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

niwrap_afni/afni/surf_measures.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF_MEASURES_METADATA = Metadata(
-    id="081416cc50152fae2d98653e2c0c325389329860.boutiques",
+    id="b94a39e16fa59659338338e4789f816c9ea37585.boutiques",
     name="SurfMeasures",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,28 @@ SURF_MEASURES_METADATA = Metadata(
 
 
 SurfMeasuresParameters = typing.TypedDict('SurfMeasuresParameters', {
-    "__STYXTYPE__": typing.Literal["SurfMeasures"],
+    "@type": typing.NotRequired[typing.Literal["afni/SurfMeasures"]],
+    "spec_file": InputPathType,
+    "surf_A": str,
+    "surf_B": typing.NotRequired[str | None],
+    "out_1D": typing.NotRequired[str | None],
+    "out_dset": str,
+    "func": typing.NotRequired[list[str] | None],
+    "surf_volume": typing.NotRequired[InputPathType | None],
+    "cmask": typing.NotRequired[str | None],
+    "debug": typing.NotRequired[int | None],
+    "dnode": typing.NotRequired[float | None],
+    "nodes_1D": typing.NotRequired[InputPathType | None],
+    "info_all": bool,
+    "info_area": bool,
+    "info_norms": bool,
+    "info_thick": bool,
+    "info_vol": bool,
+    "info_volg": bool,
+    "ver": bool,
+})
+SurfMeasuresParametersTagged = typing.TypedDict('SurfMeasuresParametersTagged', {
+    "@type": typing.Literal["afni/SurfMeasures"],
     "spec_file": InputPathType,
     "surf_A": str,
     "surf_B": typing.NotRequired[str | None],
@@ -34,43 +55,11 @@ SurfMeasuresParameters = typing.TypedDict('SurfMeasuresParameters', {
     "info_volg": bool,
     "ver": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "SurfMeasures": surf_measures_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 {
-        "SurfMeasures": surf_measures_outputs,
-    }.get(t)
 
 
 class SurfMeasuresOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf_measures(...)`.
+    Output object returned when calling `SurfMeasuresParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +88,7 @@ def surf_measures_params(
     info_vol: bool = False,
     info_volg: bool = False,
     ver: bool = False,
-) -> SurfMeasuresParameters:
+) -> SurfMeasuresParametersTagged:
     """
     Build parameters.
     
@@ -127,7 +116,7 @@ def surf_measures_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SurfMeasures",
+        "@type": "afni/SurfMeasures",
         "spec_file": spec_file,
         "surf_A": surf_a,
         "out_dset": out_dset,
@@ -175,69 +164,69 @@ def surf_measures_cargs(
     cargs.append("SurfMeasures")
     cargs.extend([
         "-spec",
-        execution.input_file(params.get("spec_file"))
+        execution.input_file(params.get("spec_file", 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)
         ])
-    if params.get("out_1D") is not None:
+    if params.get("out_1D", None) is not None:
         cargs.extend([
             "-out_1D",
-            params.get("out_1D")
+            params.get("out_1D", None)
         ])
     cargs.extend([
         "-out",
-        params.get("out_dset")
+        params.get("out_dset", None)
     ])
-    if params.get("func") is not None:
+    if params.get("func", None) is not None:
         cargs.extend([
             "-func",
-            *params.get("func")
+            *params.get("func", None)
         ])
-    if params.get("surf_volume") is not None:
+    if params.get("surf_volume", None) is not None:
         cargs.extend([
             "-sv",
-            execution.input_file(params.get("surf_volume"))
+            execution.input_file(params.get("surf_volume", None))
         ])
-    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("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("nodes_1D") is not None:
+    if params.get("nodes_1D", None) is not None:
         cargs.extend([
             "-nodes_1D",
-            execution.input_file(params.get("nodes_1D"))
+            execution.input_file(params.get("nodes_1D", None))
         ])
-    if params.get("info_all"):
+    if params.get("info_all", False):
         cargs.append("-info_all")
-    if params.get("info_area"):
+    if params.get("info_area", False):
         cargs.append("-info_area")
-    if params.get("info_norms"):
+    if params.get("info_norms", False):
         cargs.append("-info_norms")
-    if params.get("info_thick"):
+    if params.get("info_thick", False):
         cargs.append("-info_thick")
-    if params.get("info_vol"):
+    if params.get("info_vol", False):
         cargs.append("-info_vol")
-    if params.get("info_volg"):
+    if params.get("info_volg", False):
         cargs.append("-info_volg")
-    if params.get("ver"):
+    if params.get("ver", False):
         cargs.append("-ver")
     return cargs
 
@@ -257,17 +246,19 @@ def surf_measures_outputs(
     """
     ret = SurfMeasuresOutputs(
         root=execution.output_file("."),
-        output_1_d=execution.output_file(params.get("out_1D") + ".1D") if (params.get("out_1D") is not None) else None,
-        output_dset=execution.output_file(params.get("out_dset")),
+        output_1_d=execution.output_file(params.get("out_1D", None) + ".1D") if (params.get("out_1D") is not None) else None,
+        output_dset=execution.output_file(params.get("out_dset", None)),
     )
     return ret
 
 
 def surf_measures_execute(
     params: SurfMeasuresParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfMeasuresOutputs:
     """
+    SurfMeasures
+    
     Compute measures from surface dataset(s).
     
     Author: AFNI Developers
@@ -276,10 +267,12 @@ def surf_measures_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfMeasuresOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_MEASURES_METADATA)
     params = execution.params(params)
     cargs = surf_measures_cargs(params, execution)
     ret = surf_measures_outputs(params, execution)
@@ -309,6 +302,8 @@ def surf_measures(
     runner: Runner | None = None,
 ) -> SurfMeasuresOutputs:
     """
+    SurfMeasures
+    
     Compute measures from surface dataset(s).
     
     Author: AFNI Developers
@@ -339,8 +334,6 @@ def surf_measures(
     Returns:
         NamedTuple of outputs (described in `SurfMeasuresOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF_MEASURES_METADATA)
     params = surf_measures_params(
         spec_file=spec_file,
         surf_a=surf_a,
@@ -361,13 +354,13 @@ def surf_measures(
         info_volg=info_volg,
         ver=ver,
     )
-    return surf_measures_execute(params, execution)
+    return surf_measures_execute(params, runner)
 
 
 __all__ = [
     "SURF_MEASURES_METADATA",
     "SurfMeasuresOutputs",
-    "SurfMeasuresParameters",
     "surf_measures",
+    "surf_measures_execute",
     "surf_measures_params",
 ]

niwrap_afni/afni/surf_mesh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF_MESH_METADATA = Metadata(
-    id="6066359d8c294ca53c640b4ebcdab63e664ed84c.boutiques",
+    id="af151bca250ded8682ed75de04495e4b9cd36e51.boutiques",
     name="SurfMesh",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ SURF_MESH_METADATA = Metadata(
 
 
 SurfMeshParameters = typing.TypedDict('SurfMeshParameters', {
-    "__STYXTYPE__": typing.Literal["SurfMesh"],
+    "@type": typing.NotRequired[typing.Literal["afni/SurfMesh"]],
+    "input_surface": str,
+    "output_surface": str,
+    "edge_fraction": float,
+    "surface_volume": typing.NotRequired[InputPathType | None],
+    "one_state": bool,
+    "anatomical_label": bool,
+    "no_volume_registration": bool,
+    "set_env": typing.NotRequired[str | None],
+})
+SurfMeshParametersTagged = typing.TypedDict('SurfMeshParametersTagged', {
+    "@type": typing.Literal["afni/SurfMesh"],
     "input_surface": str,
     "output_surface": str,
     "edge_fraction": float,
@@ -24,43 +35,11 @@ SurfMeshParameters = typing.TypedDict('SurfMeshParameters', {
     "no_volume_registration": bool,
     "set_env": 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 {
-        "SurfMesh": surf_mesh_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 {
-        "SurfMesh": surf_mesh_outputs,
-    }.get(t)
 
 
 class SurfMeshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf_mesh(...)`.
+    Output object returned when calling `SurfMeshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def surf_mesh_params(
     anatomical_label: bool = False,
     no_volume_registration: bool = False,
     set_env: str | None = None,
-) -> SurfMeshParameters:
+) -> SurfMeshParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +74,7 @@ def surf_mesh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SurfMesh",
+        "@type": "afni/SurfMesh",
         "input_surface": input_surface,
         "output_surface": output_surface,
         "edge_fraction": edge_fraction,
@@ -127,31 +106,31 @@ def surf_mesh_cargs(
     cargs.append("SurfMesh")
     cargs.extend([
         "-i_TYPE",
-        params.get("input_surface")
+        params.get("input_surface", None)
     ])
     cargs.extend([
         "-o_TYPE",
-        params.get("output_surface")
+        params.get("output_surface", None)
     ])
     cargs.extend([
         "-edges",
-        str(params.get("edge_fraction"))
+        str(params.get("edge_fraction", 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("one_state"):
+    if params.get("one_state", False):
         cargs.append("-onestate")
-    if params.get("anatomical_label"):
+    if params.get("anatomical_label", False):
         cargs.append("-anatomical")
-    if params.get("no_volume_registration"):
+    if params.get("no_volume_registration", False):
         cargs.append("-novolreg")
-    if params.get("set_env") is not None:
+    if params.get("set_env", None) is not None:
         cargs.extend([
             "-setenv",
-            params.get("set_env")
+            params.get("set_env", None)
         ])
     return cargs
 
@@ -171,16 +150,18 @@ def surf_mesh_outputs(
     """
     ret = SurfMeshOutputs(
         root=execution.output_file("."),
-        output_surface_file=execution.output_file(params.get("output_surface") + ".surface"),
+        output_surface_file=execution.output_file(params.get("output_surface", None) + ".surface"),
     )
     return ret
 
 
 def surf_mesh_execute(
     params: SurfMeshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfMeshOutputs:
     """
+    SurfMesh
+    
     Surface mesh manipulation tool.
     
     Author: AFNI Developers
@@ -189,10 +170,12 @@ def surf_mesh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfMeshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_MESH_METADATA)
     params = execution.params(params)
     cargs = surf_mesh_cargs(params, execution)
     ret = surf_mesh_outputs(params, execution)
@@ -212,6 +195,8 @@ def surf_mesh(
     runner: Runner | None = None,
 ) -> SurfMeshOutputs:
     """
+    SurfMesh
+    
     Surface mesh manipulation tool.
     
     Author: AFNI Developers
@@ -232,8 +217,6 @@ def surf_mesh(
     Returns:
         NamedTuple of outputs (described in `SurfMeshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF_MESH_METADATA)
     params = surf_mesh_params(
         input_surface=input_surface,
         output_surface=output_surface,
@@ -244,13 +227,13 @@ def surf_mesh(
         no_volume_registration=no_volume_registration,
         set_env=set_env,
     )
-    return surf_mesh_execute(params, execution)
+    return surf_mesh_execute(params, runner)
 
 
 __all__ = [
     "SURF_MESH_METADATA",
     "SurfMeshOutputs",
-    "SurfMeshParameters",
     "surf_mesh",
+    "surf_mesh_execute",
     "surf_mesh_params",
 ]