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

niwrap_afni/afni/pta.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PTA_METADATA = Metadata(
-    id="d6f381ad3d83e22142bf2f95cc5bcacf92678029.boutiques",
+    id="68b75e168798ae5dc1df3f812b938ff85744d71e.boutiques",
     name="PTA",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ PTA_METADATA = Metadata(
 
 
 PtaParameters = typing.TypedDict('PtaParameters', {
-    "__STYXTYPE__": typing.Literal["PTA"],
+    "@type": typing.NotRequired[typing.Literal["afni/PTA"]],
+    "prefix": str,
+    "input_file": InputPathType,
+    "model_formula": str,
+    "vt_formulation": typing.NotRequired[str | None],
+    "prediction_table": typing.NotRequired[InputPathType | None],
+    "verbosity_level": typing.NotRequired[float | None],
+    "response_var": typing.NotRequired[str | None],
+    "dbg_args": bool,
+})
+PtaParametersTagged = typing.TypedDict('PtaParametersTagged', {
+    "@type": typing.Literal["afni/PTA"],
     "prefix": str,
     "input_file": InputPathType,
     "model_formula": str,
@@ -24,43 +35,11 @@ PtaParameters = typing.TypedDict('PtaParameters', {
     "response_var": typing.NotRequired[str | None],
     "dbg_args": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "PTA": pta_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 {
-        "PTA": pta_outputs,
-    }.get(t)
 
 
 class PtaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `pta(...)`.
+    Output object returned when calling `PtaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +58,7 @@ def pta_params(
     verbosity_level: float | None = None,
     response_var: str | None = None,
     dbg_args: bool = False,
-) -> PtaParameters:
+) -> PtaParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +81,7 @@ def pta_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "PTA",
+        "@type": "afni/PTA",
         "prefix": prefix,
         "input_file": input_file,
         "model_formula": model_formula,
@@ -136,37 +115,37 @@ def pta_cargs(
     cargs.append("PTA")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-model",
-        params.get("model_formula")
+        params.get("model_formula", None)
     ])
-    if params.get("vt_formulation") is not None:
+    if params.get("vt_formulation", None) is not None:
         cargs.extend([
             "-vt",
-            params.get("vt_formulation")
+            params.get("vt_formulation", None)
         ])
-    if params.get("prediction_table") is not None:
+    if params.get("prediction_table", None) is not None:
         cargs.extend([
             "-prediction",
-            execution.input_file(params.get("prediction_table"))
+            execution.input_file(params.get("prediction_table", None))
         ])
-    if params.get("verbosity_level") is not None:
+    if params.get("verbosity_level", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity_level"))
+            str(params.get("verbosity_level", None))
         ])
-    if params.get("response_var") is not None:
+    if params.get("response_var", None) is not None:
         cargs.extend([
             "-Y",
-            params.get("response_var")
+            params.get("response_var", None)
         ])
-    if params.get("dbg_args"):
+    if params.get("dbg_args", False):
         cargs.append("-dbgArgs")
     return cargs
 
@@ -186,19 +165,21 @@ def pta_outputs(
     """
     ret = PtaOutputs(
         root=execution.output_file("."),
-        stat_output=execution.output_file(params.get("prefix") + "-stat.txt"),
-        prediction_output=execution.output_file(params.get("prefix") + "-prediction.txt"),
+        stat_output=execution.output_file(params.get("prefix", None) + "-stat.txt"),
+        prediction_output=execution.output_file(params.get("prefix", None) + "-prediction.txt"),
     )
     return ret
 
 
 def pta_execute(
     params: PtaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> PtaOutputs:
     """
-    Program for Profile Tracking Analysis - estimates nonlinear trajectories through
-    smoothing splines.
+    PTA
+    
+    Program for Profile Tracking Analysis - estimates nonlinear trajectories
+    through smoothing splines.
     
     Author: AFNI Developers
     
@@ -206,10 +187,12 @@ def pta_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `PtaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PTA_METADATA)
     params = execution.params(params)
     cargs = pta_cargs(params, execution)
     ret = pta_outputs(params, execution)
@@ -229,8 +212,10 @@ def pta(
     runner: Runner | None = None,
 ) -> PtaOutputs:
     """
-    Program for Profile Tracking Analysis - estimates nonlinear trajectories through
-    smoothing splines.
+    PTA
+    
+    Program for Profile Tracking Analysis - estimates nonlinear trajectories
+    through smoothing splines.
     
     Author: AFNI Developers
     
@@ -255,8 +240,6 @@ def pta(
     Returns:
         NamedTuple of outputs (described in `PtaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(PTA_METADATA)
     params = pta_params(
         prefix=prefix,
         input_file=input_file,
@@ -267,13 +250,13 @@ def pta(
         response_var=response_var,
         dbg_args=dbg_args,
     )
-    return pta_execute(params, execution)
+    return pta_execute(params, runner)
 
 
 __all__ = [
     "PTA_METADATA",
     "PtaOutputs",
-    "PtaParameters",
     "pta",
+    "pta_execute",
     "pta_params",
 ]

niwrap_afni/afni/qdelaunay.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 QDELAUNAY_METADATA = Metadata(
-    id="a916e82e97bc11f21ddb66b1db2b18fd597bc7b9.boutiques",
+    id="ecc6f97824991f4e3883e38ef135e15cee110aeb.boutiques",
     name="qdelaunay",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,43 @@ QDELAUNAY_METADATA = Metadata(
 
 
 QdelaunayParameters = typing.TypedDict('QdelaunayParameters', {
-    "__STYXTYPE__": typing.Literal["qdelaunay"],
+    "@type": typing.NotRequired[typing.Literal["afni/qdelaunay"]],
+    "input_file": InputPathType,
+    "furthest_site": bool,
+    "triangulated_output": bool,
+    "joggled_input": bool,
+    "joggle_range": typing.NotRequired[float | None],
+    "search_simplex": bool,
+    "point_infinity": bool,
+    "delaunay_visible": typing.NotRequired[str | None],
+    "delaunay_regions": typing.NotRequired[str | None],
+    "trace_level": typing.NotRequired[float | None],
+    "check": bool,
+    "statistics": bool,
+    "verify": bool,
+    "output_stdout": bool,
+    "facets_summary": typing.NotRequired[float | None],
+    "input_file_option": typing.NotRequired[InputPathType | None],
+    "output_file_option": typing.NotRequired[InputPathType | None],
+    "trace_point": typing.NotRequired[float | None],
+    "trace_merge": typing.NotRequired[float | None],
+    "trace_merge_width": typing.NotRequired[float | None],
+    "stop_point": typing.NotRequired[float | None],
+    "stop_cone_point": typing.NotRequired[float | None],
+    "centrum_radius": typing.NotRequired[float | None],
+    "max_angle_cosine": typing.NotRequired[float | None],
+    "perturb_factor": typing.NotRequired[float | None],
+    "min_facet_width": typing.NotRequired[float | None],
+    "facet_dump": bool,
+    "geomview": bool,
+    "vertices_incident": bool,
+    "mathematica": bool,
+    "off_format": bool,
+    "point_coordinates": bool,
+    "summary": bool,
+})
+QdelaunayParametersTagged = typing.TypedDict('QdelaunayParametersTagged', {
+    "@type": typing.Literal["afni/qdelaunay"],
     "input_file": InputPathType,
     "furthest_site": bool,
     "triangulated_output": bool,
@@ -49,42 +85,11 @@ QdelaunayParameters = typing.TypedDict('QdelaunayParameters', {
     "point_coordinates": bool,
     "summary": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "qdelaunay": qdelaunay_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 QdelaunayOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `qdelaunay(...)`.
+    Output object returned when calling `QdelaunayParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -124,7 +129,7 @@ def qdelaunay_params(
     off_format: bool = False,
     point_coordinates: bool = False,
     summary: bool = False,
-) -> QdelaunayParameters:
+) -> QdelaunayParametersTagged:
     """
     Build parameters.
     
@@ -171,7 +176,7 @@ def qdelaunay_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "qdelaunay",
+        "@type": "afni/qdelaunay",
         "input_file": input_file,
         "furthest_site": furthest_site,
         "triangulated_output": triangulated_output,
@@ -240,118 +245,118 @@ def qdelaunay_cargs(
     """
     cargs = []
     cargs.append("qdelaunay")
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("furthest_site"):
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    if params.get("furthest_site", False):
         cargs.append("Qu")
-    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("joggle_range") is not None:
+    if params.get("joggle_range", None) is not None:
         cargs.extend([
             "QJn",
-            str(params.get("joggle_range"))
+            str(params.get("joggle_range", None))
         ])
-    if params.get("search_simplex"):
+    if params.get("search_simplex", False):
         cargs.append("Qs")
-    if params.get("point_infinity"):
+    if params.get("point_infinity", False):
         cargs.append("Qz")
-    if params.get("delaunay_visible") is not None:
+    if params.get("delaunay_visible", None) is not None:
         cargs.extend([
             "QGn",
-            params.get("delaunay_visible")
+            params.get("delaunay_visible", None)
         ])
-    if params.get("delaunay_regions") is not None:
+    if params.get("delaunay_regions", None) is not None:
         cargs.extend([
             "QVn",
-            params.get("delaunay_regions")
+            params.get("delaunay_regions", None)
         ])
-    if params.get("trace_level") is not None:
+    if params.get("trace_level", None) is not None:
         cargs.extend([
             "T4",
-            str(params.get("trace_level"))
+            str(params.get("trace_level", None))
         ])
-    if params.get("check"):
+    if params.get("check", False):
         cargs.append("Tc")
-    if params.get("statistics"):
+    if params.get("statistics", False):
         cargs.append("Ts")
-    if params.get("verify"):
+    if params.get("verify", False):
         cargs.append("Tv")
-    if params.get("output_stdout"):
+    if params.get("output_stdout", False):
         cargs.append("Tz")
-    if params.get("facets_summary") is not None:
+    if params.get("facets_summary", None) is not None:
         cargs.extend([
             "TFn",
-            str(params.get("facets_summary"))
+            str(params.get("facets_summary", None))
         ])
-    if params.get("input_file_option") is not None:
+    if params.get("input_file_option", None) is not None:
         cargs.extend([
             "TI",
-            execution.input_file(params.get("input_file_option"))
+            execution.input_file(params.get("input_file_option", None))
         ])
-    if params.get("output_file_option") is not None:
+    if params.get("output_file_option", None) is not None:
         cargs.extend([
             "TO",
-            execution.input_file(params.get("output_file_option"))
+            execution.input_file(params.get("output_file_option", None))
         ])
-    if params.get("trace_point") is not None:
+    if params.get("trace_point", None) is not None:
         cargs.extend([
             "TPn",
-            str(params.get("trace_point"))
+            str(params.get("trace_point", None))
         ])
-    if params.get("trace_merge") is not None:
+    if params.get("trace_merge", None) is not None:
         cargs.extend([
             "TMn",
-            str(params.get("trace_merge"))
+            str(params.get("trace_merge", None))
         ])
-    if params.get("trace_merge_width") is not None:
+    if params.get("trace_merge_width", None) is not None:
         cargs.extend([
             "TWn",
-            str(params.get("trace_merge_width"))
+            str(params.get("trace_merge_width", None))
         ])
-    if params.get("stop_point") is not None:
+    if params.get("stop_point", None) is not None:
         cargs.extend([
             "TVn",
-            str(params.get("stop_point"))
+            str(params.get("stop_point", None))
         ])
-    if params.get("stop_cone_point") is not None:
+    if params.get("stop_cone_point", None) is not None:
         cargs.extend([
             "TCn",
-            str(params.get("stop_cone_point"))
+            str(params.get("stop_cone_point", None))
         ])
-    if params.get("centrum_radius") is not None:
+    if params.get("centrum_radius", None) is not None:
         cargs.extend([
             "Cn",
-            str(params.get("centrum_radius"))
+            str(params.get("centrum_radius", None))
         ])
-    if params.get("max_angle_cosine") is not None:
+    if params.get("max_angle_cosine", None) is not None:
         cargs.extend([
             "An",
-            str(params.get("max_angle_cosine"))
+            str(params.get("max_angle_cosine", None))
         ])
-    if params.get("perturb_factor") is not None:
+    if params.get("perturb_factor", None) is not None:
         cargs.extend([
             "Rn",
-            str(params.get("perturb_factor"))
+            str(params.get("perturb_factor", None))
         ])
-    if params.get("min_facet_width") is not None:
+    if params.get("min_facet_width", None) is not None:
         cargs.extend([
             "Wn",
-            str(params.get("min_facet_width"))
+            str(params.get("min_facet_width", None))
         ])
-    if params.get("facet_dump"):
+    if params.get("facet_dump", False):
         cargs.append("f")
-    if params.get("geomview"):
+    if params.get("geomview", False):
         cargs.append("G")
-    if params.get("vertices_incident"):
+    if params.get("vertices_incident", False):
         cargs.append("i")
-    if params.get("mathematica"):
+    if params.get("mathematica", False):
         cargs.append("m")
-    if params.get("off_format"):
+    if params.get("off_format", False):
         cargs.append("o")
-    if params.get("point_coordinates"):
+    if params.get("point_coordinates", False):
         cargs.append("p")
-    if params.get("summary"):
+    if params.get("summary", False):
         cargs.append("s")
     return cargs
 
@@ -377,9 +382,11 @@ def qdelaunay_outputs(
 
 def qdelaunay_execute(
     params: QdelaunayParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> QdelaunayOutputs:
     """
+    qdelaunay
+    
     Compute the Delaunay triangulation using Qhull.
     
     Author: AFNI Developers
@@ -388,10 +395,12 @@ def qdelaunay_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `QdelaunayOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QDELAUNAY_METADATA)
     params = execution.params(params)
     cargs = qdelaunay_cargs(params, execution)
     ret = qdelaunay_outputs(params, execution)
@@ -436,6 +445,8 @@ def qdelaunay(
     runner: Runner | None = None,
 ) -> QdelaunayOutputs:
     """
+    qdelaunay
+    
     Compute the Delaunay triangulation using Qhull.
     
     Author: AFNI Developers
@@ -485,8 +496,6 @@ def qdelaunay(
     Returns:
         NamedTuple of outputs (described in `QdelaunayOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(QDELAUNAY_METADATA)
     params = qdelaunay_params(
         input_file=input_file,
         furthest_site=furthest_site,
@@ -522,13 +531,13 @@ def qdelaunay(
         point_coordinates=point_coordinates,
         summary=summary,
     )
-    return qdelaunay_execute(params, execution)
+    return qdelaunay_execute(params, runner)
 
 
 __all__ = [
     "QDELAUNAY_METADATA",
     "QdelaunayOutputs",
-    "QdelaunayParameters",
     "qdelaunay",
+    "qdelaunay_execute",
     "qdelaunay_params",
 ]