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

niwrap_afni/afni/v_3d_local_pv.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LOCAL_PV_METADATA = Metadata(
-    id="d8fdcea80bb2e245dc9877549e950e2a4c50d742.boutiques",
+    id="8390b49d7516417de04bf15a124a704a00105410.boutiques",
     name="3dLocalPV",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ V_3D_LOCAL_PV_METADATA = Metadata(
 
 
 V3dLocalPvParameters = typing.TypedDict('V3dLocalPvParameters', {
-    "__STYXTYPE__": typing.Literal["3dLocalPV"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLocalPV"]],
+    "input_dataset": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "prefix": typing.NotRequired[str | None],
+    "prefix2": typing.NotRequired[str | None],
+    "evprefix": typing.NotRequired[str | None],
+    "neighborhood": typing.NotRequired[str | None],
+    "despike": bool,
+    "polort": typing.NotRequired[float | None],
+    "vnorm": bool,
+    "vproj": typing.NotRequired[str | None],
+})
+V3dLocalPvParametersTagged = typing.TypedDict('V3dLocalPvParametersTagged', {
+    "@type": typing.Literal["afni/3dLocalPV"],
     "input_dataset": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "automask": bool,
@@ -27,43 +41,11 @@ V3dLocalPvParameters = typing.TypedDict('V3dLocalPvParameters', {
     "vnorm": bool,
     "vproj": 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 {
-        "3dLocalPV": v_3d_local_pv_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 {
-        "3dLocalPV": v_3d_local_pv_outputs,
-    }.get(t)
 
 
 class V3dLocalPvOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_local_pv(...)`.
+    Output object returned when calling `V3dLocalPvParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +69,7 @@ def v_3d_local_pv_params(
     polort: float | None = None,
     vnorm: bool = False,
     vproj: str | None = None,
-) -> V3dLocalPvParameters:
+) -> V3dLocalPvParametersTagged:
     """
     Build parameters.
     
@@ -114,7 +96,7 @@ def v_3d_local_pv_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLocalPV",
+        "@type": "afni/3dLocalPV",
         "input_dataset": input_dataset,
         "automask": automask,
         "despike": despike,
@@ -152,47 +134,47 @@ def v_3d_local_pv_cargs(
     """
     cargs = []
     cargs.append("3dLocalPV")
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    if params.get("mask") is not None:
+    cargs.append(execution.input_file(params.get("input_dataset", 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("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("prefix2") is not None:
+    if params.get("prefix2", None) is not None:
         cargs.extend([
             "-prefix2",
-            params.get("prefix2")
+            params.get("prefix2", None)
         ])
-    if params.get("evprefix") is not None:
+    if params.get("evprefix", None) is not None:
         cargs.extend([
             "-evprefix",
-            params.get("evprefix")
+            params.get("evprefix", None)
         ])
-    if params.get("neighborhood") is not None:
+    if params.get("neighborhood", None) is not None:
         cargs.extend([
             "-nbhd",
-            params.get("neighborhood")
+            params.get("neighborhood", None)
         ])
-    if params.get("despike"):
+    if params.get("despike", False):
         cargs.append("-despike")
-    if params.get("polort") is not None:
+    if params.get("polort", None) is not None:
         cargs.extend([
             "-polort",
-            str(params.get("polort"))
+            str(params.get("polort", None))
         ])
-    if params.get("vnorm"):
+    if params.get("vnorm", False):
         cargs.append("-vnorm")
-    if params.get("vproj") is not None:
+    if params.get("vproj", None) is not None:
         cargs.extend([
             "-vproj",
-            params.get("vproj")
+            params.get("vproj", None)
         ])
     return cargs
 
@@ -212,18 +194,20 @@ def v_3d_local_pv_outputs(
     """
     ret = V3dLocalPvOutputs(
         root=execution.output_file("."),
-        svd_vector_result=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
-        second_principal_vector=execution.output_file(params.get("prefix2") + ".nii.gz") if (params.get("prefix2") is not None) else None,
-        singular_value=execution.output_file(params.get("evprefix") + ".nii.gz") if (params.get("evprefix") is not None) else None,
+        svd_vector_result=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
+        second_principal_vector=execution.output_file(params.get("prefix2", None) + ".nii.gz") if (params.get("prefix2") is not None) else None,
+        singular_value=execution.output_file(params.get("evprefix", None) + ".nii.gz") if (params.get("evprefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_local_pv_execute(
     params: V3dLocalPvParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLocalPvOutputs:
     """
+    3dLocalPV
+    
     Computes the Singular Value Decomposition (SVD) of the time series from a
     neighborhood of each voxel in a 3D+time dataset, which serves as a smoothing
     method for the dataset.
@@ -234,10 +218,12 @@ def v_3d_local_pv_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLocalPvOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCAL_PV_METADATA)
     params = execution.params(params)
     cargs = v_3d_local_pv_cargs(params, execution)
     ret = v_3d_local_pv_outputs(params, execution)
@@ -260,6 +246,8 @@ def v_3d_local_pv(
     runner: Runner | None = None,
 ) -> V3dLocalPvOutputs:
     """
+    3dLocalPV
+    
     Computes the Singular Value Decomposition (SVD) of the time series from a
     neighborhood of each voxel in a 3D+time dataset, which serves as a smoothing
     method for the dataset.
@@ -291,8 +279,6 @@ def v_3d_local_pv(
     Returns:
         NamedTuple of outputs (described in `V3dLocalPvOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LOCAL_PV_METADATA)
     params = v_3d_local_pv_params(
         input_dataset=input_dataset,
         mask=mask,
@@ -306,13 +292,13 @@ def v_3d_local_pv(
         vnorm=vnorm,
         vproj=vproj,
     )
-    return v_3d_local_pv_execute(params, execution)
+    return v_3d_local_pv_execute(params, runner)
 
 
 __all__ = [
     "V3dLocalPvOutputs",
-    "V3dLocalPvParameters",
     "V_3D_LOCAL_PV_METADATA",
     "v_3d_local_pv",
+    "v_3d_local_pv_execute",
     "v_3d_local_pv_params",
 ]

niwrap_afni/afni/v_3d_local_svd.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LOCAL_SVD_METADATA = Metadata(
-    id="f1614ff47ed09d8614f9811ea2b7772cb319daa0.boutiques",
+    id="a7863df1586bb3bd5cd811b383b5caf113d92580.boutiques",
     name="3dLocalSVD",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_LOCAL_SVD_METADATA = Metadata(
 
 
 V3dLocalSvdParameters = typing.TypedDict('V3dLocalSvdParameters', {
-    "__STYXTYPE__": typing.Literal["3dLocalSVD"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLocalSVD"]],
+    "auto_mask": bool,
+    "input_file": InputPathType,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "output_file": str,
+    "nbhd": typing.NotRequired[str | None],
+    "polort": typing.NotRequired[str | None],
+    "vnorm": bool,
+    "vproj": typing.NotRequired[float | None],
+})
+V3dLocalSvdParametersTagged = typing.TypedDict('V3dLocalSvdParametersTagged', {
+    "@type": typing.Literal["afni/3dLocalSVD"],
     "auto_mask": bool,
     "input_file": InputPathType,
     "mask_file": typing.NotRequired[InputPathType | None],
@@ -24,42 +35,11 @@ V3dLocalSvdParameters = typing.TypedDict('V3dLocalSvdParameters', {
     "vnorm": bool,
     "vproj": 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 {
-        "3dLocalSVD": v_3d_local_svd_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 V3dLocalSvdOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_local_svd(...)`.
+    Output object returned when calling `V3dLocalSvdParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def v_3d_local_svd_params(
     polort: str | None = None,
     vnorm: bool = False,
     vproj: float | None = None,
-) -> V3dLocalSvdParameters:
+) -> V3dLocalSvdParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +72,7 @@ def v_3d_local_svd_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLocalSVD",
+        "@type": "afni/3dLocalSVD",
         "auto_mask": auto_mask,
         "input_file": input_file,
         "output_file": output_file,
@@ -124,37 +104,37 @@ def v_3d_local_svd_cargs(
     """
     cargs = []
     cargs.append("3dLocalSVD")
-    if params.get("auto_mask"):
+    if params.get("auto_mask", False):
         cargs.append("-automask")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", 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))
         ])
     cargs.extend([
         "-prefix",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("nbhd") is not None:
+    if params.get("nbhd", None) is not None:
         cargs.extend([
             "-nbhd",
-            params.get("nbhd")
+            params.get("nbhd", None)
         ])
-    if params.get("polort") is not None:
+    if params.get("polort", None) is not None:
         cargs.extend([
             "-polort",
-            params.get("polort")
+            params.get("polort", None)
         ])
-    if params.get("vnorm"):
+    if params.get("vnorm", False):
         cargs.append("-vnorm")
-    if params.get("vproj") is not None:
+    if params.get("vproj", None) is not None:
         cargs.extend([
             "-vproj",
-            str(params.get("vproj"))
+            str(params.get("vproj", None))
         ])
     return cargs
 
@@ -180,9 +160,11 @@ def v_3d_local_svd_outputs(
 
 def v_3d_local_svd_execute(
     params: V3dLocalSvdParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLocalSvdOutputs:
     """
+    3dLocalSVD
+    
     Computes the SVD of time series from a neighborhood of each voxel.
     
     Author: AFNI Developers
@@ -191,10 +173,12 @@ def v_3d_local_svd_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLocalSvdOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCAL_SVD_METADATA)
     params = execution.params(params)
     cargs = v_3d_local_svd_cargs(params, execution)
     ret = v_3d_local_svd_outputs(params, execution)
@@ -214,6 +198,8 @@ def v_3d_local_svd(
     runner: Runner | None = None,
 ) -> V3dLocalSvdOutputs:
     """
+    3dLocalSVD
+    
     Computes the SVD of time series from a neighborhood of each voxel.
     
     Author: AFNI Developers
@@ -234,8 +220,6 @@ def v_3d_local_svd(
     Returns:
         NamedTuple of outputs (described in `V3dLocalSvdOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LOCAL_SVD_METADATA)
     params = v_3d_local_svd_params(
         auto_mask=auto_mask,
         input_file=input_file,
@@ -246,13 +230,13 @@ def v_3d_local_svd(
         vnorm=vnorm,
         vproj=vproj,
     )
-    return v_3d_local_svd_execute(params, execution)
+    return v_3d_local_svd_execute(params, runner)
 
 
 __all__ = [
     "V3dLocalSvdOutputs",
-    "V3dLocalSvdParameters",
     "V_3D_LOCAL_SVD_METADATA",
     "v_3d_local_svd",
+    "v_3d_local_svd_execute",
     "v_3d_local_svd_params",
 ]

niwrap_afni/afni/v_3d_local_unifize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LOCAL_UNIFIZE_METADATA = Metadata(
-    id="e06d5f8fb3dc8d180368304a8bb1866d04d34859.boutiques",
+    id="d5b07f6e88c0009118f7ff6ae0483052c78712ee.boutiques",
     name="3dLocalUnifize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_LOCAL_UNIFIZE_METADATA = Metadata(
 
 
 V3dLocalUnifizeParameters = typing.TypedDict('V3dLocalUnifizeParameters', {
-    "__STYXTYPE__": typing.Literal["3dLocalUnifize"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLocalUnifize"]],
+    "input": InputPathType,
+    "output": str,
+    "working_dir": typing.NotRequired[str | None],
+    "echo": bool,
+    "no_clean": bool,
+    "local_rad": typing.NotRequired[float | None],
+    "local_perc": typing.NotRequired[float | None],
+    "local_mask": typing.NotRequired[str | None],
+    "filter_thr": typing.NotRequired[float | None],
+})
+V3dLocalUnifizeParametersTagged = typing.TypedDict('V3dLocalUnifizeParametersTagged', {
+    "@type": typing.Literal["afni/3dLocalUnifize"],
     "input": InputPathType,
     "output": str,
     "working_dir": typing.NotRequired[str | None],
@@ -25,43 +37,11 @@ V3dLocalUnifizeParameters = typing.TypedDict('V3dLocalUnifizeParameters', {
     "local_mask": typing.NotRequired[str | None],
     "filter_thr": 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 {
-        "3dLocalUnifize": v_3d_local_unifize_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 {
-        "3dLocalUnifize": v_3d_local_unifize_outputs,
-    }.get(t)
 
 
 class V3dLocalUnifizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_local_unifize(...)`.
+    Output object returned when calling `V3dLocalUnifizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def v_3d_local_unifize_params(
     local_perc: float | None = None,
     local_mask: str | None = None,
     filter_thr: float | None = None,
-) -> V3dLocalUnifizeParameters:
+) -> V3dLocalUnifizeParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +83,7 @@ def v_3d_local_unifize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLocalUnifize",
+        "@type": "afni/3dLocalUnifize",
         "input": input_,
         "output": output,
         "echo": echo,
@@ -137,39 +117,39 @@ def v_3d_local_unifize_cargs(
     """
     cargs = []
     cargs.append("3dLocalUnifize")
-    cargs.append(execution.input_file(params.get("input")))
+    cargs.append(execution.input_file(params.get("input", None)))
     cargs.extend([
         "-prefix",
-        params.get("output")
+        params.get("output", None)
     ])
-    if params.get("working_dir") is not None:
+    if params.get("working_dir", None) is not None:
         cargs.extend([
             "-wdir_name",
-            params.get("working_dir")
+            params.get("working_dir", 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")
-    if params.get("local_rad") is not None:
+    if params.get("local_rad", None) is not None:
         cargs.extend([
             "-local_rad",
-            str(params.get("local_rad"))
+            str(params.get("local_rad", None))
         ])
-    if params.get("local_perc") is not None:
+    if params.get("local_perc", None) is not None:
         cargs.extend([
             "-local_perc",
-            str(params.get("local_perc"))
+            str(params.get("local_perc", None))
         ])
-    if params.get("local_mask") is not None:
+    if params.get("local_mask", None) is not None:
         cargs.extend([
             "-local_mask",
-            params.get("local_mask")
+            params.get("local_mask", None)
         ])
-    if params.get("filter_thr") is not None:
+    if params.get("filter_thr", None) is not None:
         cargs.extend([
             "-filter_thr",
-            str(params.get("filter_thr"))
+            str(params.get("filter_thr", None))
         ])
     return cargs
 
@@ -189,18 +169,20 @@ def v_3d_local_unifize_outputs(
     """
     ret = V3dLocalUnifizeOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output")),
+        output_file=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def v_3d_local_unifize_execute(
     params: V3dLocalUnifizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLocalUnifizeOutputs:
     """
-    This program generates a 'unifized' output volume by estimating the median in
-    the local neighborhood of each voxel and using that to scale each voxel's
+    3dLocalUnifize
+    
+    This program generates a 'unifized' output volume by estimating the median
+    in the local neighborhood of each voxel and using that to scale each voxel's
     brightness.
     
     Author: AFNI Developers
@@ -209,10 +191,12 @@ def v_3d_local_unifize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLocalUnifizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCAL_UNIFIZE_METADATA)
     params = execution.params(params)
     cargs = v_3d_local_unifize_cargs(params, execution)
     ret = v_3d_local_unifize_outputs(params, execution)
@@ -233,8 +217,10 @@ def v_3d_local_unifize(
     runner: Runner | None = None,
 ) -> V3dLocalUnifizeOutputs:
     """
-    This program generates a 'unifized' output volume by estimating the median in
-    the local neighborhood of each voxel and using that to scale each voxel's
+    3dLocalUnifize
+    
+    This program generates a 'unifized' output volume by estimating the median
+    in the local neighborhood of each voxel and using that to scale each voxel's
     brightness.
     
     Author: AFNI Developers
@@ -261,8 +247,6 @@ def v_3d_local_unifize(
     Returns:
         NamedTuple of outputs (described in `V3dLocalUnifizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LOCAL_UNIFIZE_METADATA)
     params = v_3d_local_unifize_params(
         input_=input_,
         output=output,
@@ -274,13 +258,13 @@ def v_3d_local_unifize(
         local_mask=local_mask,
         filter_thr=filter_thr,
     )
-    return v_3d_local_unifize_execute(params, execution)
+    return v_3d_local_unifize_execute(params, runner)
 
 
 __all__ = [
     "V3dLocalUnifizeOutputs",
-    "V3dLocalUnifizeParameters",
     "V_3D_LOCAL_UNIFIZE_METADATA",
     "v_3d_local_unifize",
+    "v_3d_local_unifize_execute",
     "v_3d_local_unifize_params",
 ]