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

niwrap_afni/afni/v_3d_local_acf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LOCAL_ACF_METADATA = Metadata(
-    id="32095b9bbd35f01f1c52608c8dca1936fd86022e.boutiques",
+    id="13a5cf4d62e86aaa1c39140c70391cd1c06bc003.boutiques",
     name="3dLocalACF",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V_3D_LOCAL_ACF_METADATA = Metadata(
 
 
 V3dLocalAcfParameters = typing.TypedDict('V3dLocalAcfParameters', {
-    "__STYXTYPE__": typing.Literal["3dLocalACF"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLocalACF"]],
+    "prefix": str,
+    "input_file": InputPathType,
+    "neighborhood": typing.NotRequired[str | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "auto_mask": bool,
+})
+V3dLocalAcfParametersTagged = typing.TypedDict('V3dLocalAcfParametersTagged', {
+    "@type": typing.Literal["afni/3dLocalACF"],
     "prefix": str,
     "input_file": InputPathType,
     "neighborhood": typing.NotRequired[str | None],
     "mask_file": typing.NotRequired[InputPathType | None],
     "auto_mask": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dLocalACF": v_3d_local_acf_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 {
-        "3dLocalACF": v_3d_local_acf_outputs,
-    }.get(t)
 
 
 class V3dLocalAcfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_local_acf(...)`.
+    Output object returned when calling `V3dLocalAcfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def v_3d_local_acf_params(
     neighborhood: str | None = None,
     mask_file: InputPathType | None = None,
     auto_mask: bool = False,
-) -> V3dLocalAcfParameters:
+) -> V3dLocalAcfParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def v_3d_local_acf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLocalACF",
+        "@type": "afni/3dLocalACF",
         "prefix": prefix,
         "input_file": input_file,
         "auto_mask": auto_mask,
@@ -114,20 +90,20 @@ def v_3d_local_acf_cargs(
     cargs.append("3dLocalACF")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("neighborhood") is not None:
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    if params.get("neighborhood", None) is not None:
         cargs.extend([
             "-nbhd",
-            params.get("neighborhood")
+            params.get("neighborhood", 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("auto_mask"):
+    if params.get("auto_mask", False):
         cargs.append("-automask")
     return cargs
 
@@ -147,18 +123,20 @@ def v_3d_local_acf_outputs(
     """
     ret = V3dLocalAcfOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
+        output_file=execution.output_file(params.get("prefix", None) + ".nii.gz"),
     )
     return ret
 
 
 def v_3d_local_acf_execute(
     params: V3dLocalAcfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLocalAcfOutputs:
     """
-    Estimate the spatial AutoCorrelation Function (ACF) locally in a neighborhood
-    around each voxel.
+    3dLocalACF
+    
+    Estimate the spatial AutoCorrelation Function (ACF) locally in a
+    neighborhood around each voxel.
     
     Author: AFNI Developers
     
@@ -166,10 +144,12 @@ def v_3d_local_acf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLocalAcfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCAL_ACF_METADATA)
     params = execution.params(params)
     cargs = v_3d_local_acf_cargs(params, execution)
     ret = v_3d_local_acf_outputs(params, execution)
@@ -186,8 +166,10 @@ def v_3d_local_acf(
     runner: Runner | None = None,
 ) -> V3dLocalAcfOutputs:
     """
-    Estimate the spatial AutoCorrelation Function (ACF) locally in a neighborhood
-    around each voxel.
+    3dLocalACF
+    
+    Estimate the spatial AutoCorrelation Function (ACF) locally in a
+    neighborhood around each voxel.
     
     Author: AFNI Developers
     
@@ -203,8 +185,6 @@ def v_3d_local_acf(
     Returns:
         NamedTuple of outputs (described in `V3dLocalAcfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LOCAL_ACF_METADATA)
     params = v_3d_local_acf_params(
         prefix=prefix,
         input_file=input_file,
@@ -212,13 +192,13 @@ def v_3d_local_acf(
         mask_file=mask_file,
         auto_mask=auto_mask,
     )
-    return v_3d_local_acf_execute(params, execution)
+    return v_3d_local_acf_execute(params, runner)
 
 
 __all__ = [
     "V3dLocalAcfOutputs",
-    "V3dLocalAcfParameters",
     "V_3D_LOCAL_ACF_METADATA",
     "v_3d_local_acf",
+    "v_3d_local_acf_execute",
     "v_3d_local_acf_params",
 ]

niwrap_afni/afni/v_3d_local_bistat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LOCAL_BISTAT_METADATA = Metadata(
-    id="f2b736bc414186f493c90278602c279b6976ba7d.boutiques",
+    id="bd3b4e7f6f4fe6509303def6d9ffdfba8fcba781.boutiques",
     name="3dLocalBistat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ V_3D_LOCAL_BISTAT_METADATA = Metadata(
 
 
 V3dLocalBistatParameters = typing.TypedDict('V3dLocalBistatParameters', {
-    "__STYXTYPE__": typing.Literal["3dLocalBistat"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLocalBistat"]],
+    "nbhd": str,
+    "stats": list[str],
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "weight": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "histpow": typing.NotRequired[float | None],
+    "histbin": typing.NotRequired[float | None],
+    "hclip1": typing.NotRequired[list[str] | None],
+    "hclip2": typing.NotRequired[list[str] | None],
+    "dataset1": InputPathType,
+    "dataset2": InputPathType,
+})
+V3dLocalBistatParametersTagged = typing.TypedDict('V3dLocalBistatParametersTagged', {
+    "@type": typing.Literal["afni/3dLocalBistat"],
     "nbhd": str,
     "stats": list[str],
     "mask": typing.NotRequired[InputPathType | None],
@@ -28,43 +43,11 @@ V3dLocalBistatParameters = typing.TypedDict('V3dLocalBistatParameters', {
     "dataset1": InputPathType,
     "dataset2": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dLocalBistat": v_3d_local_bistat_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 {
-        "3dLocalBistat": v_3d_local_bistat_outputs,
-    }.get(t)
 
 
 class V3dLocalBistatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_local_bistat(...)`.
+    Output object returned when calling `V3dLocalBistatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +70,7 @@ def v_3d_local_bistat_params(
     histbin: float | None = None,
     hclip1: list[str] | None = None,
     hclip2: list[str] | None = None,
-) -> V3dLocalBistatParameters:
+) -> V3dLocalBistatParametersTagged:
     """
     Build parameters.
     
@@ -116,7 +99,7 @@ def v_3d_local_bistat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLocalBistat",
+        "@type": "afni/3dLocalBistat",
         "nbhd": nbhd,
         "stats": stats,
         "automask": automask,
@@ -156,50 +139,50 @@ def v_3d_local_bistat_cargs(
     cargs.append("3dLocalBistat")
     cargs.extend([
         "-nbhd",
-        params.get("nbhd")
+        params.get("nbhd", None)
     ])
     cargs.extend([
         "-stat",
-        *params.get("stats")
+        *params.get("stats", 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("weight") is not None:
+    if params.get("weight", None) is not None:
         cargs.extend([
             "-weight",
-            execution.input_file(params.get("weight"))
+            execution.input_file(params.get("weight", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("histpow") is not None:
+    if params.get("histpow", None) is not None:
         cargs.extend([
             "-histpow",
-            str(params.get("histpow"))
+            str(params.get("histpow", None))
         ])
-    if params.get("histbin") is not None:
+    if params.get("histbin", None) is not None:
         cargs.extend([
             "-histbin",
-            str(params.get("histbin"))
+            str(params.get("histbin", None))
         ])
-    if params.get("hclip1") is not None:
+    if params.get("hclip1", None) is not None:
         cargs.extend([
             "-hclip1",
-            *params.get("hclip1")
+            *params.get("hclip1", None)
         ])
-    if params.get("hclip2") is not None:
+    if params.get("hclip2", None) is not None:
         cargs.extend([
             "-hclip2",
-            *params.get("hclip2")
+            *params.get("hclip2", None)
         ])
-    cargs.append(execution.input_file(params.get("dataset1")))
-    cargs.append(execution.input_file(params.get("dataset2")))
+    cargs.append(execution.input_file(params.get("dataset1", None)))
+    cargs.append(execution.input_file(params.get("dataset2", None)))
     return cargs
 
 
@@ -218,17 +201,19 @@ def v_3d_local_bistat_outputs(
     """
     ret = V3dLocalBistatOutputs(
         root=execution.output_file("."),
-        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
-        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+        output_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD"),
+        output_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK"),
     )
     return ret
 
 
 def v_3d_local_bistat_execute(
     params: V3dLocalBistatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLocalBistatOutputs:
     """
+    3dLocalBistat
+    
     Compute statistics between 2 datasets at each voxel based on a local
     neighborhood.
     
@@ -238,10 +223,12 @@ def v_3d_local_bistat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLocalBistatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCAL_BISTAT_METADATA)
     params = execution.params(params)
     cargs = v_3d_local_bistat_cargs(params, execution)
     ret = v_3d_local_bistat_outputs(params, execution)
@@ -265,6 +252,8 @@ def v_3d_local_bistat(
     runner: Runner | None = None,
 ) -> V3dLocalBistatOutputs:
     """
+    3dLocalBistat
+    
     Compute statistics between 2 datasets at each voxel based on a local
     neighborhood.
     
@@ -297,8 +286,6 @@ def v_3d_local_bistat(
     Returns:
         NamedTuple of outputs (described in `V3dLocalBistatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LOCAL_BISTAT_METADATA)
     params = v_3d_local_bistat_params(
         nbhd=nbhd,
         stats=stats,
@@ -313,13 +300,13 @@ def v_3d_local_bistat(
         dataset1=dataset1,
         dataset2=dataset2,
     )
-    return v_3d_local_bistat_execute(params, execution)
+    return v_3d_local_bistat_execute(params, runner)
 
 
 __all__ = [
     "V3dLocalBistatOutputs",
-    "V3dLocalBistatParameters",
     "V_3D_LOCAL_BISTAT_METADATA",
     "v_3d_local_bistat",
+    "v_3d_local_bistat_execute",
     "v_3d_local_bistat_params",
 ]

niwrap_afni/afni/v_3d_local_histog.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LOCAL_HISTOG_METADATA = Metadata(
-    id="a76400adcb984e82c7f568b9ba39dc70fabc3b25.boutiques",
+    id="29b9c068d0dd2ea7db278ff9e7df60f9fb5c6103.boutiques",
     name="3dLocalHistog",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ V_3D_LOCAL_HISTOG_METADATA = Metadata(
 
 
 V3dLocalHistogParameters = typing.TypedDict('V3dLocalHistogParameters', {
-    "__STYXTYPE__": typing.Literal["3dLocalHistog"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLocalHistog"]],
+    "nbhd_option": typing.NotRequired[str | None],
+    "prefix": str,
+    "hsave": typing.NotRequired[str | None],
+    "lab_file": typing.NotRequired[InputPathType | None],
+    "exclude": typing.NotRequired[list[str] | None],
+    "exc_nonlab": bool,
+    "mincount": typing.NotRequired[float | None],
+    "probability": bool,
+    "quiet": bool,
+    "input_datasets": list[InputPathType],
+})
+V3dLocalHistogParametersTagged = typing.TypedDict('V3dLocalHistogParametersTagged', {
+    "@type": typing.Literal["afni/3dLocalHistog"],
     "nbhd_option": typing.NotRequired[str | None],
     "prefix": str,
     "hsave": typing.NotRequired[str | None],
@@ -26,43 +39,11 @@ V3dLocalHistogParameters = typing.TypedDict('V3dLocalHistogParameters', {
     "quiet": bool,
     "input_datasets": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dLocalHistog": v_3d_local_histog_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 {
-        "3dLocalHistog": v_3d_local_histog_outputs,
-    }.get(t)
 
 
 class V3dLocalHistogOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_local_histog(...)`.
+    Output object returned when calling `V3dLocalHistogParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +66,7 @@ def v_3d_local_histog_params(
     mincount: float | None = None,
     probability: bool = False,
     quiet: bool = False,
-) -> V3dLocalHistogParameters:
+) -> V3dLocalHistogParametersTagged:
     """
     Build parameters.
     
@@ -111,7 +92,7 @@ def v_3d_local_histog_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLocalHistog",
+        "@type": "afni/3dLocalHistog",
         "prefix": prefix,
         "exc_nonlab": exc_nonlab,
         "probability": probability,
@@ -146,42 +127,42 @@ def v_3d_local_histog_cargs(
     """
     cargs = []
     cargs.append("3dLocalHistog")
-    if params.get("nbhd_option") is not None:
+    if params.get("nbhd_option", None) is not None:
         cargs.extend([
             "-nbhd",
-            params.get("nbhd_option")
+            params.get("nbhd_option", None)
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("hsave") is not None:
+    if params.get("hsave", None) is not None:
         cargs.extend([
             "-hsave",
-            params.get("hsave")
+            params.get("hsave", None)
         ])
-    if params.get("lab_file") is not None:
+    if params.get("lab_file", None) is not None:
         cargs.extend([
             "-lab_file",
-            execution.input_file(params.get("lab_file"))
+            execution.input_file(params.get("lab_file", None))
         ])
-    if params.get("exclude") is not None:
+    if params.get("exclude", None) is not None:
         cargs.extend([
             "-exclude",
-            *params.get("exclude")
+            *params.get("exclude", None)
         ])
-    if params.get("exc_nonlab"):
+    if params.get("exc_nonlab", False):
         cargs.append("-excNONLAB")
-    if params.get("mincount") is not None:
+    if params.get("mincount", None) is not None:
         cargs.extend([
             "-mincount",
-            str(params.get("mincount"))
+            str(params.get("mincount", None))
         ])
-    if params.get("probability"):
+    if params.get("probability", False):
         cargs.append("-prob")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    cargs.extend([execution.input_file(f) for f in params.get("input_datasets")])
+    cargs.extend([execution.input_file(f) for f in params.get("input_datasets", None)])
     return cargs
 
 
@@ -200,18 +181,20 @@ def v_3d_local_histog_outputs(
     """
     ret = V3dLocalHistogOutputs(
         root=execution.output_file("."),
-        output_dataset_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
-        output_dataset_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
-        histogram_file=execution.output_file(params.get("hsave")) if (params.get("hsave") is not None) else None,
+        output_dataset_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD"),
+        output_dataset_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK"),
+        histogram_file=execution.output_file(params.get("hsave", None)) if (params.get("hsave") is not None) else None,
     )
     return ret
 
 
 def v_3d_local_histog_execute(
     params: V3dLocalHistogParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLocalHistogOutputs:
     """
+    3dLocalHistog
+    
     This program computes a local histogram at each voxel in the input datasets.
     
     Author: AFNI Developers
@@ -220,10 +203,12 @@ def v_3d_local_histog_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLocalHistogOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCAL_HISTOG_METADATA)
     params = execution.params(params)
     cargs = v_3d_local_histog_cargs(params, execution)
     ret = v_3d_local_histog_outputs(params, execution)
@@ -245,6 +230,8 @@ def v_3d_local_histog(
     runner: Runner | None = None,
 ) -> V3dLocalHistogOutputs:
     """
+    3dLocalHistog
+    
     This program computes a local histogram at each voxel in the input datasets.
     
     Author: AFNI Developers
@@ -273,8 +260,6 @@ def v_3d_local_histog(
     Returns:
         NamedTuple of outputs (described in `V3dLocalHistogOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LOCAL_HISTOG_METADATA)
     params = v_3d_local_histog_params(
         nbhd_option=nbhd_option,
         prefix=prefix,
@@ -287,13 +272,13 @@ def v_3d_local_histog(
         quiet=quiet,
         input_datasets=input_datasets,
     )
-    return v_3d_local_histog_execute(params, execution)
+    return v_3d_local_histog_execute(params, runner)
 
 
 __all__ = [
     "V3dLocalHistogOutputs",
-    "V3dLocalHistogParameters",
     "V_3D_LOCAL_HISTOG_METADATA",
     "v_3d_local_histog",
+    "v_3d_local_histog_execute",
     "v_3d_local_histog_params",
 ]