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

niwrap_afni/afni/v_3d_ecm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ECM_METADATA = Metadata(
-    id="5765fcd4fd9cde03d3bff59f1b7e35b7ffb1d691.boutiques",
+    id="dc84c4ba00debbcb6bece9fbb3dc81531d184e64.boutiques",
     name="3dECM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,27 @@ V_3D_ECM_METADATA = Metadata(
 
 
 V3dEcmParameters = typing.TypedDict('V3dEcmParameters', {
-    "__STYXTYPE__": typing.Literal["3dECM"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dECM"]],
+    "in_file": InputPathType,
+    "autoclip": bool,
+    "automask": bool,
+    "eps": typing.NotRequired[float | None],
+    "fecm": bool,
+    "full": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "max_iter": typing.NotRequired[int | None],
+    "memory": typing.NotRequired[float | None],
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "out_file": typing.NotRequired[str | None],
+    "polort": typing.NotRequired[int | None],
+    "scale": typing.NotRequired[float | None],
+    "shift": typing.NotRequired[float | None],
+    "sparsity": typing.NotRequired[float | None],
+    "thresh": typing.NotRequired[float | None],
+})
+V3dEcmParametersTagged = typing.TypedDict('V3dEcmParametersTagged', {
+    "@type": typing.Literal["afni/3dECM"],
     "in_file": InputPathType,
     "autoclip": bool,
     "automask": bool,
@@ -33,43 +53,11 @@ V3dEcmParameters = typing.TypedDict('V3dEcmParameters', {
     "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 {
-        "3dECM": v_3d_ecm_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 {
-        "3dECM": v_3d_ecm_outputs,
-    }.get(t)
 
 
 class V3dEcmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_ecm(...)`.
+    Output object returned when calling `V3dEcmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -97,7 +85,7 @@ def v_3d_ecm_params(
     shift: float | None = None,
     sparsity: float | None = None,
     thresh: float | None = None,
-) -> V3dEcmParameters:
+) -> V3dEcmParametersTagged:
     """
     Build parameters.
     
@@ -132,7 +120,7 @@ def v_3d_ecm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dECM",
+        "@type": "afni/3dECM",
         "in_file": in_file,
         "autoclip": autoclip,
         "automask": automask,
@@ -181,68 +169,68 @@ def v_3d_ecm_cargs(
     """
     cargs = []
     cargs.append("3dECM")
-    cargs.append(execution.input_file(params.get("in_file")))
-    if params.get("autoclip"):
+    cargs.append(execution.input_file(params.get("in_file", None)))
+    if params.get("autoclip", False):
         cargs.append("-autoclip")
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("eps") is not None:
+    if params.get("eps", None) is not None:
         cargs.extend([
             "-eps",
-            str(params.get("eps"))
+            str(params.get("eps", None))
         ])
-    if params.get("fecm"):
+    if params.get("fecm", False):
         cargs.append("-fecm")
-    if params.get("full"):
+    if params.get("full", False):
         cargs.append("-full")
-    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("max_iter") is not None:
+    if params.get("max_iter", None) is not None:
         cargs.extend([
             "-max_iter",
-            str(params.get("max_iter"))
+            str(params.get("max_iter", None))
         ])
-    if params.get("memory") is not None:
+    if params.get("memory", None) is not None:
         cargs.extend([
             "-memory",
-            str(params.get("memory"))
+            str(params.get("memory", None))
         ])
-    if params.get("num_threads") is not None:
-        cargs.append(str(params.get("num_threads")))
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    if params.get("out_file") is not None:
+    if params.get("num_threads", None) is not None:
+        cargs.append(str(params.get("num_threads", None)))
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
+    if params.get("out_file", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("out_file")
+            params.get("out_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("scale") is not None:
+    if params.get("scale", None) is not None:
         cargs.extend([
             "-scale",
-            str(params.get("scale"))
+            str(params.get("scale", None))
         ])
-    if params.get("shift") is not None:
+    if params.get("shift", None) is not None:
         cargs.extend([
             "-shift",
-            str(params.get("shift"))
+            str(params.get("shift", 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
 
@@ -262,7 +250,7 @@ def v_3d_ecm_outputs(
     """
     ret = V3dEcmOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(pathlib.Path(params.get("in_file")).name + "_afni"),
+        out_file=execution.output_file(pathlib.Path(params.get("in_file", None)).name + "_afni"),
         out_file_=execution.output_file("out_file"),
     )
     return ret
@@ -270,9 +258,11 @@ def v_3d_ecm_outputs(
 
 def v_3d_ecm_execute(
     params: V3dEcmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dEcmOutputs:
     """
+    3dECM
+    
     Performs degree centrality on a dataset using a given maskfile via the 3dECM
     command.
     
@@ -282,10 +272,12 @@ def v_3d_ecm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dEcmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ECM_METADATA)
     params = execution.params(params)
     cargs = v_3d_ecm_cargs(params, execution)
     ret = v_3d_ecm_outputs(params, execution)
@@ -314,6 +306,8 @@ def v_3d_ecm(
     runner: Runner | None = None,
 ) -> V3dEcmOutputs:
     """
+    3dECM
+    
     Performs degree centrality on a dataset using a given maskfile via the 3dECM
     command.
     
@@ -352,8 +346,6 @@ def v_3d_ecm(
     Returns:
         NamedTuple of outputs (described in `V3dEcmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ECM_METADATA)
     params = v_3d_ecm_params(
         in_file=in_file,
         autoclip=autoclip,
@@ -373,13 +365,13 @@ def v_3d_ecm(
         sparsity=sparsity,
         thresh=thresh,
     )
-    return v_3d_ecm_execute(params, execution)
+    return v_3d_ecm_execute(params, runner)
 
 
 __all__ = [
     "V3dEcmOutputs",
-    "V3dEcmParameters",
     "V_3D_ECM_METADATA",
     "v_3d_ecm",
+    "v_3d_ecm_execute",
     "v_3d_ecm_params",
 ]

niwrap_afni/afni/v_3d_edu_01_scale.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_EDU_01_SCALE_METADATA = Metadata(
-    id="882d93a008679bc5297ea9ae14de61c1a4182b85.boutiques",
+    id="bf9e7a5bd7bc4419390243111049a4474109df28.boutiques",
     name="3dEdu_01_scale",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,55 +14,27 @@ V_3D_EDU_01_SCALE_METADATA = Metadata(
 
 
 V3dEdu01ScaleParameters = typing.TypedDict('V3dEdu01ScaleParameters', {
-    "__STYXTYPE__": typing.Literal["3dEdu_01_scale"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dEdu_01_scale"]],
+    "input": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "mult_factors": typing.NotRequired[list[float] | None],
+    "option_flag": bool,
+})
+V3dEdu01ScaleParametersTagged = typing.TypedDict('V3dEdu01ScaleParametersTagged', {
+    "@type": typing.Literal["afni/3dEdu_01_scale"],
     "input": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "mult_factors": typing.NotRequired[list[float] | None],
     "option_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dEdu_01_scale": v_3d_edu_01_scale_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 {
-        "3dEdu_01_scale": v_3d_edu_01_scale_outputs,
-    }.get(t)
 
 
 class V3dEdu01ScaleOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_edu_01_scale(...)`.
+    Output object returned when calling `V3dEdu01ScaleParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    outfile: OutputPathType
-    """Output scaled and/or masked copy of the [0]th volume of the input
-    dataset"""
 
 
 def v_3d_edu_01_scale_params(
@@ -70,7 +42,7 @@ def v_3d_edu_01_scale_params(
     mask: InputPathType | None = None,
     mult_factors: list[float] | None = None,
     option_flag: bool = False,
-) -> V3dEdu01ScaleParameters:
+) -> V3dEdu01ScaleParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +56,7 @@ def v_3d_edu_01_scale_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dEdu_01_scale",
+        "@type": "afni/3dEdu_01_scale",
         "input": input_,
         "option_flag": option_flag,
     }
@@ -110,18 +82,18 @@ def v_3d_edu_01_scale_cargs(
     """
     cargs = []
     cargs.append("3dEdu_01_scale")
-    cargs.append(execution.input_file(params.get("input")))
-    if params.get("mask") is not None:
+    cargs.append(execution.input_file(params.get("input", 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("mult_factors") is not None:
+    if params.get("mult_factors", None) is not None:
         cargs.extend([
             "-mult_facs",
-            *map(str, params.get("mult_factors"))
+            *map(str, params.get("mult_factors", None))
         ])
-    if params.get("option_flag"):
+    if params.get("option_flag", False):
         cargs.append("-some_opt")
     return cargs
 
@@ -141,16 +113,17 @@ def v_3d_edu_01_scale_outputs(
     """
     ret = V3dEdu01ScaleOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file("OUT_edu_[1-9]*"),
     )
     return ret
 
 
 def v_3d_edu_01_scale_execute(
     params: V3dEdu01ScaleParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dEdu01ScaleOutputs:
     """
+    3dEdu_01_scale
+    
     Educational program to create a new AFNI program. Scales and masks dataset
     volumes.
     
@@ -160,10 +133,12 @@ def v_3d_edu_01_scale_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dEdu01ScaleOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EDU_01_SCALE_METADATA)
     params = execution.params(params)
     cargs = v_3d_edu_01_scale_cargs(params, execution)
     ret = v_3d_edu_01_scale_outputs(params, execution)
@@ -179,6 +154,8 @@ def v_3d_edu_01_scale(
     runner: Runner | None = None,
 ) -> V3dEdu01ScaleOutputs:
     """
+    3dEdu_01_scale
+    
     Educational program to create a new AFNI program. Scales and masks dataset
     volumes.
     
@@ -196,21 +173,19 @@ def v_3d_edu_01_scale(
     Returns:
         NamedTuple of outputs (described in `V3dEdu01ScaleOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_EDU_01_SCALE_METADATA)
     params = v_3d_edu_01_scale_params(
         input_=input_,
         mask=mask,
         mult_factors=mult_factors,
         option_flag=option_flag,
     )
-    return v_3d_edu_01_scale_execute(params, execution)
+    return v_3d_edu_01_scale_execute(params, runner)
 
 
 __all__ = [
     "V3dEdu01ScaleOutputs",
-    "V3dEdu01ScaleParameters",
     "V_3D_EDU_01_SCALE_METADATA",
     "v_3d_edu_01_scale",
+    "v_3d_edu_01_scale_execute",
     "v_3d_edu_01_scale_params",
 ]

niwrap_afni/afni/v_3d_eigs_to_dt.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_EIGS_TO_DT_METADATA = Metadata(
-    id="2a859820023438ce7134628316920f709603fea4.boutiques",
+    id="dbdc99d3e2baf249bb90fe77b70d558550d64576.boutiques",
     name="3dEigsToDT",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_EIGS_TO_DT_METADATA = Metadata(
 
 
 V3dEigsToDtParameters = typing.TypedDict('V3dEigsToDtParameters', {
-    "__STYXTYPE__": typing.Literal["3dEigsToDT"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dEigsToDT"]],
+    "eig_vals": str,
+    "eig_vecs": str,
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "scale_eigs": typing.NotRequired[float | None],
+})
+V3dEigsToDtParametersTagged = typing.TypedDict('V3dEigsToDtParametersTagged', {
+    "@type": typing.Literal["afni/3dEigsToDT"],
     "eig_vals": str,
     "eig_vecs": str,
     "prefix": str,
@@ -24,43 +35,11 @@ V3dEigsToDtParameters = typing.TypedDict('V3dEigsToDtParameters', {
     "flip_z": bool,
     "scale_eigs": 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 {
-        "3dEigsToDT": v_3d_eigs_to_dt_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 {
-        "3dEigsToDT": v_3d_eigs_to_dt_outputs,
-    }.get(t)
 
 
 class V3dEigsToDtOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_eigs_to_dt(...)`.
+    Output object returned when calling `V3dEigsToDtParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +58,7 @@ def v_3d_eigs_to_dt_params(
     flip_y: bool = False,
     flip_z: bool = False,
     scale_eigs: float | None = None,
-) -> V3dEigsToDtParameters:
+) -> V3dEigsToDtParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +81,7 @@ def v_3d_eigs_to_dt_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dEigsToDT",
+        "@type": "afni/3dEigsToDT",
         "eig_vals": eig_vals,
         "eig_vecs": eig_vecs,
         "prefix": prefix,
@@ -134,31 +113,31 @@ def v_3d_eigs_to_dt_cargs(
     cargs.append("3dEigsToDT")
     cargs.extend([
         "-eig_vals",
-        params.get("eig_vals")
+        params.get("eig_vals", None)
     ])
     cargs.extend([
         "-eig_vecs",
-        params.get("eig_vecs")
+        params.get("eig_vecs", None)
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("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("flip_x"):
+    if params.get("flip_x", False):
         cargs.append("-flip_x")
-    if params.get("flip_y"):
+    if params.get("flip_y", False):
         cargs.append("-flip_y")
-    if params.get("flip_z"):
+    if params.get("flip_z", False):
         cargs.append("-flip_z")
-    if params.get("scale_eigs") is not None:
+    if params.get("scale_eigs", None) is not None:
         cargs.extend([
             "-scale_eigs",
-            str(params.get("scale_eigs"))
+            str(params.get("scale_eigs", None))
         ])
     return cargs
 
@@ -178,17 +157,19 @@ def v_3d_eigs_to_dt_outputs(
     """
     ret = V3dEigsToDtOutputs(
         root=execution.output_file("."),
-        dt_brik_output=execution.output_file(params.get("prefix") + "_DT+orig.BRIK"),
-        dt_head_output=execution.output_file(params.get("prefix") + "_DT+orig.HEAD"),
+        dt_brik_output=execution.output_file(params.get("prefix", None) + "_DT+orig.BRIK"),
+        dt_head_output=execution.output_file(params.get("prefix", None) + "_DT+orig.HEAD"),
     )
     return ret
 
 
 def v_3d_eigs_to_dt_execute(
     params: V3dEigsToDtParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dEigsToDtOutputs:
     """
+    3dEigsToDT
+    
     Convert set of DTI eigenvectors and eigenvalues to a diffusion tensor, with
     optional value-scaling and vector-flipping.
     
@@ -198,10 +179,12 @@ def v_3d_eigs_to_dt_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dEigsToDtOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EIGS_TO_DT_METADATA)
     params = execution.params(params)
     cargs = v_3d_eigs_to_dt_cargs(params, execution)
     ret = v_3d_eigs_to_dt_outputs(params, execution)
@@ -221,6 +204,8 @@ def v_3d_eigs_to_dt(
     runner: Runner | None = None,
 ) -> V3dEigsToDtOutputs:
     """
+    3dEigsToDT
+    
     Convert set of DTI eigenvectors and eigenvalues to a diffusion tensor, with
     optional value-scaling and vector-flipping.
     
@@ -247,8 +232,6 @@ def v_3d_eigs_to_dt(
     Returns:
         NamedTuple of outputs (described in `V3dEigsToDtOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_EIGS_TO_DT_METADATA)
     params = v_3d_eigs_to_dt_params(
         eig_vals=eig_vals,
         eig_vecs=eig_vecs,
@@ -259,13 +242,13 @@ def v_3d_eigs_to_dt(
         flip_z=flip_z,
         scale_eigs=scale_eigs,
     )
-    return v_3d_eigs_to_dt_execute(params, execution)
+    return v_3d_eigs_to_dt_execute(params, runner)
 
 
 __all__ = [
     "V3dEigsToDtOutputs",
-    "V3dEigsToDtParameters",
     "V_3D_EIGS_TO_DT_METADATA",
     "v_3d_eigs_to_dt",
+    "v_3d_eigs_to_dt_execute",
     "v_3d_eigs_to_dt_params",
 ]