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

niwrap_afni/afni/v__roi_decluster.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__ROI_DECLUSTER_METADATA = Metadata(
-    id="520624870be5948640fb42dcdddf40d7764da2c4.boutiques",
+    id="cbc503162b576cbf2707a1fe573e7f99a6511b70.boutiques",
     name="@ROI_decluster",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V__ROI_DECLUSTER_METADATA = Metadata(
 
 
 VRoiDeclusterParameters = typing.TypedDict('VRoiDeclusterParameters', {
-    "__STYXTYPE__": typing.Literal["@ROI_decluster"],
+    "@type": typing.NotRequired[typing.Literal["afni/@ROI_decluster"]],
+    "input_dset": InputPathType,
+    "output_dir": typing.NotRequired[str | None],
+    "nvox_thresh": typing.NotRequired[float | None],
+    "frac_thresh": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "neighborhood_type": typing.NotRequired[int | None],
+})
+VRoiDeclusterParametersTagged = typing.TypedDict('VRoiDeclusterParametersTagged', {
+    "@type": typing.Literal["afni/@ROI_decluster"],
     "input_dset": InputPathType,
     "output_dir": typing.NotRequired[str | None],
     "nvox_thresh": typing.NotRequired[float | None],
@@ -22,43 +31,11 @@ VRoiDeclusterParameters = typing.TypedDict('VRoiDeclusterParameters', {
     "prefix": typing.NotRequired[str | None],
     "neighborhood_type": typing.NotRequired[int | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@ROI_decluster": v__roi_decluster_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 {
-        "@ROI_decluster": v__roi_decluster_outputs,
-    }.get(t)
 
 
 class VRoiDeclusterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__roi_decluster(...)`.
+    Output object returned when calling `VRoiDeclusterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def v__roi_decluster_params(
     frac_thresh: float | None = None,
     prefix: str | None = None,
     neighborhood_type: int | None = None,
-) -> VRoiDeclusterParameters:
+) -> VRoiDeclusterParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +69,7 @@ def v__roi_decluster_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@ROI_decluster",
+        "@type": "afni/@ROI_decluster",
         "input_dset": input_dset,
     }
     if output_dir is not None:
@@ -125,32 +102,32 @@ def v__roi_decluster_cargs(
     cargs.append("@ROI_decluster")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_dset"))
+        execution.input_file(params.get("input_dset", None))
     ])
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "-outdir",
-            params.get("output_dir")
+            params.get("output_dir", None)
         ])
-    if params.get("nvox_thresh") is not None:
+    if params.get("nvox_thresh", None) is not None:
         cargs.extend([
             "-nvox_thresh",
-            str(params.get("nvox_thresh"))
+            str(params.get("nvox_thresh", None))
         ])
-    if params.get("frac_thresh") is not None:
+    if params.get("frac_thresh", None) is not None:
         cargs.extend([
             "-frac_thresh",
-            str(params.get("frac_thresh"))
+            str(params.get("frac_thresh", None))
         ])
-    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("neighborhood_type") is not None:
+    if params.get("neighborhood_type", None) is not None:
         cargs.extend([
             "-NN",
-            str(params.get("neighborhood_type"))
+            str(params.get("neighborhood_type", None))
         ])
     return cargs
 
@@ -170,17 +147,20 @@ def v__roi_decluster_outputs(
     """
     ret = VRoiDeclusterOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v__roi_decluster_execute(
     params: VRoiDeclusterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VRoiDeclusterOutputs:
     """
-    Script to remove small clusters or standalone voxels from an ROI/atlas dataset.
+    @ROI_decluster
+    
+    Script to remove small clusters or standalone voxels from an ROI/atlas
+    dataset.
     
     Author: AFNI Developers
     
@@ -188,10 +168,12 @@ def v__roi_decluster_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VRoiDeclusterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ROI_DECLUSTER_METADATA)
     params = execution.params(params)
     cargs = v__roi_decluster_cargs(params, execution)
     ret = v__roi_decluster_outputs(params, execution)
@@ -209,7 +191,10 @@ def v__roi_decluster(
     runner: Runner | None = None,
 ) -> VRoiDeclusterOutputs:
     """
-    Script to remove small clusters or standalone voxels from an ROI/atlas dataset.
+    @ROI_decluster
+    
+    Script to remove small clusters or standalone voxels from an ROI/atlas
+    dataset.
     
     Author: AFNI Developers
     
@@ -230,8 +215,6 @@ def v__roi_decluster(
     Returns:
         NamedTuple of outputs (described in `VRoiDeclusterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__ROI_DECLUSTER_METADATA)
     params = v__roi_decluster_params(
         input_dset=input_dset,
         output_dir=output_dir,
@@ -240,13 +223,13 @@ def v__roi_decluster(
         prefix=prefix,
         neighborhood_type=neighborhood_type,
     )
-    return v__roi_decluster_execute(params, execution)
+    return v__roi_decluster_execute(params, runner)
 
 
 __all__ = [
     "VRoiDeclusterOutputs",
-    "VRoiDeclusterParameters",
     "V__ROI_DECLUSTER_METADATA",
     "v__roi_decluster",
+    "v__roi_decluster_execute",
     "v__roi_decluster_params",
 ]

niwrap_afni/afni/v__roi_modal_grow.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__ROI_MODAL_GROW_METADATA = Metadata(
-    id="569ed3bfade748be8a4eae1d8812ba05b410fe8f.boutiques",
+    id="cbe874e807b49a60306d540b573e406e97399117.boutiques",
     name="@ROI_modal_grow",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V__ROI_MODAL_GROW_METADATA = Metadata(
 
 
 VRoiModalGrowParameters = typing.TypedDict('VRoiModalGrowParameters', {
-    "__STYXTYPE__": typing.Literal["@ROI_modal_grow"],
+    "@type": typing.NotRequired[typing.Literal["afni/@ROI_modal_grow"]],
+    "input_dset": InputPathType,
+    "niters": float,
+    "outdir": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "neighborhood_type": typing.NotRequired[int | None],
+})
+VRoiModalGrowParametersTagged = typing.TypedDict('VRoiModalGrowParametersTagged', {
+    "@type": typing.Literal["afni/@ROI_modal_grow"],
     "input_dset": InputPathType,
     "niters": float,
     "outdir": typing.NotRequired[str | None],
@@ -22,43 +31,11 @@ VRoiModalGrowParameters = typing.TypedDict('VRoiModalGrowParameters', {
     "prefix": typing.NotRequired[str | None],
     "neighborhood_type": typing.NotRequired[int | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@ROI_modal_grow": v__roi_modal_grow_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 {
-        "@ROI_modal_grow": v__roi_modal_grow_outputs,
-    }.get(t)
 
 
 class VRoiModalGrowOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__roi_modal_grow(...)`.
+    Output object returned when calling `VRoiModalGrowParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def v__roi_modal_grow_params(
     mask: InputPathType | None = None,
     prefix: str | None = None,
     neighborhood_type: int | None = None,
-) -> VRoiModalGrowParameters:
+) -> VRoiModalGrowParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +72,7 @@ def v__roi_modal_grow_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@ROI_modal_grow",
+        "@type": "afni/@ROI_modal_grow",
         "input_dset": input_dset,
         "niters": niters,
     }
@@ -127,31 +104,31 @@ def v__roi_modal_grow_cargs(
     cargs.append("@ROI_modal_grow")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_dset"))
+        execution.input_file(params.get("input_dset", None))
     ])
     cargs.extend([
         "-niters",
-        str(params.get("niters"))
+        str(params.get("niters", 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("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("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("neighborhood_type") is not None:
+    if params.get("neighborhood_type", None) is not None:
         cargs.extend([
             "-NN",
-            str(params.get("neighborhood_type"))
+            str(params.get("neighborhood_type", None))
         ])
     return cargs
 
@@ -171,17 +148,20 @@ def v__roi_modal_grow_outputs(
     """
     ret = VRoiModalGrowOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("outdir") + "/" + params.get("prefix") + ".nii.gz") if (params.get("outdir") is not None and params.get("prefix") is not None) else None,
+        output_file=execution.output_file(params.get("outdir", None) + "/" + params.get("prefix", None) + ".nii.gz") if (params.get("outdir") is not None and params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v__roi_modal_grow_execute(
     params: VRoiModalGrowParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VRoiModalGrowOutputs:
     """
-    Script to grow a set of regions in a volumetric dataset using modal smoothing.
+    @ROI_modal_grow
+    
+    Script to grow a set of regions in a volumetric dataset using modal
+    smoothing.
     
     Author: AFNI Developers
     
@@ -189,10 +169,12 @@ def v__roi_modal_grow_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VRoiModalGrowOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ROI_MODAL_GROW_METADATA)
     params = execution.params(params)
     cargs = v__roi_modal_grow_cargs(params, execution)
     ret = v__roi_modal_grow_outputs(params, execution)
@@ -210,7 +192,10 @@ def v__roi_modal_grow(
     runner: Runner | None = None,
 ) -> VRoiModalGrowOutputs:
     """
-    Script to grow a set of regions in a volumetric dataset using modal smoothing.
+    @ROI_modal_grow
+    
+    Script to grow a set of regions in a volumetric dataset using modal
+    smoothing.
     
     Author: AFNI Developers
     
@@ -234,8 +219,6 @@ def v__roi_modal_grow(
     Returns:
         NamedTuple of outputs (described in `VRoiModalGrowOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__ROI_MODAL_GROW_METADATA)
     params = v__roi_modal_grow_params(
         input_dset=input_dset,
         niters=niters,
@@ -244,13 +227,13 @@ def v__roi_modal_grow(
         prefix=prefix,
         neighborhood_type=neighborhood_type,
     )
-    return v__roi_modal_grow_execute(params, execution)
+    return v__roi_modal_grow_execute(params, runner)
 
 
 __all__ = [
     "VRoiModalGrowOutputs",
-    "VRoiModalGrowParameters",
     "V__ROI_MODAL_GROW_METADATA",
     "v__roi_modal_grow",
+    "v__roi_modal_grow_execute",
     "v__roi_modal_grow_params",
 ]

niwrap_afni/afni/v__scale_volume.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SCALE_VOLUME_METADATA = Metadata(
-    id="6987f91c483f861633afc3be82cefdcfd48e7a50.boutiques",
+    id="38e29f0a503eb7393584f6500f816808bb70e0b9.boutiques",
     name="@ScaleVolume",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V__SCALE_VOLUME_METADATA = Metadata(
 
 
 VScaleVolumeParameters = typing.TypedDict('VScaleVolumeParameters', {
-    "__STYXTYPE__": typing.Literal["@ScaleVolume"],
+    "@type": typing.NotRequired[typing.Literal["afni/@ScaleVolume"]],
+    "input_dset": InputPathType,
+    "prefix": str,
+    "val_clip": typing.NotRequired[list[float] | None],
+    "perc_clip": typing.NotRequired[list[float] | None],
+    "scale_by_mean": bool,
+    "scale_by_median": bool,
+    "norm": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+})
+VScaleVolumeParametersTagged = typing.TypedDict('VScaleVolumeParametersTagged', {
+    "@type": typing.Literal["afni/@ScaleVolume"],
     "input_dset": InputPathType,
     "prefix": str,
     "val_clip": typing.NotRequired[list[float] | None],
@@ -24,43 +35,11 @@ VScaleVolumeParameters = typing.TypedDict('VScaleVolumeParameters', {
     "norm": bool,
     "mask": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@ScaleVolume": v__scale_volume_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 {
-        "@ScaleVolume": v__scale_volume_outputs,
-    }.get(t)
 
 
 class VScaleVolumeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__scale_volume(...)`.
+    Output object returned when calling `VScaleVolumeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def v__scale_volume_params(
     scale_by_median: bool = False,
     norm: bool = False,
     mask: InputPathType | None = None,
-) -> VScaleVolumeParameters:
+) -> VScaleVolumeParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +74,7 @@ def v__scale_volume_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@ScaleVolume",
+        "@type": "afni/@ScaleVolume",
         "input_dset": input_dset,
         "prefix": prefix,
         "scale_by_mean": scale_by_mean,
@@ -126,28 +105,28 @@ def v__scale_volume_cargs(
     """
     cargs = []
     cargs.append("@ScaleVolume")
-    cargs.append(execution.input_file(params.get("input_dset")))
-    cargs.append(params.get("prefix"))
-    if params.get("val_clip") is not None:
+    cargs.append(execution.input_file(params.get("input_dset", None)))
+    cargs.append(params.get("prefix", None))
+    if params.get("val_clip", None) is not None:
         cargs.extend([
             "-val_clip",
-            *map(str, params.get("val_clip"))
+            *map(str, params.get("val_clip", None))
         ])
-    if params.get("perc_clip") is not None:
+    if params.get("perc_clip", None) is not None:
         cargs.extend([
             "-perc_clip",
-            *map(str, params.get("perc_clip"))
+            *map(str, params.get("perc_clip", None))
         ])
-    if params.get("scale_by_mean"):
+    if params.get("scale_by_mean", False):
         cargs.append("-scale_by_mean")
-    if params.get("scale_by_median"):
+    if params.get("scale_by_median", False):
         cargs.append("-scale_by_median")
-    if params.get("norm"):
+    if params.get("norm", False):
         cargs.append("-norm")
-    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))
         ])
     return cargs
 
@@ -167,16 +146,18 @@ def v__scale_volume_outputs(
     """
     ret = VScaleVolumeOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file("<-prefix PREFIX>_scaled"),
+        output_file=execution.output_file(params.get("prefix", None) + "_scaled"),
     )
     return ret
 
 
 def v__scale_volume_execute(
     params: VScaleVolumeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VScaleVolumeOutputs:
     """
+    @ScaleVolume
+    
     A tool to scale the volume of datasets.
     
     Author: AFNI Developers
@@ -185,10 +166,12 @@ def v__scale_volume_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VScaleVolumeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SCALE_VOLUME_METADATA)
     params = execution.params(params)
     cargs = v__scale_volume_cargs(params, execution)
     ret = v__scale_volume_outputs(params, execution)
@@ -208,6 +191,8 @@ def v__scale_volume(
     runner: Runner | None = None,
 ) -> VScaleVolumeOutputs:
     """
+    @ScaleVolume
+    
     A tool to scale the volume of datasets.
     
     Author: AFNI Developers
@@ -228,8 +213,6 @@ def v__scale_volume(
     Returns:
         NamedTuple of outputs (described in `VScaleVolumeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SCALE_VOLUME_METADATA)
     params = v__scale_volume_params(
         input_dset=input_dset,
         prefix=prefix,
@@ -240,13 +223,13 @@ def v__scale_volume(
         norm=norm,
         mask=mask,
     )
-    return v__scale_volume_execute(params, execution)
+    return v__scale_volume_execute(params, runner)
 
 
 __all__ = [
     "VScaleVolumeOutputs",
-    "VScaleVolumeParameters",
     "V__SCALE_VOLUME_METADATA",
     "v__scale_volume",
+    "v__scale_volume_execute",
     "v__scale_volume_params",
 ]