Propagate CaImAn quality metrics #1436
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Hi, see comments on #1414 (comment) to see how to move forward with this. Feel free to reach me in slack for a call if things are not clear. |
| @@ -950,6 +980,12 @@ def _add_plane_segmentation( | |||
| data=is_id_rejected, | |||
| ) | |||
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| if include_quality_metrics and quality_metrics is not None: | |||
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default_descriptions = {"snr": "signal_to_noise_ratio_orwhatever", "other_property": "default_description}"
If your property is named like that then you used this description, otherwise, you use empty string or no description.
src/neuroconv/datainterfaces/ophys/caiman/caimandatainterface.py
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| @@ -823,6 +843,7 @@ def add_plane_segmentation_to_nwbfile( | |||
| include_roi_acceptance=include_roi_acceptance, | |||
| mask_type=mask_type, | |||
| iterator_options=iterator_options, | |||
| quality_metrics=quality_metrics, | |||
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We should call this segmentation_extractor_properties because it is not only quality metrics.
| @@ -950,6 +969,13 @@ def _add_plane_segmentation( | |||
| data=is_id_rejected, | |||
| ) | |||
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| # Always add quality metrics if they are available | |||
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I think the default definitions should be here:
quality_metrics_definitions = {
"snr": "Signal-to-noise ratio for each component",
"r_values": "Spatial correlation values for each component",
"cnn_preds": "CNN classifier predictions for component quality",
}
close to where they are used.
| @@ -536,6 +536,26 @@ def test_rejected_roi_ids(self, rejected_list, expected_rejected_roi_ids): | |||
| plane_segmentation_accepted_roi_ids = plane_segmentation["Accepted"].data | |||
| assert_array_equal(plane_segmentation_accepted_roi_ids, accepted_roi_ids) | |||
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| def test_add_plane_segmentation_with_quality_metrics(self): | |||
| """Test that available quality metrics in the segmentation extractor are added as columns to the PlaneSegmentation when available.""" | |||
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This looks fishy,
if & is intersection I think this test will always pass. or am I wrong?
Anyway, for these test here we have absolute control. Can you add some specific properties to the segmentation extractor here and test:
- that they are added
- their values match what we just added.
So just create a segmentation extractor, add properties with values that you control of various dtypes and check that they are written correctly.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1436 +/- ##
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+ Coverage 87.04% 87.06% +0.01%
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Files 145 145
Lines 9681 9691 +10
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+ Hits 8427 8437 +10
Misses 1254 1254
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Fix #1414 : propagate quality metrics and add multiplane stub files to testing.