WIP logging and validations in CompCor, SignalExtraction, ApplyTopUp

nipype/algorithms/confounds.py

@@ -281,10 +281,10 @@ def _list_outputs(self):
 class CompCorInputSpec(BaseInterfaceInputSpec):
  realigned_file = File(exists=True, mandatory=True,
  desc='already realigned brain image (4D)')
- mask_file = File(exists=True, mandatory=False,
+ mask_file = File(exists=True,
  desc='mask file that determines ROI (3D)')
  components_file = File('components_file.txt', exists=False,
- mandatory=False, usedefault=True,
+ usedefault=True,
  desc='filename to store physiological components')
  num_components = traits.Int(6, usedefault=True) # 6 for BOLD, 4 for ASL
  use_regress_poly = traits.Bool(True, usedefault=True,
@@ -330,6 +330,13 @@ class CompCor(BaseInterface):
  def _run_interface(self, runtime):
  imgseries = nb.load(self.inputs.realigned_file).get_data()
  mask = nb.load(self.inputs.mask_file).get_data()
+
+ if imgseries.shape[:3] != mask.shape:
+ raise ValueError('Inputs for CompCor, func {} and mask {}, do not have matching '
+ 'spatial dimensions ({} and {}, respectively)'
+ .format(self.inputs.realigned_file, self.inputs.mask_file,
+ imgseries.shape[:3], mask.shape))
+
  voxel_timecourses = imgseries[mask > 0]
  # Zero-out any bad values
  voxel_timecourses[np.isnan(np.sum(voxel_timecourses, axis=1)), :] = 0
@@ -402,6 +409,11 @@ class TCompCor(CompCor):
  def _run_interface(self, runtime):
  imgseries = nb.load(self.inputs.realigned_file).get_data()
 
+ if imgseries.ndim != 4:
+ raise ValueError('tCompCor expected a 4-D nifti file. Input {} has {} dimensions '
+ '(shape {})'
+ .format(self.inputs.realigned_file, imgseries.ndim, imgseries.shape))
+
  # From the paper:
  # "For each voxel time series, the temporal standard deviation is
  # defined as the standard deviation of the time series after the removal
@@ -420,11 +432,13 @@ def _run_interface(self, runtime):
  threshold_index = int(num_voxels * (1. - self.inputs.percentile_threshold))
  threshold_std = sortSTD[threshold_index]
  mask = tSTD >= threshold_std
- mask = mask.astype(int)
+ mask = mask.astype(int).T
 
  # save mask
- mask_file = 'mask.nii'
+ mask_file = os.path.abspath('mask.nii')
  nb.nifti1.save(nb.Nifti1Image(mask, np.eye(4)), mask_file)
+ IFLOG.debug('tCompcor computed and saved mask of shape {} to mask_file {}'
+ .format(mask.shape, mask_file))
  self.inputs.mask_file = mask_file
 
  super(TCompCor, self)._run_interface(runtime)
@@ -513,6 +527,8 @@ def regress_poly(degree, data, remove_mean=True, axis=-1):
  If remove_mean is True (default), the data is demeaned (i.e. degree 0).
  If remove_mean is false, the data is not.
  '''
+ IFLOG.debug('Performing polynomial regression on data of shape ' + str(data.shape))
+
  datashape = data.shape
  timepoints = datashape[axis]
 

nipype/algorithms/tests/test_auto_ArtifactDetect.py

@@ -17,7 +17,7 @@ def test_ArtifactDetect_inputs():
  mask_type=dict(mandatory=True,
  ),
  norm_threshold=dict(mandatory=True,
- xor=[u'rotation_threshold', u'translation_threshold'],
+ xor=['rotation_threshold', 'translation_threshold'],
  ),
  parameter_source=dict(mandatory=True,
  ),
@@ -28,18 +28,18 @@ def test_ArtifactDetect_inputs():
  realignment_parameters=dict(mandatory=True,
  ),
  rotation_threshold=dict(mandatory=True,
- xor=[u'norm_threshold'],
+ xor=['norm_threshold'],
  ),
  save_plot=dict(usedefault=True,
  ),
  translation_threshold=dict(mandatory=True,
- xor=[u'norm_threshold'],
+ xor=['norm_threshold'],
  ),
  use_differences=dict(maxlen=2,
  minlen=2,
  usedefault=True,
  ),
- use_norm=dict(requires=[u'norm_threshold'],
+ use_norm=dict(requires=['norm_threshold'],
  usedefault=True,
  ),
  zintensity_threshold=dict(mandatory=True,

nipype/algorithms/tests/test_auto_CompCor.py

@@ -4,14 +4,12 @@
 
 
 def test_CompCor_inputs():
- input_map = dict(components_file=dict(mandatory=False,
- usedefault=True,
+ input_map = dict(components_file=dict(usedefault=True,
  ),
  ignore_exception=dict(nohash=True,
  usedefault=True,
  ),
- mask_file=dict(mandatory=False,
- ),
+ mask_file=dict(),
  num_components=dict(usedefault=True,
  ),
  realigned_file=dict(mandatory=True,

nipype/algorithms/tests/test_auto_FramewiseDisplacement.py

@@ -11,7 +11,8 @@ def test_FramewiseDisplacement_inputs():
  ignore_exception=dict(nohash=True,
  usedefault=True,
  ),
- in_plots=dict(),
+ in_plots=dict(mandatory=True,
+ ),
  normalize=dict(usedefault=True,
  ),
  out_figure=dict(usedefault=True,

nipype/algorithms/tests/test_auto_SpecifyModel.py

@@ -5,7 +5,7 @@
 
 def test_SpecifyModel_inputs():
  input_map = dict(event_files=dict(mandatory=True,
- xor=[u'subject_info', u'event_files'],
+ xor=['subject_info', 'event_files'],
  ),
  functional_runs=dict(copyfile=False,
  mandatory=True,
@@ -22,7 +22,7 @@ def test_SpecifyModel_inputs():
  realignment_parameters=dict(copyfile=False,
  ),
  subject_info=dict(mandatory=True,
- xor=[u'subject_info', u'event_files'],
+ xor=['subject_info', 'event_files'],
  ),
  time_repetition=dict(mandatory=True,
  ),

nipype/algorithms/tests/test_auto_SpecifySPMModel.py

@@ -7,7 +7,7 @@ def test_SpecifySPMModel_inputs():
  input_map = dict(concatenate_runs=dict(usedefault=True,
  ),
  event_files=dict(mandatory=True,
- xor=[u'subject_info', u'event_files'],
+ xor=['subject_info', 'event_files'],
  ),
  functional_runs=dict(copyfile=False,
  mandatory=True,
@@ -26,7 +26,7 @@ def test_SpecifySPMModel_inputs():
  realignment_parameters=dict(copyfile=False,
  ),
  subject_info=dict(mandatory=True,
- xor=[u'subject_info', u'event_files'],
+ xor=['subject_info', 'event_files'],
  ),
  time_repetition=dict(mandatory=True,
  ),

nipype/algorithms/tests/test_auto_SpecifySparseModel.py

@@ -5,7 +5,7 @@
 
 def test_SpecifySparseModel_inputs():
  input_map = dict(event_files=dict(mandatory=True,
- xor=[u'subject_info', u'event_files'],
+ xor=['subject_info', 'event_files'],
  ),
  functional_runs=dict(copyfile=False,
  mandatory=True,
@@ -30,13 +30,13 @@ def test_SpecifySparseModel_inputs():
  stimuli_as_impulses=dict(usedefault=True,
  ),
  subject_info=dict(mandatory=True,
- xor=[u'subject_info', u'event_files'],
+ xor=['subject_info', 'event_files'],
  ),
  time_acquisition=dict(mandatory=True,
  ),
  time_repetition=dict(mandatory=True,
  ),
- use_temporal_deriv=dict(requires=[u'model_hrf'],
+ use_temporal_deriv=dict(requires=['model_hrf'],
  ),
  volumes_in_cluster=dict(usedefault=True,
  ),

nipype/algorithms/tests/test_auto_TCompCor.py

@@ -4,14 +4,12 @@
 
 
 def test_TCompCor_inputs():
- input_map = dict(components_file=dict(mandatory=False,
- usedefault=True,
+ input_map = dict(components_file=dict(usedefault=True,
  ),
  ignore_exception=dict(nohash=True,
  usedefault=True,
  ),
- mask_file=dict(mandatory=False,
- ),
+ mask_file=dict(),
  num_components=dict(usedefault=True,
  ),
  percentile_threshold=dict(usedefault=True,

nipype/algorithms/tests/test_compcor.py

@@ -74,6 +74,28 @@ def test_compcor_no_regress_poly(self):
  ['-0.5367548139', '0.0059943226'],
  ['-0.0520809054', '0.2940637551']])
 
+ def test_tcompcor_asymmetric_dim(self):
+ asymmetric_shape = (2, 3, 4, 5)
+ asymmetric_data = utils.save_toy_nii(np.zeros(asymmetric_shape), 'asymmetric.nii')
+
+ TCompCor(realigned_file=asymmetric_data).run()
+ self.assertEqual(nb.load('mask.nii').get_data().shape, asymmetric_shape[:3])
+
+ def test_compcor_bad_input_shapes(self):
+ shape_less_than = (1, 2, 2, 5) # dim 0 is < dim 0 of self.mask_file (2)
+ shape_more_than = (3, 3, 3, 5) # dim 0 is > dim 0 of self.mask_file (2)
+
+ for data_shape in (shape_less_than, shape_more_than):
+ data_file = utils.save_toy_nii(np.zeros(data_shape), 'temp.nii')
+ interface = CompCor(realigned_file=data_file, mask_file=self.mask_file)
+ self.assertRaisesRegexp(ValueError, "dimensions", interface.run)
+
+ def test_tcompcor_bad_input_dim(self):
+ bad_dims = (2, 2, 2)
+ data_file = utils.save_toy_nii(np.zeros(bad_dims), 'temp.nii')
+ interface = TCompCor(realigned_file=data_file)
+ self.assertRaisesRegexp(ValueError, '4-D', interface.run)
+
  def run_cc(self, ccinterface, expected_components):
  # run
  ccresult = ccinterface.run()

nipype/interfaces/afni/tests/test_auto_AFNICommand.py

@@ -13,7 +13,7 @@ def test_AFNICommand_inputs():
  usedefault=True,
  ),
  out_file=dict(argstr='-prefix %s',
- name_source=[u'in_file'],
+ name_source=['in_file'],
  name_template='%s_afni',
  ),
  outputtype=dict(),

nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py

@@ -22,10 +22,10 @@ def test_AutoTcorrelate_inputs():
  mask=dict(argstr='-mask %s',
  ),
  mask_only_targets=dict(argstr='-mask_only_targets',
- xor=[u'mask_source'],
+ xor=['mask_source'],
  ),
  mask_source=dict(argstr='-mask_source %s',
- xor=[u'mask_only_targets'],
+ xor=['mask_only_targets'],
  ),
  out_file=dict(argstr='-prefix %s',
  name_source='in_file',

nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py

@@ -26,7 +26,7 @@ def test_BlurToFWHM_inputs():
  mask=dict(argstr='-blurmaster %s',
  ),
  out_file=dict(argstr='-prefix %s',
- name_source=[u'in_file'],
+ name_source=['in_file'],
  name_template='%s_afni',
  ),
  outputtype=dict(),

nipype/interfaces/afni/tests/test_auto_BrickStat.py

@@ -23,7 +23,7 @@ def test_BrickStat_inputs():
  position=1,
  ),
  out_file=dict(argstr='-prefix %s',
- name_source=[u'in_file'],
+ name_source=['in_file'],
  name_template='%s_afni',
  ),
  outputtype=dict(),

nipype/interfaces/afni/tests/test_auto_Calc.py

@@ -34,9 +34,9 @@ def test_Calc_inputs():
  ),
  outputtype=dict(),
  single_idx=dict(),
- start_idx=dict(requires=[u'stop_idx'],
+ start_idx=dict(requires=['stop_idx'],
  ),
- stop_idx=dict(requires=[u'start_idx'],
+ stop_idx=dict(requires=['start_idx'],
  ),
  terminal_output=dict(nohash=True,
  ),

nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py

@@ -26,7 +26,7 @@ def test_DegreeCentrality_inputs():
  oned_file=dict(argstr='-out1D %s',
  ),
  out_file=dict(argstr='-prefix %s',
- name_source=[u'in_file'],
+ name_source=['in_file'],
  name_template='%s_afni',
  ),
  outputtype=dict(),

nipype/interfaces/afni/tests/test_auto_ECM.py

@@ -34,7 +34,7 @@ def test_ECM_inputs():
  memory=dict(argstr='-memory %f',
  ),
  out_file=dict(argstr='-prefix %s',
- name_source=[u'in_file'],
+ name_source=['in_file'],
  name_template='%s_afni',
  ),
  outputtype=dict(),

nipype/interfaces/afni/tests/test_auto_Eval.py

@@ -36,9 +36,9 @@ def test_Eval_inputs():
  ),
  outputtype=dict(),
  single_idx=dict(),
- start_idx=dict(requires=[u'stop_idx'],
+ start_idx=dict(requires=['stop_idx'],
  ),
- stop_idx=dict(requires=[u'start_idx'],
+ stop_idx=dict(requires=['start_idx'],
  ),
  terminal_output=dict(nohash=True,
  ),

nipype/interfaces/afni/tests/test_auto_FWHMx.py

@@ -10,7 +10,7 @@ def test_FWHMx_inputs():
  args=dict(argstr='%s',
  ),
  arith=dict(argstr='-arith',
- xor=[u'geom'],
+ xor=['geom'],
  ),
  automask=dict(argstr='-automask',
  usedefault=True,
@@ -20,17 +20,17 @@ def test_FWHMx_inputs():
  compat=dict(argstr='-compat',
  ),
  demed=dict(argstr='-demed',
- xor=[u'detrend'],
+ xor=['detrend'],
  ),
  detrend=dict(argstr='-detrend',
  usedefault=True,
- xor=[u'demed'],
+ xor=['demed'],
  ),
  environ=dict(nohash=True,
  usedefault=True,
  ),
  geom=dict(argstr='-geom',
- xor=[u'arith'],
+ xor=['arith'],
  ),
  ignore_exception=dict(nohash=True,
  usedefault=True,

nipype/interfaces/afni/tests/test_auto_Hist.py

@@ -29,7 +29,7 @@ def test_Hist_inputs():
  ),
  out_file=dict(argstr='-prefix %s',
  keep_extension=False,
- name_source=[u'in_file'],
+ name_source=['in_file'],
  name_template='%s_hist',
  ),
  out_show=dict(argstr='> %s',

nipype/interfaces/afni/tests/test_auto_LFCD.py

@@ -24,7 +24,7 @@ def test_LFCD_inputs():
  mask=dict(argstr='-mask %s',
  ),
  out_file=dict(argstr='-prefix %s',
- name_source=[u'in_file'],
+ name_source=['in_file'],
  name_template='%s_afni',
  ),
  outputtype=dict(),

nipype/interfaces/afni/tests/test_auto_MaskTool.py

@@ -19,7 +19,7 @@ def test_MaskTool_inputs():
  usedefault=True,
  ),
  fill_dirs=dict(argstr='-fill_dirs %s',
- requires=[u'fill_holes'],
+ requires=['fill_holes'],
  ),
  fill_holes=dict(argstr='-fill_holes',
  ),

nipype/interfaces/afni/tests/test_auto_Notes.py

@@ -7,7 +7,7 @@ def test_Notes_inputs():
  input_map = dict(add=dict(argstr='-a "%s"',
  ),
  add_history=dict(argstr='-h "%s"',
- xor=[u'rep_history'],
+ xor=['rep_history'],
  ),
  args=dict(argstr='%s',
  ),
@@ -28,7 +28,7 @@ def test_Notes_inputs():
  ),
  outputtype=dict(),
  rep_history=dict(argstr='-HH "%s"',
- xor=[u'add_history'],
+ xor=['add_history'],
  ),
  ses=dict(argstr='-ses',
  ),