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

niwrap_afni/afni/v_3d_clust_count.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_CLUST_COUNT_METADATA = Metadata(
-    id="69d4eb9bd4a197a90cb255e74008d918a4d6fbec.boutiques",
+    id="bba3556a01bcefede9729b43d63f695d828f84e3.boutiques",
     name="3dClustCount",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3D_CLUST_COUNT_METADATA = Metadata(
 
 
 V3dClustCountParameters = typing.TypedDict('V3dClustCountParameters', {
-    "__STYXTYPE__": typing.Literal["3dClustCount"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dClustCount"]],
+    "datasets": list[InputPathType],
+    "prefix": typing.NotRequired[str | None],
+    "final": bool,
+    "quiet": bool,
+})
+V3dClustCountParametersTagged = typing.TypedDict('V3dClustCountParametersTagged', {
+    "@type": typing.Literal["afni/3dClustCount"],
     "datasets": list[InputPathType],
     "prefix": typing.NotRequired[str | None],
     "final": bool,
     "quiet": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dClustCount": v_3d_clust_count_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 {
-        "3dClustCount": v_3d_clust_count_outputs,
-    }.get(t)
 
 
 class V3dClustCountOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_clust_count(...)`.
+    Output object returned when calling `V3dClustCountParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +48,7 @@ def v_3d_clust_count_params(
     prefix: str | None = None,
     final: bool = False,
     quiet: bool = False,
-) -> V3dClustCountParameters:
+) -> V3dClustCountParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +68,7 @@ def v_3d_clust_count_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dClustCount",
+        "@type": "afni/3dClustCount",
         "datasets": datasets,
         "final": final,
         "quiet": quiet,
@@ -118,15 +93,15 @@ def v_3d_clust_count_cargs(
     """
     cargs = []
     cargs.append("3dClustCount")
-    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
-    if params.get("prefix") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("datasets", None)])
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("final"):
+    if params.get("final", False):
         cargs.append("-final")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
     return cargs
 
@@ -146,18 +121,20 @@ def v_3d_clust_count_outputs(
     """
     ret = V3dClustCountOutputs(
         root=execution.output_file("."),
-        clustcount_niml=execution.output_file(params.get("prefix") + ".clustcount.niml") if (params.get("prefix") is not None) else None,
-        clustcount_1_d=execution.output_file(params.get("prefix") + ".1D") if (params.get("prefix") is not None) else None,
-        final_clustcount_niml=execution.output_file(params.get("prefix") + ".niml") if (params.get("prefix") is not None) else None,
+        clustcount_niml=execution.output_file(params.get("prefix", None) + ".clustcount.niml") if (params.get("prefix") is not None) else None,
+        clustcount_1_d=execution.output_file(params.get("prefix", None) + ".1D") if (params.get("prefix") is not None) else None,
+        final_clustcount_niml=execution.output_file(params.get("prefix", None) + ".niml") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_clust_count_execute(
     params: V3dClustCountParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dClustCountOutputs:
     """
+    3dClustCount
+    
     This program takes as input 1 or more datasets, thresholds them at various
     levels, and counts up the number of clusters of various sizes.
     
@@ -167,10 +144,12 @@ def v_3d_clust_count_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dClustCountOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CLUST_COUNT_METADATA)
     params = execution.params(params)
     cargs = v_3d_clust_count_cargs(params, execution)
     ret = v_3d_clust_count_outputs(params, execution)
@@ -186,6 +165,8 @@ def v_3d_clust_count(
     runner: Runner | None = None,
 ) -> V3dClustCountOutputs:
     """
+    3dClustCount
+    
     This program takes as input 1 or more datasets, thresholds them at various
     levels, and counts up the number of clusters of various sizes.
     
@@ -209,21 +190,19 @@ def v_3d_clust_count(
     Returns:
         NamedTuple of outputs (described in `V3dClustCountOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_CLUST_COUNT_METADATA)
     params = v_3d_clust_count_params(
         datasets=datasets,
         prefix=prefix,
         final=final,
         quiet=quiet,
     )
-    return v_3d_clust_count_execute(params, execution)
+    return v_3d_clust_count_execute(params, runner)
 
 
 __all__ = [
     "V3dClustCountOutputs",
-    "V3dClustCountParameters",
     "V_3D_CLUST_COUNT_METADATA",
     "v_3d_clust_count",
+    "v_3d_clust_count_execute",
     "v_3d_clust_count_params",
 ]

niwrap_afni/afni/v_3d_clust_sim.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_CLUST_SIM_METADATA = Metadata(
-    id="3538a0525d6d878ecea30110b69b1f8b3e739d8a.boutiques",
+    id="0c35843247cd8857e9d84ff47e38d9298db2301a.boutiques",
     name="3dClustSim",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,32 @@ V_3D_CLUST_SIM_METADATA = Metadata(
 
 
 V3dClustSimParameters = typing.TypedDict('V3dClustSimParameters', {
-    "__STYXTYPE__": typing.Literal["3dClustSim"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dClustSim"]],
+    "nxyz": typing.NotRequired[str | None],
+    "dxyz": typing.NotRequired[str | None],
+    "ball": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "oksmallmask": bool,
+    "inset": typing.NotRequired[list[InputPathType] | None],
+    "fwhm": typing.NotRequired[float | None],
+    "acf": typing.NotRequired[str | None],
+    "nopad": bool,
+    "pthr": typing.NotRequired[str | None],
+    "athr": typing.NotRequired[str | None],
+    "lots": bool,
+    "mega": bool,
+    "iter": typing.NotRequired[float | None],
+    "nodec": bool,
+    "seed": typing.NotRequired[float | None],
+    "niml": bool,
+    "both": bool,
+    "prefix": typing.NotRequired[str | None],
+    "cmd": typing.NotRequired[str | None],
+    "quiet": bool,
+    "ssave": typing.NotRequired[str | None],
+})
+V3dClustSimParametersTagged = typing.TypedDict('V3dClustSimParametersTagged', {
+    "@type": typing.Literal["afni/3dClustSim"],
     "nxyz": typing.NotRequired[str | None],
     "dxyz": typing.NotRequired[str | None],
     "ball": bool,
@@ -38,43 +63,11 @@ V3dClustSimParameters = typing.TypedDict('V3dClustSimParameters', {
     "quiet": bool,
     "ssave": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dClustSim": v_3d_clust_sim_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 {
-        "3dClustSim": v_3d_clust_sim_outputs,
-    }.get(t)
 
 
 class V3dClustSimOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_clust_sim(...)`.
+    Output object returned when calling `V3dClustSimParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -123,7 +116,7 @@ def v_3d_clust_sim_params(
     cmd_: str | None = None,
     quiet: bool = False,
     ssave: str | None = None,
-) -> V3dClustSimParameters:
+) -> V3dClustSimParametersTagged:
     """
     Build parameters.
     
@@ -156,7 +149,7 @@ def v_3d_clust_sim_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dClustSim",
+        "@type": "afni/3dClustSim",
         "ball": ball,
         "oksmallmask": oksmallmask,
         "nopad": nopad,
@@ -211,88 +204,88 @@ def v_3d_clust_sim_cargs(
     """
     cargs = []
     cargs.append("3dClustSim")
-    if params.get("nxyz") is not None:
+    if params.get("nxyz", None) is not None:
         cargs.extend([
             "-nxyz",
-            params.get("nxyz")
+            params.get("nxyz", None)
         ])
-    if params.get("dxyz") is not None:
+    if params.get("dxyz", None) is not None:
         cargs.extend([
             "-dxyz",
-            params.get("dxyz")
+            params.get("dxyz", None)
         ])
-    if params.get("ball"):
+    if params.get("ball", False):
         cargs.append("-BALL")
-    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("oksmallmask"):
+    if params.get("oksmallmask", False):
         cargs.append("-OKsmallmask")
-    if params.get("inset") is not None:
+    if params.get("inset", None) is not None:
         cargs.extend([
             "-inset",
-            *[execution.input_file(f) for f in params.get("inset")]
+            *[execution.input_file(f) for f in params.get("inset", None)]
         ])
-    if params.get("fwhm") is not None:
+    if params.get("fwhm", None) is not None:
         cargs.extend([
             "-fwhm",
-            str(params.get("fwhm"))
+            str(params.get("fwhm", None))
         ])
-    if params.get("acf") is not None:
+    if params.get("acf", None) is not None:
         cargs.extend([
             "-acf",
-            params.get("acf")
+            params.get("acf", None)
         ])
-    if params.get("nopad"):
+    if params.get("nopad", False):
         cargs.append("-nopad")
-    if params.get("pthr") is not None:
+    if params.get("pthr", None) is not None:
         cargs.extend([
             "-pthr",
-            params.get("pthr")
+            params.get("pthr", None)
         ])
-    if params.get("athr") is not None:
+    if params.get("athr", None) is not None:
         cargs.extend([
             "-athr",
-            params.get("athr")
+            params.get("athr", None)
         ])
-    if params.get("lots"):
+    if params.get("lots", False):
         cargs.append("-LOTS")
-    if params.get("mega"):
+    if params.get("mega", False):
         cargs.append("-MEGA")
-    if params.get("iter") is not None:
+    if params.get("iter", None) is not None:
         cargs.extend([
             "-iter",
-            str(params.get("iter"))
+            str(params.get("iter", None))
         ])
-    if params.get("nodec"):
+    if params.get("nodec", False):
         cargs.append("-nodec")
-    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))
         ])
-    if params.get("niml"):
+    if params.get("niml", False):
         cargs.append("-niml")
-    if params.get("both"):
+    if params.get("both", False):
         cargs.append("-both")
-    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("cmd") is not None:
+    if params.get("cmd", None) is not None:
         cargs.extend([
             "-cmd",
-            params.get("cmd")
+            params.get("cmd", None)
         ])
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("ssave") is not None:
+    if params.get("ssave", None) is not None:
         cargs.extend([
             "-ssave",
-            params.get("ssave")
+            params.get("ssave", None)
         ])
     return cargs
 
@@ -312,25 +305,27 @@ def v_3d_clust_sim_outputs(
     """
     ret = V3dClustSimOutputs(
         root=execution.output_file("."),
-        output_nn1_1sided=execution.output_file(params.get("prefix") + ".NN1_1sided.1D") if (params.get("prefix") is not None) else None,
-        output_nn1_2sided=execution.output_file(params.get("prefix") + ".NN1_2sided.1D") if (params.get("prefix") is not None) else None,
-        output_nn1_bisided=execution.output_file(params.get("prefix") + ".NN1_bisided.1D") if (params.get("prefix") is not None) else None,
-        output_nn2_1sided=execution.output_file(params.get("prefix") + ".NN2_1sided.1D") if (params.get("prefix") is not None) else None,
-        output_nn2_2sided=execution.output_file(params.get("prefix") + ".NN2_2sided.1D") if (params.get("prefix") is not None) else None,
-        output_nn2_bisided=execution.output_file(params.get("prefix") + ".NN2_bisided.1D") if (params.get("prefix") is not None) else None,
-        output_nn3_1sided=execution.output_file(params.get("prefix") + ".NN3_1sided.1D") if (params.get("prefix") is not None) else None,
-        output_nn3_2sided=execution.output_file(params.get("prefix") + ".NN3_2sided.1D") if (params.get("prefix") is not None) else None,
-        output_nn3_bisided=execution.output_file(params.get("prefix") + ".NN3_bisided.1D") if (params.get("prefix") is not None) else None,
-        mask_compressed=execution.output_file(params.get("prefix") + ".mask") if (params.get("prefix") is not None) else None,
+        output_nn1_1sided=execution.output_file(params.get("prefix", None) + ".NN1_1sided.1D") if (params.get("prefix") is not None) else None,
+        output_nn1_2sided=execution.output_file(params.get("prefix", None) + ".NN1_2sided.1D") if (params.get("prefix") is not None) else None,
+        output_nn1_bisided=execution.output_file(params.get("prefix", None) + ".NN1_bisided.1D") if (params.get("prefix") is not None) else None,
+        output_nn2_1sided=execution.output_file(params.get("prefix", None) + ".NN2_1sided.1D") if (params.get("prefix") is not None) else None,
+        output_nn2_2sided=execution.output_file(params.get("prefix", None) + ".NN2_2sided.1D") if (params.get("prefix") is not None) else None,
+        output_nn2_bisided=execution.output_file(params.get("prefix", None) + ".NN2_bisided.1D") if (params.get("prefix") is not None) else None,
+        output_nn3_1sided=execution.output_file(params.get("prefix", None) + ".NN3_1sided.1D") if (params.get("prefix") is not None) else None,
+        output_nn3_2sided=execution.output_file(params.get("prefix", None) + ".NN3_2sided.1D") if (params.get("prefix") is not None) else None,
+        output_nn3_bisided=execution.output_file(params.get("prefix", None) + ".NN3_bisided.1D") if (params.get("prefix") is not None) else None,
+        mask_compressed=execution.output_file(params.get("prefix", None) + ".mask") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_clust_sim_execute(
     params: V3dClustSimParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dClustSimOutputs:
     """
+    3dClustSim
+    
     Program to estimate the probability of false positive (noise-only) clusters.
     
     Author: AFNI Developers
@@ -339,10 +334,12 @@ def v_3d_clust_sim_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dClustSimOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CLUST_SIM_METADATA)
     params = execution.params(params)
     cargs = v_3d_clust_sim_cargs(params, execution)
     ret = v_3d_clust_sim_outputs(params, execution)
@@ -376,6 +373,8 @@ def v_3d_clust_sim(
     runner: Runner | None = None,
 ) -> V3dClustSimOutputs:
     """
+    3dClustSim
+    
     Program to estimate the probability of false positive (noise-only) clusters.
     
     Author: AFNI Developers
@@ -411,8 +410,6 @@ def v_3d_clust_sim(
     Returns:
         NamedTuple of outputs (described in `V3dClustSimOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_CLUST_SIM_METADATA)
     params = v_3d_clust_sim_params(
         nxyz=nxyz,
         dxyz=dxyz,
@@ -437,13 +434,13 @@ def v_3d_clust_sim(
         quiet=quiet,
         ssave=ssave,
     )
-    return v_3d_clust_sim_execute(params, execution)
+    return v_3d_clust_sim_execute(params, runner)
 
 
 __all__ = [
     "V3dClustSimOutputs",
-    "V3dClustSimParameters",
     "V_3D_CLUST_SIM_METADATA",
     "v_3d_clust_sim",
+    "v_3d_clust_sim_execute",
     "v_3d_clust_sim_params",
 ]