[ENH] Add DICOM header checking and `DicomDirMap` to `DicomReorgWorkflow`

[michellewang]

Closes #225

Remaining TODOs

• [x] Add tests for DicomDirMap
• [x] Add tests for new validation functions
• [x] Add yet more tests

Summary:

• Add the pydicom header check for whether ImageType contains "DERIVED"
• Add new fields to global config for configuring DICOM reorganization (i.e. in <DATASET_ROOT>/scratch/raw_dicom):
  • DICOM_DIR_MAP_FILE: custom CSV with participant_id, session and participant_dicom_dir columns
  • DICOM_DIR_PARTICIPANT_FIRST: alternative option for choosing between <DATASET_ROOT>/scratch/raw_dicom/<PARTICIPANT_ID>/<SESSION> (default) or <DATASET_ROOT>/scratch/raw_dicom/<SESSION>/<PARTICIPANT_ID>
  • (These options are mutually exclusive, by the way)
• Some changes to logger to fix testing (previously wasn't able to make the caplog fixture work)
• Added some validators for user-provided tabular/config files (i.e. participant_id cannot have sub- prefix, and session must have ses- prefix)

Note that this ONLY allows the contents of raw_dicom to be somewhat arbitrary. For sourcedata I think it makes more sense to enforce <PARTICIPANT_ID>/<SESSION>, though that might break some of the existing PPMI/QPN data. But I think it is better for things to already be more BIDS-like after the reorg step.

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 52.66%. Comparing base (cccdbf6) to head (d6785a9).

:exclamation: Current head d6785a9 differs from pull request most recent head 8a37516

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #229 +/- ## =========================================== - Coverage 97.40% 52.66% -44.74% =========================================== Files 25 47 +22 Lines 1541 3334 +1793 =========================================== + Hits 1501 1756 +255 - Misses 40 1578 +1538 ```

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