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

niwrap_freesurfer/freesurfer/mris_exvivo_surfaces.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_EXVIVO_SURFACES_METADATA = Metadata(
-    id="7ce3e563615260c1b6239fcc9ac31d31931b5872.boutiques",
+    id="7d3fdab622259a0ec052ecdb11e294b79bf1ccfc.boutiques",
     name="mris_exvivo_surfaces",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRIS_EXVIVO_SURFACES_METADATA = Metadata(
 
 
 MrisExvivoSurfacesParameters = typing.TypedDict('MrisExvivoSurfacesParameters', {
-    "__STYXTYPE__": typing.Literal["mris_exvivo_surfaces"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_exvivo_surfaces"]],
+    "subject_name": str,
+    "hemisphere": str,
+    "omit_self_intersection": bool,
+    "create_curvature_area": bool,
+    "average_curvature": typing.NotRequired[float | None],
+    "white_only": bool,
+    "formalin": typing.NotRequired[int | None],
+})
+MrisExvivoSurfacesParametersTagged = typing.TypedDict('MrisExvivoSurfacesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_exvivo_surfaces"],
     "subject_name": str,
     "hemisphere": str,
     "omit_self_intersection": bool,
@@ -23,43 +33,11 @@ MrisExvivoSurfacesParameters = typing.TypedDict('MrisExvivoSurfacesParameters',
     "white_only": bool,
     "formalin": typing.NotRequired[int | 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_exvivo_surfaces": mris_exvivo_surfaces_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_exvivo_surfaces": mris_exvivo_surfaces_outputs,
-    }.get(t)
 
 
 class MrisExvivoSurfacesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_exvivo_surfaces(...)`.
+    Output object returned when calling `MrisExvivoSurfacesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,10 +56,10 @@ def mris_exvivo_surfaces_params(
     hemisphere: str,
     omit_self_intersection: bool = False,
     create_curvature_area: bool = False,
-    average_curvature: float | None = 10,
+    average_curvature: float | None = None,
     white_only: bool = False,
     formalin: int | None = None,
-) -> MrisExvivoSurfacesParameters:
+) -> MrisExvivoSurfacesParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +79,7 @@ def mris_exvivo_surfaces_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_exvivo_surfaces",
+        "@type": "freesurfer/mris_exvivo_surfaces",
         "subject_name": subject_name,
         "hemisphere": hemisphere,
         "omit_self_intersection": omit_self_intersection,
@@ -130,23 +108,23 @@ def mris_exvivo_surfaces_cargs(
     """
     cargs = []
     cargs.append("mris_exvivo_surfaces")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("hemisphere"))
-    if params.get("omit_self_intersection"):
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("hemisphere", None))
+    if params.get("omit_self_intersection", False):
         cargs.append("-q")
-    if params.get("create_curvature_area"):
+    if params.get("create_curvature_area", False):
         cargs.append("-c")
-    if params.get("average_curvature") is not None:
+    if params.get("average_curvature", None) is not None:
         cargs.extend([
             "-a",
-            str(params.get("average_curvature"))
+            str(params.get("average_curvature", None))
         ])
-    if params.get("white_only"):
+    if params.get("white_only", False):
         cargs.append("-whiteonly")
-    if params.get("formalin") is not None:
+    if params.get("formalin", None) is not None:
         cargs.extend([
             "-formalin",
-            str(params.get("formalin"))
+            str(params.get("formalin", None))
         ])
     return cargs
 
@@ -166,21 +144,23 @@ def mris_exvivo_surfaces_outputs(
     """
     ret = MrisExvivoSurfacesOutputs(
         root=execution.output_file("."),
-        white_surface=execution.output_file("<subject_name>_<hemisphere>_white"),
-        gray_surface=execution.output_file("<subject_name>_<hemisphere>_gray"),
-        curvature_file=execution.output_file("<subject_name>_<hemisphere>_curvature"),
-        layer_iv_surface=execution.output_file("<subject_name>_<hemisphere>_layerIV"),
+        white_surface=execution.output_file(params.get("subject_name", None) + "_" + params.get("hemisphere", None) + "_white"),
+        gray_surface=execution.output_file(params.get("subject_name", None) + "_" + params.get("hemisphere", None) + "_gray"),
+        curvature_file=execution.output_file(params.get("subject_name", None) + "_" + params.get("hemisphere", None) + "_curvature"),
+        layer_iv_surface=execution.output_file(params.get("subject_name", None) + "_" + params.get("hemisphere", None) + "_layerIV"),
     )
     return ret
 
 
 def mris_exvivo_surfaces_execute(
     params: MrisExvivoSurfacesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisExvivoSurfacesOutputs:
     """
-    FreeSurfer tool to position tessellation of the cortical surface at the white
-    and gray matter surfaces, and generate relevant surface files.
+    mris_exvivo_surfaces
+    
+    FreeSurfer tool to position tessellation of the cortical surface at the
+    white and gray matter surfaces, and generate relevant surface files.
     
     Author: FreeSurfer Developers
     
@@ -188,10 +168,12 @@ def mris_exvivo_surfaces_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisExvivoSurfacesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_EXVIVO_SURFACES_METADATA)
     params = execution.params(params)
     cargs = mris_exvivo_surfaces_cargs(params, execution)
     ret = mris_exvivo_surfaces_outputs(params, execution)
@@ -204,14 +186,16 @@ def mris_exvivo_surfaces(
     hemisphere: str,
     omit_self_intersection: bool = False,
     create_curvature_area: bool = False,
-    average_curvature: float | None = 10,
+    average_curvature: float | None = None,
     white_only: bool = False,
     formalin: int | None = None,
     runner: Runner | None = None,
 ) -> MrisExvivoSurfacesOutputs:
     """
-    FreeSurfer tool to position tessellation of the cortical surface at the white
-    and gray matter surfaces, and generate relevant surface files.
+    mris_exvivo_surfaces
+    
+    FreeSurfer tool to position tessellation of the cortical surface at the
+    white and gray matter surfaces, and generate relevant surface files.
     
     Author: FreeSurfer Developers
     
@@ -233,8 +217,6 @@ def mris_exvivo_surfaces(
     Returns:
         NamedTuple of outputs (described in `MrisExvivoSurfacesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_EXVIVO_SURFACES_METADATA)
     params = mris_exvivo_surfaces_params(
         subject_name=subject_name,
         hemisphere=hemisphere,
@@ -244,13 +226,13 @@ def mris_exvivo_surfaces(
         white_only=white_only,
         formalin=formalin,
     )
-    return mris_exvivo_surfaces_execute(params, execution)
+    return mris_exvivo_surfaces_execute(params, runner)
 
 
 __all__ = [
     "MRIS_EXVIVO_SURFACES_METADATA",
     "MrisExvivoSurfacesOutputs",
-    "MrisExvivoSurfacesParameters",
     "mris_exvivo_surfaces",
+    "mris_exvivo_surfaces_execute",
     "mris_exvivo_surfaces_params",
 ]

niwrap_freesurfer/freesurfer/mris_fill.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_FILL_METADATA = Metadata(
-    id="84be80e9010c7bb92225d5144415ad385491eea0.boutiques",
+    id="54d3ccd6e5feb1b210594124e0c140fe183541aa.boutiques",
     name="mris_fill",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_FILL_METADATA = Metadata(
 
 
 MrisFillParameters = typing.TypedDict('MrisFillParameters', {
-    "__STYXTYPE__": typing.Literal["mris_fill"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_fill"]],
+    "resolution": typing.NotRequired[float | None],
+    "conform": bool,
+    "input_surface": InputPathType,
+    "output_volume": str,
+})
+MrisFillParametersTagged = typing.TypedDict('MrisFillParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_fill"],
     "resolution": typing.NotRequired[float | None],
     "conform": bool,
     "input_surface": InputPathType,
     "output_volume": 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_fill": mris_fill_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_fill": mris_fill_outputs,
-    }.get(t)
 
 
 class MrisFillOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_fill(...)`.
+    Output object returned when calling `MrisFillParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_fill_params(
     output_volume: str,
     resolution: float | None = None,
     conform: bool = False,
-) -> MrisFillParameters:
+) -> MrisFillParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def mris_fill_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_fill",
+        "@type": "freesurfer/mris_fill",
         "conform": conform,
         "input_surface": input_surface,
         "output_volume": output_volume,
@@ -108,15 +83,15 @@ def mris_fill_cargs(
     """
     cargs = []
     cargs.append("mris_fill")
-    if params.get("resolution") is not None:
+    if params.get("resolution", None) is not None:
         cargs.extend([
             "-r",
-            str(params.get("resolution"))
+            str(params.get("resolution", None))
         ])
-    if params.get("conform"):
+    if params.get("conform", False):
         cargs.append("-c")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(params.get("output_volume"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -135,18 +110,20 @@ def mris_fill_outputs(
     """
     ret = MrisFillOutputs(
         root=execution.output_file("."),
-        filled_volume=execution.output_file(params.get("output_volume")),
+        filled_volume=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mris_fill_execute(
     params: MrisFillParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisFillOutputs:
     """
-    A tool that floodfills the interior of a surface and writes the results into a
-    volume of specified resolution.
+    mris_fill
+    
+    A tool that floodfills the interior of a surface and writes the results into
+    a volume of specified resolution.
     
     Author: FreeSurfer Developers
     
@@ -154,10 +131,12 @@ def mris_fill_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisFillOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_FILL_METADATA)
     params = execution.params(params)
     cargs = mris_fill_cargs(params, execution)
     ret = mris_fill_outputs(params, execution)
@@ -173,8 +152,10 @@ def mris_fill(
     runner: Runner | None = None,
 ) -> MrisFillOutputs:
     """
-    A tool that floodfills the interior of a surface and writes the results into a
-    volume of specified resolution.
+    mris_fill
+    
+    A tool that floodfills the interior of a surface and writes the results into
+    a volume of specified resolution.
     
     Author: FreeSurfer Developers
     
@@ -190,21 +171,19 @@ def mris_fill(
     Returns:
         NamedTuple of outputs (described in `MrisFillOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_FILL_METADATA)
     params = mris_fill_params(
         resolution=resolution,
         conform=conform,
         input_surface=input_surface,
         output_volume=output_volume,
     )
-    return mris_fill_execute(params, execution)
+    return mris_fill_execute(params, runner)
 
 
 __all__ = [
     "MRIS_FILL_METADATA",
     "MrisFillOutputs",
-    "MrisFillParameters",
     "mris_fill",
+    "mris_fill_execute",
     "mris_fill_params",
 ]

niwrap_freesurfer/freesurfer/mris_find_flat_regions.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_FIND_FLAT_REGIONS_METADATA = Metadata(
-    id="44372d93aad1a76a59c052c0d483b056d5c709e5.boutiques",
+    id="be573f569b90034ae9f6de163479dc51f840a2dd.boutiques",
     name="mris_find_flat_regions",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRIS_FIND_FLAT_REGIONS_METADATA = Metadata(
 
 
 MrisFindFlatRegionsParameters = typing.TypedDict('MrisFindFlatRegionsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_find_flat_regions"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_find_flat_regions"]],
+    "surface": InputPathType,
+    "wfile": str,
+    "threshold": typing.NotRequired[float | None],
+})
+MrisFindFlatRegionsParametersTagged = typing.TypedDict('MrisFindFlatRegionsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_find_flat_regions"],
     "surface": InputPathType,
     "wfile": str,
     "threshold": 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_find_flat_regions": mris_find_flat_regions_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_find_flat_regions": mris_find_flat_regions_outputs,
-    }.get(t)
 
 
 class MrisFindFlatRegionsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_find_flat_regions(...)`.
+    Output object returned when calling `MrisFindFlatRegionsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,8 +41,8 @@ class MrisFindFlatRegionsOutputs(typing.NamedTuple):
 def mris_find_flat_regions_params(
     surface: InputPathType,
     wfile: str,
-    threshold: float | None = 0.99,
-) -> MrisFindFlatRegionsParameters:
+    threshold: float | None = None,
+) -> MrisFindFlatRegionsParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def mris_find_flat_regions_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_find_flat_regions",
+        "@type": "freesurfer/mris_find_flat_regions",
         "surface": surface,
         "wfile": wfile,
     }
@@ -104,12 +78,12 @@ def mris_find_flat_regions_cargs(
     """
     cargs = []
     cargs.append("mris_find_flat_regions")
-    cargs.append(execution.input_file(params.get("surface")))
-    cargs.append(params.get("wfile"))
-    if params.get("threshold") is not None:
+    cargs.append(execution.input_file(params.get("surface", None)))
+    cargs.append(params.get("wfile", None))
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-t",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
     return cargs
 
@@ -129,16 +103,18 @@ def mris_find_flat_regions_outputs(
     """
     ret = MrisFindFlatRegionsOutputs(
         root=execution.output_file("."),
-        output_label_file=execution.output_file(params.get("wfile")),
+        output_label_file=execution.output_file(params.get("wfile", None)),
     )
     return ret
 
 
 def mris_find_flat_regions_execute(
     params: MrisFindFlatRegionsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisFindFlatRegionsOutputs:
     """
+    mris_find_flat_regions
+    
     Compute regions in which the surface is almost perpendicular to one of the
     cardinal axes and write the results to a label file.
     
@@ -148,10 +124,12 @@ def mris_find_flat_regions_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisFindFlatRegionsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_FIND_FLAT_REGIONS_METADATA)
     params = execution.params(params)
     cargs = mris_find_flat_regions_cargs(params, execution)
     ret = mris_find_flat_regions_outputs(params, execution)
@@ -162,10 +140,12 @@ def mris_find_flat_regions_execute(
 def mris_find_flat_regions(
     surface: InputPathType,
     wfile: str,
-    threshold: float | None = 0.99,
+    threshold: float | None = None,
     runner: Runner | None = None,
 ) -> MrisFindFlatRegionsOutputs:
     """
+    mris_find_flat_regions
+    
     Compute regions in which the surface is almost perpendicular to one of the
     cardinal axes and write the results to a label file.
     
@@ -181,20 +161,18 @@ def mris_find_flat_regions(
     Returns:
         NamedTuple of outputs (described in `MrisFindFlatRegionsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_FIND_FLAT_REGIONS_METADATA)
     params = mris_find_flat_regions_params(
         surface=surface,
         wfile=wfile,
         threshold=threshold,
     )
-    return mris_find_flat_regions_execute(params, execution)
+    return mris_find_flat_regions_execute(params, runner)
 
 
 __all__ = [
     "MRIS_FIND_FLAT_REGIONS_METADATA",
     "MrisFindFlatRegionsOutputs",
-    "MrisFindFlatRegionsParameters",
     "mris_find_flat_regions",
+    "mris_find_flat_regions_execute",
     "mris_find_flat_regions_params",
 ]