Merge remote-tracking branch 'Januzz/jacobian_determinant'

Conflicts:
	CHANGES

Author: chrisgorgo

CHANGES

@@ -2,7 +2,7 @@ Next release
 ============
 
 * ENH: Add basic support for LSF plugin.
-* ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool
+* ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool, ants.JacobianDeterminant
 * ENH: New workflows: ants template building (both using 'ANTS' and the new 'antsRegistration')
 * ENH: New examples: how to use ANTS template building workflows (smri_ants_build_tmeplate), 
 	  how to set SGE specific options (smri_ants_build_template_new)

nipype/interfaces/ants/__init__.py

@@ -14,4 +14,4 @@
 from .segmentation import Atropos, N4BiasFieldCorrection
 
 # Utility Programs
-from .utils import AverageAffineTransform, AverageImages, MultiplyImages
+from .utils import AverageAffineTransform, AverageImages, MultiplyImages, JacobianDeterminant

nipype/interfaces/ants/utils.py

@@ -16,14 +16,18 @@
 from ...utils.filemanip import split_filename
 from nipype.interfaces.base import InputMultiPath
 
+
 class AverageAffineTransformInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(3, 2, argstr='%d', usedefault=False, mandatory=True, position=0, desc='image dimension (2 or 3)')
     output_affine_transform = File(argstr='%s', mandatory=True, position=1, desc='Outputfname.txt: the name of the resulting transform.')
-    transforms = InputMultiPath(File(exists=True), argstr='%s', mandatory=True, position=3, desc=('transforms to average') )
+    transforms = InputMultiPath(File(exists=True), argstr='%s', mandatory=True,
+                                position=3, desc=('transforms to average'))
+
 
 class AverageAffineTransformOutputSpec(TraitedSpec):
     affine_transform = File(exists=True, desc='average transform file')
 
+
 class AverageAffineTransform(ANTSCommand):
     """
     Examples
@@ -45,20 +49,24 @@ def _format_arg(self, opt, spec, val):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs['affine_transform'] = os.path.abspath(self.inputs.output_affine_transform)
+        outputs['affine_transform'] = os.path.abspath(
+            self.inputs.output_affine_transform)
         return outputs
 
 
 class AverageImagesInputSpec(ANTSCommandInputSpec):
-    dimension = traits.Enum(3, 2, argstr='%d', mandatory=True, position=0, desc='image dimension (2 or 3)')
+    dimension = traits.Enum(3, 2, argstr='%d', mandatory=True,
+                            position=0, desc='image dimension (2 or 3)')
     output_average_image = File("average.nii", argstr='%s', position=1, desc='the name of the resulting image.', usedefault=True, hash_files=False)
     normalize = traits.Bool(argstr="%d", mandatory=True, position=2, desc='Normalize: if true, the 2nd image' +
                             'is divided by its mean. This will select the largest image to average into.')
-    images = InputMultiPath(File(exists=True), argstr='%s', mandatory=True, position=3, desc=('image to apply transformation to (generally a coregistered functional)') )
+    images = InputMultiPath(File(exists=True), argstr='%s', mandatory=True, position=3, desc=('image to apply transformation to (generally a coregistered functional)'))
+
 
 class AverageImagesOutputSpec(TraitedSpec):
     output_average_image = File(exists=True, desc='average image file')
 
+
 class AverageImages(ANTSCommand):
     """
     Examples
@@ -81,18 +89,23 @@ def _format_arg(self, opt, spec, val):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs['output_average_image'] = os.path.realpath(self.inputs.output_average_image)
+        outputs['output_average_image'] = os.path.realpath(
+            self.inputs.output_average_image)
         return outputs
 
+
 class MultiplyImagesInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(3, 2, argstr='%d', usedefault=False, mandatory=True, position=0, desc='image dimension (2 or 3)')
-    first_input = File(argstr='%s', exists=True, mandatory=True, position=1, desc='image 1')
+    first_input = File(
+        argstr='%s', exists=True, mandatory=True, position=1, desc='image 1')
     second_input = traits.Either(File(exists=True), traits.Float, argstr='%s', mandatory=True, position=2, desc='image 2 or multiplication weight')
     output_product_image = File(argstr='%s', mandatory=True, position=3, desc='Outputfname.nii.gz: the name of the resulting image.')
 
+
 class MultiplyImagesOutputSpec(TraitedSpec):
     output_product_image = File(exists=True, desc='average image file')
 
+
 class MultiplyImages(ANTSCommand):
     """
     Examples
@@ -115,5 +128,61 @@ def _format_arg(self, opt, spec, val):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs['output_product_image'] = os.path.abspath(self.inputs.output_product_image)
+        outputs['output_product_image'] = os.path.abspath(
+            self.inputs.output_product_image)
+        return outputs
+
+
+class JacobianDeterminantInputSpec(ANTSCommandInputSpec):
+    dimension = traits.Enum(3, 2, argstr='%d', usedefault=False, mandatory=True, position=0, desc='image dimension (2 or 3)')
+    warp_file = File(argstr='%s', exists=True, mandatory=True,
+                     position=1, desc='input warp file')
+    output_prefix = File(argstr='%s', genfile=True, hash_files=False, position=2, desc='prefix of the output image filename: PREFIX(log)jacobian.nii.gz')
+    use_log = traits.Enum(0, 1, argstr='%d', mandatory=False, position=3,
+                          desc='log transform the jacobian determinant')
+    template_mask = File(argstr='%s', exists=True, mandatory=False, position=4,
+                         desc='template mask to adjust for head size')
+    norm_by_total = traits.Enum(0, 1, argstr='%d', mandatory=False, position=5, desc='normalize jacobian by total in mask to adjust for head size')
+    projection_vector = traits.List(traits.Float(), argstr='%s', sep='x', mandatory=False, position=6, desc='vector to project warp against')
+
+
+class JacobianDeterminantOutputSpec(TraitedSpec):
+    jacobian_image = File(exists=True, desc='(log transformed) jacobian image')
+
+
+class JacobianDeterminant(ANTSCommand):
+    """
+    Examples
+    --------
+    >>> from nipype.interfaces.ants import JacobianDeterminant
+    >>> jacobian = JacobianDeterminant()
+    >>> jacobian.inputs.dimension = 3
+    >>> jacobian.inputs.warp_file = 'ants_Warp.nii.gz'
+    >>> jacobian.inputs.output_prefix = 'Sub001_'
+    >>> jacobian.inputs.use_log = 1
+    >>> jacobian.cmdline
+    'ANTSJacobian 3 ants_Warp.nii.gz Sub001_ 1'
+    """
+
+    _cmd = 'ANTSJacobian'
+    input_spec = JacobianDeterminantInputSpec
+    output_spec = JacobianDeterminantOutputSpec
+
+    def _gen_filename(self, name):
+        if name == 'output_prefix':
+            output = self.inputs.output_prefix
+            if not isdefined(output):
+                _, name, ext = split_filename(self.inputs.warp_file)
+                output = name + '_'
+            return output
+        return None
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        if self.inputs.use_log == 1:
+            outputs['jacobian_image'] = os.path.abspath(
+                self._gen_filename('output_prefix') + 'logjacobian.nii.gz')
+        else:
+            outputs['jacobian_image'] = os.path.abspath(
+                self._gen_filename('output_prefix') + 'jacobian.nii.gz')
         return outputs