key groups and param groups work!

bond/bond.py

@@ -3,17 +3,21 @@
 import json
 from pathlib import Path
 from bids.layout import parse_file_entities
-from bids.layout import BIDSFile
+import pandas as pd
 
 bids.config.set_option('extension_initial_dot', True)
 
 NON_KEY_ENTITIES = set(["subject", "session", "extension"])
 # Multi-dimensional keys SliceTiming
-IMAGING_PARAMS = set(["ParallelReductionFactorInPlane", "ParallelAcquisitionTechnique",
+IMAGING_PARAMS = set([
+ "ParallelReductionFactorInPlane", "ParallelAcquisitionTechnique",
  "ParallelAcquisitionTechnique", "PartialFourier", "PhaseEncodingDirection",
- "EffectiveEchoSpacing", "TotalReadoutTime", "EchoTime", "SliceEncodingDirection",
- "DwellTime", "FlipAngle", "MultibandAccelerationFactor", "RepetitionTime", "SliceTiming",
- "VolumeTiming", "NumberOfVolumesDiscardedByScanner", "NumberOfVolumesDiscardedByUser"])
+ "EffectiveEchoSpacing", "TotalReadoutTime", "EchoTime",
+ "SliceEncodingDirection", "DwellTime", "FlipAngle",
+ "MultibandAccelerationFactor", "RepetitionTime", "SliceTiming",
+ "VolumeTiming", "NumberOfVolumesDiscardedByScanner",
+ "NumberOfVolumesDiscardedByUser"])
+
 
 class BOnD(object):
 
@@ -49,16 +53,17 @@ def rename_files(self, filters, pattern, replacement):
 
  def get_param_groups(self, key_group):
  key_entities = _key_group_to_entities(key_group)
+ key_entities["extension"] = ".nii[.gz]*"
  matching_files = self.layout.get(return_type="file", scope="self",
- **key_entities)
- return _get_param_groups(matching_files)
+ regex_search=True, **key_entities)
+ return _get_param_groups(matching_files, self.layout)
 
  def get_key_groups(self):
  key_groups = set()
  for path in Path(self.path).rglob("*.*"):
  if path.suffix == ".json":
  continue
- key_groups.update(_file_to_key_group(path),)
+ key_groups.update((_file_to_key_group(path),))
  return sorted(key_groups)
 
  def change_metadata(self, filters, pattern, metadata):
@@ -81,7 +86,7 @@ def change_metadata(self, filters, pattern, metadata):
 
  json_file = [x for x in bidsjson_file if 'json' in x.filename]
 
- if len(json_file) is not 1:
+ if not len(json_file) == 1:
 
  print("FOUND IRREGULAR ASSOCIATIONS")
 
@@ -135,7 +140,7 @@ def _file_to_key_group(filename):
  return _entities_to_key_group(entities)
 
 
-def _get_param_groups(files):
+def _get_param_groups(files, layout):
  """Finds a list of *parameter groups* from a list of files.
 
  Parameters:
@@ -153,4 +158,19 @@ def _get_param_groups(files):
  For each file in `files`, find critical parameters for metadata. Then find
  unique sets of these critical parameters.
  """
- pass
+ dfs = []
+ for path in files:
+ metadata = layout.get_metadata(path)
+ wanted_keys = metadata.keys() & IMAGING_PARAMS
+ example_data = {key: metadata[key] for key in wanted_keys}
+
+ # Expand slice timing to multiple columns
+ SliceTime = example_data.get('SliceTiming')
+ if SliceTime:
+ example_data.update(
+ {"SliceTime%03d" % SliceNum: time for
+ SliceNum, time in enumerate(SliceTime)})
+ del example_data['SliceTiming']
+ dfs.append(example_data)
+
+ return pd.DataFrame(dfs).drop_duplicates()