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

niwrap_afni/afni/v_3ddot_beta.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DDOT_BETA_METADATA = Metadata(
-    id="713d46495fc511b0c705f51aedcff3425be6c314.boutiques",
+    id="29f85c73d1e8013050b3f32ac425b1405e6a97d0.boutiques",
     name="3ddot_beta",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3DDOT_BETA_METADATA = Metadata(
 
 
 V3ddotBetaParameters = typing.TypedDict('V3ddotBetaParameters', {
-    "__STYXTYPE__": typing.Literal["3ddot_beta"],
+    "@type": typing.NotRequired[typing.Literal["afni/3ddot_beta"]],
+    "input_file": InputPathType,
+    "prefix": str,
+    "doeta2": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+})
+V3ddotBetaParametersTagged = typing.TypedDict('V3ddotBetaParametersTagged', {
+    "@type": typing.Literal["afni/3ddot_beta"],
     "input_file": InputPathType,
     "prefix": str,
     "doeta2": 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 {
-        "3ddot_beta": v_3ddot_beta_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 {
-        "3ddot_beta": v_3ddot_beta_outputs,
-    }.get(t)
 
 
 class V3ddotBetaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3ddot_beta(...)`.
+    Output object returned when calling `V3ddotBetaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def v_3ddot_beta_params(
     prefix: str,
     doeta2: bool = False,
     mask: InputPathType | None = None,
-) -> V3ddotBetaParameters:
+) -> V3ddotBetaParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def v_3ddot_beta_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3ddot_beta",
+        "@type": "afni/3ddot_beta",
         "input_file": input_file,
         "prefix": prefix,
         "doeta2": doeta2,
@@ -109,18 +84,18 @@ def v_3ddot_beta_cargs(
     cargs.append("3ddot_beta")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("doeta2"):
+    if params.get("doeta2", False):
         cargs.append("-doeta2")
-    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
 
@@ -140,16 +115,18 @@ def v_3ddot_beta_outputs(
     """
     ret = V3ddotBetaOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + "_eta2.dat"),
+        output_file=execution.output_file(params.get("prefix", None) + "_eta2.dat"),
     )
     return ret
 
 
 def v_3ddot_beta_execute(
     params: V3ddotBetaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3ddotBetaOutputs:
     """
+    3ddot_beta
+    
     Beta version of updating 3ddot, currently only performing eta2 tests and
     outputting a full matrix to a text file.
     
@@ -159,10 +136,12 @@ def v_3ddot_beta_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3ddotBetaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DDOT_BETA_METADATA)
     params = execution.params(params)
     cargs = v_3ddot_beta_cargs(params, execution)
     ret = v_3ddot_beta_outputs(params, execution)
@@ -178,6 +157,8 @@ def v_3ddot_beta(
     runner: Runner | None = None,
 ) -> V3ddotBetaOutputs:
     """
+    3ddot_beta
+    
     Beta version of updating 3ddot, currently only performing eta2 tests and
     outputting a full matrix to a text file.
     
@@ -194,21 +175,19 @@ def v_3ddot_beta(
     Returns:
         NamedTuple of outputs (described in `V3ddotBetaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DDOT_BETA_METADATA)
     params = v_3ddot_beta_params(
         input_file=input_file,
         prefix=prefix,
         doeta2=doeta2,
         mask=mask,
     )
-    return v_3ddot_beta_execute(params, execution)
+    return v_3ddot_beta_execute(params, runner)
 
 
 __all__ = [
     "V3ddotBetaOutputs",
-    "V3ddotBetaParameters",
     "V_3DDOT_BETA_METADATA",
     "v_3ddot_beta",
+    "v_3ddot_beta_execute",
     "v_3ddot_beta_params",
 ]

niwrap_afni/afni/v_3dedge3.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DEDGE3_METADATA = Metadata(
-    id="d7d3b3b44cb6ea512aa961c541a8cbc9f1d748d8.boutiques",
+    id="92d42181803ad681b388ede7c21f06e69a56a8b2.boutiques",
     name="3dedge3",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3DEDGE3_METADATA = Metadata(
 
 
 V3dedge3Parameters = typing.TypedDict('V3dedge3Parameters', {
-    "__STYXTYPE__": typing.Literal["3dedge3"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dedge3"]],
+    "input_file": InputPathType,
+    "verbose": bool,
+    "prefix": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[str | None],
+    "fscale": bool,
+    "gscale": bool,
+    "nscale": bool,
+    "scale_floats": typing.NotRequired[float | None],
+    "automask": bool,
+})
+V3dedge3ParametersTagged = typing.TypedDict('V3dedge3ParametersTagged', {
+    "@type": typing.Literal["afni/3dedge3"],
     "input_file": InputPathType,
     "verbose": bool,
     "prefix": typing.NotRequired[str | None],
@@ -25,43 +37,11 @@ V3dedge3Parameters = typing.TypedDict('V3dedge3Parameters', {
     "scale_floats": typing.NotRequired[float | None],
     "automask": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dedge3": v_3dedge3_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 {
-        "3dedge3": v_3dedge3_outputs,
-    }.get(t)
 
 
 class V3dedge3Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dedge3(...)`.
+    Output object returned when calling `V3dedge3Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def v_3dedge3_params(
     nscale: bool = False,
     scale_floats: float | None = None,
     automask: bool = False,
-) -> V3dedge3Parameters:
+) -> V3dedge3ParametersTagged:
     """
     Build parameters.
     
@@ -100,7 +80,7 @@ def v_3dedge3_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dedge3",
+        "@type": "afni/3dedge3",
         "input_file": input_file,
         "verbose": verbose,
         "fscale": fscale,
@@ -134,32 +114,32 @@ def v_3dedge3_cargs(
     cargs.append("3dedge3")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verbose")
-    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("datum") is not None:
+    if params.get("datum", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datum")
+            params.get("datum", None)
         ])
-    if params.get("fscale"):
+    if params.get("fscale", False):
         cargs.append("-fscale")
-    if params.get("gscale"):
+    if params.get("gscale", False):
         cargs.append("-gscale")
-    if params.get("nscale"):
+    if params.get("nscale", False):
         cargs.append("-nscale")
-    if params.get("scale_floats") is not None:
+    if params.get("scale_floats", None) is not None:
         cargs.extend([
             "-scale_floats",
-            str(params.get("scale_floats"))
+            str(params.get("scale_floats", None))
         ])
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
     return cargs
 
@@ -179,16 +159,18 @@ def v_3dedge3_outputs(
     """
     ret = V3dedge3Outputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3dedge3_execute(
     params: V3dedge3Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dedge3Outputs:
     """
+    3dedge3
+    
     Does 3D Edge detection using the library 3DEdge.
     
     Author: AFNI Developers
@@ -197,10 +179,12 @@ def v_3dedge3_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dedge3Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DEDGE3_METADATA)
     params = execution.params(params)
     cargs = v_3dedge3_cargs(params, execution)
     ret = v_3dedge3_outputs(params, execution)
@@ -221,6 +205,8 @@ def v_3dedge3(
     runner: Runner | None = None,
 ) -> V3dedge3Outputs:
     """
+    3dedge3
+    
     Does 3D Edge detection using the library 3DEdge.
     
     Author: AFNI Developers
@@ -244,8 +230,6 @@ def v_3dedge3(
     Returns:
         NamedTuple of outputs (described in `V3dedge3Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DEDGE3_METADATA)
     params = v_3dedge3_params(
         input_file=input_file,
         verbose=verbose,
@@ -257,13 +241,13 @@ def v_3dedge3(
         scale_floats=scale_floats,
         automask=automask,
     )
-    return v_3dedge3_execute(params, execution)
+    return v_3dedge3_execute(params, runner)
 
 
 __all__ = [
     "V3dedge3Outputs",
-    "V3dedge3Parameters",
     "V_3DEDGE3_METADATA",
     "v_3dedge3",
+    "v_3dedge3_execute",
     "v_3dedge3_params",
 ]

niwrap_afni/afni/v_3dedgedog.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DEDGEDOG_METADATA = Metadata(
-    id="d8ea0ba3919d19e8494c7f6b252c74f682d34b17.boutiques",
+    id="1c3d8f0c9e39b26a708590d37d0905a6facb7f27.boutiques",
     name="3dedgedog",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ V_3DEDGEDOG_METADATA = Metadata(
 
 
 V3dedgedogParameters = typing.TypedDict('V3dedgedogParameters', {
-    "__STYXTYPE__": typing.Literal["3dedgedog"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dedgedog"]],
+    "input": InputPathType,
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": typing.NotRequired[str | None],
+    "sigma_rad": typing.NotRequired[float | None],
+    "sigma_nvox": typing.NotRequired[float | None],
+    "ratio_sigma": typing.NotRequired[float | None],
+    "output_intermed": bool,
+    "edge_bnd_nn": typing.NotRequired[float | None],
+    "edge_bnd_side": typing.NotRequired[str | None],
+    "edge_bnd_scale": bool,
+    "only2d": typing.NotRequired[str | None],
+})
+V3dedgedogParametersTagged = typing.TypedDict('V3dedgedogParametersTagged', {
+    "@type": typing.Literal["afni/3dedgedog"],
     "input": InputPathType,
     "prefix": str,
     "mask": typing.NotRequired[InputPathType | None],
@@ -28,43 +43,11 @@ V3dedgedogParameters = typing.TypedDict('V3dedgedogParameters', {
     "edge_bnd_scale": bool,
     "only2d": 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 {
-        "3dedgedog": v_3dedgedog_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 {
-        "3dedgedog": v_3dedgedog_outputs,
-    }.get(t)
 
 
 class V3dedgedogOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dedgedog(...)`.
+    Output object returned when calling `V3dedgedogParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +76,7 @@ def v_3dedgedog_params(
     edge_bnd_side: str | None = None,
     edge_bnd_scale: bool = False,
     only2d: str | None = None,
-) -> V3dedgedogParameters:
+) -> V3dedgedogParametersTagged:
     """
     Build parameters.
     
@@ -126,7 +109,7 @@ def v_3dedgedog_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dedgedog",
+        "@type": "afni/3dedgedog",
         "input": input_,
         "prefix": prefix,
         "output_intermed": output_intermed,
@@ -166,51 +149,51 @@ def v_3dedgedog_cargs(
     """
     cargs = []
     cargs.append("3dedgedog")
-    cargs.append(execution.input_file(params.get("input")))
-    cargs.append(params.get("prefix"))
-    if params.get("mask") is not None:
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(params.get("prefix", 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("automask") is not None:
+    if params.get("automask", None) is not None:
         cargs.extend([
             "-automask",
-            params.get("automask")
+            params.get("automask", None)
         ])
-    if params.get("sigma_rad") is not None:
+    if params.get("sigma_rad", None) is not None:
         cargs.extend([
             "-sigma_rad",
-            str(params.get("sigma_rad"))
+            str(params.get("sigma_rad", None))
         ])
-    if params.get("sigma_nvox") is not None:
+    if params.get("sigma_nvox", None) is not None:
         cargs.extend([
             "-sigma_nvox",
-            str(params.get("sigma_nvox"))
+            str(params.get("sigma_nvox", None))
         ])
-    if params.get("ratio_sigma") is not None:
+    if params.get("ratio_sigma", None) is not None:
         cargs.extend([
             "-ratio_sigma",
-            str(params.get("ratio_sigma"))
+            str(params.get("ratio_sigma", None))
         ])
-    if params.get("output_intermed"):
+    if params.get("output_intermed", False):
         cargs.append("-output_intermed")
-    if params.get("edge_bnd_nn") is not None:
+    if params.get("edge_bnd_nn", None) is not None:
         cargs.extend([
             "-edge_bnd_NN",
-            str(params.get("edge_bnd_nn"))
+            str(params.get("edge_bnd_nn", None))
         ])
-    if params.get("edge_bnd_side") is not None:
+    if params.get("edge_bnd_side", None) is not None:
         cargs.extend([
             "-edge_bnd_side",
-            params.get("edge_bnd_side")
+            params.get("edge_bnd_side", None)
         ])
-    if params.get("edge_bnd_scale"):
+    if params.get("edge_bnd_scale", False):
         cargs.append("-edge_bnd_scale")
-    if params.get("only2d") is not None:
+    if params.get("only2d", None) is not None:
         cargs.extend([
             "-only2D",
-            params.get("only2d")
+            params.get("only2d", None)
         ])
     return cargs
 
@@ -230,22 +213,24 @@ def v_3dedgedog_outputs(
     """
     ret = V3dedgedogOutputs(
         root=execution.output_file("."),
-        out_edge=execution.output_file(params.get("prefix") + "_edge.nii.gz"),
-        out_dog=execution.output_file(params.get("prefix") + "_dog.nii.gz"),
-        out_edt2=execution.output_file(params.get("prefix") + "_edt2.nii.gz"),
-        out_blur_inner=execution.output_file(params.get("prefix") + "_blur_inner.nii.gz"),
-        out_blur_outer=execution.output_file(params.get("prefix") + "_blur_outer.nii.gz"),
+        out_edge=execution.output_file(params.get("prefix", None) + "_edge.nii.gz"),
+        out_dog=execution.output_file(params.get("prefix", None) + "_dog.nii.gz"),
+        out_edt2=execution.output_file(params.get("prefix", None) + "_edt2.nii.gz"),
+        out_blur_inner=execution.output_file(params.get("prefix", None) + "_blur_inner.nii.gz"),
+        out_blur_outer=execution.output_file(params.get("prefix", None) + "_blur_outer.nii.gz"),
     )
     return ret
 
 
 def v_3dedgedog_execute(
     params: V3dedgedogParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dedgedogOutputs:
     """
-    Calculate edges in an image using the Difference of Gaussians (DOG) method with
-    extensions/tweaks of the Marr-Hildreth algorithm.
+    3dedgedog
+    
+    Calculate edges in an image using the Difference of Gaussians (DOG) method
+    with extensions/tweaks of the Marr-Hildreth algorithm.
     
     Author: AFNI Developers
     
@@ -253,10 +238,12 @@ def v_3dedgedog_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dedgedogOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DEDGEDOG_METADATA)
     params = execution.params(params)
     cargs = v_3dedgedog_cargs(params, execution)
     ret = v_3dedgedog_outputs(params, execution)
@@ -280,8 +267,10 @@ def v_3dedgedog(
     runner: Runner | None = None,
 ) -> V3dedgedogOutputs:
     """
-    Calculate edges in an image using the Difference of Gaussians (DOG) method with
-    extensions/tweaks of the Marr-Hildreth algorithm.
+    3dedgedog
+    
+    Calculate edges in an image using the Difference of Gaussians (DOG) method
+    with extensions/tweaks of the Marr-Hildreth algorithm.
     
     Author: AFNI Developers
     
@@ -316,8 +305,6 @@ def v_3dedgedog(
     Returns:
         NamedTuple of outputs (described in `V3dedgedogOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DEDGEDOG_METADATA)
     params = v_3dedgedog_params(
         input_=input_,
         prefix=prefix,
@@ -332,13 +319,13 @@ def v_3dedgedog(
         edge_bnd_scale=edge_bnd_scale,
         only2d=only2d,
     )
-    return v_3dedgedog_execute(params, execution)
+    return v_3dedgedog_execute(params, runner)
 
 
 __all__ = [
     "V3dedgedogOutputs",
-    "V3dedgedogParameters",
     "V_3DEDGEDOG_METADATA",
     "v_3dedgedog",
+    "v_3dedgedog_execute",
     "v_3dedgedog_params",
 ]