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

niwrap_afni/afni/v_3d_zregrid.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ZREGRID_METADATA = Metadata(
-    id="db022b59eef3bb41c838694c65e5ebc0749928b2.boutiques",
+    id="b39d545c55431f2a5f0304bee7d362ad69dcd3e9.boutiques",
     name="3dZregrid",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_ZREGRID_METADATA = Metadata(
 
 
 V3dZregridParameters = typing.TypedDict('V3dZregridParameters', {
-    "__STYXTYPE__": typing.Literal["3dZregrid"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dZregrid"]],
+    "z_thickness": typing.NotRequired[float | None],
+    "slice_count": typing.NotRequired[float | None],
+    "z_size": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "infile": InputPathType,
+    "verbose": bool,
+})
+V3dZregridParametersTagged = typing.TypedDict('V3dZregridParametersTagged', {
+    "@type": typing.Literal["afni/3dZregrid"],
     "z_thickness": typing.NotRequired[float | None],
     "slice_count": typing.NotRequired[float | None],
     "z_size": typing.NotRequired[float | None],
@@ -22,43 +31,11 @@ V3dZregridParameters = typing.TypedDict('V3dZregridParameters', {
     "infile": InputPathType,
     "verbose": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dZregrid": v_3d_zregrid_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 {
-        "3dZregrid": v_3d_zregrid_outputs,
-    }.get(t)
 
 
 class V3dZregridOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_zregrid(...)`.
+    Output object returned when calling `V3dZregridParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def v_3d_zregrid_params(
     z_size: float | None = None,
     prefix: str | None = None,
     verbose: bool = False,
-) -> V3dZregridParameters:
+) -> V3dZregridParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +68,7 @@ def v_3d_zregrid_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dZregrid",
+        "@type": "afni/3dZregrid",
         "infile": infile,
         "verbose": verbose,
     }
@@ -121,28 +98,28 @@ def v_3d_zregrid_cargs(
     """
     cargs = []
     cargs.append("3dZregrid")
-    if params.get("z_thickness") is not None:
+    if params.get("z_thickness", None) is not None:
         cargs.extend([
             "-dz",
-            str(params.get("z_thickness"))
+            str(params.get("z_thickness", None))
         ])
-    if params.get("slice_count") is not None:
+    if params.get("slice_count", None) is not None:
         cargs.extend([
             "-nz",
-            str(params.get("slice_count"))
+            str(params.get("slice_count", None))
         ])
-    if params.get("z_size") is not None:
+    if params.get("z_size", None) is not None:
         cargs.extend([
             "-zsize",
-            str(params.get("z_size"))
+            str(params.get("z_size", 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)
         ])
-    cargs.append(execution.input_file(params.get("infile")))
-    if params.get("verbose"):
+    cargs.append(execution.input_file(params.get("infile", None)))
+    if params.get("verbose", False):
         cargs.append("-verb")
     return cargs
 
@@ -162,17 +139,19 @@ def v_3d_zregrid_outputs(
     """
     ret = V3dZregridOutputs(
         root=execution.output_file("."),
-        outfile_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
-        outfile_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        outfile_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        outfile_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_zregrid_execute(
     params: V3dZregridParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dZregridOutputs:
     """
+    3dZregrid
+    
     Alters the input dataset's slice thickness and/or number.
     
     Author: AFNI Developers
@@ -181,10 +160,12 @@ def v_3d_zregrid_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dZregridOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ZREGRID_METADATA)
     params = execution.params(params)
     cargs = v_3d_zregrid_cargs(params, execution)
     ret = v_3d_zregrid_outputs(params, execution)
@@ -202,6 +183,8 @@ def v_3d_zregrid(
     runner: Runner | None = None,
 ) -> V3dZregridOutputs:
     """
+    3dZregrid
+    
     Alters the input dataset's slice thickness and/or number.
     
     Author: AFNI Developers
@@ -220,8 +203,6 @@ def v_3d_zregrid(
     Returns:
         NamedTuple of outputs (described in `V3dZregridOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ZREGRID_METADATA)
     params = v_3d_zregrid_params(
         z_thickness=z_thickness,
         slice_count=slice_count,
@@ -230,13 +211,13 @@ def v_3d_zregrid(
         infile=infile,
         verbose=verbose,
     )
-    return v_3d_zregrid_execute(params, execution)
+    return v_3d_zregrid_execute(params, runner)
 
 
 __all__ = [
     "V3dZregridOutputs",
-    "V3dZregridParameters",
     "V_3D_ZREGRID_METADATA",
     "v_3d_zregrid",
+    "v_3d_zregrid_execute",
     "v_3d_zregrid_params",
 ]

niwrap_afni/afni/v_3danisosmooth.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DANISOSMOOTH_METADATA = Metadata(
-    id="1ba569c84d08290efa7b480422abdfb93ead68bf.boutiques",
+    id="dae012901f3b9c0ef9fb5a4a4f358d15d077efc3.boutiques",
     name="3danisosmooth",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,32 @@ V_3DANISOSMOOTH_METADATA = Metadata(
 
 
 V3danisosmoothParameters = typing.TypedDict('V3danisosmoothParameters', {
-    "__STYXTYPE__": typing.Literal["3danisosmooth"],
+    "@type": typing.NotRequired[typing.Literal["afni/3danisosmooth"]],
+    "input_dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "iterations": typing.NotRequired[float | None],
+    "2d_flag": bool,
+    "3d_flag": bool,
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "automask_flag": bool,
+    "viewer_flag": bool,
+    "nosmooth_flag": bool,
+    "sigma1": typing.NotRequired[float | None],
+    "sigma2": typing.NotRequired[float | None],
+    "deltat": typing.NotRequired[float | None],
+    "savetempdata_flag": bool,
+    "save_temp_with_diff_measures_flag": bool,
+    "phiding_flag": bool,
+    "phiexp_flag": bool,
+    "noneg_flag": bool,
+    "setneg_value": typing.NotRequired[float | None],
+    "edgefraction": typing.NotRequired[float | None],
+    "datum_type": typing.NotRequired[str | None],
+    "matchorig_flag": bool,
+    "help_flag": bool,
+})
+V3danisosmoothParametersTagged = typing.TypedDict('V3danisosmoothParametersTagged', {
+    "@type": typing.Literal["afni/3danisosmooth"],
     "input_dataset": InputPathType,
     "prefix": typing.NotRequired[str | None],
     "iterations": typing.NotRequired[float | None],
@@ -38,43 +63,11 @@ V3danisosmoothParameters = typing.TypedDict('V3danisosmoothParameters', {
     "matchorig_flag": bool,
     "help_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 {
-        "3danisosmooth": v_3danisosmooth_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 {
-        "3danisosmooth": v_3danisosmooth_outputs,
-    }.get(t)
 
 
 class V3danisosmoothOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3danisosmooth(...)`.
+    Output object returned when calling `V3danisosmoothParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -122,7 +115,7 @@ def v_3danisosmooth_params(
     datum_type: str | None = None,
     matchorig_flag: bool = False,
     help_flag: bool = False,
-) -> V3danisosmoothParameters:
+) -> V3danisosmoothParametersTagged:
     """
     Build parameters.
     
@@ -158,7 +151,7 @@ def v_3danisosmooth_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3danisosmooth",
+        "@type": "afni/3danisosmooth",
         "input_dataset": input_dataset,
         "2d_flag": v_2d_flag,
         "3d_flag": v_3d_flag,
@@ -209,75 +202,75 @@ def v_3danisosmooth_cargs(
     """
     cargs = []
     cargs.append("3danisosmooth")
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("iterations") is not None:
+    if params.get("iterations", None) is not None:
         cargs.extend([
             "-iters",
-            str(params.get("iterations"))
+            str(params.get("iterations", None))
         ])
-    if params.get("2d_flag"):
+    if params.get("2d_flag", False):
         cargs.append("-2D")
-    if params.get("3d_flag"):
+    if params.get("3d_flag", False):
         cargs.append("-3D")
-    if params.get("mask_dataset") is not None:
+    if params.get("mask_dataset", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_dataset"))
+            execution.input_file(params.get("mask_dataset", None))
         ])
-    if params.get("automask_flag"):
+    if params.get("automask_flag", False):
         cargs.append("-automask")
-    if params.get("viewer_flag"):
+    if params.get("viewer_flag", False):
         cargs.append("-viewer")
-    if params.get("nosmooth_flag"):
+    if params.get("nosmooth_flag", False):
         cargs.append("-nosmooth")
-    if params.get("sigma1") is not None:
+    if params.get("sigma1", None) is not None:
         cargs.extend([
             "-sigma1",
-            str(params.get("sigma1"))
+            str(params.get("sigma1", None))
         ])
-    if params.get("sigma2") is not None:
+    if params.get("sigma2", None) is not None:
         cargs.extend([
             "-sigma2",
-            str(params.get("sigma2"))
+            str(params.get("sigma2", None))
         ])
-    if params.get("deltat") is not None:
+    if params.get("deltat", None) is not None:
         cargs.extend([
             "-deltat",
-            str(params.get("deltat"))
+            str(params.get("deltat", None))
         ])
-    if params.get("savetempdata_flag"):
+    if params.get("savetempdata_flag", False):
         cargs.append("-savetempdata")
-    if params.get("save_temp_with_diff_measures_flag"):
+    if params.get("save_temp_with_diff_measures_flag", False):
         cargs.append("-save_temp_with_diff_measures")
-    if params.get("phiding_flag"):
+    if params.get("phiding_flag", False):
         cargs.append("-phiding")
-    if params.get("phiexp_flag"):
+    if params.get("phiexp_flag", False):
         cargs.append("-phiexp")
-    if params.get("noneg_flag"):
+    if params.get("noneg_flag", False):
         cargs.append("-noneg")
-    if params.get("setneg_value") is not None:
+    if params.get("setneg_value", None) is not None:
         cargs.extend([
             "-setneg",
-            str(params.get("setneg_value"))
+            str(params.get("setneg_value", None))
         ])
-    if params.get("edgefraction") is not None:
+    if params.get("edgefraction", None) is not None:
         cargs.extend([
             "-edgefraction",
-            str(params.get("edgefraction"))
+            str(params.get("edgefraction", None))
         ])
-    if params.get("datum_type") is not None:
+    if params.get("datum_type", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datum_type")
+            params.get("datum_type", None)
         ])
-    if params.get("matchorig_flag"):
+    if params.get("matchorig_flag", False):
         cargs.append("-matchorig")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-help")
     return cargs
 
@@ -297,7 +290,7 @@ def v_3danisosmooth_outputs(
     """
     ret = V3danisosmoothOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("prefix") + "+smooth") if (params.get("prefix") is not None) else None,
+        output_dataset=execution.output_file(params.get("prefix", None) + "+smooth") if (params.get("prefix") is not None) else None,
         gradient_data=execution.output_file("Gradient.ITER"),
         eigens_data=execution.output_file("Eigens.ITER"),
         phi_data=execution.output_file("phi.ITER"),
@@ -312,9 +305,11 @@ def v_3danisosmooth_outputs(
 
 def v_3danisosmooth_execute(
     params: V3danisosmoothParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3danisosmoothOutputs:
     """
+    3danisosmooth
+    
     Smooths a dataset using an anisotropic smoothing technique.
     
     Author: AFNI Developers
@@ -323,10 +318,12 @@ def v_3danisosmooth_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3danisosmoothOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DANISOSMOOTH_METADATA)
     params = execution.params(params)
     cargs = v_3danisosmooth_cargs(params, execution)
     ret = v_3danisosmooth_outputs(params, execution)
@@ -360,6 +357,8 @@ def v_3danisosmooth(
     runner: Runner | None = None,
 ) -> V3danisosmoothOutputs:
     """
+    3danisosmooth
+    
     Smooths a dataset using an anisotropic smoothing technique.
     
     Author: AFNI Developers
@@ -398,8 +397,6 @@ def v_3danisosmooth(
     Returns:
         NamedTuple of outputs (described in `V3danisosmoothOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DANISOSMOOTH_METADATA)
     params = v_3danisosmooth_params(
         input_dataset=input_dataset,
         prefix=prefix,
@@ -424,13 +421,13 @@ def v_3danisosmooth(
         matchorig_flag=matchorig_flag,
         help_flag=help_flag,
     )
-    return v_3danisosmooth_execute(params, execution)
+    return v_3danisosmooth_execute(params, runner)
 
 
 __all__ = [
     "V3danisosmoothOutputs",
-    "V3danisosmoothParameters",
     "V_3DANISOSMOOTH_METADATA",
     "v_3danisosmooth",
+    "v_3danisosmooth_execute",
     "v_3danisosmooth_params",
 ]

niwrap_afni/afni/v_3daxialize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DAXIALIZE_METADATA = Metadata(
-    id="a6d7c2a7a9db46fb00a81d8e8f737c33f01dcc59.boutiques",
+    id="c1898d45d46d749a0dc725e71c68225ccc7797f4.boutiques",
     name="3daxialize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3DAXIALIZE_METADATA = Metadata(
 
 
 V3daxializeParameters = typing.TypedDict('V3daxializeParameters', {
-    "__STYXTYPE__": typing.Literal["3daxialize"],
+    "@type": typing.NotRequired[typing.Literal["afni/3daxialize"]],
+    "infile": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "verb": bool,
+    "sagittal": bool,
+    "coronal": bool,
+    "axial": bool,
+    "orient_code": typing.NotRequired[str | None],
+    "frugal": bool,
+})
+V3daxializeParametersTagged = typing.TypedDict('V3daxializeParametersTagged', {
+    "@type": typing.Literal["afni/3daxialize"],
     "infile": InputPathType,
     "prefix": typing.NotRequired[str | None],
     "verb": bool,
@@ -24,43 +35,11 @@ V3daxializeParameters = typing.TypedDict('V3daxializeParameters', {
     "orient_code": typing.NotRequired[str | None],
     "frugal": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3daxialize": v_3daxialize_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 {
-        "3daxialize": v_3daxialize_outputs,
-    }.get(t)
 
 
 class V3daxializeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3daxialize(...)`.
+    Output object returned when calling `V3daxializeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def v_3daxialize_params(
     axial: bool = False,
     orient_code: str | None = None,
     frugal: bool = False,
-) -> V3daxializeParameters:
+) -> V3daxializeParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +76,7 @@ def v_3daxialize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3daxialize",
+        "@type": "afni/3daxialize",
         "infile": infile,
         "verb": verb,
         "sagittal": sagittal,
@@ -127,26 +106,26 @@ def v_3daxialize_cargs(
     """
     cargs = []
     cargs.append("3daxialize")
-    cargs.append(execution.input_file(params.get("infile")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("infile", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("verb"):
+    if params.get("verb", False):
         cargs.append("-verb")
-    if params.get("sagittal"):
+    if params.get("sagittal", False):
         cargs.append("-sagittal")
-    if params.get("coronal"):
+    if params.get("coronal", False):
         cargs.append("-coronal")
-    if params.get("axial"):
+    if params.get("axial", False):
         cargs.append("-axial")
-    if params.get("orient_code") is not None:
+    if params.get("orient_code", None) is not None:
         cargs.extend([
             "-orient",
-            params.get("orient_code")
+            params.get("orient_code", None)
         ])
-    if params.get("frugal"):
+    if params.get("frugal", False):
         cargs.append("-frugal")
     return cargs
 
@@ -166,17 +145,20 @@ def v_3daxialize_outputs(
     """
     ret = V3daxializeOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("prefix") + "+orig") if (params.get("prefix") is not None) else None,
+        outfile=execution.output_file(params.get("prefix", None) + "+orig") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3daxialize_execute(
     params: V3daxializeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3daxializeOutputs:
     """
-    Read and write dataset as new dataset with data brick oriented as axial slices.
+    3daxialize
+    
+    Read and write dataset as new dataset with data brick oriented as axial
+    slices.
     
     Author: AFNI Developers
     
@@ -184,10 +166,12 @@ def v_3daxialize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3daxializeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DAXIALIZE_METADATA)
     params = execution.params(params)
     cargs = v_3daxialize_cargs(params, execution)
     ret = v_3daxialize_outputs(params, execution)
@@ -207,7 +191,10 @@ def v_3daxialize(
     runner: Runner | None = None,
 ) -> V3daxializeOutputs:
     """
-    Read and write dataset as new dataset with data brick oriented as axial slices.
+    3daxialize
+    
+    Read and write dataset as new dataset with data brick oriented as axial
+    slices.
     
     Author: AFNI Developers
     
@@ -229,8 +216,6 @@ def v_3daxialize(
     Returns:
         NamedTuple of outputs (described in `V3daxializeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DAXIALIZE_METADATA)
     params = v_3daxialize_params(
         infile=infile,
         prefix=prefix,
@@ -241,13 +226,13 @@ def v_3daxialize(
         orient_code=orient_code,
         frugal=frugal,
     )
-    return v_3daxialize_execute(params, execution)
+    return v_3daxialize_execute(params, runner)
 
 
 __all__ = [
     "V3daxializeOutputs",
-    "V3daxializeParameters",
     "V_3DAXIALIZE_METADATA",
     "v_3daxialize",
+    "v_3daxialize_execute",
     "v_3daxialize_params",
 ]