Open GenevieveBuckley opened 5 years ago
Apparently podocytes_validation/51686/Images_51686/glom 8.tif
is a good example of this problem.
Traceback:
2018-12-18 14:13:35,009 Processing file: /Users/genevieb/Documents/GitHub/Code_repositories/podocytes_validation/51686/Images_51686/glom 8.tif
2018-12-18 14:13:35,243 Image:0
2018-12-18 14:13:35,244 glom 8.tif
Traceback (most recent call last):
File "podocytes/main.py", line 176, in <module>
main()
File "podocytes/main.py", line 47, in main
run_program(args)
File "podocytes/main.py", line 72, in run_program
single_image_stats = process_image_series(images, filename, args)
File "podocytes/main.py", line 137, in process_image_series
images[0].metadata['mppZ']
KeyError: 'mppZ'
I'm finding that occasionally the metadata on voxel size is missing or corrupt. This results in a
KeyError
for:images[0].metadata['mppZ']
This might be more common since we're working with cropped tiff images for validation purposes (instead of raw .lif files from the microscope), but we'll need to handle it regardless.
We refer to
images[0].metadata['mppZ']
directly in two places in main.py, but a lot of follow on statistics use the result in their calculation. Should be skip those entirely? Put a NaN value in the column there? Not sure of the best way to handle this just yet.