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MannLabs / SPARCSpy

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Segmentation not possible in TimecourseProject if `overwrite=True` #32

Open namsaraeva opened 5 months ago

namsaraeva commented 5 months ago

Segmentation with overwrite=True when initializing a TimecourseProject is not possible due to missing segmentation/input_segmentation.h5. The segmentation directory is emptied beforehand, therefore the file is missing. 

 project = TimecourseProject(project_location, 
                             config_path= "config_segmentation.yml", 
                             segmentation_f=Multithreaded_Cytosol_Cellpose_Downsampling_TimecourseSegmentation,
                             extraction_f = TimecourseHDF5CellExtraction,
                             overwrite=True,
                             debug=False)

Possible source of this error might be in base.py:163. This needs further investigation.