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

niwrap_afni/afni/v_3d_surf2_vol.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SURF2_VOL_METADATA = Metadata(
-    id="fa9697733e4cdedac6e9ad32c1f0b6636170c645.boutiques",
+    id="1f2f454c8e97201c60f42b8b26c9ecfeb795f1a7.boutiques",
     name="3dSurf2Vol",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,35 @@ V_3D_SURF2_VOL_METADATA = Metadata(
 
 
 V3dSurf2VolParameters = typing.TypedDict('V3dSurf2VolParameters', {
-    "__STYXTYPE__": typing.Literal["3dSurf2Vol"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSurf2Vol"]],
+    "spec": InputPathType,
+    "surface_volume": InputPathType,
+    "surf_a": str,
+    "surf_b": typing.NotRequired[str | None],
+    "grid_parent": InputPathType,
+    "map_func": str,
+    "prefix": str,
+    "surf_xyz_1d": typing.NotRequired[InputPathType | None],
+    "sdata_1d": typing.NotRequired[InputPathType | None],
+    "sdata": typing.NotRequired[InputPathType | None],
+    "f_steps": typing.NotRequired[float | None],
+    "f_index": typing.NotRequired[str | None],
+    "f_p1_fr": typing.NotRequired[float | None],
+    "f_pn_fr": typing.NotRequired[float | None],
+    "f_p1_mm": typing.NotRequired[float | None],
+    "f_pn_mm": typing.NotRequired[float | None],
+    "stop_gap": bool,
+    "cmask": typing.NotRequired[str | None],
+    "data_expr": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[str | None],
+    "debug": typing.NotRequired[int | None],
+    "dnode": typing.NotRequired[int | None],
+    "dvoxel": typing.NotRequired[int | None],
+    "noscale": bool,
+    "sxyz_orient_as_gpar": bool,
+})
+V3dSurf2VolParametersTagged = typing.TypedDict('V3dSurf2VolParametersTagged', {
+    "@type": typing.Literal["afni/3dSurf2Vol"],
     "spec": InputPathType,
     "surface_volume": InputPathType,
     "surf_a": str,
@@ -41,48 +69,14 @@ V3dSurf2VolParameters = typing.TypedDict('V3dSurf2VolParameters', {
     "noscale": bool,
     "sxyz_orient_as_gpar": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dSurf2Vol": v_3d_surf2_vol_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 {
-        "3dSurf2Vol": v_3d_surf2_vol_outputs,
-    }.get(t)
 
 
 class V3dSurf2VolOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_surf2_vol(...)`.
+    Output object returned when calling `V3dSurf2VolParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_file: OutputPathType
-    """Output dataset"""
 
 
 def v_3d_surf2_vol_params(
@@ -111,7 +105,7 @@ def v_3d_surf2_vol_params(
     dvoxel: int | None = None,
     noscale: bool = False,
     sxyz_orient_as_gpar: bool = False,
-) -> V3dSurf2VolParameters:
+) -> V3dSurf2VolParametersTagged:
     """
     Build parameters.
     
@@ -145,7 +139,7 @@ def v_3d_surf2_vol_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSurf2Vol",
+        "@type": "afni/3dSurf2Vol",
         "spec": spec,
         "surface_volume": surface_volume,
         "surf_a": surf_a,
@@ -208,113 +202,113 @@ def v_3d_surf2_vol_cargs(
     cargs.append("3dSurf2Vol")
     cargs.extend([
         "-spec",
-        execution.input_file(params.get("spec"))
+        execution.input_file(params.get("spec", None))
     ])
     cargs.extend([
         "-sv",
-        execution.input_file(params.get("surface_volume"))
+        execution.input_file(params.get("surface_volume", None))
     ])
     cargs.extend([
         "-surf_A",
-        params.get("surf_a")
+        params.get("surf_a", None)
     ])
-    if params.get("surf_b") is not None:
+    if params.get("surf_b", None) is not None:
         cargs.extend([
             "-surf_B",
-            params.get("surf_b")
+            params.get("surf_b", None)
         ])
     cargs.extend([
         "-grid_parent",
-        execution.input_file(params.get("grid_parent"))
+        execution.input_file(params.get("grid_parent", None))
     ])
     cargs.extend([
         "-map_func",
-        params.get("map_func")
+        params.get("map_func", None)
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("surf_xyz_1d") is not None:
+    if params.get("surf_xyz_1d", None) is not None:
         cargs.extend([
             "-surf_xyz_1D",
-            execution.input_file(params.get("surf_xyz_1d"))
+            execution.input_file(params.get("surf_xyz_1d", None))
         ])
-    if params.get("sdata_1d") is not None:
+    if params.get("sdata_1d", None) is not None:
         cargs.extend([
             "-sdata_1D",
-            execution.input_file(params.get("sdata_1d"))
+            execution.input_file(params.get("sdata_1d", None))
         ])
-    if params.get("sdata") is not None:
+    if params.get("sdata", None) is not None:
         cargs.extend([
             "-sdata",
-            execution.input_file(params.get("sdata"))
+            execution.input_file(params.get("sdata", None))
         ])
-    if params.get("f_steps") is not None:
+    if params.get("f_steps", None) is not None:
         cargs.extend([
             "-f_steps",
-            str(params.get("f_steps"))
+            str(params.get("f_steps", None))
         ])
-    if params.get("f_index") is not None:
+    if params.get("f_index", None) is not None:
         cargs.extend([
             "-f_index",
-            params.get("f_index")
+            params.get("f_index", None)
         ])
-    if params.get("f_p1_fr") is not None:
+    if params.get("f_p1_fr", None) is not None:
         cargs.extend([
             "-f_p1_fr",
-            str(params.get("f_p1_fr"))
+            str(params.get("f_p1_fr", None))
         ])
-    if params.get("f_pn_fr") is not None:
+    if params.get("f_pn_fr", None) is not None:
         cargs.extend([
             "-f_pn_fr",
-            str(params.get("f_pn_fr"))
+            str(params.get("f_pn_fr", None))
         ])
-    if params.get("f_p1_mm") is not None:
+    if params.get("f_p1_mm", None) is not None:
         cargs.extend([
             "-f_p1_mm",
-            str(params.get("f_p1_mm"))
+            str(params.get("f_p1_mm", None))
         ])
-    if params.get("f_pn_mm") is not None:
+    if params.get("f_pn_mm", None) is not None:
         cargs.extend([
             "-f_pn_mm",
-            str(params.get("f_pn_mm"))
+            str(params.get("f_pn_mm", None))
         ])
-    if params.get("stop_gap"):
+    if params.get("stop_gap", False):
         cargs.append("-stop_gap")
-    if params.get("cmask") is not None:
+    if params.get("cmask", None) is not None:
         cargs.extend([
             "-cmask",
-            params.get("cmask")
+            params.get("cmask", None)
         ])
-    if params.get("data_expr") is not None:
+    if params.get("data_expr", None) is not None:
         cargs.extend([
             "-data_expr",
-            params.get("data_expr")
+            params.get("data_expr", None)
         ])
-    if params.get("datum") is not None:
+    if params.get("datum", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datum")
+            params.get("datum", None)
         ])
-    if params.get("debug") is not None:
+    if params.get("debug", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug"))
+            str(params.get("debug", None))
         ])
-    if params.get("dnode") is not None:
+    if params.get("dnode", None) is not None:
         cargs.extend([
             "-dnode",
-            str(params.get("dnode"))
+            str(params.get("dnode", None))
         ])
-    if params.get("dvoxel") is not None:
+    if params.get("dvoxel", None) is not None:
         cargs.extend([
             "-dvoxel",
-            str(params.get("dvoxel"))
+            str(params.get("dvoxel", None))
         ])
-    if params.get("noscale"):
+    if params.get("noscale", False):
         cargs.append("-noscale")
-    if params.get("sxyz_orient_as_gpar"):
+    if params.get("sxyz_orient_as_gpar", False):
         cargs.append("-sxyz_orient_as_gpar")
     return cargs
 
@@ -334,16 +328,17 @@ def v_3d_surf2_vol_outputs(
     """
     ret = V3dSurf2VolOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + "+*[gz]"),
     )
     return ret
 
 
 def v_3d_surf2_vol_execute(
     params: V3dSurf2VolParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSurf2VolOutputs:
     """
+    3dSurf2Vol
+    
     Map data from a surface domain to an AFNI volume domain.
     
     Author: AFNI Developers
@@ -352,10 +347,12 @@ def v_3d_surf2_vol_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSurf2VolOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SURF2_VOL_METADATA)
     params = execution.params(params)
     cargs = v_3d_surf2_vol_cargs(params, execution)
     ret = v_3d_surf2_vol_outputs(params, execution)
@@ -392,6 +389,8 @@ def v_3d_surf2_vol(
     runner: Runner | None = None,
 ) -> V3dSurf2VolOutputs:
     """
+    3dSurf2Vol
+    
     Map data from a surface domain to an AFNI volume domain.
     
     Author: AFNI Developers
@@ -428,8 +427,6 @@ def v_3d_surf2_vol(
     Returns:
         NamedTuple of outputs (described in `V3dSurf2VolOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SURF2_VOL_METADATA)
     params = v_3d_surf2_vol_params(
         spec=spec,
         surface_volume=surface_volume,
@@ -457,13 +454,13 @@ def v_3d_surf2_vol(
         noscale=noscale,
         sxyz_orient_as_gpar=sxyz_orient_as_gpar,
     )
-    return v_3d_surf2_vol_execute(params, execution)
+    return v_3d_surf2_vol_execute(params, runner)
 
 
 __all__ = [
     "V3dSurf2VolOutputs",
-    "V3dSurf2VolParameters",
     "V_3D_SURF2_VOL_METADATA",
     "v_3d_surf2_vol",
+    "v_3d_surf2_vol_execute",
     "v_3d_surf2_vol_params",
 ]

niwrap_afni/afni/v_3d_surf_mask.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SURF_MASK_METADATA = Metadata(
-    id="8c0ff8c2071e2a01164c6a3e3d4790c519002089.boutiques",
+    id="0c8c0c85cb938597bc328e04d5ab913c255457c7.boutiques",
     name="3dSurfMask",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_SURF_MASK_METADATA = Metadata(
 
 
 V3dSurfMaskParameters = typing.TypedDict('V3dSurfMaskParameters', {
-    "__STYXTYPE__": typing.Literal["3dSurfMask"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSurfMask"]],
+    "surface_type": str,
+    "surface_file": InputPathType,
+    "prefix": str,
+    "grid_parent": InputPathType,
+    "fill_method": typing.NotRequired[str | None],
+    "surface_volume": typing.NotRequired[InputPathType | None],
+    "mask_only": bool,
+    "flip_orientation": bool,
+    "no_distance": bool,
+})
+V3dSurfMaskParametersTagged = typing.TypedDict('V3dSurfMaskParametersTagged', {
+    "@type": typing.Literal["afni/3dSurfMask"],
     "surface_type": str,
     "surface_file": InputPathType,
     "prefix": str,
@@ -25,43 +37,11 @@ V3dSurfMaskParameters = typing.TypedDict('V3dSurfMaskParameters', {
     "flip_orientation": bool,
     "no_distance": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dSurfMask": v_3d_surf_mask_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 {
-        "3dSurfMask": v_3d_surf_mask_outputs,
-    }.get(t)
 
 
 class V3dSurfMaskOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_surf_mask(...)`.
+    Output object returned when calling `V3dSurfMaskParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def v_3d_surf_mask_params(
     mask_only: bool = False,
     flip_orientation: bool = False,
     no_distance: bool = False,
-) -> V3dSurfMaskParameters:
+) -> V3dSurfMaskParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +81,7 @@ def v_3d_surf_mask_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSurfMask",
+        "@type": "afni/3dSurfMask",
         "surface_type": surface_type,
         "surface_file": surface_file,
         "prefix": prefix,
@@ -132,25 +112,25 @@ def v_3d_surf_mask_cargs(
     """
     cargs = []
     cargs.append("3dSurfMask")
-    cargs.append(params.get("surface_type"))
-    cargs.append(execution.input_file(params.get("surface_file")))
-    cargs.append(params.get("prefix"))
-    cargs.append(execution.input_file(params.get("grid_parent")))
-    if params.get("fill_method") is not None:
+    cargs.append(params.get("surface_type", None))
+    cargs.append(execution.input_file(params.get("surface_file", None)))
+    cargs.append(params.get("prefix", None))
+    cargs.append(execution.input_file(params.get("grid_parent", None)))
+    if params.get("fill_method", None) is not None:
         cargs.extend([
             "-fill_method",
-            params.get("fill_method")
+            params.get("fill_method", None)
         ])
-    if params.get("surface_volume") is not None:
+    if params.get("surface_volume", None) is not None:
         cargs.extend([
             "-sv",
-            execution.input_file(params.get("surface_volume"))
+            execution.input_file(params.get("surface_volume", None))
         ])
-    if params.get("mask_only"):
+    if params.get("mask_only", False):
         cargs.append("-mask_only")
-    if params.get("flip_orientation"):
+    if params.get("flip_orientation", False):
         cargs.append("-flip_orientation")
-    if params.get("no_distance"):
+    if params.get("no_distance", False):
         cargs.append("-no_dist")
     return cargs
 
@@ -170,19 +150,21 @@ def v_3d_surf_mask_outputs(
     """
     ret = V3dSurfMaskOutputs(
         root=execution.output_file("."),
-        output_mask=execution.output_file(params.get("prefix") + ".m+orig.BRIK"),
-        distance_dataset=execution.output_file(params.get("prefix") + ".d+orig.BRIK"),
+        output_mask=execution.output_file(params.get("prefix", None) + ".m+orig.BRIK"),
+        distance_dataset=execution.output_file(params.get("prefix", None) + ".d+orig.BRIK"),
     )
     return ret
 
 
 def v_3d_surf_mask_execute(
     params: V3dSurfMaskParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSurfMaskOutputs:
     """
-    Creates volumetric datasets marking voxels based on their location relative to a
-    surface.
+    3dSurfMask
+    
+    Creates volumetric datasets marking voxels based on their location relative
+    to a surface.
     
     Author: AFNI Developers
     
@@ -190,10 +172,12 @@ def v_3d_surf_mask_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSurfMaskOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SURF_MASK_METADATA)
     params = execution.params(params)
     cargs = v_3d_surf_mask_cargs(params, execution)
     ret = v_3d_surf_mask_outputs(params, execution)
@@ -214,8 +198,10 @@ def v_3d_surf_mask(
     runner: Runner | None = None,
 ) -> V3dSurfMaskOutputs:
     """
-    Creates volumetric datasets marking voxels based on their location relative to a
-    surface.
+    3dSurfMask
+    
+    Creates volumetric datasets marking voxels based on their location relative
+    to a surface.
     
     Author: AFNI Developers
     
@@ -237,8 +223,6 @@ def v_3d_surf_mask(
     Returns:
         NamedTuple of outputs (described in `V3dSurfMaskOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SURF_MASK_METADATA)
     params = v_3d_surf_mask_params(
         surface_type=surface_type,
         surface_file=surface_file,
@@ -250,13 +234,13 @@ def v_3d_surf_mask(
         flip_orientation=flip_orientation,
         no_distance=no_distance,
     )
-    return v_3d_surf_mask_execute(params, execution)
+    return v_3d_surf_mask_execute(params, runner)
 
 
 __all__ = [
     "V3dSurfMaskOutputs",
-    "V3dSurfMaskParameters",
     "V_3D_SURF_MASK_METADATA",
     "v_3d_surf_mask",
+    "v_3d_surf_mask_execute",
     "v_3d_surf_mask_params",
 ]