amd64-3.7\cellfinder\detect\filters\volume_filters
copying cellfinder\detect\filters\volume_filters\__init__.py -> build\lib.win-amd64-3.7\cellfinder\detect\filters\volume_filters
package init file 'tests\tests\__init__.py' not found (or not a regular file)
package init file 'tests\tests\test_integration\__init__.py' not found (or not a regular file)
creating build\lib.win-amd64-3.7\tests
creating build\lib.win-amd64-3.7\tests\tests
creating build\lib.win-amd64-3.7\tests\tests\test_integration
copying tests\tests\test_integration\test_detection.py -> build\lib.win-amd64-3.7\tests\tests\test_integration
copying tests\tests\test_integration\test_extract.py -> build\lib.win-amd64-3.7\tests\tests\test_integration
copying tests\tests\test_integration\test_train.py -> build\lib.win-amd64-3.7\tests\tests\test_integration
package init file 'tests\tests\test_unit\__init__.py' not found (or not a regular file)
package init file 'tests\tests\test_integration\test_utils\__init__.py' not found (or not a regular file)
creating build\lib.win-amd64-3.7\tests\tests\test_integration\test_utils
copying tests\tests\test_integration\test_utils\test_xml_scale.py -> build\lib.win-amd64-3.7\tests\tests\test_integration\test_utils
package init file 'tests\tests\test_unit\test_analyse\__init__.py' not found (or not a regular file)
package init file 'tests\tests\test_unit\test_detect\__init__.py' not found (or not a regular file)
package init file 'tests\tests\test_unit\test_tools\__init__.py' not found (or not a regular file)
creating build\lib.win-amd64-3.7\tests\tests\test_unit
creating build\lib.win-amd64-3.7\tests\tests\test_unit\test_tools
copying tests\tests\test_unit\test_tools\test_geometry.py -> build\lib.win-amd64-3.7\tests\tests\test_unit\test_tools
copying tests\tests\test_unit\test_tools\test_image_processing.py -> build\lib.win-amd64-3.7\tests\tests\test_unit\test_tools
copying tests\tests\test_unit\test_tools\test_prep.py -> build\lib.win-amd64-3.7\tests\tests\test_unit\test_tools
copying tests\tests\test_unit\test_tools\test_system.py -> build\lib.win-amd64-3.7\tests\tests\test_unit\test_tools
copying tests\tests\test_unit\test_tools\test_tools_general.py -> build\lib.win-amd64-3.7\tests\tests\test_unit\test_tools
package init file 'tests\tests\test_unit\test_analyse\test_group\__init__.py' not found (or not a regular file)
creating build\lib.win-amd64-3.7\tests\tests\test_unit\test_analyse
creating build\lib.win-amd64-3.7\tests\tests\test_unit\test_analyse\test_group
copying tests\tests\test_unit\test_analyse\test_group\test_region_summary.py -> build\lib.win-amd64-3.7\tests\tests\test_unit\test_analyse\test_group
package init file 'tests\tests\test_unit\test_detect\test_filters\__init__.py' not found (or not a regular file)
package init file 'tests\tests\test_unit\test_detect\test_filters\test_volume_filters\__init__.py' not found (or not a regular file)
creating build\lib.win-amd64-3.7\tests\tests\test_unit\test_detect
creating build\lib.win-amd64-3.7\tests\tests\test_unit\test_detect\test_filters
creating build\lib.win-amd64-3.7\tests\tests\test_unit\test_detect\test_filters\test_volume_filters
copying tests\tests\test_unit\test_detect\test_filters\test_volume_filters\test_structure_detection.py -> build\lib.win-amd64-3.7\tests\tests\test_unit\test_detect\test_filters\test_volume_filters
running egg_info
writing cellfinder.egg-info\PKG-INFO
writing dependency_links to cellfinder.egg-info\dependency_links.txt
writing entry points to cellfinder.egg-info\entry_points.txt
writing requirements to cellfinder.egg-info\requires.txt
writing top-level names to cellfinder.egg-info\top_level.txt
reading manifest file 'cellfinder.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'cellfinder.egg-info\SOURCES.txt'
copying cellfinder\config\cellfinder.conf -> build\lib.win-amd64-3.7\cellfinder\config
copying cellfinder\detect\filters\typedefs.pxd -> build\lib.win-amd64-3.7\cellfinder\detect\filters
copying cellfinder\detect\filters\plane_filters\base_tile_filter.cpp -> build\lib.win-amd64-3.7\cellfinder\detect\filters\plane_filters
copying cellfinder\detect\filters\volume_filters\ball_filter.c -> build\lib.win-amd64-3.7\cellfinder\detect\filters\volume_filters
copying cellfinder\detect\filters\volume_filters\structure_detection.cpp -> build\lib.win-amd64-3.7\cellfinder\detect\filters\volume_filters
running build_ext
cythoning cellfinder/detect/filters/volume_filters/ball_filter.pyx to cellfinder/detect/filters/volume_filters\ball_filter.c
error: C:\Users\LPETRU~1\AppData\Local\Temp\pip-install-0_weoiei\cellfinder\cellfinder\detect\filters\volume_filters\ball_filter.pyx
----------------------------------------
ERROR: Command errored out with exit status 1: 'C:\Users\lpetrucco\anaconda3\envs\amap_env\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\LPETRU~1\\AppData\\Local\\Temp\\pip-install-0_weoiei\\cellfinder\\setup.py'"'"'; __file__='"'"'C:\\Users\\LPETRU~1\\AppData\\Local\\Temp\\pip-install-0_weoiei\\cellfinder\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\LPETRU~1\AppData\Local\Temp\pip-record-iqkxei9h\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\lpetrucco\anaconda3\envs\amap_env\Include\cellfinder' Check the logs for full command output.
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adamltyson
commented on May 30, 2024
Not sure why this is happening, but I seem to think it happened before on linux. I've uploaded a wheel for windows, can you try pip install cellfinder==0.3.12rc0 --no-cache-dir, and see if that works?
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vigji
commented on May 30, 2024
it does!
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adamltyson
commented on May 30, 2024
But it fails if you try to install locally?
How are you installing locally, something like pip install cellfinder/?
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vigji
commented on May 30, 2024
pip install path_to/cellfinder, a locally cloned branch up-to-date with commit 3ac3a2b
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adamltyson
commented on May 30, 2024
Strange, on my machine (Win10) this works:
conda create --name cellfindertest python=3.7
conda activate cellfindertest
cd C:\Users\adam\projects\cellfinder
git checkout 3ac3a2b
pip install .
But I can't install locally from the source archive on PyPI. They must be linked, but not sure why.
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adamltyson
commented on May 30, 2024
I think this must be a compiler issue. Can you try looking up what compiler you need for your systems?
Cellfinder compiles without issue on macOS and windows now on Travis.
From Version 0.3.12, prebuilt wheels will be released for macOS, Windows and Linux, which should get around this issue.
I'm not planning on supporting macOS to the same extent as the others, but it's there and seems to work. If you could test these versions (pip install cellfinder==0.3.12rc8), that would be great.
I'm going to close this issue, but let me know if you can't get cellfinder compiled locally for development.
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Related Issues (20)
- Pin to latest version of cellfinder-core HOT 1
- [BUG] Issue on cell detection cellfinder v0.4.15 vs cellfinder v0.4.3 HOT 3
- [BUG] cell candidate detection failing with cellfinder 0.4.15 HOT 4
- [BUG] Need to reimplement loading from a text file for cell detection HOT 2
- [BUG] Registering Failed HOT 5
- Classification + Analysis step Inefficiencies HOT 1
- [BUG] figures not generating HOT 1
- Cell detection and analysis without cell classification HOT 1
- 'No cells detected' line when positives have been classified HOT 3
- Create docker container
- [BUG] is the tox file required?
- [Feature] storing config files in local data/output directory instead of in conda env installation directory HOT 1
- [Feature]Could you please supply you .npy file in your ouput from you example data HOT 1
- [BUG] cellfinder interacts badly with multiprocessing_logging on Python 3.9.13 HOT 14
- Remove contributing.md and use generic brainglobe guide
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