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

niwrap_afni/afni/v_3d_clusterize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_CLUSTERIZE_METADATA = Metadata(
-    id="e4655542f19e9af1312825c39fb9645b11431092.boutiques",
+    id="725fbe8de4d68e491d4c6521feeffaddeff3ba5c.boutiques",
     name="3dClusterize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,34 @@ V_3D_CLUSTERIZE_METADATA = Metadata(
 
 
 V3dClusterizeParameters = typing.TypedDict('V3dClusterizeParameters', {
-    "__STYXTYPE__": typing.Literal["3dClusterize"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dClusterize"]],
+    "inset": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_from_hdr": bool,
+    "out_mask": typing.NotRequired[str | None],
+    "ithr": str,
+    "idat": typing.NotRequired[str | None],
+    "onesided": typing.NotRequired[str | None],
+    "twosided": typing.NotRequired[str | None],
+    "bisided": typing.NotRequired[str | None],
+    "within_range": typing.NotRequired[str | None],
+    "nn": int,
+    "clust_nvox": typing.NotRequired[int | None],
+    "clust_vol": typing.NotRequired[int | None],
+    "pref_map": typing.NotRequired[str | None],
+    "pref_dat": typing.NotRequired[str | None],
+    "one_d_format": bool,
+    "no_one_d_format": bool,
+    "summarize": bool,
+    "nosum": bool,
+    "quiet": bool,
+    "outvol_if_no_clust": bool,
+    "orient": typing.NotRequired[str | None],
+    "abs_table_data": bool,
+    "binary": bool,
+})
+V3dClusterizeParametersTagged = typing.TypedDict('V3dClusterizeParametersTagged', {
+    "@type": typing.Literal["afni/3dClusterize"],
     "inset": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "mask_from_hdr": bool,
@@ -40,43 +67,11 @@ V3dClusterizeParameters = typing.TypedDict('V3dClusterizeParameters', {
     "abs_table_data": bool,
     "binary": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dClusterize": v_3d_clusterize_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 {
-        "3dClusterize": v_3d_clusterize_outputs,
-    }.get(t)
 
 
 class V3dClusterizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_clusterize(...)`.
+    Output object returned when calling `V3dClusterizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -113,7 +108,7 @@ def v_3d_clusterize_params(
     orient: str | None = None,
     abs_table_data: bool = False,
     binary: bool = False,
-) -> V3dClusterizeParameters:
+) -> V3dClusterizeParametersTagged:
     """
     Build parameters.
     
@@ -148,7 +143,7 @@ def v_3d_clusterize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dClusterize",
+        "@type": "afni/3dClusterize",
         "inset": inset,
         "mask_from_hdr": mask_from_hdr,
         "ithr": ithr,
@@ -206,93 +201,93 @@ def v_3d_clusterize_cargs(
     cargs.append("3dClusterize")
     cargs.extend([
         "-inset",
-        execution.input_file(params.get("inset"))
+        execution.input_file(params.get("inset", 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_from_hdr"):
+    if params.get("mask_from_hdr", False):
         cargs.append("-mask_from_hdr")
-    if params.get("out_mask") is not None:
+    if params.get("out_mask", None) is not None:
         cargs.extend([
             "-out_mask",
-            params.get("out_mask")
+            params.get("out_mask", None)
         ])
     cargs.extend([
         "-ithr",
-        params.get("ithr")
+        params.get("ithr", None)
     ])
-    if params.get("idat") is not None:
+    if params.get("idat", None) is not None:
         cargs.extend([
             "-idat",
-            params.get("idat")
+            params.get("idat", None)
         ])
-    if params.get("onesided") is not None:
+    if params.get("onesided", None) is not None:
         cargs.extend([
             "-1sided",
-            params.get("onesided")
+            params.get("onesided", None)
         ])
-    if params.get("twosided") is not None:
+    if params.get("twosided", None) is not None:
         cargs.extend([
             "-2sided",
-            params.get("twosided")
+            params.get("twosided", None)
         ])
-    if params.get("bisided") is not None:
+    if params.get("bisided", None) is not None:
         cargs.extend([
             "-bisided",
-            params.get("bisided")
+            params.get("bisided", None)
         ])
-    if params.get("within_range") is not None:
+    if params.get("within_range", None) is not None:
         cargs.extend([
             "-within_range",
-            params.get("within_range")
+            params.get("within_range", None)
         ])
     cargs.extend([
         "-NN",
-        str(params.get("nn"))
+        str(params.get("nn", None))
     ])
-    if params.get("clust_nvox") is not None:
+    if params.get("clust_nvox", None) is not None:
         cargs.extend([
             "-clust_nvox",
-            str(params.get("clust_nvox"))
+            str(params.get("clust_nvox", None))
         ])
-    if params.get("clust_vol") is not None:
+    if params.get("clust_vol", None) is not None:
         cargs.extend([
             "-clust_vol",
-            str(params.get("clust_vol"))
+            str(params.get("clust_vol", None))
         ])
-    if params.get("pref_map") is not None:
+    if params.get("pref_map", None) is not None:
         cargs.extend([
             "-pref_map",
-            params.get("pref_map")
+            params.get("pref_map", None)
         ])
-    if params.get("pref_dat") is not None:
+    if params.get("pref_dat", None) is not None:
         cargs.extend([
             "-pref_dat",
-            params.get("pref_dat")
+            params.get("pref_dat", None)
         ])
-    if params.get("one_d_format"):
+    if params.get("one_d_format", False):
         cargs.append("-1Dformat")
-    if params.get("no_one_d_format"):
+    if params.get("no_one_d_format", False):
         cargs.append("-no_1Dformat")
-    if params.get("summarize"):
+    if params.get("summarize", False):
         cargs.append("-summarize")
-    if params.get("nosum"):
+    if params.get("nosum", False):
         cargs.append("-nosum")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("outvol_if_no_clust"):
+    if params.get("outvol_if_no_clust", False):
         cargs.append("-outvol_if_no_clust")
-    if params.get("orient") is not None:
+    if params.get("orient", None) is not None:
         cargs.extend([
             "-orient",
-            params.get("orient")
+            params.get("orient", None)
         ])
-    if params.get("abs_table_data"):
+    if params.get("abs_table_data", False):
         cargs.append("-abs_table_data")
-    if params.get("binary"):
+    if params.get("binary", False):
         cargs.append("-binary")
     return cargs
 
@@ -312,18 +307,20 @@ def v_3d_clusterize_outputs(
     """
     ret = V3dClusterizeOutputs(
         root=execution.output_file("."),
-        out_map_file=execution.output_file(params.get("pref_map") + "+orig.HEAD") if (params.get("pref_map") is not None) else None,
-        out_data_file=execution.output_file(params.get("pref_dat") + "+orig.HEAD") if (params.get("pref_dat") is not None) else None,
-        out_mask_file=execution.output_file(params.get("out_mask") + "+orig.HEAD") if (params.get("out_mask") is not None) else None,
+        out_map_file=execution.output_file(params.get("pref_map", None) + "+orig.HEAD") if (params.get("pref_map") is not None) else None,
+        out_data_file=execution.output_file(params.get("pref_dat", None) + "+orig.HEAD") if (params.get("pref_dat") is not None) else None,
+        out_mask_file=execution.output_file(params.get("out_mask", None) + "+orig.HEAD") if (params.get("out_mask") is not None) else None,
     )
     return ret
 
 
 def v_3d_clusterize_execute(
     params: V3dClusterizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dClusterizeOutputs:
     """
+    3dClusterize
+    
     A tool for voxelwise thresholding and clusterizing of datasets.
     
     Author: AFNI Developers
@@ -332,10 +329,12 @@ def v_3d_clusterize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dClusterizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CLUSTERIZE_METADATA)
     params = execution.params(params)
     cargs = v_3d_clusterize_cargs(params, execution)
     ret = v_3d_clusterize_outputs(params, execution)
@@ -371,6 +370,8 @@ def v_3d_clusterize(
     runner: Runner | None = None,
 ) -> V3dClusterizeOutputs:
     """
+    3dClusterize
+    
     A tool for voxelwise thresholding and clusterizing of datasets.
     
     Author: AFNI Developers
@@ -408,8 +409,6 @@ def v_3d_clusterize(
     Returns:
         NamedTuple of outputs (described in `V3dClusterizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_CLUSTERIZE_METADATA)
     params = v_3d_clusterize_params(
         inset=inset,
         mask=mask,
@@ -436,13 +435,13 @@ def v_3d_clusterize(
         abs_table_data=abs_table_data,
         binary=binary,
     )
-    return v_3d_clusterize_execute(params, execution)
+    return v_3d_clusterize_execute(params, runner)
 
 
 __all__ = [
     "V3dClusterizeOutputs",
-    "V3dClusterizeParameters",
     "V_3D_CLUSTERIZE_METADATA",
     "v_3d_clusterize",
+    "v_3d_clusterize_execute",
     "v_3d_clusterize_params",
 ]

niwrap_afni/afni/v_3d_cm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_CM_METADATA = Metadata(
-    id="86d28ac666c67b4bd4d8d68c8533d068db093ca1.boutiques",
+    id="cc4964ce8dfead0a7b95f8643fa44e42b93444ab.boutiques",
     name="3dCM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_CM_METADATA = Metadata(
 
 
 V3dCmParameters = typing.TypedDict('V3dCmParameters', {
-    "__STYXTYPE__": typing.Literal["3dCM"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dCM"]],
+    "dset": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "set_origin": typing.NotRequired[list[float] | None],
+    "local_ijk": bool,
+    "roi_vals": typing.NotRequired[list[float] | None],
+    "all_rois": bool,
+    "icent": bool,
+    "dcent": bool,
+})
+V3dCmParametersTagged = typing.TypedDict('V3dCmParametersTagged', {
+    "@type": typing.Literal["afni/3dCM"],
     "dset": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "automask": bool,
@@ -25,48 +37,16 @@ V3dCmParameters = typing.TypedDict('V3dCmParameters', {
     "icent": bool,
     "dcent": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dCM": v_3d_cm_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 {
-        "3dCM": v_3d_cm_outputs,
-    }.get(t)
 
 
 class V3dCmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_cm(...)`.
+    Output object returned when calling `V3dCmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    center_of_mass: OutputPathType
-    """Center of mass of the dataset."""
+    stdout: list[str]
+    """center of mass of the dataset"""
 
 
 def v_3d_cm_params(
@@ -79,7 +59,7 @@ def v_3d_cm_params(
     all_rois: bool = False,
     icent: bool = False,
     dcent: bool = False,
-) -> V3dCmParameters:
+) -> V3dCmParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +86,7 @@ def v_3d_cm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dCM",
+        "@type": "afni/3dCM",
         "dset": dset,
         "automask": automask,
         "local_ijk": local_ijk,
@@ -138,31 +118,31 @@ def v_3d_cm_cargs(
     """
     cargs = []
     cargs.append("3dCM")
-    cargs.append(execution.input_file(params.get("dset")))
-    if params.get("mask") is not None:
+    cargs.append(execution.input_file(params.get("dset", 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("set_origin") is not None:
+    if params.get("set_origin", None) is not None:
         cargs.extend([
             "-set",
-            *map(str, params.get("set_origin"))
+            *map(str, params.get("set_origin", None))
         ])
-    if params.get("local_ijk"):
+    if params.get("local_ijk", False):
         cargs.append("-local_ijk")
-    if params.get("roi_vals") is not None:
+    if params.get("roi_vals", None) is not None:
         cargs.extend([
             "-roi_vals",
-            *map(str, params.get("roi_vals"))
+            *map(str, params.get("roi_vals", None))
         ])
-    if params.get("all_rois"):
+    if params.get("all_rois", False):
         cargs.append("-all_rois")
-    if params.get("icent"):
+    if params.get("icent", False):
         cargs.append("-Icent")
-    if params.get("dcent"):
+    if params.get("dcent", False):
         cargs.append("-Dcent")
     return cargs
 
@@ -182,16 +162,18 @@ def v_3d_cm_outputs(
     """
     ret = V3dCmOutputs(
         root=execution.output_file("."),
-        center_of_mass=execution.output_file("<stdout>"),
+        stdout=[],
     )
     return ret
 
 
 def v_3d_cm_execute(
     params: V3dCmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dCmOutputs:
     """
+    3dCM
+    
     Tool for computing the center of mass of a dataset.
     
     Author: AFNI Developers
@@ -200,14 +182,16 @@ def v_3d_cm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dCmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CM_METADATA)
     params = execution.params(params)
     cargs = v_3d_cm_cargs(params, execution)
     ret = v_3d_cm_outputs(params, execution)
-    execution.run(cargs)
+    execution.run(cargs, handle_stdout=lambda s: ret.stdout.append(s))
     return ret
 
 
@@ -224,6 +208,8 @@ def v_3d_cm(
     runner: Runner | None = None,
 ) -> V3dCmOutputs:
     """
+    3dCM
+    
     Tool for computing the center of mass of a dataset.
     
     Author: AFNI Developers
@@ -253,8 +239,6 @@ def v_3d_cm(
     Returns:
         NamedTuple of outputs (described in `V3dCmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_CM_METADATA)
     params = v_3d_cm_params(
         dset=dset,
         mask=mask,
@@ -266,13 +250,13 @@ def v_3d_cm(
         icent=icent,
         dcent=dcent,
     )
-    return v_3d_cm_execute(params, execution)
+    return v_3d_cm_execute(params, runner)
 
 
 __all__ = [
     "V3dCmOutputs",
-    "V3dCmParameters",
     "V_3D_CM_METADATA",
     "v_3d_cm",
+    "v_3d_cm_execute",
     "v_3d_cm_params",
 ]