[ENH] more specific bids entities and fixes to be bids compatible

AFQ/afq_bids_entities.json

@@ -0,0 +1,22 @@
+{
+    "name": "bidsafq",
+    "entities": [
+      {
+        "name": "odfmodel",
+        "pattern": "[_/\\\\]+odfmodel-([a-zA-Z0-9]+)"
+      },
+      {
+        "name": "coordsys",
+        "pattern": "[_/\\\\]+coordsys-([a-zA-Z0-9]+)"
+      },
+      {
+        "name": "trkmethod",
+        "pattern": "[_/\\\\]+trkmethod-([a-zA-Z0-9]+)"
+      },
+      {
+        "name": "recogmethod",
+        "pattern": "[_/\\\\]+recogmethod-([a-zA-Z0-9]+)"
+      }
+    ]
+  }
+

AFQ/api/group.py

@@ -41,7 +41,7 @@
     using_afqb = False
 
 
-__all__ = ["GroupAFQ"]
+__all__ = ["GroupAFQ", "get_afq_bids_entities_fname"]
 
 
 logger = logging.getLogger('AFQ')
@@ -55,6 +55,11 @@ def clean_pandas_df(df):
     return df
 
 
+def get_afq_bids_entities_fname():
+    return op.dirname(op.dirname(op.abspath(
+        aus.__file__))) + "/afq_bids_entities.json"
+
+
 class GroupAFQ(object):
     f"""{AFQclass_doc}"""
 

AFQ/api/participant.py

@@ -1,6 +1,5 @@
 import nibabel as nib
 import os.path as op
-import os
 from time import time
 import logging
 from tqdm import tqdm
@@ -20,7 +19,8 @@
 from AFQ.tasks.tractography import get_tractography_plan
 from AFQ.tasks.segmentation import get_segmentation_plan
 from AFQ.tasks.viz import get_viz_plan
-from AFQ.utils.path import drop_extension, apply_cmd_to_afq_derivs
+from AFQ.tasks.utils import get_base_fname
+from AFQ.utils.path import apply_cmd_to_afq_derivs
 from AFQ.viz.utils import BEST_BUNDLE_ORIENTATIONS, trim, get_eye
 
 
@@ -104,9 +104,7 @@ def __init__(self,
             results_dir=output_dir,
             dwi_affine=nib.load(dwi_data_file).affine,
             bids_info=bids_info,
-            base_fname=op.join(
-                output_dir,
-                drop_extension(op.basename(dwi_data_file))),
+            base_fname=get_base_fname(output_dir, dwi_data_file),
             **kwargs)
         self.make_workflow()
 

AFQ/data/fetch.py

@@ -822,7 +822,8 @@ def read_cp_templates(as_img=True, resample_to=False):
         resample_to=resample_to)
 
     toc = time.perf_counter()
-    logger.debug(f'Cerebellar peduncles templates loaded in {toc - tic:0.4f} seconds')
+    logger.debug(
+        f'Cerebellar peduncles templates loaded in {toc - tic:0.4f} seconds')
 
     return template_dict
 
@@ -1084,7 +1085,7 @@ def organize_stanford_data(path=None, clear_previous_afq=None):
         else:
             apply_cmd_to_afq_derivs(
                 op.join(afq_folder, "sub-01/ses-01"),
-                op.join(afq_folder, "sub-01/ses-01/sub-01_ses-01_dwi"),
+                op.join(afq_folder, "sub-01/ses-01/sub-01_ses-01"),
                 dependent_on=clear_previous_afq)
 
     if not op.exists(derivatives_path):