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

niwrap_afni/afni/surf_layers.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF_LAYERS_METADATA = Metadata(
-    id="5e9aa050f045ea0f592f85e3b66ef116c3891cbb.boutiques",
+    id="703511de3d8b8c18aa7ffa12f03522430f692e1c.boutiques",
     name="SurfLayers",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ SURF_LAYERS_METADATA = Metadata(
 
 
 SurfLayersParameters = typing.TypedDict('SurfLayersParameters', {
-    "__STYXTYPE__": typing.Literal["SurfLayers"],
+    "@type": typing.NotRequired[typing.Literal["afni/SurfLayers"]],
+    "spec_dset": typing.NotRequired[InputPathType | None],
+    "outdir": typing.NotRequired[str | None],
+    "states": typing.NotRequired[str | None],
+    "hemi": typing.NotRequired[str | None],
+    "n_intermed_surfs": typing.NotRequired[float | None],
+    "surf_a": typing.NotRequired[InputPathType | None],
+    "surf_b": typing.NotRequired[InputPathType | None],
+    "surf_intermed_pref": typing.NotRequired[str | None],
+    "echo": bool,
+    "no_clean": bool,
+})
+SurfLayersParametersTagged = typing.TypedDict('SurfLayersParametersTagged', {
+    "@type": typing.Literal["afni/SurfLayers"],
     "spec_dset": typing.NotRequired[InputPathType | None],
     "outdir": typing.NotRequired[str | None],
     "states": typing.NotRequired[str | None],
@@ -26,52 +39,16 @@ SurfLayersParameters = typing.TypedDict('SurfLayersParameters', {
     "echo": bool,
     "no_clean": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "SurfLayers": surf_layers_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 {
-        "SurfLayers": surf_layers_outputs,
-    }.get(t)
 
 
 class SurfLayersOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf_layers(...)`.
+    Output object returned when calling `SurfLayersParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    interpolated_surfaces: OutputPathType | None
-    """Interpolated surfaces files"""
-    additional_spec_files: OutputPathType | None
-    """Additional files if -spec option was used"""
-    run_view_script: OutputPathType | None
-    """Run script to view output directly"""
+    output_dir: OutputPathType | None
+    """Directory containing output files"""
 
 
 def surf_layers_params(
@@ -85,7 +62,7 @@ def surf_layers_params(
     surf_intermed_pref: str | None = None,
     echo: bool = False,
     no_clean: bool = False,
-) -> SurfLayersParameters:
+) -> SurfLayersParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +83,7 @@ def surf_layers_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SurfLayers",
+        "@type": "afni/SurfLayers",
         "echo": echo,
         "no_clean": no_clean,
     }
@@ -144,49 +121,49 @@ def surf_layers_cargs(
     """
     cargs = []
     cargs.append("SurfLayers")
-    if params.get("spec_dset") is not None:
+    if params.get("spec_dset", None) is not None:
         cargs.extend([
             "-spec",
-            execution.input_file(params.get("spec_dset"))
+            execution.input_file(params.get("spec_dset", None))
         ])
-    if params.get("outdir") is not None:
+    if params.get("outdir", None) is not None:
         cargs.extend([
             "-outdir",
-            params.get("outdir")
+            params.get("outdir", None)
         ])
-    if params.get("states") is not None:
+    if params.get("states", None) is not None:
         cargs.extend([
             "-states",
-            params.get("states")
+            params.get("states", None)
         ])
-    if params.get("hemi") is not None:
+    if params.get("hemi", None) is not None:
         cargs.extend([
             "-hemi",
-            params.get("hemi")
+            params.get("hemi", None)
         ])
-    if params.get("n_intermed_surfs") is not None:
+    if params.get("n_intermed_surfs", None) is not None:
         cargs.extend([
             "-n_intermed_surfs",
-            str(params.get("n_intermed_surfs"))
+            str(params.get("n_intermed_surfs", None))
         ])
-    if params.get("surf_a") is not None:
+    if params.get("surf_a", None) is not None:
         cargs.extend([
             "-surf_A",
-            execution.input_file(params.get("surf_a"))
+            execution.input_file(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",
-            execution.input_file(params.get("surf_b"))
+            execution.input_file(params.get("surf_b", None))
         ])
-    if params.get("surf_intermed_pref") is not None:
+    if params.get("surf_intermed_pref", None) is not None:
         cargs.extend([
             "-surf_intermed_pref",
-            params.get("surf_intermed_pref")
+            params.get("surf_intermed_pref", None)
         ])
-    if params.get("echo"):
+    if params.get("echo", False):
         cargs.append("-echo")
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
     return cargs
 
@@ -206,18 +183,18 @@ def surf_layers_outputs(
     """
     ret = SurfLayersOutputs(
         root=execution.output_file("."),
-        interpolated_surfaces=execution.output_file(params.get("outdir") + "/isurf." + params.get("hemi") + ".*.gii") if (params.get("outdir") is not None and params.get("hemi") is not None) else None,
-        additional_spec_files=execution.output_file(params.get("outdir") + "/*") if (params.get("outdir") is not None) else None,
-        run_view_script=execution.output_file(params.get("outdir") + "/run*tcsh") if (params.get("outdir") is not None) else None,
+        output_dir=execution.output_file(params.get("outdir", None)) if (params.get("outdir") is not None) else None,
     )
     return ret
 
 
 def surf_layers_execute(
     params: SurfLayersParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfLayersOutputs:
     """
+    SurfLayers
+    
     Compute intermediate equi-distant surfaces between two boundary surfaces.
     
     Author: AFNI Developers
@@ -226,10 +203,12 @@ def surf_layers_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfLayersOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_LAYERS_METADATA)
     params = execution.params(params)
     cargs = surf_layers_cargs(params, execution)
     ret = surf_layers_outputs(params, execution)
@@ -251,6 +230,8 @@ def surf_layers(
     runner: Runner | None = None,
 ) -> SurfLayersOutputs:
     """
+    SurfLayers
+    
     Compute intermediate equi-distant surfaces between two boundary surfaces.
     
     Author: AFNI Developers
@@ -274,8 +255,6 @@ def surf_layers(
     Returns:
         NamedTuple of outputs (described in `SurfLayersOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF_LAYERS_METADATA)
     params = surf_layers_params(
         spec_dset=spec_dset,
         outdir=outdir,
@@ -288,13 +267,13 @@ def surf_layers(
         echo=echo,
         no_clean=no_clean,
     )
-    return surf_layers_execute(params, execution)
+    return surf_layers_execute(params, runner)
 
 
 __all__ = [
     "SURF_LAYERS_METADATA",
     "SurfLayersOutputs",
-    "SurfLayersParameters",
     "surf_layers",
+    "surf_layers_execute",
     "surf_layers_params",
 ]

niwrap_afni/afni/surf_localstat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF_LOCALSTAT_METADATA = Metadata(
-    id="68d36b45710d5771191842721ee9dc58a7e2c6f9.boutiques",
+    id="8a12a6d69e93058f704ee707c378a9b21f748a8e.boutiques",
     name="SurfLocalstat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ SURF_LOCALSTAT_METADATA = Metadata(
 
 
 SurfLocalstatParameters = typing.TypedDict('SurfLocalstatParameters', {
-    "__STYXTYPE__": typing.Literal["SurfLocalstat"],
+    "@type": typing.NotRequired[typing.Literal["afni/SurfLocalstat"]],
+    "hood": typing.NotRequired[float | None],
+    "nbhd_rad": typing.NotRequired[float | None],
+    "prefix": str,
+    "stat": typing.Literal["mean", "mode", "num", "FWHM", "ALL"],
+    "input_dataset": InputPathType,
+    "surface": InputPathType,
+})
+SurfLocalstatParametersTagged = typing.TypedDict('SurfLocalstatParametersTagged', {
+    "@type": typing.Literal["afni/SurfLocalstat"],
     "hood": typing.NotRequired[float | None],
     "nbhd_rad": typing.NotRequired[float | None],
     "prefix": str,
@@ -22,43 +31,11 @@ SurfLocalstatParameters = typing.TypedDict('SurfLocalstatParameters', {
     "input_dataset": InputPathType,
     "surface": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "SurfLocalstat": surf_localstat_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 {
-        "SurfLocalstat": surf_localstat_outputs,
-    }.get(t)
 
 
 class SurfLocalstatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf_localstat(...)`.
+    Output object returned when calling `SurfLocalstatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def surf_localstat_params(
     surface: InputPathType,
     hood: float | None = None,
     nbhd_rad: float | None = None,
-) -> SurfLocalstatParameters:
+) -> SurfLocalstatParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def surf_localstat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SurfLocalstat",
+        "@type": "afni/SurfLocalstat",
         "prefix": prefix,
         "stat": stat_,
         "input_dataset": input_dataset,
@@ -118,31 +95,31 @@ def surf_localstat_cargs(
     """
     cargs = []
     cargs.append("SurfLocalstat")
-    if params.get("hood") is not None:
+    if params.get("hood", None) is not None:
         cargs.extend([
             "-hood",
-            str(params.get("hood"))
+            str(params.get("hood", None))
         ])
-    if params.get("nbhd_rad") is not None:
+    if params.get("nbhd_rad", None) is not None:
         cargs.extend([
             "-nbhd_rad",
-            str(params.get("nbhd_rad"))
+            str(params.get("nbhd_rad", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "-stat",
-        params.get("stat")
+        params.get("stat", None)
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_dataset"))
+        execution.input_file(params.get("input_dataset", None))
     ])
     cargs.extend([
         "-i_gii",
-        execution.input_file(params.get("surface"))
+        execution.input_file(params.get("surface", None))
     ])
     return cargs
 
@@ -162,16 +139,18 @@ def surf_localstat_outputs(
     """
     ret = SurfLocalstatOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".niml.dset"),
+        output_file=execution.output_file(params.get("prefix", None) + ".niml.dset"),
     )
     return ret
 
 
 def surf_localstat_execute(
     params: SurfLocalstatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfLocalstatOutputs:
     """
+    SurfLocalstat
+    
     Compute local statistics on a surface mesh.
     
     Author: AFNI Developers
@@ -180,10 +159,12 @@ def surf_localstat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfLocalstatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_LOCALSTAT_METADATA)
     params = execution.params(params)
     cargs = surf_localstat_cargs(params, execution)
     ret = surf_localstat_outputs(params, execution)
@@ -201,6 +182,8 @@ def surf_localstat(
     runner: Runner | None = None,
 ) -> SurfLocalstatOutputs:
     """
+    SurfLocalstat
+    
     Compute local statistics on a surface mesh.
     
     Author: AFNI Developers
@@ -220,8 +203,6 @@ def surf_localstat(
     Returns:
         NamedTuple of outputs (described in `SurfLocalstatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF_LOCALSTAT_METADATA)
     params = surf_localstat_params(
         hood=hood,
         nbhd_rad=nbhd_rad,
@@ -230,13 +211,13 @@ def surf_localstat(
         input_dataset=input_dataset,
         surface=surface,
     )
-    return surf_localstat_execute(params, execution)
+    return surf_localstat_execute(params, runner)
 
 
 __all__ = [
     "SURF_LOCALSTAT_METADATA",
     "SurfLocalstatOutputs",
-    "SurfLocalstatParameters",
     "surf_localstat",
+    "surf_localstat_execute",
     "surf_localstat_params",
 ]