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

niwrap_freesurfer/freesurfer/mris_volmask_novtk.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_VOLMASK_NOVTK_METADATA = Metadata(
-    id="4e1cb80a05cb3eaf1f94144ef1674e45ce0528db.boutiques",
+    id="fd403da0a6d85ed4d975553ad02bba60b13e64a4.boutiques",
     name="mris_volmask_novtk",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,28 @@ MRIS_VOLMASK_NOVTK_METADATA = Metadata(
 
 
 MrisVolmaskNovtkParameters = typing.TypedDict('MrisVolmaskNovtkParameters', {
-    "__STYXTYPE__": typing.Literal["mris_volmask_novtk"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_volmask_novtk"]],
+    "io": str,
+    "cap_distance": typing.NotRequired[float | None],
+    "label_background": typing.NotRequired[float | None],
+    "label_left_white": typing.NotRequired[float | None],
+    "label_left_ribbon": typing.NotRequired[float | None],
+    "label_right_white": typing.NotRequired[float | None],
+    "label_right_ribbon": typing.NotRequired[float | None],
+    "surf_white": typing.NotRequired[str | None],
+    "surf_pial": typing.NotRequired[str | None],
+    "aseg_name": typing.NotRequired[str | None],
+    "out_root": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "save_distance": bool,
+    "lh_only": bool,
+    "rh_only": bool,
+    "parallel": bool,
+    "edit_aseg": bool,
+    "save_ribbon": bool,
+})
+MrisVolmaskNovtkParametersTagged = typing.TypedDict('MrisVolmaskNovtkParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_volmask_novtk"],
     "io": str,
     "cap_distance": typing.NotRequired[float | None],
     "label_background": typing.NotRequired[float | None],
@@ -34,42 +55,11 @@ MrisVolmaskNovtkParameters = typing.TypedDict('MrisVolmaskNovtkParameters', {
     "edit_aseg": bool,
     "save_ribbon": 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_volmask_novtk": mris_volmask_novtk_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 MrisVolmaskNovtkOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_volmask_novtk(...)`.
+    Output object returned when calling `MrisVolmaskNovtkParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -94,7 +84,7 @@ def mris_volmask_novtk_params(
     parallel: bool = False,
     edit_aseg: bool = False,
     save_ribbon: bool = False,
-) -> MrisVolmaskNovtkParameters:
+) -> MrisVolmaskNovtkParametersTagged:
     """
     Build parameters.
     
@@ -125,7 +115,7 @@ def mris_volmask_novtk_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_volmask_novtk",
+        "@type": "freesurfer/mris_volmask_novtk",
         "io": io_,
         "save_distance": save_distance,
         "lh_only": lh_only,
@@ -174,73 +164,73 @@ def mris_volmask_novtk_cargs(
     """
     cargs = []
     cargs.append("mris_volmask_novtk")
-    cargs.append(params.get("io"))
-    if params.get("cap_distance") is not None:
+    cargs.append(params.get("io", None))
+    if params.get("cap_distance", None) is not None:
         cargs.extend([
             "--cap_distance",
-            str(params.get("cap_distance"))
+            str(params.get("cap_distance", None))
         ])
-    if params.get("label_background") is not None:
+    if params.get("label_background", None) is not None:
         cargs.extend([
             "--label_background",
-            str(params.get("label_background"))
+            str(params.get("label_background", None))
         ])
-    if params.get("label_left_white") is not None:
+    if params.get("label_left_white", None) is not None:
         cargs.extend([
             "--label_left_white",
-            str(params.get("label_left_white"))
+            str(params.get("label_left_white", None))
         ])
-    if params.get("label_left_ribbon") is not None:
+    if params.get("label_left_ribbon", None) is not None:
         cargs.extend([
             "--label_left_ribbon",
-            str(params.get("label_left_ribbon"))
+            str(params.get("label_left_ribbon", None))
         ])
-    if params.get("label_right_white") is not None:
+    if params.get("label_right_white", None) is not None:
         cargs.extend([
             "--label_right_white",
-            str(params.get("label_right_white"))
+            str(params.get("label_right_white", None))
         ])
-    if params.get("label_right_ribbon") is not None:
+    if params.get("label_right_ribbon", None) is not None:
         cargs.extend([
             "--label_right_ribbon",
-            str(params.get("label_right_ribbon"))
+            str(params.get("label_right_ribbon", None))
         ])
-    if params.get("surf_white") is not None:
+    if params.get("surf_white", None) is not None:
         cargs.extend([
             "--surf_white",
-            params.get("surf_white")
+            params.get("surf_white", None)
         ])
-    if params.get("surf_pial") is not None:
+    if params.get("surf_pial", None) is not None:
         cargs.extend([
             "--surf_pial",
-            params.get("surf_pial")
+            params.get("surf_pial", None)
         ])
-    if params.get("aseg_name") is not None:
+    if params.get("aseg_name", None) is not None:
         cargs.extend([
             "--aseg_name",
-            params.get("aseg_name")
+            params.get("aseg_name", None)
         ])
-    if params.get("out_root") is not None:
+    if params.get("out_root", None) is not None:
         cargs.extend([
             "--out_root",
-            params.get("out_root")
+            params.get("out_root", None)
         ])
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("save_distance"):
+    if params.get("save_distance", False):
         cargs.append("--save_distance")
-    if params.get("lh_only"):
+    if params.get("lh_only", False):
         cargs.append("--lh-only")
-    if params.get("rh_only"):
+    if params.get("rh_only", False):
         cargs.append("--rh-only")
-    if params.get("parallel"):
+    if params.get("parallel", False):
         cargs.append("--parallel")
-    if params.get("edit_aseg"):
+    if params.get("edit_aseg", False):
         cargs.append("--edit_aseg")
-    if params.get("save_ribbon"):
+    if params.get("save_ribbon", False):
         cargs.append("--save_ribbon")
     return cargs
 
@@ -266,9 +256,11 @@ def mris_volmask_novtk_outputs(
 
 def mris_volmask_novtk_execute(
     params: MrisVolmaskNovtkParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisVolmaskNovtkOutputs:
     """
+    mris_volmask_novtk
+    
     Computes a volume mask at the same resolution as <subject>/mri/brain.mgz and
     labels voxels based on the signed-distance function from the surface.
     
@@ -278,10 +270,12 @@ def mris_volmask_novtk_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisVolmaskNovtkOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_VOLMASK_NOVTK_METADATA)
     params = execution.params(params)
     cargs = mris_volmask_novtk_cargs(params, execution)
     ret = mris_volmask_novtk_outputs(params, execution)
@@ -311,6 +305,8 @@ def mris_volmask_novtk(
     runner: Runner | None = None,
 ) -> MrisVolmaskNovtkOutputs:
     """
+    mris_volmask_novtk
+    
     Computes a volume mask at the same resolution as <subject>/mri/brain.mgz and
     labels voxels based on the signed-distance function from the surface.
     
@@ -345,8 +341,6 @@ def mris_volmask_novtk(
     Returns:
         NamedTuple of outputs (described in `MrisVolmaskNovtkOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_VOLMASK_NOVTK_METADATA)
     params = mris_volmask_novtk_params(
         io_=io_,
         cap_distance=cap_distance,
@@ -367,13 +361,13 @@ def mris_volmask_novtk(
         edit_aseg=edit_aseg,
         save_ribbon=save_ribbon,
     )
-    return mris_volmask_novtk_execute(params, execution)
+    return mris_volmask_novtk_execute(params, runner)
 
 
 __all__ = [
     "MRIS_VOLMASK_NOVTK_METADATA",
     "MrisVolmaskNovtkOutputs",
-    "MrisVolmaskNovtkParameters",
     "mris_volmask_novtk",
+    "mris_volmask_novtk_execute",
     "mris_volmask_novtk_params",
 ]

niwrap_freesurfer/freesurfer/mris_volmask_vtk.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_VOLMASK_VTK_METADATA = Metadata(
-    id="a3c789f55e6c7a3e7227b6c9374dfc58b3c098e4.boutiques",
+    id="18075f3e0f86b04df853ca3f2d12d30d3e8248fb.boutiques",
     name="mris_volmask_vtk",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,28 @@ MRIS_VOLMASK_VTK_METADATA = Metadata(
 
 
 MrisVolmaskVtkParameters = typing.TypedDict('MrisVolmaskVtkParameters', {
-    "__STYXTYPE__": typing.Literal["mris_volmask_vtk"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_volmask_vtk"]],
+    "cap_distance": typing.NotRequired[float | None],
+    "label_background": typing.NotRequired[float | None],
+    "label_left_white": typing.NotRequired[float | None],
+    "label_left_ribbon": typing.NotRequired[float | None],
+    "label_right_white": typing.NotRequired[float | None],
+    "label_right_ribbon": typing.NotRequired[float | None],
+    "surf_white": typing.NotRequired[str | None],
+    "surf_pial": typing.NotRequired[str | None],
+    "aseg_name": typing.NotRequired[str | None],
+    "out_root": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "save_distance": bool,
+    "lh_only": bool,
+    "rh_only": bool,
+    "parallel": bool,
+    "edit_aseg": bool,
+    "save_ribbon": bool,
+    "io_param": str,
+})
+MrisVolmaskVtkParametersTagged = typing.TypedDict('MrisVolmaskVtkParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_volmask_vtk"],
     "cap_distance": typing.NotRequired[float | None],
     "label_background": typing.NotRequired[float | None],
     "label_left_white": typing.NotRequired[float | None],
@@ -34,43 +55,11 @@ MrisVolmaskVtkParameters = typing.TypedDict('MrisVolmaskVtkParameters', {
     "save_ribbon": bool,
     "io_param": 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_volmask_vtk": mris_volmask_vtk_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_volmask_vtk": mris_volmask_vtk_outputs,
-    }.get(t)
 
 
 class MrisVolmaskVtkOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_volmask_vtk(...)`.
+    Output object returned when calling `MrisVolmaskVtkParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -82,10 +71,14 @@ class MrisVolmaskVtkOutputs(typing.NamedTuple):
     """Right hemisphere ribbon output file."""
     edited_aseg_output: OutputPathType
     """Edited aseg output using ribbons."""
-    dwhite_output: OutputPathType
-    """Signed distance output for the white matter."""
-    dpial_output: OutputPathType
-    """Signed distance output for the pial surface."""
+    lh_dwhite_output: OutputPathType
+    """Signed distance output for the left hemisphere white matter."""
+    lh_dpial_output: OutputPathType
+    """Signed distance output for the left hemisphere pial surface."""
+    rh_dwhite_output: OutputPathType
+    """Signed distance output for the right hemisphere white matter."""
+    rh_dpial_output: OutputPathType
+    """Signed distance output for the right hemisphere pial surface."""
 
 
 def mris_volmask_vtk_params(
@@ -107,7 +100,7 @@ def mris_volmask_vtk_params(
     parallel: bool = False,
     edit_aseg: bool = False,
     save_ribbon: bool = False,
-) -> MrisVolmaskVtkParameters:
+) -> MrisVolmaskVtkParametersTagged:
     """
     Build parameters.
     
@@ -139,7 +132,7 @@ def mris_volmask_vtk_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_volmask_vtk",
+        "@type": "freesurfer/mris_volmask_vtk",
         "save_distance": save_distance,
         "lh_only": lh_only,
         "rh_only": rh_only,
@@ -188,74 +181,74 @@ def mris_volmask_vtk_cargs(
     """
     cargs = []
     cargs.append("mris_volmask_vtk")
-    if params.get("cap_distance") is not None:
+    if params.get("cap_distance", None) is not None:
         cargs.extend([
             "--cap_distance",
-            str(params.get("cap_distance"))
+            str(params.get("cap_distance", None))
         ])
-    if params.get("label_background") is not None:
+    if params.get("label_background", None) is not None:
         cargs.extend([
             "--label_background",
-            str(params.get("label_background"))
+            str(params.get("label_background", None))
         ])
-    if params.get("label_left_white") is not None:
+    if params.get("label_left_white", None) is not None:
         cargs.extend([
             "--label_left_white",
-            str(params.get("label_left_white"))
+            str(params.get("label_left_white", None))
         ])
-    if params.get("label_left_ribbon") is not None:
+    if params.get("label_left_ribbon", None) is not None:
         cargs.extend([
             "--label_left_ribbon",
-            str(params.get("label_left_ribbon"))
+            str(params.get("label_left_ribbon", None))
         ])
-    if params.get("label_right_white") is not None:
+    if params.get("label_right_white", None) is not None:
         cargs.extend([
             "--label_right_white",
-            str(params.get("label_right_white"))
+            str(params.get("label_right_white", None))
         ])
-    if params.get("label_right_ribbon") is not None:
+    if params.get("label_right_ribbon", None) is not None:
         cargs.extend([
             "--label_right_ribbon",
-            str(params.get("label_right_ribbon"))
+            str(params.get("label_right_ribbon", None))
         ])
-    if params.get("surf_white") is not None:
+    if params.get("surf_white", None) is not None:
         cargs.extend([
             "--surf_white",
-            params.get("surf_white")
+            params.get("surf_white", None)
         ])
-    if params.get("surf_pial") is not None:
+    if params.get("surf_pial", None) is not None:
         cargs.extend([
             "--surf_pial",
-            params.get("surf_pial")
+            params.get("surf_pial", None)
         ])
-    if params.get("aseg_name") is not None:
+    if params.get("aseg_name", None) is not None:
         cargs.extend([
             "--aseg_name",
-            params.get("aseg_name")
+            params.get("aseg_name", None)
         ])
-    if params.get("out_root") is not None:
+    if params.get("out_root", None) is not None:
         cargs.extend([
             "--out_root",
-            params.get("out_root")
+            params.get("out_root", None)
         ])
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("save_distance"):
+    if params.get("save_distance", False):
         cargs.append("--save_distance")
-    if params.get("lh_only"):
+    if params.get("lh_only", False):
         cargs.append("--lh-only")
-    if params.get("rh_only"):
+    if params.get("rh_only", False):
         cargs.append("--rh-only")
-    if params.get("parallel"):
+    if params.get("parallel", False):
         cargs.append("--parallel")
-    if params.get("edit_aseg"):
+    if params.get("edit_aseg", False):
         cargs.append("--edit_aseg")
-    if params.get("save_ribbon"):
+    if params.get("save_ribbon", False):
         cargs.append("--save_ribbon")
-    cargs.append(params.get("io_param"))
+    cargs.append(params.get("io_param", None))
     return cargs
 
 
@@ -274,21 +267,25 @@ def mris_volmask_vtk_outputs(
     """
     ret = MrisVolmaskVtkOutputs(
         root=execution.output_file("."),
-        output_volume_mask=execution.output_file("mri/" + params.get("out_root") + ".mgz") if (params.get("out_root") is not None) else None,
-        left_ribbon_output=execution.output_file("mri/lh." + params.get("out_root") + ".mgz") if (params.get("out_root") is not None) else None,
-        right_ribbon_output=execution.output_file("mri/rh." + params.get("out_root") + ".mgz") if (params.get("out_root") is not None) else None,
+        output_volume_mask=execution.output_file("mri/" + params.get("out_root", None) + ".mgz") if (params.get("out_root") is not None) else None,
+        left_ribbon_output=execution.output_file("mri/lh." + params.get("out_root", None) + ".mgz") if (params.get("out_root") is not None) else None,
+        right_ribbon_output=execution.output_file("mri/rh." + params.get("out_root", None) + ".mgz") if (params.get("out_root") is not None) else None,
         edited_aseg_output=execution.output_file("mri/aseg.ribbon.mgz"),
-        dwhite_output=execution.output_file("mri/?h.dwhite.mgz"),
-        dpial_output=execution.output_file("mri/?h.dpial.mgz"),
+        lh_dwhite_output=execution.output_file("mri/lh.dwhite.mgz"),
+        lh_dpial_output=execution.output_file("mri/lh.dpial.mgz"),
+        rh_dwhite_output=execution.output_file("mri/rh.dwhite.mgz"),
+        rh_dpial_output=execution.output_file("mri/rh.dpial.mgz"),
     )
     return ret
 
 
 def mris_volmask_vtk_execute(
     params: MrisVolmaskVtkParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisVolmaskVtkOutputs:
     """
+    mris_volmask_vtk
+    
     Computes a volume mask at the resolution of the brain.mgz file, containing
     labels for various brain structures using surface files.
     
@@ -298,10 +295,12 @@ def mris_volmask_vtk_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisVolmaskVtkOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_VOLMASK_VTK_METADATA)
     params = execution.params(params)
     cargs = mris_volmask_vtk_cargs(params, execution)
     ret = mris_volmask_vtk_outputs(params, execution)
@@ -331,6 +330,8 @@ def mris_volmask_vtk(
     runner: Runner | None = None,
 ) -> MrisVolmaskVtkOutputs:
     """
+    mris_volmask_vtk
+    
     Computes a volume mask at the resolution of the brain.mgz file, containing
     labels for various brain structures using surface files.
     
@@ -366,8 +367,6 @@ def mris_volmask_vtk(
     Returns:
         NamedTuple of outputs (described in `MrisVolmaskVtkOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_VOLMASK_VTK_METADATA)
     params = mris_volmask_vtk_params(
         cap_distance=cap_distance,
         label_background=label_background,
@@ -388,13 +387,13 @@ def mris_volmask_vtk(
         save_ribbon=save_ribbon,
         io_param=io_param,
     )
-    return mris_volmask_vtk_execute(params, execution)
+    return mris_volmask_vtk_execute(params, runner)
 
 
 __all__ = [
     "MRIS_VOLMASK_VTK_METADATA",
     "MrisVolmaskVtkOutputs",
-    "MrisVolmaskVtkParameters",
     "mris_volmask_vtk",
+    "mris_volmask_vtk_execute",
     "mris_volmask_vtk_params",
 ]