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

niwrap_freesurfer/freesurfer/mris_distance_to_label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_DISTANCE_TO_LABEL_METADATA = Metadata(
-    id="0538a932ce0052cc0bb4e77e20e1d20d65106c51.boutiques",
+    id="22e44fd776ac40400214cd24d7f9a0b1bcbea8e7.boutiques",
     name="mris_distance_to_label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ MRIS_DISTANCE_TO_LABEL_METADATA = Metadata(
 
 
 MrisDistanceToLabelParameters = typing.TypedDict('MrisDistanceToLabelParameters', {
-    "__STYXTYPE__": typing.Literal["mris_distance_to_label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_distance_to_label"]],
+    "hemisphere": str,
+    "subject_1": str,
+})
+MrisDistanceToLabelParametersTagged = typing.TypedDict('MrisDistanceToLabelParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_distance_to_label"],
     "hemisphere": str,
     "subject_1": 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_distance_to_label": mris_distance_to_label_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 MrisDistanceToLabelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_distance_to_label(...)`.
+    Output object returned when calling `MrisDistanceToLabelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class MrisDistanceToLabelOutputs(typing.NamedTuple):
 def mris_distance_to_label_params(
     hemisphere: str,
     subject_1: str,
-) -> MrisDistanceToLabelParameters:
+) -> MrisDistanceToLabelParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +48,7 @@ def mris_distance_to_label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_distance_to_label",
+        "@type": "freesurfer/mris_distance_to_label",
         "hemisphere": hemisphere,
         "subject_1": subject_1,
     }
@@ -96,8 +70,8 @@ def mris_distance_to_label_cargs(
     """
     cargs = []
     cargs.append("mris_distance_to_label")
-    cargs.append(params.get("hemisphere"))
-    cargs.append(params.get("subject_1"))
+    cargs.append(params.get("hemisphere", None))
+    cargs.append(params.get("subject_1", None))
     return cargs
 
 
@@ -122,11 +96,13 @@ def mris_distance_to_label_outputs(
 
 def mris_distance_to_label_execute(
     params: MrisDistanceToLabelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisDistanceToLabelOutputs:
     """
-    A tool for measuring the distance between vertices on a surface and a labeled
-    region.
+    mris_distance_to_label
+    
+    A tool for measuring the distance between vertices on a surface and a
+    labeled region.
     
     Author: FreeSurfer Developers
     
@@ -134,10 +110,12 @@ def mris_distance_to_label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisDistanceToLabelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_DISTANCE_TO_LABEL_METADATA)
     params = execution.params(params)
     cargs = mris_distance_to_label_cargs(params, execution)
     ret = mris_distance_to_label_outputs(params, execution)
@@ -151,8 +129,10 @@ def mris_distance_to_label(
     runner: Runner | None = None,
 ) -> MrisDistanceToLabelOutputs:
     """
-    A tool for measuring the distance between vertices on a surface and a labeled
-    region.
+    mris_distance_to_label
+    
+    A tool for measuring the distance between vertices on a surface and a
+    labeled region.
     
     Author: FreeSurfer Developers
     
@@ -166,19 +146,17 @@ def mris_distance_to_label(
     Returns:
         NamedTuple of outputs (described in `MrisDistanceToLabelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_DISTANCE_TO_LABEL_METADATA)
     params = mris_distance_to_label_params(
         hemisphere=hemisphere,
         subject_1=subject_1,
     )
-    return mris_distance_to_label_execute(params, execution)
+    return mris_distance_to_label_execute(params, runner)
 
 
 __all__ = [
     "MRIS_DISTANCE_TO_LABEL_METADATA",
     "MrisDistanceToLabelOutputs",
-    "MrisDistanceToLabelParameters",
     "mris_distance_to_label",
+    "mris_distance_to_label_execute",
     "mris_distance_to_label_params",
 ]

niwrap_freesurfer/freesurfer/mris_distance_transform.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_DISTANCE_TRANSFORM_METADATA = Metadata(
-    id="26327fdeedfb1e1343a77de6d926663c874f15f0.boutiques",
+    id="c8724f1b368418a2816a0e1c0b66d8c2321403ff.boutiques",
     name="mris_distance_transform",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRIS_DISTANCE_TRANSFORM_METADATA = Metadata(
 
 
 MrisDistanceTransformParameters = typing.TypedDict('MrisDistanceTransformParameters', {
-    "__STYXTYPE__": typing.Literal["mris_distance_transform"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_distance_transform"]],
+    "surface": InputPathType,
+    "label": InputPathType,
+    "mode": typing.Literal["signed", "unsigned", "outside"],
+    "output_file": str,
+    "anterior": typing.NotRequired[float | None],
+    "posterior": typing.NotRequired[float | None],
+    "divide": typing.NotRequired[float | None],
+    "olabel": bool,
+})
+MrisDistanceTransformParametersTagged = typing.TypedDict('MrisDistanceTransformParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_distance_transform"],
     "surface": InputPathType,
     "label": InputPathType,
     "mode": typing.Literal["signed", "unsigned", "outside"],
@@ -24,43 +35,11 @@ MrisDistanceTransformParameters = typing.TypedDict('MrisDistanceTransformParamet
     "divide": typing.NotRequired[float | None],
     "olabel": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_distance_transform": mris_distance_transform_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_distance_transform": mris_distance_transform_outputs,
-    }.get(t)
 
 
 class MrisDistanceTransformOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_distance_transform(...)`.
+    Output object returned when calling `MrisDistanceTransformParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def mris_distance_transform_params(
     posterior: float | None = None,
     divide: float | None = None,
     olabel: bool = False,
-) -> MrisDistanceTransformParameters:
+) -> MrisDistanceTransformParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +74,7 @@ def mris_distance_transform_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_distance_transform",
+        "@type": "freesurfer/mris_distance_transform",
         "surface": surface,
         "label": label,
         "mode": mode,
@@ -126,26 +105,26 @@ def mris_distance_transform_cargs(
     """
     cargs = []
     cargs.append("mris_distance_transform")
-    cargs.append(execution.input_file(params.get("surface")))
-    cargs.append(execution.input_file(params.get("label")))
-    cargs.append(params.get("mode"))
-    cargs.append(params.get("output_file"))
-    if params.get("anterior") is not None:
+    cargs.append(execution.input_file(params.get("surface", None)))
+    cargs.append(execution.input_file(params.get("label", None)))
+    cargs.append(params.get("mode", None))
+    cargs.append(params.get("output_file", None))
+    if params.get("anterior", None) is not None:
         cargs.extend([
             "-anterior",
-            str(params.get("anterior"))
+            str(params.get("anterior", None))
         ])
-    if params.get("posterior") is not None:
+    if params.get("posterior", None) is not None:
         cargs.extend([
             "-posterior",
-            str(params.get("posterior"))
+            str(params.get("posterior", None))
         ])
-    if params.get("divide") is not None:
+    if params.get("divide", None) is not None:
         cargs.extend([
             "-divide",
-            str(params.get("divide"))
+            str(params.get("divide", None))
         ])
-    if params.get("olabel"):
+    if params.get("olabel", False):
         cargs.append("-olabel")
     return cargs
 
@@ -165,16 +144,18 @@ def mris_distance_transform_outputs(
     """
     ret = MrisDistanceTransformOutputs(
         root=execution.output_file("."),
-        result_file=execution.output_file(params.get("output_file")),
+        result_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mris_distance_transform_execute(
     params: MrisDistanceTransformParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisDistanceTransformOutputs:
     """
+    mris_distance_transform
+    
     Computes the distance transform of a label on the surface.
     
     Author: FreeSurfer Developers
@@ -183,10 +164,12 @@ def mris_distance_transform_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisDistanceTransformOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_DISTANCE_TRANSFORM_METADATA)
     params = execution.params(params)
     cargs = mris_distance_transform_cargs(params, execution)
     ret = mris_distance_transform_outputs(params, execution)
@@ -206,6 +189,8 @@ def mris_distance_transform(
     runner: Runner | None = None,
 ) -> MrisDistanceTransformOutputs:
     """
+    mris_distance_transform
+    
     Computes the distance transform of a label on the surface.
     
     Author: FreeSurfer Developers
@@ -226,8 +211,6 @@ def mris_distance_transform(
     Returns:
         NamedTuple of outputs (described in `MrisDistanceTransformOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_DISTANCE_TRANSFORM_METADATA)
     params = mris_distance_transform_params(
         surface=surface,
         label=label,
@@ -238,13 +221,13 @@ def mris_distance_transform(
         divide=divide,
         olabel=olabel,
     )
-    return mris_distance_transform_execute(params, execution)
+    return mris_distance_transform_execute(params, runner)
 
 
 __all__ = [
     "MRIS_DISTANCE_TRANSFORM_METADATA",
     "MrisDistanceTransformOutputs",
-    "MrisDistanceTransformParameters",
     "mris_distance_transform",
+    "mris_distance_transform_execute",
     "mris_distance_transform_params",
 ]

niwrap_freesurfer/freesurfer/mris_divide_parcellation.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_DIVIDE_PARCELLATION_METADATA = Metadata(
-    id="eb4ef7e4768c5312c5386818b3df847302db121f.boutiques",
+    id="073744a9dd46d03ed520a3c051ec5f427a86f468.boutiques",
     name="mris_divide_parcellation",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRIS_DIVIDE_PARCELLATION_METADATA = Metadata(
 
 
 MrisDivideParcellationParameters = typing.TypedDict('MrisDivideParcellationParameters', {
-    "__STYXTYPE__": typing.Literal["mris_divide_parcellation"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_divide_parcellation"]],
+    "subject": str,
+    "hemi": str,
+    "sourceannot": InputPathType,
+    "splitfile_or_areathresh": str,
+    "outannot": str,
+    "scale": typing.NotRequired[float | None],
+    "label_name": typing.NotRequired[str | None],
+})
+MrisDivideParcellationParametersTagged = typing.TypedDict('MrisDivideParcellationParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_divide_parcellation"],
     "subject": str,
     "hemi": str,
     "sourceannot": InputPathType,
@@ -23,43 +33,11 @@ MrisDivideParcellationParameters = typing.TypedDict('MrisDivideParcellationParam
     "scale": typing.NotRequired[float | None],
     "label_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_divide_parcellation": mris_divide_parcellation_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_divide_parcellation": mris_divide_parcellation_outputs,
-    }.get(t)
 
 
 class MrisDivideParcellationOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_divide_parcellation(...)`.
+    Output object returned when calling `MrisDivideParcellationParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mris_divide_parcellation_params(
     outannot: str,
     scale: float | None = None,
     label_name: str | None = None,
-) -> MrisDivideParcellationParameters:
+) -> MrisDivideParcellationParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +70,7 @@ def mris_divide_parcellation_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_divide_parcellation",
+        "@type": "freesurfer/mris_divide_parcellation",
         "subject": subject,
         "hemi": hemi,
         "sourceannot": sourceannot,
@@ -121,20 +99,20 @@ def mris_divide_parcellation_cargs(
     """
     cargs = []
     cargs.append("mris_divide_parcellation")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("sourceannot")))
-    cargs.append(params.get("splitfile_or_areathresh"))
-    cargs.append(params.get("outannot"))
-    if params.get("scale") is not None:
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("sourceannot", None)))
+    cargs.append(params.get("splitfile_or_areathresh", None))
+    cargs.append(params.get("outannot", None))
+    if params.get("scale", None) is not None:
         cargs.extend([
             "-scale",
-            str(params.get("scale"))
+            str(params.get("scale", None))
         ])
-    if params.get("label_name") is not None:
+    if params.get("label_name", None) is not None:
         cargs.extend([
             "-l",
-            params.get("label_name")
+            params.get("label_name", None)
         ])
     return cargs
 
@@ -154,18 +132,20 @@ def mris_divide_parcellation_outputs(
     """
     ret = MrisDivideParcellationOutputs(
         root=execution.output_file("."),
-        outannot_file=execution.output_file(params.get("outannot")),
+        outannot_file=execution.output_file(params.get("outannot", None)),
     )
     return ret
 
 
 def mris_divide_parcellation_execute(
     params: MrisDivideParcellationParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisDivideParcellationOutputs:
     """
-    Divides one or more parcellations into divisions perpendicular to the long axis
-    of the label.
+    mris_divide_parcellation
+    
+    Divides one or more parcellations into divisions perpendicular to the long
+    axis of the label.
     
     Author: FreeSurfer Developers
     
@@ -173,10 +153,12 @@ def mris_divide_parcellation_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisDivideParcellationOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_DIVIDE_PARCELLATION_METADATA)
     params = execution.params(params)
     cargs = mris_divide_parcellation_cargs(params, execution)
     ret = mris_divide_parcellation_outputs(params, execution)
@@ -195,8 +177,10 @@ def mris_divide_parcellation(
     runner: Runner | None = None,
 ) -> MrisDivideParcellationOutputs:
     """
-    Divides one or more parcellations into divisions perpendicular to the long axis
-    of the label.
+    mris_divide_parcellation
+    
+    Divides one or more parcellations into divisions perpendicular to the long
+    axis of the label.
     
     Author: FreeSurfer Developers
     
@@ -215,8 +199,6 @@ def mris_divide_parcellation(
     Returns:
         NamedTuple of outputs (described in `MrisDivideParcellationOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_DIVIDE_PARCELLATION_METADATA)
     params = mris_divide_parcellation_params(
         subject=subject,
         hemi=hemi,
@@ -226,13 +208,13 @@ def mris_divide_parcellation(
         scale=scale,
         label_name=label_name,
     )
-    return mris_divide_parcellation_execute(params, execution)
+    return mris_divide_parcellation_execute(params, runner)
 
 
 __all__ = [
     "MRIS_DIVIDE_PARCELLATION_METADATA",
     "MrisDivideParcellationOutputs",
-    "MrisDivideParcellationParameters",
     "mris_divide_parcellation",
+    "mris_divide_parcellation_execute",
     "mris_divide_parcellation_params",
 ]