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

niwrap_freesurfer/freesurfer/mris_merge_parcellations.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MERGE_PARCELLATIONS_METADATA = Metadata(
-    id="59eb13227975afaa7a05e9947ae25c61de64b8ec.boutiques",
+    id="a05f2598fc622c439488b0d5084f9127865f9812.boutiques",
     name="mris_merge_parcellations",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ MRIS_MERGE_PARCELLATIONS_METADATA = Metadata(
 
 
 MrisMergeParcellationsParameters = typing.TypedDict('MrisMergeParcellationsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_merge_parcellations"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_merge_parcellations"]],
+    "surface": InputPathType,
+    "label1": InputPathType,
+    "label2": InputPathType,
+    "annot_name": typing.NotRequired[str | None],
+})
+MrisMergeParcellationsParametersTagged = typing.TypedDict('MrisMergeParcellationsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_merge_parcellations"],
     "surface": InputPathType,
     "label1": InputPathType,
     "label2": InputPathType,
     "annot_name": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_merge_parcellations": mris_merge_parcellations_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 {
-    }.get(t)
 
 
 class MrisMergeParcellationsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_merge_parcellations(...)`.
+    Output object returned when calling `MrisMergeParcellationsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def mris_merge_parcellations_params(
     label1: InputPathType,
     label2: InputPathType,
     annot_name: str | None = None,
-) -> MrisMergeParcellationsParameters:
+) -> MrisMergeParcellationsParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def mris_merge_parcellations_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_merge_parcellations",
+        "@type": "freesurfer/mris_merge_parcellations",
         "surface": surface,
         "label1": label1,
         "label2": label2,
@@ -104,13 +80,13 @@ def mris_merge_parcellations_cargs(
     """
     cargs = []
     cargs.append("mris_merge_parcellations")
-    cargs.append(execution.input_file(params.get("surface")))
-    cargs.append(execution.input_file(params.get("label1")))
-    cargs.append(execution.input_file(params.get("label2")))
-    if params.get("annot_name") is not None:
+    cargs.append(execution.input_file(params.get("surface", None)))
+    cargs.append(execution.input_file(params.get("label1", None)))
+    cargs.append(execution.input_file(params.get("label2", None)))
+    if params.get("annot_name", None) is not None:
         cargs.extend([
             "-a",
-            params.get("annot_name")
+            params.get("annot_name", None)
         ])
     return cargs
 
@@ -136,10 +112,13 @@ def mris_merge_parcellations_outputs(
 
 def mris_merge_parcellations_execute(
     params: MrisMergeParcellationsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMergeParcellationsOutputs:
     """
-    This program computes the Hausdorff distance between two labels on the surface.
+    mris_merge_parcellations
+    
+    This program computes the Hausdorff distance between two labels on the
+    surface.
     
     Author: FreeSurfer Developers
     
@@ -147,10 +126,12 @@ def mris_merge_parcellations_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMergeParcellationsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MERGE_PARCELLATIONS_METADATA)
     params = execution.params(params)
     cargs = mris_merge_parcellations_cargs(params, execution)
     ret = mris_merge_parcellations_outputs(params, execution)
@@ -166,7 +147,10 @@ def mris_merge_parcellations(
     runner: Runner | None = None,
 ) -> MrisMergeParcellationsOutputs:
     """
-    This program computes the Hausdorff distance between two labels on the surface.
+    mris_merge_parcellations
+    
+    This program computes the Hausdorff distance between two labels on the
+    surface.
     
     Author: FreeSurfer Developers
     
@@ -181,21 +165,19 @@ def mris_merge_parcellations(
     Returns:
         NamedTuple of outputs (described in `MrisMergeParcellationsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MERGE_PARCELLATIONS_METADATA)
     params = mris_merge_parcellations_params(
         surface=surface,
         label1=label1,
         label2=label2,
         annot_name=annot_name,
     )
-    return mris_merge_parcellations_execute(params, execution)
+    return mris_merge_parcellations_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MERGE_PARCELLATIONS_METADATA",
     "MrisMergeParcellationsOutputs",
-    "MrisMergeParcellationsParameters",
     "mris_merge_parcellations",
+    "mris_merge_parcellations_execute",
     "mris_merge_parcellations_params",
 ]

niwrap_freesurfer/freesurfer/mris_mesh_subdivide.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MESH_SUBDIVIDE_METADATA = Metadata(
-    id="43ce90cf6a44f8bcd3a24d12daa3e2183baa4a31.boutiques",
+    id="01bbf56fb52c81246c889b051a38d5054ff5195c.boutiques",
     name="mris_mesh_subdivide",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_MESH_SUBDIVIDE_METADATA = Metadata(
 
 
 MrisMeshSubdivideParameters = typing.TypedDict('MrisMeshSubdivideParameters', {
-    "__STYXTYPE__": typing.Literal["mris_mesh_subdivide"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_mesh_subdivide"]],
+    "input_surface": InputPathType,
+    "output_surface": str,
+    "subdivision_method": typing.NotRequired[typing.Literal["butterfly", "loop", "linear"] | None],
+    "iterations": typing.NotRequired[float | None],
+})
+MrisMeshSubdivideParametersTagged = typing.TypedDict('MrisMeshSubdivideParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_mesh_subdivide"],
     "input_surface": InputPathType,
     "output_surface": str,
     "subdivision_method": typing.NotRequired[typing.Literal["butterfly", "loop", "linear"] | None],
     "iterations": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_mesh_subdivide": mris_mesh_subdivide_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_mesh_subdivide": mris_mesh_subdivide_outputs,
-    }.get(t)
 
 
 class MrisMeshSubdivideOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_mesh_subdivide(...)`.
+    Output object returned when calling `MrisMeshSubdivideParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_mesh_subdivide_params(
     output_surface: str,
     subdivision_method: typing.Literal["butterfly", "loop", "linear"] | None = None,
     iterations: float | None = None,
-) -> MrisMeshSubdivideParameters:
+) -> MrisMeshSubdivideParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +59,7 @@ def mris_mesh_subdivide_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_mesh_subdivide",
+        "@type": "freesurfer/mris_mesh_subdivide",
         "input_surface": input_surface,
         "output_surface": output_surface,
     }
@@ -112,21 +87,21 @@ def mris_mesh_subdivide_cargs(
     cargs.append("mris_mesh_subdivide")
     cargs.extend([
         "--surf",
-        execution.input_file(params.get("input_surface"))
+        execution.input_file(params.get("input_surface", None))
     ])
     cargs.extend([
         "--out",
-        params.get("output_surface")
+        params.get("output_surface", None)
     ])
-    if params.get("subdivision_method") is not None:
+    if params.get("subdivision_method", None) is not None:
         cargs.extend([
             "--method",
-            params.get("subdivision_method")
+            params.get("subdivision_method", None)
         ])
-    if params.get("iterations") is not None:
+    if params.get("iterations", None) is not None:
         cargs.extend([
             "--iter",
-            str(params.get("iterations"))
+            str(params.get("iterations", None))
         ])
     return cargs
 
@@ -146,16 +121,18 @@ def mris_mesh_subdivide_outputs(
     """
     ret = MrisMeshSubdivideOutputs(
         root=execution.output_file("."),
-        subdivided_surface=execution.output_file(params.get("output_surface")),
+        subdivided_surface=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mris_mesh_subdivide_execute(
     params: MrisMeshSubdivideParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMeshSubdivideOutputs:
     """
+    mris_mesh_subdivide
+    
     This program will subdivide a triangular mesh surface.
     
     Author: FreeSurfer Developers
@@ -164,10 +141,12 @@ def mris_mesh_subdivide_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMeshSubdivideOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MESH_SUBDIVIDE_METADATA)
     params = execution.params(params)
     cargs = mris_mesh_subdivide_cargs(params, execution)
     ret = mris_mesh_subdivide_outputs(params, execution)
@@ -183,6 +162,8 @@ def mris_mesh_subdivide(
     runner: Runner | None = None,
 ) -> MrisMeshSubdivideOutputs:
     """
+    mris_mesh_subdivide
+    
     This program will subdivide a triangular mesh surface.
     
     Author: FreeSurfer Developers
@@ -200,21 +181,19 @@ def mris_mesh_subdivide(
     Returns:
         NamedTuple of outputs (described in `MrisMeshSubdivideOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MESH_SUBDIVIDE_METADATA)
     params = mris_mesh_subdivide_params(
         input_surface=input_surface,
         output_surface=output_surface,
         subdivision_method=subdivision_method,
         iterations=iterations,
     )
-    return mris_mesh_subdivide_execute(params, execution)
+    return mris_mesh_subdivide_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MESH_SUBDIVIDE_METADATA",
     "MrisMeshSubdivideOutputs",
-    "MrisMeshSubdivideParameters",
     "mris_mesh_subdivide",
+    "mris_mesh_subdivide_execute",
     "mris_mesh_subdivide_params",
 ]

niwrap_freesurfer/freesurfer/mris_morph_stats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MORPH_STATS_METADATA = Metadata(
-    id="da593f1d8b569bcf1c57e65563ce3b6eb93b2e86.boutiques",
+    id="3362e55d8942bbd7f975ead6fc19ef456b999c8f.boutiques",
     name="mris_morph_stats",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_MORPH_STATS_METADATA = Metadata(
 
 
 MrisMorphStatsParameters = typing.TypedDict('MrisMorphStatsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_morph_stats"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_morph_stats"]],
+    "subject_name": str,
+    "hemisphere": typing.Literal["lh", "rh"],
+    "morphed_surface": InputPathType,
+    "output_name": str,
+})
+MrisMorphStatsParametersTagged = typing.TypedDict('MrisMorphStatsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_morph_stats"],
     "subject_name": str,
     "hemisphere": typing.Literal["lh", "rh"],
     "morphed_surface": InputPathType,
     "output_name": 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_morph_stats": mris_morph_stats_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_morph_stats": mris_morph_stats_outputs,
-    }.get(t)
 
 
 class MrisMorphStatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_morph_stats(...)`.
+    Output object returned when calling `MrisMorphStatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_morph_stats_params(
     hemisphere: typing.Literal["lh", "rh"],
     morphed_surface: InputPathType,
     output_name: str,
-) -> MrisMorphStatsParameters:
+) -> MrisMorphStatsParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def mris_morph_stats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_morph_stats",
+        "@type": "freesurfer/mris_morph_stats",
         "subject_name": subject_name,
         "hemisphere": hemisphere,
         "morphed_surface": morphed_surface,
@@ -107,10 +82,10 @@ def mris_morph_stats_cargs(
     """
     cargs = []
     cargs.append("mris_morph_stats")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("hemisphere"))
-    cargs.append(execution.input_file(params.get("morphed_surface")))
-    cargs.append(params.get("output_name"))
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("hemisphere", None))
+    cargs.append(execution.input_file(params.get("morphed_surface", None)))
+    cargs.append(params.get("output_name", None))
     return cargs
 
 
@@ -129,18 +104,20 @@ def mris_morph_stats_outputs(
     """
     ret = MrisMorphStatsOutputs(
         root=execution.output_file("."),
-        stats_output=execution.output_file(params.get("output_name")),
+        stats_output=execution.output_file(params.get("output_name", None)),
     )
     return ret
 
 
 def mris_morph_stats_execute(
     params: MrisMorphStatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMorphStatsOutputs:
     """
-    This program generates statistics which characterize a surface-based deformation
-    field.
+    mris_morph_stats
+    
+    This program generates statistics which characterize a surface-based
+    deformation field.
     
     Author: FreeSurfer Developers
     
@@ -148,10 +125,12 @@ def mris_morph_stats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMorphStatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MORPH_STATS_METADATA)
     params = execution.params(params)
     cargs = mris_morph_stats_cargs(params, execution)
     ret = mris_morph_stats_outputs(params, execution)
@@ -167,8 +146,10 @@ def mris_morph_stats(
     runner: Runner | None = None,
 ) -> MrisMorphStatsOutputs:
     """
-    This program generates statistics which characterize a surface-based deformation
-    field.
+    mris_morph_stats
+    
+    This program generates statistics which characterize a surface-based
+    deformation field.
     
     Author: FreeSurfer Developers
     
@@ -184,21 +165,19 @@ def mris_morph_stats(
     Returns:
         NamedTuple of outputs (described in `MrisMorphStatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MORPH_STATS_METADATA)
     params = mris_morph_stats_params(
         subject_name=subject_name,
         hemisphere=hemisphere,
         morphed_surface=morphed_surface,
         output_name=output_name,
     )
-    return mris_morph_stats_execute(params, execution)
+    return mris_morph_stats_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MORPH_STATS_METADATA",
     "MrisMorphStatsOutputs",
-    "MrisMorphStatsParameters",
     "mris_morph_stats",
+    "mris_morph_stats_execute",
     "mris_morph_stats_params",
 ]