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

niwrap_freesurfer/freesurfer/mris_smooth.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SMOOTH_METADATA = Metadata(
-    id="de9358e87f1400c4ea7c69099e7d714065b4d1f6.boutiques",
+    id="00da8d7d3a54e8839cd5f2f0f460ce08b83100a6.boutiques",
     name="mris_smooth",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ MRIS_SMOOTH_METADATA = Metadata(
 
 
 MrisSmoothParameters = typing.TypedDict('MrisSmoothParameters', {
-    "__STYXTYPE__": typing.Literal["mris_smooth"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_smooth"]],
+    "input_surface": InputPathType,
+    "output_surface": str,
+    "average_iters": typing.NotRequired[float | None],
+    "smoothing_iters": typing.NotRequired[float | None],
+    "no_write": bool,
+    "curvature_name": typing.NotRequired[str | None],
+    "area_name": typing.NotRequired[str | None],
+    "gaussian_params": typing.NotRequired[list[float] | None],
+    "normalize_area": bool,
+    "momentum": typing.NotRequired[float | None],
+    "snapshot_interval": typing.NotRequired[float | None],
+})
+MrisSmoothParametersTagged = typing.TypedDict('MrisSmoothParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_smooth"],
     "input_surface": InputPathType,
     "output_surface": str,
     "average_iters": typing.NotRequired[float | None],
@@ -27,43 +41,11 @@ MrisSmoothParameters = typing.TypedDict('MrisSmoothParameters', {
     "momentum": typing.NotRequired[float | None],
     "snapshot_interval": 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_smooth": mris_smooth_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_smooth": mris_smooth_outputs,
-    }.get(t)
 
 
 class MrisSmoothOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_smooth(...)`.
+    Output object returned when calling `MrisSmoothParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,16 +60,16 @@ class MrisSmoothOutputs(typing.NamedTuple):
 def mris_smooth_params(
     input_surface: InputPathType,
     output_surface: str,
-    average_iters: float | None = 10,
-    smoothing_iters: float | None = 10,
+    average_iters: float | None = None,
+    smoothing_iters: float | None = None,
     no_write: bool = False,
-    curvature_name: str | None = "curv",
-    area_name: str | None = "area",
+    curvature_name: str | None = None,
+    area_name: str | None = None,
     gaussian_params: list[float] | None = None,
     normalize_area: bool = False,
     momentum: float | None = None,
     snapshot_interval: float | None = None,
-) -> MrisSmoothParameters:
+) -> MrisSmoothParametersTagged:
     """
     Build parameters.
     
@@ -111,7 +93,7 @@ def mris_smooth_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_smooth",
+        "@type": "freesurfer/mris_smooth",
         "input_surface": input_surface,
         "output_surface": output_surface,
         "no_write": no_write,
@@ -149,46 +131,46 @@ def mris_smooth_cargs(
     """
     cargs = []
     cargs.append("mris_smooth")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(params.get("output_surface"))
-    if params.get("average_iters") is not None:
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(params.get("output_surface", None))
+    if params.get("average_iters", None) is not None:
         cargs.extend([
             "-a",
-            str(params.get("average_iters"))
+            str(params.get("average_iters", None))
         ])
-    if params.get("smoothing_iters") is not None:
+    if params.get("smoothing_iters", None) is not None:
         cargs.extend([
             "-n",
-            str(params.get("smoothing_iters"))
+            str(params.get("smoothing_iters", None))
         ])
-    if params.get("no_write"):
+    if params.get("no_write", False):
         cargs.append("-nw")
-    if params.get("curvature_name") is not None:
+    if params.get("curvature_name", None) is not None:
         cargs.extend([
             "-c",
-            params.get("curvature_name")
+            params.get("curvature_name", None)
         ])
-    if params.get("area_name") is not None:
+    if params.get("area_name", None) is not None:
         cargs.extend([
             "-b",
-            params.get("area_name")
+            params.get("area_name", None)
         ])
-    if params.get("gaussian_params") is not None:
+    if params.get("gaussian_params", None) is not None:
         cargs.extend([
             "-g",
-            *map(str, params.get("gaussian_params"))
+            *map(str, params.get("gaussian_params", None))
         ])
-    if params.get("normalize_area"):
+    if params.get("normalize_area", False):
         cargs.append("-area")
-    if params.get("momentum") is not None:
+    if params.get("momentum", None) is not None:
         cargs.extend([
             "-m",
-            str(params.get("momentum"))
+            str(params.get("momentum", None))
         ])
-    if params.get("snapshot_interval") is not None:
+    if params.get("snapshot_interval", None) is not None:
         cargs.extend([
             "-w",
-            str(params.get("snapshot_interval"))
+            str(params.get("snapshot_interval", None))
         ])
     return cargs
 
@@ -208,7 +190,7 @@ def mris_smooth_outputs(
     """
     ret = MrisSmoothOutputs(
         root=execution.output_file("."),
-        output_surface_file=execution.output_file(params.get("output_surface")),
+        output_surface_file=execution.output_file(params.get("output_surface", None)),
         curvature_file=execution.output_file("${OUTPUT_SURFACE}_curvature"),
         area_file=execution.output_file("${OUTPUT_SURFACE}_area"),
     )
@@ -217,11 +199,13 @@ def mris_smooth_outputs(
 
 def mris_smooth_execute(
     params: MrisSmoothParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSmoothOutputs:
     """
-    This program smooths the tessellation of a cortical surface and writes out the
-    mean curvature and area files.
+    mris_smooth
+    
+    This program smooths the tessellation of a cortical surface and writes out
+    the mean curvature and area files.
     
     Author: FreeSurfer Developers
     
@@ -229,10 +213,12 @@ def mris_smooth_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSmoothOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SMOOTH_METADATA)
     params = execution.params(params)
     cargs = mris_smooth_cargs(params, execution)
     ret = mris_smooth_outputs(params, execution)
@@ -243,11 +229,11 @@ def mris_smooth_execute(
 def mris_smooth(
     input_surface: InputPathType,
     output_surface: str,
-    average_iters: float | None = 10,
-    smoothing_iters: float | None = 10,
+    average_iters: float | None = None,
+    smoothing_iters: float | None = None,
     no_write: bool = False,
-    curvature_name: str | None = "curv",
-    area_name: str | None = "area",
+    curvature_name: str | None = None,
+    area_name: str | None = None,
     gaussian_params: list[float] | None = None,
     normalize_area: bool = False,
     momentum: float | None = None,
@@ -255,8 +241,10 @@ def mris_smooth(
     runner: Runner | None = None,
 ) -> MrisSmoothOutputs:
     """
-    This program smooths the tessellation of a cortical surface and writes out the
-    mean curvature and area files.
+    mris_smooth
+    
+    This program smooths the tessellation of a cortical surface and writes out
+    the mean curvature and area files.
     
     Author: FreeSurfer Developers
     
@@ -282,8 +270,6 @@ def mris_smooth(
     Returns:
         NamedTuple of outputs (described in `MrisSmoothOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SMOOTH_METADATA)
     params = mris_smooth_params(
         input_surface=input_surface,
         output_surface=output_surface,
@@ -297,13 +283,13 @@ def mris_smooth(
         momentum=momentum,
         snapshot_interval=snapshot_interval,
     )
-    return mris_smooth_execute(params, execution)
+    return mris_smooth_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SMOOTH_METADATA",
     "MrisSmoothOutputs",
-    "MrisSmoothParameters",
     "mris_smooth",
+    "mris_smooth_execute",
     "mris_smooth_params",
 ]

niwrap_freesurfer/freesurfer/mris_smooth_intracortical.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SMOOTH_INTRACORTICAL_METADATA = Metadata(
-    id="40a15a33b82c63e11e7ab868f6bbf4b236de01b3.boutiques",
+    id="0d8141b48c8789db47136b6c9b336006cfc8494d.boutiques",
     name="mris_smooth_intracortical",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ MRIS_SMOOTH_INTRACORTICAL_METADATA = Metadata(
 
 
 MrisSmoothIntracorticalParameters = typing.TypedDict('MrisSmoothIntracorticalParameters', {
-    "__STYXTYPE__": typing.Literal["mris_smooth_intracortical"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_smooth_intracortical"]],
+    "surf_dir": str,
+    "surf_name": str,
+    "overlay_dir": str,
+    "overlay_name": str,
+    "output_dir": typing.NotRequired[str | None],
+    "output_name": typing.NotRequired[str | None],
+    "tan_size": typing.NotRequired[int | None],
+    "rad_size": typing.NotRequired[float | None],
+    "rad_start": typing.NotRequired[float | None],
+    "tan_weights": typing.NotRequired[str | None],
+})
+MrisSmoothIntracorticalParametersTagged = typing.TypedDict('MrisSmoothIntracorticalParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_smooth_intracortical"],
     "surf_dir": str,
     "surf_name": str,
     "overlay_dir": str,
@@ -26,43 +39,11 @@ MrisSmoothIntracorticalParameters = typing.TypedDict('MrisSmoothIntracorticalPar
     "rad_start": typing.NotRequired[float | None],
     "tan_weights": 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_smooth_intracortical": mris_smooth_intracortical_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_smooth_intracortical": mris_smooth_intracortical_outputs,
-    }.get(t)
 
 
 class MrisSmoothIntracorticalOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_smooth_intracortical(...)`.
+    Output object returned when calling `MrisSmoothIntracorticalParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,13 +56,13 @@ def mris_smooth_intracortical_params(
     surf_name: str,
     overlay_dir: str,
     overlay_name: str,
-    output_dir: str | None = "[OVERLAY_DIR]",
+    output_dir: str | None = None,
     output_name: str | None = None,
     tan_size: int | None = None,
     rad_size: float | None = None,
     rad_start: float | None = None,
     tan_weights: str | None = None,
-) -> MrisSmoothIntracorticalParameters:
+) -> MrisSmoothIntracorticalParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +87,7 @@ def mris_smooth_intracortical_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_smooth_intracortical",
+        "@type": "freesurfer/mris_smooth_intracortical",
         "surf_dir": surf_dir,
         "surf_name": surf_name,
         "overlay_dir": overlay_dir,
@@ -144,49 +125,49 @@ def mris_smooth_intracortical_cargs(
     cargs.append("mris_smooth_intracortical")
     cargs.extend([
         "--surf_dir",
-        params.get("surf_dir")
+        params.get("surf_dir", None)
     ])
     cargs.extend([
         "--surf_name",
-        params.get("surf_name")
+        params.get("surf_name", None)
     ])
     cargs.extend([
         "--overlay_dir",
-        params.get("overlay_dir")
+        params.get("overlay_dir", None)
     ])
     cargs.extend([
         "--overlay_name",
-        params.get("overlay_name")
+        params.get("overlay_name", None)
     ])
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "--output_dir",
-            "[" + params.get("output_dir") + "]"
+            "[" + params.get("output_dir", None) + "]"
         ])
-    if params.get("output_name") is not None:
+    if params.get("output_name", None) is not None:
         cargs.extend([
             "--output_name",
-            "[" + params.get("output_name") + "]"
+            "[" + params.get("output_name", None) + "]"
         ])
-    if params.get("tan_size") is not None:
+    if params.get("tan_size", None) is not None:
         cargs.extend([
             "--tan-size",
-            "[" + str(params.get("tan_size")) + "]"
+            "[" + str(params.get("tan_size", None)) + "]"
         ])
-    if params.get("rad_size") is not None:
+    if params.get("rad_size", None) is not None:
         cargs.extend([
             "--rad-size",
-            "[" + str(params.get("rad_size")) + "]"
+            "[" + str(params.get("rad_size", None)) + "]"
         ])
-    if params.get("rad_start") is not None:
+    if params.get("rad_start", None) is not None:
         cargs.extend([
             "--rad-start",
-            "[" + str(params.get("rad_start")) + "]"
+            "[" + str(params.get("rad_start", None)) + "]"
         ])
-    if params.get("tan_weights") is not None:
+    if params.get("tan_weights", None) is not None:
         cargs.extend([
             "--tan-weights",
-            "[" + params.get("tan_weights") + "]"
+            "[" + params.get("tan_weights", None) + "]"
         ])
     return cargs
 
@@ -206,18 +187,20 @@ def mris_smooth_intracortical_outputs(
     """
     ret = MrisSmoothIntracorticalOutputs(
         root=execution.output_file("."),
-        output_overlay=execution.output_file(params.get("output_dir") + "/" + params.get("output_name")) if (params.get("output_dir") is not None and params.get("output_name") is not None) else None,
+        output_overlay=execution.output_file(params.get("output_dir", None) + "/" + params.get("output_name", None)) if (params.get("output_dir") is not None and params.get("output_name") is not None) else None,
     )
     return ret
 
 
 def mris_smooth_intracortical_execute(
     params: MrisSmoothIntracorticalParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSmoothIntracorticalOutputs:
     """
-    Smooths data overlaid onto cortical surface meshes using specified tangential
-    and radial extents.
+    mris_smooth_intracortical
+    
+    Smooths data overlaid onto cortical surface meshes using specified
+    tangential and radial extents.
     
     Author: FreeSurfer Developers
     
@@ -225,10 +208,12 @@ def mris_smooth_intracortical_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSmoothIntracorticalOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SMOOTH_INTRACORTICAL_METADATA)
     params = execution.params(params)
     cargs = mris_smooth_intracortical_cargs(params, execution)
     ret = mris_smooth_intracortical_outputs(params, execution)
@@ -241,7 +226,7 @@ def mris_smooth_intracortical(
     surf_name: str,
     overlay_dir: str,
     overlay_name: str,
-    output_dir: str | None = "[OVERLAY_DIR]",
+    output_dir: str | None = None,
     output_name: str | None = None,
     tan_size: int | None = None,
     rad_size: float | None = None,
@@ -250,8 +235,10 @@ def mris_smooth_intracortical(
     runner: Runner | None = None,
 ) -> MrisSmoothIntracorticalOutputs:
     """
-    Smooths data overlaid onto cortical surface meshes using specified tangential
-    and radial extents.
+    mris_smooth_intracortical
+    
+    Smooths data overlaid onto cortical surface meshes using specified
+    tangential and radial extents.
     
     Author: FreeSurfer Developers
     
@@ -278,8 +265,6 @@ def mris_smooth_intracortical(
     Returns:
         NamedTuple of outputs (described in `MrisSmoothIntracorticalOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SMOOTH_INTRACORTICAL_METADATA)
     params = mris_smooth_intracortical_params(
         surf_dir=surf_dir,
         surf_name=surf_name,
@@ -292,13 +277,13 @@ def mris_smooth_intracortical(
         rad_start=rad_start,
         tan_weights=tan_weights,
     )
-    return mris_smooth_intracortical_execute(params, execution)
+    return mris_smooth_intracortical_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SMOOTH_INTRACORTICAL_METADATA",
     "MrisSmoothIntracorticalOutputs",
-    "MrisSmoothIntracorticalParameters",
     "mris_smooth_intracortical",
+    "mris_smooth_intracortical_execute",
     "mris_smooth_intracortical_params",
 ]

niwrap_freesurfer/freesurfer/mris_sphere.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SPHERE_METADATA = Metadata(
-    id="fc663f61c3446a5af498e7708ae7ba01b8237606.boutiques",
+    id="7ddef7e57280aba6e64ffebd2b3c6fee383fd738.boutiques",
     name="mris_sphere",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRIS_SPHERE_METADATA = Metadata(
 
 
 MrisSphereParameters = typing.TypedDict('MrisSphereParameters', {
-    "__STYXTYPE__": typing.Literal["mris_sphere"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_sphere"]],
+    "surface_file": InputPathType,
+    "patch_file": InputPathType,
+    "output_patch": str,
+})
+MrisSphereParametersTagged = typing.TypedDict('MrisSphereParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_sphere"],
     "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_sphere": mris_sphere_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_sphere": mris_sphere_outputs,
-    }.get(t)
 
 
 class MrisSphereOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_sphere(...)`.
+    Output object returned when calling `MrisSphereParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mris_sphere_params(
     surface_file: InputPathType,
     patch_file: InputPathType,
     output_patch: str,
-) -> MrisSphereParameters:
+) -> MrisSphereParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mris_sphere_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_sphere",
+        "@type": "freesurfer/mris_sphere",
         "surface_file": surface_file,
         "patch_file": patch_file,
         "output_patch": output_patch,
@@ -102,9 +76,9 @@ def mris_sphere_cargs(
     """
     cargs = []
     cargs.append("mris_sphere")
-    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_sphere_outputs(
     """
     ret = MrisSphereOutputs(
         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_sphere_execute(
     params: MrisSphereParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSphereOutputs:
     """
+    mris_sphere
+    
     This program will add a template into an average surface.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def mris_sphere_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSphereOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SPHERE_METADATA)
     params = execution.params(params)
     cargs = mris_sphere_cargs(params, execution)
     ret = mris_sphere_outputs(params, execution)
@@ -159,6 +137,8 @@ def mris_sphere(
     runner: Runner | None = None,
 ) -> MrisSphereOutputs:
     """
+    mris_sphere
+    
     This program will add a template into an average surface.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def mris_sphere(
     Returns:
         NamedTuple of outputs (described in `MrisSphereOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SPHERE_METADATA)
     params = mris_sphere_params(
         surface_file=surface_file,
         patch_file=patch_file,
         output_patch=output_patch,
     )
-    return mris_sphere_execute(params, execution)
+    return mris_sphere_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SPHERE_METADATA",
     "MrisSphereOutputs",
-    "MrisSphereParameters",
     "mris_sphere",
+    "mris_sphere_execute",
     "mris_sphere_params",
 ]