fix: Fix checking if channel requested by MeasurementProfile exists #1165
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WalkthroughThe recent updates enhance measurement functionality and channel validation across various components, particularly in Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant MeasurementWidget
participant PartSegImage
User->>MeasurementWidget: Request measurement with channel number
MeasurementWidget->>PartSegImage: Check channel with has_channel()
PartSegImage-->>MeasurementWidget: Return channel existence
MeasurementWidget->>User: Display result or error message
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Files selected for processing (2)
- package/PartSeg/_roi_analysis/measurement_widget.py (1 hunks)
- package/PartSegImage/image.py (2 hunks)
Additional comments not posted (5)
package/PartSeg/_roi_analysis/measurement_widget.py (2)
370-373: LGTM! The channel validation is now more robust.The use of
has_channel(num)method improves the robustness of the channel validation.
374-376: Update the warning message for clarity.The warning message now correctly references the channel number without incrementing it by one.
package/PartSegImage/image.py (3)
529-533: LGTM! The method now handlesChannelobjects and strings for theCkeyword argument.The change improves the flexibility of the method by allowing it to accept a broader range of input types for channel identification.
575-576: LGTM! The method now handlesChannelobjects and strings.The change improves the flexibility of the method by allowing it to accept a broader range of input types for channel identification.
577-584: LGTM! The newhas_channelmethod enhances functionality.The method provides a straightforward way to verify the existence of a channel before attempting to access it.
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #1165 +/- ##
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+ Coverage 93.06% 93.10% +0.04%
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Files 209 209
Lines 32829 32876 +47
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+ Hits 30552 30609 +57
+ Misses 2277 2267 -10 ☔ View full report in Codecov by Sentry. |
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Files selected for processing (1)
- package/PartSeg/_roi_analysis/measurement_widget.py (1 hunks)
Files skipped from review as they are similar to previous changes (1)
- package/PartSeg/_roi_analysis/measurement_widget.py
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Files selected for processing (14)
- package/PartSeg/_roi_analysis/advanced_window.py (1 hunks)
- package/PartSeg/common_gui/napari_image_view.py (1 hunks)
- package/PartSeg/plugins/napari_widgets/measurement_widget.py (2 hunks)
- package/PartSeg/plugins/napari_widgets/utils.py (1 hunks)
- package/PartSegCore/analysis/measurement_base.py (1 hunks)
- package/tests/conftest.py (3 hunks)
- package/tests/test_PartSeg/conftest.py (3 hunks)
- package/tests/test_PartSeg/roi_analysis/test_advanced_window.py (1 hunks)
- package/tests/test_PartSeg/test_analysis.py (4 hunks)
- package/tests/test_PartSeg/test_napari_widgets.py (3 hunks)
- package/tests/test_PartSeg/test_roi_analysis_batch.py (1 hunks)
- package/tests/test_PartSeg/test_viewer.py (1 hunks)
- package/tests/test_PartSegImage/test_image.py (1 hunks)
- package/tests/test_data/napari_measurements_profile.json (1 hunks)
Files skipped from review due to trivial changes (1)
- package/tests/test_PartSeg/conftest.py
Additional comments not posted (30)
package/PartSeg/plugins/napari_widgets/utils.py (2)
64-65: LGTM! Enhanced flexibility with type check.The type check to handle both string inputs and
Channelobjects enhances the function's flexibility.
67-67: LGTM! Correct usage ofname.value.The usage of
name.valueensures that the correct layer is accessed based on the new input handling.package/tests/test_PartSeg/test_analysis.py (4)
21-21: LGTM! Updated measurement type count.The update to the
measurement_typecount from 3 to 4 reflects the expected behavior of theMeasurementWidget.
37-37: LGTM! Updated measurement type count.The update to the
measurement_typecount from 3 to 4 reflects the expected behavior of theMeasurementWidget.
55-55: LGTM! Updated measurement type count.The update to the
measurement_typecount from 3 to 4 reflects the expected behavior of theMeasurementWidget.
67-83: LGTM! New test case for channel measurements.The new test case
test_base_channelsexpands the coverage of theMeasurementWidgetfunctionality, particularly in scenarios involving channel measurements.package/tests/test_PartSeg/test_viewer.py (3)
78-78: LGTM! Updated expected number of layers.The update to the expected number of layers in the
viewerobject reflects the revised understanding of how many layers should be present after each operation.
81-81: LGTM! Updated expected number of layers.The update to the expected number of layers in the
viewerobject reflects the revised understanding of how many layers should be present after each operation.
84-84: LGTM! Updated expected number of layers.The update to the expected number of layers in the
viewerobject reflects the revised understanding of how many layers should be present after each operation.package/PartSeg/plugins/napari_widgets/measurement_widget.py (2)
62-62: Ensurename.valueis correct.The change to use
name.valueinstead ofnameimproves accuracy in channel validation. Verify thatname.valueis the correct attribute to use.
66-67: Wrap channel name inChannelobject.Wrapping the channel name in a
Channelobject improves type safety and aligns with the expected data structure for channel representation.package/tests/test_PartSeg/roi_analysis/test_advanced_window.py (2)
151-151: Update assertion to reflect new expected state.The assertion has been updated to check for a length of 3, indicating a change in the expected state of
measurement_profiles.
154-154: Update assertion to reflect new expected state.The assertion has been updated to check for a length of 4, indicating a change in the expected state of
measurement_profiles.package/tests/conftest.py (2)
77-77: Update data shape to handle multi-channel images.The data shape has been updated to
[20, 40, 40, 2], allowing the tests to handle multi-channel image data.
209-216: Add newMeasurementProfileforstatistic3.The addition of a new
MeasurementProfileforstatistic3enhances the testing framework to support colocalization measurements.package/PartSegCore/analysis/measurement_base.py (1)
398-401: LGTM! The changes enhance method functionality.The inclusion of a conditional check for the
__argument_class__attribute improves the method's robustness.package/tests/test_data/napari_measurements_profile.json (8)
3-7: LGTM! The structural changes enhance compatibility tracking.Replacing the root key with
__class__and__class_version_dkt__indicates a shift towards a more robust class-based representation.
11-15: LGTM! The changes improve schema uniformity.Using
__class__and__class_version_dkt__instead of__Serializable__and__subtype__enhances the schema's extensibility and maintainability.
18-19: LGTM! The renaming enhances clarity.Including "ROI" in measurement names improves the context-specific application of the measurements.
20-24: LGTM! The restructuring improves clarity.Using
__class__and__values__consistently in calculation trees enhances the understanding of measurement calculations.
25-49: LGTM! The changes align with the new schema.Updating the
ROI Volumemeasurement to use the new schema is consistent with the overall improvements in the file.
53-92: LGTM! The changes align with the new schema.Updating the
ROI Volume per componentmeasurement to use the new schema is consistent with the overall improvements in the file.
94-174: LGTM! The changes align with the new schema.Updating the
ROI Volume per component /ROI Volumemeasurement to use the new schema is consistent with the overall improvements in the file.
176-215: LGTM! The changes align with the new schema.Updating the
ROI Mean pixel brightnessmeasurement to use the new schema is consistent with the overall improvements in the file.package/tests/test_PartSeg/test_napari_widgets.py (1)
Line range hint
226-257:
LGTM! The changes enhance test functionality.The alterations to the function's parameters and the additional assertions improve the test's robustness.
package/tests/test_PartSegImage/test_image.py (2)
291-292: Ensure channel existence checks are meaningful.The assertions
assert image.has_channel(1)andassert not image.has_channel(5)verify that channel 1 exists and channel 5 does not. These checks enhance the robustness of the test.
295-296: Ensure channel existence checks are meaningful.The assertions
assert image.has_channel("b")andassert not image.has_channel("d")verify that channel "b" exists and channel "d" does not. These checks enhance the robustness of the test.package/tests/test_PartSeg/test_roi_analysis_batch.py (1)
538-538: Update the expected count in the assertion.The assertion
assert widget.measurements_list.count() == 3ensures that themeasurements_listcontains the correct number of items, reflecting the updated expected state of the widget.package/PartSeg/_roi_analysis/advanced_window.py (1)
808-808: Enhance dialog management by adding parent parameter.The addition of the
parentparameter to theImportDialoginstantiation improves the dialog's integration within the application's window hierarchy.package/PartSeg/common_gui/napari_image_view.py (1)
416-416: LGTM! But verify the method usage in the codebase.The code changes are approved.
However, ensure that all usages of the
mask_colormethod correctly handle the newNonekey in the returned dictionary.
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- package/tests/test_PartSegCore/test_napari_plugins.py (2 hunks)
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package/tests/test_PartSegCore/test_napari_plugins.py (4)
30-30: Update the expected number of layers to 4.The expected number of layers has been updated from 3 to 4, reflecting an enhancement in the
project_to_layersfunction.
35-35: Update the index for the second layer.The index for the second layer has been updated from
res[1]tores[2]to accommodate the additional layer.
39-39: Update the index for the third layer.The index for the third layer has been updated from
res[2]tores[3]to accommodate the additional layer.
58-58: Update the expected number of layers to 3.The expected number of layers has been updated from 2 to 3, reflecting an enhancement in the
project_to_layersfunction.
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Files selected for processing (2)
- package/PartSegCore/analysis/measurement_base.py (1 hunks)
- package/tests/test_PartSegImage/test_image.py (1 hunks)
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- package/PartSegCore/analysis/measurement_base.py
- package/tests/test_PartSegImage/test_image.py
fix PARTSEG-VA
Summary by CodeRabbit
Summary by CodeRabbit
New Features
Channelobjects and strings for improved flexibility.Bug Fixes