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

niwrap_afni/afni/surface_metrics.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURFACE_METRICS_METADATA = Metadata(
-    id="1ef3c8a44dad85904fd6b95c168fae520751be00.boutiques",
+    id="b315e5bce71dcb571710c69e747d37245226be55.boutiques",
     name="SurfaceMetrics",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,33 @@ SURFACE_METRICS_METADATA = Metadata(
 
 
 SurfaceMetricsParameters = typing.TypedDict('SurfaceMetricsParameters', {
-    "__STYXTYPE__": typing.Literal["SurfaceMetrics"],
+    "@type": typing.NotRequired[typing.Literal["afni/SurfaceMetrics"]],
+    "volume": bool,
+    "convexity": bool,
+    "closest_node": typing.NotRequired[InputPathType | None],
+    "area": bool,
+    "tri_sines": bool,
+    "tri_cosines": bool,
+    "tri_CoSines": bool,
+    "tri_angles": bool,
+    "node_angles": bool,
+    "curvature": bool,
+    "edges": bool,
+    "node_normals": bool,
+    "face_normals": bool,
+    "normals_scale": typing.NotRequired[float | None],
+    "coords": bool,
+    "sph_coords": bool,
+    "sph_coords_center": typing.NotRequired[list[float] | None],
+    "boundary_nodes": bool,
+    "boundary_triangles": bool,
+    "internal_nodes": bool,
+    "surf1": str,
+    "tlrc": bool,
+    "prefix": typing.NotRequired[str | None],
+})
+SurfaceMetricsParametersTagged = typing.TypedDict('SurfaceMetricsParametersTagged', {
+    "@type": typing.Literal["afni/SurfaceMetrics"],
     "volume": bool,
     "convexity": bool,
     "closest_node": typing.NotRequired[InputPathType | None],
@@ -39,42 +65,11 @@ SurfaceMetricsParameters = typing.TypedDict('SurfaceMetricsParameters', {
     "tlrc": bool,
     "prefix": 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 {
-        "SurfaceMetrics": surface_metrics_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 SurfaceMetricsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surface_metrics(...)`.
+    Output object returned when calling `SurfaceMetricsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -104,7 +99,7 @@ def surface_metrics_params(
     internal_nodes: bool = False,
     tlrc: bool = False,
     prefix: str | None = None,
-) -> SurfaceMetricsParameters:
+) -> SurfaceMetricsParametersTagged:
     """
     Build parameters.
     
@@ -138,7 +133,7 @@ def surface_metrics_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SurfaceMetrics",
+        "@type": "afni/SurfaceMetrics",
         "volume": volume,
         "convexity": convexity,
         "area": area,
@@ -185,65 +180,65 @@ def surface_metrics_cargs(
     """
     cargs = []
     cargs.append("SurfaceMetrics")
-    if params.get("volume"):
+    if params.get("volume", False):
         cargs.append("-vol")
-    if params.get("convexity"):
+    if params.get("convexity", False):
         cargs.append("-conv")
-    if params.get("closest_node") is not None:
+    if params.get("closest_node", None) is not None:
         cargs.extend([
             "-closest_node",
-            execution.input_file(params.get("closest_node"))
+            execution.input_file(params.get("closest_node", None))
         ])
-    if params.get("area"):
+    if params.get("area", False):
         cargs.append("-area")
-    if params.get("tri_sines"):
+    if params.get("tri_sines", False):
         cargs.append("-tri_sines")
-    if params.get("tri_cosines"):
+    if params.get("tri_cosines", False):
         cargs.append("-tri_cosines")
-    if params.get("tri_CoSines"):
+    if params.get("tri_CoSines", False):
         cargs.append("-tri_CoSines")
-    if params.get("tri_angles"):
+    if params.get("tri_angles", False):
         cargs.append("-tri_angles")
-    if params.get("node_angles"):
+    if params.get("node_angles", False):
         cargs.append("-node_angles")
-    if params.get("curvature"):
+    if params.get("curvature", False):
         cargs.append("-curv")
-    if params.get("edges"):
+    if params.get("edges", False):
         cargs.append("-edges")
-    if params.get("node_normals"):
+    if params.get("node_normals", False):
         cargs.append("-node_normals")
-    if params.get("face_normals"):
+    if params.get("face_normals", False):
         cargs.append("-face_normals")
-    if params.get("normals_scale") is not None:
+    if params.get("normals_scale", None) is not None:
         cargs.extend([
             "-normals_scale",
-            str(params.get("normals_scale"))
+            str(params.get("normals_scale", None))
         ])
-    if params.get("coords"):
+    if params.get("coords", False):
         cargs.append("-coords")
-    if params.get("sph_coords"):
+    if params.get("sph_coords", False):
         cargs.append("-sph_coords")
-    if params.get("sph_coords_center") is not None:
+    if params.get("sph_coords_center", None) is not None:
         cargs.extend([
             "-sph_coords_center",
-            *map(str, params.get("sph_coords_center"))
+            *map(str, params.get("sph_coords_center", None))
         ])
-    if params.get("boundary_nodes"):
+    if params.get("boundary_nodes", False):
         cargs.append("-boundary_nodes")
-    if params.get("boundary_triangles"):
+    if params.get("boundary_triangles", False):
         cargs.append("-boundary_triangles")
-    if params.get("internal_nodes"):
+    if params.get("internal_nodes", False):
         cargs.append("-internal_nodes")
     cargs.extend([
         "-SURF_1",
-        params.get("surf1")
+        params.get("surf1", None)
     ])
-    if params.get("tlrc"):
+    if params.get("tlrc", False):
         cargs.append("-tlrc")
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
     return cargs
 
@@ -269,9 +264,11 @@ def surface_metrics_outputs(
 
 def surface_metrics_execute(
     params: SurfaceMetricsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfaceMetricsOutputs:
     """
+    SurfaceMetrics
+    
     Outputs information about a surface's mesh.
     
     Author: AFNI Developers
@@ -280,10 +277,12 @@ def surface_metrics_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfaceMetricsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURFACE_METRICS_METADATA)
     params = execution.params(params)
     cargs = surface_metrics_cargs(params, execution)
     ret = surface_metrics_outputs(params, execution)
@@ -318,6 +317,8 @@ def surface_metrics(
     runner: Runner | None = None,
 ) -> SurfaceMetricsOutputs:
     """
+    SurfaceMetrics
+    
     Outputs information about a surface's mesh.
     
     Author: AFNI Developers
@@ -354,8 +355,6 @@ def surface_metrics(
     Returns:
         NamedTuple of outputs (described in `SurfaceMetricsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURFACE_METRICS_METADATA)
     params = surface_metrics_params(
         volume=volume,
         convexity=convexity,
@@ -381,13 +380,13 @@ def surface_metrics(
         tlrc=tlrc,
         prefix=prefix,
     )
-    return surface_metrics_execute(params, execution)
+    return surface_metrics_execute(params, runner)
 
 
 __all__ = [
     "SURFACE_METRICS_METADATA",
     "SurfaceMetricsOutputs",
-    "SurfaceMetricsParameters",
     "surface_metrics",
+    "surface_metrics_execute",
     "surface_metrics_params",
 ]

niwrap_afni/afni/tedana_wrapper_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TEDANA_WRAPPER_PY_METADATA = Metadata(
-    id="062c0aea0577a5fde96bac4b23ec34f8ab38f7ae.boutiques",
+    id="35e559ddd827c563b8387bf1e45614d747bf5d09.boutiques",
     name="tedana_wrapper.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ TEDANA_WRAPPER_PY_METADATA = Metadata(
 
 
 TedanaWrapperPyParameters = typing.TypedDict('TedanaWrapperPyParameters', {
-    "__STYXTYPE__": typing.Literal["tedana_wrapper.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/tedana_wrapper.py"]],
+    "input_files": list[InputPathType],
+    "echo_times": list[float],
+    "mask": InputPathType,
+    "results_dir": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "save_all": bool,
+    "prep_only": bool,
+    "tedana_prog": typing.NotRequired[str | None],
+    "tedana_is_exec": bool,
+    "ted_label": typing.NotRequired[str | None],
+    "tedana_opts": typing.NotRequired[str | None],
+    "help": bool,
+    "detailed_help": bool,
+})
+TedanaWrapperPyParametersTagged = typing.TypedDict('TedanaWrapperPyParametersTagged', {
+    "@type": typing.Literal["afni/tedana_wrapper.py"],
     "input_files": list[InputPathType],
     "echo_times": list[float],
     "mask": InputPathType,
@@ -29,43 +45,11 @@ TedanaWrapperPyParameters = typing.TypedDict('TedanaWrapperPyParameters', {
     "help": bool,
     "detailed_help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "tedana_wrapper.py": tedana_wrapper_py_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 {
-        "tedana_wrapper.py": tedana_wrapper_py_outputs,
-    }.get(t)
 
 
 class TedanaWrapperPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tedana_wrapper_py(...)`.
+    Output object returned when calling `TedanaWrapperPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +73,7 @@ def tedana_wrapper_py_params(
     tedana_opts: str | None = None,
     help_: bool = False,
     detailed_help: bool = False,
-) -> TedanaWrapperPyParameters:
+) -> TedanaWrapperPyParametersTagged:
     """
     Build parameters.
     
@@ -116,7 +100,7 @@ def tedana_wrapper_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tedana_wrapper.py",
+        "@type": "afni/tedana_wrapper.py",
         "input_files": input_files,
         "echo_times": echo_times,
         "mask": mask,
@@ -156,50 +140,50 @@ def tedana_wrapper_py_cargs(
     cargs.append("tedana_wrapper.py")
     cargs.extend([
         "-input",
-        *[execution.input_file(f) for f in params.get("input_files")]
+        *[execution.input_file(f) for f in params.get("input_files", None)]
     ])
     cargs.extend([
         "-TE",
-        *map(str, params.get("echo_times"))
+        *map(str, params.get("echo_times", None))
     ])
     cargs.extend([
         "-mask",
-        execution.input_file(params.get("mask"))
+        execution.input_file(params.get("mask", None))
     ])
-    if params.get("results_dir") is not None:
+    if params.get("results_dir", None) is not None:
         cargs.extend([
             "-results_dir",
-            params.get("results_dir")
+            params.get("results_dir", None)
         ])
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("save_all"):
+    if params.get("save_all", False):
         cargs.append("-save_all")
-    if params.get("prep_only"):
+    if params.get("prep_only", False):
         cargs.append("-prep_only")
-    if params.get("tedana_prog") is not None:
+    if params.get("tedana_prog", None) is not None:
         cargs.extend([
             "-tedana_prog",
-            params.get("tedana_prog")
+            params.get("tedana_prog", None)
         ])
-    if params.get("tedana_is_exec"):
+    if params.get("tedana_is_exec", False):
         cargs.append("-tedana_is_exec")
-    if params.get("ted_label") is not None:
+    if params.get("ted_label", None) is not None:
         cargs.extend([
             "-ted_label",
-            params.get("ted_label")
+            params.get("ted_label", None)
         ])
-    if params.get("tedana_opts") is not None:
+    if params.get("tedana_opts", None) is not None:
         cargs.extend([
             "-tedana_opts",
-            params.get("tedana_opts")
+            params.get("tedana_opts", None)
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-h")
-    if params.get("detailed_help"):
+    if params.get("detailed_help", False):
         cargs.append("-help")
     return cargs
 
@@ -219,17 +203,19 @@ def tedana_wrapper_py_outputs(
     """
     ret = TedanaWrapperPyOutputs(
         root=execution.output_file("."),
-        tedana_output=execution.output_file(params.get("results_dir") + "/" + params.get("prefix") + "_ted_output") if (params.get("results_dir") is not None and params.get("prefix") is not None) else None,
-        tedana_report=execution.output_file(params.get("results_dir") + "/" + params.get("prefix") + "_tedana_report.txt") if (params.get("results_dir") is not None and params.get("prefix") is not None) else None,
+        tedana_output=execution.output_file(params.get("results_dir", None) + "/" + params.get("prefix", None) + "_ted_output") if (params.get("results_dir") is not None and params.get("prefix") is not None) else None,
+        tedana_report=execution.output_file(params.get("results_dir", None) + "/" + params.get("prefix", None) + "_tedana_report.txt") if (params.get("results_dir") is not None and params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def tedana_wrapper_py_execute(
     params: TedanaWrapperPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TedanaWrapperPyOutputs:
     """
+    tedana_wrapper.py
+    
     Internal wrapper to run tedana.py, typically used within afni_proc.py.
     
     Author: AFNI Developers
@@ -238,10 +224,12 @@ def tedana_wrapper_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TedanaWrapperPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TEDANA_WRAPPER_PY_METADATA)
     params = execution.params(params)
     cargs = tedana_wrapper_py_cargs(params, execution)
     ret = tedana_wrapper_py_outputs(params, execution)
@@ -266,6 +254,8 @@ def tedana_wrapper_py(
     runner: Runner | None = None,
 ) -> TedanaWrapperPyOutputs:
     """
+    tedana_wrapper.py
+    
     Internal wrapper to run tedana.py, typically used within afni_proc.py.
     
     Author: AFNI Developers
@@ -295,8 +285,6 @@ def tedana_wrapper_py(
     Returns:
         NamedTuple of outputs (described in `TedanaWrapperPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TEDANA_WRAPPER_PY_METADATA)
     params = tedana_wrapper_py_params(
         input_files=input_files,
         echo_times=echo_times,
@@ -312,13 +300,13 @@ def tedana_wrapper_py(
         help_=help_,
         detailed_help=detailed_help,
     )
-    return tedana_wrapper_py_execute(params, execution)
+    return tedana_wrapper_py_execute(params, runner)
 
 
 __all__ = [
     "TEDANA_WRAPPER_PY_METADATA",
     "TedanaWrapperPyOutputs",
-    "TedanaWrapperPyParameters",
     "tedana_wrapper_py",
+    "tedana_wrapper_py_execute",
     "tedana_wrapper_py_params",
 ]