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

niwrap_freesurfer/freesurfer/mris_ms_refine.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MS_REFINE_METADATA = Metadata(
-    id="91b7755f469e5c9dbb00e033cd00aadb63d9ea59.boutiques",
+    id="debc4c2551398adeb5c36c7e39a3e3e7c1ae900c.boutiques",
     name="mris_ms_refine",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ MRIS_MS_REFINE_METADATA = Metadata(
 
 
 MrisMsRefineParameters = typing.TypedDict('MrisMsRefineParameters', {
-    "__STYXTYPE__": typing.Literal["mris_ms_refine"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_ms_refine"]],
+    "subject_name": str,
+    "hemisphere": str,
+    "xform": InputPathType,
+    "flash_files": list[InputPathType],
+    "residuals": InputPathType,
+    "omit_self_intersection": bool,
+    "create_curvature_files": bool,
+    "average_curvature": typing.NotRequired[float | None],
+    "white_only": bool,
+})
+MrisMsRefineParametersTagged = typing.TypedDict('MrisMsRefineParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_ms_refine"],
     "subject_name": str,
     "hemisphere": str,
     "xform": InputPathType,
@@ -25,43 +37,11 @@ MrisMsRefineParameters = typing.TypedDict('MrisMsRefineParameters', {
     "average_curvature": typing.NotRequired[float | None],
     "white_only": 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_ms_refine": mris_ms_refine_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_ms_refine": mris_ms_refine_outputs,
-    }.get(t)
 
 
 class MrisMsRefineOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_ms_refine(...)`.
+    Output object returned when calling `MrisMsRefineParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,9 +63,9 @@ def mris_ms_refine_params(
     residuals: InputPathType,
     omit_self_intersection: bool = False,
     create_curvature_files: bool = False,
-    average_curvature: float | None = 10,
+    average_curvature: float | None = None,
     white_only: bool = False,
-) -> MrisMsRefineParameters:
+) -> MrisMsRefineParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +86,7 @@ def mris_ms_refine_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_ms_refine",
+        "@type": "freesurfer/mris_ms_refine",
         "subject_name": subject_name,
         "hemisphere": hemisphere,
         "xform": xform,
@@ -136,21 +116,21 @@ def mris_ms_refine_cargs(
     """
     cargs = []
     cargs.append("mris_ms_refine")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("hemisphere"))
-    cargs.append(execution.input_file(params.get("xform")))
-    cargs.extend([execution.input_file(f) for f in params.get("flash_files")])
-    cargs.append(execution.input_file(params.get("residuals")))
-    if params.get("omit_self_intersection"):
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("hemisphere", None))
+    cargs.append(execution.input_file(params.get("xform", None)))
+    cargs.extend([execution.input_file(f) for f in params.get("flash_files", None)])
+    cargs.append(execution.input_file(params.get("residuals", None)))
+    if params.get("omit_self_intersection", False):
         cargs.append("-q")
-    if params.get("create_curvature_files"):
+    if params.get("create_curvature_files", 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")
     return cargs
 
@@ -170,23 +150,25 @@ def mris_ms_refine_outputs(
     """
     ret = MrisMsRefineOutputs(
         root=execution.output_file("."),
-        white_surface=execution.output_file("<subject name>/<hemisphere>.white"),
-        pial_surface=execution.output_file("<subject name>/<hemisphere>.pial"),
-        curvature_file=execution.output_file("<subject name>/<hemisphere>.curv"),
-        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"),
+        pial_surface=execution.output_file(params.get("subject_name", None) + "/" + params.get("hemisphere", None) + ".pial"),
+        curvature_file=execution.output_file(params.get("subject_name", None) + "/" + params.get("hemisphere", None) + ".curv"),
+        layer_iv_surface=execution.output_file(params.get("subject_name", None) + "/" + params.get("hemisphere", None) + ".layerIV"),
     )
     return ret
 
 
 def mris_ms_refine_execute(
     params: MrisMsRefineParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMsRefineOutputs:
     """
+    mris_ms_refine
+    
     This program positions the tessellation of the cortical surface at the white
     matter surface, then the gray matter surface. It generates surface files for
-    these surfaces as well as a 'curvature' file for the cortical thickness, and a
-    surface file which approximates layer IV of the cortical sheet.
+    these surfaces as well as a 'curvature' file for the cortical thickness, and
+    a surface file which approximates layer IV of the cortical sheet.
     
     Author: FreeSurfer Developers
     
@@ -194,10 +176,12 @@ def mris_ms_refine_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMsRefineOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MS_REFINE_METADATA)
     params = execution.params(params)
     cargs = mris_ms_refine_cargs(params, execution)
     ret = mris_ms_refine_outputs(params, execution)
@@ -213,15 +197,17 @@ def mris_ms_refine(
     residuals: InputPathType,
     omit_self_intersection: bool = False,
     create_curvature_files: bool = False,
-    average_curvature: float | None = 10,
+    average_curvature: float | None = None,
     white_only: bool = False,
     runner: Runner | None = None,
 ) -> MrisMsRefineOutputs:
     """
+    mris_ms_refine
+    
     This program positions the tessellation of the cortical surface at the white
     matter surface, then the gray matter surface. It generates surface files for
-    these surfaces as well as a 'curvature' file for the cortical thickness, and a
-    surface file which approximates layer IV of the cortical sheet.
+    these surfaces as well as a 'curvature' file for the cortical thickness, and
+    a surface file which approximates layer IV of the cortical sheet.
     
     Author: FreeSurfer Developers
     
@@ -244,8 +230,6 @@ def mris_ms_refine(
     Returns:
         NamedTuple of outputs (described in `MrisMsRefineOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MS_REFINE_METADATA)
     params = mris_ms_refine_params(
         subject_name=subject_name,
         hemisphere=hemisphere,
@@ -257,13 +241,13 @@ def mris_ms_refine(
         average_curvature=average_curvature,
         white_only=white_only,
     )
-    return mris_ms_refine_execute(params, execution)
+    return mris_ms_refine_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MS_REFINE_METADATA",
     "MrisMsRefineOutputs",
-    "MrisMsRefineParameters",
     "mris_ms_refine",
+    "mris_ms_refine_execute",
     "mris_ms_refine_params",
 ]

niwrap_freesurfer/freesurfer/mris_multimodal.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MULTIMODAL_METADATA = Metadata(
-    id="31df0ef92422bdefc56b3c5c0422ab3e36e55274.boutiques",
+    id="e3efa26567b53a98c02ce5d99d25b2ca7ca916fb.boutiques",
     name="mris_multimodal",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ MRIS_MULTIMODAL_METADATA = Metadata(
 
 
 MrisMultimodalParameters = typing.TypedDict('MrisMultimodalParameters', {
-    "__STYXTYPE__": typing.Literal["mris_multimodal"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_multimodal"]],
+    "input_surface": InputPathType,
+    "target_surface": InputPathType,
+    "output_surface": str,
+    "fill_holes": bool,
+    "curvature": bool,
+    "thickness": bool,
+    "annotation_output": str,
+    "overlay_output": str,
+    "csv_output": str,
+    "vtk_output": bool,
+})
+MrisMultimodalParametersTagged = typing.TypedDict('MrisMultimodalParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_multimodal"],
     "input_surface": InputPathType,
     "target_surface": InputPathType,
     "output_surface": str,
@@ -26,43 +39,11 @@ MrisMultimodalParameters = typing.TypedDict('MrisMultimodalParameters', {
     "csv_output": str,
     "vtk_output": 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_multimodal": mris_multimodal_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_multimodal": mris_multimodal_outputs,
-    }.get(t)
 
 
 class MrisMultimodalOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_multimodal(...)`.
+    Output object returned when calling `MrisMultimodalParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +68,7 @@ def mris_multimodal_params(
     curvature: bool = False,
     thickness: bool = False,
     vtk_output: bool = False,
-) -> MrisMultimodalParameters:
+) -> MrisMultimodalParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +87,7 @@ def mris_multimodal_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_multimodal",
+        "@type": "freesurfer/mris_multimodal",
         "input_surface": input_surface,
         "target_surface": target_surface,
         "output_surface": output_surface,
@@ -138,35 +119,35 @@ def mris_multimodal_cargs(
     cargs.append("mris_multimodal")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_surface"))
+        execution.input_file(params.get("input_surface", None))
     ])
     cargs.extend([
         "-t",
-        execution.input_file(params.get("target_surface"))
+        execution.input_file(params.get("target_surface", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_surface")
+        params.get("output_surface", None)
     ])
-    if params.get("fill_holes"):
+    if params.get("fill_holes", False):
         cargs.append("-fillHoles")
-    if params.get("curvature"):
+    if params.get("curvature", False):
         cargs.append("--curvature")
-    if params.get("thickness"):
+    if params.get("thickness", False):
         cargs.append("--thickness")
     cargs.extend([
         "-a",
-        params.get("annotation_output")
+        params.get("annotation_output", None)
     ])
     cargs.extend([
         "-v",
-        params.get("overlay_output")
+        params.get("overlay_output", None)
     ])
     cargs.extend([
         "-c",
-        params.get("csv_output")
+        params.get("csv_output", None)
     ])
-    if params.get("vtk_output"):
+    if params.get("vtk_output", False):
         cargs.append("-vtk")
     return cargs
 
@@ -186,19 +167,21 @@ def mris_multimodal_outputs(
     """
     ret = MrisMultimodalOutputs(
         root=execution.output_file("."),
-        processed_output_surface=execution.output_file(params.get("output_surface")),
-        annotation_output_file=execution.output_file(params.get("annotation_output")),
-        overlay_output_file=execution.output_file(params.get("overlay_output")),
-        csv_output_file=execution.output_file(params.get("csv_output")),
+        processed_output_surface=execution.output_file(params.get("output_surface", None)),
+        annotation_output_file=execution.output_file(params.get("annotation_output", None)),
+        overlay_output_file=execution.output_file(params.get("overlay_output", None)),
+        csv_output_file=execution.output_file(params.get("csv_output", None)),
     )
     return ret
 
 
 def mris_multimodal_execute(
     params: MrisMultimodalParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMultimodalOutputs:
     """
+    mris_multimodal
+    
     A FreeSurfer tool for processing multimodal surface data.
     
     Author: FreeSurfer Developers
@@ -207,10 +190,12 @@ def mris_multimodal_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMultimodalOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MULTIMODAL_METADATA)
     params = execution.params(params)
     cargs = mris_multimodal_cargs(params, execution)
     ret = mris_multimodal_outputs(params, execution)
@@ -232,6 +217,8 @@ def mris_multimodal(
     runner: Runner | None = None,
 ) -> MrisMultimodalOutputs:
     """
+    mris_multimodal
+    
     A FreeSurfer tool for processing multimodal surface data.
     
     Author: FreeSurfer Developers
@@ -253,8 +240,6 @@ def mris_multimodal(
     Returns:
         NamedTuple of outputs (described in `MrisMultimodalOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MULTIMODAL_METADATA)
     params = mris_multimodal_params(
         input_surface=input_surface,
         target_surface=target_surface,
@@ -267,13 +252,13 @@ def mris_multimodal(
         csv_output=csv_output,
         vtk_output=vtk_output,
     )
-    return mris_multimodal_execute(params, execution)
+    return mris_multimodal_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MULTIMODAL_METADATA",
     "MrisMultimodalOutputs",
-    "MrisMultimodalParameters",
     "mris_multimodal",
+    "mris_multimodal_execute",
     "mris_multimodal_params",
 ]

niwrap_freesurfer/freesurfer/mris_multimodal_surface_placement.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MULTIMODAL_SURFACE_PLACEMENT_METADATA = Metadata(
-    id="92026e98ad5a95dddbebbf0c2d425303698ac22a.boutiques",
+    id="c20f8e5e3b61083baa016effc3eb556a13403d62.boutiques",
     name="mris_multimodal_surface_placement",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,26 @@ MRIS_MULTIMODAL_SURFACE_PLACEMENT_METADATA = Metadata(
 
 
 MrisMultimodalSurfacePlacementParameters = typing.TypedDict('MrisMultimodalSurfacePlacementParameters', {
-    "__STYXTYPE__": typing.Literal["mris_multimodal_surface_placement"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_multimodal_surface_placement"]],
+    "input_surface": InputPathType,
+    "output_surface": InputPathType,
+    "sphere_surface": InputPathType,
+    "normals": str,
+    "values": str,
+    "debug_vertex": typing.NotRequired[float | None],
+    "step_size": float,
+    "number_of_steps": float,
+    "gradient_sigma": float,
+    "aseg_aparc": InputPathType,
+    "white_surface": InputPathType,
+    "prob_of_csf": float,
+    "t1_image": InputPathType,
+    "t2_image": InputPathType,
+    "flair_image": InputPathType,
+    "min_max": bool,
+})
+MrisMultimodalSurfacePlacementParametersTagged = typing.TypedDict('MrisMultimodalSurfacePlacementParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_multimodal_surface_placement"],
     "input_surface": InputPathType,
     "output_surface": InputPathType,
     "sphere_surface": InputPathType,
@@ -32,42 +51,11 @@ MrisMultimodalSurfacePlacementParameters = typing.TypedDict('MrisMultimodalSurfa
     "flair_image": InputPathType,
     "min_max": 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_multimodal_surface_placement": mris_multimodal_surface_placement_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 MrisMultimodalSurfacePlacementOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_multimodal_surface_placement(...)`.
+    Output object returned when calling `MrisMultimodalSurfacePlacementParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -90,7 +78,7 @@ def mris_multimodal_surface_placement_params(
     flair_image: InputPathType,
     debug_vertex: float | None = None,
     min_max: bool = False,
-) -> MrisMultimodalSurfacePlacementParameters:
+) -> MrisMultimodalSurfacePlacementParametersTagged:
     """
     Build parameters.
     
@@ -115,7 +103,7 @@ def mris_multimodal_surface_placement_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_multimodal_surface_placement",
+        "@type": "freesurfer/mris_multimodal_surface_placement",
         "input_surface": input_surface,
         "output_surface": output_surface,
         "sphere_surface": sphere_surface,
@@ -154,66 +142,66 @@ def mris_multimodal_surface_placement_cargs(
     cargs.append("mris_multimodal_surface_placement")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_surface"))
+        execution.input_file(params.get("input_surface", None))
     ])
     cargs.extend([
         "-o",
-        execution.input_file(params.get("output_surface"))
+        execution.input_file(params.get("output_surface", None))
     ])
     cargs.extend([
         "-b",
-        execution.input_file(params.get("sphere_surface"))
+        execution.input_file(params.get("sphere_surface", None))
     ])
     cargs.extend([
         "-n",
-        params.get("normals")
+        params.get("normals", None)
     ])
     cargs.extend([
         "-v",
-        params.get("values")
+        params.get("values", None)
     ])
-    if params.get("debug_vertex") is not None:
+    if params.get("debug_vertex", None) is not None:
         cargs.extend([
             "-d",
-            str(params.get("debug_vertex"))
+            str(params.get("debug_vertex", None))
         ])
     cargs.extend([
         "-s",
-        str(params.get("step_size"))
+        str(params.get("step_size", None))
     ])
     cargs.extend([
         "-k",
-        str(params.get("number_of_steps"))
+        str(params.get("number_of_steps", None))
     ])
     cargs.extend([
         "-g",
-        str(params.get("gradient_sigma"))
+        str(params.get("gradient_sigma", None))
     ])
     cargs.extend([
         "-a",
-        execution.input_file(params.get("aseg_aparc"))
+        execution.input_file(params.get("aseg_aparc", None))
     ])
     cargs.extend([
         "-w",
-        execution.input_file(params.get("white_surface"))
+        execution.input_file(params.get("white_surface", None))
     ])
     cargs.extend([
         "-p",
-        str(params.get("prob_of_csf"))
+        str(params.get("prob_of_csf", None))
     ])
     cargs.extend([
         "-t1",
-        execution.input_file(params.get("t1_image"))
+        execution.input_file(params.get("t1_image", None))
     ])
     cargs.extend([
         "-t2",
-        execution.input_file(params.get("t2_image"))
+        execution.input_file(params.get("t2_image", None))
     ])
     cargs.extend([
         "-flair",
-        execution.input_file(params.get("flair_image"))
+        execution.input_file(params.get("flair_image", None))
     ])
-    if params.get("min_max"):
+    if params.get("min_max", False):
         cargs.append("-min/max")
     return cargs
 
@@ -239,9 +227,11 @@ def mris_multimodal_surface_placement_outputs(
 
 def mris_multimodal_surface_placement_execute(
     params: MrisMultimodalSurfacePlacementParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMultimodalSurfacePlacementOutputs:
     """
+    mris_multimodal_surface_placement
+    
     FreeSurfer command for multimodal surface placement.
     
     Author: FreeSurfer Developers
@@ -250,10 +240,12 @@ def mris_multimodal_surface_placement_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMultimodalSurfacePlacementOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MULTIMODAL_SURFACE_PLACEMENT_METADATA)
     params = execution.params(params)
     cargs = mris_multimodal_surface_placement_cargs(params, execution)
     ret = mris_multimodal_surface_placement_outputs(params, execution)
@@ -281,6 +273,8 @@ def mris_multimodal_surface_placement(
     runner: Runner | None = None,
 ) -> MrisMultimodalSurfacePlacementOutputs:
     """
+    mris_multimodal_surface_placement
+    
     FreeSurfer command for multimodal surface placement.
     
     Author: FreeSurfer Developers
@@ -308,8 +302,6 @@ def mris_multimodal_surface_placement(
     Returns:
         NamedTuple of outputs (described in `MrisMultimodalSurfacePlacementOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MULTIMODAL_SURFACE_PLACEMENT_METADATA)
     params = mris_multimodal_surface_placement_params(
         input_surface=input_surface,
         output_surface=output_surface,
@@ -328,13 +320,13 @@ def mris_multimodal_surface_placement(
         flair_image=flair_image,
         min_max=min_max,
     )
-    return mris_multimodal_surface_placement_execute(params, execution)
+    return mris_multimodal_surface_placement_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MULTIMODAL_SURFACE_PLACEMENT_METADATA",
     "MrisMultimodalSurfacePlacementOutputs",
-    "MrisMultimodalSurfacePlacementParameters",
     "mris_multimodal_surface_placement",
+    "mris_multimodal_surface_placement_execute",
     "mris_multimodal_surface_placement_params",
 ]