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made ezbids formatting conditional, formatted code with black #345

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Merged
merged 3 commits into from
May 23, 2025
Merged

made ezbids formatting conditional, formatted code with black #345

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f473e76
made ezbids formatting conditional, formatted code with black
bendhouseart May 23, 2025
335f982
removed type from argument declaration
bendhouseart May 23, 2025
279384c
removing python 3.8 due to lock issues w/ poetry
bendhouseart May 23, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/python.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ jobs:
strategy:
matrix:
os: [macOS-latest, ubuntu-latest]
python: ['3.8', '3.9', '3.10']
python: ['3.9', '3.10']

steps:
- name: Checkout Repo
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2 changes: 1 addition & 1 deletion .github/workflows/windows.yaml
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Expand Up @@ -13,7 +13,7 @@ jobs:
strategy:
matrix:
os: [windows-latest]
python: ['3.8', '3.9', '3.10']
python: ['3.9', '3.10']

steps:
- name: Checkout Repo
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1,368 changes: 971 additions & 397 deletions pypet2bids/poetry.lock
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14 changes: 8 additions & 6 deletions pypet2bids/pypet2bids/dcm2niix4pet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ def __init__(
file_format="%p_%i_%t_%s",
silent=False,
tempdir_location=None,
ezbids=False
ezbids=False,
):
"""
This class is a simple wrapper for dcm2niix and contains methods to do the following in order:
Expand Down Expand Up @@ -216,7 +216,7 @@ def __init__(
self.blood_json = None
self.blood_tsv = None
self.telemetry_data = {}
self.ezbids=ezbids
self.ezbids = ezbids
self.dcm2niix_path = self.check_for_dcm2niix()
if not self.dcm2niix_path:
logger.error(
Expand Down Expand Up @@ -763,9 +763,11 @@ def run_dcm2niix(self):
if self.session_id:
collection_of_fields["ses"] = self.session_id

hash_string = helper_functions.hash_fields(**collection_of_fields)

sidecar_json.update({"SeriesDescription": hash_string})
if self.ezbids:
hash_string = helper_functions.hash_fields(
**collection_of_fields
)
sidecar_json.update({"SeriesDescription": hash_string})

# if there's a subject id rename the output file to use it
if self.subject_id:
Expand Down Expand Up @@ -1170,7 +1172,7 @@ def cli():
action="store_true",
default=False,
help="Add fields to json output that are useful for ezBIDS or other conversion software. This will de-anonymize"
" pet2bids output and add AcquisitionDate an AcquisitionTime into the output json."
" pet2bids output and add AcquisitionDate an AcquisitionTime into the output json.",
)
return parser

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