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[ENH] Allow import from zip files, and allow export with newer versions of dcm2bids#374

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DESm1th merged 49 commits intoTIGRLab:mainfrom
DESm1th:bids
Aug 19, 2025
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[ENH] Allow import from zip files, and allow export with newer versions of dcm2bids#374
DESm1th merged 49 commits intoTIGRLab:mainfrom
DESm1th:bids

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@DESm1th DESm1th commented Aug 19, 2025

This PR makes the following changes:

  • dm_xnat_extract.py: Adds the '--use-zips' option and the ability to extract directly from zip files. Also allows arbitrary dcm2bids arguments to be passed to the tool, and removes the BidsOptions class (moved to the exporters modules)
  • datman.exporters: Removed exporters.py and replaced with a folder of exporter modules. The version of BidsExporter (and its BidsOption class) can now be changed depending on user environment. NiiLinkExporter has also been updated to be usable without reliance on a specific version of dcm2bid

DESm1th and others added 30 commits February 28, 2025 14:41
@DESm1th
[ENH] Start adding zip file importer (and move XNAT classes)
3fb30fb
@DESm1th
[ENH] Add missing methods to zip importers. Still need testing
fd53d07
@DESm1th
[ENH] Update extract to allow zip files to be used as input
f6ce3ab
@DESm1th
[FIX] Bug fixes (name issues, repeated resource exports)
b5253e7
@DESm1th
[FIX] Handle headers with an empty image_type field
ab49032
@DESm1th
[FIX] Allow an ident to be stored with the XNATExperiment importer
390e8ff
@DESm1th
[FIX] Renamed SessionImporter dcm_dir -> dcm_subdir
4240cfe 
SessionImporter and SeriesImporter both used dcm_dir but for
different functions (and with SeriesImporter sometimes being None).

Renamed SessionImporter variable to better reflect differences.
@DESm1th
[FIX] Rename some vars, add missing items to interface classes
a8d0f34
@DESm1th
[CONF] Update pylint settings to ignore more messages
ac8cb20
@DESm1th
[PEP8] Fix formatting issues
e7e175d
@DESm1th
[FIX] Stop repeated export for NiiLinkExporter
f255904
@DESm1th
[FIX] Update timeout for uploading zip files
0a6d72c
@DESm1th
Merge remote-tracking branch 'origin/zip_export' into zip_export
1e7d521
@DESm1th
[FIX] Attribute referenced before assignment
169271b
@DESm1th
[FIX] Fix ZipImporter string and let NiiLinkExporter remove broken sy…
4549a6e 
…mlinks
@DESm1th
[FIX] Ensure is_usable is consistent across SeriesImporters
276e9b3
@DESm1th
[FIX] Added required additional attributes
ac398d8
@DESm1th
[FIX] typo when referencing timeout exception
cb1ea63
@DESm1th
[FIX] Greatly increase timeout value, update upload options
d5c7744
@DESm1th
[FIX] Update function reference
dcd98e1
@DESm1th
[FIX] Correct errors with zip parsing and alternate file types
0edbcac
@DESm1th
Merge remote-tracking branch 'origin/zip_export' into zip_export
c8d50ed
@DESm1th
[FIX] Allow zip parsing when dicoms have no extension
b4006dc
@DESm1th
Merge remote-tracking branch 'origin/zip_export' into zip_export
4065ff8
@DESm1th
[FIX] Update scan importer repr + bids inventory to catch error files
ef8724e 
Error files needed the session number to be match-able to the
right scan session + bids inventory needs to include error files
to ensure blacklisting removal etc. can correctly handle them.
@DESm1th
[FIX] Update references to datman.scanid
81bee31 
At somepoint in the past I changed the import to scanid but
didnt fully update all references so I just switched it back
to avoid name reference errors
@DESm1th
[FIX] Ensure series number is always integer
6f9f270
@DESm1th
[FIX] Fix type in reference to parse function
6ff603c
@DESm1th
[FIX] Move .err parser to utils, catch blacklisted err files
2090221
@DESm1th
[FIX] Move .err parser to utils, catch blacklisted err files
23fae5e
DESm1th and others added 19 commits April 25, 2025 22:21
@DESm1th
Merge remote-tracking branch 'origin/zip_export' into zip_export
4565a93
@DESm1th
[FIX] Ensure zip resources extract to same path as XNAT resources
0fb9d85
@DESm1th
[FIX] Stop index error from happening when no gold standards found
82e35d6
@DESm1th
[FIX] Update function call
cdcc264
@DESm1th
[FIX] Make err file regex more general for XNAT import errors
cc692e7
@DESm1th
[FIX] Started adding a fix for handling repeat sessions
c6b2660
@DESm1th
[FIX] Handle expected scans when repeat sessions exist
224addb
@DESm1th
[FIX] Address bug when bids split series exists in repeat session
b7aafab
@DESm1th
[FIX] Add check for direction as well, if configured
755b5db
@DESm1th
[REF] Reorganize the exporters into submodules
c45ab66 
To prep for multiple versions of dcm2bids I've divided up
the exporters and the bids classes will now be imported based on
user environment.
@DESm1th
[REF] Move BidsOptions, accept arbitrary dcm2bids options
b73e2c8 
- BidsOptions class is now specific to each bids exporter module
- dm_xnat_extract will more flexibly handle options for dcm2bids
	and other future wrapped tools.
@DESm1th
[WIP] Add some functionality back to new bids class
4cd5399
@DESm1th
[ENH] Update the NiiLinkExporter to better locate bids files
601dabf
@DESm1th
[FIX] Make NiiLinkExporter less spammy, handle ints in config
b7fe7af
@DESm1th
[FIX] Correct typos and missing imports
72a3e0c
@DESm1th
[FIX] Update bids version selection, re-add bids functionality
b650226
@DESm1th
[FIX] Ensure extra bids opts always defaults to list
6d72159
@DESm1th
[PEP8] Fix style issues
05f3554
@DESm1th
[ENH] Refactor away the old NiiLinkExporter
a3bd702
@DESm1th DESm1th requested a review from a team as a code owner August 19, 2025 01:09
@DESm1th DESm1th requested review from kimjetwav and slimnsour August 19, 2025 01:09
@DESm1th DESm1th merged commit 97ce68a into TIGRLab:main Aug 19, 2025
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