feat: Add visualization module with environment detection for Jupyter notebooks #223
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In old version, bounding box was a single voxel. Now is expanded to at least the minimum dimension default. - **New Features** - Now, users can optionally specify a desired size when generating image bounding boxes for enhanced control. - **Chores** - Updated the software version from 1.21.1 to 1.22.0.
…method to Scan class for improved string representation
…g and error messages
In old version, bounding box was a single voxel. Now is expanded to at least the minimum dimension default. - **New Features** - Now, users can optionally specify a desired size when generating image bounding boxes for enhanced control. - **Chores** - Updated the software version from 1.21.1 to 1.22.0.
… in an image (#221) This works the same way as `_adjust_negative_coordinates`, but requires the image as an addition input and modifies the RegionBox object directly. A message is logged in the debugger if a dimension is adjusted. I also updated the `crop_image` function to call this before applying the crop.
…notebooks (future feature)
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Actionable comments posted: 0
🧹 Nitpick comments (7)
src/imgtools/vizualize/visualizer.py (5)
33-34: Consider adding a class-level docstring.While the methods in
ImageSlicesare reasonably documented, a brief class-level docstring would improve clarity about its overall purpose.
37-42: Clarify dictionary keys in thefrom_dictmethod.Here, you convert the
dict[tuple[int, int], Image.Image]into a sorted list of images, but the significance of thetuple[int, int]keys is not immediately clear from the docstring. A brief explanation would help future maintainers understand their meaning and sorting logic.
73-75: Class docstring references mask overlay color incorrectly.The docstring says the mask is overlaid in red, but the
_generate_slicemethod actually uses the green channel to display the mask. Please update the docstring or the overlay color to keep them consistent.- """Generates 2D slices from a 3D SimpleITK image and optionally overlays a mask.""" + """Generates 2D slices from a 3D SimpleITK image and optionally overlays a green mask."""
185-186: Remove or update reference to metadata text.The docstring mentions "metadata text in the bottom right corner," but no text is drawn. You might consider removing this statement or implementing the metadata overlay.
343-349: Unused variablesz.The logic here conditionally assigns
szbased ondim, but immediately overwrites it withSize3D(new_size, new_size, new_size)on line 349 without further usage. This might be leftover code.- if dim == 0: - sz = Size3D(new_size, new_size, 0) - elif dim == 1: - sz = Size3D(new_size, 0, new_size) - sz = Size3D(new_size, new_size, new_size)src/imgtools/vizualize/__init__.py (1)
1-14: Add a brief module-level docstring.A short explanation of the module’s purpose, such as how it ties
utilsandvisualizertogether, will enhance readability and maintainability.src/imgtools/vizualize/utils.py (1)
5-23: Reflect QtConsole detection in enum usage.The docstring mentions a
JUPYTER_QTCONSOLEenvironment type, but the code does not explicitly differentiate QtConsole from standard Jupyter Notebook. Consider adjusting the detection logic or updating the docstring to avoid confusion.
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src/imgtools/vizualize/__init__.py(1 hunks)src/imgtools/vizualize/utils.py(1 hunks)src/imgtools/vizualize/visualizer.py(1 hunks)
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`src/**/*.py`: Review the Python code for compliance with PE...
src/**/*.py: Review the Python code for compliance with PEP 8 and PEP 257 (docstring conventions). Ensure the following: - Variables and functions follow meaningful naming conventions. - Docstrings are present, accurate, and align with the implementation. - Code is efficient and avoids redundancy while adhering to DRY principles. - Consider suggestions to enhance readability and maintainability. - Highlight any potential performance issues, edge cases, or logical errors. - Ensure all imported libraries are used and necessary.
src/imgtools/vizualize/utils.pysrc/imgtools/vizualize/__init__.pysrc/imgtools/vizualize/visualizer.py
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🔇 Additional comments (3)
src/imgtools/vizualize/visualizer.py (2)
1-2: Good top-level docstring.This concise top-level docstring accurately summarizes the file's purpose and functionality.
131-134: Validate the slice dimension to prevent IndexErrors.While the docstring states the dimension should be 0, 1, or 2, there is no explicit check, so passing invalid values (like 3) would cause out-of-bounds issues. Consider adding a validation check.
+ if dim not in (0, 1, 2): + raise ValueError(f"Invalid dimension {dim}. Must be 0, 1, or 2.")src/imgtools/vizualize/utils.py (1)
5-65: Good coverage of environment detection logic.The structured approach to detect IPython-related environments and fall back to standard Python is clear and comprehensive. Nicely done!
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## development #223 +/- ##
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Coverage 63.33% 63.33%
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Files 52 52
Lines 3758 3758
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Hits 2380 2380
Misses 1378 1378 ☔ View full report in Codecov by Sentry. |
…interaction refactor: update import path for get_modality_metadata function
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