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Optimize DICOM processing and enhance logging and testing framework - #14

Merged

NicholasLeotta99 merged 89 commits into

mainfrom

feature/hpc-singularity

Jun 11, 2026

Merged

Optimize DICOM processing and enhance logging and testing framework#14
NicholasLeotta99 merged 89 commits into
mainfrom
feature/hpc-singularity

Commits on Mar 16, 2026
- Optimize Removed_fully.csv logging loop in 02_parseDicom.py
  
  google-labs-jules[bot]
  and
  NicholasLeotta99
  committed
  1e88eb8
- Merge pull request #12 from TheParraLab/fix-parsedicom-removal-perf-12338934965225293055
  NicholasLeotta99
  authored
  1655cbc
Commits on Mar 17, 2026
Commits on Mar 18, 2026
- Refactor DICOM processing logic to enhance scan handling and improve Data_table boolean flag normalization. Allowing supplemental scanning to skip when results saved
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Commits on Mar 23, 2026
- Refactor DICOM processing to improve directory creation and data loading. Added checks for existing split and ordered tables, enhancing logging for relocation processes.
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Commits on Apr 21, 2026
- fix(DICOMextract): enhance modality extraction and fix glob pattern usage for DICOM files
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  4516e67
- Merge branch 'develop' of https://github.com/TheParraLab/MRI_preprocessing into develop
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  abc01fc
Commits on Apr 22, 2026
- Enhance testing framework for DICOM processing
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Commits on Apr 23, 2026
- Removed deprecated web interface
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- Simplifying base container deployment
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- fix(docs): update README for WSL compose file and clarify DATA_DIRECTORY_PATH
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Commits on Apr 24, 2026
- refactor(docs): update README to enhance clarity and structure for MRI preprocessing pipeline
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  8eff3e1
- refactor: remove disk space check and related logic from DICOM parsing script
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Commits on Apr 30, 2026
Commits on May 1, 2026
Commits on May 2, 2026
- Refactor tests to utilize ScanConfig and improve logging; streamline integration and unit tests for DICOM processing
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  a1379e1
- Refactor 01_scanDicom.py to improve logging and streamline DICOM extraction; add review documentation for clarity on implementation and test coverage
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Commits on May 4, 2026
- Add normalization script for MRI data processing; implement directory selection and percentile calculation
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Commits on May 5, 2026
Commits on May 6, 2026
- Add scripts for comparing and scanning checksum data; implement JSON output for results
  
  NicholasLeotta99
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  Copilot
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Commits on May 7, 2026
- Refactor temporary save directory handling and improve user prompts for overwriting files
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  69fe48b
Commits on May 11, 2026
- Optimize data aggregation and compilation in DICOM parsing script
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  da178e2
- Enhance scan comparison script with detailed loading messages and refined reporting structure
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Commits on May 12, 2026
Commits on May 19, 2026
Commits on May 26, 2026
- Add extraction of body part examined in DICOM files
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  e09d979
- Add disk space check to prevent processing with insufficient storage
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Commits on May 27, 2026
- Add 'BodyPartExamined' and 'Part' fields for DICOM metadata consistency
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Commits on May 28, 2026
- Add functions to save and load split relocations for persistent symlink management
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Commits on Jun 1, 2026
Commits on Jun 2, 2026
- Enhance DICOMextract to accept pre-computed number of slices and optimize slice retrieval
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  b3d4eea
Commits on Jun 3, 2026
Commits on Jun 4, 2026
Commits on Jun 5, 2026
- Update 01_scanDicom.py review: refine summary, enhance metadata extraction details, and address dead code cleanup
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  committed
  4ec9edb
- Implement hybrid chunk worker for improved parallel processing in toolbox.py
  NicholasLeotta99
  committed
  7b1e8f9
Commits on Jun 11, 2026

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