yoda-vid
commented
2 years ago Thanks for reporting this! Glad you are trying the GUI for cell counting and hope I can help.
File "/home/toolboxes/magellanmapper/magmap/io/libmag.py", line 1212, in get_version ver = metadata.version(config.APP_NAME.lower())
I was getting this error as well and just recently fixed it in commit 99294555e0d6dbbbd40030ffc942d895a52f5573. If you update mag on git (eg git checkout master; git pull), does it fix the GUI error for you?
root - ERROR - /home/anaconda3/envs/mag/lib/python3.6/site-packages/traits/observation/_has_traits_helpers.py:83: RuntimeWarning: Trait '_wrappers' (trait type: List) on class ActionItem is defined with comparison_mode=<ComparisonMode.equality: 2>. Mutations and extended traits cannot be observed if a new container compared equally to the old one is set. Redefine the trait with List(..., comparison_mode=<ComparisonMode.identity: 1>) to avoid this.
Hm I haven't seen these errors before, not sure if they're also causing the GUI issue or coincidental. Would you mind posting the output of conda list to see what version of Traits is installed? I'm hoping the above update will fix at least the GUI start.
SaibotMagd
Sorry I worked only with the CLI for most of the time, but today I started to work on the cell-counting and now I can start the GUI anymore: " python run.py Starting MagellanMapper run script... magmap.io.cli - INFO - Launched MagellanMapper from run.py magmap.io.cli - INFO - Set default (channel 0) ROI profile: default magmap.io.cli - INFO - Set atlas profile to default root - INFO - setting up Matplotlib style default root - INFO - applying theme DEFAULT root - INFO - Loaded database from /home/.local/share/MagellanMapper/magmap.db root - INFO - set multiprocessing start method to fork root - INFO - No image filename set for processing files, skipping root - ERROR - /home/anaconda3/envs/mag/lib/python3.6/site-packages/traits/observation/_has_traits_helpers.py:83: RuntimeWarning: Trait '_wrappers' (trait type: List) on class ActionItem is defined with comparison_mode=<ComparisonMode.equality: 2>. Mutations and extended traits cannot be observed if a new container compared equally to the old one is set. Redefine the trait with List(..., comparison_mode=<ComparisonMode.identity: 1>) to avoid this. RuntimeWarning, root - ERROR - /home/anaconda3/envs/mag/lib/python3.6/site-packages/traits/observation/_has_traits_helpers.py:83: RuntimeWarning: Trait 'adapters' (trait type: List) on class SegmentsArrayAdapter is defined with comparison_mode=<ComparisonMode.equality: 2>. Mutations and extended traits cannot be observed if a new container compared equally to the old one is set. Redefine the trait with List(..., comparison_mode=<ComparisonMode.identity: 1>) to avoid this. RuntimeWarning, root - ERROR - /home/anaconda3/envs/mag/lib/python3.6/site-packages/traits/observation/_has_traits_helpers.py:83: RuntimeWarning: Trait 'adapters' (trait type: List) on class ProfilesArrayAdapter is defined with comparison_mode=<ComparisonMode.equality: 2>. Mutations and extended traits cannot be observed if a new container compared equally to the old one is set. Redefine the trait with List(..., comparison_mode=<ComparisonMode.identity: 1>) to avoid this. RuntimeWarning, root - ERROR - /home/anaconda3/envs/mag/lib/python3.6/site-packages/traits/observation/_has_traits_helpers.py:83: RuntimeWarning: Trait 'adapters' (trait type: List) on class ImportFilesArrayAdapter is defined with comparison_mode=<ComparisonMode.equality: 2>. Mutations and extended traits cannot be observed if a new container compared equally to the old one is set. Redefine the trait with List(..., comparison_mode=<ComparisonMode.identity: 1>) to avoid this. RuntimeWarning, root - INFO - set border to zeros root - INFO - set border to [0. 0. 0.] root - CRITICAL - Unhandled exception. Additional log saved to: /tmp/magellanmapper_error_45tywcdt.log Traceback (most recent call last): File "run.py", line 237, in
main()
File "run.py", line 170, in main
launch_magmap()
File "run.py", line 128, in launch_magmap
visualizer.main()
File "/home/toolboxes/magellanmapper/magmap/gui/visualizer.py", line 85, in main
visualization = Visualization()
File "/home/toolboxes/magellanmapper/magmap/gui/visualizer.py", line 832, in init
self._profiles_ver = libmag.get_version(True)
File "/home/toolboxes/magellanmapper/magmap/io/libmag.py", line 1212, in get_version
ver = metadata.version(config.APP_NAME.lower())
File "/home/anaconda3/envs/mag/lib/python3.6/site-packages/importlib_metadata/init.py", line 861, in version
return distribution(distribution_name).version
File "/home/anaconda3/envs/mag/lib/python3.6/site-packages/importlib_metadata/init.py", line 834, in distribution
return Distribution.from_name(distribution_name)
File "/home/anaconda3/envs/mag/lib/python3.6/site-packages/importlib_metadata/init.py", line 449, in from_name
raise PackageNotFoundError(name)
importlib_metadata.PackageNotFoundError: No package metadata was found for magellanmapper
"
I'm importing the datafile using an old version of mag and then try to start the GUI by loading the dataset. Maybe this will work