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Merge pull request #283 from UNFmontreal/fix_issue_282
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Fetch all descriptions: id list
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@arnaudbore
arnaudbore authored Dec 2, 2023
2 parents 0a13c49 + b455cc4 commit 4955ac5
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Showing 6 changed files with 112 additions and 17 deletions.
2 changes: 1 addition & 1 deletion dcm2bids/acquisition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -278,7 +278,7 @@ def dstSidecarData(self, idList):
values.append(idList.get(val, val))
if values[-1] != val:
if isinstance(values[-1], list):
values[-1] = "bids::" + values[-1][0]
values[-1] = ["bids::" + img_dest for img_dest in values[-1]]
else:
values[-1] = "bids::" + values[-1]

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33 changes: 33 additions & 0 deletions tests/data/config_test_multiple_intendedfor.json
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@@ -0,0 +1,33 @@
{
"search_method": "fnmatch",
"extractors": {"SeriesDescription": ["task-(?P<task>[a-zA-Z0-9]+)"]},
"descriptions": [
{
"id": "localizer",
"datatype": "localizer",
"suffix": "localizer",
"criteria": {
"SeriesDescription": "locali*"
}
},
{
"id": "T1",
"datatype": "anat",
"suffix": "T1w",
"criteria": {
"SidecarFilename": "*MPRAGE*"
}
},
{
"datatype": "fmap",
"suffix": "fmap",
"criteria": {
"EchoNumber": 1,
"EchoTime": 0.00492
},
"sidecar_changes": {
"IntendedFor": ["localizer", "T1"]
}
}
]
}
1 change: 1 addition & 0 deletions tests/data/sidecars/001_localizer_20100603125600_i00001.nii
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DUMMY_FILE_FOR_TEST
1 change: 1 addition & 0 deletions tests/data/sidecars/001_localizer_20100603125600_i00002.nii
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DUMMY_FILE_FOR_TEST
1 change: 1 addition & 0 deletions tests/data/sidecars/001_localizer_20100603125600_i00003.nii
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DUMMY_FILE_FOR_TEST
91 changes: 75 additions & 16 deletions tests/test_dcm2bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,9 @@ def test_dcm2bids():
"sub-01_echo-738_fmap.json")
data = load_json(fmapFile)
fmapMtime = os.stat(fmapFile).st_mtime
assert data["IntendedFor"] == "bids::" + os.path.join("sub-01", "dwi", "sub-01_dwi.nii.gz")
assert data["IntendedFor"] == "bids::" + os.path.join("sub-01",
"dwi",
"sub-01_dwi.nii.gz")

data = load_json(
os.path.join(
Expand Down Expand Up @@ -231,16 +233,22 @@ def test_dcm2bids_case_sensitive():
"fmap",
"sub-01_echo-492_fmap.json")
data = load_json(fmapFile)
assert data["IntendedFor"] == ["bids::" + os.path.join("sub-01", "dwi", "sub-01_dwi.nii.gz"),
"bids::" + os.path.join("sub-01", "anat", "sub-01_T1w.nii")]
assert data["IntendedFor"] == ["bids::" + os.path.join("sub-01",
"dwi",
"sub-01_dwi.nii.gz"),
"bids::" + os.path.join("sub-01",
"anat",
"sub-01_T1w.nii")]

fmapFile = os.path.join(bids_dir.name,
"sub-01",
"fmap",
"sub-01_echo-738_fmap.json")
data = load_json(fmapFile)
fmapMtime = os.stat(fmapFile).st_mtime
assert data["IntendedFor"] == "bids::" + os.path.join("sub-01", "dwi", "sub-01_dwi.nii.gz")
assert data["IntendedFor"] == "bids::" + os.path.join("sub-01",
"dwi",
"sub-01_dwi.nii.gz")

data = load_json(
os.path.join(
Expand Down Expand Up @@ -288,8 +296,12 @@ def test_dcm2bids_auto_extract():
data = load_json(epi_file)

assert os.path.exists(epi_file)
assert data["IntendedFor"] == ["bids::" + os.path.join("sub-01", "dwi", "sub-01_dwi.nii.gz"),
"bids::" + os.path.join("sub-01", "anat", "sub-01_T1w.nii")]
assert data["IntendedFor"] == ["bids::" + os.path.join("sub-01",
"dwi",
"sub-01_dwi.nii.gz"),
"bids::" + os.path.join("sub-01",
"anat",
"sub-01_T1w.nii")]

func_task = os.path.join(bids_dir.name, "sub-01",
"func",
Expand Down Expand Up @@ -459,8 +471,6 @@ def test_dcm2bids_sidecar():
session="dev")
app.run()

layout = BIDSLayout(bids_dir.name, validate=False)

# existing field
data = load_json(os.path.join(bids_dir.name,
"sub-01",
Expand All @@ -483,8 +493,8 @@ def test_dcm2bids_sidecar():
"ses-dev",
"fmap",
"sub-01_ses-dev_echo-492_fmap.json"))
assert data["MTState"] == True
assert data["MTState"]

# boolean value if input as a string
data = load_json(os.path.join(bids_dir.name,
"sub-01",
Expand All @@ -499,16 +509,65 @@ def test_dcm2bids_sidecar():
"ses-dev",
"dwi",
"sub-01_ses-dev_desc-fa01_dwi.json"))
assert data["IntendedFor"] == ["bids::" + os.path.join("sub-01", "ses-dev", "dwi", "sub-01_ses-dev_dwi.nii.gz"),
"bids::" + os.path.join("sub-01", "ses-dev", "anat", "sub-01_ses-dev_T1w.nii")]
assert data["Sources"] == ["bids::" + os.path.join("sub-01", "ses-dev", "anat", "sub-01_ses-dev_T1w.nii"),
"bids::" + os.path.join("sub-01", "ses-dev", "dwi", "sub-01_ses-dev_dwi.nii.gz")]
assert data["IntendedFor"] == ["bids::" + os.path.join("sub-01",
"ses-dev",
"dwi",
"sub-01_ses-dev_dwi.nii.gz"),
"bids::" + os.path.join("sub-01",
"ses-dev",
"anat",
"sub-01_ses-dev_T1w.nii")]
assert data["Sources"] == ["bids::" + os.path.join("sub-01",
"ses-dev",
"anat",
"sub-01_ses-dev_T1w.nii"),
"bids::" + os.path.join("sub-01",
"ses-dev",
"dwi",
"sub-01_ses-dev_dwi.nii.gz")]

# list with 1 item
data = load_json(os.path.join(bids_dir.name,
"sub-01",
"ses-dev",
"dwi",
"sub-01_ses-dev_desc-trace_dwi.json"))
assert data["IntendedFor"] == "bids::" + os.path.join("sub-01", "ses-dev", "dwi", "sub-01_ses-dev_dwi.nii.gz")
assert data["Sources"] == "bids::" + os.path.join("sub-01", "ses-dev", "anat", "sub-01_ses-dev_T1w.nii")
assert data["IntendedFor"] == "bids::" + os.path.join("sub-01",
"ses-dev",
"dwi",
"sub-01_ses-dev_dwi.nii.gz")
assert data["Sources"] == "bids::" + os.path.join("sub-01",
"ses-dev",
"anat",
"sub-01_ses-dev_T1w.nii")


def test_dcm2bids_multiple_intendedFor():
bids_dir = TemporaryDirectory()

tmp_sub_dir = os.path.join(bids_dir.name, DEFAULT.tmp_dir_name, "sub-01")
shutil.copytree(os.path.join(TEST_DATA_DIR, "sidecars"), tmp_sub_dir)

app = Dcm2BidsGen(TEST_DATA_DIR, "01",
os.path.join(TEST_DATA_DIR,
"config_test_multiple_intendedfor.json"),
bids_dir.name,
auto_extract_entities=True)
app.run()

epi_file = os.path.join(bids_dir.name, "sub-01", "fmap", "sub-01_fmap.json")
data = load_json(epi_file)

assert os.path.exists(epi_file)
assert data["IntendedFor"] == ["bids::" + os.path.join("sub-01",
"localizer",
"sub-01_run-01_localizer.nii"),
"bids::" + os.path.join("sub-01",
"localizer",
"sub-01_run-02_localizer.nii"),
"bids::" + os.path.join("sub-01",
"localizer",
"sub-01_run-03_localizer.nii"),
"bids::" + os.path.join("sub-01",
"anat",
"sub-01_T1w.nii")]

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