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

niwrap_freesurfer/freesurfer/mris_spherical_average.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SPHERICAL_AVERAGE_METADATA = Metadata(
-    id="4f03c5890f4e5fcc3807326ef8dcefa4c44a5776.boutiques",
+    id="49fbe3a280d7a2c1507533169db06a97eaf05a25.boutiques",
     name="mris_spherical_average",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ MRIS_SPHERICAL_AVERAGE_METADATA = Metadata(
 
 
 MrisSphericalAverageParameters = typing.TypedDict('MrisSphericalAverageParameters', {
-    "__STYXTYPE__": typing.Literal["mris_spherical_average"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_spherical_average"]],
+    "which": typing.Literal["coords", "label", "vals", "curv", "area"],
+    "fname": str,
+    "hemi": typing.Literal["lh", "rh"],
+    "spherical_surf": str,
+    "subjects": list[str],
+    "output": str,
+    "segment": bool,
+    "normalize": bool,
+    "orig": typing.NotRequired[str | None],
+    "output_subject_name": typing.NotRequired[str | None],
+    "output_subject_dir": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "average_area": bool,
+    "summary_statistics": typing.NotRequired[str | None],
+})
+MrisSphericalAverageParametersTagged = typing.TypedDict('MrisSphericalAverageParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_spherical_average"],
     "which": typing.Literal["coords", "label", "vals", "curv", "area"],
     "fname": str,
     "hemi": typing.Literal["lh", "rh"],
@@ -30,42 +47,11 @@ MrisSphericalAverageParameters = typing.TypedDict('MrisSphericalAverageParameter
     "average_area": bool,
     "summary_statistics": 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_spherical_average": mris_spherical_average_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 MrisSphericalAverageOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_spherical_average(...)`.
+    Output object returned when calling `MrisSphericalAverageParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -86,7 +72,7 @@ def mris_spherical_average_params(
     subjects_dir: str | None = None,
     average_area: bool = False,
     summary_statistics: str | None = None,
-) -> MrisSphericalAverageParameters:
+) -> MrisSphericalAverageParametersTagged:
     """
     Build parameters.
     
@@ -113,7 +99,7 @@ def mris_spherical_average_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_spherical_average",
+        "@type": "freesurfer/mris_spherical_average",
         "which": which,
         "fname": fname,
         "hemi": hemi,
@@ -152,42 +138,42 @@ def mris_spherical_average_cargs(
     """
     cargs = []
     cargs.append("mris_spherical_average")
-    cargs.append(params.get("which"))
-    cargs.append(params.get("fname"))
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("spherical_surf"))
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output"))
-    if params.get("segment"):
+    cargs.append(params.get("which", None))
+    cargs.append(params.get("fname", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("spherical_surf", None))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output", None))
+    if params.get("segment", False):
         cargs.append("-segment")
-    if params.get("normalize"):
+    if params.get("normalize", False):
         cargs.append("-n")
-    if params.get("orig") is not None:
+    if params.get("orig", None) is not None:
         cargs.extend([
             "-orig",
-            params.get("orig")
+            params.get("orig", None)
         ])
-    if params.get("output_subject_name") is not None:
+    if params.get("output_subject_name", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_subject_name")
+            params.get("output_subject_name", None)
         ])
-    if params.get("output_subject_dir") is not None:
+    if params.get("output_subject_dir", None) is not None:
         cargs.extend([
             "-osdir",
-            params.get("output_subject_dir")
+            params.get("output_subject_dir", None)
         ])
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "-sdir",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("average_area"):
+    if params.get("average_area", False):
         cargs.append("-average_area")
-    if params.get("summary_statistics") is not None:
+    if params.get("summary_statistics", None) is not None:
         cargs.extend([
             "-s",
-            params.get("summary_statistics")
+            params.get("summary_statistics", None)
         ])
     return cargs
 
@@ -213,9 +199,11 @@ def mris_spherical_average_outputs(
 
 def mris_spherical_average_execute(
     params: MrisSphericalAverageParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSphericalAverageOutputs:
     """
+    mris_spherical_average
+    
     This tool adds a template into an average surface in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -224,10 +212,12 @@ def mris_spherical_average_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSphericalAverageOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SPHERICAL_AVERAGE_METADATA)
     params = execution.params(params)
     cargs = mris_spherical_average_cargs(params, execution)
     ret = mris_spherical_average_outputs(params, execution)
@@ -253,6 +243,8 @@ def mris_spherical_average(
     runner: Runner | None = None,
 ) -> MrisSphericalAverageOutputs:
     """
+    mris_spherical_average
+    
     This tool adds a template into an average surface in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -282,8 +274,6 @@ def mris_spherical_average(
     Returns:
         NamedTuple of outputs (described in `MrisSphericalAverageOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SPHERICAL_AVERAGE_METADATA)
     params = mris_spherical_average_params(
         which=which,
         fname=fname,
@@ -300,13 +290,13 @@ def mris_spherical_average(
         average_area=average_area,
         summary_statistics=summary_statistics,
     )
-    return mris_spherical_average_execute(params, execution)
+    return mris_spherical_average_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SPHERICAL_AVERAGE_METADATA",
     "MrisSphericalAverageOutputs",
-    "MrisSphericalAverageParameters",
     "mris_spherical_average",
+    "mris_spherical_average_execute",
     "mris_spherical_average_params",
 ]

niwrap_freesurfer/freesurfer/mris_surf2vtk.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SURF2VTK_METADATA = Metadata(
-    id="90077d9e6ee2cb5405978b32562110c8626e38e7.boutiques",
+    id="f5871efb4fe7c8319d01e2ffecab50e8cd8d5b55.boutiques",
     name="mris_surf2vtk",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRIS_SURF2VTK_METADATA = Metadata(
 
 
 MrisSurf2vtkParameters = typing.TypedDict('MrisSurf2vtkParameters', {
-    "__STYXTYPE__": typing.Literal["mris_surf2vtk"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_surf2vtk"]],
+    "input_surface": InputPathType,
+    "output_surface": str,
+})
+MrisSurf2vtkParametersTagged = typing.TypedDict('MrisSurf2vtkParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_surf2vtk"],
     "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_surf2vtk": mris_surf2vtk_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_surf2vtk": mris_surf2vtk_outputs,
-    }.get(t)
 
 
 class MrisSurf2vtkOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_surf2vtk(...)`.
+    Output object returned when calling `MrisSurf2vtkParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MrisSurf2vtkOutputs(typing.NamedTuple):
 def mris_surf2vtk_params(
     input_surface: InputPathType,
     output_surface: str,
-) -> MrisSurf2vtkParameters:
+) -> MrisSurf2vtkParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mris_surf2vtk_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_surf2vtk",
+        "@type": "freesurfer/mris_surf2vtk",
         "input_surface": input_surface,
         "output_surface": output_surface,
     }
@@ -100,11 +73,11 @@ def mris_surf2vtk_cargs(
     cargs.append("mris_surf2vtk")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_surface"))
+        execution.input_file(params.get("input_surface", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_surface")
+        params.get("output_surface", None)
     ])
     return cargs
 
@@ -124,16 +97,18 @@ def mris_surf2vtk_outputs(
     """
     ret = MrisSurf2vtkOutputs(
         root=execution.output_file("."),
-        vtk_surface=execution.output_file(params.get("output_surface")),
+        vtk_surface=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mris_surf2vtk_execute(
     params: MrisSurf2vtkParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSurf2vtkOutputs:
     """
+    mris_surf2vtk
+    
     Conversion tool to convert surface files to VTK format.
     
     Author: FreeSurfer Developers
@@ -142,10 +117,12 @@ def mris_surf2vtk_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSurf2vtkOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SURF2VTK_METADATA)
     params = execution.params(params)
     cargs = mris_surf2vtk_cargs(params, execution)
     ret = mris_surf2vtk_outputs(params, execution)
@@ -159,6 +136,8 @@ def mris_surf2vtk(
     runner: Runner | None = None,
 ) -> MrisSurf2vtkOutputs:
     """
+    mris_surf2vtk
+    
     Conversion tool to convert surface files to VTK format.
     
     Author: FreeSurfer Developers
@@ -172,19 +151,17 @@ def mris_surf2vtk(
     Returns:
         NamedTuple of outputs (described in `MrisSurf2vtkOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SURF2VTK_METADATA)
     params = mris_surf2vtk_params(
         input_surface=input_surface,
         output_surface=output_surface,
     )
-    return mris_surf2vtk_execute(params, execution)
+    return mris_surf2vtk_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SURF2VTK_METADATA",
     "MrisSurf2vtkOutputs",
-    "MrisSurf2vtkParameters",
     "mris_surf2vtk",
+    "mris_surf2vtk_execute",
     "mris_surf2vtk_params",
 ]

niwrap_freesurfer/freesurfer/mris_surface_stats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SURFACE_STATS_METADATA = Metadata(
-    id="707a5f1a6a689ddf45132cc3c368f2c68cdc956c.boutiques",
+    id="a421298f7c018fc93544a2d37b58d3c5d3bf6405.boutiques",
     name="mris_surface_stats",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ MRIS_SURFACE_STATS_METADATA = Metadata(
 
 
 MrisSurfaceStatsParameters = typing.TypedDict('MrisSurfaceStatsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_surface_stats"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_surface_stats"]],
+    "nsmooth": typing.NotRequired[float | None],
+    "surf_name": InputPathType,
+    "mask_name": typing.NotRequired[InputPathType | None],
+    "out_name": str,
+    "mean": typing.NotRequired[str | None],
+    "absmean": typing.NotRequired[str | None],
+    "absstd": typing.NotRequired[str | None],
+    "zscore": typing.NotRequired[str | None],
+    "first_group_size": typing.NotRequired[float | None],
+    "src_type": typing.NotRequired[str | None],
+    "trg_type": typing.NotRequired[str | None],
+    "debug": typing.NotRequired[float | None],
+    "data_files": list[InputPathType],
+})
+MrisSurfaceStatsParametersTagged = typing.TypedDict('MrisSurfaceStatsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_surface_stats"],
     "nsmooth": typing.NotRequired[float | None],
     "surf_name": InputPathType,
     "mask_name": typing.NotRequired[InputPathType | None],
@@ -29,43 +45,11 @@ MrisSurfaceStatsParameters = typing.TypedDict('MrisSurfaceStatsParameters', {
     "debug": typing.NotRequired[float | None],
     "data_files": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_surface_stats": mris_surface_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_surface_stats": mris_surface_stats_outputs,
-    }.get(t)
 
 
 class MrisSurfaceStatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_surface_stats(...)`.
+    Output object returned when calling `MrisSurfaceStatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +79,7 @@ def mris_surface_stats_params(
     src_type: str | None = None,
     trg_type: str | None = None,
     debug: float | None = None,
-) -> MrisSurfaceStatsParameters:
+) -> MrisSurfaceStatsParametersTagged:
     """
     Build parameters.
     
@@ -119,7 +103,7 @@ def mris_surface_stats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_surface_stats",
+        "@type": "freesurfer/mris_surface_stats",
         "surf_name": surf_name,
         "out_name": out_name,
         "data_files": data_files,
@@ -162,65 +146,65 @@ def mris_surface_stats_cargs(
     """
     cargs = []
     cargs.append("mris_surface_stats")
-    if params.get("nsmooth") is not None:
+    if params.get("nsmooth", None) is not None:
         cargs.extend([
             "-nsmooth",
-            str(params.get("nsmooth"))
+            str(params.get("nsmooth", None))
         ])
     cargs.extend([
         "-surf_name",
-        execution.input_file(params.get("surf_name"))
+        execution.input_file(params.get("surf_name", None))
     ])
-    if params.get("mask_name") is not None:
+    if params.get("mask_name", None) is not None:
         cargs.extend([
             "-mask_name",
-            execution.input_file(params.get("mask_name"))
+            execution.input_file(params.get("mask_name", None))
         ])
     cargs.extend([
         "-out_name",
-        params.get("out_name")
+        params.get("out_name", None)
     ])
-    if params.get("mean") is not None:
+    if params.get("mean", None) is not None:
         cargs.extend([
             "-mean",
-            params.get("mean")
+            params.get("mean", None)
         ])
-    if params.get("absmean") is not None:
+    if params.get("absmean", None) is not None:
         cargs.extend([
             "-absmean",
-            params.get("absmean")
+            params.get("absmean", None)
         ])
-    if params.get("absstd") is not None:
+    if params.get("absstd", None) is not None:
         cargs.extend([
             "-absstd",
-            params.get("absstd")
+            params.get("absstd", None)
         ])
-    if params.get("zscore") is not None:
+    if params.get("zscore", None) is not None:
         cargs.extend([
             "-zscore",
-            params.get("zscore")
+            params.get("zscore", None)
         ])
-    if params.get("first_group_size") is not None:
+    if params.get("first_group_size", None) is not None:
         cargs.extend([
             "-first_group_size",
-            str(params.get("first_group_size"))
+            str(params.get("first_group_size", None))
         ])
-    if params.get("src_type") is not None:
+    if params.get("src_type", None) is not None:
         cargs.extend([
             "-src_type",
-            params.get("src_type")
+            params.get("src_type", None)
         ])
-    if params.get("trg_type") is not None:
+    if params.get("trg_type", None) is not None:
         cargs.extend([
             "-trg_type",
-            params.get("trg_type")
+            params.get("trg_type", None)
         ])
-    if params.get("debug") is not None:
+    if params.get("debug", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug"))
+            str(params.get("debug", None))
         ])
-    cargs.extend([execution.input_file(f) for f in params.get("data_files")])
+    cargs.extend([execution.input_file(f) for f in params.get("data_files", None)])
     return cargs
 
 
@@ -239,22 +223,24 @@ def mris_surface_stats_outputs(
     """
     ret = MrisSurfaceStatsOutputs(
         root=execution.output_file("."),
-        std_output=execution.output_file(params.get("out_name")),
-        mean_output=execution.output_file(params.get("mean")) if (params.get("mean") is not None) else None,
-        absmean_output=execution.output_file(params.get("absmean")) if (params.get("absmean") is not None) else None,
-        absstd_output=execution.output_file(params.get("absstd")) if (params.get("absstd") is not None) else None,
-        zscore_output=execution.output_file(params.get("zscore")) if (params.get("zscore") is not None) else None,
+        std_output=execution.output_file(params.get("out_name", None)),
+        mean_output=execution.output_file(params.get("mean", None)) if (params.get("mean") is not None) else None,
+        absmean_output=execution.output_file(params.get("absmean", None)) if (params.get("absmean") is not None) else None,
+        absstd_output=execution.output_file(params.get("absstd", None)) if (params.get("absstd") is not None) else None,
+        zscore_output=execution.output_file(params.get("zscore", None)) if (params.get("zscore") is not None) else None,
     )
     return ret
 
 
 def mris_surface_stats_execute(
     params: MrisSurfaceStatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSurfaceStatsOutputs:
     """
-    Computes the group-wise mean and standard deviation of thickness differences at
-    every vertex of the template surface.
+    mris_surface_stats
+    
+    Computes the group-wise mean and standard deviation of thickness differences
+    at every vertex of the template surface.
     
     Author: FreeSurfer Developers
     
@@ -262,10 +248,12 @@ def mris_surface_stats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSurfaceStatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SURFACE_STATS_METADATA)
     params = execution.params(params)
     cargs = mris_surface_stats_cargs(params, execution)
     ret = mris_surface_stats_outputs(params, execution)
@@ -290,8 +278,10 @@ def mris_surface_stats(
     runner: Runner | None = None,
 ) -> MrisSurfaceStatsOutputs:
     """
-    Computes the group-wise mean and standard deviation of thickness differences at
-    every vertex of the template surface.
+    mris_surface_stats
+    
+    Computes the group-wise mean and standard deviation of thickness differences
+    at every vertex of the template surface.
     
     Author: FreeSurfer Developers
     
@@ -317,8 +307,6 @@ def mris_surface_stats(
     Returns:
         NamedTuple of outputs (described in `MrisSurfaceStatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SURFACE_STATS_METADATA)
     params = mris_surface_stats_params(
         nsmooth=nsmooth,
         surf_name=surf_name,
@@ -334,13 +322,13 @@ def mris_surface_stats(
         debug=debug,
         data_files=data_files,
     )
-    return mris_surface_stats_execute(params, execution)
+    return mris_surface_stats_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SURFACE_STATS_METADATA",
     "MrisSurfaceStatsOutputs",
-    "MrisSurfaceStatsParameters",
     "mris_surface_stats",
+    "mris_surface_stats_execute",
     "mris_surface_stats_params",
 ]