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fractal-analytics-platform / fractal-tasks-core

Main tasks for the Fractal analytics platform
https://fractal-analytics-platform.github.io/fractal-tasks-core/
BSD 3-Clause "New" or "Revised" License
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Create OME-Zarr structure Task failure when metadata does not match acquisition #627

Open nrepina opened 7 months ago

nrepina commented 7 months ago

Task fails when Yokogawa mrl metadata contains channels of different pixel dimensions (e.g. due to different binning settings). See example metadata; channel 5 was not used during acquisition but it is still in metadata due to inheritance from a previous acquisition, and causes the task to fail. Perhaps best to check consistency only on channels used for creating ome-zarr structure. 

ValueError: During metadata parsing, a consistency check failed: 
Image dimensions
Difference dataframe: 
horiz_pixel_dim       0.325
vert_pixel_dim        0.325
horiz_pixels       1000.000
vert_pixels        1000.000
bit_depth             0.000
dtype: float64

MeasurementDetail.txt MeasurementData.txt

jluethi commented 7 months ago

Agreed, we should refactor the consistency check to only run for channels that are actually present. Either based on allowed_channels or based on channels present in the mlf file.

jluethi commented 6 months ago

For future reference: See also additional description in https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/287 And here: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/586