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

niwrap_afni/afni/v_3d_nwarp_cat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_NWARP_CAT_METADATA = Metadata(
-    id="8375fa045d633a347594fc067d7b9dc9dbfedbed.boutiques",
+    id="62adbc513d6c3a93a1b123ab55b3308c6a6d676e.boutiques",
     name="3dNwarpCat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_NWARP_CAT_METADATA = Metadata(
 
 
 V3dNwarpCatParameters = typing.TypedDict('V3dNwarpCatParameters', {
-    "__STYXTYPE__": typing.Literal["3dNwarpCat"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dNwarpCat"]],
+    "interpolation": typing.NotRequired[str | None],
+    "verbosity": bool,
+    "output_prefix": str,
+    "space_marker": typing.NotRequired[str | None],
+    "warp1": InputPathType,
+    "warp2": InputPathType,
+    "additional_warps": typing.NotRequired[list[InputPathType] | None],
+    "invert_final_warp": bool,
+    "extra_padding": typing.NotRequired[float | None],
+})
+V3dNwarpCatParametersTagged = typing.TypedDict('V3dNwarpCatParametersTagged', {
+    "@type": typing.Literal["afni/3dNwarpCat"],
     "interpolation": typing.NotRequired[str | None],
     "verbosity": bool,
     "output_prefix": str,
@@ -25,43 +37,11 @@ V3dNwarpCatParameters = typing.TypedDict('V3dNwarpCatParameters', {
     "invert_final_warp": bool,
     "extra_padding": 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 {
-        "3dNwarpCat": v_3d_nwarp_cat_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 {
-        "3dNwarpCat": v_3d_nwarp_cat_outputs,
-    }.get(t)
 
 
 class V3dNwarpCatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_nwarp_cat(...)`.
+    Output object returned when calling `V3dNwarpCatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def v_3d_nwarp_cat_params(
     additional_warps: list[InputPathType] | None = None,
     invert_final_warp: bool = False,
     extra_padding: float | None = None,
-) -> V3dNwarpCatParameters:
+) -> V3dNwarpCatParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +82,7 @@ def v_3d_nwarp_cat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dNwarpCat",
+        "@type": "afni/3dNwarpCat",
         "verbosity": verbosity,
         "output_prefix": output_prefix,
         "warp1": warp1,
@@ -135,38 +115,38 @@ def v_3d_nwarp_cat_cargs(
     """
     cargs = []
     cargs.append("3dNwarpCat")
-    if params.get("interpolation") is not None:
+    if params.get("interpolation", None) is not None:
         cargs.extend([
             "-interp",
-            params.get("interpolation")
+            params.get("interpolation", None)
         ])
-    if params.get("verbosity"):
+    if params.get("verbosity", False):
         cargs.append("-verb")
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
-    if params.get("space_marker") is not None:
+    if params.get("space_marker", None) is not None:
         cargs.extend([
             "-space",
-            params.get("space_marker")
+            params.get("space_marker", None)
         ])
     cargs.extend([
         "-warp1",
-        execution.input_file(params.get("warp1"))
+        execution.input_file(params.get("warp1", None))
     ])
     cargs.extend([
         "-warp2",
-        execution.input_file(params.get("warp2"))
+        execution.input_file(params.get("warp2", None))
     ])
-    if params.get("additional_warps") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("additional_warps")])
-    if params.get("invert_final_warp"):
+    if params.get("additional_warps", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("additional_warps", None)])
+    if params.get("invert_final_warp", False):
         cargs.append("-iwarp")
-    if params.get("extra_padding") is not None:
+    if params.get("extra_padding", None) is not None:
         cargs.extend([
             "-expad",
-            str(params.get("extra_padding"))
+            str(params.get("extra_padding", None))
         ])
     return cargs
 
@@ -186,17 +166,19 @@ def v_3d_nwarp_cat_outputs(
     """
     ret = V3dNwarpCatOutputs(
         root=execution.output_file("."),
-        output_matrix=execution.output_file(params.get("output_prefix") + ".aff12.1D"),
-        output_dataset=execution.output_file(params.get("output_prefix") + "+tlrc.HEAD"),
+        output_matrix=execution.output_file(params.get("output_prefix", None) + ".aff12.1D"),
+        output_dataset=execution.output_file(params.get("output_prefix", None) + "+tlrc.HEAD"),
     )
     return ret
 
 
 def v_3d_nwarp_cat_execute(
     params: V3dNwarpCatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dNwarpCatOutputs:
     """
+    3dNwarpCat
+    
     Catenates (composes) 3D warps defined on a grid or via a matrix.
     
     Author: AFNI Developers
@@ -205,10 +187,12 @@ def v_3d_nwarp_cat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dNwarpCatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NWARP_CAT_METADATA)
     params = execution.params(params)
     cargs = v_3d_nwarp_cat_cargs(params, execution)
     ret = v_3d_nwarp_cat_outputs(params, execution)
@@ -229,6 +213,8 @@ def v_3d_nwarp_cat(
     runner: Runner | None = None,
 ) -> V3dNwarpCatOutputs:
     """
+    3dNwarpCat
+    
     Catenates (composes) 3D warps defined on a grid or via a matrix.
     
     Author: AFNI Developers
@@ -252,8 +238,6 @@ def v_3d_nwarp_cat(
     Returns:
         NamedTuple of outputs (described in `V3dNwarpCatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_NWARP_CAT_METADATA)
     params = v_3d_nwarp_cat_params(
         interpolation=interpolation,
         verbosity=verbosity,
@@ -265,13 +249,13 @@ def v_3d_nwarp_cat(
         invert_final_warp=invert_final_warp,
         extra_padding=extra_padding,
     )
-    return v_3d_nwarp_cat_execute(params, execution)
+    return v_3d_nwarp_cat_execute(params, runner)
 
 
 __all__ = [
     "V3dNwarpCatOutputs",
-    "V3dNwarpCatParameters",
     "V_3D_NWARP_CAT_METADATA",
     "v_3d_nwarp_cat",
+    "v_3d_nwarp_cat_execute",
     "v_3d_nwarp_cat_params",
 ]

niwrap_afni/afni/v_3d_nwarp_funcs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_NWARP_FUNCS_METADATA = Metadata(
-    id="1eff17eabae05eb35c5c1d7331dcbdcf39fb85a8.boutiques",
+    id="35ae1d7095534556f19806b182ded46e4021aa28.boutiques",
     name="3dNwarpFuncs",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_NWARP_FUNCS_METADATA = Metadata(
 
 
 V3dNwarpFuncsParameters = typing.TypedDict('V3dNwarpFuncsParameters', {
-    "__STYXTYPE__": typing.Literal["3dNwarpFuncs"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dNwarpFuncs"]],
+    "input_warp": InputPathType,
+    "output_prefix": str,
+    "bulk_flag": bool,
+    "shear_flag": bool,
+    "vorticity_flag": bool,
+    "all_flag": bool,
+})
+V3dNwarpFuncsParametersTagged = typing.TypedDict('V3dNwarpFuncsParametersTagged', {
+    "@type": typing.Literal["afni/3dNwarpFuncs"],
     "input_warp": InputPathType,
     "output_prefix": str,
     "bulk_flag": bool,
@@ -22,43 +31,11 @@ V3dNwarpFuncsParameters = typing.TypedDict('V3dNwarpFuncsParameters', {
     "vorticity_flag": bool,
     "all_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dNwarpFuncs": v_3d_nwarp_funcs_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 {
-        "3dNwarpFuncs": v_3d_nwarp_funcs_outputs,
-    }.get(t)
 
 
 class V3dNwarpFuncsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_nwarp_funcs(...)`.
+    Output object returned when calling `V3dNwarpFuncsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def v_3d_nwarp_funcs_params(
     shear_flag: bool = False,
     vorticity_flag: bool = False,
     all_flag: bool = False,
-) -> V3dNwarpFuncsParameters:
+) -> V3dNwarpFuncsParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def v_3d_nwarp_funcs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dNwarpFuncs",
+        "@type": "afni/3dNwarpFuncs",
         "input_warp": input_warp,
         "output_prefix": output_prefix,
         "bulk_flag": bulk_flag,
@@ -118,19 +95,19 @@ def v_3d_nwarp_funcs_cargs(
     cargs.append("3dNwarpFuncs")
     cargs.extend([
         "-nwarp",
-        execution.input_file(params.get("input_warp"))
+        execution.input_file(params.get("input_warp", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
-    if params.get("bulk_flag"):
+    if params.get("bulk_flag", False):
         cargs.append("-bulk")
-    if params.get("shear_flag"):
+    if params.get("shear_flag", False):
         cargs.append("-shear")
-    if params.get("vorticity_flag"):
+    if params.get("vorticity_flag", False):
         cargs.append("-vorticity")
-    if params.get("all_flag"):
+    if params.get("all_flag", False):
         cargs.append("-all")
     return cargs
 
@@ -150,18 +127,20 @@ def v_3d_nwarp_funcs_outputs(
     """
     ret = V3dNwarpFuncsOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_prefix") + "_output.nii.gz"),
+        output_file=execution.output_file(params.get("output_prefix", None) + "_output.nii.gz"),
     )
     return ret
 
 
 def v_3d_nwarp_funcs_execute(
     params: V3dNwarpFuncsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dNwarpFuncsOutputs:
     """
-    Compute functions of 3D warp displacements, such as bulk volume change, shear
-    energy, and vorticity energy.
+    3dNwarpFuncs
+    
+    Compute functions of 3D warp displacements, such as bulk volume change,
+    shear energy, and vorticity energy.
     
     Author: AFNI Developers
     
@@ -169,10 +148,12 @@ def v_3d_nwarp_funcs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dNwarpFuncsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NWARP_FUNCS_METADATA)
     params = execution.params(params)
     cargs = v_3d_nwarp_funcs_cargs(params, execution)
     ret = v_3d_nwarp_funcs_outputs(params, execution)
@@ -190,8 +171,10 @@ def v_3d_nwarp_funcs(
     runner: Runner | None = None,
 ) -> V3dNwarpFuncsOutputs:
     """
-    Compute functions of 3D warp displacements, such as bulk volume change, shear
-    energy, and vorticity energy.
+    3dNwarpFuncs
+    
+    Compute functions of 3D warp displacements, such as bulk volume change,
+    shear energy, and vorticity energy.
     
     Author: AFNI Developers
     
@@ -210,8 +193,6 @@ def v_3d_nwarp_funcs(
     Returns:
         NamedTuple of outputs (described in `V3dNwarpFuncsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_NWARP_FUNCS_METADATA)
     params = v_3d_nwarp_funcs_params(
         input_warp=input_warp,
         output_prefix=output_prefix,
@@ -220,13 +201,13 @@ def v_3d_nwarp_funcs(
         vorticity_flag=vorticity_flag,
         all_flag=all_flag,
     )
-    return v_3d_nwarp_funcs_execute(params, execution)
+    return v_3d_nwarp_funcs_execute(params, runner)
 
 
 __all__ = [
     "V3dNwarpFuncsOutputs",
-    "V3dNwarpFuncsParameters",
     "V_3D_NWARP_FUNCS_METADATA",
     "v_3d_nwarp_funcs",
+    "v_3d_nwarp_funcs_execute",
     "v_3d_nwarp_funcs_params",
 ]

niwrap_afni/afni/v_3d_nwarp_xyz.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_NWARP_XYZ_METADATA = Metadata(
-    id="67cdd4619b5c8cf49e16cb21278fc3347a324697.boutiques",
+    id="b3e50bef18db95c8d2cd2dc41d63b8a7d7da7351.boutiques",
     name="3dNwarpXYZ",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3D_NWARP_XYZ_METADATA = Metadata(
 
 
 V3dNwarpXyzParameters = typing.TypedDict('V3dNwarpXyzParameters', {
-    "__STYXTYPE__": typing.Literal["3dNwarpXYZ"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dNwarpXYZ"]],
+    "xyzfile": InputPathType,
+    "warp_spec": str,
+    "iwarp": bool,
+    "output_file": str,
+})
+V3dNwarpXyzParametersTagged = typing.TypedDict('V3dNwarpXyzParametersTagged', {
+    "@type": typing.Literal["afni/3dNwarpXYZ"],
     "xyzfile": InputPathType,
     "warp_spec": str,
     "iwarp": bool,
     "output_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dNwarpXYZ": v_3d_nwarp_xyz_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 {
-        "3dNwarpXYZ": v_3d_nwarp_xyz_outputs,
-    }.get(t)
 
 
 class V3dNwarpXyzOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_nwarp_xyz(...)`.
+    Output object returned when calling `V3dNwarpXyzParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def v_3d_nwarp_xyz_params(
     warp_spec: str,
     output_file: str,
     iwarp: bool = False,
-) -> V3dNwarpXyzParameters:
+) -> V3dNwarpXyzParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def v_3d_nwarp_xyz_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dNwarpXYZ",
+        "@type": "afni/3dNwarpXYZ",
         "xyzfile": xyzfile,
         "warp_spec": warp_spec,
         "iwarp": iwarp,
@@ -106,14 +81,14 @@ def v_3d_nwarp_xyz_cargs(
     """
     cargs = []
     cargs.append("3dNwarpXYZ")
-    cargs.append(execution.input_file(params.get("xyzfile")))
+    cargs.append(execution.input_file(params.get("xyzfile", None)))
     cargs.extend([
         "-nwarp",
-        params.get("warp_spec")
+        params.get("warp_spec", None)
     ])
-    if params.get("iwarp"):
+    if params.get("iwarp", False):
         cargs.append("-iwarp")
-    cargs.append("> " + params.get("output_file"))
+    cargs.append("> " + params.get("output_file", None))
     return cargs
 
 
@@ -132,18 +107,20 @@ def v_3d_nwarp_xyz_outputs(
     """
     ret = V3dNwarpXyzOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")),
+        output_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def v_3d_nwarp_xyz_execute(
     params: V3dNwarpXyzParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dNwarpXyzOutputs:
     """
-    Transforms the DICOM xyz coordinates in the input XYZfile.1D based on specified
-    warp.
+    3dNwarpXYZ
+    
+    Transforms the DICOM xyz coordinates in the input XYZfile.1D based on
+    specified warp.
     
     Author: AFNI Developers
     
@@ -151,10 +128,12 @@ def v_3d_nwarp_xyz_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dNwarpXyzOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NWARP_XYZ_METADATA)
     params = execution.params(params)
     cargs = v_3d_nwarp_xyz_cargs(params, execution)
     ret = v_3d_nwarp_xyz_outputs(params, execution)
@@ -170,8 +149,10 @@ def v_3d_nwarp_xyz(
     runner: Runner | None = None,
 ) -> V3dNwarpXyzOutputs:
     """
-    Transforms the DICOM xyz coordinates in the input XYZfile.1D based on specified
-    warp.
+    3dNwarpXYZ
+    
+    Transforms the DICOM xyz coordinates in the input XYZfile.1D based on
+    specified warp.
     
     Author: AFNI Developers
     
@@ -186,21 +167,19 @@ def v_3d_nwarp_xyz(
     Returns:
         NamedTuple of outputs (described in `V3dNwarpXyzOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_NWARP_XYZ_METADATA)
     params = v_3d_nwarp_xyz_params(
         xyzfile=xyzfile,
         warp_spec=warp_spec,
         iwarp=iwarp,
         output_file=output_file,
     )
-    return v_3d_nwarp_xyz_execute(params, execution)
+    return v_3d_nwarp_xyz_execute(params, runner)
 
 
 __all__ = [
     "V3dNwarpXyzOutputs",
-    "V3dNwarpXyzParameters",
     "V_3D_NWARP_XYZ_METADATA",
     "v_3d_nwarp_xyz",
+    "v_3d_nwarp_xyz_execute",
     "v_3d_nwarp_xyz_params",
 ]