Plugin Crashes Q when attempting to save ROI to training input, opens multiple new Q windows

[macromicrobe]

I apologize if this is a resolved issue, but I am a relatively new user of Q from the field of microbiology.

Whenever I go to save a temporary ROI to training input, Q attempts to open 3 new windows that give these warnings/errors in the log messages panel:

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2021-01-09T13:40:48 WARNING Plugin processing : This plugin is disabled because it previously crashed QGIS. 2021-01-09T13:40:50 CRITICAL Invalid Data Source : /-c is not a valid or recognized data source. 2021-01-09T13:40:50 CRITICAL Invalid Data Source : /from multiprocessing.spawn import spawn_main; spawn_main(tracker_fd=57, pipe_handle=59) is not a valid or recognized data source. 2021-01-09T13:40:50 CRITICAL Invalid Data Source : /--multiprocessing-fork is not a valid or recognized data source.

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Here is the Python error I get:

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An error has occurred while executing Python code:

ValueError: need at least one array to stack Traceback (most recent call last): File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/dock/scpdock.py", line 2036, in saveROItoShapefile cfg.utls.calculateSignature(cfg.shpLay, cfg.bandSetsList[bandSetNumber][8], [self.ROILastID], cfg.ROIMacroID, cfg.ROIMacroClassInfo, cfg.ROIID, cfg.ROIInfo, 50, 40, 'No', 'No', UID, bandSetNumber = bandSetNumber) File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/core/utils.py", line 1591, in calculateSignature covMat = cfg.utls.calculateCovMatrix(ROIArray) File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/core/utils.py", line 825, in calculateCovMatrix matrix = cfg.np.stack(arrayList) File "", line 6, in stack File "/Applications/QGIS.app/Contents/MacOS/lib/python3.7/site-packages/numpy-1.19.1-py3.7-macosx-10.13.0-x86_64.egg/numpy/core/shape_base.py", line 423, in stack raise ValueError('need at least one array to stack') ValueError: need at least one array to stack

Python version: 3.7.7 (default, Sep 22 2020, 10:25:18) [Clang 12.0.0 (clang-1200.0.32.2)] QGIS version: 3.16.2-Hannover Hannover, c6ac5a6052

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And it just remains at 80% completion indefinitely on "creating ROI".

I have attached the log file from attempting this action ("save_ROI_error_log.txt").

I also have log file when I click the "Check Dependencies" button ("check_dependencies_error_log.txt"). Clicking this button triggers the same effect as I have described above. Please find the log file attached.

I am using SCP Version 7.3.7 with Q Version 3.16.2 on a MacBook Pro (BigSur).

I tried reinstalling Q and reinstalling the plugin. I tried this on a different computer with an entirely fresh install of Q, with the same error.

Any help is greatly appreciated. save_ROI_error_log.txt check_dependencies_error_log.txt

[semiautomaticgit]

Hello @macromicrobe , I think it is related to this issue https://github.com/semiautomaticgit/SemiAutomaticClassificationPlugin/issues/144

Please update to the latest version 7.4.0, click the button "Test dependencies" and report the log file.

[macromicrobe]

Hello @semiautomaticgit , Many thanks for your reply. I have updated to the latest version, and have attached the log file.

It no longer attempts to open multiple new instances of Q, but still throws a Python error and cannot save the ROI. Please find below the Python errors for both attempting to save an ROI, and from the "Test dependencies" run.

2021-01-10T13:44:52 WARNING Traceback (most recent call last): File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/dock/scpdock.py", line 2036, in saveROItoShapefile cfg.utls.calculateSignature(cfg.shpLay, cfg.bandSetsList[bandSetNumber][8], [self.ROILastID], cfg.ROIMacroID, cfg.ROIMacroClassInfo, cfg.ROIID, cfg.ROIInfo, 50, 40, 'No', 'No', UID, bandSetNumber = bandSetNumber) File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/core/utils.py", line 1591, in calculateSignature covMat = cfg.utls.calculateCovMatrix(ROIArray) File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/core/utils.py", line 825, in calculateCovMatrix matrix = cfg.np.stack(arrayList) File "", line 6, in stack File "/Applications/QGIS.app/Contents/MacOS/lib/python3.7/site-packages/numpy-1.19.1-py3.7-macosx-10.13.0-x86_64.egg/numpy/core/shape_base.py", line 423, in stack raise ValueError('need at least one array to stack') ValueError: need at least one array to stack

2021-01-10T13:45:14 WARNING Traceback (most recent call last): File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/maininterface/settings.py", line 262, in testDependencies testMultiprocess = self.testMultiprocess() File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/maininterface/settings.py", line 307, in testMultiprocess mp.set_executable(flPrefPy) NameError: name 'mp' is not defined

test_dependencies_7.4.txt

[semiautomaticgit]

Hello @macromicrobe , please update again to version 7.4.2

[macromicrobe]

Hello @semiautomaticgit ,

Many thanks for your continued help.

Apologies for not updating to the most recent version. I am now at 7.4.2, and have attached the log.

test_dependencies_7_4_2.txt

[semiautomaticgit]

Thank you.

Please open the tab Processing setting and try to enter in Python executable path: /usr/bin/python3

Also, in GDAL directory you should enter the path to the directory containing tools such as gdal_translate and gdalwarp

[macromicrobe]

Hello @semiautomaticgit ,

I have now added the Python path, and the path to GDAL directory, in Processing settings. Here is the log file from "test dependencies" after adding these paths and restarting.

test.txt

[semiautomaticgit]

Thank you, I think we are getting closer to finding the cause of the issue. Please update to version 7.4.3 and copy the log file again.

[macromicrobe]

Hello @semiautomaticgit ,

Thank you for your continued help! I have updated to 7.4.3, and attached the log file.

test.txt

[semiautomaticgit]

Thank you very much. Please update to version 7.4.4. It shouldn't solve the issue, but should provide information about the cause of the issue.

[macromicrobe]

Thank you, @semiautomaticgit .

I have now updated. Please find attached the new log. log.txt

[semiautomaticgit]

The good thing is that GDAL was correctly found. Please update again to version 7.4.5, hopefully this will provide information about Python multiprocessing.

[macromicrobe]

@semiautomaticgit ,

The "Test dependencies" now fails with a Python error:

2021-01-10T17:44:44 WARNING Traceback (most recent call last): File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/maininterface/settings.py", line 262, in testDependencies testMultiprocess = self.testMultiprocess() File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/maininterface/settings.py", line 334, in testMultiprocess dPref = [cfg.ui.python_path_lineEdit.text()].rstrip('python3') AttributeError: 'list' object has no attribute 'rstrip'

2021-01-10T17:45:02 WARNING Traceback (most recent call last): File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/maininterface/settings.py", line 262, in testDependencies testMultiprocess = self.testMultiprocess() File "/Users/cissell/Library/Application Support/QGIS/QGIS3/profiles/default/python/plugins/SemiAutomaticClassificationPlugin/maininterface/settings.py", line 334, in testMultiprocess dPref = [cfg.ui.python_path_lineEdit.text()].rstrip('python3') AttributeError: 'list' object has no attribute 'rstrip'

[semiautomaticgit]

sorry, that was my fault, please update to version 7.4.6

[macromicrobe]

My apologies for posting this reply on the wrong issue. I will repost it here for continuity on this specific issue.

Clicking the "Test dependencies" button now causes Q to not respond, and will not generate a log file or errors. I have attempted 10 times now, all with the same result.

Thank you again for your support.

[semiautomaticgit]

Thank you, please try version 7.4.7

[macromicrobe]

Unfortunately, I am still encountering the same issue with version 7.4.7 where Q stops responding and I am unable to generate a log or receive errors.

[semiautomaticgit]

Thank you for your cooperation. Please try version 7.4.8

[macromicrobe]

@semiautomaticgit ,

Thank you for your continued effort! Please find attached the log from 7.4.8.

log_7_4_8.txt

[macromicrobe]

Just a note - when I restarted Q, I encounter the previous crashing issue when attempting to check dependencies.

[semiautomaticgit]

Thank you. Did you set also the Python path?

[macromicrobe]

I did. Currently it is set as /usr/bin/python3 under the Python executable path in Processing setting.

[semiautomaticgit]

OK, maybe you can check if there are other directories containing python3 However I think it is an installation issue. Other users reported that SCP works with KyngChaos package QGIS 3.16.2-2, maybe you can try this

[macromicrobe]

I will try this. Many thanks for all of your help, @semiautomaticgit !

[semiautomaticgit]

Hello, it seems that /usr/local is not created by default. A possible solution from https://www.facebook.com/groups/SemiAutomaticClassificationPlugin/permalink/3722826171146887/?comment_id=3740311452731692 In a Terminal: (if you have a libcrypto and libssl in /usr/local/lib this will overwrite them) sudo ln -sf /Library/Frameworks/Python.framework/Versions/3.9/lib/libssl.dylib /usr/local/lib/libssl.dylib sudo ln -sf /Library/Frameworks/Python.framework/Versions/3.9/lib/libcrypto.dylib /usr/local/lib/libcrypto.dylib If usr/local doesn't exist, though it should, even if it's empty. Try: sudo mkdir -p /usr/local/lib Then, the ln commands and try to do processing on QGIS.

[semiautomaticgit]

I'm closing this because of the new version 8 of SCP. Please reopen it if it is still relevant in the new version. Thank you!