👔 Strip space and res from atlas keys

FCP-INDI · Jan 27, 2023 · 2ab869f · 2ab869f
1 parent 91054ac
commit 2ab869f
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Showing 3 changed files with 34 additions and 4 deletions.
diff --git a/CPAC/resources/templates/BIDS_identifiers.tsv b/CPAC/resources/templates/BIDS_identifiers.tsv
@@ -21,10 +21,10 @@
 /ndmg_atlases/label/Human/HarvardOxfordcort-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz	HOCPA	th25
 /ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz	HOSPA	th25
 /ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-2x2x2.nii.gz	Juelich	
-/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-200Parcels17NetworksOrder.nii.gz	Schaefer2018	p200n17
-/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-300Parcels17NetworksOrder.nii.gz	Schaefer2018	p300n17
-/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-400Parcels17NetworksOrder.nii.gz	Schaefer2018	p400n17
-/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-1000Parcels17NetworksOrder.nii.gz	Schaefer2018	p1000n17
+/ndmg_atlases/label/Human/Schaefer[^_-]*200.*.nii(\.gz){0,1}	Schaefer2018	p200n17
+/ndmg_atlases/label/Human/Schaefer[^_-]*300.*.nii(\.gz){0,1}	Schaefer2018	p300n17
+/ndmg_atlases/label/Human/Schaefer[^_-]*400.*.nii(\.gz){0,1}	Schaefer2018	p400n17
+/ndmg_atlases/label/Human/Schaefer[^_-]*1000.*.nii(\.gz){0,1}	Schaefer2018	p1000n17
 /ndmg_atlases/label/Human/Yeo-7_space-MNI152NLin6_res-2x2x2.nii.gz	Yeo	7
 /ndmg_atlases/label/Human/Yeo-7-liberal_space-MNI152NLin6_res-2x2x2.nii.gz	Yeo	7liberal
 /ndmg_atlases/label/Human/Yeo-17_space-MNI152NLin6_res-2x2x2.nii.gz	Yeo	17

diff --git a/CPAC/utils/bids_utils.py b/CPAC/utils/bids_utils.py
@@ -198,6 +198,32 @@ def bids_match_entities(file_list, entities, suffix):
     return matches
 
 
+def bids_remove_entity(name, key):
+    """Remove an entity from a BIDS string by key
+
+    Parameters
+    ----------
+    name : str
+        BIDS string to remove entity from
+    key : str
+        BIDS key of entity to remove
+
+    Returns
+    -------
+    str
+        BIDS name with entity removed
+
+    Examples
+    --------
+    >>> bids_remove_entity('atlas-Yeo_space-MNI152NLin6_res-2x2x2', 'space')
+    'atlas-Yeo_res-2x2x2'
+    >>> bids_remove_entity('atlas-Yeo_space-MNI152NLin6_res-2x2x2', 'res')
+    'atlas-Yeo_space-MNI152NLin6'
+    """
+    return '_'.join(entity for entity in bids_entities_from_filename(name)
+                    if not entity.startswith(f'{key.rstrip("-")}-'))
+
+
 def bids_retrieve_params(bids_config_dict, f_dict, dbg=False):
     """
 

diff --git a/CPAC/utils/datasource.py b/CPAC/utils/datasource.py
@@ -24,6 +24,7 @@
 from CPAC.resources.templates.lookup_table import format_identifier, \
                                                   lookup_identifier
 from CPAC.utils import function
+from CPAC.utils.bids_utils import bids_remove_entity
 from CPAC.utils.interfaces.function import Function
 from CPAC.utils.utils import get_scan_params
 
@@ -1031,6 +1032,9 @@ def create_roi_mask_dataflow(masks, wf_name='datasource_roi_mask'):
                     if base_file.endswith(ext)
                     ][0]
 
+                for key in ['res', 'space']:
+                    base_name = bids_remove_entity(base_name, key)
+
             except IndexError:
                 # pylint: disable=raise-missing-from
                 raise ValueError('Error in spatial_map_dataflow: File '