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

niwrap_afni/afni/qhull.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 QHULL_METADATA = Metadata(
-    id="36c4abb8c29f69fab57cfb4a2bc32d5fb32edf2e.boutiques",
+    id="7cf282f989e22a92a6d1e41d86ce6515a481efaa.boutiques",
     name="qhull",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,31 @@ QHULL_METADATA = Metadata(
 
 
 QhullParameters = typing.TypedDict('QhullParameters', {
-    "__STYXTYPE__": typing.Literal["qhull"],
+    "@type": typing.NotRequired[typing.Literal["afni/qhull"]],
+    "input_coords": str,
+    "delaunay": bool,
+    "furthest_delaunay": bool,
+    "voronoi": bool,
+    "furthest_voronoi": bool,
+    "halfspace_intersection": bool,
+    "triangulated_output": bool,
+    "joggled_input": bool,
+    "verify": bool,
+    "summary": bool,
+    "vertices_incident": bool,
+    "normals": bool,
+    "vertex_coordinates": bool,
+    "halfspace_intersections": bool,
+    "extreme_points": bool,
+    "total_area_volume": bool,
+    "off_format": bool,
+    "geomview_output": bool,
+    "mathematica_output": bool,
+    "print_facets": typing.NotRequired[str | None],
+    "output_file": typing.NotRequired[str | None],
+})
+QhullParametersTagged = typing.TypedDict('QhullParametersTagged', {
+    "@type": typing.Literal["afni/qhull"],
     "input_coords": str,
     "delaunay": bool,
     "furthest_delaunay": bool,
@@ -37,43 +61,11 @@ QhullParameters = typing.TypedDict('QhullParameters', {
     "print_facets": typing.NotRequired[str | None],
     "output_file": 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 {
-        "qhull": qhull_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 {
-        "qhull": qhull_outputs,
-    }.get(t)
 
 
 class QhullOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `qhull(...)`.
+    Output object returned when calling `QhullParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +95,7 @@ def qhull_params(
     mathematica_output: bool = False,
     print_facets: str | None = None,
     output_file: str | None = None,
-) -> QhullParameters:
+) -> QhullParametersTagged:
     """
     Build parameters.
     
@@ -139,7 +131,7 @@ def qhull_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "qhull",
+        "@type": "afni/qhull",
         "input_coords": input_coords,
         "delaunay": delaunay,
         "furthest_delaunay": furthest_delaunay,
@@ -182,52 +174,52 @@ def qhull_cargs(
     """
     cargs = []
     cargs.append("qhull")
-    cargs.append(params.get("input_coords"))
-    if params.get("delaunay"):
+    cargs.append(params.get("input_coords", None))
+    if params.get("delaunay", False):
         cargs.append("d")
-    if params.get("furthest_delaunay"):
+    if params.get("furthest_delaunay", False):
         cargs.append("d Qu")
-    if params.get("voronoi"):
+    if params.get("voronoi", False):
         cargs.append("v")
-    if params.get("furthest_voronoi"):
+    if params.get("furthest_voronoi", False):
         cargs.append("v Qu")
-    if params.get("halfspace_intersection"):
+    if params.get("halfspace_intersection", False):
         cargs.append("H1,1")
-    if params.get("triangulated_output"):
+    if params.get("triangulated_output", False):
         cargs.append("Qt")
-    if params.get("joggled_input"):
+    if params.get("joggled_input", False):
         cargs.append("QJ")
-    if params.get("verify"):
+    if params.get("verify", False):
         cargs.append("Tv")
-    if params.get("summary"):
+    if params.get("summary", False):
         cargs.append("s")
-    if params.get("vertices_incident"):
+    if params.get("vertices_incident", False):
         cargs.append("i")
-    if params.get("normals"):
+    if params.get("normals", False):
         cargs.append("n")
-    if params.get("vertex_coordinates"):
+    if params.get("vertex_coordinates", False):
         cargs.append("p")
-    if params.get("halfspace_intersections"):
+    if params.get("halfspace_intersections", False):
         cargs.append("Fp")
-    if params.get("extreme_points"):
+    if params.get("extreme_points", False):
         cargs.append("Fx")
-    if params.get("total_area_volume"):
+    if params.get("total_area_volume", False):
         cargs.append("FA")
-    if params.get("off_format"):
+    if params.get("off_format", False):
         cargs.append("o")
-    if params.get("geomview_output"):
+    if params.get("geomview_output", False):
         cargs.append("G")
-    if params.get("mathematica_output"):
+    if params.get("mathematica_output", False):
         cargs.append("m")
-    if params.get("print_facets") is not None:
+    if params.get("print_facets", None) is not None:
         cargs.extend([
             "QVn",
-            params.get("print_facets")
+            params.get("print_facets", None)
         ])
-    if params.get("output_file") is not None:
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "TO",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
     return cargs
 
@@ -247,16 +239,18 @@ def qhull_outputs(
     """
     ret = QhullOutputs(
         root=execution.output_file("."),
-        output_results=execution.output_file(params.get("output_file") + ".txt") if (params.get("output_file") is not None) else None,
+        output_results=execution.output_file(params.get("output_file", None) + ".txt") if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def qhull_execute(
     params: QhullParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> QhullOutputs:
     """
+    qhull
+    
     Tool to compute convex hulls and related structures.
     
     Author: AFNI Developers
@@ -265,10 +259,12 @@ def qhull_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `QhullOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QHULL_METADATA)
     params = execution.params(params)
     cargs = qhull_cargs(params, execution)
     ret = qhull_outputs(params, execution)
@@ -301,6 +297,8 @@ def qhull(
     runner: Runner | None = None,
 ) -> QhullOutputs:
     """
+    qhull
+    
     Tool to compute convex hulls and related structures.
     
     Author: AFNI Developers
@@ -339,8 +337,6 @@ def qhull(
     Returns:
         NamedTuple of outputs (described in `QhullOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(QHULL_METADATA)
     params = qhull_params(
         input_coords=input_coords,
         delaunay=delaunay,
@@ -364,13 +360,13 @@ def qhull(
         print_facets=print_facets,
         output_file=output_file,
     )
-    return qhull_execute(params, execution)
+    return qhull_execute(params, runner)
 
 
 __all__ = [
     "QHULL_METADATA",
     "QhullOutputs",
-    "QhullParameters",
     "qhull",
+    "qhull_execute",
     "qhull_params",
 ]

niwrap_afni/afni/quick_alpha_vals_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 QUICK_ALPHA_VALS_PY_METADATA = Metadata(
-    id="43400d28d72275606480ec0f8739d52a9c960123.boutiques",
+    id="240a9d3e24a1a2d167b06636e882d90d255a2a3c.boutiques",
     name="quick.alpha.vals.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,20 @@ QUICK_ALPHA_VALS_PY_METADATA = Metadata(
 
 
 QuickAlphaValsPyParameters = typing.TypedDict('QuickAlphaValsPyParameters', {
-    "__STYXTYPE__": typing.Literal["quick.alpha.vals.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/quick.alpha.vals.py"]],
+    "niter": typing.NotRequired[int | None],
+    "max_file": InputPathType,
+})
+QuickAlphaValsPyParametersTagged = typing.TypedDict('QuickAlphaValsPyParametersTagged', {
+    "@type": typing.Literal["afni/quick.alpha.vals.py"],
     "niter": typing.NotRequired[int | None],
     "max_file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "quick.alpha.vals.py": quick_alpha_vals_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 {
-        "quick.alpha.vals.py": quick_alpha_vals_py_outputs,
-    }.get(t)
 
 
 class QuickAlphaValsPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `quick_alpha_vals_py(...)`.
+    Output object returned when calling `QuickAlphaValsPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class QuickAlphaValsPyOutputs(typing.NamedTuple):
 def quick_alpha_vals_py_params(
     max_file: InputPathType,
     niter: int | None = None,
-) -> QuickAlphaValsPyParameters:
+) -> QuickAlphaValsPyParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def quick_alpha_vals_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "quick.alpha.vals.py",
+        "@type": "afni/quick.alpha.vals.py",
         "max_file": max_file,
     }
     if niter is not None:
@@ -99,12 +72,12 @@ def quick_alpha_vals_py_cargs(
     """
     cargs = []
     cargs.append("quick.alpha.vals.py")
-    if params.get("niter") is not None:
+    if params.get("niter", None) is not None:
         cargs.extend([
             "-niter",
-            str(params.get("niter"))
+            str(params.get("niter", None))
         ])
-    cargs.append(execution.input_file(params.get("max_file")))
+    cargs.append(execution.input_file(params.get("max_file", None)))
     return cargs
 
 
@@ -130,9 +103,11 @@ def quick_alpha_vals_py_outputs(
 
 def quick_alpha_vals_py_execute(
     params: QuickAlphaValsPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> QuickAlphaValsPyOutputs:
     """
+    quick.alpha.vals.py
+    
     Generate an alpha table from slow_surf_clustsim.py results.
     
     Author: AFNI Developers
@@ -141,10 +116,12 @@ def quick_alpha_vals_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `QuickAlphaValsPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QUICK_ALPHA_VALS_PY_METADATA)
     params = execution.params(params)
     cargs = quick_alpha_vals_py_cargs(params, execution)
     ret = quick_alpha_vals_py_outputs(params, execution)
@@ -158,6 +135,8 @@ def quick_alpha_vals_py(
     runner: Runner | None = None,
 ) -> QuickAlphaValsPyOutputs:
     """
+    quick.alpha.vals.py
+    
     Generate an alpha table from slow_surf_clustsim.py results.
     
     Author: AFNI Developers
@@ -171,19 +150,17 @@ def quick_alpha_vals_py(
     Returns:
         NamedTuple of outputs (described in `QuickAlphaValsPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(QUICK_ALPHA_VALS_PY_METADATA)
     params = quick_alpha_vals_py_params(
         niter=niter,
         max_file=max_file,
     )
-    return quick_alpha_vals_py_execute(params, execution)
+    return quick_alpha_vals_py_execute(params, runner)
 
 
 __all__ = [
     "QUICK_ALPHA_VALS_PY_METADATA",
     "QuickAlphaValsPyOutputs",
-    "QuickAlphaValsPyParameters",
     "quick_alpha_vals_py",
+    "quick_alpha_vals_py_execute",
     "quick_alpha_vals_py_params",
 ]

niwrap_afni/afni/quickspec.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 QUICKSPEC_METADATA = Metadata(
-    id="46432d665730d07674145b924b55e89f5ce5660b.boutiques",
+    id="280e96292648ffe2c737c44b5d806c26bc44f50f.boutiques",
     name="quickspec",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ QUICKSPEC_METADATA = Metadata(
 
 
 QuickspecParameters = typing.TypedDict('QuickspecParameters', {
-    "__STYXTYPE__": typing.Literal["quickspec"],
+    "@type": typing.NotRequired[typing.Literal["afni/quickspec"]],
+    "tn": list[str],
+    "tsn": list[str],
+    "tsnad": typing.NotRequired[list[str] | None],
+    "tsnadm": typing.NotRequired[list[str] | None],
+    "tsnadl": typing.NotRequired[list[str] | None],
+    "spec": typing.NotRequired[str | None],
+    "help": bool,
+})
+QuickspecParametersTagged = typing.TypedDict('QuickspecParametersTagged', {
+    "@type": typing.Literal["afni/quickspec"],
     "tn": list[str],
     "tsn": list[str],
     "tsnad": typing.NotRequired[list[str] | None],
@@ -23,43 +33,11 @@ QuickspecParameters = typing.TypedDict('QuickspecParameters', {
     "spec": typing.NotRequired[str | None],
     "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 {
-        "quickspec": quickspec_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 {
-        "quickspec": quickspec_outputs,
-    }.get(t)
 
 
 class QuickspecOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `quickspec(...)`.
+    Output object returned when calling `QuickspecParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def quickspec_params(
     tsnadl: list[str] | None = None,
     spec: str | None = None,
     help_: bool = False,
-) -> QuickspecParameters:
+) -> QuickspecParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +72,7 @@ def quickspec_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "quickspec",
+        "@type": "afni/quickspec",
         "tn": tn,
         "tsn": tsn,
         "help": help_,
@@ -127,33 +105,33 @@ def quickspec_cargs(
     cargs.append("quickspec")
     cargs.extend([
         "-tn",
-        *params.get("tn")
+        *params.get("tn", None)
     ])
     cargs.extend([
         "-tsn",
-        *params.get("tsn")
+        *params.get("tsn", None)
     ])
-    if params.get("tsnad") is not None:
+    if params.get("tsnad", None) is not None:
         cargs.extend([
             "-tsnad",
-            *params.get("tsnad")
+            *params.get("tsnad", None)
         ])
-    if params.get("tsnadm") is not None:
+    if params.get("tsnadm", None) is not None:
         cargs.extend([
             "-tsnadm",
-            *params.get("tsnadm")
+            *params.get("tsnadm", None)
         ])
-    if params.get("tsnadl") is not None:
+    if params.get("tsnadl", None) is not None:
         cargs.extend([
             "-tsnadl",
-            *params.get("tsnadl")
+            *params.get("tsnadl", None)
         ])
-    if params.get("spec") is not None:
+    if params.get("spec", None) is not None:
         cargs.extend([
             "-spec",
-            params.get("spec")
+            params.get("spec", None)
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-h")
     return cargs
 
@@ -173,18 +151,20 @@ def quickspec_outputs(
     """
     ret = QuickspecOutputs(
         root=execution.output_file("."),
-        out_specfile=execution.output_file(params.get("spec")) if (params.get("spec") is not None) else None,
+        out_specfile=execution.output_file(params.get("spec", None)) if (params.get("spec") is not None) else None,
     )
     return ret
 
 
 def quickspec_execute(
     params: QuickspecParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> QuickspecOutputs:
     """
-    A quick and dirty way of loading a surface into SUMA or command line programs
-    using a spec file.
+    quickspec
+    
+    A quick and dirty way of loading a surface into SUMA or command line
+    programs using a spec file.
     
     Author: AFNI Developers
     
@@ -192,10 +172,12 @@ def quickspec_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `QuickspecOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QUICKSPEC_METADATA)
     params = execution.params(params)
     cargs = quickspec_cargs(params, execution)
     ret = quickspec_outputs(params, execution)
@@ -214,8 +196,10 @@ def quickspec(
     runner: Runner | None = None,
 ) -> QuickspecOutputs:
     """
-    A quick and dirty way of loading a surface into SUMA or command line programs
-    using a spec file.
+    quickspec
+    
+    A quick and dirty way of loading a surface into SUMA or command line
+    programs using a spec file.
     
     Author: AFNI Developers
     
@@ -236,8 +220,6 @@ def quickspec(
     Returns:
         NamedTuple of outputs (described in `QuickspecOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(QUICKSPEC_METADATA)
     params = quickspec_params(
         tn=tn,
         tsn=tsn,
@@ -247,13 +229,13 @@ def quickspec(
         spec=spec,
         help_=help_,
     )
-    return quickspec_execute(params, execution)
+    return quickspec_execute(params, runner)
 
 
 __all__ = [
     "QUICKSPEC_METADATA",
     "QuickspecOutputs",
-    "QuickspecParameters",
     "quickspec",
+    "quickspec_execute",
     "quickspec_params",
 ]