miblab_data.tristan.rat_fetch#

miblab_data.tristan.rat_fetch(dataset: str | None = None, *, folder: str | Path = './tristanrat', unzip: bool = True, convert: bool = False, keep_archives: bool = False) → List[str][source]#

Download, recursively extract, and (optionally) convert TRISTAN rat MRI studies from Zenodo (record 15747417).

The helper understands the 15 published studies S01 … S15. Pass dataset="all" (or leave dataset empty) to fetch every archive in one go.

Parameters:

dataset – "S01" … "S15" to grab a single study "all" or None to fetch them all.
folder – Root directory that will hold the SXX.zip files and the extracted DICOM tree. A sibling directory <folder>_nifti/ is used for conversion output.
unzip – If True, each ZIP is unpacked recursively (handles inner ZIP-in-ZIP structures).
convert – If True, every DICOM folder is converted to compressed NIfTI (requires the dicom2nifti wheel and unzip=True).
keep_archives – Forwarded to _unzip_nested(); set True to retain each inner ZIP after extraction (useful for auditing).

Returns:

Absolute paths to every SXX.zip that was downloaded (whether new or cached).

Return type:

list[str]

Examples

Download a single study and leave it zipped

>>> from miblab_data.tristan import rat_fetch

Single study, leave zipped

>>> rat_fetch("S01", folder="./rat_data", unzip=False)
['/home/you/rat_data/S01.zip']

Single study, unzip everything and convert to NIfTI (requires dicom2nifti)

>>> rat_fetch("S01", folder="./rat_data", unzip=True, convert=True)

Download by group (friendly names):

rifampicin_effect_size → S01, S02, S03, S04
six_compound → S05, S06, S07, S08, S09, S10, S12
field_strength → S13
chronic → S11, S14, S15

Example of download by group: Rifampicin effect-size (S01–S04)

>>> rat_fetch("rifampicin_effect_size", folder="./rat_data", unzip=True, convert=False)

Example of download by group: Six-compound set (S05, S06, S07, S08, S10, S12)

>>> rat_fetch("six_compound", folder="./rat_data", unzip=True, convert=False)

Example of download by group: Field-strength (S13)

>>> rat_fetch("field_strength", folder="./rat_data", unzip=True, convert=False)

Example of download by group: Chronic studies (S11, S14, S15)

>>> rat_fetch("chronic", folder="./rat_data", unzip=True, convert=False)

Fetch the entire collection, unzip, but skip conversion

>>> rat_fetch(dataset="all",
...           folder="./rat_data",
...           unzip=True,
...           convert=False)

Full end-to-end pipeline (requires dicom2nifti)

>>> rat_fetch("S03",
...           folder="./rat_data",
...           unzip=True,
...           convert=True)

The call returns the list of ZIP paths; side-effects are files extracted (and optionally NIfTI volumes) under folder.

Notes

unzip=True recursively extracts any inner ZIPs.
convert=True writes compressed NIfTI files alongside the DICOM tree (requires dicom2nifti; installed via miblab[data]).
You may pass “S01” or “s01”; labels are case-insensitive.

miblab_data.tristan.rat_fetch#

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