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

niwrap_afni/afni/v_3d_degree_centrality.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DEGREE_CENTRALITY_METADATA = Metadata(
-    id="6b26eb322a598bdf48e84565bbf6674c9e7c8cf4.boutiques",
+    id="92d1c07bfff26718b69be19ce1645a7154290cb7.boutiques",
     name="3dDegreeCentrality",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_DEGREE_CENTRALITY_METADATA = Metadata(
 
 
 V3dDegreeCentralityParameters = typing.TypedDict('V3dDegreeCentralityParameters', {
-    "__STYXTYPE__": typing.Literal["3dDegreeCentrality"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDegreeCentrality"]],
+    "autoclip": bool,
+    "automask": bool,
+    "in_file": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "oned_file": typing.NotRequired[str | None],
+    "polort": typing.NotRequired[int | None],
+    "sparsity": typing.NotRequired[float | None],
+    "thresh": typing.NotRequired[float | None],
+})
+V3dDegreeCentralityParametersTagged = typing.TypedDict('V3dDegreeCentralityParametersTagged', {
+    "@type": typing.Literal["afni/3dDegreeCentrality"],
     "autoclip": bool,
     "automask": bool,
     "in_file": InputPathType,
@@ -24,43 +35,11 @@ V3dDegreeCentralityParameters = typing.TypedDict('V3dDegreeCentralityParameters'
     "sparsity": typing.NotRequired[float | None],
     "thresh": 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 {
-        "3dDegreeCentrality": v_3d_degree_centrality_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 {
-        "3dDegreeCentrality": v_3d_degree_centrality_outputs,
-    }.get(t)
 
 
 class V3dDegreeCentralityOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_degree_centrality(...)`.
+    Output object returned when calling `V3dDegreeCentralityParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +60,7 @@ def v_3d_degree_centrality_params(
     polort: int | None = None,
     sparsity: float | None = None,
     thresh: float | None = None,
-) -> V3dDegreeCentralityParameters:
+) -> V3dDegreeCentralityParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +77,7 @@ def v_3d_degree_centrality_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDegreeCentrality",
+        "@type": "afni/3dDegreeCentrality",
         "autoclip": autoclip,
         "automask": automask,
         "in_file": in_file,
@@ -131,35 +110,35 @@ def v_3d_degree_centrality_cargs(
     """
     cargs = []
     cargs.append("3dDegreeCentrality")
-    if params.get("autoclip"):
+    if params.get("autoclip", False):
         cargs.append("-autoclip")
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    cargs.append(execution.input_file(params.get("in_file")))
-    if params.get("mask") is not None:
+    cargs.append(execution.input_file(params.get("in_file", 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("oned_file") is not None:
+    if params.get("oned_file", None) is not None:
         cargs.extend([
             "-out1D",
-            params.get("oned_file")
+            params.get("oned_file", None)
         ])
-    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("sparsity") is not None:
+    if params.get("sparsity", None) is not None:
         cargs.extend([
             "-sparsity",
-            str(params.get("sparsity"))
+            str(params.get("sparsity", None))
         ])
-    if params.get("thresh") is not None:
+    if params.get("thresh", None) is not None:
         cargs.extend([
             "-thresh",
-            str(params.get("thresh"))
+            str(params.get("thresh", None))
         ])
     return cargs
 
@@ -179,21 +158,23 @@ def v_3d_degree_centrality_outputs(
     """
     ret = V3dDegreeCentralityOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(pathlib.Path(params.get("in_file")).name),
-        oned_file_outfile=execution.output_file(params.get("oned_file")) if (params.get("oned_file") is not None) else None,
+        out_file=execution.output_file(pathlib.Path(params.get("in_file", None)).name),
+        oned_file_outfile=execution.output_file(params.get("oned_file", None)) if (params.get("oned_file") is not None) else None,
     )
     return ret
 
 
 def v_3d_degree_centrality_execute(
     params: V3dDegreeCentralityParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDegreeCentralityOutputs:
     """
-    Computes voxelwise weighted and binary degree centrality and stores the result
-    in a new 3D bucket dataset as floats to preserve their values. Degree centrality
-    reflects the strength and extent of the correlation of a voxel with every other
-    voxel in the brain. .
+    3dDegreeCentrality
+    
+    Computes voxelwise weighted and binary degree centrality and stores the
+    result in a new 3D bucket dataset as floats to preserve their values. Degree
+    centrality reflects the strength and extent of the correlation of a voxel
+    with every other voxel in the brain. .
     
     Author: AFNI Developers
     
@@ -201,10 +182,12 @@ def v_3d_degree_centrality_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDegreeCentralityOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DEGREE_CENTRALITY_METADATA)
     params = execution.params(params)
     cargs = v_3d_degree_centrality_cargs(params, execution)
     ret = v_3d_degree_centrality_outputs(params, execution)
@@ -224,10 +207,12 @@ def v_3d_degree_centrality(
     runner: Runner | None = None,
 ) -> V3dDegreeCentralityOutputs:
     """
-    Computes voxelwise weighted and binary degree centrality and stores the result
-    in a new 3D bucket dataset as floats to preserve their values. Degree centrality
-    reflects the strength and extent of the correlation of a voxel with every other
-    voxel in the brain. .
+    3dDegreeCentrality
+    
+    Computes voxelwise weighted and binary degree centrality and stores the
+    result in a new 3D bucket dataset as floats to preserve their values. Degree
+    centrality reflects the strength and extent of the correlation of a voxel
+    with every other voxel in the brain. .
     
     Author: AFNI Developers
     
@@ -246,8 +231,6 @@ def v_3d_degree_centrality(
     Returns:
         NamedTuple of outputs (described in `V3dDegreeCentralityOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DEGREE_CENTRALITY_METADATA)
     params = v_3d_degree_centrality_params(
         autoclip=autoclip,
         automask=automask,
@@ -258,13 +241,13 @@ def v_3d_degree_centrality(
         sparsity=sparsity,
         thresh=thresh,
     )
-    return v_3d_degree_centrality_execute(params, execution)
+    return v_3d_degree_centrality_execute(params, runner)
 
 
 __all__ = [
     "V3dDegreeCentralityOutputs",
-    "V3dDegreeCentralityParameters",
     "V_3D_DEGREE_CENTRALITY_METADATA",
     "v_3d_degree_centrality",
+    "v_3d_degree_centrality_execute",
     "v_3d_degree_centrality_params",
 ]

niwrap_afni/afni/v_3d_depth_map.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DEPTH_MAP_METADATA = Metadata(
-    id="b4b586aabaa0388928e52c39e0a960a38ea18d5b.boutiques",
+    id="08e415c1078b5105d214367ddc3e04f3759931bf.boutiques",
     name="3dDepthMap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ V_3D_DEPTH_MAP_METADATA = Metadata(
 
 
 V3dDepthMapParameters = typing.TypedDict('V3dDepthMapParameters', {
-    "__STYXTYPE__": typing.Literal["3dDepthMap"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDepthMap"]],
+    "input_dataset": InputPathType,
+    "output_prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "dist_squared": bool,
+    "ignore_voxdims": bool,
+    "rimify": typing.NotRequired[float | None],
+    "zeros_are_zero": bool,
+    "zeros_are_neg": bool,
+    "nz_are_neg": bool,
+    "bounds_are_not_zero": bool,
+    "only2D": typing.NotRequired[str | None],
+    "binary_only": bool,
+    "verbosity": typing.NotRequired[float | None],
+})
+V3dDepthMapParametersTagged = typing.TypedDict('V3dDepthMapParametersTagged', {
+    "@type": typing.Literal["afni/3dDepthMap"],
     "input_dataset": InputPathType,
     "output_prefix": str,
     "mask": typing.NotRequired[InputPathType | None],
@@ -29,43 +45,11 @@ V3dDepthMapParameters = typing.TypedDict('V3dDepthMapParameters', {
     "binary_only": bool,
     "verbosity": 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 {
-        "3dDepthMap": v_3d_depth_map_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 {
-        "3dDepthMap": v_3d_depth_map_outputs,
-    }.get(t)
 
 
 class V3dDepthMapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_depth_map(...)`.
+    Output object returned when calling `V3dDepthMapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +71,7 @@ def v_3d_depth_map_params(
     only2_d: str | None = None,
     binary_only: bool = False,
     verbosity: float | None = None,
-) -> V3dDepthMapParameters:
+) -> V3dDepthMapParametersTagged:
     """
     Build parameters.
     
@@ -113,7 +97,7 @@ def v_3d_depth_map_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDepthMap",
+        "@type": "afni/3dDepthMap",
         "input_dataset": input_dataset,
         "output_prefix": output_prefix,
         "dist_squared": dist_squared,
@@ -152,45 +136,45 @@ def v_3d_depth_map_cargs(
     cargs.append("3dDepthMap")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_dataset"))
+        execution.input_file(params.get("input_dataset", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", 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("dist_squared"):
+    if params.get("dist_squared", False):
         cargs.append("-dist_sq")
-    if params.get("ignore_voxdims"):
+    if params.get("ignore_voxdims", False):
         cargs.append("-ignore_voxdims")
-    if params.get("rimify") is not None:
+    if params.get("rimify", None) is not None:
         cargs.extend([
             "-rimify",
-            str(params.get("rimify"))
+            str(params.get("rimify", None))
         ])
-    if params.get("zeros_are_zero"):
+    if params.get("zeros_are_zero", False):
         cargs.append("-zeros_are_zero")
-    if params.get("zeros_are_neg"):
+    if params.get("zeros_are_neg", False):
         cargs.append("-zeros_are_neg")
-    if params.get("nz_are_neg"):
+    if params.get("nz_are_neg", False):
         cargs.append("-nz_are_neg")
-    if params.get("bounds_are_not_zero"):
+    if params.get("bounds_are_not_zero", False):
         cargs.append("-bounds_are_not_zero")
-    if params.get("only2D") is not None:
+    if params.get("only2D", None) is not None:
         cargs.extend([
             "-only2D",
-            params.get("only2D")
+            params.get("only2D", None)
         ])
-    if params.get("binary_only"):
+    if params.get("binary_only", False):
         cargs.append("-binary_only")
-    if params.get("verbosity") is not None:
+    if params.get("verbosity", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity"))
+            str(params.get("verbosity", None))
         ])
     return cargs
 
@@ -210,19 +194,21 @@ def v_3d_depth_map_outputs(
     """
     ret = V3dDepthMapOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_prefix") + ".nii.gz"),
+        output_file=execution.output_file(params.get("output_prefix", None) + ".nii.gz"),
     )
     return ret
 
 
 def v_3d_depth_map_execute(
     params: V3dDepthMapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDepthMapOutputs:
     """
+    3dDepthMap
+    
     Calculates the Euclidean Distance Transform (EDT) for 3D volumes, allowing
-    computation of ROI depth maps and applying various adjustments like masking and
-    rimification.
+    computation of ROI depth maps and applying various adjustments like masking
+    and rimification.
     
     Author: AFNI Developers
     
@@ -230,10 +216,12 @@ def v_3d_depth_map_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDepthMapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DEPTH_MAP_METADATA)
     params = execution.params(params)
     cargs = v_3d_depth_map_cargs(params, execution)
     ret = v_3d_depth_map_outputs(params, execution)
@@ -258,9 +246,11 @@ def v_3d_depth_map(
     runner: Runner | None = None,
 ) -> V3dDepthMapOutputs:
     """
+    3dDepthMap
+    
     Calculates the Euclidean Distance Transform (EDT) for 3D volumes, allowing
-    computation of ROI depth maps and applying various adjustments like masking and
-    rimification.
+    computation of ROI depth maps and applying various adjustments like masking
+    and rimification.
     
     Author: AFNI Developers
     
@@ -288,8 +278,6 @@ def v_3d_depth_map(
     Returns:
         NamedTuple of outputs (described in `V3dDepthMapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DEPTH_MAP_METADATA)
     params = v_3d_depth_map_params(
         input_dataset=input_dataset,
         output_prefix=output_prefix,
@@ -305,13 +293,13 @@ def v_3d_depth_map(
         binary_only=binary_only,
         verbosity=verbosity,
     )
-    return v_3d_depth_map_execute(params, execution)
+    return v_3d_depth_map_execute(params, runner)
 
 
 __all__ = [
     "V3dDepthMapOutputs",
-    "V3dDepthMapParameters",
     "V_3D_DEPTH_MAP_METADATA",
     "v_3d_depth_map",
+    "v_3d_depth_map_execute",
     "v_3d_depth_map_params",
 ]

niwrap_afni/afni/v_3d_despike.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DESPIKE_METADATA = Metadata(
-    id="25879c99c0ec4a24f082b425a60ad7b7f6e906a2.boutiques",
+    id="0d9ca0fdaa93ca1595d1563a20d7d4f183471790.boutiques",
     name="3dDespike",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,20 @@ V_3D_DESPIKE_METADATA = Metadata(
 
 
 V3dDespikeParameters = typing.TypedDict('V3dDespikeParameters', {
-    "__STYXTYPE__": typing.Literal["3dDespike"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDespike"]],
+    "prefix": typing.NotRequired[str | None],
+    "in_file": InputPathType,
+})
+V3dDespikeParametersTagged = typing.TypedDict('V3dDespikeParametersTagged', {
+    "@type": typing.Literal["afni/3dDespike"],
     "prefix": typing.NotRequired[str | None],
     "in_file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dDespike": v_3d_despike_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 {
-        "3dDespike": v_3d_despike_outputs,
-    }.get(t)
 
 
 class V3dDespikeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_despike(...)`.
+    Output object returned when calling `V3dDespikeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class V3dDespikeOutputs(typing.NamedTuple):
 def v_3d_despike_params(
     in_file: InputPathType,
     prefix: str | None = None,
-) -> V3dDespikeParameters:
+) -> V3dDespikeParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def v_3d_despike_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDespike",
+        "@type": "afni/3dDespike",
         "in_file": in_file,
     }
     if prefix is not None:
@@ -99,12 +72,12 @@ def v_3d_despike_cargs(
     """
     cargs = []
     cargs.append("3dDespike")
-    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)
         ])
-    cargs.append(execution.input_file(params.get("in_file")))
+    cargs.append(execution.input_file(params.get("in_file", None)))
     return cargs
 
 
@@ -123,18 +96,20 @@ def v_3d_despike_outputs(
     """
     ret = V3dDespikeOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        out_file=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_despike_execute(
     params: V3dDespikeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDespikeOutputs:
     """
-    Removes 'spikes' from the 3D+time input dataset and writes a new dataset with
-    the spike values replaced by something more pleasing to the eye.
+    3dDespike
+    
+    Removes 'spikes' from the 3D+time input dataset and writes a new dataset
+    with the spike values replaced by something more pleasing to the eye.
     
     Author: AFNI Developers
     
@@ -142,10 +117,12 @@ def v_3d_despike_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDespikeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DESPIKE_METADATA)
     params = execution.params(params)
     cargs = v_3d_despike_cargs(params, execution)
     ret = v_3d_despike_outputs(params, execution)
@@ -159,8 +136,10 @@ def v_3d_despike(
     runner: Runner | None = None,
 ) -> V3dDespikeOutputs:
     """
-    Removes 'spikes' from the 3D+time input dataset and writes a new dataset with
-    the spike values replaced by something more pleasing to the eye.
+    3dDespike
+    
+    Removes 'spikes' from the 3D+time input dataset and writes a new dataset
+    with the spike values replaced by something more pleasing to the eye.
     
     Author: AFNI Developers
     
@@ -173,19 +152,17 @@ def v_3d_despike(
     Returns:
         NamedTuple of outputs (described in `V3dDespikeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DESPIKE_METADATA)
     params = v_3d_despike_params(
         prefix=prefix,
         in_file=in_file,
     )
-    return v_3d_despike_execute(params, execution)
+    return v_3d_despike_execute(params, runner)
 
 
 __all__ = [
     "V3dDespikeOutputs",
-    "V3dDespikeParameters",
     "V_3D_DESPIKE_METADATA",
     "v_3d_despike",
+    "v_3d_despike_execute",
     "v_3d_despike_params",
 ]