Correct TPM and dartel shooting template format;

Improved code.

Author: mfmachado

nipype/interfaces/cat12/preprocess.py

@@ -18,6 +18,8 @@
 )
 from nipype.utils.filemanip import split_filename, fname_presuffix
 
+from src.interfaces.cat12.surface import Cell
+
 
 class CAT12SegmentInputSpec(SPMCommandInputSpec):
     in_files = InputMultiPath(
@@ -41,6 +43,27 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
         copyfile=False,
     )
 
+    _help_shoots_tpm = (
+        'Shooting Template %d.  The Shooting template must be in multi-volume nifti format and should contain GM,'
+        ' WM, and background segmentations and have to be saved with at least 16 bit. '
+    )
+
+    shooting_tpm = ImageFileSPM(exists=True, field="extopts.registration.shooting.shootingtpm",
+                                desc=_help_shoots_tpm % 0, mandatory=False, copyfile=False)
+
+    shooting_tpm_template_1 = ImageFileSPM(
+        exists=True, desc=_help_shoots_tpm % 1, mandatory=False, copyfile=False
+    )
+    shooting_tpm_template_2 = ImageFileSPM(
+        exists=True, desc=_help_shoots_tpm % 2, mandatory=False, copyfile=False
+    )
+    shooting_tpm_template_3 = ImageFileSPM(
+        exists=True, desc=_help_shoots_tpm % 3, mandatory=False, copyfile=False
+    )
+    shooting_tpm_template_4 = ImageFileSPM(
+        exists=True, desc=_help_shoots_tpm % 4, mandatory=False, copyfile=False
+    )
+
     n_jobs = traits.Int(
         1, usedefault=True, mandatory=True, field="nproc", desc="Number of threads"
     )
@@ -239,13 +262,6 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
         copyfile=False,
     )
 
-    _dartel_help = (
-        "This option is to export data into a form that can be used with DARTEL. The SPM default is to "
-        "only apply rigid body transformation. However, a more appropriate option is to apply affine "
-        "transformation, because the additional scaling of the images requires less deformations to "
-        "non-linearly register brains to the template."
-    )
-
     # Grey matter
     gm_output_native = traits.Bool(
         False,
@@ -495,11 +511,14 @@ def __init__(self, **inputs):
 
     def _format_arg(self, opt, spec, val):
         """Convert input to appropriate format for spm"""
-        if opt in ["in_files"]:
+        if opt == "in_files":
             if isinstance(val, list):
                 return scans_for_fnames(val)
             else:
                 return scans_for_fname(val)
+        elif opt in ["tpm", "shooting_tpm"]:
+            return Cell2Str(val)
+
         return super(CAT12Segment, self)._format_arg(opt, spec, val)
 
     def _list_outputs(self):
@@ -513,9 +532,7 @@ def _list_outputs(self):
 
         for tidx, tissue in enumerate(["gm", "wm", "csf"]):
 
-            for idx, (image, prefix) in enumerate(
-                [("modulated", "mw"), ("dartel", "r"), ("native", "")]
-            ):
+            for image, prefix in [("modulated", "mw"), ("dartel", "r"), ("native", "")]:
                 outtype = f"{tissue}_output_{image}"
                 if isdefined(getattr(self.inputs, outtype)) and getattr(
                     self.inputs, outtype
@@ -552,7 +569,7 @@ def _list_outputs(self):
             str(report) for report in Path(pth).glob("report/*") if report.is_file()
         ]
 
-        outputs[f"report"] = fname_presuffix(
+        outputs["report"] = fname_presuffix(
             f, prefix=os.path.join("report", f"cat_"), suffix=".xml", use_ext=False
         )
 
@@ -561,10 +578,18 @@ def _list_outputs(self):
         ]
 
         outputs["label_rois"] = fname_presuffix(
-            f, prefix=os.path.join("label", f"catROIs_"), suffix=".xml", use_ext=False
+            f, prefix=os.path.join("label", "catROIs_"), suffix=".xml", use_ext=False
         )
         outputs["label_roi"] = fname_presuffix(
-            f, prefix=os.path.join("label", f"catROI_"), suffix=".xml", use_ext=False
+            f, prefix=os.path.join("label", "catROI_"), suffix=".xml", use_ext=False
         )
 
         return outputs
+
+
+class Cell2Str(Cell):
+
+    def __str__(self):
+        """Convert input to appropriate format for cat12
+        """
+        return "{'%s'}" % self.to_string()

nipype/interfaces/cat12/surface.py

@@ -1,9 +1,7 @@
 import os
 from pathlib import Path
 
-from traits.trait_base import _Undefined
-
-from nipype.interfaces.base import File, InputMultiPath, TraitedSpec, traits
+from nipype.interfaces.base import File, InputMultiPath, TraitedSpec, traits, isdefined
 from nipype.interfaces.spm import SPMCommand
 from nipype.interfaces.spm.base import SPMCommandInputSpec
 from nipype.utils.filemanip import split_filename
@@ -137,14 +135,14 @@ def _list_outputs(self):
             pth, base, ext = split_filename(filename)
             # The first part of the filename is rh.central or lh.central
             original_filename = base.split(".", 2)[-1]
-            for i, (extracted_parameter, parameter_name) in enumerate(names_outputs):
+            for extracted_parameter, parameter_name in names_outputs:
                 if extracted_parameter:
                     for hemisphere in ["rh", "lh"]:
                         all_files_hemisphere = hemisphere + "_extracted_files"
                         name_hemisphere = hemisphere + "_" + parameter_name
-                        if isinstance(outputs[name_hemisphere], _Undefined):
+                        if not isdefined(outputs[name_hemisphere]):
                             outputs[name_hemisphere] = []
-                        if isinstance(outputs[all_files_hemisphere], _Undefined):
+                        if not isdefined(outputs[all_files_hemisphere]):
                             outputs[all_files_hemisphere] = []
                         generated_filename = ".".join(
                             [hemisphere, parameter_name, original_filename]