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

niwrap_afni/afni/v_3d_localstat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LOCALSTAT_METADATA = Metadata(
-    id="b6832c9a6c0ede2cc09453d38680dba0ddb4cbb6.boutiques",
+    id="15d18f8099c45acdfeb4986ad42670c840553014.boutiques",
     name="3dLocalstat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,30 @@ V_3D_LOCALSTAT_METADATA = Metadata(
 
 
 V3dLocalstatParameters = typing.TypedDict('V3dLocalstatParameters', {
-    "__STYXTYPE__": typing.Literal["3dLocalstat"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLocalstat"]],
+    "dataset": InputPathType,
+    "nbhd": str,
+    "stat": typing.NotRequired[list[str] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "use_nonmask": bool,
+    "prefix": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[str | None],
+    "label_ext": typing.NotRequired[str | None],
+    "reduce_grid": typing.NotRequired[list[float] | None],
+    "reduce_restore_grid": typing.NotRequired[list[float] | None],
+    "reduce_max_vox": typing.NotRequired[float | None],
+    "grid_rmode": typing.NotRequired[str | None],
+    "quiet": bool,
+    "verbose": bool,
+    "proceed_small_N": bool,
+    "fillvalue": typing.NotRequired[float | None],
+    "unfillvalue": typing.NotRequired[float | None],
+    "maskvalue": typing.NotRequired[float | None],
+    "maskvalue2": typing.NotRequired[float | None],
+})
+V3dLocalstatParametersTagged = typing.TypedDict('V3dLocalstatParametersTagged', {
+    "@type": typing.Literal["afni/3dLocalstat"],
     "dataset": InputPathType,
     "nbhd": str,
     "stat": typing.NotRequired[list[str] | None],
@@ -36,43 +59,11 @@ V3dLocalstatParameters = typing.TypedDict('V3dLocalstatParameters', {
     "maskvalue": typing.NotRequired[float | None],
     "maskvalue2": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dLocalstat": v_3d_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 {
-        "3dLocalstat": v_3d_localstat_outputs,
-    }.get(t)
 
 
 class V3dLocalstatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_localstat(...)`.
+    Output object returned when calling `V3dLocalstatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +92,7 @@ def v_3d_localstat_params(
     unfillvalue: float | None = None,
     maskvalue: float | None = None,
     maskvalue2: float | None = None,
-) -> V3dLocalstatParameters:
+) -> V3dLocalstatParametersTagged:
     """
     Build parameters.
     
@@ -142,7 +133,7 @@ def v_3d_localstat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLocalstat",
+        "@type": "afni/3dLocalstat",
         "dataset": dataset,
         "nbhd": nbhd,
         "automask": automask,
@@ -195,85 +186,85 @@ def v_3d_localstat_cargs(
     """
     cargs = []
     cargs.append("3dLocalstat")
-    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(execution.input_file(params.get("dataset", None)))
     cargs.extend([
         "-nbhd",
-        params.get("nbhd")
+        params.get("nbhd", None)
     ])
-    if params.get("stat") is not None:
+    if params.get("stat", None) is not None:
         cargs.extend([
             "-stat",
-            *params.get("stat")
+            *params.get("stat", None)
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("use_nonmask"):
+    if params.get("use_nonmask", False):
         cargs.append("-use_nonmask")
-    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("datum") is not None:
+    if params.get("datum", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datum")
+            params.get("datum", None)
         ])
-    if params.get("label_ext") is not None:
+    if params.get("label_ext", None) is not None:
         cargs.extend([
             "-label_ext",
-            params.get("label_ext")
+            params.get("label_ext", None)
         ])
-    if params.get("reduce_grid") is not None:
+    if params.get("reduce_grid", None) is not None:
         cargs.extend([
             "-reduce_grid",
-            *map(str, params.get("reduce_grid"))
+            *map(str, params.get("reduce_grid", None))
         ])
-    if params.get("reduce_restore_grid") is not None:
+    if params.get("reduce_restore_grid", None) is not None:
         cargs.extend([
             "-reduce_restore_grid",
-            *map(str, params.get("reduce_restore_grid"))
+            *map(str, params.get("reduce_restore_grid", None))
         ])
-    if params.get("reduce_max_vox") is not None:
+    if params.get("reduce_max_vox", None) is not None:
         cargs.extend([
             "-reduce_max_vox",
-            str(params.get("reduce_max_vox"))
+            str(params.get("reduce_max_vox", None))
         ])
-    if params.get("grid_rmode") is not None:
+    if params.get("grid_rmode", None) is not None:
         cargs.extend([
             "-grid_rmode",
-            params.get("grid_rmode")
+            params.get("grid_rmode", None)
         ])
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("proceed_small_N"):
+    if params.get("proceed_small_N", False):
         cargs.append("-proceed_small_N")
-    if params.get("fillvalue") is not None:
+    if params.get("fillvalue", None) is not None:
         cargs.extend([
             "-fillvalue",
-            str(params.get("fillvalue"))
+            str(params.get("fillvalue", None))
         ])
-    if params.get("unfillvalue") is not None:
+    if params.get("unfillvalue", None) is not None:
         cargs.extend([
             "-unfillvalue",
-            str(params.get("unfillvalue"))
+            str(params.get("unfillvalue", None))
         ])
-    if params.get("maskvalue") is not None:
+    if params.get("maskvalue", None) is not None:
         cargs.extend([
             "-maskvalue",
-            str(params.get("maskvalue"))
+            str(params.get("maskvalue", None))
         ])
-    if params.get("maskvalue2") is not None:
+    if params.get("maskvalue2", None) is not None:
         cargs.extend([
             "-maskvalue2",
-            str(params.get("maskvalue2"))
+            str(params.get("maskvalue2", None))
         ])
     return cargs
 
@@ -293,18 +284,20 @@ def v_3d_localstat_outputs(
     """
     ret = V3dLocalstatOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        outfile=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_localstat_execute(
     params: V3dLocalstatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLocalstatOutputs:
     """
-    This program computes statistics at each voxel, based on a local neighborhood of
-    that voxel.
+    3dLocalstat
+    
+    This program computes statistics at each voxel, based on a local
+    neighborhood of that voxel.
     
     Author: AFNI Developers
     
@@ -312,10 +305,12 @@ def v_3d_localstat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLocalstatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCALSTAT_METADATA)
     params = execution.params(params)
     cargs = v_3d_localstat_cargs(params, execution)
     ret = v_3d_localstat_outputs(params, execution)
@@ -347,8 +342,10 @@ def v_3d_localstat(
     runner: Runner | None = None,
 ) -> V3dLocalstatOutputs:
     """
-    This program computes statistics at each voxel, based on a local neighborhood of
-    that voxel.
+    3dLocalstat
+    
+    This program computes statistics at each voxel, based on a local
+    neighborhood of that voxel.
     
     Author: AFNI Developers
     
@@ -391,8 +388,6 @@ def v_3d_localstat(
     Returns:
         NamedTuple of outputs (described in `V3dLocalstatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LOCALSTAT_METADATA)
     params = v_3d_localstat_params(
         dataset=dataset,
         nbhd=nbhd,
@@ -415,13 +410,13 @@ def v_3d_localstat(
         maskvalue=maskvalue,
         maskvalue2=maskvalue2,
     )
-    return v_3d_localstat_execute(params, execution)
+    return v_3d_localstat_execute(params, runner)
 
 
 __all__ = [
     "V3dLocalstatOutputs",
-    "V3dLocalstatParameters",
     "V_3D_LOCALSTAT_METADATA",
     "v_3d_localstat",
+    "v_3d_localstat_execute",
     "v_3d_localstat_params",
 ]

niwrap_afni/afni/v_3d_lomb_scargle.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LOMB_SCARGLE_METADATA = Metadata(
-    id="9e597a7312ee6b69d649017dd3754eea9c3d47b9.boutiques",
+    id="3eb111bc9d1c9d69174403521850d208bfb9c167.boutiques",
     name="3dLombScargle",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_LOMB_SCARGLE_METADATA = Metadata(
 
 
 V3dLombScargleParameters = typing.TypedDict('V3dLombScargleParameters', {
-    "__STYXTYPE__": typing.Literal["3dLombScargle"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLombScargle"]],
+    "prefix": str,
+    "inset": InputPathType,
+    "censor_1d": typing.NotRequired[InputPathType | None],
+    "censor_string": typing.NotRequired[str | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "out_pow_spec": bool,
+    "nyquist_multiplier": typing.NotRequired[int | None],
+    "nifti": bool,
+})
+V3dLombScargleParametersTagged = typing.TypedDict('V3dLombScargleParametersTagged', {
+    "@type": typing.Literal["afni/3dLombScargle"],
     "prefix": str,
     "inset": InputPathType,
     "censor_1d": typing.NotRequired[InputPathType | None],
@@ -24,43 +35,11 @@ V3dLombScargleParameters = typing.TypedDict('V3dLombScargleParameters', {
     "nyquist_multiplier": typing.NotRequired[int | None],
     "nifti": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dLombScargle": v_3d_lomb_scargle_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 {
-        "3dLombScargle": v_3d_lomb_scargle_outputs,
-    }.get(t)
 
 
 class V3dLombScargleOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_lomb_scargle(...)`.
+    Output object returned when calling `V3dLombScargleParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +64,7 @@ def v_3d_lomb_scargle_params(
     out_pow_spec: bool = False,
     nyquist_multiplier: int | None = None,
     nifti: bool = False,
-) -> V3dLombScargleParameters:
+) -> V3dLombScargleParametersTagged:
     """
     Build parameters.
     
@@ -119,7 +98,7 @@ def v_3d_lomb_scargle_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLombScargle",
+        "@type": "afni/3dLombScargle",
         "prefix": prefix,
         "inset": inset,
         "out_pow_spec": out_pow_spec,
@@ -153,35 +132,35 @@ def v_3d_lomb_scargle_cargs(
     cargs.append("3dLombScargle")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "-inset",
-        execution.input_file(params.get("inset"))
+        execution.input_file(params.get("inset", None))
     ])
-    if params.get("censor_1d") is not None:
+    if params.get("censor_1d", None) is not None:
         cargs.extend([
             "-censor_1D",
-            execution.input_file(params.get("censor_1d"))
+            execution.input_file(params.get("censor_1d", None))
         ])
-    if params.get("censor_string") is not None:
+    if params.get("censor_string", None) is not None:
         cargs.extend([
             "-censor_str",
-            params.get("censor_string")
+            params.get("censor_string", None)
         ])
-    if params.get("mask_file") is not None:
+    if params.get("mask_file", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_file"))
+            execution.input_file(params.get("mask_file", None))
         ])
-    if params.get("out_pow_spec"):
+    if params.get("out_pow_spec", False):
         cargs.append("-out_pow_spec")
-    if params.get("nyquist_multiplier") is not None:
+    if params.get("nyquist_multiplier", None) is not None:
         cargs.extend([
             "-nyq_mult",
-            str(params.get("nyquist_multiplier"))
+            str(params.get("nyquist_multiplier", None))
         ])
-    if params.get("nifti"):
+    if params.get("nifti", False):
         cargs.append("-nifti")
     return cargs
 
@@ -201,19 +180,21 @@ def v_3d_lomb_scargle_outputs(
     """
     ret = V3dLombScargleOutputs(
         root=execution.output_file("."),
-        time_points=execution.output_file(params.get("prefix") + "_time.1D"),
-        frequency_points=execution.output_file(params.get("prefix") + "_freq.1D"),
-        amplitude_spectrum=execution.output_file(params.get("prefix") + "_amp+orig"),
-        power_spectrum=execution.output_file(params.get("prefix") + "_pow+orig"),
+        time_points=execution.output_file(params.get("prefix", None) + "_time.1D"),
+        frequency_points=execution.output_file(params.get("prefix", None) + "_freq.1D"),
+        amplitude_spectrum=execution.output_file(params.get("prefix", None) + "_amp+orig"),
+        power_spectrum=execution.output_file(params.get("prefix", None) + "_pow+orig"),
     )
     return ret
 
 
 def v_3d_lomb_scargle_execute(
     params: V3dLombScargleParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLombScargleOutputs:
     """
+    3dLombScargle
+    
     Make a periodogram or amplitude-spectrum of a time series that has a
     non-constant sampling rate.
     
@@ -223,10 +204,12 @@ def v_3d_lomb_scargle_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLombScargleOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOMB_SCARGLE_METADATA)
     params = execution.params(params)
     cargs = v_3d_lomb_scargle_cargs(params, execution)
     ret = v_3d_lomb_scargle_outputs(params, execution)
@@ -246,6 +229,8 @@ def v_3d_lomb_scargle(
     runner: Runner | None = None,
 ) -> V3dLombScargleOutputs:
     """
+    3dLombScargle
+    
     Make a periodogram or amplitude-spectrum of a time series that has a
     non-constant sampling rate.
     
@@ -283,8 +268,6 @@ def v_3d_lomb_scargle(
     Returns:
         NamedTuple of outputs (described in `V3dLombScargleOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LOMB_SCARGLE_METADATA)
     params = v_3d_lomb_scargle_params(
         prefix=prefix,
         inset=inset,
@@ -295,13 +278,13 @@ def v_3d_lomb_scargle(
         nyquist_multiplier=nyquist_multiplier,
         nifti=nifti,
     )
-    return v_3d_lomb_scargle_execute(params, execution)
+    return v_3d_lomb_scargle_execute(params, runner)
 
 
 __all__ = [
     "V3dLombScargleOutputs",
-    "V3dLombScargleParameters",
     "V_3D_LOMB_SCARGLE_METADATA",
     "v_3d_lomb_scargle",
+    "v_3d_lomb_scargle_execute",
     "v_3d_lomb_scargle_params",
 ]