@@ -127,111 +127,6 @@ def _unique(inlist):
127127 return {k : _unique (v ) for k , v in entities .items ()}
128128
129129
130- def group_bolds_ref (* , layout , subject , sessions = None ):
131- """
132- Extracts BOLD files from a BIDS dataset and combines them into buckets.
133- Files in a bucket share:
134- 1) Session
135- 2) Phase-encoding direction (PEdir)
136- 3) Total readout time (TRT)
137-
138- Any files with missing data for (2) or (3) are put in their own bucket.
139-
140- Parameters
141- ----------
142- layout : pybids.layout.BIDSLayout
143- Initialized BIDSLayout
144- subject : str
145- The subject ID
146- sessions : None
147-
148- Outputs
149- -------
150- combinations : list of tuples
151- Each tuple is composed of (session, PEdir, TRT)
152- files : list of lists
153- Files matching each combination.
154-
155- Limitations
156- -----------
157- Single-band reference (sbref) are excluded.
158- """
159- import re
160- from contextlib import suppress
161- from itertools import product
162-
163- from sdcflows .utils .epimanip import get_trt
164-
165- base_entities = {
166- "subject" : subject ,
167- "extension" : (".nii" , ".nii.gz" ),
168- "scope" : "raw" , # Ensure derivatives are not captured
169- }
170- # dictionary containing unique Groupings and files
171- groupings = {}
172- # list of all BOLDS encountered
173- all_bolds = []
174-
175- sessions = sessions if sessions else layout .get_sessions (subject = subject , scope = "raw" )
176-
177- for ses , suffix in sorted (product (sessions or (None ,), {"bold" })):
178- # bold files same session
179- bolds = layout .get (suffix = suffix , session = ses , ** base_entities )
180- # some sessions may not have BOLD scans
181- if bolds is None :
182- continue
183-
184- for i , bold in enumerate (bolds ):
185- multiecho_id = None
186- # multi-echo should be grouped together
187- if 'echo' in bold .entities :
188- # create unique id by dropping "_echo-{i}"
189- multiecho_id = re .sub (r"_echo-\d+" , "" , bold .filename )
190-
191- # session, pe, ro
192- meta = bold .get_metadata ()
193- pe_dir = meta .get ("PhaseEncodingDirection" )
194-
195- ro = None
196- with suppress (ValueError ):
197- ro = get_trt (meta , bold .path )
198- if ro is not None :
199- meta .update ({"TotalReadoutTime" : ro })
200-
201- grouping = BOLDGrouping (
202- session = ses ,
203- pe_dir = pe_dir ,
204- readout = ro ,
205- multiecho_id = multiecho_id ,
206- )
207-
208- if any (v is None for v in (pe_dir , ro )):
209- # cannot be certain so treat as unique
210- grouping .add_file (bold .path )
211- groupings [f'unknown{ i } ] = grouping
212- else :
213- try :
214- grouping = groupings [grouping .name ]
215- except KeyError :
216- groupings [grouping .name ] = grouping
217-
218- grouping .add_file (bold .path )
219-
220- all_bolds += bolds
221-
222- if len (all_bolds ) != sum ([len (g .files ) for _ , g in groupings .items ()]):
223- msg = f"""Error encountered when grouping BOLD runs.
224- Combinations: { groupings }
225- BOLD files: { bolds }
226-
227- Please file a bug-report with the nibabies developers at:
228- https://github.com/nipreps/nibabies/issues/new/choose
229- """
230- raise RuntimeError (msg )
231-
232- return groupings
233-
234-
235130def validate_input_dir (exec_env , bids_dir , participant_label ):
236131 # Ignore issues and warnings that should not influence NiBabies
237132 import subprocess
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