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Include PV360's CMN_study_ parameters in the subject metadata group #218

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Merged
headmeister merged 1 commit into from
Aug 24, 2026
Merged

Include PV360's CMN_study_ parameters in the subject metadata group #218

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2 changes: 1 addition & 1 deletion brukerapi/dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,7 @@
"visu_series": (("VisuSeries",), ("VisuExperimentNumber", "VisuProcessingNumber")),
"visu_equipment": ((), ("VisuManufacturer", "VisuAcqSoftwareVersion", "VisuInstitution", "VisuStation")),
"visu_acq": (("VisuAcq", "VisuAcquisition"), ()),
"subject": (("SUBJECT_",), ()),
"subject": (("SUBJECT_", "CMN_study_"), ()),
}

# What "could not read this parameter file" looks like. FileNotFoundError is the
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16 changes: 16 additions & 0 deletions test/test_api.py
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Expand Up @@ -69,6 +69,22 @@ def test_metadata_groups_follow_the_specification(tmp_path):
assert "uisition_protocol" not in metadata["visu_acq"]


def test_subject_group_carries_the_pv360_study_level_cmn_parameters(tmp_path):
"""PV360 writes two CMN_ parameters into `subject`, next to SUBJECT_study_*.

`CMN_study_use_ats` says whether the Animal Transport System was in use,
which shifts the coordinate origin; selecting the group by `SUBJECT_` alone
dropped it and `CMN_study_bed` silently.
"""
root = tmp_path / "20200612_094625_study_1_1"
write_jcampdx(root / "subject", {"SUBJECT_id": ["<phantom>"], "SUBJECT_study_nr": 1, "CMN_study_use_ats": "Yes", "CMN_study_bed": ["<Rat bed>"]})
dataset = Dataset(write_2dseq(root / "8" / "pdata" / "1"), add_parameters=["subject"], load=LOAD_STAGES["properties"])

assert dataset.metadata["subject"]["id"] == "phantom"
assert dataset.metadata["subject"]["use_ats"] == "Yes"
assert dataset.metadata["subject"]["bed"] == "Rat bed"


def test_metadata_reports_the_same_string_as_the_property_that_reads_it(tmp_path):
"""`subj_id` and `metadata` read VisuSubjectName; they must agree.

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