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

niwrap_freesurfer/freesurfer/mris_register_to_volume.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_REGISTER_TO_VOLUME_METADATA = Metadata(
-    id="75f22b681c3c24e94cf09ba0a51bea93311a01be.boutiques",
+    id="60c56ada6b1c4db76b113b110ab2c2c2aa2119c5.boutiques",
     name="mris_register_to_volume",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,38 @@ MRIS_REGISTER_TO_VOLUME_METADATA = Metadata(
 
 
 MrisRegisterToVolumeParameters = typing.TypedDict('MrisRegisterToVolumeParameters', {
-    "__STYXTYPE__": typing.Literal["mris_register_to_volume"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_register_to_volume"]],
+    "surface": str,
+    "pial": str,
+    "pial_only": typing.NotRequired[str | None],
+    "reg": str,
+    "noglobal": bool,
+    "median": bool,
+    "mri_reg": str,
+    "tx_mmd": typing.NotRequired[list[float] | None],
+    "ty_mmd": typing.NotRequired[list[float] | None],
+    "tz_mmd": typing.NotRequired[list[float] | None],
+    "ax_mmd": typing.NotRequired[list[float] | None],
+    "ay_mmd": typing.NotRequired[list[float] | None],
+    "az_mmd": typing.NotRequired[list[float] | None],
+    "cost": typing.NotRequired[str | None],
+    "interp": typing.NotRequired[str | None],
+    "noise": typing.NotRequired[float | None],
+    "seed": typing.NotRequired[float | None],
+    "skip": typing.NotRequired[list[float] | None],
+    "sigma": typing.NotRequired[list[float] | None],
+    "cnr": bool,
+    "max_rot": typing.NotRequired[float | None],
+    "max_trans": typing.NotRequired[float | None],
+    "border": typing.NotRequired[float | None],
+    "subject": typing.NotRequired[str | None],
+    "dilate": typing.NotRequired[float | None],
+    "patch": typing.NotRequired[str | None],
+    "label": typing.NotRequired[str | None],
+    "out_reg": typing.NotRequired[str | None],
+})
+MrisRegisterToVolumeParametersTagged = typing.TypedDict('MrisRegisterToVolumeParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_register_to_volume"],
     "surface": str,
     "pial": str,
     "pial_only": typing.NotRequired[str | None],
@@ -44,42 +75,11 @@ MrisRegisterToVolumeParameters = typing.TypedDict('MrisRegisterToVolumeParameter
     "label": typing.NotRequired[str | None],
     "out_reg": 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_register_to_volume": mris_register_to_volume_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 MrisRegisterToVolumeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_register_to_volume(...)`.
+    Output object returned when calling `MrisRegisterToVolumeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -114,7 +114,7 @@ def mris_register_to_volume_params(
     patch: str | None = None,
     label: str | None = None,
     out_reg: str | None = None,
-) -> MrisRegisterToVolumeParameters:
+) -> MrisRegisterToVolumeParametersTagged:
     """
     Build parameters.
     
@@ -151,7 +151,7 @@ def mris_register_to_volume_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_register_to_volume",
+        "@type": "freesurfer/mris_register_to_volume",
         "surface": surface,
         "pial": pial,
         "reg": reg,
@@ -222,130 +222,130 @@ def mris_register_to_volume_cargs(
     cargs.append("mris_register_to_volume")
     cargs.extend([
         "--surf",
-        params.get("surface")
+        params.get("surface", None)
     ])
     cargs.extend([
         "--pial",
-        params.get("pial")
+        params.get("pial", None)
     ])
-    if params.get("pial_only") is not None:
+    if params.get("pial_only", None) is not None:
         cargs.extend([
             "--pial_only",
-            params.get("pial_only")
+            params.get("pial_only", None)
         ])
     cargs.extend([
         "--reg",
-        params.get("reg")
+        params.get("reg", None)
     ])
-    if params.get("noglobal"):
+    if params.get("noglobal", False):
         cargs.append("--noglobal")
-    if params.get("median"):
+    if params.get("median", False):
         cargs.append("--median")
     cargs.extend([
         "--mri_reg",
-        params.get("mri_reg")
+        params.get("mri_reg", None)
     ])
-    if params.get("tx_mmd") is not None:
+    if params.get("tx_mmd", None) is not None:
         cargs.extend([
             "--tx-mmd",
-            *map(str, params.get("tx_mmd"))
+            *map(str, params.get("tx_mmd", None))
         ])
-    if params.get("ty_mmd") is not None:
+    if params.get("ty_mmd", None) is not None:
         cargs.extend([
             "--ty-mmd",
-            *map(str, params.get("ty_mmd"))
+            *map(str, params.get("ty_mmd", None))
         ])
-    if params.get("tz_mmd") is not None:
+    if params.get("tz_mmd", None) is not None:
         cargs.extend([
             "--tz-mmd",
-            *map(str, params.get("tz_mmd"))
+            *map(str, params.get("tz_mmd", None))
         ])
-    if params.get("ax_mmd") is not None:
+    if params.get("ax_mmd", None) is not None:
         cargs.extend([
             "--ax-mmd",
-            *map(str, params.get("ax_mmd"))
+            *map(str, params.get("ax_mmd", None))
         ])
-    if params.get("ay_mmd") is not None:
+    if params.get("ay_mmd", None) is not None:
         cargs.extend([
             "--ay-mmd",
-            *map(str, params.get("ay_mmd"))
+            *map(str, params.get("ay_mmd", None))
         ])
-    if params.get("az_mmd") is not None:
+    if params.get("az_mmd", None) is not None:
         cargs.extend([
             "--az-mmd",
-            *map(str, params.get("az_mmd"))
+            *map(str, params.get("az_mmd", None))
         ])
-    if params.get("cost") is not None:
+    if params.get("cost", None) is not None:
         cargs.extend([
             "--cost",
-            params.get("cost")
+            params.get("cost", None)
         ])
-    if params.get("interp") is not None:
+    if params.get("interp", None) is not None:
         cargs.extend([
             "--interp",
-            params.get("interp")
+            params.get("interp", None)
         ])
-    if params.get("noise") is not None:
+    if params.get("noise", None) is not None:
         cargs.extend([
             "--noise",
-            str(params.get("noise"))
+            str(params.get("noise", None))
         ])
-    if params.get("seed") is not None:
+    if params.get("seed", None) is not None:
         cargs.extend([
             "--seed",
-            str(params.get("seed"))
+            str(params.get("seed", None))
         ])
-    if params.get("skip") is not None:
+    if params.get("skip", None) is not None:
         cargs.extend([
             "--skip",
-            *map(str, params.get("skip"))
+            *map(str, params.get("skip", None))
         ])
-    if params.get("sigma") is not None:
+    if params.get("sigma", None) is not None:
         cargs.extend([
             "--sigma",
-            *map(str, params.get("sigma"))
+            *map(str, params.get("sigma", None))
         ])
-    if params.get("cnr"):
+    if params.get("cnr", False):
         cargs.append("--CNR")
-    if params.get("max_rot") is not None:
+    if params.get("max_rot", None) is not None:
         cargs.extend([
             "--max_rot",
-            str(params.get("max_rot"))
+            str(params.get("max_rot", None))
         ])
-    if params.get("max_trans") is not None:
+    if params.get("max_trans", None) is not None:
         cargs.extend([
             "--max_trans",
-            str(params.get("max_trans"))
+            str(params.get("max_trans", None))
         ])
-    if params.get("border") is not None:
+    if params.get("border", None) is not None:
         cargs.extend([
             "--border",
-            str(params.get("border"))
+            str(params.get("border", None))
         ])
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "--s",
-            params.get("subject")
+            params.get("subject", None)
         ])
-    if params.get("dilate") is not None:
+    if params.get("dilate", None) is not None:
         cargs.extend([
             "--dilate",
-            str(params.get("dilate"))
+            str(params.get("dilate", None))
         ])
-    if params.get("patch") is not None:
+    if params.get("patch", None) is not None:
         cargs.extend([
             "--patch",
-            params.get("patch")
+            params.get("patch", None)
         ])
-    if params.get("label") is not None:
+    if params.get("label", None) is not None:
         cargs.extend([
             "--label",
-            params.get("label")
+            params.get("label", None)
         ])
-    if params.get("out_reg") is not None:
+    if params.get("out_reg", None) is not None:
         cargs.extend([
             "--out-reg",
-            params.get("out_reg")
+            params.get("out_reg", None)
         ])
     return cargs
 
@@ -371,9 +371,11 @@ def mris_register_to_volume_outputs(
 
 def mris_register_to_volume_execute(
     params: MrisRegisterToVolumeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisRegisterToVolumeOutputs:
     """
+    mris_register_to_volume
+    
     Aligns cortical surfaces to a volumetric template.
     
     Author: FreeSurfer Developers
@@ -382,10 +384,12 @@ def mris_register_to_volume_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisRegisterToVolumeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_REGISTER_TO_VOLUME_METADATA)
     params = execution.params(params)
     cargs = mris_register_to_volume_cargs(params, execution)
     ret = mris_register_to_volume_outputs(params, execution)
@@ -425,6 +429,8 @@ def mris_register_to_volume(
     runner: Runner | None = None,
 ) -> MrisRegisterToVolumeOutputs:
     """
+    mris_register_to_volume
+    
     Aligns cortical surfaces to a volumetric template.
     
     Author: FreeSurfer Developers
@@ -464,8 +470,6 @@ def mris_register_to_volume(
     Returns:
         NamedTuple of outputs (described in `MrisRegisterToVolumeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_REGISTER_TO_VOLUME_METADATA)
     params = mris_register_to_volume_params(
         surface=surface,
         pial=pial,
@@ -496,13 +500,13 @@ def mris_register_to_volume(
         label=label,
         out_reg=out_reg,
     )
-    return mris_register_to_volume_execute(params, execution)
+    return mris_register_to_volume_execute(params, runner)
 
 
 __all__ = [
     "MRIS_REGISTER_TO_VOLUME_METADATA",
     "MrisRegisterToVolumeOutputs",
-    "MrisRegisterToVolumeParameters",
     "mris_register_to_volume",
+    "mris_register_to_volume_execute",
     "mris_register_to_volume_params",
 ]

niwrap_freesurfer/freesurfer/mris_remesh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_REMESH_METADATA = Metadata(
-    id="040169fbc540d467ef423e58c64e1b78e83cb580.boutiques",
+    id="ddaf1cccfdae82e80600ea00ed9aea4f252f25e9.boutiques",
     name="mris_remesh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRIS_REMESH_METADATA = Metadata(
 
 
 MrisRemeshParameters = typing.TypedDict('MrisRemeshParameters', {
-    "__STYXTYPE__": typing.Literal["mris_remesh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_remesh"]],
+    "input": InputPathType,
+    "output": str,
+    "edge_length": typing.NotRequired[float | None],
+    "num_vertices": typing.NotRequired[float | None],
+    "face_area": typing.NotRequired[float | None],
+    "remesh": bool,
+    "iterations": typing.NotRequired[float | None],
+})
+MrisRemeshParametersTagged = typing.TypedDict('MrisRemeshParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_remesh"],
     "input": InputPathType,
     "output": str,
     "edge_length": typing.NotRequired[float | None],
@@ -23,43 +33,11 @@ MrisRemeshParameters = typing.TypedDict('MrisRemeshParameters', {
     "remesh": bool,
     "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_remesh": mris_remesh_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_remesh": mris_remesh_outputs,
-    }.get(t)
 
 
 class MrisRemeshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_remesh(...)`.
+    Output object returned when calling `MrisRemeshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mris_remesh_params(
     face_area: float | None = None,
     remesh: bool = False,
     iterations: float | None = None,
-) -> MrisRemeshParameters:
+) -> MrisRemeshParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +70,7 @@ def mris_remesh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_remesh",
+        "@type": "freesurfer/mris_remesh",
         "input": input_,
         "output": output,
         "remesh": remesh,
@@ -125,33 +103,33 @@ def mris_remesh_cargs(
     cargs.append("mris_remesh")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input"))
+        execution.input_file(params.get("input", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output")
+        params.get("output", None)
     ])
-    if params.get("edge_length") is not None:
+    if params.get("edge_length", None) is not None:
         cargs.extend([
             "--edge-len",
-            str(params.get("edge_length"))
+            str(params.get("edge_length", None))
         ])
-    if params.get("num_vertices") is not None:
+    if params.get("num_vertices", None) is not None:
         cargs.extend([
             "--nvert",
-            str(params.get("num_vertices"))
+            str(params.get("num_vertices", None))
         ])
-    if params.get("face_area") is not None:
+    if params.get("face_area", None) is not None:
         cargs.extend([
             "--desired-face-area",
-            str(params.get("face_area"))
+            str(params.get("face_area", None))
         ])
-    if params.get("remesh"):
+    if params.get("remesh", False):
         cargs.append("--remesh")
-    if params.get("iterations") is not None:
+    if params.get("iterations", None) is not None:
         cargs.extend([
             "--iters",
-            str(params.get("iterations"))
+            str(params.get("iterations", None))
         ])
     return cargs
 
@@ -171,18 +149,20 @@ def mris_remesh_outputs(
     """
     ret = MrisRemeshOutputs(
         root=execution.output_file("."),
-        remeshed_output=execution.output_file(params.get("output")),
+        remeshed_output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def mris_remesh_execute(
     params: MrisRemeshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisRemeshOutputs:
     """
-    Remeshes a surface to a desired edge length, number of vertices, or average face
-    area.
+    mris_remesh
+    
+    Remeshes a surface to a desired edge length, number of vertices, or average
+    face area.
     
     Author: FreeSurfer Developers
     
@@ -190,10 +170,12 @@ def mris_remesh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisRemeshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_REMESH_METADATA)
     params = execution.params(params)
     cargs = mris_remesh_cargs(params, execution)
     ret = mris_remesh_outputs(params, execution)
@@ -212,8 +194,10 @@ def mris_remesh(
     runner: Runner | None = None,
 ) -> MrisRemeshOutputs:
     """
-    Remeshes a surface to a desired edge length, number of vertices, or average face
-    area.
+    mris_remesh
+    
+    Remeshes a surface to a desired edge length, number of vertices, or average
+    face area.
     
     Author: FreeSurfer Developers
     
@@ -232,8 +216,6 @@ def mris_remesh(
     Returns:
         NamedTuple of outputs (described in `MrisRemeshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_REMESH_METADATA)
     params = mris_remesh_params(
         input_=input_,
         output=output,
@@ -243,13 +225,13 @@ def mris_remesh(
         remesh=remesh,
         iterations=iterations,
     )
-    return mris_remesh_execute(params, execution)
+    return mris_remesh_execute(params, runner)
 
 
 __all__ = [
     "MRIS_REMESH_METADATA",
     "MrisRemeshOutputs",
-    "MrisRemeshParameters",
     "mris_remesh",
+    "mris_remesh_execute",
     "mris_remesh_params",
 ]