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cytomining / cytominer-database

[DEPRECATED] A package for storing morphological profiling data.
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Don't ingest objects when cell count = 0 #91

Open shntnu opened 6 years ago

shntnu commented 6 years ago

When we get a Some files were invalid error, that's almost always because the number of cells were zero. So handle this explicitly, i.e., if *_Count exists and is zero and then don't ingest the objects

INFO [2018-01-10 16:29:36] Ingesting...
Some files were invalid: Cells.csv,Nuclei.csv,Cytoplasm.csv. Skipping ../../analysis/2017_12_05_Batch2/BR00092746/analysis/BR00092746-C07-2.
mcquin commented 6 years ago

@shntnu To clarify, the CSV for that particular object should be skipped but not the others. For example, if Cells_Count is 0, but Nuclei_Count and Cytoplasm_Count are non-zero, then we should ingest Nuclei.csv and Cytoplasm.csv (but not Cells.csv).

shntnu commented 6 years ago

Cell (or other compartment) count may not always be present in the Image.csv. Instead, first check whether all the compartments CSVs have zero rows; if so, log that (as opposed to a more generic Some files were invalid) and proceed