niwrap-freesurfer 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_remove_intersection.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_REMOVE_INTERSECTION_METADATA = Metadata(
-    id="35105f4c486e8643420cf4f167c32a531bdc3428.boutiques",
+    id="88b4ff5041cef2806f183cade65dd8196d2b1360.boutiques",
     name="mris_remove_intersection",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRIS_REMOVE_INTERSECTION_METADATA = Metadata(
 
 
 MrisRemoveIntersectionParameters = typing.TypedDict('MrisRemoveIntersectionParameters', {
-    "__STYXTYPE__": typing.Literal["mris_remove_intersection"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_remove_intersection"]],
+    "surface_in_file": InputPathType,
+    "corrected_surface_out_file": str,
+    "fill_holes": bool,
+    "map_option": typing.NotRequired[InputPathType | None],
+    "projdistmm": typing.NotRequired[float | None],
+})
+MrisRemoveIntersectionParametersTagged = typing.TypedDict('MrisRemoveIntersectionParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_remove_intersection"],
     "surface_in_file": InputPathType,
     "corrected_surface_out_file": str,
     "fill_holes": bool,
     "map_option": typing.NotRequired[InputPathType | None],
     "projdistmm": 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_remove_intersection": mris_remove_intersection_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_remove_intersection": mris_remove_intersection_outputs,
-    }.get(t)
 
 
 class MrisRemoveIntersectionOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_remove_intersection(...)`.
+    Output object returned when calling `MrisRemoveIntersectionParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +49,7 @@ def mris_remove_intersection_params(
     fill_holes: bool = False,
     map_option: InputPathType | None = None,
     projdistmm: float | None = None,
-) -> MrisRemoveIntersectionParameters:
+) -> MrisRemoveIntersectionParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +64,7 @@ def mris_remove_intersection_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_remove_intersection",
+        "@type": "freesurfer/mris_remove_intersection",
         "surface_in_file": surface_in_file,
         "corrected_surface_out_file": corrected_surface_out_file,
         "fill_holes": fill_holes,
@@ -115,17 +91,17 @@ def mris_remove_intersection_cargs(
     """
     cargs = []
     cargs.append("mris_remove_intersection")
-    cargs.append(execution.input_file(params.get("surface_in_file")))
-    cargs.append(params.get("corrected_surface_out_file"))
-    if params.get("fill_holes"):
+    cargs.append(execution.input_file(params.get("surface_in_file", None)))
+    cargs.append(params.get("corrected_surface_out_file", None))
+    if params.get("fill_holes", False):
         cargs.append("-fill-holes")
-    if params.get("map_option") is not None:
+    if params.get("map_option", None) is not None:
         cargs.extend([
             "-map",
-            execution.input_file(params.get("map_option"))
+            execution.input_file(params.get("map_option", None))
         ])
-    if params.get("projdistmm") is not None:
-        cargs.append(str(params.get("projdistmm")))
+    if params.get("projdistmm", None) is not None:
+        cargs.append(str(params.get("projdistmm", None)))
     return cargs
 
 
@@ -144,17 +120,19 @@ def mris_remove_intersection_outputs(
     """
     ret = MrisRemoveIntersectionOutputs(
         root=execution.output_file("."),
-        out_corrected_surface=execution.output_file(params.get("corrected_surface_out_file")),
-        out_map_file=execution.output_file(pathlib.Path(params.get("map_option")).name) if (params.get("map_option") is not None) else None,
+        out_corrected_surface=execution.output_file(params.get("corrected_surface_out_file", None)),
+        out_map_file=execution.output_file(pathlib.Path(params.get("map_option", None)).name) if (params.get("map_option") is not None) else None,
     )
     return ret
 
 
 def mris_remove_intersection_execute(
     params: MrisRemoveIntersectionParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisRemoveIntersectionOutputs:
     """
+    mris_remove_intersection
+    
     Tool to remove intersections in surface files.
     
     Author: FreeSurfer Developers
@@ -163,10 +141,12 @@ def mris_remove_intersection_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisRemoveIntersectionOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_REMOVE_INTERSECTION_METADATA)
     params = execution.params(params)
     cargs = mris_remove_intersection_cargs(params, execution)
     ret = mris_remove_intersection_outputs(params, execution)
@@ -183,6 +163,8 @@ def mris_remove_intersection(
     runner: Runner | None = None,
 ) -> MrisRemoveIntersectionOutputs:
     """
+    mris_remove_intersection
+    
     Tool to remove intersections in surface files.
     
     Author: FreeSurfer Developers
@@ -200,8 +182,6 @@ def mris_remove_intersection(
     Returns:
         NamedTuple of outputs (described in `MrisRemoveIntersectionOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_REMOVE_INTERSECTION_METADATA)
     params = mris_remove_intersection_params(
         surface_in_file=surface_in_file,
         corrected_surface_out_file=corrected_surface_out_file,
@@ -209,13 +189,13 @@ def mris_remove_intersection(
         map_option=map_option,
         projdistmm=projdistmm,
     )
-    return mris_remove_intersection_execute(params, execution)
+    return mris_remove_intersection_execute(params, runner)
 
 
 __all__ = [
     "MRIS_REMOVE_INTERSECTION_METADATA",
     "MrisRemoveIntersectionOutputs",
-    "MrisRemoveIntersectionParameters",
     "mris_remove_intersection",
+    "mris_remove_intersection_execute",
     "mris_remove_intersection_params",
 ]

niwrap_freesurfer/freesurfer/mris_remove_negative_vertices.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_REMOVE_NEGATIVE_VERTICES_METADATA = Metadata(
-    id="5a68aabeda2f4e6811f224288d7f4d9c8c795765.boutiques",
+    id="e5a89fc26e32cd844efa516970b571cf6064fcde.boutiques",
     name="mris_remove_negative_vertices",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRIS_REMOVE_NEGATIVE_VERTICES_METADATA = Metadata(
 
 
 MrisRemoveNegativeVerticesParameters = typing.TypedDict('MrisRemoveNegativeVerticesParameters', {
-    "__STYXTYPE__": typing.Literal["mris_remove_negative_vertices"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_remove_negative_vertices"]],
+    "surface_file": InputPathType,
+    "patch_file": InputPathType,
+    "output_patch": str,
+})
+MrisRemoveNegativeVerticesParametersTagged = typing.TypedDict('MrisRemoveNegativeVerticesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_remove_negative_vertices"],
     "surface_file": InputPathType,
     "patch_file": InputPathType,
     "output_patch": 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_remove_negative_vertices": mris_remove_negative_vertices_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_remove_negative_vertices": mris_remove_negative_vertices_outputs,
-    }.get(t)
 
 
 class MrisRemoveNegativeVerticesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_remove_negative_vertices(...)`.
+    Output object returned when calling `MrisRemoveNegativeVerticesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mris_remove_negative_vertices_params(
     surface_file: InputPathType,
     patch_file: InputPathType,
     output_patch: str,
-) -> MrisRemoveNegativeVerticesParameters:
+) -> MrisRemoveNegativeVerticesParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mris_remove_negative_vertices_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_remove_negative_vertices",
+        "@type": "freesurfer/mris_remove_negative_vertices",
         "surface_file": surface_file,
         "patch_file": patch_file,
         "output_patch": output_patch,
@@ -102,9 +76,9 @@ def mris_remove_negative_vertices_cargs(
     """
     cargs = []
     cargs.append("mris_remove_negative_vertices")
-    cargs.append(execution.input_file(params.get("surface_file")))
-    cargs.append(execution.input_file(params.get("patch_file")))
-    cargs.append(params.get("output_patch"))
+    cargs.append(execution.input_file(params.get("surface_file", None)))
+    cargs.append(execution.input_file(params.get("patch_file", None)))
+    cargs.append(params.get("output_patch", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def mris_remove_negative_vertices_outputs(
     """
     ret = MrisRemoveNegativeVerticesOutputs(
         root=execution.output_file("."),
-        output_patch_file=execution.output_file(params.get("output_patch")),
+        output_patch_file=execution.output_file(params.get("output_patch", None)),
     )
     return ret
 
 
 def mris_remove_negative_vertices_execute(
     params: MrisRemoveNegativeVerticesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisRemoveNegativeVerticesOutputs:
     """
+    mris_remove_negative_vertices
+    
     This program adds a template into an average surface.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def mris_remove_negative_vertices_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisRemoveNegativeVerticesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_REMOVE_NEGATIVE_VERTICES_METADATA)
     params = execution.params(params)
     cargs = mris_remove_negative_vertices_cargs(params, execution)
     ret = mris_remove_negative_vertices_outputs(params, execution)
@@ -159,6 +137,8 @@ def mris_remove_negative_vertices(
     runner: Runner | None = None,
 ) -> MrisRemoveNegativeVerticesOutputs:
     """
+    mris_remove_negative_vertices
+    
     This program adds a template into an average surface.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def mris_remove_negative_vertices(
     Returns:
         NamedTuple of outputs (described in `MrisRemoveNegativeVerticesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_REMOVE_NEGATIVE_VERTICES_METADATA)
     params = mris_remove_negative_vertices_params(
         surface_file=surface_file,
         patch_file=patch_file,
         output_patch=output_patch,
     )
-    return mris_remove_negative_vertices_execute(params, execution)
+    return mris_remove_negative_vertices_execute(params, runner)
 
 
 __all__ = [
     "MRIS_REMOVE_NEGATIVE_VERTICES_METADATA",
     "MrisRemoveNegativeVerticesOutputs",
-    "MrisRemoveNegativeVerticesParameters",
     "mris_remove_negative_vertices",
+    "mris_remove_negative_vertices_execute",
     "mris_remove_negative_vertices_params",
 ]

niwrap_freesurfer/freesurfer/mris_remove_variance.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_REMOVE_VARIANCE_METADATA = Metadata(
-    id="f725b8052ca4cdae9b81c460bf2279cdcc7e582b.boutiques",
+    id="a233d0c60ef8e39a89e40a91dfdf170763167129.boutiques",
     name="mris_remove_variance",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_REMOVE_VARIANCE_METADATA = Metadata(
 
 
 MrisRemoveVarianceParameters = typing.TypedDict('MrisRemoveVarianceParameters', {
-    "__STYXTYPE__": typing.Literal["mris_remove_variance"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_remove_variance"]],
+    "input_surface_file": InputPathType,
+    "curvature_file": InputPathType,
+    "curvature_file_to_remove": InputPathType,
+    "output_curvature_file": str,
+})
+MrisRemoveVarianceParametersTagged = typing.TypedDict('MrisRemoveVarianceParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_remove_variance"],
     "input_surface_file": InputPathType,
     "curvature_file": InputPathType,
     "curvature_file_to_remove": InputPathType,
     "output_curvature_file": 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_remove_variance": mris_remove_variance_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_remove_variance": mris_remove_variance_outputs,
-    }.get(t)
 
 
 class MrisRemoveVarianceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_remove_variance(...)`.
+    Output object returned when calling `MrisRemoveVarianceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_remove_variance_params(
     curvature_file: InputPathType,
     curvature_file_to_remove: InputPathType,
     output_curvature_file: str,
-) -> MrisRemoveVarianceParameters:
+) -> MrisRemoveVarianceParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def mris_remove_variance_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_remove_variance",
+        "@type": "freesurfer/mris_remove_variance",
         "input_surface_file": input_surface_file,
         "curvature_file": curvature_file,
         "curvature_file_to_remove": curvature_file_to_remove,
@@ -107,10 +82,10 @@ def mris_remove_variance_cargs(
     """
     cargs = []
     cargs.append("mris_remove_variance")
-    cargs.append(execution.input_file(params.get("input_surface_file")))
-    cargs.append(execution.input_file(params.get("curvature_file")))
-    cargs.append(execution.input_file(params.get("curvature_file_to_remove")))
-    cargs.append(params.get("output_curvature_file"))
+    cargs.append(execution.input_file(params.get("input_surface_file", None)))
+    cargs.append(execution.input_file(params.get("curvature_file", None)))
+    cargs.append(execution.input_file(params.get("curvature_file_to_remove", None)))
+    cargs.append(params.get("output_curvature_file", None))
     return cargs
 
 
@@ -129,18 +104,20 @@ def mris_remove_variance_outputs(
     """
     ret = MrisRemoveVarianceOutputs(
         root=execution.output_file("."),
-        resulting_curvature_file=execution.output_file(params.get("output_curvature_file")),
+        resulting_curvature_file=execution.output_file(params.get("output_curvature_file", None)),
     )
     return ret
 
 
 def mris_remove_variance_execute(
     params: MrisRemoveVarianceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisRemoveVarianceOutputs:
     """
-    This program removes the linear component of the variance accounted for by one
-    curvature vector from another.
+    mris_remove_variance
+    
+    This program removes the linear component of the variance accounted for by
+    one curvature vector from another.
     
     Author: FreeSurfer Developers
     
@@ -148,10 +125,12 @@ def mris_remove_variance_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisRemoveVarianceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_REMOVE_VARIANCE_METADATA)
     params = execution.params(params)
     cargs = mris_remove_variance_cargs(params, execution)
     ret = mris_remove_variance_outputs(params, execution)
@@ -167,8 +146,10 @@ def mris_remove_variance(
     runner: Runner | None = None,
 ) -> MrisRemoveVarianceOutputs:
     """
-    This program removes the linear component of the variance accounted for by one
-    curvature vector from another.
+    mris_remove_variance
+    
+    This program removes the linear component of the variance accounted for by
+    one curvature vector from another.
     
     Author: FreeSurfer Developers
     
@@ -184,21 +165,19 @@ def mris_remove_variance(
     Returns:
         NamedTuple of outputs (described in `MrisRemoveVarianceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_REMOVE_VARIANCE_METADATA)
     params = mris_remove_variance_params(
         input_surface_file=input_surface_file,
         curvature_file=curvature_file,
         curvature_file_to_remove=curvature_file_to_remove,
         output_curvature_file=output_curvature_file,
     )
-    return mris_remove_variance_execute(params, execution)
+    return mris_remove_variance_execute(params, runner)
 
 
 __all__ = [
     "MRIS_REMOVE_VARIANCE_METADATA",
     "MrisRemoveVarianceOutputs",
-    "MrisRemoveVarianceParameters",
     "mris_remove_variance",
+    "mris_remove_variance_execute",
     "mris_remove_variance_params",
 ]