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

niwrap_afni/afni/v_3d_twoto_complex.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TWOTO_COMPLEX_METADATA = Metadata(
-    id="aa8fbbdea4d3caa146b57ec824c11fc1f44cb810.boutiques",
+    id="17b73527b00b0f307fb5ced607e1099690f5ba4e.boutiques",
     name="3dTwotoComplex",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_TWOTO_COMPLEX_METADATA = Metadata(
 
 
 V3dTwotoComplexParameters = typing.TypedDict('V3dTwotoComplexParameters', {
-    "__STYXTYPE__": typing.Literal["3dTwotoComplex"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTwotoComplex"]],
+    "dataset1": InputPathType,
+    "dataset2": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "ri": bool,
+    "mp": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+})
+V3dTwotoComplexParametersTagged = typing.TypedDict('V3dTwotoComplexParametersTagged', {
+    "@type": typing.Literal["afni/3dTwotoComplex"],
     "dataset1": InputPathType,
     "dataset2": typing.NotRequired[InputPathType | None],
     "prefix": typing.NotRequired[str | None],
@@ -22,43 +31,11 @@ V3dTwotoComplexParameters = typing.TypedDict('V3dTwotoComplexParameters', {
     "mp": bool,
     "mask": 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 {
-        "3dTwotoComplex": v_3d_twoto_complex_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 {
-        "3dTwotoComplex": v_3d_twoto_complex_outputs,
-    }.get(t)
 
 
 class V3dTwotoComplexOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_twoto_complex(...)`.
+    Output object returned when calling `V3dTwotoComplexParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def v_3d_twoto_complex_params(
     ri: bool = False,
     mp: bool = False,
     mask: InputPathType | None = None,
-) -> V3dTwotoComplexParameters:
+) -> V3dTwotoComplexParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +71,7 @@ def v_3d_twoto_complex_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTwotoComplex",
+        "@type": "afni/3dTwotoComplex",
         "dataset1": dataset1,
         "ri": ri,
         "mp": mp,
@@ -123,22 +100,22 @@ def v_3d_twoto_complex_cargs(
     """
     cargs = []
     cargs.append("3dTwotoComplex")
-    cargs.append(execution.input_file(params.get("dataset1")))
-    if params.get("dataset2") is not None:
-        cargs.append(execution.input_file(params.get("dataset2")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("dataset1", None)))
+    if params.get("dataset2", None) is not None:
+        cargs.append(execution.input_file(params.get("dataset2", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("ri"):
+    if params.get("ri", False):
         cargs.append("-RI")
-    if params.get("mp"):
+    if params.get("mp", False):
         cargs.append("-MP")
-    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))
         ])
     return cargs
 
@@ -158,17 +135,19 @@ def v_3d_twoto_complex_outputs(
     """
     ret = V3dTwotoComplexOutputs(
         root=execution.output_file("."),
-        out_brick=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
-        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        out_brick=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        out_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_twoto_complex_execute(
     params: V3dTwotoComplexParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTwotoComplexOutputs:
     """
+    3dTwotoComplex
+    
     Converts 2 sub-bricks of input to a complex-valued dataset.
     
     Author: AFNI Developers
@@ -177,10 +156,12 @@ def v_3d_twoto_complex_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTwotoComplexOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TWOTO_COMPLEX_METADATA)
     params = execution.params(params)
     cargs = v_3d_twoto_complex_cargs(params, execution)
     ret = v_3d_twoto_complex_outputs(params, execution)
@@ -198,6 +179,8 @@ def v_3d_twoto_complex(
     runner: Runner | None = None,
 ) -> V3dTwotoComplexOutputs:
     """
+    3dTwotoComplex
+    
     Converts 2 sub-bricks of input to a complex-valued dataset.
     
     Author: AFNI Developers
@@ -219,8 +202,6 @@ def v_3d_twoto_complex(
     Returns:
         NamedTuple of outputs (described in `V3dTwotoComplexOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TWOTO_COMPLEX_METADATA)
     params = v_3d_twoto_complex_params(
         dataset1=dataset1,
         dataset2=dataset2,
@@ -229,13 +210,13 @@ def v_3d_twoto_complex(
         mp=mp,
         mask=mask,
     )
-    return v_3d_twoto_complex_execute(params, execution)
+    return v_3d_twoto_complex_execute(params, runner)
 
 
 __all__ = [
     "V3dTwotoComplexOutputs",
-    "V3dTwotoComplexParameters",
     "V_3D_TWOTO_COMPLEX_METADATA",
     "v_3d_twoto_complex",
+    "v_3d_twoto_complex_execute",
     "v_3d_twoto_complex_params",
 ]

niwrap_afni/afni/v_3d_undump.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_UNDUMP_METADATA = Metadata(
-    id="a42a3e34bb6d7324060b71b7ded981c6489cdfe0.boutiques",
+    id="e0919ef65f657db4fbb40c7df0c11d28b1620a3e.boutiques",
     name="3dUndump",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,26 @@ V_3D_UNDUMP_METADATA = Metadata(
 
 
 V3dUndumpParameters = typing.TypedDict('V3dUndumpParameters', {
-    "__STYXTYPE__": typing.Literal["3dUndump"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dUndump"]],
+    "input_files": list[InputPathType],
+    "prefix": typing.NotRequired[str | None],
+    "master": typing.NotRequired[InputPathType | None],
+    "dimensions": typing.NotRequired[list[float] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "datatype": typing.NotRequired[str | None],
+    "dval": typing.NotRequired[float | None],
+    "fval": typing.NotRequired[float | None],
+    "ijk": bool,
+    "xyz": bool,
+    "sphere_radius": typing.NotRequired[float | None],
+    "cube_mode": bool,
+    "orient": typing.NotRequired[str | None],
+    "head_only": bool,
+    "roimask": typing.NotRequired[InputPathType | None],
+    "allow_nan": bool,
+})
+V3dUndumpParametersTagged = typing.TypedDict('V3dUndumpParametersTagged', {
+    "@type": typing.Literal["afni/3dUndump"],
     "input_files": list[InputPathType],
     "prefix": typing.NotRequired[str | None],
     "master": typing.NotRequired[InputPathType | None],
@@ -32,43 +51,11 @@ V3dUndumpParameters = typing.TypedDict('V3dUndumpParameters', {
     "roimask": typing.NotRequired[InputPathType | None],
     "allow_nan": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dUndump": v_3d_undump_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 {
-        "3dUndump": v_3d_undump_outputs,
-    }.get(t)
 
 
 class V3dUndumpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_undump(...)`.
+    Output object returned when calling `V3dUndumpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +80,7 @@ def v_3d_undump_params(
     head_only: bool = False,
     roimask: InputPathType | None = None,
     allow_nan: bool = False,
-) -> V3dUndumpParameters:
+) -> V3dUndumpParametersTagged:
     """
     Build parameters.
     
@@ -130,7 +117,7 @@ def v_3d_undump_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dUndump",
+        "@type": "afni/3dUndump",
         "input_files": input_files,
         "ijk": ijk,
         "xyz": xyz,
@@ -176,66 +163,66 @@ def v_3d_undump_cargs(
     """
     cargs = []
     cargs.append("3dUndump")
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
-    if params.get("prefix") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("master") is not None:
+    if params.get("master", None) is not None:
         cargs.extend([
             "-master",
-            execution.input_file(params.get("master"))
+            execution.input_file(params.get("master", None))
         ])
-    if params.get("dimensions") is not None:
+    if params.get("dimensions", None) is not None:
         cargs.extend([
             "-dimen",
-            *map(str, params.get("dimensions"))
+            *map(str, params.get("dimensions", 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("datatype") is not None:
+    if params.get("datatype", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datatype")
+            params.get("datatype", None)
         ])
-    if params.get("dval") is not None:
+    if params.get("dval", None) is not None:
         cargs.extend([
             "-dval",
-            str(params.get("dval"))
+            str(params.get("dval", None))
         ])
-    if params.get("fval") is not None:
+    if params.get("fval", None) is not None:
         cargs.extend([
             "-fval",
-            str(params.get("fval"))
+            str(params.get("fval", None))
         ])
-    if params.get("ijk"):
+    if params.get("ijk", False):
         cargs.append("-ijk")
-    if params.get("xyz"):
+    if params.get("xyz", False):
         cargs.append("-xyz")
-    if params.get("sphere_radius") is not None:
+    if params.get("sphere_radius", None) is not None:
         cargs.extend([
             "-srad",
-            str(params.get("sphere_radius"))
+            str(params.get("sphere_radius", None))
         ])
-    if params.get("cube_mode"):
+    if params.get("cube_mode", False):
         cargs.append("-cubes")
-    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("head_only"):
+    if params.get("head_only", False):
         cargs.append("-head_only")
-    if params.get("roimask") is not None:
+    if params.get("roimask", None) is not None:
         cargs.extend([
             "-ROImask",
-            execution.input_file(params.get("roimask"))
+            execution.input_file(params.get("roimask", None))
         ])
-    if params.get("allow_nan"):
+    if params.get("allow_nan", False):
         cargs.append("-allow_NaN")
     return cargs
 
@@ -255,17 +242,20 @@ def v_3d_undump_outputs(
     """
     ret = V3dUndumpOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        outfile=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_undump_execute(
     params: V3dUndumpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dUndumpOutputs:
     """
-    Assembles a 3D dataset from an ASCII list of coordinates and optionally values.
+    3dUndump
+    
+    Assembles a 3D dataset from an ASCII list of coordinates and optionally
+    values.
     
     Author: AFNI Developers
     
@@ -273,10 +263,12 @@ def v_3d_undump_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dUndumpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_UNDUMP_METADATA)
     params = execution.params(params)
     cargs = v_3d_undump_cargs(params, execution)
     ret = v_3d_undump_outputs(params, execution)
@@ -304,7 +296,10 @@ def v_3d_undump(
     runner: Runner | None = None,
 ) -> V3dUndumpOutputs:
     """
-    Assembles a 3D dataset from an ASCII list of coordinates and optionally values.
+    3dUndump
+    
+    Assembles a 3D dataset from an ASCII list of coordinates and optionally
+    values.
     
     Author: AFNI Developers
     
@@ -343,8 +338,6 @@ def v_3d_undump(
     Returns:
         NamedTuple of outputs (described in `V3dUndumpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_UNDUMP_METADATA)
     params = v_3d_undump_params(
         input_files=input_files,
         prefix=prefix,
@@ -363,13 +356,13 @@ def v_3d_undump(
         roimask=roimask,
         allow_nan=allow_nan,
     )
-    return v_3d_undump_execute(params, execution)
+    return v_3d_undump_execute(params, runner)
 
 
 __all__ = [
     "V3dUndumpOutputs",
-    "V3dUndumpParameters",
     "V_3D_UNDUMP_METADATA",
     "v_3d_undump",
+    "v_3d_undump_execute",
     "v_3d_undump_params",
 ]