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

niwrap_afni/afni/v_3d_rank.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_RANK_METADATA = Metadata(
-    id="3ed67a52ba31b18e397b5efcfba13ef05031c91f.boutiques",
+    id="5a23cfc12c0e4363654019cb91a34ed7f2b61e4e.boutiques",
     name="3dRank",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3D_RANK_METADATA = Metadata(
 
 
 V3dRankParameters = typing.TypedDict('V3dRankParameters', {
-    "__STYXTYPE__": typing.Literal["3dRank"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dRank"]],
+    "input_datasets": list[InputPathType],
+    "output_prefix": typing.NotRequired[str | None],
+    "version_info": bool,
+    "help_info": bool,
+})
+V3dRankParametersTagged = typing.TypedDict('V3dRankParametersTagged', {
+    "@type": typing.Literal["afni/3dRank"],
     "input_datasets": list[InputPathType],
     "output_prefix": typing.NotRequired[str | None],
     "version_info": bool,
     "help_info": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dRank": v_3d_rank_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 {
-        "3dRank": v_3d_rank_outputs,
-    }.get(t)
 
 
 class V3dRankOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_rank(...)`.
+    Output object returned when calling `V3dRankParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +49,7 @@ def v_3d_rank_params(
     output_prefix: str | None = None,
     version_info: bool = False,
     help_info: bool = False,
-) -> V3dRankParameters:
+) -> V3dRankParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +65,7 @@ def v_3d_rank_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dRank",
+        "@type": "afni/3dRank",
         "input_datasets": input_datasets,
         "version_info": version_info,
         "help_info": help_info,
@@ -115,15 +90,15 @@ def v_3d_rank_cargs(
     """
     cargs = []
     cargs.append("3dRank")
-    cargs.extend([execution.input_file(f) for f in params.get("input_datasets")])
-    if params.get("output_prefix") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("input_datasets", None)])
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("version_info"):
+    if params.get("version_info", False):
         cargs.append("-ver")
-    if params.get("help_info"):
+    if params.get("help_info", False):
         cargs.append("-help")
     return cargs
 
@@ -143,18 +118,20 @@ def v_3d_rank_outputs(
     """
     ret = V3dRankOutputs(
         root=execution.output_file("."),
-        output_dataset_head=execution.output_file(params.get("output_prefix") + "*.HEAD") if (params.get("output_prefix") is not None) else None,
-        output_dataset_brik=execution.output_file(params.get("output_prefix") + "*.BRIK") if (params.get("output_prefix") is not None) else None,
-        rank_map_file=execution.output_file(params.get("output_prefix") + "*.1D") if (params.get("output_prefix") is not None) else None,
+        output_dataset_head=execution.output_file(params.get("output_prefix", None) + ".HEAD") if (params.get("output_prefix") is not None) else None,
+        output_dataset_brik=execution.output_file(params.get("output_prefix", None) + ".BRIK") if (params.get("output_prefix") is not None) else None,
+        rank_map_file=execution.output_file(params.get("output_prefix", None) + ".1D") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_rank_execute(
     params: V3dRankParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dRankOutputs:
     """
+    3dRank
+    
     Replaces voxel values by their rank in the set of values collected over all
     voxels in all input datasets.
     
@@ -164,10 +141,12 @@ def v_3d_rank_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRankOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RANK_METADATA)
     params = execution.params(params)
     cargs = v_3d_rank_cargs(params, execution)
     ret = v_3d_rank_outputs(params, execution)
@@ -183,6 +162,8 @@ def v_3d_rank(
     runner: Runner | None = None,
 ) -> V3dRankOutputs:
     """
+    3dRank
+    
     Replaces voxel values by their rank in the set of values collected over all
     voxels in all input datasets.
     
@@ -202,21 +183,19 @@ def v_3d_rank(
     Returns:
         NamedTuple of outputs (described in `V3dRankOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_RANK_METADATA)
     params = v_3d_rank_params(
         input_datasets=input_datasets,
         output_prefix=output_prefix,
         version_info=version_info,
         help_info=help_info,
     )
-    return v_3d_rank_execute(params, execution)
+    return v_3d_rank_execute(params, runner)
 
 
 __all__ = [
     "V3dRankOutputs",
-    "V3dRankParameters",
     "V_3D_RANK_METADATA",
     "v_3d_rank",
+    "v_3d_rank_execute",
     "v_3d_rank_params",
 ]

niwrap_afni/afni/v_3d_rankizer.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_RANKIZER_METADATA = Metadata(
-    id="d25cd53dac78c92a658be818b365fd56efd0a2bb.boutiques",
+    id="d17c4c35340ecaaf4825b74baad438e208b71e64.boutiques",
     name="3dRankizer",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_RANKIZER_METADATA = Metadata(
 
 
 V3dRankizerParameters = typing.TypedDict('V3dRankizerParameters', {
-    "__STYXTYPE__": typing.Literal["3dRankizer"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dRankizer"]],
+    "dataset": InputPathType,
+    "base_rank": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "percentize": bool,
+    "percentize_mask": bool,
+})
+V3dRankizerParametersTagged = typing.TypedDict('V3dRankizerParametersTagged', {
+    "@type": typing.Literal["afni/3dRankizer"],
     "dataset": InputPathType,
     "base_rank": typing.NotRequired[float | None],
     "mask": typing.NotRequired[InputPathType | None],
@@ -22,43 +31,11 @@ V3dRankizerParameters = typing.TypedDict('V3dRankizerParameters', {
     "percentize": bool,
     "percentize_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 {
-        "3dRankizer": v_3d_rankizer_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 {
-        "3dRankizer": v_3d_rankizer_outputs,
-    }.get(t)
 
 
 class V3dRankizerOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_rankizer(...)`.
+    Output object returned when calling `V3dRankizerParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def v_3d_rankizer_params(
     mask: InputPathType | None = None,
     percentize: bool = False,
     percentize_mask: bool = False,
-) -> V3dRankizerParameters:
+) -> V3dRankizerParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +69,7 @@ def v_3d_rankizer_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dRankizer",
+        "@type": "afni/3dRankizer",
         "dataset": dataset,
         "prefix": prefix,
         "percentize": percentize,
@@ -120,24 +97,24 @@ def v_3d_rankizer_cargs(
     """
     cargs = []
     cargs.append("3dRankizer")
-    cargs.append(execution.input_file(params.get("dataset")))
-    if params.get("base_rank") is not None:
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    if params.get("base_rank", None) is not None:
         cargs.extend([
             "-brank",
-            str(params.get("base_rank"))
+            str(params.get("base_rank", 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))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("percentize"):
+    if params.get("percentize", False):
         cargs.append("-percentize")
-    if params.get("percentize_mask"):
+    if params.get("percentize_mask", False):
         cargs.append("-percentize_mask")
     return cargs
 
@@ -157,18 +134,20 @@ def v_3d_rankizer_outputs(
     """
     ret = V3dRankizerOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("prefix") + "+tlrc.HEAD"),
+        output_dataset=execution.output_file(params.get("prefix", None) + "+tlrc.HEAD"),
     )
     return ret
 
 
 def v_3d_rankizer_execute(
     params: V3dRankizerParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dRankizerOutputs:
     """
-    Tool to rank each voxel as sorted into increasing value. Ties get the average
-    rank.
+    3dRankizer
+    
+    Tool to rank each voxel as sorted into increasing value. Ties get the
+    average rank.
     
     Author: AFNI Developers
     
@@ -176,10 +155,12 @@ def v_3d_rankizer_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRankizerOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RANKIZER_METADATA)
     params = execution.params(params)
     cargs = v_3d_rankizer_cargs(params, execution)
     ret = v_3d_rankizer_outputs(params, execution)
@@ -197,8 +178,10 @@ def v_3d_rankizer(
     runner: Runner | None = None,
 ) -> V3dRankizerOutputs:
     """
-    Tool to rank each voxel as sorted into increasing value. Ties get the average
-    rank.
+    3dRankizer
+    
+    Tool to rank each voxel as sorted into increasing value. Ties get the
+    average rank.
     
     Author: AFNI Developers
     
@@ -219,8 +202,6 @@ def v_3d_rankizer(
     Returns:
         NamedTuple of outputs (described in `V3dRankizerOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_RANKIZER_METADATA)
     params = v_3d_rankizer_params(
         dataset=dataset,
         base_rank=base_rank,
@@ -229,13 +210,13 @@ def v_3d_rankizer(
         percentize=percentize,
         percentize_mask=percentize_mask,
     )
-    return v_3d_rankizer_execute(params, execution)
+    return v_3d_rankizer_execute(params, runner)
 
 
 __all__ = [
     "V3dRankizerOutputs",
-    "V3dRankizerParameters",
     "V_3D_RANKIZER_METADATA",
     "v_3d_rankizer",
+    "v_3d_rankizer_execute",
     "v_3d_rankizer_params",
 ]

niwrap_afni/afni/v_3d_re_ho.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_RE_HO_METADATA = Metadata(
-    id="3a27e09e4e1a042595724b1260fd5708eb32b082.boutiques",
+    id="c46ec7166950d75a3ca69b019838d644b481ce05.boutiques",
     name="3dReHo",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_RE_HO_METADATA = Metadata(
 
 
 V3dReHoParameters = typing.TypedDict('V3dReHoParameters', {
-    "__STYXTYPE__": typing.Literal["3dReHo"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dReHo"]],
+    "prefix": str,
+    "inset": InputPathType,
+    "nneigh": typing.NotRequired[str | None],
+    "chi_sq": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "neigh_rad": typing.NotRequired[float | None],
+    "neigh_x": typing.NotRequired[float | None],
+    "neigh_y": typing.NotRequired[float | None],
+    "neigh_z": typing.NotRequired[float | None],
+    "box_rad": typing.NotRequired[float | None],
+    "box_x": typing.NotRequired[float | None],
+    "box_y": typing.NotRequired[float | None],
+    "box_z": typing.NotRequired[float | None],
+    "in_rois": typing.NotRequired[InputPathType | None],
+})
+V3dReHoParametersTagged = typing.TypedDict('V3dReHoParametersTagged', {
+    "@type": typing.Literal["afni/3dReHo"],
     "prefix": str,
     "inset": InputPathType,
     "nneigh": typing.NotRequired[str | None],
@@ -30,43 +47,11 @@ V3dReHoParameters = typing.TypedDict('V3dReHoParameters', {
     "box_z": typing.NotRequired[float | None],
     "in_rois": 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 {
-        "3dReHo": v_3d_re_ho_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 {
-        "3dReHo": v_3d_re_ho_outputs,
-    }.get(t)
 
 
 class V3dReHoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_re_ho(...)`.
+    Output object returned when calling `V3dReHoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -96,7 +81,7 @@ def v_3d_re_ho_params(
     box_y: float | None = None,
     box_z: float | None = None,
     in_rois: InputPathType | None = None,
-) -> V3dReHoParameters:
+) -> V3dReHoParametersTagged:
     """
     Build parameters.
     
@@ -130,7 +115,7 @@ def v_3d_re_ho_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dReHo",
+        "@type": "afni/3dReHo",
         "prefix": prefix,
         "inset": inset,
         "chi_sq": chi_sq,
@@ -177,68 +162,68 @@ def v_3d_re_ho_cargs(
     cargs.append("3dReHo")
     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("nneigh") is not None:
+    if params.get("nneigh", None) is not None:
         cargs.extend([
             "-nneigh",
-            params.get("nneigh")
+            params.get("nneigh", None)
         ])
-    if params.get("chi_sq"):
+    if params.get("chi_sq", False):
         cargs.append("-chi_sq")
-    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("neigh_rad") is not None:
+    if params.get("neigh_rad", None) is not None:
         cargs.extend([
             "-neigh_RAD",
-            str(params.get("neigh_rad"))
+            str(params.get("neigh_rad", None))
         ])
-    if params.get("neigh_x") is not None:
+    if params.get("neigh_x", None) is not None:
         cargs.extend([
             "-neigh_X",
-            str(params.get("neigh_x"))
+            str(params.get("neigh_x", None))
         ])
-    if params.get("neigh_y") is not None:
+    if params.get("neigh_y", None) is not None:
         cargs.extend([
             "-neigh_Y",
-            str(params.get("neigh_y"))
+            str(params.get("neigh_y", None))
         ])
-    if params.get("neigh_z") is not None:
+    if params.get("neigh_z", None) is not None:
         cargs.extend([
             "-neigh_Z",
-            str(params.get("neigh_z"))
+            str(params.get("neigh_z", None))
         ])
-    if params.get("box_rad") is not None:
+    if params.get("box_rad", None) is not None:
         cargs.extend([
             "-box_RAD",
-            str(params.get("box_rad"))
+            str(params.get("box_rad", None))
         ])
-    if params.get("box_x") is not None:
+    if params.get("box_x", None) is not None:
         cargs.extend([
             "-box_X",
-            str(params.get("box_x"))
+            str(params.get("box_x", None))
         ])
-    if params.get("box_y") is not None:
+    if params.get("box_y", None) is not None:
         cargs.extend([
             "-box_Y",
-            str(params.get("box_y"))
+            str(params.get("box_y", None))
         ])
-    if params.get("box_z") is not None:
+    if params.get("box_z", None) is not None:
         cargs.extend([
             "-box_Z",
-            str(params.get("box_z"))
+            str(params.get("box_z", None))
         ])
-    if params.get("in_rois") is not None:
+    if params.get("in_rois", None) is not None:
         cargs.extend([
             "-in_rois",
-            execution.input_file(params.get("in_rois"))
+            execution.input_file(params.get("in_rois", None))
         ])
     return cargs
 
@@ -258,21 +243,23 @@ def v_3d_re_ho_outputs(
     """
     ret = V3dReHoOutputs(
         root=execution.output_file("."),
-        reho_output=execution.output_file(params.get("prefix") + "+orig.BRIK"),
-        roi_reho_vals=execution.output_file(params.get("prefix") + "_ROI_reho.vals"),
-        chi_square=execution.output_file(params.get("prefix") + "+orig.BRIK[1]"),
-        roi_chi_vals=execution.output_file(params.get("prefix") + "_ROI_reho.chi"),
+        reho_output=execution.output_file(params.get("prefix", None) + "+orig.BRIK"),
+        roi_reho_vals=execution.output_file(params.get("prefix", None) + "_ROI_reho.vals"),
+        chi_square=execution.output_file(params.get("prefix", None) + "+orig.BRIK[1]"),
+        roi_chi_vals=execution.output_file(params.get("prefix", None) + "_ROI_reho.chi"),
     )
     return ret
 
 
 def v_3d_re_ho_execute(
     params: V3dReHoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dReHoOutputs:
     """
-    3dReHo calculates Kendall's W per voxel using neighborhood voxels from 4D time
-    series data set.
+    3dReHo
+    
+    3dReHo calculates Kendall's W per voxel using neighborhood voxels from 4D
+    time series data set.
     
     Author: AFNI Developers
     
@@ -280,10 +267,12 @@ def v_3d_re_ho_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dReHoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RE_HO_METADATA)
     params = execution.params(params)
     cargs = v_3d_re_ho_cargs(params, execution)
     ret = v_3d_re_ho_outputs(params, execution)
@@ -309,8 +298,10 @@ def v_3d_re_ho(
     runner: Runner | None = None,
 ) -> V3dReHoOutputs:
     """
-    3dReHo calculates Kendall's W per voxel using neighborhood voxels from 4D time
-    series data set.
+    3dReHo
+    
+    3dReHo calculates Kendall's W per voxel using neighborhood voxels from 4D
+    time series data set.
     
     Author: AFNI Developers
     
@@ -346,8 +337,6 @@ def v_3d_re_ho(
     Returns:
         NamedTuple of outputs (described in `V3dReHoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_RE_HO_METADATA)
     params = v_3d_re_ho_params(
         prefix=prefix,
         inset=inset,
@@ -364,13 +353,13 @@ def v_3d_re_ho(
         box_z=box_z,
         in_rois=in_rois,
     )
-    return v_3d_re_ho_execute(params, execution)
+    return v_3d_re_ho_execute(params, runner)
 
 
 __all__ = [
     "V3dReHoOutputs",
-    "V3dReHoParameters",
     "V_3D_RE_HO_METADATA",
     "v_3d_re_ho",
+    "v_3d_re_ho_execute",
     "v_3d_re_ho_params",
 ]