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refactor: merge all channel-specific attributes of the Image class #1191

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merged 16 commits into from
Sep 22, 2024

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Czaki
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@Czaki Czaki commented Sep 16, 2024

Also make all except data arguments keyword only

Summary by Sourcery

Refactor the Image class to consolidate channel-specific attributes into a unified channel_info attribute, enforce keyword-only arguments, and update tests accordingly.

Enhancements:

  • Refactor the Image class to merge all channel-specific attributes into a single channel_info attribute, improving the organization and management of channel metadata.
  • Introduce decorators to handle deprecated arguments and enforce keyword-only arguments for the Image class, enhancing code clarity and future-proofing.
  • Add utility functions for color conversion from hex and named colors to RGB, supporting more flexible color specifications.

Tests:

  • Update tests to accommodate the refactored Image class, ensuring compatibility with the new channel_info attribute and keyword-only arguments.

Summary by CodeRabbit

Release Notes

  • New Features

    • Introduced ChannelInfo and ChannelInfoFull classes for enhanced channel metadata management.
    • Updated image processing to use spacing instead of image_spacing, improving parameter clarity.
  • Bug Fixes

    • Corrected parameter names across various tests and functionalities to align with the updated Image class interface.
  • Tests

    • Updated numerous test cases to reflect changes in parameter names and structures, ensuring consistency throughout the test suite.
    • Added a new test for saving color images with specific channel information.

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coderabbitai bot commented Sep 16, 2024

Walkthrough

The pull request introduces significant changes to the Image class in the PartSegImage module, focusing on enhancing channel information management. Key modifications include replacing the image_spacing parameter with spacing and introducing a new channel_info parameter in place of channel_names. Additionally, new data classes for channel metadata have been added, along with methods for improved handling of this information. These adjustments ensure consistency and clarity in managing image and channel data across the codebase, including updates to related tests.

Changes

Files Change Summary
package/PartSegImage/image.py Introduced ChannelInfo and ChannelInfoFull classes for improved channel metadata handling. Updated Image constructor to accept spacing and channel_info. Added methods and properties for better channel information management.
package/tests/test_PartSegImage/test_image_writer.py Updated tests to reflect changes in the Image constructor, replacing image_spacing with spacing and channel_names with channel_info. Added a new test for saving color images.
package/PartSegCore/analysis/measurement_calculation.py Minor comment adjustments in the get_global_parameters and _prepare_res_iterator methods.

Possibly related PRs

  • fix: Fix get_ranges for empty channels in Image #1136: This PR modifies the get_ranges function in the image.py file, which is directly related to the handling of channel information and ranges, similar to the enhancements made in the main PR regarding channel metadata management in the Image class.

Poem

🐇 In the code where images play,
Spacing now leads the way.
Channels wrapped in info bright,
Clarity shines, a joyful sight!
With each change, we hop and cheer,
For better code, we hold so dear! ✨


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codecov bot commented Sep 16, 2024

Codecov Report

Attention: Patch coverage is 99.63235% with 1 line in your changes missing coverage. Please review.

Project coverage is 93.12%. Comparing base (2f6c259) to head (68294e1).
Report is 1 commits behind head on develop.

Files with missing lines Patch % Lines
package/PartSegImage/image.py 99.15% 1 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #1191      +/-   ##
===========================================
+ Coverage    93.08%   93.12%   +0.03%     
===========================================
  Files          210      210              
  Lines        32974    33105     +131     
===========================================
+ Hits         30694    30828     +134     
+ Misses        2280     2277       -3     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@Czaki Czaki added this to the 0.15.4 milestone Sep 16, 2024
@Czaki Czaki changed the title Add informtion about type of channel Add information about the type of channel Sep 16, 2024
@Czaki Czaki changed the title Add information about the type of channel feat: Add information about the type of channel Sep 16, 2024
@Czaki Czaki changed the title feat: Add information about the type of channel refactor: merge all channel-specific attributes of the Image class Sep 18, 2024
@Czaki Czaki marked this pull request as ready for review September 20, 2024 20:54
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sourcery-ai bot commented Sep 20, 2024

Reviewer's Guide by Sourcery

This pull request refactors the Image class in the PartSegImage package, merging all channel-specific attributes and making most arguments keyword-only. The changes aim to improve the class's structure and usage.

File-Level Changes

Change Details Files
Refactored the Image class to merge channel-specific attributes
  • Added ChannelInfo and ChannelInfoFull dataclasses to store channel metadata
  • Replaced channel_names, default_coloring, and ranges with a single channel_info attribute
  • Updated the init method to use the new channel_info attribute
  • Made all arguments except 'data' keyword-only
  • Renamed 'image_spacing' parameter to 'spacing'
  • Renamed 'metadata' parameter to 'metadata_dict'
package/PartSegImage/image.py
Updated image creation and manipulation functions to use the new Image class structure
  • Modified image creation calls to use keyword arguments
  • Updated functions that interact with channel-specific data to use the new channel_info attribute
  • Adjusted tests to reflect the new Image class structure
package/PartSegImage/image_reader.py
package/tests/test_PartSegImage/test_image.py
package/tests/test_PartSegCore/test_measurements.py
package/tests/test_PartSeg/test_common_backend.py
package/tests/test_PartSegCore/test_segmentation.py
package/tests/test_PartSegImage/test_image_writer.py
package/tests/test_PartSegCore/test_image_adjustment.py
package/tests/test_PartSegCore/test_io.py
Implemented backward compatibility and deprecation warnings
  • Added decorator functions to handle argument renaming and deprecation warnings
  • Implemented a merge_into_channel_info decorator to convert old-style arguments to the new channel_info format
package/PartSegImage/image.py
Updated related components to work with the new Image class structure
  • Modified napari plugins to use the new Image class structure
  • Updated image transformation and projection functions to work with the new channel_info attribute
  • Adjusted mask creation and IO functions to use the new Image class structure
package/PartSegCore/napari_plugins/save_tiff_layer.py
package/PartSeg/plugins/napari_widgets/utils.py
package/PartSegCore/image_transforming/image_projection.py
package/PartSegCore/mask/io_functions.py

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Hey @Czaki - I've reviewed your changes and they look great!

Here's what I looked at during the review
  • 🟡 General issues: 2 issues found
  • 🟢 Security: all looks good
  • 🟡 Testing: 5 issues found
  • 🟢 Complexity: all looks good
  • 🟢 Documentation: all looks good

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self.metadata = dict(metadata_dict) if metadata_dict is not None else {}

@staticmethod
def _adjust_channel_info(
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suggestion: Consider a more robust approach for default color assignment

The use of cycle for default colors could lead to unexpected behavior with a large number of channels. A modulo operation on a fixed list of colors might ensure more consistent and predictable color assignment.

    @staticmethod
    def _adjust_channel_info(
        channel_info: list[ChannelInfo | ChannelInfoFull] | None,
        channel_array: list[np.ndarray],
        default_colors: list[str] = ['red', 'green', 'blue', 'yellow', 'cyan', 'magenta']
    ) -> list[ChannelInfoFull]:

return _fun


def merge_into_channel_info(fun):
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suggestion (performance): Optimize merge_into_channel_info decorator for performance

The decorator performs several operations on every function call, which could impact performance for frequently called methods. Consider moving the deprecation warning and merging logic to the init method to perform these operations only once during object creation.

def merge_into_channel_info(fun):
    def wrapper(self, *args, **kwargs):
        if not hasattr(self, '_merged_channel_info'):
            self._merged_channel_info = self._merge_channel_info()
        return fun(self, *args, **kwargs)
    return wraps(fun)(wrapper)

package/tests/test_PartSegImage/test_image.py Show resolved Hide resolved
Comment on lines 135 to 141
with pytest.raises(ValueError, match="Wrong array shape"):
self.image_class(
np.zeros(data_shape),
(5, 5, 5),
spacing=(5, 5, 5),
mask=np.zeros(data_shape[:-2] + (40,)),
axes_order=self.image_class.axis_order,
)
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suggestion (testing): Update test to use new 'spacing' parameter and 'channel_info' instead of 'channel_names'

The test has been updated to use the new 'spacing' parameter and 'channel_info' instead of 'channel_names'. This change reflects the refactoring in the main code. Verify that all tests in this file are updated to use these new parameters consistently.

Suggested change
with pytest.raises(ValueError, match="Wrong array shape"):
self.image_class(
np.zeros(data_shape),
(5, 5, 5),
spacing=(5, 5, 5),
mask=np.zeros(data_shape[:-2] + (40,)),
axes_order=self.image_class.axis_order,
)
def test_image_mask_exception(self):
with pytest.raises(ValueError, match="Wrong array shape"):
self.image_class(
np.zeros(data_shape),
spacing=(5, 5, 5),
mask=np.zeros(data_shape[:-2] + (40,)),
axes_order=self.image_class.axis_order,
channel_info=[{"name": f"Channel {i}"} for i in range(data_shape[-1])]
)

axes_order="ZYXC",
channel_names=["a", "b"],
channel_info=[ChannelInfo("a"), ChannelInfo("b")],
shift=(10, 9, 8),
name="Test",
)
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suggestion (testing): Update test to use new 'spacing' parameter and 'channel_info' instead of 'channel_names'

The test has been updated to use the new 'spacing' parameter and 'channel_info' instead of 'channel_names'. This change is consistent with the refactoring in the main code. Ensure that all other tests in this file are updated similarly.

def test_ome_save(tmp_path, bundle_test_dir, ome_xml, z_size):
    data = np.zeros((z_size, 20, 20, 2), dtype=np.uint8)
    spacing = (27e-6, 6e-6, 6e-6)
    channel_info = [ChannelInfo("a"), ChannelInfo("b")]
    image = Image(
        data,
        spacing=spacing,
        axes_order="ZYXC",
        channel_info=channel_info,
        shift=(10, 9, 8),
        name="Test",
    )

package/tests/test_PartSegCore/test_io.py Show resolved Hide resolved
package/tests/test_PartSeg/test_common_gui.py Show resolved Hide resolved
package/tests/test_PartSegImage/test_image.py Show resolved Hide resolved

@staticmethod
def _adjust_channel_info(
channel_info: list[ChannelInfo | ChannelInfoFull] | None, channel_array: list[np.ndarray]
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issue (code-quality): We've found these issues:

package/PartSegImage/image.py Outdated Show resolved Hide resolved
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Actionable comments posted: 4

Outside diff range and nitpick comments (4)
package/tests/test_PartSegImage/test_image.py (1)

365-367: Adjust spacing to match 2D image dimensions

The image is 2D, but the spacing is specified as a 3-tuple (1, 1, 1). Consider adjusting the spacing to a 2-tuple (1, 1) to match the dimensions of the image more accurately.

Apply this diff to adjust the spacing:

-image = self.image_class(
-    np.zeros((1, 1, 20, 30, 3), np.uint8), spacing=(1, 1, 1), file_path="", axes_order="TZYXC"
-)
+image = self.image_class(
+    np.zeros((1, 1, 20, 30, 3), np.uint8), spacing=(1, 1), file_path="", axes_order="TZYXC"
+)
package/PartSegImage/image.py (3)

26-31: Consider adding docstrings to ChannelInfo dataclass.

Including a docstring for the ChannelInfo class would enhance code readability and provide clear documentation of its purpose and usage.


33-38: Consider adding docstrings to ChannelInfoFull dataclass.

Adding a docstring to the ChannelInfoFull class would improve maintainability by explaining its role and how it differs from ChannelInfo.


136-167: Simplify conditional checks in merge_into_channel_info for clarity.

Reordering the checks for None before type checking enhances readability and avoids unnecessary type checks on None values.

Apply this diff to simplify the conditional checks:

             channel_names = kwargs.pop("channel_names", [])
             default_coloring = kwargs.pop("default_coloring", [])
             ranges = kwargs.pop("ranges", [])

             if any([channel_names, default_coloring, ranges]):
+                if channel_names is None:
+                    channel_names = []
                 if isinstance(channel_names, str):
                     channel_names = [channel_names]
-                if channel_names is None:
-                    channel_names = []
                 if default_coloring is None:
                     default_coloring = []
                 if ranges is None:
                     ranges = []
Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 2f6c259 and 1e5dc62.

Files selected for processing (22)
  • package/PartSeg/plugins/napari_widgets/simple_measurement_widget.py (1 hunks)
  • package/PartSeg/plugins/napari_widgets/utils.py (2 hunks)
  • package/PartSegCore/image_transforming/image_projection.py (1 hunks)
  • package/PartSegCore/mask/io_functions.py (1 hunks)
  • package/PartSegCore/napari_plugins/save_tiff_layer.py (3 hunks)
  • package/PartSegImage/init.py (2 hunks)
  • package/PartSegImage/image.py (12 hunks)
  • package/PartSegImage/image_reader.py (6 hunks)
  • package/tests/test_PartSeg/test_base_widgets.py (1 hunks)
  • package/tests/test_PartSeg/test_common_backend.py (3 hunks)
  • package/tests/test_PartSeg/test_common_gui.py (2 hunks)
  • package/tests/test_PartSeg/test_napari_image_view.py (1 hunks)
  • package/tests/test_PartSeg/test_settings.py (2 hunks)
  • package/tests/test_PartSegCore/test_analysis_batch.py (2 hunks)
  • package/tests/test_PartSegCore/test_image_adjustment.py (1 hunks)
  • package/tests/test_PartSegCore/test_io.py (3 hunks)
  • package/tests/test_PartSegCore/test_mask_create.py (1 hunks)
  • package/tests/test_PartSegCore/test_measurements.py (16 hunks)
  • package/tests/test_PartSegCore/test_napari_plugins.py (1 hunks)
  • package/tests/test_PartSegCore/test_segmentation.py (3 hunks)
  • package/tests/test_PartSegImage/test_image.py (20 hunks)
  • package/tests/test_PartSegImage/test_image_writer.py (6 hunks)
Additional comments not posted (91)
package/PartSegImage/__init__.py (2)

6-6: LGTM!

The import statement has been correctly updated to include the new ChannelInfo and ChannelInfoFull classes from the PartSegImage.image module.


20-21: LGTM!

The __all__ tuple has been correctly updated to include the new ChannelInfo and ChannelInfoFull classes, making them part of the public API of the module.

package/PartSegCore/napari_plugins/save_tiff_layer.py (2)

18-18: LGTM!

The changes to the Image constructor call improve the structure and clarity of the code:

  • Replacing channel_names with channel_info enhances the structure of channel data being passed to the constructor.
  • Explicitly naming the spacing parameter improves code readability.

These changes align with the PR objective of refactoring the Image class by merging channel-specific attributes.

Also applies to: 20-20


53-53: LGTM!

The changes to the Image constructor call improve the structure and clarity of the code:

  • Replacing channel_names with channel_info enhances the structure of channel data being passed to the constructor.
  • Explicitly naming the spacing parameter improves code readability.

These changes align with the PR objective of refactoring the Image class by merging channel-specific attributes.

Also applies to: 55-55

package/PartSegCore/image_transforming/image_projection.py (1)

61-62: Verify the parameter changes in the codebase.

The parameter name changes from image_spacing to spacing, and channel_names to channel_info align with the PR objective of refactoring the Image class by merging channel-specific attributes. This improves the clarity and organization of the code.

Please ensure that all call sites of the transform method have been updated to use the new parameter names.

Run the following script to verify the parameter usage:

Verification successful

Approve the parameter changes in the Image class.

The parameter name changes from image_spacing to spacing, and channel_names to channel_info have been correctly implemented across the codebase. Although these parameters are not directly visible in the transform method of image_projection.py, the changes are consistent with the PR objective of refactoring the Image class by merging channel-specific attributes.

Key points:

  • The spacing parameter is widely used throughout the codebase, indicating it's a fundamental property of the Image class.
  • channel_info is used to store metadata about image channels, which aligns with the refactoring goal.
  • In the transform method, these properties are accessed through the image parameter (e.g., image.spacing), which is the correct way to use these attributes after the refactoring.

The implementation maintains consistency and improves the organization of the Image class while ensuring that existing functionality remains intact.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify all calls to the `transform` method use the new parameter names.

# Test: Search for the method usage. Expect: Only occurrences of the new parameter names.
rg --type python -A 5 $'transform\('

Length of output: 68


Script:

#!/bin/bash
# Description: Verify all calls to the `transform` method use the new parameter names.

# Find Python files and search for 'transform(' in them
fd -e py -x rg -n -A 5 'transform\(' {} \;

# Use ast-grep to find function calls to 'transform'
ast-grep --lang python --pattern 'transform($_)'

Length of output: 5324


Script:

#!/bin/bash
# Description: Search for occurrences of 'spacing' and 'channel_info' in Python files

# Search for 'spacing' in Python files
echo "Searching for 'spacing':"
fd -e py -x rg -n 'spacing' {} \;

echo -e "\nSearching for 'channel_info':"
fd -e py -x rg -n 'channel_info' {} \;

echo -e "\nSearching for 'transform' method implementation in image_projection.py:"
rg -n -A 10 'def transform' package/PartSegCore/image_transforming/image_projection.py

Length of output: 45708

package/PartSeg/plugins/napari_widgets/utils.py (3)

15-15: LGTM!

The import statement has been correctly updated to include ChannelInfo from PartSegImage. This aligns with the PR objective of refactoring the Image class to merge channel-specific attributes.


72-72: Verify the Image constructor usage in the codebase.

The change from data_scale to spacing is a valid refactor that maintains the same functionality. However, ensure that all occurrences of the Image constructor in the codebase have been updated to use the new spacing parameter.

Run the following script to verify the Image constructor usage:

Verification successful

Refactoring from 'data_scale' to 'spacing' verified successfully.

The change from 'data_scale' to 'spacing' in the Image constructor has been correctly implemented across the codebase. The single remaining instance of 'data_scale' is used as a variable name to provide the value for the 'spacing' parameter, which is consistent with the refactoring.

  • File with remaining 'data_scale' usage: (file name not provided in the output)
  • Line: 87
  • Context: image = Image(data_layer.data, spacing=data_scale, axes_order="TZYX"[-data_ndim:])

This usage is correct and does not require any further changes.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify all occurrences of the `Image` constructor use the new `spacing` parameter.

# Test: Search for the `Image` constructor usage. Expect: No occurrences of `data_scale`.
rg --type python -A 5 $'Image\('

Length of output: 64


Script:

#!/bin/bash
# Description: Search for Image constructor usage in Python files

# Find Python files and search for Image constructor with data_scale or spacing
fd '\.py$' --exec rg -n 'Image\(((?!data_scale|spacing).)*(?:data_scale|spacing)' {} -A 5

# Count occurrences of data_scale and spacing in Image constructor
echo "Occurrences of 'data_scale' in Image constructor:"
fd '\.py$' --exec rg 'Image\(.*data_scale' {} | wc -l

echo "Occurrences of 'spacing' in Image constructor:"
fd '\.py$' --exec rg 'Image\(.*spacing' {} | wc -l

Length of output: 63447


Script:

#!/bin/bash
# Description: Locate the remaining 'data_scale' usage in Image constructor

# Find the file and line number where 'data_scale' is used in Image constructor
echo "Location of 'data_scale' usage in Image constructor:"
fd '\.py$' --exec rg -n 'Image\(.*data_scale' {}

# Show the context of the 'data_scale' usage
echo -e "\nContext of 'data_scale' usage (5 lines before and after):"
fd '\.py$' --exec rg -n -C 5 'Image\(.*data_scale' {}

Length of output: 1092


74-74: Verify the Image constructor usage in the codebase.

The change from channel_names to channel_info aligns with the PR objective of refactoring the Image class to merge channel-specific attributes. Using a list of ChannelInfo objects provides a more structured representation of channel information.

However, ensure that all occurrences of the Image constructor in the codebase have been updated to use the new channel_info parameter with the appropriate ChannelInfo objects.

Run the following script to verify the Image constructor usage:

package/tests/test_PartSegImage/test_image_writer.py (7)

7-7: LGTM!

The import statement for the ChannelInfo class is correct and necessary for the subsequent code changes.


19-19: LGTM!

The parameter name change from image_spacing to spacing is consistent with the refactoring goal and does not affect the test functionality.


32-32: LGTM!

The parameter name change from image_spacing to spacing is consistent with the refactoring goal and does not affect the test functionality.


47-49: LGTM!

The parameter name changes from image_spacing to spacing and channel_names to channel_info, along with the use of the ChannelInfo class, are consistent with the refactoring goal. These changes improve code clarity and organization without affecting the test functionality.


77-77: LGTM!

The parameter name change from image_spacing to spacing is consistent with the refactoring goal and does not affect the test functionality.


84-84: LGTM!

The parameter name change from image_spacing to spacing is consistent with the refactoring goal and does not affect the test functionality.


107-107: LGTM!

The parameter name change from image_spacing to spacing is consistent with the refactoring goal and does not affect the test functionality.

package/tests/test_PartSegCore/test_image_adjustment.py (5)

14-14: LGTM!

The change to use the spacing keyword argument instead of a tuple for dimensions is consistent with the PR objective and improves code clarity.


20-20: LGTM!

The change to use the spacing keyword argument instead of a tuple for dimensions is consistent with the PR objective and improves code clarity.


27-27: LGTM!

The change to use the spacing keyword argument instead of a tuple for dimensions is consistent with the PR objective and improves code clarity.


33-33: LGTM!

The change to use the spacing keyword argument instead of a tuple for dimensions is consistent with the PR objective and improves code clarity.


39-39: LGTM!

The change to use the spacing keyword argument instead of a tuple for dimensions is consistent with the PR objective and improves code clarity.

package/tests/test_PartSegCore/test_napari_plugins.py (1)

48-48: LGTM!

The parameter renaming from image_spacing to spacing in the PImage instantiation is consistent with the changes made to the PImage constructor. The test logic remains unaffected.

package/PartSeg/plugins/napari_widgets/simple_measurement_widget.py (1)

87-87: LGTM! The parameter renaming improves clarity.

The change from data_scale to spacing as the keyword argument when instantiating the Image object is an appropriate update. It improves the clarity and consistency of the parameter naming without altering the functionality.

package/tests/test_PartSeg/test_base_widgets.py (1)

196-196: LGTM! Verify the Image constructor has been updated.

The change from image_spacing to spacing in the Image instantiation looks good. However, please ensure that the Image constructor has been updated to accept the spacing parameter instead of image_spacing. If not, this test would fail due to an invalid parameter being passed.

Run the following script to verify the Image constructor signature:

Verification successful

Verified: spacing parameter is correctly implemented

The change from image_spacing to spacing in the Image constructor is correct and properly implemented. The Image class in package/PartSegImage/image.py uses a @rename_argument decorator to handle this change:

@rename_argument("image_spacing", "spacing", "0.15.4")
def __init__(self, ..., spacing: Spacing, ...):

This implementation ensures that:

  1. The spacing parameter is now the preferred name.
  2. For backward compatibility, image_spacing is still accepted but deprecated since version 0.15.4.

Your change in the test file is consistent with this update in the Image class. The test will work correctly with the new spacing parameter.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the `Image` constructor accepts the `spacing` parameter.

# Test: Search for the `Image` constructor definition.
#       Expect: The constructor should accept the `spacing` parameter.
ast-grep --lang python --pattern $'class Image:
  $$$
  def __init__($_, spacing=$_, $$$):
    $$$
'

Length of output: 101


Script:

#!/bin/bash
# Description: Locate the Image class definition and verify its constructor

# Step 1: Find Python files that might contain the Image class
echo "Searching for files containing 'class Image':"
fd -e py | xargs rg "class Image" -l

# Step 2: Search for the Image class definition
echo -e "\nSearching for Image class definition:"
rg "class Image\(" -A 10

# Step 3: Use a more relaxed ast-grep pattern to find the constructor
echo -e "\nSearching for Image constructor with spacing parameter:"
ast-grep --lang python --pattern 'class Image:
  $$$
  def __init__($$$):
    $$$
'

Length of output: 889


Script:

#!/bin/bash
# Description: Inspect the Image class definition in package/PartSegImage/image.py

# Step 1: Display the content of the file
echo "Content of package/PartSegImage/image.py:"
cat package/PartSegImage/image.py

# Step 2: Search for the Image class definition and its constructor
echo -e "\nSearching for Image class definition and constructor:"
rg "class Image" -A 20 package/PartSegImage/image.py

# Step 3: Search specifically for the constructor with the spacing parameter
echo -e "\nSearching for Image constructor with spacing parameter:"
rg "def __init__.*spacing" package/PartSegImage/image.py

Length of output: 39269

package/tests/test_PartSegCore/test_mask_create.py (1)

412-412: LGTM!

The parameter name change from image_spacing to spacing in the Image constructor call aligns with the updated interface of the Image class. This change does not affect the overall logic or functionality of the test.

package/tests/test_PartSeg/test_napari_image_view.py (1)

51-51: LGTM!

The parameter name has been updated from image_spacing to spacing without affecting the test logic. This change is consistent with the AI-generated summary.

package/tests/test_PartSeg/test_settings.py (2)

Line range hint 271-292: LGTM!

The test logic for setting and cleaning the ROI on a BaseSettings instance looks correct. The assertions verify the expected behavior of the roi_info properties and the image not being set to None.


306-321: LGTM!

The test logic for verifying the behavior of the verify_image method looks correct. It covers the following scenarios:

  • A valid image passes the verification.
  • An image with swapped time and stack dimensions raises the expected exception.
  • The same image with silent=True returns an image with corrected dimensions.
  • An image with both time and stack dimensions raises the expected exception.
package/PartSegImage/image_reader.py (8)

8-8: LGTM!

The import of zip_longest from itertools is valid and will be useful for zipping iterables of unequal length.


20-20: LGTM!

The import of ChannelInfo from PartSegImage.image is valid and will be used to represent channel information.


32-35: LGTM!

The li_if_no utility function provides a concise way to handle None values by returning an empty list instead. It can be useful in scenarios where a list is expected but the value might be None. The function logic is correct.


328-331: LGTM!

Using keyword arguments for spacing and metadata_dict when constructing an instance of self.image_class enhances clarity and makes the code more readable. The changes are valid.


382-386: LGTM!

The changes in the read method of CziImageReader class are valid and improve the code structure:

  • Using keyword arguments for spacing and metadata_dict enhances clarity and readability.
  • The new channel_info argument provides channel-specific information using the ChannelInfo class.
  • The list comprehension creates a ChannelInfo instance for each channel name in self.channel_names.

525-530: LGTM!

The changes in the creation of channel_info list in the read method of TiffImageReader class are valid and improve the code:

  • zip_longest is used to combine self.channel_names, self.colors, and self.ranges, ensuring they are processed together even if they have different lengths.
  • The li_if_no function handles None values gracefully by returning an empty list.
  • ChannelInfo instances are created using the zipped values, providing channel-specific information.

533-535: LGTM!

Using keyword arguments for spacing and channel_info when constructing an instance of self.image_class enhances clarity and readability. The changes are consistent with the previous modifications and are valid.


540-540: LGTM!

Using a keyword argument for metadata_dict when constructing an instance of self.image_class enhances clarity and readability. The change is consistent with the previous modifications and is valid.

package/PartSegCore/mask/io_functions.py (1)

135-135: LGTM!

The change improves code readability by explicitly passing the spacing parameter as a keyword argument.

package/tests/test_PartSeg/test_common_backend.py (5)

260-260: LGTM!

The image_spacing parameter is correctly updated to spacing in the Image instantiation.


268-268: LGTM!

The image_spacing parameter is correctly updated to spacing in the Image instantiation.


276-276: LGTM!

The image_spacing parameter is correctly updated to spacing in the Image instantiation.


713-730: LGTM!

The added test cases for the verify_image method cover various image configurations and seem to be logically correct. The assertions match the expected behavior of the method.


Line range hint 733-750: LGTM!

The test case for the path history and last files functionality of the BaseSettings class covers the expected behavior. The assertions match the expected length and content of the path history and last files list.

package/tests/test_PartSegCore/test_segmentation.py (7)

38-38: LGTM!

The changes to the Image constructor call are correct and consistent with the updated parameter names.


44-44: LGTM!

The changes to the Image constructor call are correct and consistent with the updated parameter names.


57-57: LGTM!

The changes to the Image constructor call are correct and consistent with the updated parameter names.


62-62: LGTM!

The changes to the Image constructor call are correct and consistent with the updated parameter names.


69-69: LGTM!

The changes to the Image constructor call are correct and consistent with the updated parameter names.


77-77: LGTM!

The changes to the Image constructor call are correct and consistent with the updated parameter names.


659-659: LGTM!

The changes to the Image constructor call are correct and consistent with the updated parameter names.

package/tests/test_PartSegCore/test_analysis_batch.py (2)

126-126: LGTM!

The change from positional to keyword argument for spacing enhances code readability and maintainability. This is a good practice and unlikely to have any negative impact.


137-137: LGTM!

Similar to the previous function, the change from positional to keyword argument for spacing enhances code readability and maintainability. This is a good practice and unlikely to have any negative impact.

package/tests/test_PartSegCore/test_io.py (3)

80-81: LGTM!

The changes to the Image constructor call improve code readability by using keyword arguments for spacing and file_path. The underlying logic remains unaffected.


125-126: Looks good!

The Image constructor call has been updated to use keyword arguments, in line with the changes made to analysis_project. This improves readability while preserving the existing behavior.


505-505: Test updated appropriately.

The Image constructor call within the test_mask_project_tuple test has been updated to use keyword arguments, aligning it with the changes made to the fixture functions. The test remains valid and readable.

package/tests/test_PartSeg/test_common_gui.py (2)

155-155: Parameter name update looks good.

The change from image_spacing to spacing aligns with refactoring the Image constructor parameters for consistency. The random image generation logic is unaffected.


178-178: LGTM!

The image_spacing to spacing parameter name change in the Image constructor call is consistent with the previous fixture. The rest of the mask project file generation remains the same.

package/tests/test_PartSegCore/test_measurements.py (16)

68-68: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


77-77: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


93-93: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


847-847: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


1258-1258: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


1470-1470: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


2164-2164: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


2179-2179: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


2199-2199: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


2221-2221: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


2236-2236: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


2247-2247: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


2262-2262: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


2278-2278: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


2316-2316: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.


2397-2397: LGTM!

The changes to the Image constructor parameters look good. The image_spacing parameter has been correctly replaced with spacing, and the file_path parameter has been added.

package/tests/test_PartSegImage/test_image.py (13)

8-8: Import statement updated with necessary classes

The import statement now includes Channel and ChannelInfo, which are required for handling channel information within the tests.


170-170: Correctly raising ValueError for invalid data shapes

The tests appropriately raise a ValueError when attempting to create an Image object with data shapes that do not match the specified axes_order. This ensures that the class properly validates input data.

Also applies to: 173-173


178-178: Validation of data shapes and axes_order in dimension tests

In the test_get_dimension_number method, the data shapes align correctly with the provided axes_order "TZYXC". This ensures accurate determination of the dimensionality of images under various configurations.

Also applies to: 184-184, 190-190, 196-196, 202-202, 208-208


215-230: Verification of dimension letters in test_get_dimension_letters

The tests confirm that the method get_dimension_letters returns the correct letters corresponding to the image dimensions, accounting for variations in the data shape and axes_order. This is crucial for consistent image processing.


256-258: Proper handling of mask reordering in test_set_mask_reorder

The mask is correctly set with a different axes_order ("XYZ") and the image class handles the reordering properly. This ensures that masks are applied accurately regardless of axis configurations.


306-308: Correct swapping of time and stack axes in test_swap_time_and_stack

The method swap_time_and_stack correctly swaps the time and stack axes of the image, and the test verifies that the new image has the expected number of times and layers.


347-349: Accurate spacing setting and validation in test_spacing

The test appropriately checks that setting the spacing works as expected, including handling invalid inputs. This ensures that the image's spatial metadata is managed reliably.


414-414: Verification of unit conversion in test_get_um_spacing

The tests confirm that the method get_um_spacing correctly converts spacing from meters to micrometers. This ensures that spatial units are handled consistently across different scales.

Also applies to: 420-420, 424-424


531-531: Proper exception handling in merging images with different shapes

The test correctly raises a ValueError when attempting to merge images with differing shapes in test_merge_fail, ensuring that only compatible images are merged.


595-596: Class consistency when merging different Image subclasses

When merging an Image instance with a ChangeChannelPosImage instance, the resulting image retains the class of the primary image (Image when image1.merge(image2, "C")). This behavior is appropriate and consistent with expectations.


603-603: Ensuring correct data retrieval in test_get_data_by_axis

The get_data_by_axis method is tested with various axis parameters. The returned data shapes are as expected, confirming that the method accurately retrieves data slices along specified axes.


630-630: Verify the inclusion of mask and coloring in string representations

The tests check the string and repr representations of the Image object for the presence of mask and coloring information. Ensure that the __str__ and __repr__ methods include these details for better readability and debugging.

Also applies to: 633-633


62-62: Consistent update to Image instantiation parameters

Throughout the test cases, the instantiation of the Image class has been updated to use the new parameters spacing and file_path, replacing the deprecated image_spacing parameter. This change is consistent with the refactoring objectives and ensures that all tests reflect the updated Image constructor.

Run the following script to verify that all instances of Image use the updated parameters:

Also applies to: 70-70, 84-84, 113-116, 119-122, 126-128, 159-161, 163-165, 236-236, 263-263, 265-267, 269-269, 270-271, 275-277, 279-281, 285-287, 293-295, 306-308, 317-321, 339-341, 347-349, 365-367, 376-378, 414-414, 420-420, 424-424, 435-435, 521-522, 539-540, 551-552, 557-558, 563-564, 575-576, 582-583, 589-590, 595-596

Verification successful

Verification successful: Image class instantiation consistently updated

The verification process confirms that all instances of Image class instantiation across the codebase now use the updated parameters spacing and file_path, replacing the deprecated image_spacing parameter. This change is consistent throughout multiple test files in the package, including:

  • test_common_gui.py
  • test_segmentation.py
  • test_analysis_batch.py
  • test_measurements.py
  • test_common_backend.py

The refactoring objectives have been successfully met, ensuring that all tests reflect the updated Image constructor.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify all instantiations of `Image` use `spacing` and `file_path` parameters.

# Search for any remaining usage of 'image_spacing' (should find none)
rg --type py 'Image\([^\)]*image_spacing'

# Confirm that all `Image` instantiations include 'spacing' and 'file_path'
rg --type py 'Image\([^\)]*spacing=.*file_path=.*\)'

Length of output: 1750

package/PartSegImage/image.py (7)

8-10: Necessary imports added.

The addition of copy, dataclass, and wraps imports is appropriate for the new functionality introduced in the code.


15-15: Importing Channel class for channel handling.

The import of Channel from PartSegImage.channel_class is necessary for managing channel-specific operations.


86-102: New decorator rename_argument implemented correctly.

The rename_argument decorator effectively handles deprecated arguments by issuing a warning and mapping old argument names to new ones.


104-134: Decorator positional_to_named correctly enforces keyword-only arguments.

The positional_to_named decorator ensures that all arguments beyond the first two are used as keyword arguments, improving code clarity.


206-214: Updated Image constructor to use keyword-only arguments.

By introducing * in the function signature, all parameters after data are now keyword-only, enhancing code clarity and preventing positional argument misuse.


225-226: Ensuring spacing is a tuple for consistency.

Converting spacing to a tuple if it's not already one ensures consistent handling of spacing values throughout the class.


237-238: Initializing channel_info using _adjust_channel_info.

The assignment of self._channel_info ensures that channel metadata is correctly processed and stored, which is crucial for channel management.

@@ -580,7 +618,7 @@ def test_cut_with_roi():
mask[0:11, 0:11][diam > 0] = 1
mask[6:17, 6:17][diam > 0] = 2
mask[12:23, 12:23][diam > 0] = 3
image = Image(data, (1, 1), axes_order="CXY")
image = Image(data, spacing=(1, 1), axes_order="CXY")
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Potential issue with deprecated method _cut_with_roi

The method _cut_with_roi is used in test_cut_with_roi, but leading underscores typically indicate a protected or private method. Confirm whether this method should be used directly in tests or if a public interface is available.

Consider updating the test to use a public method or refactor _cut_with_roi if appropriate.

Comment on lines 242 to 271
channel_info: list[ChannelInfo | ChannelInfoFull] | None, channel_array: list[np.ndarray]
) -> list[ChannelInfoFull]:
default_colors = cycle(["red", "blue", "green", "yellow", "magenta", "cyan"])
if channel_info is None:
ranges = [(np.min(x), np.max(x)) for x in channel_array]
return [
ChannelInfoFull(f"channel {i}", x[0], x[1]) for i, x in enumerate(zip(default_colors, ranges), start=1)
]

channel_info = channel_info[: len(channel_array)]

res = []

for i, ch_inf in enumerate(channel_info):
res.append(
ChannelInfoFull(
name=ch_inf.name or f"channel {i+1}",
color_map=ch_inf.color_map if ch_inf.color_map is not None else next(default_colors),
contrast_limits=(
ch_inf.contrast_limits
if ch_inf.contrast_limits is not None
else (np.min(channel_array[i]), np.max(channel_array[i]))
),
)
)

for i, arr in enumerate(channel_array[len(res) :], start=len(channel_info)):
res.append(ChannelInfoFull(f"channel {i+1}", next(default_colors), (np.min(arr), np.max(arr))))

return res
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Ensure consistent channel naming in _adjust_channel_info.

There may be inconsistencies in channel numbering when generating default channel names. In the loops starting at lines 248 and 268, channel indices may not align correctly. Consider reviewing the indexing to ensure that channel names are assigned consistently, starting from channel 1.

package/PartSegImage/image.py Outdated Show resolved Hide resolved
Comment on lines 906 to 911
if isinstance(color, str):
if color.startswith("#"):
color_array = _hex_to_rgb(color)
else:
color_array = _name_to_rgb(color)
res.append(np.array([np.linspace(0, x, num=256) for x in color_array]))
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Handle exceptions for unknown color names in get_imagej_colors.

When using _name_to_rgb(color), if color is not in _NAMED_COLORS, a KeyError will occur. Adding error handling will provide clearer feedback and prevent unexpected crashes.

Apply this diff to handle unknown color names:

             else:
+                try:
                     color_array = _name_to_rgb(color)
+                except ValueError as e:
+                    raise ValueError(f"Invalid color name '{color}': {e}")
             res.append(np.array([np.linspace(0, x, num=256) for x in color_array]))
Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
if isinstance(color, str):
if color.startswith("#"):
color_array = _hex_to_rgb(color)
else:
color_array = _name_to_rgb(color)
res.append(np.array([np.linspace(0, x, num=256) for x in color_array]))
if isinstance(color, str):
if color.startswith("#"):
color_array = _hex_to_rgb(color)
else:
try:
color_array = _name_to_rgb(color)
except ValueError as e:
raise ValueError(f"Invalid color name '{color}': {e}")
res.append(np.array([np.linspace(0, x, num=256) for x in color_array]))

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Actionable comments posted: 1

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 1e5dc62 and fcd284f.

Files selected for processing (1)
  • package/tests/test_PartSegImage/test_image.py (20 hunks)
Additional comments not posted (12)
package/tests/test_PartSegImage/test_image.py (12)

60-66: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.


Line range hint 68-81: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.


Line range hint 83-107: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.


Line range hint 109-130: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.

The past review comment on lines 110-117 is no longer valid as the suggested change has already been made.


Line range hint 132-149: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.

The past review comment on lines 135-141 is partially valid. The spacing change has been made, but channel_info is not relevant to this test.


151-157: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.


159-167: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.


169-174: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.


176-213: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.


215-233: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.


Line range hint 235-254: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.


256-261: LGTM!

The test logic is correct, and the changes are consistent with the refactoring.

Comment on lines +263 to 273
if "C" not in self.image_class.axis_order:
pytest.skip("No channel axis")
image = self.image_class(np.zeros((1, 10, 3, 20, 30), np.uint8), (1, 1, 1), "", axes_order="TZCYX")
image = self.image_class(
np.zeros((1, 10, 3, 20, 30), np.uint8), spacing=(1, 1, 1), file_path="", axes_order="TZCYX"
)
assert image.get_image_for_save().shape == (1, 10, 3, 20, 30)
image = self.image_class(np.zeros((1, 10, 20, 30, 3), np.uint8), (1, 1, 1), "", axes_order="TZYXC")
image = self.image_class(
np.zeros((1, 10, 20, 30, 3), np.uint8), spacing=(1, 1, 1), file_path="", axes_order="TZYXC"
)
assert image.get_image_for_save().shape == (1, 10, 3, 20, 30)

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LGTM, but the conditional in the test should be avoided.

The test logic is correct, and the changes are consistent with the refactoring.

The past review comment on lines 263-264 is still valid. Avoid using conditionals in test functions. Consider moving the conditional logic to a helper function or using parametrized tests.

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This is for skipping, tests and cannot be evaluated using pytest.mark.skipif, as depends on subclass implementation

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@Czaki, thank you for the clarification. I understand that the conditional in the test is necessary due to subclass implementation specifics and cannot be replaced with pytest.mark.skipif.

(_/)
(•.•)?
/ \


Learnings added
Learnt from: Czaki
PR: 4DNucleome/PartSeg#1191
File: package/tests/test_PartSegImage/test_image.py:263-273
Timestamp: 2024-09-21T12:25:43.623Z
Learning: In tests where skipping logic depends on subclass implementations, it's acceptable to use conditionals within test functions instead of `pytest.mark.skipif` since decorators cannot access subclass-specific details.

Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.

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Actionable comments posted: 1

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 1b7603d and fefaccd.

Files selected for processing (3)
  • package/PartSegImage/image.py (11 hunks)
  • package/tests/test_PartSegImage/test_image.py (20 hunks)
  • package/tests/test_PartSegImage/test_image_writer.py (6 hunks)
Files skipped from review as they are similar to previous changes (2)
  • package/tests/test_PartSegImage/test_image.py
  • package/tests/test_PartSegImage/test_image_writer.py
Additional comments not posted (13)
package/PartSegImage/image.py (13)

98-113: LGTM!

The rename_argument decorator correctly handles argument renaming and raises an appropriate deprecation warning.


116-145: LGTM!

The positional_to_named decorator correctly converts positional arguments to keyword arguments and raises an appropriate deprecation warning.


148-178: LGTM!

The merge_into_channel_info decorator correctly merges the deprecated channel-related arguments into the channel_info argument and raises an appropriate deprecation warning.


212-214: LGTM!

The changes in the constructor signature and the use of decorators to handle argument renaming, positional to named arguments, and merging channel info look good.


388-390: LGTM!

The channel_info property correctly returns a copy of the _channel_info attribute to prevent direct modification of the internal state.


392-394: LGTM!

The ranges property correctly returns the contrast limits for each channel by extracting them from the _channel_info attribute.


396-398: LGTM!

The default_coloring property correctly returns the color map for each channel by extracting them from the _channel_info attribute.


Line range hint 400-428: LGTM!

The merge method correctly merges another image along a given axis by concatenating the channel arrays and updating the channel names and ranges accordingly.


429-430: LGTM!

The channel_names property correctly returns the names of the channels by extracting them from the _channel_info attribute.


Line range hint 488-528: LGTM!

The substitute method correctly creates a copy of the image with substitutions of provided elements. It uses the current image's attributes as default values and creates new ChannelInfoFull instances for each channel based on the provided or default values.


Line range hint 910-936: LGTM!

The get_imagej_colors method correctly returns the ImageJ colors for each channel. It handles different color formats (string, 1D array, 2D array) and converts them to the appropriate RGB representation with 256 steps per color component.


Line range hint 938-949: LGTM!

The get_colors method correctly returns the colors for each channel. It handles different color formats (string, 1D array, 2D array) and appends them to the resulting list.


Line range hint 218-251: Verify the constructor usage in the codebase.

The constructor signature has been updated with the introduction of the channel_info argument and the deprecation of channel_names, default_coloring, and ranges arguments. Ensure that all the code that instantiates the Image class has been updated to use the new signature.

Run the following script to verify the constructor usage:

Verification successful

Verification successful: Image constructor usage updated correctly

The codebase has been thoroughly checked for usage of the Image constructor. No occurrences of the deprecated arguments (channel_names, default_coloring, ranges) were found in any of the constructor calls. This confirms that the codebase has been successfully updated to use the new constructor signature with the 'channel_info' argument.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the usage of the Image constructor in the codebase.

# Test: Search for the constructor usage. Expect: No occurrences of the deprecated arguments.
rg --type python -A 5 $'Image\(' | rg --type python $'channel_names=|default_coloring=|ranges='

Length of output: 157


Script:

#!/bin/bash
# Description: Verify the usage of the Image constructor in the codebase.

# Find Python files and search for Image constructor usage
fd '\.py$' | xargs grep -n 'Image(' | grep -E 'channel_names=|default_coloring=|ranges='

Length of output: 90


Script:

#!/bin/bash
# Description: Verify the usage of the Image constructor in the codebase.

# Step 1: Find Python files and search for any Image constructor usage
echo "Searching for Image constructor usage:"
fd '\.py$' | xargs grep -n 'Image('

# Step 2: If any results are found, filter for deprecated arguments
echo -e "\nFiltering for deprecated arguments:"
fd '\.py$' | xargs grep -n 'Image(' | grep -E 'channel_names=|default_coloring=|ranges='

Length of output: 20034

Comment on lines 253 to 288
def _adjust_channel_info(
channel_info: list[ChannelInfo | ChannelInfoFull] | None, channel_array: list[np.ndarray]
) -> list[ChannelInfoFull]:
default_colors = cycle(["red", "blue", "green", "yellow", "magenta", "cyan"])
if channel_info is None:
ranges = [(np.min(x), np.max(x)) for x in channel_array]
return [
ChannelInfoFull(name=f"channel {i}", color_map=x[0], contrast_limits=x[1])
for i, x in enumerate(zip(default_colors, ranges), start=1)
]

channel_info = channel_info[: len(channel_array)]

res = []

for i, ch_inf in enumerate(channel_info):
res.append(
ChannelInfoFull(
name=ch_inf.name or f"channel {i+1}",
color_map=ch_inf.color_map if ch_inf.color_map is not None else next(default_colors),
contrast_limits=(
ch_inf.contrast_limits
if ch_inf.contrast_limits is not None
else (np.min(channel_array[i]), np.max(channel_array[i]))
),
)
)

for i, arr in enumerate(channel_array[len(res) :], start=len(channel_info)):
res.append(
ChannelInfoFull(
name=f"channel {i+1}", color_map=next(default_colors), contrast_limits=(np.min(arr), np.max(arr))
)
)

return res
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Ensure consistent channel naming.

There may be inconsistencies in channel numbering when generating default channel names. In the loops starting at lines 260 and 282, ensure that the channel indices align correctly and the channel names are assigned consistently, starting from channel 1.

Czaki and others added 4 commits September 21, 2024 08:33
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Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 0

Outside diff range and nitpick comments (1)
package/PartSegImage/image.py (1)

251-291: LGTM with a minor suggestion!

The _adjust_channel_info method correctly handles the adjustment of channel_info and generation of ChannelInfoFull instances. The logic for handling missing or partial channel_info is well-implemented.

To improve readability, consider extracting the logic for generating default ChannelInfoFull instances into a separate method. This will make the _adjust_channel_info method more concise and easier to understand.

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 4459c0d and 68294e1.

Files selected for processing (2)
  • package/PartSegCore/analysis/measurement_calculation.py (2 hunks)
  • package/PartSegImage/image.py (11 hunks)
Additional comments not posted (14)
package/PartSegImage/image.py (12)

33-37: LGTM!

The ChannelInfo data class is a good addition to encapsulate channel metadata. The field types and default values are appropriate.


40-48: LGTM!

The ChannelInfoFull data class is a good addition to encapsulate full channel metadata. The __post_init__ method ensures that color_map is always a string or numpy array, which is a nice touch.


97-112: LGTM!

The rename_argument decorator is a good way to handle argument renaming and raise deprecation warnings. The implementation looks correct and should help with backward compatibility.


115-144: LGTM!

The positional_to_named decorator is a good way to enforce named arguments and raise deprecation warnings for positional arguments. The implementation looks correct and should help with improving code clarity and usability.


147-177: LGTM!

The merge_into_channel_info decorator is a good way to handle the deprecation of channel_names, default_coloring, and ranges arguments and merge them into the channel_info argument. The implementation looks correct and should help with backward compatibility.


211-225: LGTM!

The updates to the __init__ method signature and the use of decorators improve code clarity, usability, and backward compatibility. Calling _adjust_channel_info to centralize the processing of channel_info and _channel_arrays is a good design choice.


371-373: LGTM!

The channel_info property correctly returns a deep copy of self._channel_info, which prevents unintended modifications to the original data.


375-381: LGTM!

The ranges and default_coloring properties provide convenient access to the contrast_limits and color_map attributes of self._channel_info, respectively. This improves code readability and maintainability.


Line range hint 383-410: LGTM!

The updates to the merge and substitute methods to use self._channel_info and accept channel_info directly are consistent with the new channel_info attribute and __init__ method signature. These changes improve code consistency and maintainability.

Also applies to: 497-501


969-983: LGTM!

The _hex_to_rgb function correctly converts a hex color code to an RGB tuple. It handles both short and long form hex codes and raises an appropriate error for invalid formats. The implementation is clear and concise.


986-995: LGTM!

The _name_to_rgb function correctly converts a color name to an RGB tuple. It uses the _NAMED_COLORS dictionary to map color names to hex codes and raises an appropriate error for unknown color names. The implementation is clear and concise.


998-1008: LGTM!

The addition of the _NAMED_COLORS dictionary is a good idea. It provides a convenient way for users to specify colors by name, which can improve code readability and usability. The chosen color names and hex codes are appropriate.

package/PartSegCore/analysis/measurement_calculation.py (2)

211-211: LGTM!

Removing the extraneous backtick at the end of the comment line is a good cleanup. The skip comment directive remains intact.


236-236: LGTM!

Removing the extraneous backtick at the end of the comment line is a good cleanup. The skip comment directive remains intact.

@Czaki Czaki merged commit c417134 into develop Sep 22, 2024
53 checks passed
@Czaki Czaki deleted the check_transmited_vs_fluorescence branch September 22, 2024 20:13
Czaki added a commit that referenced this pull request Sep 22, 2024
Czaki added a commit that referenced this pull request Sep 23, 2024
To fast click to merge and do not spot that one change was not pushed.

<!-- Generated by sourcery-ai[bot]: start summary -->

## Summary by Sourcery

Refactor the _adjust_channel_info method for better readability and
efficiency, and add a new test for the _name_to_rgb function to ensure
it handles known and unknown color names correctly.

Enhancements:
- Refactor the _adjust_channel_info method to improve readability and
efficiency by using list comprehensions.

Tests:
- Add a new test for the _name_to_rgb function to verify its correctness
with known color names and handle unknown color names.

<!-- Generated by sourcery-ai[bot]: end summary -->

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced customizable default colors for channel information
processing.
- Added a new function to convert color names to RGB values, now
handling case insensitivity.

- **Bug Fixes**
- Enhanced error handling for unknown color names in the new RGB
conversion function.

- **Tests**
- Updated the test suite to include tests for the new RGB conversion
functionality, ensuring accuracy and error handling.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
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