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

niwrap_freesurfer/freesurfer/mris_make_template.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MAKE_TEMPLATE_METADATA = Metadata(
-    id="f241b82eadd84acf1f6370c052eca75a53412d4e.boutiques",
+    id="40081e1d5ceb0f100df56980171d3c61a2f34b9b.boutiques",
     name="mris_make_template",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,25 @@ MRIS_MAKE_TEMPLATE_METADATA = Metadata(
 
 
 MrisMakeTemplateParameters = typing.TypedDict('MrisMakeTemplateParameters', {
-    "__STYXTYPE__": typing.Literal["mris_make_template"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_make_template"]],
+    "hemi": str,
+    "surface_name": str,
+    "subjects": list[str],
+    "output_name": str,
+    "addframe_parameters": typing.NotRequired[list[str] | None],
+    "vector": bool,
+    "norot": bool,
+    "rot": bool,
+    "annot": bool,
+    "overlay_parameters": typing.NotRequired[list[str] | None],
+    "overlay_dir": typing.NotRequired[str | None],
+    "scale": typing.NotRequired[float | None],
+    "surf_dir": typing.NotRequired[str | None],
+    "smooth_iterations": typing.NotRequired[float | None],
+    "subjects_dir": typing.NotRequired[str | None],
+})
+MrisMakeTemplateParametersTagged = typing.TypedDict('MrisMakeTemplateParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_make_template"],
     "hemi": str,
     "surface_name": str,
     "subjects": list[str],
@@ -31,42 +49,11 @@ MrisMakeTemplateParameters = typing.TypedDict('MrisMakeTemplateParameters', {
     "smooth_iterations": typing.NotRequired[float | None],
     "subjects_dir": 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_make_template": mris_make_template_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 MrisMakeTemplateOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_make_template(...)`.
+    Output object returned when calling `MrisMakeTemplateParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -88,7 +75,7 @@ def mris_make_template_params(
     surf_dir: str | None = None,
     smooth_iterations: float | None = None,
     subjects_dir: str | None = None,
-) -> MrisMakeTemplateParameters:
+) -> MrisMakeTemplateParametersTagged:
     """
     Build parameters.
     
@@ -113,7 +100,7 @@ def mris_make_template_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_make_template",
+        "@type": "freesurfer/mris_make_template",
         "hemi": hemi,
         "surface_name": surface_name,
         "subjects": subjects,
@@ -155,52 +142,52 @@ def mris_make_template_cargs(
     """
     cargs = []
     cargs.append("mris_make_template")
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("surface_name"))
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_name"))
-    if params.get("addframe_parameters") is not None:
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("surface_name", None))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_name", None))
+    if params.get("addframe_parameters", None) is not None:
         cargs.extend([
             "-addframe",
-            *params.get("addframe_parameters")
+            *params.get("addframe_parameters", None)
         ])
-    if params.get("vector"):
+    if params.get("vector", False):
         cargs.append("-vector")
-    if params.get("norot"):
+    if params.get("norot", False):
         cargs.append("-norot")
-    if params.get("rot"):
+    if params.get("rot", False):
         cargs.append("-rot")
-    if params.get("annot"):
+    if params.get("annot", False):
         cargs.append("-annot")
-    if params.get("overlay_parameters") is not None:
+    if params.get("overlay_parameters", None) is not None:
         cargs.extend([
             "-overlay",
-            *params.get("overlay_parameters")
+            *params.get("overlay_parameters", None)
         ])
-    if params.get("overlay_dir") is not None:
+    if params.get("overlay_dir", None) is not None:
         cargs.extend([
             "-overlay-dir",
-            params.get("overlay_dir")
+            params.get("overlay_dir", None)
         ])
-    if params.get("scale") is not None:
+    if params.get("scale", None) is not None:
         cargs.extend([
             "-s",
-            str(params.get("scale"))
+            str(params.get("scale", None))
         ])
-    if params.get("surf_dir") is not None:
+    if params.get("surf_dir", None) is not None:
         cargs.extend([
             "-surf_dir",
-            params.get("surf_dir")
+            params.get("surf_dir", None)
         ])
-    if params.get("smooth_iterations") is not None:
+    if params.get("smooth_iterations", None) is not None:
         cargs.extend([
             "-a",
-            str(params.get("smooth_iterations"))
+            str(params.get("smooth_iterations", None))
         ])
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "-sdir",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
     return cargs
 
@@ -226,9 +213,11 @@ def mris_make_template_outputs(
 
 def mris_make_template_execute(
     params: MrisMakeTemplateParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMakeTemplateOutputs:
     """
+    mris_make_template
+    
     This program will add a template into an average surface.
     
     Author: FreeSurfer Developers
@@ -237,10 +226,12 @@ def mris_make_template_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMakeTemplateOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MAKE_TEMPLATE_METADATA)
     params = execution.params(params)
     cargs = mris_make_template_cargs(params, execution)
     ret = mris_make_template_outputs(params, execution)
@@ -267,6 +258,8 @@ def mris_make_template(
     runner: Runner | None = None,
 ) -> MrisMakeTemplateOutputs:
     """
+    mris_make_template
+    
     This program will add a template into an average surface.
     
     Author: FreeSurfer Developers
@@ -294,8 +287,6 @@ def mris_make_template(
     Returns:
         NamedTuple of outputs (described in `MrisMakeTemplateOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MAKE_TEMPLATE_METADATA)
     params = mris_make_template_params(
         hemi=hemi,
         surface_name=surface_name,
@@ -313,13 +304,13 @@ def mris_make_template(
         smooth_iterations=smooth_iterations,
         subjects_dir=subjects_dir,
     )
-    return mris_make_template_execute(params, execution)
+    return mris_make_template_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MAKE_TEMPLATE_METADATA",
     "MrisMakeTemplateOutputs",
-    "MrisMakeTemplateParameters",
     "mris_make_template",
+    "mris_make_template_execute",
     "mris_make_template_params",
 ]

niwrap_freesurfer/freesurfer/mris_map_cuts.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MAP_CUTS_METADATA = Metadata(
-    id="c694d790811be0a427c0f191c8203d1e2914b980.boutiques",
+    id="ad8291e62ce6de8cd46297e851a11555e882b1c4.boutiques",
     name="mris_map_cuts",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ MRIS_MAP_CUTS_METADATA = Metadata(
 
 
 MrisMapCutsParameters = typing.TypedDict('MrisMapCutsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_map_cuts"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_map_cuts"]],
+    "input_patch": InputPathType,
+    "output_patch": str,
+})
+MrisMapCutsParametersTagged = typing.TypedDict('MrisMapCutsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_map_cuts"],
     "input_patch": InputPathType,
     "output_patch": 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_map_cuts": mris_map_cuts_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 MrisMapCutsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_map_cuts(...)`.
+    Output object returned when calling `MrisMapCutsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class MrisMapCutsOutputs(typing.NamedTuple):
 def mris_map_cuts_params(
     input_patch: InputPathType,
     output_patch: str,
-) -> MrisMapCutsParameters:
+) -> MrisMapCutsParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def mris_map_cuts_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_map_cuts",
+        "@type": "freesurfer/mris_map_cuts",
         "input_patch": input_patch,
         "output_patch": output_patch,
     }
@@ -95,8 +69,8 @@ def mris_map_cuts_cargs(
     """
     cargs = []
     cargs.append("mris_map_cuts")
-    cargs.append(execution.input_file(params.get("input_patch")))
-    cargs.append(params.get("output_patch"))
+    cargs.append(execution.input_file(params.get("input_patch", None)))
+    cargs.append(params.get("output_patch", None))
     return cargs
 
 
@@ -121,9 +95,11 @@ def mris_map_cuts_outputs(
 
 def mris_map_cuts_execute(
     params: MrisMapCutsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMapCutsOutputs:
     """
+    mris_map_cuts
+    
     Tool for mapping cortical surface data onto cuts.
     
     Author: FreeSurfer Developers
@@ -132,10 +108,12 @@ def mris_map_cuts_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMapCutsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MAP_CUTS_METADATA)
     params = execution.params(params)
     cargs = mris_map_cuts_cargs(params, execution)
     ret = mris_map_cuts_outputs(params, execution)
@@ -149,6 +127,8 @@ def mris_map_cuts(
     runner: Runner | None = None,
 ) -> MrisMapCutsOutputs:
     """
+    mris_map_cuts
+    
     Tool for mapping cortical surface data onto cuts.
     
     Author: FreeSurfer Developers
@@ -162,19 +142,17 @@ def mris_map_cuts(
     Returns:
         NamedTuple of outputs (described in `MrisMapCutsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MAP_CUTS_METADATA)
     params = mris_map_cuts_params(
         input_patch=input_patch,
         output_patch=output_patch,
     )
-    return mris_map_cuts_execute(params, execution)
+    return mris_map_cuts_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MAP_CUTS_METADATA",
     "MrisMapCutsOutputs",
-    "MrisMapCutsParameters",
     "mris_map_cuts",
+    "mris_map_cuts_execute",
     "mris_map_cuts_params",
 ]

niwrap_freesurfer/freesurfer/mris_mef_surfaces.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MEF_SURFACES_METADATA = Metadata(
-    id="f5e7133e280262c674ba034bd20d28f4c0e8e683.boutiques",
+    id="72ce821afd111f07a160675c0d51851ca09f1b3a.boutiques",
     name="mris_mef_surfaces",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_MEF_SURFACES_METADATA = Metadata(
 
 
 MrisMefSurfacesParameters = typing.TypedDict('MrisMefSurfacesParameters', {
-    "__STYXTYPE__": typing.Literal["mris_mef_surfaces"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_mef_surfaces"]],
+    "subject_name": str,
+    "hemisphere": str,
+    "omit_self_intersection": bool,
+    "curvature": bool,
+    "average_curvature": typing.NotRequired[float | None],
+    "white_only": bool,
+})
+MrisMefSurfacesParametersTagged = typing.TypedDict('MrisMefSurfacesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_mef_surfaces"],
     "subject_name": str,
     "hemisphere": str,
     "omit_self_intersection": bool,
@@ -22,42 +31,11 @@ MrisMefSurfacesParameters = typing.TypedDict('MrisMefSurfacesParameters', {
     "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_mef_surfaces": mris_mef_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 {
-    }.get(t)
 
 
 class MrisMefSurfacesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_mef_surfaces(...)`.
+    Output object returned when calling `MrisMefSurfacesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def mris_mef_surfaces_params(
     curvature: bool = False,
     average_curvature: float | None = None,
     white_only: bool = False,
-) -> MrisMefSurfacesParameters:
+) -> MrisMefSurfacesParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +66,7 @@ def mris_mef_surfaces_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_mef_surfaces",
+        "@type": "freesurfer/mris_mef_surfaces",
         "subject_name": subject_name,
         "hemisphere": hemisphere,
         "omit_self_intersection": omit_self_intersection,
@@ -115,18 +93,18 @@ def mris_mef_surfaces_cargs(
     """
     cargs = []
     cargs.append("mris_mef_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("curvature"):
+    if params.get("curvature", 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
 
@@ -152,13 +130,15 @@ def mris_mef_surfaces_outputs(
 
 def mris_mef_surfaces_execute(
     params: MrisMefSurfacesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMefSurfacesOutputs:
     """
-    Positions the tessellation of the cortical surface at the white matter surface,
-    then the gray matter surface and generates surface files for these surfaces.
-    Also generates 'curvature' file for cortical thickness and a surface file
-    approximating layer IV of the cortical sheet.
+    mris_mef_surfaces
+    
+    Positions the tessellation of the cortical surface at the white matter
+    surface, then the gray matter surface and generates surface files for these
+    surfaces. Also generates 'curvature' file for cortical thickness and a
+    surface file approximating layer IV of the cortical sheet.
     
     Author: FreeSurfer Developers
     
@@ -166,10 +146,12 @@ def mris_mef_surfaces_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMefSurfacesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MEF_SURFACES_METADATA)
     params = execution.params(params)
     cargs = mris_mef_surfaces_cargs(params, execution)
     ret = mris_mef_surfaces_outputs(params, execution)
@@ -187,10 +169,12 @@ def mris_mef_surfaces(
     runner: Runner | None = None,
 ) -> MrisMefSurfacesOutputs:
     """
-    Positions the tessellation of the cortical surface at the white matter surface,
-    then the gray matter surface and generates surface files for these surfaces.
-    Also generates 'curvature' file for cortical thickness and a surface file
-    approximating layer IV of the cortical sheet.
+    mris_mef_surfaces
+    
+    Positions the tessellation of the cortical surface at the white matter
+    surface, then the gray matter surface and generates surface files for these
+    surfaces. Also generates 'curvature' file for cortical thickness and a
+    surface file approximating layer IV of the cortical sheet.
     
     Author: FreeSurfer Developers
     
@@ -210,8 +194,6 @@ def mris_mef_surfaces(
     Returns:
         NamedTuple of outputs (described in `MrisMefSurfacesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MEF_SURFACES_METADATA)
     params = mris_mef_surfaces_params(
         subject_name=subject_name,
         hemisphere=hemisphere,
@@ -220,13 +202,13 @@ def mris_mef_surfaces(
         average_curvature=average_curvature,
         white_only=white_only,
     )
-    return mris_mef_surfaces_execute(params, execution)
+    return mris_mef_surfaces_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MEF_SURFACES_METADATA",
     "MrisMefSurfacesOutputs",
-    "MrisMefSurfacesParameters",
     "mris_mef_surfaces",
+    "mris_mef_surfaces_execute",
     "mris_mef_surfaces_params",
 ]