separate apply and calculate VDM in two classes

Author: Fabio Bernardoni

nipype/interfaces/spm/preprocess.py

@@ -39,21 +39,16 @@
 
 
 class FieldMapInputSpec(SPMCommandInputSpec):
- jobtype = traits.Enum(
- "calculatevdm",
- "applyvdm",
- usedefault=True,
- desc="one of: calculatevdm, applyvdm",
- )
+
  phase_file = File(
- # mandatory=True,
+ mandatory=True,
  exists=True,
  copyfile=False,
  field="subj.data.presubphasemag.phase",
  desc="presubstracted phase file",
  )
  magnitude_file = File(
- # mandatory=True,
+ mandatory=True,
  exists=True,
  copyfile=False,
  field="subj.data.presubphasemag.magnitude",
@@ -62,7 +57,7 @@ class FieldMapInputSpec(SPMCommandInputSpec):
  echo_times = traits.Tuple(
  traits.Float,
  traits.Float,
- # mandatory=True,
+ mandatory=True,
  field="subj.defaults.defaultsval.et",
  desc="short and long echo times",
  )
@@ -169,7 +164,7 @@ class FieldMapInputSpec(SPMCommandInputSpec):
  epi_file = File(
  copyfile=False,
  exists=True,
- # mandatory=True,
+ mandatory=True,
  field="subj.session.epi",
  desc="EPI to unwarp",
  )
@@ -195,6 +190,65 @@ class FieldMapInputSpec(SPMCommandInputSpec):
  desc="match anatomical image to EPI",
  )
 
+
+class FieldMapOutputSpec(TraitedSpec):
+ vdm = File(exists=True, desc="voxel difference map")
+
+
+class FieldMap(SPMCommand):
+ """Use the fieldmap toolbox from spm to calculate the voxel displacement map (VDM).
+
+ http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=173
+
+ .. important::
+
+ This interface does not deal with real/imag magnitude images nor
+ with the two phase files case.
+
+ Examples
+ --------
+ >>> from nipype.interfaces.spm import FieldMap
+ >>> fm = FieldMap()
+ >>> fm.inputs.phase_file = 'phase.nii'
+ >>> fm.inputs.magnitude_file = 'magnitude.nii'
+ >>> fm.inputs.echo_times = (5.19, 7.65)
+ >>> fm.inputs.blip_direction = 1
+ >>> fm.inputs.total_readout_time = 15.6
+ >>> fm.inputs.epi_file = 'epi.nii'
+ >>> fm.run() # doctest: +SKIP
+
+ """
+
+ input_spec = FieldMapInputSpec
+ output_spec = FieldMapOutputSpec
+ _jobtype = "tools"
+ _jobname = "fieldmap"
+
+ def _format_arg(self, opt, spec, val):
+ """Convert input to appropriate format for spm"""
+
+ if opt in ["phase_file", "magnitude_file", "anat_file", "epi_file"]:
+
+ return scans_for_fname(ensure_list(val))
+
+ return super(FieldMap, self)._format_arg(opt, spec, val)
+
+ def _parse_inputs(self):
+ """validate spm fieldmap options if set to None ignore"""
+
+ einputs = super(FieldMap, self)._parse_inputs()
+ return [{"calculatevdm": einputs[0]}]
+
+ def _list_outputs(self):
+ outputs = self._outputs().get()
+ jobtype = self.inputs.jobtype
+
+ outputs["vdm"] = fname_presuffix(self.inputs.phase_file, prefix="vdm5_sc")
+
+ return outputs
+
+class ApplyVDMInputSpec(SPMCommandInputSpec):
+
  in_files = InputMultiObject(
  traits.Either(
  ImageFileSPM(exists=True), traits.List(ImageFileSPM(exists=True))
@@ -207,7 +261,7 @@ class FieldMapInputSpec(SPMCommandInputSpec):
  vdmfile = File(
  field="data.vdmfile",
  desc="Voxel displacement map to use",
- mandatory=True,
+ #mandatory=True,
  copyfile=True,
  )
  distortion_direction = traits.Int(
@@ -253,25 +307,17 @@ class FieldMapInputSpec(SPMCommandInputSpec):
  desc="fieldmap corrected output prefix",
  )
 
-
-class FieldMapOutputSpec(TraitedSpec):
- vdm = File(exists=True, desc="voxel difference map")
-
+class ApplyVDMOutputSpec(TraitedSpec):
  out_files = OutputMultiPath(
  traits.Either(traits.List(File(exists=True)), File(exists=True)),
  desc=(
- "If jobtype is applyvdm, "
- "these will be the fieldmap corrected files."
- " Otherwise, they will be copies "
- "of in_files that have had their "
- "headers rewritten."
+ "These will be the fieldmap corrected files."
  ),
  )
  mean_image = File(exists=True, desc="Mean image")
 
-
-class FieldMap(SPMCommand):
- """Use the fieldmap toolbox from spm to calculate the voxel displacement map (VDM).
+class ApplyVDM(SPMCommand):
+ """Use the fieldmap toolbox from spm to apply the voxel displacement map (VDM) to some epi files.
 
  http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=173
 
@@ -280,114 +326,54 @@ class FieldMap(SPMCommand):
  This interface does not deal with real/imag magnitude images nor
  with the two phase files case.
 
- Examples
- --------
- >>> from nipype.interfaces.spm import FieldMap
- >>> fm = FieldMap()
- >>> fm.inputs.phase_file = 'phase.nii'
- >>> fm.inputs.magnitude_file = 'magnitude.nii'
- >>> fm.inputs.echo_times = (5.19, 7.65)
- >>> fm.inputs.blip_direction = 1
- >>> fm.inputs.total_readout_time = 15.6
- >>> fm.inputs.epi_file = 'epi.nii'
- >>> fm.run() # doctest: +SKIP
-
  """
 
- input_spec = FieldMapInputSpec
- output_spec = FieldMapOutputSpec
+ input_spec = ApplyVDMInputSpec
+ output_spec = ApplyVDMOutputSpec
  _jobtype = "tools"
  _jobname = "fieldmap"
 
  def _format_arg(self, opt, spec, val):
  """Convert input to appropriate format for spm"""
 
- if (self.inputs.jobtype == "calculatevdm") and (
- opt in ["phase_file", "magnitude_file", "anat_file", "epi_file"]
- ):
-
- return scans_for_fname(ensure_list(val))
-
- if (self.inputs.jobtype == "applyvdm") and (opt == "in_files"):
- return scans_for_fnames(ensure_list(val))
- if (self.inputs.jobtype == "applyvdm") and (opt == "vdmfile"):
+ if opt in ["in_files", "vdmfile"]:
  return scans_for_fname(ensure_list(val))
  return super(FieldMap, self)._format_arg(opt, spec, val)
 
  def _parse_inputs(self):
  """validate spm fieldmap options if set to None ignore"""
 
- if self.inputs.jobtype == "applyvdm":
- einputs = super(FieldMap, self)._parse_inputs(
- skip=(
- "jobtype",
- "phase_file",
- "magnitude_file",
- "echo_times",
- "blip_direction",
- "total_readout_time",
- "maskbrain",
- "epifm",
- "jacobian_modulation",
- "method",
- "unwarp_fwhm",
- "pad",
- "ws",
- "template",
- "mask_fwhm",
- "nerode",
- "ndilate",
- "thresh",
- "reg",
- "epi_file",
- "matchvdm",
- "sessname",
- "writeunwarped",
- "anat_file",
- "matchanat",
- )
- )
-
- else:
- einputs = super(FieldMap, self)._parse_inputs(
- skip=("jobtype", "in_files", "vdmfile")
- )
- jobtype = self.inputs.jobtype
+ einputs = super(ApplyVDM, self)._parse_inputs()
 
- return [{"%s" % (jobtype): einputs[0]}]
+ return [{"applymap": einputs[0]}]
 
  def _list_outputs(self):
  outputs = self._outputs().get()
  jobtype = self.inputs.jobtype
  resliced_all = self.inputs.write_which[0] > 0
  resliced_mean = self.inputs.write_which[1] > 0
- if jobtype == "calculatevdm":
- outputs["vdm"] = fname_presuffix(self.inputs.phase_file, prefix="vdm5_sc")
- elif jobtype == "applyvdm":
- if resliced_mean:
- if isinstance(self.inputs.in_files[0], list):
- first_image = self.inputs.in_files[0][0]
- else:
- first_image = self.inputs.in_files[0]
- outputs["mean_image"] = fname_presuffix(first_image, prefix="meanu")
+ if resliced_mean:
+ if isinstance(self.inputs.in_files[0], list):
+ first_image = self.inputs.in_files[0][0]
+ else:
+ first_image = self.inputs.in_files[0]
+ outputs["mean_image"] = fname_presuffix(first_image, prefix="meanu")
 
- if resliced_all:
- outputs["out_files"] = []
- for idx, imgf in enumerate(ensure_list(self.inputs.in_files)):
- appliedvdm_run = []
- if isinstance(imgf, list):
- for i, inner_imgf in enumerate(ensure_list(imgf)):
- newfile = fname_presuffix(
- inner_imgf, prefix=self.inputs.out_prefix
- )
- appliedvdm_run.append(newfile)
- else:
- appliedvdm_run = fname_presuffix(
- imgf, prefix=self.inputs.out_prefix
+ if resliced_all:
+ outputs["out_files"] = []
+ for idx, imgf in enumerate(ensure_list(self.inputs.in_files)):
+ appliedvdm_run = []
+ if isinstance(imgf, list):
+ for i, inner_imgf in enumerate(ensure_list(imgf)):
+ newfile = fname_presuffix(
+ inner_imgf, prefix=self.inputs.out_prefix
  )
- outputs["out_files"].append(appliedvdm_run)
- return outputs
-
+ appliedvdm_run.append(newfile)
+ else:
+ appliedvdm_run = fname_presuffix(
+ imgf, prefix=self.inputs.out_prefix
+ )
+ outputs["out_files"].append(appliedvdm_run)
  return outputs