Finished TODO items in ApplyTransforms and added option to Atropos

Added interpolation_parameters, float and verbose to ApplyTransforms and added use_random_seed and verbose to Atropos

Author: blakedewey

nipype/interfaces/ants/resampling.py

@@ -253,6 +253,9 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
     default_value = traits.Float(0.0, argstr='--default-value %g', usedefault=True)
     print_out_composite_warp_file = traits.Bool(False, requires=["output_image"],
                                                 desc='output a composite warp file instead of a transformed image')
+    float = traits.Bool(argstr='--float %d', default=False, desc='Use float instead of double for computations.')
+    # Verbose Output
+    verbose = traits.Bool(True, argstr='--verbose %d', desc='enable verbose logging', usedefault=True)
 
 
 class ApplyTransformsOutputSpec(TraitedSpec):
@@ -279,7 +282,7 @@ class ApplyTransforms(ANTSCommand):
     >>> at.cmdline
     'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation Linear \
 --output deformed_moving1.nii --reference-image fixed1.nii --transform [ trans.mat, 0 ] \
---transform [ ants_Warp.nii.gz, 0 ]'
+--transform [ ants_Warp.nii.gz, 0 ] --verbose 1'
 
     >>> at1 = ApplyTransforms()
     >>> at1.inputs.dimension = 3
@@ -294,7 +297,7 @@ class ApplyTransforms(ANTSCommand):
     >>> at1.cmdline
     'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation BSpline[ 5 ] \
 --output deformed_moving1.nii --reference-image fixed1.nii --transform [ trans.mat, 0 ] \
---transform [ ants_Warp.nii.gz, 0 ]'
+--transform [ ants_Warp.nii.gz, 0 ] --verbose 1'
 
 
     """

nipype/interfaces/ants/segmentation.py

@@ -44,13 +44,17 @@ class AtroposInputSpec(ANTSCommandInputSpec):
     n_iterations = traits.Int(argstr="%s")
     convergence_threshold = traits.Float(requires=['n_iterations'])
     posterior_formulation = traits.Str(argstr="%s")
+    use_random_seed = traits.Bool(True, argstr='--use-random-seed %d', desc='use random seed value over constant',
+                                  usedefault=True)
     use_mixture_model_proportions = traits.Bool(
         requires=['posterior_formulation'])
     out_classified_image_name = File(argstr="%s", genfile=True,
                                      hash_files=False)
     save_posteriors = traits.Bool()
     output_posteriors_name_template = traits.Str('POSTERIOR_%02d.nii.gz',
                                                  usedefault=True)
+    # Verbose Output
+    verbose = traits.Bool(True, argstr='--verbose %d', desc='enable verbose logging', usedefault=True)
 
 
 class AtroposOutputSpec(TraitedSpec):
@@ -92,7 +96,8 @@ class Atropos(ANTSCommand):
     'Atropos --image-dimensionality 3 --icm [1,1] \
 --initialization PriorProbabilityImages[2,priors/priorProbImages%02d.nii,0.8,1e-07] --intensity-image structural.nii \
 --likelihood-model Gaussian --mask-image mask.nii --mrf [0.2,1x1x1] --convergence [5,1e-06] \
---output [structural_labeled.nii,POSTERIOR_%02d.nii.gz] --posterior-formulation Socrates[1]'
+--output [structural_labeled.nii,POSTERIOR_%02d.nii.gz] --posterior-formulation Socrates[1] --use-random-seed 1 \
+--verbose 1'
     """
     input_spec = AtroposInputSpec
     output_spec = AtroposOutputSpec

nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py

@@ -14,6 +14,8 @@ def test_ApplyTransforms_inputs():
     environ=dict(nohash=True,
     usedefault=True,
     ),
+    float=dict(argstr='--float %d',
+    ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
@@ -46,6 +48,9 @@ def test_ApplyTransforms_inputs():
     transforms=dict(argstr='%s',
     mandatory=True,
     ),
+    verbose=dict(argstr='--verbose %d',
+    usedefault=True,
+    ),
     )
     inputs = ApplyTransforms.input_spec()
 

nipype/interfaces/ants/tests/test_auto_Atropos.py

@@ -61,6 +61,12 @@ def test_Atropos_inputs():
     ),
     use_mixture_model_proportions=dict(requires=['posterior_formulation'],
     ),
+    use_random_seed=dict(argstr='--use-random-seed %d',
+    usedefault=True,
+    ),
+    verbose=dict(argstr='--verbose %d',
+    usedefault=True,
+    ),
     )
     inputs = Atropos.input_spec()