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

niwrap_afni/afni/convert_surface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CONVERT_SURFACE_METADATA = Metadata(
-    id="d48b4e88fa9598a23318fbc071216469e4145c7f.boutiques",
+    id="57576de1b82aad67fcaed9b36da45f9b5b81e8fe.boutiques",
     name="ConvertSurface",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ CONVERT_SURFACE_METADATA = Metadata(
 
 
 ConvertSurfaceParameters = typing.TypedDict('ConvertSurfaceParameters', {
-    "__STYXTYPE__": typing.Literal["ConvertSurface"],
+    "@type": typing.NotRequired[typing.Literal["afni/ConvertSurface"]],
+    "input_surface": str,
+    "output_surface": str,
+    "surface_volume": typing.NotRequired[str | None],
+    "transform_tlrc": bool,
+    "mni_rai": bool,
+    "mni_lpi": bool,
+    "xmat_1D": typing.NotRequired[str | None],
+    "ixmat_1D": typing.NotRequired[str | None],
+    "seed": typing.NotRequired[str | None],
+    "native": bool,
+})
+ConvertSurfaceParametersTagged = typing.TypedDict('ConvertSurfaceParametersTagged', {
+    "@type": typing.Literal["afni/ConvertSurface"],
     "input_surface": str,
     "output_surface": str,
     "surface_volume": typing.NotRequired[str | None],
@@ -26,43 +39,11 @@ ConvertSurfaceParameters = typing.TypedDict('ConvertSurfaceParameters', {
     "seed": typing.NotRequired[str | None],
     "native": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "ConvertSurface": convert_surface_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 {
-        "ConvertSurface": convert_surface_outputs,
-    }.get(t)
 
 
 class ConvertSurfaceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `convert_surface(...)`.
+    Output object returned when calling `ConvertSurfaceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +62,7 @@ def convert_surface_params(
     ixmat_1_d: str | None = None,
     seed: str | None = None,
     native: bool = False,
-) -> ConvertSurfaceParameters:
+) -> ConvertSurfaceParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +83,7 @@ def convert_surface_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ConvertSurface",
+        "@type": "afni/ConvertSurface",
         "input_surface": input_surface,
         "output_surface": output_surface,
         "transform_tlrc": transform_tlrc,
@@ -138,39 +119,39 @@ def convert_surface_cargs(
     cargs.append("ConvertSurface")
     cargs.extend([
         "-i",
-        params.get("input_surface")
+        params.get("input_surface", None)
     ])
     cargs.extend([
         "-o",
-        params.get("output_surface")
+        params.get("output_surface", None)
     ])
-    if params.get("surface_volume") is not None:
+    if params.get("surface_volume", None) is not None:
         cargs.extend([
             "-sv",
-            params.get("surface_volume")
+            params.get("surface_volume", None)
         ])
-    if params.get("transform_tlrc"):
+    if params.get("transform_tlrc", False):
         cargs.append("-tlrc")
-    if params.get("mni_rai"):
+    if params.get("mni_rai", False):
         cargs.append("-MNI_rai")
-    if params.get("mni_lpi"):
+    if params.get("mni_lpi", False):
         cargs.append("-MNI_lpi")
-    if params.get("xmat_1D") is not None:
+    if params.get("xmat_1D", None) is not None:
         cargs.extend([
             "-xmat_1D",
-            params.get("xmat_1D")
+            params.get("xmat_1D", None)
         ])
-    if params.get("ixmat_1D") is not None:
+    if params.get("ixmat_1D", None) is not None:
         cargs.extend([
             "-ixmat_1D",
-            params.get("ixmat_1D")
+            params.get("ixmat_1D", None)
         ])
-    if params.get("seed") is not None:
+    if params.get("seed", None) is not None:
         cargs.extend([
             "-seed",
-            params.get("seed")
+            params.get("seed", None)
         ])
-    if params.get("native"):
+    if params.get("native", False):
         cargs.append("-native")
     return cargs
 
@@ -190,18 +171,20 @@ def convert_surface_outputs(
     """
     ret = ConvertSurfaceOutputs(
         root=execution.output_file("."),
-        output_surface_file=execution.output_file(params.get("output_surface")),
+        output_surface_file=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def convert_surface_execute(
     params: ConvertSurfaceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ConvertSurfaceOutputs:
     """
-    Reads in a surface and writes it out in another format. Only fields pertinent to
-    SUMA are preserved.
+    ConvertSurface
+    
+    Reads in a surface and writes it out in another format. Only fields
+    pertinent to SUMA are preserved.
     
     Author: AFNI Developers
     
@@ -209,10 +192,12 @@ def convert_surface_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ConvertSurfaceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONVERT_SURFACE_METADATA)
     params = execution.params(params)
     cargs = convert_surface_cargs(params, execution)
     ret = convert_surface_outputs(params, execution)
@@ -234,8 +219,10 @@ def convert_surface(
     runner: Runner | None = None,
 ) -> ConvertSurfaceOutputs:
     """
-    Reads in a surface and writes it out in another format. Only fields pertinent to
-    SUMA are preserved.
+    ConvertSurface
+    
+    Reads in a surface and writes it out in another format. Only fields
+    pertinent to SUMA are preserved.
     
     Author: AFNI Developers
     
@@ -258,8 +245,6 @@ def convert_surface(
     Returns:
         NamedTuple of outputs (described in `ConvertSurfaceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CONVERT_SURFACE_METADATA)
     params = convert_surface_params(
         input_surface=input_surface,
         output_surface=output_surface,
@@ -272,13 +257,13 @@ def convert_surface(
         seed=seed,
         native=native,
     )
-    return convert_surface_execute(params, execution)
+    return convert_surface_execute(params, runner)
 
 
 __all__ = [
     "CONVERT_SURFACE_METADATA",
     "ConvertSurfaceOutputs",
-    "ConvertSurfaceParameters",
     "convert_surface",
+    "convert_surface_execute",
     "convert_surface_params",
 ]

niwrap_afni/afni/convex_hull.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CONVEX_HULL_METADATA = Metadata(
-    id="212679c3e56974a08070cda35b98c1c96c0bfe04.boutiques",
+    id="79e3bac48907406f7ee6520d509c9b76000ff72f.boutiques",
     name="ConvexHull",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,26 @@ CONVEX_HULL_METADATA = Metadata(
 
 
 ConvexHullParameters = typing.TypedDict('ConvexHullParameters', {
-    "__STYXTYPE__": typing.Literal["ConvexHull"],
+    "@type": typing.NotRequired[typing.Literal["afni/ConvexHull"]],
+    "vol": typing.NotRequired[InputPathType | None],
+    "isoval": typing.NotRequired[float | None],
+    "isorange": typing.NotRequired[list[float] | None],
+    "isocmask": typing.NotRequired[str | None],
+    "xform": typing.NotRequired[str | None],
+    "surface_input": typing.NotRequired[InputPathType | None],
+    "surf_vol": typing.NotRequired[InputPathType | None],
+    "input_1d": typing.NotRequired[InputPathType | None],
+    "q_opt": typing.NotRequired[str | None],
+    "proj_xy": bool,
+    "orig_coord": bool,
+    "these_coords": typing.NotRequired[InputPathType | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "debug": typing.NotRequired[str | None],
+    "novolreg": bool,
+    "setenv": typing.NotRequired[str | None],
+})
+ConvexHullParametersTagged = typing.TypedDict('ConvexHullParametersTagged', {
+    "@type": typing.Literal["afni/ConvexHull"],
     "vol": typing.NotRequired[InputPathType | None],
     "isoval": typing.NotRequired[float | None],
     "isorange": typing.NotRequired[list[float] | None],
@@ -32,43 +51,11 @@ ConvexHullParameters = typing.TypedDict('ConvexHullParameters', {
     "novolreg": bool,
     "setenv": 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 {
-        "ConvexHull": convex_hull_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 {
-        "ConvexHull": convex_hull_outputs,
-    }.get(t)
 
 
 class ConvexHullOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `convex_hull(...)`.
+    Output object returned when calling `ConvexHullParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +80,7 @@ def convex_hull_params(
     debug: str | None = None,
     novolreg: bool = False,
     setenv: str | None = None,
-) -> ConvexHullParameters:
+) -> ConvexHullParametersTagged:
     """
     Build parameters.
     
@@ -128,7 +115,7 @@ def convex_hull_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ConvexHull",
+        "@type": "afni/ConvexHull",
         "proj_xy": proj_xy,
         "orig_coord": orig_coord,
         "novolreg": novolreg,
@@ -177,76 +164,76 @@ def convex_hull_cargs(
     """
     cargs = []
     cargs.append("ConvexHull")
-    if params.get("vol") is not None:
+    if params.get("vol", None) is not None:
         cargs.extend([
             "-input",
-            execution.input_file(params.get("vol"))
+            execution.input_file(params.get("vol", None))
         ])
-    if params.get("isoval") is not None:
+    if params.get("isoval", None) is not None:
         cargs.extend([
             "-isoval",
-            str(params.get("isoval"))
+            str(params.get("isoval", None))
         ])
-    if params.get("isorange") is not None:
+    if params.get("isorange", None) is not None:
         cargs.extend([
             "-isorange",
-            *map(str, params.get("isorange"))
+            *map(str, params.get("isorange", None))
         ])
-    if params.get("isocmask") is not None:
+    if params.get("isocmask", None) is not None:
         cargs.extend([
             "-isocmask",
-            params.get("isocmask")
+            params.get("isocmask", None)
         ])
-    if params.get("xform") is not None:
+    if params.get("xform", None) is not None:
         cargs.extend([
             "-xform",
-            params.get("xform")
+            params.get("xform", None)
         ])
-    if params.get("surface_input") is not None:
+    if params.get("surface_input", None) is not None:
         cargs.extend([
             "-i_TYPE",
-            execution.input_file(params.get("surface_input"))
+            execution.input_file(params.get("surface_input", None))
         ])
-    if params.get("surf_vol") is not None:
+    if params.get("surf_vol", None) is not None:
         cargs.extend([
             "-sv",
-            execution.input_file(params.get("surf_vol"))
+            execution.input_file(params.get("surf_vol", None))
         ])
-    if params.get("input_1d") is not None:
+    if params.get("input_1d", None) is not None:
         cargs.extend([
             "-input_1D",
-            execution.input_file(params.get("input_1d"))
+            execution.input_file(params.get("input_1d", None))
         ])
-    if params.get("q_opt") is not None:
+    if params.get("q_opt", None) is not None:
         cargs.extend([
             "-q_opt",
-            params.get("q_opt")
+            params.get("q_opt", None)
         ])
-    if params.get("proj_xy"):
+    if params.get("proj_xy", False):
         cargs.append("-proj_xy")
-    if params.get("orig_coord"):
+    if params.get("orig_coord", False):
         cargs.append("-orig_coord")
-    if params.get("these_coords") is not None:
+    if params.get("these_coords", None) is not None:
         cargs.extend([
             "-these_coords",
-            execution.input_file(params.get("these_coords"))
+            execution.input_file(params.get("these_coords", None))
         ])
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-o_TYPE",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("debug") is not None:
+    if params.get("debug", None) is not None:
         cargs.extend([
             "-debug",
-            params.get("debug")
+            params.get("debug", None)
         ])
-    if params.get("novolreg"):
+    if params.get("novolreg", False):
         cargs.append("-novolreg")
-    if params.get("setenv") is not None:
+    if params.get("setenv", None) is not None:
         cargs.extend([
             "-setenv",
-            params.get("setenv")
+            params.get("setenv", None)
         ])
     return cargs
 
@@ -266,18 +253,20 @@ def convex_hull_outputs(
     """
     ret = ConvexHullOutputs(
         root=execution.output_file("."),
-        out_surf=execution.output_file(params.get("output_prefix")) if (params.get("output_prefix") is not None) else None,
+        out_surf=execution.output_file(params.get("output_prefix", None)) if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def convex_hull_execute(
     params: ConvexHullParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ConvexHullOutputs:
     """
-    A program to find the convex hull, or perform a Delaunay triangulation of a set
-    of points.
+    ConvexHull
+    
+    A program to find the convex hull, or perform a Delaunay triangulation of a
+    set of points.
     
     Author: AFNI Developers
     
@@ -285,10 +274,12 @@ def convex_hull_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ConvexHullOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONVEX_HULL_METADATA)
     params = execution.params(params)
     cargs = convex_hull_cargs(params, execution)
     ret = convex_hull_outputs(params, execution)
@@ -316,8 +307,10 @@ def convex_hull(
     runner: Runner | None = None,
 ) -> ConvexHullOutputs:
     """
-    A program to find the convex hull, or perform a Delaunay triangulation of a set
-    of points.
+    ConvexHull
+    
+    A program to find the convex hull, or perform a Delaunay triangulation of a
+    set of points.
     
     Author: AFNI Developers
     
@@ -354,8 +347,6 @@ def convex_hull(
     Returns:
         NamedTuple of outputs (described in `ConvexHullOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CONVEX_HULL_METADATA)
     params = convex_hull_params(
         vol=vol,
         isoval=isoval,
@@ -374,13 +365,13 @@ def convex_hull(
         novolreg=novolreg,
         setenv=setenv,
     )
-    return convex_hull_execute(params, execution)
+    return convex_hull_execute(params, runner)
 
 
 __all__ = [
     "CONVEX_HULL_METADATA",
     "ConvexHullOutputs",
-    "ConvexHullParameters",
     "convex_hull",
+    "convex_hull_execute",
     "convex_hull_params",
 ]