Compile

childmindresearch · Dec 20, 2024 · 86301d1 · 86301d1
1 parent b8fa66a
commit 86301d1
Show file tree

Hide file tree

Showing 81 changed files with 411 additions and 411 deletions.
diff --git a/python/src/niwrap/afni/apsearch.py b/python/src/niwrap/afni/apsearch.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 APSEARCH_METADATA = Metadata(
-    id="daa8fa19d4d15fe37e1fd44af2f41bbb1e0649d7.boutiques",
+    id="d759bc178b2620ea44d398387e0405f577daa6c5.boutiques",
     name="apsearch",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -26,7 +26,7 @@ class ApsearchOutputs(typing.NamedTuple):
 
 def apsearch(
     search_term: str,
-    file_output: InputPathType | None = None,
+    file_output: str | None = None,
     verbose: bool = False,
     runner: Runner | None = None,
 ) -> ApsearchOutputs:
@@ -51,12 +51,12 @@ def apsearch(
     cargs.append("apsearch")
     cargs.append(search_term)
     if file_output is not None:
-        cargs.append(execution.input_file(file_output))
+        cargs.append(file_output)
     if verbose:
         cargs.append("-v")
     ret = ApsearchOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(pathlib.Path(file_output).name) if (file_output is not None) else None,
+        output_file=execution.output_file(file_output) if (file_output is not None) else None,
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/afni/imand.py b/python/src/niwrap/afni/imand.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 IMAND_METADATA = Metadata(
-    id="c48ca42cf72c91b13a658c727dcfb9f75ba40bf0.boutiques",
+    id="0afb6402a062c937d946cf010c86102b9c4a0c96.boutiques",
     name="imand",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -26,7 +26,7 @@ class ImandOutputs(typing.NamedTuple):
 
 def imand(
     input_images: list[InputPathType],
-    output_image: InputPathType,
+    output_image: str,
     threshold: float | None = None,
     runner: Runner | None = None,
 ) -> ImandOutputs:
@@ -58,10 +58,10 @@ def imand(
             str(threshold)
         ])
     cargs.extend([execution.input_file(f) for f in input_images])
-    cargs.append(execution.input_file(output_image))
+    cargs.append(output_image)
     ret = ImandOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(pathlib.Path(output_image).name),
+        outfile=execution.output_file(output_image),
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/afni/imrotate.py b/python/src/niwrap/afni/imrotate.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 IMROTATE_METADATA = Metadata(
-    id="91ce2622ebf37f0ee8816748397e7f0cf65a832b.boutiques",
+    id="046eb12264816ed4b6d2246d2d697caf596e0670.boutiques",
     name="imrotate",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -29,7 +29,7 @@ def imrotate(
     dy: float,
     phi: float,
     input_image: InputPathType,
-    output_image: InputPathType,
+    output_image: str,
     fourier_interpolation: bool = False,
     runner: Runner | None = None,
 ) -> ImrotateOutputs:
@@ -61,10 +61,10 @@ def imrotate(
     cargs.append(str(dy))
     cargs.append(str(phi))
     cargs.append(execution.input_file(input_image))
-    cargs.append(execution.input_file(output_image))
+    cargs.append(output_image)
     ret = ImrotateOutputs(
         root=execution.output_file("."),
-        output_image_file=execution.output_file(pathlib.Path(output_image).name),
+        output_image_file=execution.output_file(output_image),
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/afni/qhull.py b/python/src/niwrap/afni/qhull.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 QHULL_METADATA = Metadata(
-    id="c66bd98623328e49e50c28ca6d4ac9a47c26c314.boutiques",
+    id="d25dad9388d53afd5a2f6019c508abe651c2e611.boutiques",
     name="qhull",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -45,7 +45,7 @@ def qhull(
     geomview_output: bool = False,
     mathematica_output: bool = False,
     print_facets: str | None = None,
-    output_file: InputPathType | None = None,
+    output_file: str | None = None,
     runner: Runner | None = None,
 ) -> QhullOutputs:
     """
@@ -136,11 +136,11 @@ def qhull(
     if output_file is not None:
         cargs.extend([
             "TO",
-            execution.input_file(output_file)
+            output_file
         ])
     ret = QhullOutputs(
         root=execution.output_file("."),
-        output_results=execution.output_file(pathlib.Path(output_file).name + ".txt") if (output_file is not None) else None,
+        output_results=execution.output_file(output_file + ".txt") if (output_file is not None) else None,
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/afni/quotize.py b/python/src/niwrap/afni/quotize.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 QUOTIZE_METADATA = Metadata(
-    id="6c4eed808717d714bfc54617b8f18dc0c60724e7.boutiques",
+    id="d23de9ba9a8a0ec51eec10d409b73d3f766156d0.boutiques",
     name="quotize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -27,7 +27,7 @@ class QuotizeOutputs(typing.NamedTuple):
 def quotize(
     name: str,
     input_file: InputPathType,
-    output_file: InputPathType,
+    output_file: str,
     runner: Runner | None = None,
 ) -> QuotizeOutputs:
     """
@@ -52,10 +52,10 @@ def quotize(
     cargs.append("quotize")
     cargs.append(name)
     cargs.append(execution.input_file(input_file))
-    cargs.append(execution.input_file(output_file))
+    cargs.append(output_file)
     ret = QuotizeOutputs(
         root=execution.output_file("."),
-        array_output=execution.output_file(pathlib.Path(output_file).name),
+        array_output=execution.output_file(output_file),
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/afni/surf_smooth.py b/python/src/niwrap/afni/surf_smooth.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 SURF_SMOOTH_METADATA = Metadata(
-    id="9567232249acc1b0e69c280f3ce45f44bb256c86.boutiques",
+    id="d12bfab32f106014ff3d8c52a7b720c737313260.boutiques",
     name="SurfSmooth",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -31,7 +31,7 @@ def surf_smooth(
     target_fwhm: float | None = None,
     fwhm: float | None = None,
     number_iterations: float | None = None,
-    output_file: InputPathType | None = None,
+    output_file: str | None = None,
     band_pass_frequency: float | None = None,
     lambda_mu: str | None = None,
     interp_weights: str | None = None,
@@ -118,7 +118,7 @@ def surf_smooth(
     if output_file is not None:
         cargs.extend([
             "-output",
-            execution.input_file(output_file)
+            output_file
         ])
     if band_pass_frequency is not None:
         cargs.extend([
@@ -161,7 +161,7 @@ def surf_smooth(
         ])
     ret = SurfSmoothOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(pathlib.Path(output_file).name) if (output_file is not None) else None,
+        out_file=execution.output_file(output_file) if (output_file is not None) else None,
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/ants/add_noise_to_image.py b/python/src/niwrap/ants/add_noise_to_image.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 ADD_NOISE_TO_IMAGE_METADATA = Metadata(
-    id="e8efbf11871081a5ad3301baf672f8de93471bd0.boutiques",
+    id="5da8ee75f74c156a91ae2c476ce7533d884a9bda.boutiques",
     name="AddNoiseToImage",
     package="ants",
     container_image_tag="antsx/ants:v2.5.3",
@@ -27,7 +27,7 @@ class AddNoiseToImageOutputs(typing.NamedTuple):
 def add_noise_to_image(
     input_image: InputPathType,
     noise_model: typing.Literal["AdditiveGaussian", "SaltAndPepper", "Shot", "Speckle"],
-    output: InputPathType,
+    output: str,
     image_dimensionality: typing.Literal[2, 3, 4] | None = None,
     verbose: typing.Literal[0, 1] | None = None,
     runner: Runner | None = None,
@@ -72,7 +72,7 @@ def add_noise_to_image(
     ])
     cargs.extend([
         "--output",
-        execution.input_file(output)
+        output
     ])
     if verbose is not None:
         cargs.extend([
@@ -81,7 +81,7 @@ def add_noise_to_image(
         ])
     ret = AddNoiseToImageOutputs(
         root=execution.output_file("."),
-        noise_corrupted_image=execution.output_file(pathlib.Path(output).name),
+        noise_corrupted_image=execution.output_file(output),
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/ants/ants_align_origin.py b/python/src/niwrap/ants/ants_align_origin.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 ANTS_ALIGN_ORIGIN_METADATA = Metadata(
-    id="6857aca2f492ef8646affc2ca57d3ca2675b0b13.boutiques",
+    id="74cc71ee1dbe0d0c58e8719cd30215507f2ae81e.boutiques",
     name="antsAlignOrigin",
     package="ants",
     container_image_tag="antsx/ants:v2.5.3",
@@ -27,7 +27,7 @@ class AntsAlignOriginOutputs(typing.NamedTuple):
 def ants_align_origin(
     input_: InputPathType,
     reference_image: InputPathType,
-    output: InputPathType,
+    output: str,
     dimensionality: typing.Literal[2, 3] | None = None,
     runner: Runner | None = None,
 ) -> AntsAlignOriginOutputs:
@@ -74,11 +74,11 @@ def ants_align_origin(
     ])
     cargs.extend([
         "--output",
-        execution.input_file(output)
+        output
     ])
     ret = AntsAlignOriginOutputs(
         root=execution.output_file("."),
-        aligned_image=execution.output_file(pathlib.Path(output).name),
+        aligned_image=execution.output_file(output),
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/ants/ants_landmark_based_transform_initializer.py b/python/src/niwrap/ants/ants_landmark_based_transform_initializer.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 ANTS_LANDMARK_BASED_TRANSFORM_INITIALIZER_METADATA = Metadata(
-    id="e680d25c4b1661ea27d0968828f088b5d76779fa.boutiques",
+    id="0a1f0f529ca0b132289382b0bfa307fd1e5cda95.boutiques",
     name="antsLandmarkBasedTransformInitializer",
     package="ants",
     container_image_tag="antsx/ants:v2.5.3",
@@ -29,7 +29,7 @@ def ants_landmark_based_transform_initializer(
     fixed_image: InputPathType,
     moving_image: InputPathType,
     transform_type: typing.Literal["rigid", "affine", "bspline"],
-    output_transform: InputPathType,
+    output_transform: str,
     mesh_size: str | None = None,
     number_of_levels: int | None = None,
     order: int | None = None,
@@ -74,7 +74,7 @@ def ants_landmark_based_transform_initializer(
     cargs.append(execution.input_file(fixed_image))
     cargs.append(execution.input_file(moving_image))
     cargs.append(transform_type)
-    cargs.append(execution.input_file(output_transform))
+    cargs.append(output_transform)
     if mesh_size is not None:
         cargs.append(mesh_size)
     if number_of_levels is not None:
@@ -87,7 +87,7 @@ def ants_landmark_based_transform_initializer(
         cargs.append(execution.input_file(landmark_weights))
     ret = AntsLandmarkBasedTransformInitializerOutputs(
         root=execution.output_file("."),
-        output_transform=execution.output_file(pathlib.Path(output_transform).name),
+        output_transform=execution.output_file(output_transform),
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/ants/ants_motion_corr_stats.py b/python/src/niwrap/ants/ants_motion_corr_stats.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 ANTS_MOTION_CORR_STATS_METADATA = Metadata(
-    id="d29996fec64fd395bafc8947a76eea2b5d1ba04c.boutiques",
+    id="ae93cc3983b8309bee22c105a3b82c9e97354cf5.boutiques",
     name="antsMotionCorrStats",
     package="ants",
     container_image_tag="antsx/ants:v2.5.3",
@@ -27,7 +27,7 @@ class AntsMotionCorrStatsOutputs(typing.NamedTuple):
 def ants_motion_corr_stats(
     mask: InputPathType,
     moco_params: InputPathType,
-    output: InputPathType,
+    output: str,
     transform_index: int | None = None,
     framewise: typing.Literal[0, 1] | None = None,
     spatial_map: bool = False,
@@ -72,7 +72,7 @@ def ants_motion_corr_stats(
     ])
     cargs.extend([
         "-o",
-        execution.input_file(output)
+        output
     ])
     if transform_index is not None:
         cargs.extend([
@@ -90,7 +90,7 @@ def ants_motion_corr_stats(
         cargs.append("-d")
     ret = AntsMotionCorrStatsOutputs(
         root=execution.output_file("."),
-        corrected_csv=execution.output_file(pathlib.Path(output).name),
+        corrected_csv=execution.output_file(output),
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/ants/convert_scalar_image_to_rgb.py b/python/src/niwrap/ants/convert_scalar_image_to_rgb.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 CONVERT_SCALAR_IMAGE_TO_RGB_METADATA = Metadata(
-    id="bd90be2304f55e5624a9a746b1b00f9df35ab8d6.boutiques",
+    id="9ca4a7950c397eac7a9318ce90e2920bf4776ea6.boutiques",
     name="ConvertScalarImageToRGB",
     package="ants",
     container_image_tag="antsx/ants:v2.5.3",
@@ -27,7 +27,7 @@ class ConvertScalarImageToRgbOutputs(typing.NamedTuple):
 def convert_scalar_image_to_rgb(
     image_dimension: int,
     input_image: InputPathType,
-    output_image: InputPathType,
+    output_image: str,
     mask: InputPathType,
     colormap: typing.Literal["grey", "red", "green", "blue", "copper", "jet", "hsv", "spring", "summer", "autumn", "winter", "hot", "cool", "overunder", "custom"],
     custom_colormap_file: InputPathType | None = None,
@@ -72,7 +72,7 @@ def convert_scalar_image_to_rgb(
     cargs.append("ConvertScalarImageToRGB")
     cargs.append(str(image_dimension))
     cargs.append(execution.input_file(input_image))
-    cargs.append(execution.input_file(output_image))
+    cargs.append(output_image)
     cargs.append(execution.input_file(mask))
     cargs.append(colormap)
     if custom_colormap_file is not None:
@@ -89,7 +89,7 @@ def convert_scalar_image_to_rgb(
         cargs.append(vtk_lookup_table)
     ret = ConvertScalarImageToRgbOutputs(
         root=execution.output_file("."),
-        output_rgb_image=execution.output_file(pathlib.Path(output_image).name),
+        output_rgb_image=execution.output_file(output_image),
     )
     execution.run(cargs)
     return ret