Add gzip compression option for tar archives

[Copilot]

Adds optional gzip compression for tar archives to reduce storage footprint, particularly beneficial for non-Enhanced MR DICOMs.

Changes

CLI: New --gzip flag creates .tar.gz files instead of .tar

cfmm2tar --gzip -d '20240101' output_dir

API: Added use_gzip parameter to download_studies() and download_studies_from_metadata()

from cfmm2tar.api import download_studies
download_studies(output_dir="/path/to/output", use_gzip=True)

Core: Modified DicomSorter.tar() to use tarfile gzip mode when enabled

• Creates .tar.gz and .attached.tar.gz files
• Refactored attached tar logic to collect items before writing (gzip doesn't support append mode)
• Updated .uid file generation to handle both extensions

Backward compatibility: Defaults to False throughout. Existing workflows unchanged.

Original prompt

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This section details on the original issue you should resolve

<issue_title>gzip the tarballs</issue_title>
<issue_description>What do you guys think about providing an option to gzip the tar files? Will save some space, especially for old-school non-Enhanced MR DICOMs.</issue_description>

<agent_instructions>add an option to cfmm2tar (api and cli) to provide gzipped tar files instead of regular tar files</agent_instructions>

Comments on the Issue (you are @copilot in this section)

@akhanf Ya I think that’s a good idea.. I think the downstream scripts (e.g. tar2bids) should still work with tar.gz files too anyways.. Can add the same flag perhaps to dicom2tar as well..

On Oct 17, 2018, at 3:06 PM, isolovey-robarts <notifications@github.commailto:notifications@github.com> wrote:

What do you guys think about providing an option to gzip the tar files? Will save some space, especially for old-school non-Enhanced MR DICOMs.

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• Fixes gzip the tarballs #4

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[akhanf]

tested this and works