Add multi-run workflow synchronized with BIDS dataset

phys2bids/bids.py

@@ -1,5 +1,6 @@
 import logging
 import os
+import re
 from csv import reader
 from pathlib import Path
 
@@ -52,6 +53,86 @@
 }
 
 
+def update_bids_name(basename, **kwargs):
+    """
+    Add entities, suffix, and/or extension to a BIDS filename while retaining
+    BIDS compatibility.
+
+    Parameters
+    ----------
+    basename : str
+        Name of valid BIDS file.
+    kwargs : dict
+        Keyword arguments indicating entities and/or suffix and/or extension
+        to update/add to the BIDS filename. If a keyword's value is None, then
+        the entity will be removed from the filename.
+
+    Returns
+    -------
+    outname : str
+        Valid BIDS filename with updated entities/suffix/extension.
+    """
+    # This is hardcoded, but would be nice to use the yaml-fied BIDS entity
+    # table when that's up and running.
+    ENTITY_ORDER = ['sub', 'ses', 'task', 'acq', 'ce', 'rec', 'dir', 'run',
+                    'mod', 'echo', 'fa', 'inv', 'mt', 'part', 'ch',
+                    'recording', 'proc', 'space', 'split']
+
+    outdir = os.path.dirname(basename)
+    outname = os.path.basename(basename)
+
+    # Determine scan suffix (should always be physio)
+    suffix = outname.split('_')[-1].split('.')[0]
+    extension = '.' + '.'.join(outname.split('_')[-1].split('.')[1:])
+    filetype = suffix + extension
+
+    for key, val in kwargs.items():
+        if key == 'suffix':
+            if not val.startswith('_'):
+                val = '_' + val
+
+            if not val.endswith('.'):
+                val = val + '.'
+
+            outname = outname.replace('_' + suffix + '.', val)
+        elif key == 'extension':
+            # add leading . if not ''
+            if val and not val.startswith('.'):
+                val = '.' + val
+            outname = outname.replace(extension, val)
+        else:
+            # entities
+            if key not in ENTITY_ORDER:
+                raise ValueError('Key {} not understood.'.format(key))
+
+            if val is None:
+                # remove entity from filename if kwarg val is None
+                regex = '_{}-[0-9a-zA-Z]+'.format(key)
+                outname = re.sub(regex, '', outname)
+            elif '_{}-{}'.format(key, val) in basename:
+                LGR.warning('Key-value pair {}/{} already found in '
+                            'basename {}. Skipping.'.format(key, val, basename))
+            elif '_{}-'.format(key) in basename:
+                LGR.warning('Key {} already found in basename {}. '
+                            'Overwriting.'.format(key, basename))
+                regex = '_{}-[0-9a-zA-Z]+'.format(key)
+                outname = re.sub(regex, '_{}-{}'.format(key, val), outname)
+            else:
+                loc = ENTITY_ORDER.index(key)
+                entities_to_check = ENTITY_ORDER[loc:]
+                entities_to_check = ['_{}-'.format(etc) for etc in entities_to_check]
+                entities_to_check.append('_{}'.format(filetype))
+                for etc in entities_to_check:
+                    if etc in outname:
+                        outname = outname.replace(
+                            etc,
+                            '_{}-{}{}'.format(key, val, etc)
+                        )
+                        break
+    outname = os.path.join(outdir, outname)
+    return outname
+
+
 def bidsify_units(orig_unit):
     """
     Read the input unit of measure and use the dictionary of aliases