niwrap-freesurfer 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_topo_fixer.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_TOPO_FIXER_METADATA = Metadata(
-    id="8f80d79d55bacb40b2cbd2f6150f071f3dec1313.boutiques",
+    id="130981631be6b9b28baff8c72da137e074e52936.boutiques",
     name="mris_topo_fixer",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRIS_TOPO_FIXER_METADATA = Metadata(
 
 
 MrisTopoFixerParameters = typing.TypedDict('MrisTopoFixerParameters', {
-    "__STYXTYPE__": typing.Literal["mris_topo_fixer"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_topo_fixer"]],
+    "input_surface": InputPathType,
+    "output_surface": str,
+})
+MrisTopoFixerParametersTagged = typing.TypedDict('MrisTopoFixerParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_topo_fixer"],
     "input_surface": InputPathType,
     "output_surface": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_topo_fixer": mris_topo_fixer_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "mris_topo_fixer": mris_topo_fixer_outputs,
-    }.get(t)
 
 
 class MrisTopoFixerOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_topo_fixer(...)`.
+    Output object returned when calling `MrisTopoFixerParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MrisTopoFixerOutputs(typing.NamedTuple):
 def mris_topo_fixer_params(
     input_surface: InputPathType,
     output_surface: str,
-) -> MrisTopoFixerParameters:
+) -> MrisTopoFixerParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mris_topo_fixer_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_topo_fixer",
+        "@type": "freesurfer/mris_topo_fixer",
         "input_surface": input_surface,
         "output_surface": output_surface,
     }
@@ -98,8 +71,8 @@ def mris_topo_fixer_cargs(
     """
     cargs = []
     cargs.append("mris_topo_fixer")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(params.get("output_surface"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(params.get("output_surface", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def mris_topo_fixer_outputs(
     """
     ret = MrisTopoFixerOutputs(
         root=execution.output_file("."),
-        fixed_surface=execution.output_file(params.get("output_surface")),
+        fixed_surface=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mris_topo_fixer_execute(
     params: MrisTopoFixerParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisTopoFixerOutputs:
     """
+    mris_topo_fixer
+    
     FreeSurfer tool for fixing topological defects in cortical surface meshes.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def mris_topo_fixer_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisTopoFixerOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_TOPO_FIXER_METADATA)
     params = execution.params(params)
     cargs = mris_topo_fixer_cargs(params, execution)
     ret = mris_topo_fixer_outputs(params, execution)
@@ -153,6 +130,8 @@ def mris_topo_fixer(
     runner: Runner | None = None,
 ) -> MrisTopoFixerOutputs:
     """
+    mris_topo_fixer
+    
     FreeSurfer tool for fixing topological defects in cortical surface meshes.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def mris_topo_fixer(
     Returns:
         NamedTuple of outputs (described in `MrisTopoFixerOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_TOPO_FIXER_METADATA)
     params = mris_topo_fixer_params(
         input_surface=input_surface,
         output_surface=output_surface,
     )
-    return mris_topo_fixer_execute(params, execution)
+    return mris_topo_fixer_execute(params, runner)
 
 
 __all__ = [
     "MRIS_TOPO_FIXER_METADATA",
     "MrisTopoFixerOutputs",
-    "MrisTopoFixerParameters",
     "mris_topo_fixer",
+    "mris_topo_fixer_execute",
     "mris_topo_fixer_params",
 ]

niwrap_freesurfer/freesurfer/mris_transform.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_TRANSFORM_METADATA = Metadata(
-    id="e6c41caaf057c6f68a1db006d796ff5fd5cf374b.boutiques",
+    id="3726d6539bff096984bce03233ea9266224ec279.boutiques",
     name="mris_transform",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_TRANSFORM_METADATA = Metadata(
 
 
 MrisTransformParameters = typing.TypedDict('MrisTransformParameters', {
-    "__STYXTYPE__": typing.Literal["mris_transform"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_transform"]],
+    "input_surface": InputPathType,
+    "transform": InputPathType,
+    "output_surface": str,
+    "trx_src": typing.NotRequired[InputPathType | None],
+    "trx_dst": typing.NotRequired[InputPathType | None],
+    "is_inverse": bool,
+})
+MrisTransformParametersTagged = typing.TypedDict('MrisTransformParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_transform"],
     "input_surface": InputPathType,
     "transform": InputPathType,
     "output_surface": str,
@@ -22,43 +31,11 @@ MrisTransformParameters = typing.TypedDict('MrisTransformParameters', {
     "trx_dst": typing.NotRequired[InputPathType | None],
     "is_inverse": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_transform": mris_transform_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "mris_transform": mris_transform_outputs,
-    }.get(t)
 
 
 class MrisTransformOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_transform(...)`.
+    Output object returned when calling `MrisTransformParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mris_transform_params(
     trx_src: InputPathType | None = None,
     trx_dst: InputPathType | None = None,
     is_inverse: bool = False,
-) -> MrisTransformParameters:
+) -> MrisTransformParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +68,7 @@ def mris_transform_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_transform",
+        "@type": "freesurfer/mris_transform",
         "input_surface": input_surface,
         "transform": transform,
         "output_surface": output_surface,
@@ -119,20 +96,20 @@ def mris_transform_cargs(
     """
     cargs = []
     cargs.append("mris_transform")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("transform")))
-    cargs.append(params.get("output_surface"))
-    if params.get("trx_src") is not None:
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("transform", None)))
+    cargs.append(params.get("output_surface", None))
+    if params.get("trx_src", None) is not None:
         cargs.extend([
             "--trx-src",
-            execution.input_file(params.get("trx_src"))
+            execution.input_file(params.get("trx_src", None))
         ])
-    if params.get("trx_dst") is not None:
+    if params.get("trx_dst", None) is not None:
         cargs.extend([
             "--trx-dst",
-            execution.input_file(params.get("trx_dst"))
+            execution.input_file(params.get("trx_dst", None))
         ])
-    if params.get("is_inverse"):
+    if params.get("is_inverse", False):
         cargs.append("--is-inverse")
     return cargs
 
@@ -152,17 +129,20 @@ def mris_transform_outputs(
     """
     ret = MrisTransformOutputs(
         root=execution.output_file("."),
-        transformed_output_surface=execution.output_file(params.get("output_surface")),
+        transformed_output_surface=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mris_transform_execute(
     params: MrisTransformParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisTransformOutputs:
     """
-    A tool to transform surfaces from one space to another using image transforms.
+    mris_transform
+    
+    A tool to transform surfaces from one space to another using image
+    transforms.
     
     Author: FreeSurfer Developers
     
@@ -170,10 +150,12 @@ def mris_transform_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisTransformOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_TRANSFORM_METADATA)
     params = execution.params(params)
     cargs = mris_transform_cargs(params, execution)
     ret = mris_transform_outputs(params, execution)
@@ -191,7 +173,10 @@ def mris_transform(
     runner: Runner | None = None,
 ) -> MrisTransformOutputs:
     """
-    A tool to transform surfaces from one space to another using image transforms.
+    mris_transform
+    
+    A tool to transform surfaces from one space to another using image
+    transforms.
     
     Author: FreeSurfer Developers
     
@@ -211,8 +196,6 @@ def mris_transform(
     Returns:
         NamedTuple of outputs (described in `MrisTransformOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_TRANSFORM_METADATA)
     params = mris_transform_params(
         input_surface=input_surface,
         transform=transform,
@@ -221,13 +204,13 @@ def mris_transform(
         trx_dst=trx_dst,
         is_inverse=is_inverse,
     )
-    return mris_transform_execute(params, execution)
+    return mris_transform_execute(params, runner)
 
 
 __all__ = [
     "MRIS_TRANSFORM_METADATA",
     "MrisTransformOutputs",
-    "MrisTransformParameters",
     "mris_transform",
+    "mris_transform_execute",
     "mris_transform_params",
 ]

niwrap_freesurfer/freesurfer/mris_translate_annotation.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_TRANSLATE_ANNOTATION_METADATA = Metadata(
-    id="6c13abe344cff5acfb63f7aed4a6a067fb093515.boutiques",
+    id="ff0cfbba26df08e97c0f75744311fd74364e37d6.boutiques",
     name="mris_translate_annotation",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRIS_TRANSLATE_ANNOTATION_METADATA = Metadata(
 
 
 MrisTranslateAnnotationParameters = typing.TypedDict('MrisTranslateAnnotationParameters', {
-    "__STYXTYPE__": typing.Literal["mris_translate_annotation"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_translate_annotation"]],
+    "subject": str,
+    "hemi": str,
+    "in_annot": InputPathType,
+    "translation_file": InputPathType,
+    "out_annot": str,
+})
+MrisTranslateAnnotationParametersTagged = typing.TypedDict('MrisTranslateAnnotationParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_translate_annotation"],
     "subject": str,
     "hemi": str,
     "in_annot": InputPathType,
     "translation_file": InputPathType,
     "out_annot": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_translate_annotation": mris_translate_annotation_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "mris_translate_annotation": mris_translate_annotation_outputs,
-    }.get(t)
 
 
 class MrisTranslateAnnotationOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_translate_annotation(...)`.
+    Output object returned when calling `MrisTranslateAnnotationParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mris_translate_annotation_params(
     in_annot: InputPathType,
     translation_file: InputPathType,
     out_annot: str,
-) -> MrisTranslateAnnotationParameters:
+) -> MrisTranslateAnnotationParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def mris_translate_annotation_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_translate_annotation",
+        "@type": "freesurfer/mris_translate_annotation",
         "subject": subject,
         "hemi": hemi,
         "in_annot": in_annot,
@@ -110,11 +86,11 @@ def mris_translate_annotation_cargs(
     """
     cargs = []
     cargs.append("mris_translate_annotation")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("in_annot")))
-    cargs.append(execution.input_file(params.get("translation_file")))
-    cargs.append(params.get("out_annot"))
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("in_annot", None)))
+    cargs.append(execution.input_file(params.get("translation_file", None)))
+    cargs.append(params.get("out_annot", None))
     return cargs
 
 
@@ -133,16 +109,18 @@ def mris_translate_annotation_outputs(
     """
     ret = MrisTranslateAnnotationOutputs(
         root=execution.output_file("."),
-        output_annotation=execution.output_file(params.get("out_annot")),
+        output_annotation=execution.output_file(params.get("out_annot", None)),
     )
     return ret
 
 
 def mris_translate_annotation_execute(
     params: MrisTranslateAnnotationParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisTranslateAnnotationOutputs:
     """
+    mris_translate_annotation
+    
     This program applies a translation table to an annotation file.
     
     Author: FreeSurfer Developers
@@ -151,10 +129,12 @@ def mris_translate_annotation_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisTranslateAnnotationOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_TRANSLATE_ANNOTATION_METADATA)
     params = execution.params(params)
     cargs = mris_translate_annotation_cargs(params, execution)
     ret = mris_translate_annotation_outputs(params, execution)
@@ -171,6 +151,8 @@ def mris_translate_annotation(
     runner: Runner | None = None,
 ) -> MrisTranslateAnnotationOutputs:
     """
+    mris_translate_annotation
+    
     This program applies a translation table to an annotation file.
     
     Author: FreeSurfer Developers
@@ -187,8 +169,6 @@ def mris_translate_annotation(
     Returns:
         NamedTuple of outputs (described in `MrisTranslateAnnotationOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_TRANSLATE_ANNOTATION_METADATA)
     params = mris_translate_annotation_params(
         subject=subject,
         hemi=hemi,
@@ -196,13 +176,13 @@ def mris_translate_annotation(
         translation_file=translation_file,
         out_annot=out_annot,
     )
-    return mris_translate_annotation_execute(params, execution)
+    return mris_translate_annotation_execute(params, runner)
 
 
 __all__ = [
     "MRIS_TRANSLATE_ANNOTATION_METADATA",
     "MrisTranslateAnnotationOutputs",
-    "MrisTranslateAnnotationParameters",
     "mris_translate_annotation",
+    "mris_translate_annotation_execute",
     "mris_translate_annotation_params",
 ]