feat: Add option to combine channels using sum and max #1159
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Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (8)
- package/PartSeg/_roi_analysis/partseg_settings.py (1 hunks)
- package/PartSeg/common_gui/image_adjustment.py (1 hunks)
- package/PartSegCore/image_transforming/init.py (1 hunks)
- package/PartSegCore/image_transforming/combine_channels.py (1 hunks)
- package/PartSegCore/image_transforming/image_projection.py (2 hunks)
- package/PartSegCore/image_transforming/interpolate_image.py (1 hunks)
- package/PartSegCore/image_transforming/swap_time_stack.py (1 hunks)
- package/PartSegCore/image_transforming/transform_base.py (1 hunks)
Additional comments not posted (13)
package/PartSegCore/image_transforming/__init__.py (3)
2-2: LGTM! Import statement forCombineChannels.The import statement for
CombineChannelsis correctly added.
8-8: LGTM! Update toimage_transform_dict.The
CombineChannelsclass is correctly added to theimage_transform_dict.
10-10: LGTM! Update to__all__.The
__all__list is correctly updated to includeCombineChannels.package/PartSegCore/image_transforming/transform_base.py (1)
21-21: LGTM! Update to method signature forget_fields_per_dimension.The method signature change to accept an
Imageobject is consistent with the new functionality.However, ensure that all calls to
get_fields_per_dimensionare updated to match the new signature.Verification successful
LGTM! Update to method signature for
get_fields_per_dimension.The method signature change to accept an
Imageobject is consistent with the new functionality. All calls toget_fields_per_dimensionhave been updated to match the new signature.
Definitions:
package/PartSegCore/image_transforming/combine_channels.pypackage/PartSegCore/image_transforming/swap_time_stack.pypackage/PartSegCore/image_transforming/image_projection.pypackage/PartSegCore/image_transforming/interpolate_image.pypackage/PartSegCore/image_transforming/transform_base.pyUsage:
package/PartSeg/common_gui/image_adjustment.pyScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all calls to `get_fields_per_dimension` match the new signature. # Test: Search for the method usage. Expect: Only occurrences of the new signature. rg --type python -A 5 'get_fields_per_dimension'Length of output: 79
Script:
#!/bin/bash # Description: Verify all calls to `get_fields_per_dimension` match the new signature. # Test: Search for the method usage. Expect: Only occurrences of the new signature. rg --type py -A 5 'get_fields_per_dimension'Length of output: 3601
package/PartSegCore/image_transforming/swap_time_stack.py (1)
21-21: LGTM! Update to method signature forget_fields_per_dimension.The method signature change to accept an
Imageobject is consistent with the new functionality.However, ensure that all calls to
get_fields_per_dimensionare updated to match the new signature.Verification successful
All calls to
get_fields_per_dimensionhave been updated to match the new signature.The method signature change to accept an
Imageobject is consistently applied across the codebase.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all calls to `get_fields_per_dimension` match the new signature. # Test: Search for the method usage. Expect: Only occurrences of the new signature. rg --type python -A 5 'get_fields_per_dimension'Length of output: 79
Script:
#!/bin/bash # Description: Verify all calls to `get_fields_per_dimension` match the new signature. # Test: Search for the method usage. Expect: Only occurrences of the new signature. rg --type py -A 5 'get_fields_per_dimension'Length of output: 3601
package/PartSeg/common_gui/image_adjustment.py (1)
25-25: LGTM! Update toFormWidgetinstantiation.The change simplifies the code by passing the
imageobject directly.However, ensure that the
FormWidgetclass can handle theimageobject correctly.package/PartSegCore/image_transforming/interpolate_image.py (1)
17-18: LGTM! But verify the function usage in the codebase.The code changes are approved.
However, ensure that all function calls to
get_fields_per_dimensionmatch the new signature.Verification successful
Verify the function calls to
get_fields_per_dimensionmatch the new signature.The function
get_fields_per_dimensionis used in multiple files. Ensure that all calls to this function pass anImageobject as an argument.
package/PartSeg/common_gui/image_adjustment.py
- Line:
form_widget = FormWidget(val.get_fields_per_dimension(image), initial_values)package/PartSegCore/image_transforming/swap_time_stack.py
- Line:
def get_fields_per_dimension(cls, image: Image):package/PartSegCore/image_transforming/interpolate_image.py
- Line:
def get_fields_per_dimension(cls, image: Image) -> List[Union[str, AlgorithmProperty]]:package/PartSegCore/image_transforming/image_projection.py
- Line:
def get_fields_per_dimension(cls, image: Image):package/PartSegCore/image_transforming/transform_base.py
- Line:
def get_fields_per_dimension(cls, image: Image) -> List[Union[str, AlgorithmProperty]]:package/PartSegCore/image_transforming/combine_channels.py
- Line:
def get_fields_per_dimension(cls, image: Image) -> List[Union[str, AlgorithmProperty]]:All instances appear to follow the new signature, passing an
Imageobject as an argument.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `get_fields_per_dimension` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg --type python -A 5 $'get_fields_per_dimension'Length of output: 79
Script:
#!/bin/bash # Description: Verify all function calls to `get_fields_per_dimension` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg --type py -A 5 $'get_fields_per_dimension'Length of output: 3601
package/PartSegCore/image_transforming/combine_channels.py (4)
19-20: LGTM!The method correctly returns a list of algorithm properties with a default combine mode.
23-27: LGTM!The method correctly returns a list of algorithm properties for each channel in the image.
34-53: LGTM!The method correctly combines channels in the image based on the specified combine mode and updates the image accordingly.
56-60: LGTM!The method correctly calculates initial values for the algorithm properties based on the image spacing.
package/PartSegCore/image_transforming/image_projection.py (1)
70-70: LGTM! But verify the function usage in the codebase.The code changes are approved.
However, ensure that all function calls to
get_fields_per_dimensionmatch the new signature.Verification successful
Let's correct the
rgcommand to use the appropriate file type for Python files and re-run the script to verify the function usage in the codebase.
Verified: All function calls to
get_fields_per_dimensionmatch the new signature.The code changes are consistent across the codebase, and the function usage has been updated appropriately.
package/PartSeg/common_gui/image_adjustment.pypackage/PartSegCore/image_transforming/transform_base.pypackage/PartSegCore/image_transforming/swap_time_stack.pypackage/PartSegCore/image_transforming/interpolate_image.pypackage/PartSegCore/image_transforming/image_projection.pypackage/PartSegCore/image_transforming/combine_channels.pyScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `get_fields_per_dimension` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg --type python -A 5 $'get_fields_per_dimension'Length of output: 79
Script:
#!/bin/bash # Description: Verify all function calls to `get_fields_per_dimension` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg --type py -A 5 $'get_fields_per_dimension'Length of output: 3601
package/PartSeg/_roi_analysis/partseg_settings.py (1)
109-113: LGTM!The method now correctly includes a check for the equality of
image.channelsto ensure consistency.
Czaki
changed the title
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #1159 +/- ##
===========================================
+ Coverage 93.05% 93.06% +0.01%
===========================================
Files 208 209 +1
Lines 32763 32830 +67
===========================================
+ Hits 30486 30553 +67
Misses 2277 2277 ☔ View full report in Codecov by Sentry. |
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There was a problem hiding this comment.
Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (3)
- package/PartSegCore/image_transforming/init.py (1 hunks)
- package/PartSegCore/image_transforming/combine_channels.py (1 hunks)
- package/tests/test_PartSegCore/test_image_adjustment.py (3 hunks)
Files skipped from review as they are similar to previous changes (2)
- package/PartSegCore/image_transforming/init.py
- package/PartSegCore/image_transforming/combine_channels.py
Additional comments not posted (6)
package/tests/test_PartSegCore/test_image_adjustment.py (6)
5-5: Imports look good.The imported classes
CombineChannels,CombineMode, andInterpolateImageare necessary for the new tests.
23-27: Functionget_cube_image_2chlooks good.The function correctly creates a 2-channel cube image and returns an
Imageobject.
118-125: Test methodtest_simplelooks good.The test correctly sets up the image, applies the
CombineChannelstransformation with theMaxmode, and verifies the results.
126-130: Test methodtest_no_channelslooks good.The test correctly sets up the image, applies the
CombineChannelstransformation with no specific channel settings, and verifies the results.
131-138: Test methodtest_sumlooks good.The test correctly sets up the image, applies the
CombineChannelstransformation with theSummode, and verifies the results.
139-145: Test methodtest_maxlooks good.The test correctly sets up the image, applies the
CombineChannelstransformation with theMaxmode, and verifies the results.
Summary by CodeRabbit
New Features
CombineChannelsclass, allowing users to combine image channels using modes like Max or Sum.Bug Fixes
ImageProjectionto improve image handling.Tests