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

niwrap_afni/afni/v_3d_gen_priors.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_GEN_PRIORS_METADATA = Metadata(
-    id="91092ee429c6a7122831a6a12f5cca172e9717de.boutiques",
+    id="2ef1d36ab8521e473da2eeb01af4267f96ee82d4.boutiques",
     name="3dGenPriors",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,36 @@ V_3D_GEN_PRIORS_METADATA = Metadata(
 
 
 V3dGenPriorsParameters = typing.TypedDict('V3dGenPriorsParameters', {
-    "__STYXTYPE__": typing.Literal["3dGenPriors"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dGenPriors"]],
+    "sigs": InputPathType,
+    "tdist": InputPathType,
+    "cprefix": str,
+    "pprefix": str,
+    "labeltable": InputPathType,
+    "do": str,
+    "prefix": typing.NotRequired[str | None],
+    "cmask": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[str | None],
+    "mrange": typing.NotRequired[list[float] | None],
+    "debug": typing.NotRequired[float | None],
+    "vox_debug": typing.NotRequired[str | None],
+    "vox_debug_file": typing.NotRequired[str | None],
+    "uid": typing.NotRequired[str | None],
+    "use_tmp": bool,
+    "no_tmp": bool,
+    "pset": typing.NotRequired[str | None],
+    "cset": typing.NotRequired[str | None],
+    "regroup_classes": typing.NotRequired[str | None],
+    "classes": typing.NotRequired[str | None],
+    "features": typing.NotRequired[str | None],
+    "strict_feature_match": bool,
+    "featgroups": typing.NotRequired[str | None],
+    "show_this_dist": typing.NotRequired[str | None],
+    "fast": bool,
+    "slow": bool,
+})
+V3dGenPriorsParametersTagged = typing.TypedDict('V3dGenPriorsParametersTagged', {
+    "@type": typing.Literal["afni/3dGenPriors"],
     "sigs": InputPathType,
     "tdist": InputPathType,
     "cprefix": str,
@@ -42,43 +71,11 @@ V3dGenPriorsParameters = typing.TypedDict('V3dGenPriorsParameters', {
     "fast": bool,
     "slow": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dGenPriors": v_3d_gen_priors_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 {
-        "3dGenPriors": v_3d_gen_priors_outputs,
-    }.get(t)
 
 
 class V3dGenPriorsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_gen_priors(...)`.
+    Output object returned when calling `V3dGenPriorsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -115,7 +112,7 @@ def v_3d_gen_priors_params(
     show_this_dist: str | None = None,
     fast: bool = False,
     slow: bool = False,
-) -> V3dGenPriorsParameters:
+) -> V3dGenPriorsParametersTagged:
     """
     Build parameters.
     
@@ -155,7 +152,7 @@ def v_3d_gen_priors_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dGenPriors",
+        "@type": "afni/3dGenPriors",
         "sigs": sigs,
         "tdist": tdist,
         "cprefix": cprefix,
@@ -218,112 +215,112 @@ def v_3d_gen_priors_cargs(
     cargs.append("3dGenPriors")
     cargs.extend([
         "-sig",
-        execution.input_file(params.get("sigs"))
+        execution.input_file(params.get("sigs", None))
     ])
     cargs.extend([
         "-tdist",
-        execution.input_file(params.get("tdist"))
+        execution.input_file(params.get("tdist", None))
     ])
     cargs.extend([
         "-cprefix",
-        params.get("cprefix")
+        params.get("cprefix", None)
     ])
     cargs.extend([
         "-pprefix",
-        params.get("pprefix")
+        params.get("pprefix", None)
     ])
     cargs.extend([
         "-labeltable",
-        execution.input_file(params.get("labeltable"))
+        execution.input_file(params.get("labeltable", None))
     ])
     cargs.extend([
         "-do",
-        params.get("do")
+        params.get("do", 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("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("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            params.get("mask")
+            params.get("mask", None)
         ])
-    if params.get("mrange") is not None:
+    if params.get("mrange", None) is not None:
         cargs.extend([
             "-mrange",
-            *map(str, params.get("mrange"))
+            *map(str, params.get("mrange", None))
         ])
-    if params.get("debug") is not None:
+    if params.get("debug", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug"))
+            str(params.get("debug", None))
         ])
-    if params.get("vox_debug") is not None:
+    if params.get("vox_debug", None) is not None:
         cargs.extend([
             "-vox_debug",
-            params.get("vox_debug")
+            params.get("vox_debug", None)
         ])
-    if params.get("vox_debug_file") is not None:
+    if params.get("vox_debug_file", None) is not None:
         cargs.extend([
             "-vox_debug_file",
-            params.get("vox_debug_file")
+            params.get("vox_debug_file", None)
         ])
-    if params.get("uid") is not None:
+    if params.get("uid", None) is not None:
         cargs.extend([
             "-uid",
-            params.get("uid")
+            params.get("uid", None)
         ])
-    if params.get("use_tmp"):
+    if params.get("use_tmp", False):
         cargs.append("-use_tmp")
-    if params.get("no_tmp"):
+    if params.get("no_tmp", False):
         cargs.append("-no_tmp")
-    if params.get("pset") is not None:
+    if params.get("pset", None) is not None:
         cargs.extend([
             "-pset",
-            params.get("pset")
+            params.get("pset", None)
         ])
-    if params.get("cset") is not None:
+    if params.get("cset", None) is not None:
         cargs.extend([
             "-cset",
-            params.get("cset")
+            params.get("cset", None)
         ])
-    if params.get("regroup_classes") is not None:
+    if params.get("regroup_classes", None) is not None:
         cargs.extend([
             "-regroup_classes",
-            params.get("regroup_classes")
+            params.get("regroup_classes", None)
         ])
-    if params.get("classes") is not None:
+    if params.get("classes", None) is not None:
         cargs.extend([
             "-classes",
-            params.get("classes")
+            params.get("classes", None)
         ])
-    if params.get("features") is not None:
+    if params.get("features", None) is not None:
         cargs.extend([
             "-features",
-            params.get("features")
+            params.get("features", None)
         ])
-    if params.get("strict_feature_match"):
+    if params.get("strict_feature_match", False):
         cargs.append("-strict_feature_match")
-    if params.get("featgroups") is not None:
+    if params.get("featgroups", None) is not None:
         cargs.extend([
             "-featgroups",
-            params.get("featgroups")
+            params.get("featgroups", None)
         ])
-    if params.get("show_this_dist") is not None:
+    if params.get("show_this_dist", None) is not None:
         cargs.extend([
             "-ShowThisDist",
-            params.get("show_this_dist")
+            params.get("show_this_dist", None)
         ])
-    if params.get("fast"):
+    if params.get("fast", False):
         cargs.append("-fast")
-    if params.get("slow"):
+    if params.get("slow", False):
         cargs.append("-slow")
     return cargs
 
@@ -343,17 +340,19 @@ def v_3d_gen_priors_outputs(
     """
     ret = V3dGenPriorsOutputs(
         root=execution.output_file("."),
-        out_cprefix=execution.output_file(params.get("cprefix") + ".nii.gz"),
-        out_pprefix=execution.output_file(params.get("pprefix") + ".nii.gz"),
+        out_cprefix=execution.output_file(params.get("cprefix", None) + ".nii.gz"),
+        out_pprefix=execution.output_file(params.get("pprefix", None) + ".nii.gz"),
     )
     return ret
 
 
 def v_3d_gen_priors_execute(
     params: V3dGenPriorsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dGenPriorsOutputs:
     """
+    3dGenPriors
+    
     Produces classification priors based on voxel signatures.
     
     Author: AFNI Developers
@@ -362,10 +361,12 @@ def v_3d_gen_priors_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dGenPriorsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_GEN_PRIORS_METADATA)
     params = execution.params(params)
     cargs = v_3d_gen_priors_cargs(params, execution)
     ret = v_3d_gen_priors_outputs(params, execution)
@@ -403,6 +404,8 @@ def v_3d_gen_priors(
     runner: Runner | None = None,
 ) -> V3dGenPriorsOutputs:
     """
+    3dGenPriors
+    
     Produces classification priors based on voxel signatures.
     
     Author: AFNI Developers
@@ -445,8 +448,6 @@ def v_3d_gen_priors(
     Returns:
         NamedTuple of outputs (described in `V3dGenPriorsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_GEN_PRIORS_METADATA)
     params = v_3d_gen_priors_params(
         sigs=sigs,
         tdist=tdist,
@@ -475,13 +476,13 @@ def v_3d_gen_priors(
         fast=fast,
         slow=slow,
     )
-    return v_3d_gen_priors_execute(params, execution)
+    return v_3d_gen_priors_execute(params, runner)
 
 
 __all__ = [
     "V3dGenPriorsOutputs",
-    "V3dGenPriorsParameters",
     "V_3D_GEN_PRIORS_METADATA",
     "v_3d_gen_priors",
+    "v_3d_gen_priors_execute",
     "v_3d_gen_priors_params",
 ]

niwrap_afni/afni/v_3d_getrow.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_GETROW_METADATA = Metadata(
-    id="07f583964934ab4d2f12cc2751f27623c441a893.boutiques",
+    id="fe2cbb2a6fe1ed79c57056bfe6ae512bbf863d90.boutiques",
     name="3dGetrow",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V_3D_GETROW_METADATA = Metadata(
 
 
 V3dGetrowParameters = typing.TypedDict('V3dGetrowParameters', {
-    "__STYXTYPE__": typing.Literal["3dGetrow"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dGetrow"]],
+    "xrow": typing.NotRequired[list[int] | None],
+    "yrow": typing.NotRequired[list[int] | None],
+    "zrow": typing.NotRequired[list[int] | None],
+    "input_file": typing.NotRequired[InputPathType | None],
+    "output_file": typing.NotRequired[str | None],
+})
+V3dGetrowParametersTagged = typing.TypedDict('V3dGetrowParametersTagged', {
+    "@type": typing.Literal["afni/3dGetrow"],
     "xrow": typing.NotRequired[list[int] | None],
     "yrow": typing.NotRequired[list[int] | None],
     "zrow": typing.NotRequired[list[int] | None],
     "input_file": typing.NotRequired[InputPathType | None],
     "output_file": 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 {
-        "3dGetrow": v_3d_getrow_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 {
-        "3dGetrow": v_3d_getrow_outputs,
-    }.get(t)
 
 
 class V3dGetrowOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_getrow(...)`.
+    Output object returned when calling `V3dGetrowParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def v_3d_getrow_params(
     zrow: list[int] | None = None,
     input_file: InputPathType | None = None,
     output_file: str | None = None,
-) -> V3dGetrowParameters:
+) -> V3dGetrowParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +66,7 @@ def v_3d_getrow_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dGetrow",
+        "@type": "afni/3dGetrow",
     }
     if xrow is not None:
         params["xrow"] = xrow
@@ -120,30 +96,30 @@ def v_3d_getrow_cargs(
     """
     cargs = []
     cargs.append("3dGetrow")
-    if params.get("xrow") is not None:
+    if params.get("xrow", None) is not None:
         cargs.extend([
             "-xrow",
-            *map(str, params.get("xrow"))
+            *map(str, params.get("xrow", None))
         ])
-    if params.get("yrow") is not None:
+    if params.get("yrow", None) is not None:
         cargs.extend([
             "-yrow",
-            *map(str, params.get("yrow"))
+            *map(str, params.get("yrow", None))
         ])
-    if params.get("zrow") is not None:
+    if params.get("zrow", None) is not None:
         cargs.extend([
             "-zrow",
-            *map(str, params.get("zrow"))
+            *map(str, params.get("zrow", None))
         ])
-    if params.get("input_file") is not None:
+    if params.get("input_file", None) is not None:
         cargs.extend([
             "-input",
-            execution.input_file(params.get("input_file"))
+            execution.input_file(params.get("input_file", None))
         ])
-    if params.get("output_file") is not None:
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-output",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
     return cargs
 
@@ -163,16 +139,18 @@ def v_3d_getrow_outputs(
     """
     ret = V3dGetrowOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("output_file") + ".1D") if (params.get("output_file") is not None) else None,
+        out_file=execution.output_file(params.get("output_file", None) + ".1D") if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def v_3d_getrow_execute(
     params: V3dGetrowParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dGetrowOutputs:
     """
+    3dGetrow
+    
     Program to extract 1 row from a dataset and write it as a .1D file.
     
     Author: AFNI Developers
@@ -181,10 +159,12 @@ def v_3d_getrow_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dGetrowOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_GETROW_METADATA)
     params = execution.params(params)
     cargs = v_3d_getrow_cargs(params, execution)
     ret = v_3d_getrow_outputs(params, execution)
@@ -201,6 +181,8 @@ def v_3d_getrow(
     runner: Runner | None = None,
 ) -> V3dGetrowOutputs:
     """
+    3dGetrow
+    
     Program to extract 1 row from a dataset and write it as a .1D file.
     
     Author: AFNI Developers
@@ -222,8 +204,6 @@ def v_3d_getrow(
     Returns:
         NamedTuple of outputs (described in `V3dGetrowOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_GETROW_METADATA)
     params = v_3d_getrow_params(
         xrow=xrow,
         yrow=yrow,
@@ -231,13 +211,13 @@ def v_3d_getrow(
         input_file=input_file,
         output_file=output_file,
     )
-    return v_3d_getrow_execute(params, execution)
+    return v_3d_getrow_execute(params, runner)
 
 
 __all__ = [
     "V3dGetrowOutputs",
-    "V3dGetrowParameters",
     "V_3D_GETROW_METADATA",
     "v_3d_getrow",
+    "v_3d_getrow_execute",
     "v_3d_getrow_params",
 ]