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

niwrap_freesurfer/freesurfer/mris_reposition_surface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_REPOSITION_SURFACE_METADATA = Metadata(
-    id="0c77cbb7786fb79ce602e33afe3529727da1fb02.boutiques",
+    id="30d5faac758f4d4e79dcb635f98b995e59376ddf.boutiques",
     name="mris_reposition_surface",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRIS_REPOSITION_SURFACE_METADATA = Metadata(
 
 
 MrisRepositionSurfaceParameters = typing.TypedDict('MrisRepositionSurfaceParameters', {
-    "__STYXTYPE__": typing.Literal["mris_reposition_surface"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_reposition_surface"]],
+    "surf": InputPathType,
+    "volume": InputPathType,
+    "points": InputPathType,
+    "output": str,
+    "size": typing.NotRequired[float | None],
+    "sigma": typing.NotRequired[float | None],
+    "iterations": typing.NotRequired[float | None],
+})
+MrisRepositionSurfaceParametersTagged = typing.TypedDict('MrisRepositionSurfaceParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_reposition_surface"],
     "surf": InputPathType,
     "volume": InputPathType,
     "points": InputPathType,
@@ -23,43 +33,11 @@ MrisRepositionSurfaceParameters = typing.TypedDict('MrisRepositionSurfaceParamet
     "sigma": typing.NotRequired[float | None],
     "iterations": 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_reposition_surface": mris_reposition_surface_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_reposition_surface": mris_reposition_surface_outputs,
-    }.get(t)
 
 
 class MrisRepositionSurfaceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_reposition_surface(...)`.
+    Output object returned when calling `MrisRepositionSurfaceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,10 +50,10 @@ def mris_reposition_surface_params(
     volume: InputPathType,
     points: InputPathType,
     output: str,
-    size: float | None = 1,
-    sigma: float | None = 2.0,
-    iterations: float | None = 1,
-) -> MrisRepositionSurfaceParameters:
+    size: float | None = None,
+    sigma: float | None = None,
+    iterations: float | None = None,
+) -> MrisRepositionSurfaceParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +69,7 @@ def mris_reposition_surface_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_reposition_surface",
+        "@type": "freesurfer/mris_reposition_surface",
         "surf": surf,
         "volume": volume,
         "points": points,
@@ -123,34 +101,34 @@ def mris_reposition_surface_cargs(
     cargs.append("mris_reposition_surface")
     cargs.extend([
         "-s",
-        execution.input_file(params.get("surf"))
+        execution.input_file(params.get("surf", None))
     ])
     cargs.extend([
         "-v",
-        execution.input_file(params.get("volume"))
+        execution.input_file(params.get("volume", None))
     ])
     cargs.extend([
         "-p",
-        execution.input_file(params.get("points"))
+        execution.input_file(params.get("points", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output")
+        params.get("output", None)
     ])
-    if params.get("size") is not None:
+    if params.get("size", None) is not None:
         cargs.extend([
             "-z",
-            str(params.get("size"))
+            str(params.get("size", None))
         ])
-    if params.get("sigma") is not None:
+    if params.get("sigma", None) is not None:
         cargs.extend([
             "-g",
-            str(params.get("sigma"))
+            str(params.get("sigma", None))
         ])
-    if params.get("iterations") is not None:
+    if params.get("iterations", None) is not None:
         cargs.extend([
             "-i",
-            str(params.get("iterations"))
+            str(params.get("iterations", None))
         ])
     return cargs
 
@@ -170,16 +148,18 @@ def mris_reposition_surface_outputs(
     """
     ret = MrisRepositionSurfaceOutputs(
         root=execution.output_file("."),
-        output_surface=execution.output_file(params.get("output")),
+        output_surface=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def mris_reposition_surface_execute(
     params: MrisRepositionSurfaceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisRepositionSurfaceOutputs:
     """
+    mris_reposition_surface
+    
     Reposition a surface based on the given control points (in JSON format).
     
     Author: FreeSurfer Developers
@@ -188,10 +168,12 @@ def mris_reposition_surface_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisRepositionSurfaceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_REPOSITION_SURFACE_METADATA)
     params = execution.params(params)
     cargs = mris_reposition_surface_cargs(params, execution)
     ret = mris_reposition_surface_outputs(params, execution)
@@ -204,12 +186,14 @@ def mris_reposition_surface(
     volume: InputPathType,
     points: InputPathType,
     output: str,
-    size: float | None = 1,
-    sigma: float | None = 2.0,
-    iterations: float | None = 1,
+    size: float | None = None,
+    sigma: float | None = None,
+    iterations: float | None = None,
     runner: Runner | None = None,
 ) -> MrisRepositionSurfaceOutputs:
     """
+    mris_reposition_surface
+    
     Reposition a surface based on the given control points (in JSON format).
     
     Author: FreeSurfer Developers
@@ -228,8 +212,6 @@ def mris_reposition_surface(
     Returns:
         NamedTuple of outputs (described in `MrisRepositionSurfaceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_REPOSITION_SURFACE_METADATA)
     params = mris_reposition_surface_params(
         surf=surf,
         volume=volume,
@@ -239,13 +221,13 @@ def mris_reposition_surface(
         sigma=sigma,
         iterations=iterations,
     )
-    return mris_reposition_surface_execute(params, execution)
+    return mris_reposition_surface_execute(params, runner)
 
 
 __all__ = [
     "MRIS_REPOSITION_SURFACE_METADATA",
     "MrisRepositionSurfaceOutputs",
-    "MrisRepositionSurfaceParameters",
     "mris_reposition_surface",
+    "mris_reposition_surface_execute",
     "mris_reposition_surface_params",
 ]

niwrap_freesurfer/freesurfer/mris_resample.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_RESAMPLE_METADATA = Metadata(
-    id="33f6025deb7a5ce712fd1bc0d45af2a272896018.boutiques",
+    id="daadddee27729e6853f086ff1ecfaef6e4baf449.boutiques",
     name="mris_resample",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_RESAMPLE_METADATA = Metadata(
 
 
 MrisResampleParameters = typing.TypedDict('MrisResampleParameters', {
-    "__STYXTYPE__": typing.Literal["mris_resample"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_resample"]],
+    "atlas_reg": InputPathType,
+    "subject_reg": InputPathType,
+    "subject_surf": InputPathType,
+    "output": str,
+    "annot_in": typing.NotRequired[InputPathType | None],
+    "annot_out": typing.NotRequired[str | None],
+})
+MrisResampleParametersTagged = typing.TypedDict('MrisResampleParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_resample"],
     "atlas_reg": InputPathType,
     "subject_reg": InputPathType,
     "subject_surf": InputPathType,
@@ -22,43 +31,11 @@ MrisResampleParameters = typing.TypedDict('MrisResampleParameters', {
     "annot_in": typing.NotRequired[InputPathType | None],
     "annot_out": 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_resample": mris_resample_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_resample": mris_resample_outputs,
-    }.get(t)
 
 
 class MrisResampleOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_resample(...)`.
+    Output object returned when calling `MrisResampleParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def mris_resample_params(
     output: str,
     annot_in: InputPathType | None = None,
     annot_out: str | None = None,
-) -> MrisResampleParameters:
+) -> MrisResampleParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +69,7 @@ def mris_resample_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_resample",
+        "@type": "freesurfer/mris_resample",
         "atlas_reg": atlas_reg,
         "subject_reg": subject_reg,
         "subject_surf": subject_surf,
@@ -122,29 +99,29 @@ def mris_resample_cargs(
     cargs.append("mris_resample")
     cargs.extend([
         "-atlas_reg",
-        execution.input_file(params.get("atlas_reg"))
+        execution.input_file(params.get("atlas_reg", None))
     ])
     cargs.extend([
         "-subject_reg",
-        execution.input_file(params.get("subject_reg"))
+        execution.input_file(params.get("subject_reg", None))
     ])
     cargs.extend([
         "-subject_surf",
-        execution.input_file(params.get("subject_surf"))
+        execution.input_file(params.get("subject_surf", None))
     ])
     cargs.extend([
         "-out",
-        params.get("output")
+        params.get("output", None)
     ])
-    if params.get("annot_in") is not None:
+    if params.get("annot_in", None) is not None:
         cargs.extend([
             "--annot_in",
-            execution.input_file(params.get("annot_in"))
+            execution.input_file(params.get("annot_in", None))
         ])
-    if params.get("annot_out") is not None:
+    if params.get("annot_out", None) is not None:
         cargs.extend([
             "--annot_out",
-            params.get("annot_out")
+            params.get("annot_out", None)
         ])
     return cargs
 
@@ -164,17 +141,19 @@ def mris_resample_outputs(
     """
     ret = MrisResampleOutputs(
         root=execution.output_file("."),
-        resampled_surface_output=execution.output_file(params.get("output")),
-        resampled_annotation_output=execution.output_file(params.get("annot_out")) if (params.get("annot_out") is not None) else None,
+        resampled_surface_output=execution.output_file(params.get("output", None)),
+        resampled_annotation_output=execution.output_file(params.get("annot_out", None)) if (params.get("annot_out") is not None) else None,
     )
     return ret
 
 
 def mris_resample_execute(
     params: MrisResampleParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisResampleOutputs:
     """
+    mris_resample
+    
     Resample cortical surfaces in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -183,10 +162,12 @@ def mris_resample_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisResampleOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_RESAMPLE_METADATA)
     params = execution.params(params)
     cargs = mris_resample_cargs(params, execution)
     ret = mris_resample_outputs(params, execution)
@@ -204,6 +185,8 @@ def mris_resample(
     runner: Runner | None = None,
 ) -> MrisResampleOutputs:
     """
+    mris_resample
+    
     Resample cortical surfaces in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -223,8 +206,6 @@ def mris_resample(
     Returns:
         NamedTuple of outputs (described in `MrisResampleOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_RESAMPLE_METADATA)
     params = mris_resample_params(
         atlas_reg=atlas_reg,
         subject_reg=subject_reg,
@@ -233,13 +214,13 @@ def mris_resample(
         annot_in=annot_in,
         annot_out=annot_out,
     )
-    return mris_resample_execute(params, execution)
+    return mris_resample_execute(params, runner)
 
 
 __all__ = [
     "MRIS_RESAMPLE_METADATA",
     "MrisResampleOutputs",
-    "MrisResampleParameters",
     "mris_resample",
+    "mris_resample_execute",
     "mris_resample_params",
 ]

niwrap_freesurfer/freesurfer/mris_rescale.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_RESCALE_METADATA = Metadata(
-    id="7c34665e3228c1d75cd583cfdaebcd5129ccb2cf.boutiques",
+    id="ed45dab6599c3ba280a7565b2f7a8cd93e1db782.boutiques",
     name="mris_rescale",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRIS_RESCALE_METADATA = Metadata(
 
 
 MrisRescaleParameters = typing.TypedDict('MrisRescaleParameters', {
-    "__STYXTYPE__": typing.Literal["mris_rescale"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_rescale"]],
+    "input_surface": InputPathType,
+    "output_surface": str,
+})
+MrisRescaleParametersTagged = typing.TypedDict('MrisRescaleParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_rescale"],
     "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_rescale": mris_rescale_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_rescale": mris_rescale_outputs,
-    }.get(t)
 
 
 class MrisRescaleOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_rescale(...)`.
+    Output object returned when calling `MrisRescaleParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MrisRescaleOutputs(typing.NamedTuple):
 def mris_rescale_params(
     input_surface: InputPathType,
     output_surface: str,
-) -> MrisRescaleParameters:
+) -> MrisRescaleParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mris_rescale_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_rescale",
+        "@type": "freesurfer/mris_rescale",
         "input_surface": input_surface,
         "output_surface": output_surface,
     }
@@ -98,8 +71,8 @@ def mris_rescale_cargs(
     """
     cargs = []
     cargs.append("mris_rescale")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(params.get("output_surface"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(params.get("output_surface", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def mris_rescale_outputs(
     """
     ret = MrisRescaleOutputs(
         root=execution.output_file("."),
-        rescaled_output_surface=execution.output_file(params.get("output_surface")),
+        rescaled_output_surface=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mris_rescale_execute(
     params: MrisRescaleParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisRescaleOutputs:
     """
+    mris_rescale
+    
     This program will rescale a surface representation.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def mris_rescale_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisRescaleOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_RESCALE_METADATA)
     params = execution.params(params)
     cargs = mris_rescale_cargs(params, execution)
     ret = mris_rescale_outputs(params, execution)
@@ -153,6 +130,8 @@ def mris_rescale(
     runner: Runner | None = None,
 ) -> MrisRescaleOutputs:
     """
+    mris_rescale
+    
     This program will rescale a surface representation.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def mris_rescale(
     Returns:
         NamedTuple of outputs (described in `MrisRescaleOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_RESCALE_METADATA)
     params = mris_rescale_params(
         input_surface=input_surface,
         output_surface=output_surface,
     )
-    return mris_rescale_execute(params, execution)
+    return mris_rescale_execute(params, runner)
 
 
 __all__ = [
     "MRIS_RESCALE_METADATA",
     "MrisRescaleOutputs",
-    "MrisRescaleParameters",
     "mris_rescale",
+    "mris_rescale_execute",
     "mris_rescale_params",
 ]