niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v_3dkmeans.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DKMEANS_METADATA = Metadata(
-    id="75badc8d9b45ae3a536b3127bd2f907364fc748e.boutiques",
+    id="4659eac7c7853548ba4e9fb9cedfdec6b3bfd618.boutiques",
     name="3dkmeans",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,29 @@ V_3DKMEANS_METADATA = Metadata(
 
 
 V3dkmeansParameters = typing.TypedDict('V3dkmeansParameters', {
-    "__STYXTYPE__": typing.Literal["3dkmeans"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dkmeans"]],
+    "version": bool,
+    "input": list[InputPathType],
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_range": typing.NotRequired[list[float] | None],
+    "cmask": typing.NotRequired[str | None],
+    "jobname": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "distance_measure": typing.NotRequired[float | None],
+    "num_clusters": typing.NotRequired[float | None],
+    "remap_method": typing.NotRequired[str | None],
+    "labeltable": typing.NotRequired[InputPathType | None],
+    "clabels": typing.NotRequired[list[str] | None],
+    "clust_init": typing.NotRequired[InputPathType | None],
+    "num_repeats": typing.NotRequired[float | None],
+    "rsigs": typing.NotRequired[InputPathType | None],
+    "verbose": bool,
+    "write_dists": bool,
+    "voxdbg": typing.NotRequired[list[float] | None],
+    "seed": typing.NotRequired[float | None],
+})
+V3dkmeansParametersTagged = typing.TypedDict('V3dkmeansParametersTagged', {
+    "@type": typing.Literal["afni/3dkmeans"],
     "version": bool,
     "input": list[InputPathType],
     "mask": typing.NotRequired[InputPathType | None],
@@ -35,43 +57,11 @@ V3dkmeansParameters = typing.TypedDict('V3dkmeansParameters', {
     "voxdbg": typing.NotRequired[list[float] | None],
     "seed": 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 {
-        "3dkmeans": v_3dkmeans_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 {
-        "3dkmeans": v_3dkmeans_outputs,
-    }.get(t)
 
 
 class V3dkmeansOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dkmeans(...)`.
+    Output object returned when calling `V3dkmeansParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -111,7 +101,7 @@ def v_3dkmeans_params(
     write_dists: bool = False,
     voxdbg: list[float] | None = None,
     seed: float | None = None,
-) -> V3dkmeansParameters:
+) -> V3dkmeansParametersTagged:
     """
     Build parameters.
     
@@ -154,7 +144,7 @@ def v_3dkmeans_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dkmeans",
+        "@type": "afni/3dkmeans",
         "version": version,
         "input": input_,
         "verbose": verbose,
@@ -208,90 +198,90 @@ def v_3dkmeans_cargs(
     """
     cargs = []
     cargs.append("3dkmeans")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     cargs.extend([
         "-f",
-        *[execution.input_file(f) for f in params.get("input")]
+        *[execution.input_file(f) for f in params.get("input", 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("mask_range") is not None:
+    if params.get("mask_range", None) is not None:
         cargs.extend([
             "-mrange",
-            *map(str, params.get("mask_range"))
+            *map(str, params.get("mask_range", None))
         ])
-    if params.get("cmask") is not None:
+    if params.get("cmask", None) is not None:
         cargs.extend([
             "-cmask",
-            params.get("cmask")
+            params.get("cmask", None)
         ])
-    if params.get("jobname") is not None:
+    if params.get("jobname", None) is not None:
         cargs.extend([
             "-u",
-            params.get("jobname")
+            params.get("jobname", 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("distance_measure") is not None:
+    if params.get("distance_measure", None) is not None:
         cargs.extend([
             "-g",
-            str(params.get("distance_measure"))
+            str(params.get("distance_measure", None))
         ])
-    if params.get("num_clusters") is not None:
+    if params.get("num_clusters", None) is not None:
         cargs.extend([
             "-k",
-            str(params.get("num_clusters"))
+            str(params.get("num_clusters", None))
         ])
-    if params.get("remap_method") is not None:
+    if params.get("remap_method", None) is not None:
         cargs.extend([
             "-remap",
-            params.get("remap_method")
+            params.get("remap_method", None)
         ])
-    if params.get("labeltable") is not None:
+    if params.get("labeltable", None) is not None:
         cargs.extend([
             "-labeltable",
-            execution.input_file(params.get("labeltable"))
+            execution.input_file(params.get("labeltable", None))
         ])
-    if params.get("clabels") is not None:
+    if params.get("clabels", None) is not None:
         cargs.extend([
             "-clabels",
-            *params.get("clabels")
+            *params.get("clabels", None)
         ])
-    if params.get("clust_init") is not None:
+    if params.get("clust_init", None) is not None:
         cargs.extend([
             "-clust_init",
-            execution.input_file(params.get("clust_init"))
+            execution.input_file(params.get("clust_init", None))
         ])
-    if params.get("num_repeats") is not None:
+    if params.get("num_repeats", None) is not None:
         cargs.extend([
             "-r",
-            str(params.get("num_repeats"))
+            str(params.get("num_repeats", None))
         ])
-    if params.get("rsigs") is not None:
+    if params.get("rsigs", None) is not None:
         cargs.extend([
             "-rsigs",
-            execution.input_file(params.get("rsigs"))
+            execution.input_file(params.get("rsigs", None))
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("write_dists"):
+    if params.get("write_dists", False):
         cargs.append("-write_dists")
-    if params.get("voxdbg") is not None:
+    if params.get("voxdbg", None) is not None:
         cargs.extend([
             "-voxdbg",
-            *map(str, params.get("voxdbg"))
+            *map(str, params.get("voxdbg", None))
         ])
-    if params.get("seed") is not None:
+    if params.get("seed", None) is not None:
         cargs.extend([
             "-seed",
-            str(params.get("seed"))
+            str(params.get("seed", None))
         ])
     return cargs
 
@@ -311,8 +301,8 @@ def v_3dkmeans_outputs(
     """
     ret = V3dkmeansOutputs(
         root=execution.output_file("."),
-        cluster_membership=execution.output_file(params.get("jobname") + "_membership.nii.gz") if (params.get("jobname") is not None) else None,
-        cluster_distance=execution.output_file(params.get("jobname") + "_distance.nii.gz") if (params.get("jobname") is not None) else None,
+        cluster_membership=execution.output_file(params.get("jobname", None) + "_membership.nii.gz") if (params.get("jobname") is not None) else None,
+        cluster_distance=execution.output_file(params.get("jobname", None) + "_distance.nii.gz") if (params.get("jobname") is not None) else None,
         distances_text_file=execution.output_file("FILE.dis.1D"),
         centroids_text_file=execution.output_file("FILE.cen.1D"),
         within_cluster_sum_text_file=execution.output_file("FILE.info1.1D"),
@@ -324,9 +314,11 @@ def v_3dkmeans_outputs(
 
 def v_3dkmeans_execute(
     params: V3dkmeansParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dkmeansOutputs:
     """
+    3dkmeans
+    
     3d+t Clustering segmentation based on The C clustering library.
     
     Author: AFNI Developers
@@ -335,10 +327,12 @@ def v_3dkmeans_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dkmeansOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DKMEANS_METADATA)
     params = execution.params(params)
     cargs = v_3dkmeans_cargs(params, execution)
     ret = v_3dkmeans_outputs(params, execution)
@@ -369,6 +363,8 @@ def v_3dkmeans(
     runner: Runner | None = None,
 ) -> V3dkmeansOutputs:
     """
+    3dkmeans
+    
     3d+t Clustering segmentation based on The C clustering library.
     
     Author: AFNI Developers
@@ -414,8 +410,6 @@ def v_3dkmeans(
     Returns:
         NamedTuple of outputs (described in `V3dkmeansOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DKMEANS_METADATA)
     params = v_3dkmeans_params(
         version=version,
         input_=input_,
@@ -437,13 +431,13 @@ def v_3dkmeans(
         voxdbg=voxdbg,
         seed=seed,
     )
-    return v_3dkmeans_execute(params, execution)
+    return v_3dkmeans_execute(params, runner)
 
 
 __all__ = [
     "V3dkmeansOutputs",
-    "V3dkmeansParameters",
     "V_3DKMEANS_METADATA",
     "v_3dkmeans",
+    "v_3dkmeans_execute",
     "v_3dkmeans_params",
 ]

niwrap_afni/afni/v_3dmask_svd.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DMASK_SVD_METADATA = Metadata(
-    id="d590df9b7bd7af7769a60fa5f7ef2b1ffe4dc148.boutiques",
+    id="3afaca16d6ee198be8fa2aef83a6ea126609e032.boutiques",
     name="3dmaskSVD",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3DMASK_SVD_METADATA = Metadata(
 
 
 V3dmaskSvdParameters = typing.TypedDict('V3dmaskSvdParameters', {
-    "__STYXTYPE__": typing.Literal["3dmaskSVD"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dmaskSVD"]],
+    "input_dataset": InputPathType,
+    "vnorm": bool,
+    "sval": typing.NotRequired[float | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "polort": typing.NotRequired[float | None],
+    "bandpass": typing.NotRequired[list[str] | None],
+    "ort": typing.NotRequired[list[InputPathType] | None],
+    "alt_input": typing.NotRequired[InputPathType | None],
+})
+V3dmaskSvdParametersTagged = typing.TypedDict('V3dmaskSvdParametersTagged', {
+    "@type": typing.Literal["afni/3dmaskSVD"],
     "input_dataset": InputPathType,
     "vnorm": bool,
     "sval": typing.NotRequired[float | None],
@@ -25,43 +37,11 @@ V3dmaskSvdParameters = typing.TypedDict('V3dmaskSvdParameters', {
     "ort": typing.NotRequired[list[InputPathType] | None],
     "alt_input": 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 {
-        "3dmaskSVD": v_3dmask_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 {
-        "3dmaskSVD": v_3dmask_svd_outputs,
-    }.get(t)
 
 
 class V3dmaskSvdOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dmask_svd(...)`.
+    Output object returned when calling `V3dmaskSvdParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def v_3dmask_svd_params(
     bandpass: list[str] | None = None,
     ort: list[InputPathType] | None = None,
     alt_input: InputPathType | None = None,
-) -> V3dmaskSvdParameters:
+) -> V3dmaskSvdParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +78,7 @@ def v_3dmask_svd_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dmaskSVD",
+        "@type": "afni/3dmaskSVD",
         "input_dataset": input_dataset,
         "vnorm": vnorm,
         "automask": automask,
@@ -133,40 +113,40 @@ def v_3dmask_svd_cargs(
     """
     cargs = []
     cargs.append("3dmaskSVD")
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    if params.get("vnorm"):
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
+    if params.get("vnorm", False):
         cargs.append("-vnorm")
-    if params.get("sval") is not None:
+    if params.get("sval", None) is not None:
         cargs.extend([
             "-sval",
-            str(params.get("sval"))
+            str(params.get("sval", 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("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    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("bandpass") is not None:
+    if params.get("bandpass", None) is not None:
         cargs.extend([
             "-bpass",
-            *params.get("bandpass")
+            *params.get("bandpass", None)
         ])
-    if params.get("ort") is not None:
+    if params.get("ort", None) is not None:
         cargs.extend([
             "-ort",
-            *[execution.input_file(f) for f in params.get("ort")]
+            *[execution.input_file(f) for f in params.get("ort", None)]
         ])
-    if params.get("alt_input") is not None:
+    if params.get("alt_input", None) is not None:
         cargs.extend([
             "-input",
-            execution.input_file(params.get("alt_input"))
+            execution.input_file(params.get("alt_input", None))
         ])
     return cargs
 
@@ -193,11 +173,13 @@ def v_3dmask_svd_outputs(
 
 def v_3dmask_svd_execute(
     params: V3dmaskSvdParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dmaskSvdOutputs:
     """
-    Computes the principal singular vector of the time series vectors extracted from
-    the input dataset over the input mask.
+    3dmaskSVD
+    
+    Computes the principal singular vector of the time series vectors extracted
+    from the input dataset over the input mask.
     
     Author: AFNI Developers
     
@@ -205,10 +187,12 @@ def v_3dmask_svd_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dmaskSvdOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMASK_SVD_METADATA)
     params = execution.params(params)
     cargs = v_3dmask_svd_cargs(params, execution)
     ret = v_3dmask_svd_outputs(params, execution)
@@ -229,8 +213,10 @@ def v_3dmask_svd(
     runner: Runner | None = None,
 ) -> V3dmaskSvdOutputs:
     """
-    Computes the principal singular vector of the time series vectors extracted from
-    the input dataset over the input mask.
+    3dmaskSVD
+    
+    Computes the principal singular vector of the time series vectors extracted
+    from the input dataset over the input mask.
     
     Author: AFNI Developers
     
@@ -251,8 +237,6 @@ def v_3dmask_svd(
     Returns:
         NamedTuple of outputs (described in `V3dmaskSvdOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DMASK_SVD_METADATA)
     params = v_3dmask_svd_params(
         input_dataset=input_dataset,
         vnorm=vnorm,
@@ -264,13 +248,13 @@ def v_3dmask_svd(
         ort=ort,
         alt_input=alt_input,
     )
-    return v_3dmask_svd_execute(params, execution)
+    return v_3dmask_svd_execute(params, runner)
 
 
 __all__ = [
     "V3dmaskSvdOutputs",
-    "V3dmaskSvdParameters",
     "V_3DMASK_SVD_METADATA",
     "v_3dmask_svd",
+    "v_3dmask_svd_execute",
     "v_3dmask_svd_params",
 ]