fix: make specs

Author: oesteban

nipype/interfaces/ants/__init__.py

@@ -3,7 +3,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Top-level namespace for ants."""
 
-# RegistratIon programs
+# Registration programs
 from .registration import (
     ANTS,
     CompositeTransformUtil,

nipype/interfaces/ants/tests/test_auto_AI.py

@@ -0,0 +1,37 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..utils import AI
+
+
+def test_AI_inputs():
+    input_map = dict(
+        args=dict(argstr="%s",),
+        convergence=dict(argstr="-c [%d,%g,%d]", usedefault=True,),
+        dimension=dict(argstr="-d %d", usedefault=True,),
+        environ=dict(nohash=True, usedefault=True,),
+        fixed_image=dict(extensions=None, mandatory=True,),
+        fixed_image_mask=dict(argstr="-x %s", extensions=None,),
+        metric=dict(argstr="-m %s", mandatory=True,),
+        moving_image=dict(extensions=None, mandatory=True,),
+        moving_image_mask=dict(extensions=None, requires=["fixed_image_mask"],),
+        num_threads=dict(nohash=True, usedefault=True,),
+        output_transform=dict(argstr="-o %s", extensions=None, usedefault=True,),
+        principal_axes=dict(argstr="-p %d", usedefault=True, xor=["blobs"],),
+        search_factor=dict(argstr="-s [%g,%g]", usedefault=True,),
+        search_grid=dict(argstr="-g %s",),
+        transform=dict(argstr="-t %s[%g]", usedefault=True,),
+        verbose=dict(argstr="-v %d", usedefault=True,),
+    )
+    inputs = AI.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_AI_outputs():
+    output_map = dict(output_transform=dict(extensions=None,),)
+    outputs = AI.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/ants/tests/test_auto_Atropos.py

@@ -13,6 +13,7 @@ def test_Atropos_inputs():
             argstr="%s", mandatory=True, requires=["number_of_tissue_classes"],
         ),
         intensity_images=dict(argstr="--intensity-image %s...", mandatory=True,),
+        kmeans_init_centers=dict(),
         likelihood_model=dict(argstr="--likelihood-model %s",),
         mask_image=dict(argstr="--mask-image %s", extensions=None, mandatory=True,),
         maximum_number_of_icm_terations=dict(requires=["icm_use_synchronous_update"],),
@@ -26,7 +27,7 @@ def test_Atropos_inputs():
         ),
         output_posteriors_name_template=dict(usedefault=True,),
         posterior_formulation=dict(argstr="%s",),
-        prior_probability_images=dict(),
+        prior_image=dict(),
         prior_probability_threshold=dict(requires=["prior_weighting"],),
         prior_weighting=dict(),
         save_posteriors=dict(),

nipype/interfaces/ants/tests/test_auto_ImageMath.py

@@ -0,0 +1,37 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..utils import ImageMath
+
+
+def test_ImageMath_inputs():
+    input_map = dict(
+        args=dict(argstr="%s",),
+        copy_header=dict(usedefault=True,),
+        dimension=dict(argstr="%d", position=1, usedefault=True,),
+        environ=dict(nohash=True, usedefault=True,),
+        num_threads=dict(nohash=True, usedefault=True,),
+        op1=dict(argstr="%s", extensions=None, mandatory=True, position=-2,),
+        op2=dict(argstr="%s", position=-1,),
+        operation=dict(argstr="%s", mandatory=True, position=3,),
+        output_image=dict(
+            argstr="%s",
+            extensions=None,
+            keep_extension=True,
+            name_source=["op1"],
+            name_template="%s_maths",
+            position=2,
+        ),
+    )
+    inputs = ImageMath.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_ImageMath_outputs():
+    output_map = dict(output_image=dict(extensions=None,),)
+    outputs = ImageMath.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/ants/tests/test_auto_JointFusion.py

@@ -0,0 +1,59 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..segmentation import JointFusion
+
+
+def test_JointFusion_inputs():
+    input_map = dict(
+        alpha=dict(argstr="-a %s", usedefault=True,),
+        args=dict(argstr="%s",),
+        atlas_image=dict(argstr="-g %s...", mandatory=True,),
+        atlas_segmentation_image=dict(argstr="-l %s...", mandatory=True,),
+        beta=dict(argstr="-b %s", usedefault=True,),
+        constrain_nonnegative=dict(argstr="-c", usedefault=True,),
+        dimension=dict(argstr="-d %d",),
+        environ=dict(nohash=True, usedefault=True,),
+        exclusion_image=dict(),
+        exclusion_image_label=dict(argstr="-e %s", requires=["exclusion_image"],),
+        mask_image=dict(argstr="-x %s", extensions=None,),
+        num_threads=dict(nohash=True, usedefault=True,),
+        out_atlas_voting_weight_name_format=dict(
+            requires=[
+                "out_label_fusion",
+                "out_intensity_fusion_name_format",
+                "out_label_post_prob_name_format",
+            ],
+        ),
+        out_intensity_fusion_name_format=dict(argstr="",),
+        out_label_fusion=dict(argstr="%s", extensions=None, hash_files=False,),
+        out_label_post_prob_name_format=dict(
+            requires=["out_label_fusion", "out_intensity_fusion_name_format"],
+        ),
+        patch_metric=dict(argstr="-m %s",),
+        patch_radius=dict(argstr="-p %s", maxlen=3, minlen=3,),
+        retain_atlas_voting_images=dict(argstr="-f", usedefault=True,),
+        retain_label_posterior_images=dict(
+            argstr="-r", requires=["atlas_segmentation_image"], usedefault=True,
+        ),
+        search_radius=dict(argstr="-s %s", usedefault=True,),
+        target_image=dict(argstr="-t %s", mandatory=True,),
+        verbose=dict(argstr="-v",),
+    )
+    inputs = JointFusion.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_JointFusion_outputs():
+    output_map = dict(
+        out_atlas_voting_weight=dict(),
+        out_intensity_fusion=dict(),
+        out_label_fusion=dict(extensions=None,),
+        out_label_post_prob=dict(),
+    )
+    outputs = JointFusion.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/ants/tests/test_auto_ResampleImageBySpacing.py

@@ -0,0 +1,38 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..utils import ResampleImageBySpacing
+
+
+def test_ResampleImageBySpacing_inputs():
+    input_map = dict(
+        addvox=dict(argstr="%d", position=6, requires=["apply_smoothing"],),
+        apply_smoothing=dict(argstr="%d", position=5,),
+        args=dict(argstr="%s",),
+        dimension=dict(argstr="%d", position=1, usedefault=True,),
+        environ=dict(nohash=True, usedefault=True,),
+        input_image=dict(argstr="%s", extensions=None, mandatory=True, position=2,),
+        nn_interp=dict(argstr="%d", position=-1, requires=["addvox"],),
+        num_threads=dict(nohash=True, usedefault=True,),
+        out_spacing=dict(argstr="%s", mandatory=True, position=4,),
+        output_image=dict(
+            argstr="%s",
+            extensions=None,
+            keep_extension=True,
+            name_source=["input_image"],
+            name_template="%s_resampled",
+            position=3,
+        ),
+    )
+    inputs = ResampleImageBySpacing.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_ResampleImageBySpacing_outputs():
+    output_map = dict(output_image=dict(extensions=None,),)
+    outputs = ResampleImageBySpacing.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/ants/tests/test_auto_ThresholdImage.py

@@ -0,0 +1,47 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..utils import ThresholdImage
+
+
+def test_ThresholdImage_inputs():
+    input_map = dict(
+        args=dict(argstr="%s",),
+        copy_header=dict(mandatory=True, usedefault=True,),
+        dimension=dict(argstr="%d", position=1, usedefault=True,),
+        environ=dict(nohash=True, usedefault=True,),
+        input_image=dict(argstr="%s", extensions=None, mandatory=True, position=2,),
+        input_mask=dict(argstr="%s", extensions=None, requires=["num_thresholds"],),
+        inside_value=dict(argstr="%f", position=6, requires=["th_low"],),
+        mode=dict(
+            argstr="%s",
+            position=4,
+            requires=["num_thresholds"],
+            xor=["th_low", "th_high"],
+        ),
+        num_threads=dict(nohash=True, usedefault=True,),
+        num_thresholds=dict(argstr="%d", position=5,),
+        output_image=dict(
+            argstr="%s",
+            extensions=None,
+            keep_extension=True,
+            name_source=["input_image"],
+            name_template="%s_resampled",
+            position=3,
+        ),
+        outside_value=dict(argstr="%f", position=7, requires=["th_low"],),
+        th_high=dict(argstr="%f", position=5, xor=["mode"],),
+        th_low=dict(argstr="%f", position=4, xor=["mode"],),
+    )
+    inputs = ThresholdImage.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_ThresholdImage_outputs():
+    output_map = dict(output_image=dict(extensions=None,),)
+    outputs = ThresholdImage.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value