- Jan 20, 2025
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LEGRAND Jonathan authored
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LEGRAND Jonathan authored
Enhanced the multi-angle image fusion script with improved argument descriptions, a more robust transformation computation using indexed dictionaries, and refined logging for clarity. Removed redundant code for image reordering, streamlining the function to default behaviors where applicable.
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LEGRAND Jonathan authored
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LEGRAND Jonathan authored
Revised the example code to ensure `flo_points` and `ref_points` are explicitly converted to numpy arrays.
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LEGRAND Jonathan authored
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LEGRAND Jonathan authored
Simplify and streamline initial transformation computations by refining logic for rigid registrations. Added logging to clarify usage of provided or updated transformations.
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LEGRAND Jonathan authored
Standardized logger parameter descriptions in multiple files to improve readability and consistency
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LEGRAND Jonathan authored
Provide detailed documentation for the `_integer_indexed_json` function, explaining its purpose, parameters, return values, and behavior.
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LEGRAND Jonathan authored
Enhanced `compute_rigid_initial_trsf` to handle the shortest path composition and improved transformation refinement. Introduced `rigid_iso_blockmatching` for streamlined isometric rigid block matching with detailed parameter validation.
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LEGRAND Jonathan authored
Ensure the `list_trsf` parameter is not empty and is a proper list of `Trsf` objects. This improves robustness by catching invalid inputs early and providing clear error messages.
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- Jan 17, 2025
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Jonathan Legrand authored
Provide a brief summary of the `algorithm` module, highlighting its tools for image enhancement, transformation, and feature extraction.
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Jonathan Legrand authored
Standardize type annotations in parameter docstrings by replacing `Path` with `pathlib.Path` for clarity and consistency across modules. Also, remove an unnecessary blank line in a test file to improve formatting.
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Jonathan Legrand authored
Updated type annotations to modern Python conventions (e.g., `list[Type]`) across multiple modules. This improves code readability and compliance with newer Python standards, ensuring consistent type hinting throughout the project.
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Jonathan Legrand authored
Updated all docstring type annotations to consistently use `timagetk` module class names (e.g., `timagetk.SpatialImage`, `timagetk.LabelledImage`). Corrected minor typos in explanations and improved readability in certain sections.
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Jonathan Legrand authored
Eliminated unnecessary blank lines within docstring sections across multiple files.
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Jonathan Legrand authored
Updated clustering-related imports to use `clustering_estimators` for clarity and organization. Standardized terminology to British English (e.g., "visualization" → "visualisation", "labeled" → "labelled") across the project for consistency.
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Jonathan Legrand authored
Expanded and detailed module docstrings across various algorithms, including watershed, linear filtering, peak detection, and quaternion transformations. Added usage examples, key functionalities, and improved descriptions for better usability and clarity in image processing workflows.
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Jonathan Legrand authored
Moved core clustering metric functions (e.g., diameters, separation, global distances) from `clustering.py` to a new `clustering_estimators.py` module. This change improves code organization.
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- Jan 16, 2025
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Jonathan Legrand authored
Replaced `only` with `rules` for greater flexibility and streamlined branch-specific execution logic. Removed unused jobs and redundant platform conversions, added retry logic for documentation builds, and optimized upload scripts to target the `noarch` package.
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Jonathan Legrand authored
Previously, the identity transformation was always removed. This change ensures that it is only removed when `fuse_reference` is set, aligning the behavior with the intended logic.
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Jonathan Legrand authored
New test cases validate the `fusion_on_reference` and `iterative_fusion` methods, covering both low-resolution and super-resolution scenarios. Updated an existing test to correct the directional edges in the transformation graph.
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Jonathan Legrand authored
Enhanced the image fusion module by adding support for reference image selection and robust handling of transformation graphs. Refined parameter descriptions, error handling, and added new examples to illustrate diverse use cases. This update facilitates more precise and flexible image fusion workflows.
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Jonathan Legrand authored
Adjusted copyright range from 2022 to 2018-2025 in all headers.
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Jonathan Legrand authored
Introduce detailed docstring to describe functionalities and datasets available in the shared data module. Includes descriptions and access links for experimental and synthetic datasets hosted on Zenodo. Enhances module clarity for biological research use cases.
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Jonathan Legrand authored
Update function parameter types, return types, and descriptions to enhance clarity and consistency in the `trsf.py` module. Improved docstrings for better readability and alignment with the `timagetk` framework. Removed unnecessary optional tags.
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Jonathan Legrand authored
Enhanced `Trsf` class documentation with clearer attribute definitions, consistent method behavior, and expanded examples for key functionalities. Updated module and class docstrings to better explain core concepts, usage scenarios, and supported transformation types.
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Jonathan Legrand authored
Updated `get_pne` to account for files without directories, handle missing or multiple extensions more robustly, and provide clearer warnings.
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Jonathan Legrand authored
Updated the return type annotation to include dict[pathlib.Path], ensuring accurate documentation of the method's output.
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Jonathan Legrand authored
Introduce `guess_delimiter` to identify the most frequent delimiter in a filename and `find_common_segments` to extract shared segments from a list of filenames. These utilities enhance filename parsing and processing, especially for cases with structured naming conventions.
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Jonathan Legrand authored
Reorganized data entries into ZENODO_RECORDS and LOCAL_RECORDS for clarity and modularity. Added descriptive metadata as comments for each dataset. Unified DATA_REGISTRY to combine ZENODO and LOCAL entries, and fixed casing in synthetic registry reference.
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- Jan 15, 2025
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LEGRAND Jonathan authored
Introduces tests for `initial_transformation_graph` and `check_all_nodes_connected_to_reference` methods. These validate node creation, graph connections, and edge cases like empty or improperly connected graphs.
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LEGRAND Jonathan authored
Updated image fusion tasks to handle dictionaries of images and transformations instead of lists, leveraging transformation graphs for improved flexibility. Added support for refining transformations, checking graph connectivity, and computing rigid transformations. Updated docstrings and examples for clarity and additional use cases.
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LEGRAND Jonathan authored
Renamed `registry` to `DATA_REGISTRY` across the codebase for clarity and consistency. Improved URL file handling by adding proper filename extraction and ensuring hash validation support in `_image_from_url`. Updated function examples and docstrings to reflect these changes.
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- Jan 14, 2025
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Jonathan Legrand authored
Added checks to verify conda installation and handle build failures gracefully. Updated the build script for noarch packaging and adjusted cleanup logic to prevent accidental deletions Applied `noarch: python` to simplify distribution across platforms.
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Jonathan Legrand authored
Restructured the developer installation guide to provide clear, step-by-step instructions, including a quick setup section and a detailed version. Improved formatting, added explanations for dependencies, and clarified the installation process for `timagetk` and related packages.
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Jonathan Legrand authored
Updated the Python dependency to a fixed version (3.10) in both `timagetk_dev.yaml` and `timagetk.yaml` environment files. This ensures consistency and resolves any potential compatibility issues.
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Jonathan Legrand authored
Standardize the syntax for `pip install` commands by enclosing the `[all]` option in single quotes. This ensures compatibility across different shells and improves clarity in installation instructions.
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Jonathan Legrand authored
This change aligns with the updated API usage.
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Jonathan Legrand authored
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Jonathan Legrand authored
The `ctrl` package has been removed from the `timagetk` environment file and related installation instructions.
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