AFM-SPM/TopoStats
Sep 2024 – May 2026
12 Months active
Languages Used
PythonMarkdownNumPyBinaryYAMLpythonyamlCSV
Technical Skills
PythonPython programmingdata analysismathematicsscientific computingtesting
SylviaWhittle
PROFILE
Sylviawhittle
Over two years, contributed to AFM-SPM/TopoStats by building and refining a robust grain analysis and image processing pipeline. Developed features for multi-class segmentation, configurable thresholding, and dynamic cropping, while maintaining backward compatibility and improving test coverage. Leveraged Python, NumPy, and Pandas to implement data validation, modular design, and efficient tensor manipulation. Enhanced the command-line interface for user configurability and streamlined configuration management. Focused on code clarity, maintainability, and documentation, enabling reliable deployment and easier onboarding. Regularly addressed bugs, refactored core modules, and updated documentation to align with evolving requirements, ensuring the repository remains stable and adaptable for scientific workflows.
Overall Statistics
Feature vs Bugs
56%Features
Repository Contributions
353Total
Bugs
78
Commits
353
Features
101
Lines of code
2,502,299
Activity Months12
Your Network
10 peopleWork History
May 2026
2 Commits • 1 Features
May 1, 2026May 2026 focused on removing the height profile extraction feature from grain statistics processing in TopoStats (AFM-SPM/TopoStats). Completed removal of the feature and related deprecated references, cleaned up configurations and tests, and updated documentation to reflect the change. This reduces maintenance surface and aligns the repository with the current roadmap.
2 Commits • 1 Features
May 1, 2026May 2026 focused on removing the height profile extraction feature from grain statistics processing in TopoStats (AFM-SPM/TopoStats). Completed removal of the feature and related deprecated references, cleaned up configurations and tests, and updated documentation to reflect the change. This reduces maintenance surface and aligns the repository with the current roadmap.
May 2026
April 2026
5 Commits • 2 Features
Apr 1, 2026In April 2026, AFM-SPM/TopoStats advanced maintainability, onboarding, and predictability through documentation enhancements and project scaffolding. The work emphasized Python 3.10 compatibility, clearer configuration guidance, and code cleanliness, laying groundwork for faster feature delivery and lower support overhead.
April 2026
5 Commits • 2 Features
Apr 1, 2026In April 2026, AFM-SPM/TopoStats advanced maintainability, onboarding, and predictability through documentation enhancements and project scaffolding. The work emphasized Python 3.10 compatibility, clearer configuration guidance, and code cleanliness, laying groundwork for faster feature delivery and lower support overhead.
June 2025
3 Commits • 1 Features
Jun 1, 2025June 2025 monthly summary for AFM-SPM/TopoStats focused on delivering user-facing improvements, loader robustness, and documentation accuracy. The team shipped a new grain image cropping option, hardened backward compatibility with legacy Bruker file extensions, and maintained quality through targeted tests and clear docs. These efforts reduce processing errors, improve workflow control for grain analysis, and strengthen maintainability for upcoming releases.
3 Commits • 1 Features
Jun 1, 2025June 2025 monthly summary for AFM-SPM/TopoStats focused on delivering user-facing improvements, loader robustness, and documentation accuracy. The team shipped a new grain image cropping option, hardened backward compatibility with legacy Bruker file extensions, and maintained quality through targeted tests and clear docs. These efforts reduce processing errors, improve workflow control for grain analysis, and strengthen maintainability for upcoming releases.
June 2025
May 2025
25 Commits • 10 Features
May 1, 2025May 2025 performance summary for AFM-SPM/TopoStats. Focused on delivering configurable model behavior, strengthening data preprocessing, and expanding test coverage to improve reliability, maintainability, and business value across the pipeline.
May 2025
25 Commits • 10 Features
May 1, 2025May 2025 performance summary for AFM-SPM/TopoStats. Focused on delivering configurable model behavior, strengthening data preprocessing, and expanding test coverage to improve reliability, maintainability, and business value across the pipeline.
April 2025
78 Commits • 14 Features
Apr 1, 2025April 2025 focused on delivering high-value features, improving configurability, and strengthening code quality for AFM-SPM/TopoStats. Key work included introducing multi_class_thresholding with accompanying tests and config to support multi-class behavior (including class merges and thresholds initialization fixes), expanding threshold configuration (adding whole_grain_size_thresholds and renaming absolute_area_thresholds to area_thresholds) with robust list-based initialization, and extensive code cleanup that re-added the regionprops wrapper. Plotting structure and run_grains logging were revamped for better traceability, while the test suite and fixtures were stabilized (including minicircle fixtures overhaul and removal of deprecated tests), enhancing CI reliability. These changes collectively improve measurement accuracy, configurability, and maintainability, accelerating reliable deployment of advanced grain analysis features across projects.
78 Commits • 14 Features
Apr 1, 2025April 2025 focused on delivering high-value features, improving configurability, and strengthening code quality for AFM-SPM/TopoStats. Key work included introducing multi_class_thresholding with accompanying tests and config to support multi-class behavior (including class merges and thresholds initialization fixes), expanding threshold configuration (adding whole_grain_size_thresholds and renaming absolute_area_thresholds to area_thresholds) with robust list-based initialization, and extensive code cleanup that re-added the regionprops wrapper. Plotting structure and run_grains logging were revamped for better traceability, while the test suite and fixtures were stabilized (including minicircle fixtures overhaul and removal of deprecated tests), enhancing CI reliability. These changes collectively improve measurement accuracy, configurability, and maintainability, accelerating reliable deployment of advanced grain analysis features across projects.
April 2025
March 2025
14 Commits • 3 Features
Mar 1, 2025March 2025: Summary focused on delivering business value through TopoStats improvements in three core areas: U-Net integration, thresholding modernization, and grains processing vetting. Deliverables include clearer TensorFlow model usage/docs and a new remove_disconnected_grains option; a modernized thresholding framework supporting lists, multi-threshold processing, and None bounds with new thresholding tensors; and a grains processing overhaul with enhanced vetting, border handling, and storage organization. These changes enable more robust, scalable segmentation, cleaner data, and more efficient workflows for downstream analytics.
March 2025
14 Commits • 3 Features
Mar 1, 2025March 2025: Summary focused on delivering business value through TopoStats improvements in three core areas: U-Net integration, thresholding modernization, and grains processing vetting. Deliverables include clearer TensorFlow model usage/docs and a new remove_disconnected_grains option; a modernized thresholding framework supporting lists, multi-threshold processing, and None bounds with new thresholding tensors; and a grains processing overhaul with enhanced vetting, border handling, and storage organization. These changes enable more robust, scalable segmentation, cleaner data, and more efficient workflows for downstream analytics.
February 2025
32 Commits • 11 Features
Feb 1, 2025February 2025 focused on strengthening reliability and widening capabilities in AFM-SPM/TopoStats. Delivered a robust GrainCrop validation flow, comprehensive test coverage for grain crops and full mask tensors, and a major GrainCrop refactor to validate on construction with support for non-square images. Cleaned and hardened codebase with linting, test stability fixes, and logical cleanups across processing, grainstats, and tracing modules. Updated topostats to store full mask tensors and enhanced documentation and config options. These actions improved CI reliability, data integrity for tensor-based analyses, and overall business value of the grain statistics pipeline.
32 Commits • 11 Features
Feb 1, 2025February 2025 focused on strengthening reliability and widening capabilities in AFM-SPM/TopoStats. Delivered a robust GrainCrop validation flow, comprehensive test coverage for grain crops and full mask tensors, and a major GrainCrop refactor to validate on construction with support for non-square images. Cleaned and hardened codebase with linting, test stability fixes, and logical cleanups across processing, grainstats, and tracing modules. Updated topostats to store full mask tensors and enhanced documentation and config options. These actions improved CI reliability, data integrity for tensor-based analyses, and overall business value of the grain statistics pipeline.
February 2025
January 2025
66 Commits • 13 Features
Jan 1, 2025January 2025 monthly summary for AFM-SPM/TopoStats focusing on data model enhancements, test infrastructure, pipeline robustness, and visualization improvements. The team delivered notable features, stabilized test fixtures, and fixed critical regressions to support reliable, scalable analysis workflows.
January 2025
66 Commits • 13 Features
Jan 1, 2025January 2025 monthly summary for AFM-SPM/TopoStats focusing on data model enhancements, test infrastructure, pipeline robustness, and visualization improvements. The team delivered notable features, stabilized test fixtures, and fixed critical regressions to support reliable, scalable analysis workflows.
December 2024
10 Commits • 3 Features
Dec 1, 2024In 2024-12, delivered targeted improvements to TopoStats: enhanced disordered tracing and grain processing configuration, hardened grain crop data pipeline, refactored GrainCrop validation, and expanded topostats analytics for grain crops. These changes improve trace accuracy, data integrity, maintainability, and visibility into grain crop analytics, enabling more reliable experiments and faster iteration.
10 Commits • 3 Features
Dec 1, 2024In 2024-12, delivered targeted improvements to TopoStats: enhanced disordered tracing and grain processing configuration, hardened grain crop data pipeline, refactored GrainCrop validation, and expanded topostats analytics for grain crops. These changes improve trace accuracy, data integrity, maintainability, and visibility into grain crop analytics, enabling more reliable experiments and faster iteration.
December 2024
November 2024
80 Commits • 27 Features
Nov 1, 2024November 2024 (2024-11) focused on delivering core multi-class handling capabilities, strengthening data validation, and improving the GrainCrops/GrainStats pipeline. Key features delivered include a unified merge_classes utility, configurable grain statistics by class, and extended grain crop extraction with bounding box and padding. The month also advanced testing and configuration robustness through vet_grains enhancements, Haribo debugging scaffolding, and related API improvements. Collectively these workstreams increased data integrity, model accuracy, and deployment confidence, while enabling easier future refactors and scalability.
November 2024
80 Commits • 27 Features
Nov 1, 2024November 2024 (2024-11) focused on delivering core multi-class handling capabilities, strengthening data validation, and improving the GrainCrops/GrainStats pipeline. Key features delivered include a unified merge_classes utility, configurable grain statistics by class, and extended grain crop extraction with bounding box and padding. The month also advanced testing and configuration robustness through vet_grains enhancements, Haribo debugging scaffolding, and related API improvements. Collectively these workstreams increased data integrity, model accuracy, and deployment confidence, while enabling easier future refactors and scalability.
October 2024
35 Commits • 15 Features
Oct 1, 2024October 2024 performance summary for AFM-SPM/TopoStats: Delivered core multi-class analytics capabilities, expanded documentation, and improved configuration reliability. Strengthened testing coverage across new grain-level and region-relationship utilities, enabling more accurate model evaluation and easier onboarding. Result: higher segmentation accuracy, clearer configuration onboarding, and improved stability for downstream analytics.
35 Commits • 15 Features
Oct 1, 2024October 2024 performance summary for AFM-SPM/TopoStats: Delivered core multi-class analytics capabilities, expanded documentation, and improved configuration reliability. Strengthened testing coverage across new grain-level and region-relationship utilities, enabling more accurate model evaluation and easier onboarding. Result: higher segmentation accuracy, clearer configuration onboarding, and improved stability for downstream analytics.
October 2024
September 2024
3 Commits • 1 Features
Sep 1, 2024September 2024 focused on establishing a robust curvature analytics foundation for AFM-SPM/TopoStats, enabling reliable 2D curvature metrics and downstream analytics.
September 2024
3 Commits • 1 Features
Sep 1, 2024September 2024 focused on establishing a robust curvature analytics foundation for AFM-SPM/TopoStats, enabling reliable 2D curvature metrics and downstream analytics.
Activity
Loading activity data...
Quality Metrics
Correctness89.4%
Maintainability90.6%
Architecture85.4%
Performance80.8%
AI Usage20.2%
Skills & Technologies
Programming Languages
BinaryCSVMarkdownNoneNumPyNumpyPKLPandasPythonShell
Technical Skills
Algorithm DevelopmentAlgorithm ImplementationArgument ParsingBackend DevelopmentBug FixBug FixingCI/CDClass MergingCode ClarityCode CleanupCode MaintenanceCode OrganizationCode RefactoringCode RenamingCode Revert
Repositories Contributed To
Overview of all repositories you've contributed to across your timeline