ENH: Calculate TA and store in run_info

bids/analysis/analysis.py

@@ -388,13 +388,22 @@ def get_design_matrix(self, names=None, format='long', mode='both',
 
  if sampling_rate == 'TR':
  trs = {var.run_info[0].tr for var in self.collection.variables.values()}
+ tas = {var.run_info[0].ta for var in self.collection.variables.values()}
  if not trs:
  raise ValueError("Repetition time unavailable; specify sampling_rate "
  "explicitly")
  elif len(trs) > 1:
  raise ValueError("Non-unique Repetition times found ({!r}); specify "
- "sampling_rate explicitly")
- sampling_rate = 1. / trs.pop()
+ "sampling_rate explicitly".format(trs))
+ TR = trs.pop()
+ if not tas:
+ warnings.warn("Acquisition time unavailable; assuming TA = TR")
+ tas = {TR}
+ elif len(tas) > 1:
+ raise ValueError("Non-unique acquisition times found ({!r})".format(tas))
+
+ sampling_rate = 1. / TR
+ acquisition_time = tas.pop()
  elif sampling_rate == 'highest':
  sampling_rate = None
  dense_df = coll.to_df(names, format='wide',

bids/variables/entities.py

@@ -36,23 +36,25 @@ class RunNode(Node):
  image_file (str): The full path to the corresponding nifti image.
  duration (float): Duration of the run, in seconds.
  repetition_time (float): TR for the run.
+ acquisition_time (float): TA for the run.
  task (str): The task name for this run.
  '''
 
- def __init__(self, entities, image_file, duration, repetition_time):
+ def __init__(self, entities, image_file, duration, repetition_time, acquisition_time):
  self.image_file = image_file
  self.duration = duration
  self.repetition_time = repetition_time
+ self.acquisition_time = acquisition_time
  super(RunNode, self).__init__('run', entities)
 
  def get_info(self):
 
  return RunInfo(self.entities, self.duration, self.repetition_time,
- self.image_file)
+ self.acquisition_time, self.image_file)
 
 
 # Stores key information for each Run.
-RunInfo = namedtuple('RunInfo', ['entities', 'duration', 'tr', 'image'])
+RunInfo = namedtuple('RunInfo', ['entities', 'duration', 'tr', 'ta', 'image'])
 
 
 class NodeIndex(Node):

bids/variables/io.py

@@ -82,6 +82,24 @@ def load_variables(layout, types=None, levels=None, skip_empty=True,
  return dataset
 
 
+def _get_timing_info(img_md):
+ if 'RepetitionTime' in img_md:
+ tr = img_md['RepetitionTime']
+ if 'DelayTime' in img_md:
+ ta = tr - img_md['DelayTime']
+ elif 'SliceTiming' in img_md:
+ slicetimes = sorted(img_md['SliceTiming'])
+ # a, b ... z
+ # z = final slice onset, b - a = slice duration
+ ta = slicetimes[-1] + slicetimes[1] - slicetimes[0]
+ else:
+ ta = tr
+ elif 'VolumeTiming' in img_md:
+ return NotImplemented
+
+ return tr, ta
+
+
 def _load_time_variables(layout, dataset=None, columns=None, scan_length=None,
  drop_na=True, events=True, physio=True, stim=True,
  regressors=True, skip_empty=True, **selectors):
@@ -141,8 +159,9 @@ def _load_time_variables(layout, dataset=None, columns=None, scan_length=None,
  if 'run' in entities:
  entities['run'] = int(entities['run'])
 
- tr = layout.get_metadata(img_f, suffix='bold', domains=domains,
- full_search=True)['RepetitionTime']
+ img_md = layout.get_metadata(img_f, suffix='bold', domains=domains,
+ full_search=True)
+ tr, ta = _get_timing_info(img_md)
 
  # Get duration of run: first try to get it directly from the image
  # header; if that fails, try to get NumberOfVolumes from the
@@ -162,7 +181,8 @@ def _load_time_variables(layout, dataset=None, columns=None, scan_length=None,
  raise ValueError(msg)
 
  run = dataset.get_or_create_node('run', entities, image_file=img_f,
- duration=duration, repetition_time=tr)
+ duration=duration, repetition_time=tr,
+ acquisition_time=ta)
  run_info = run.get_info()
 
  # Process event files