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

niwrap_afni/afni/v_3d_automask.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_AUTOMASK_METADATA = Metadata(
-    id="856ea5835596fc570c8d957e8bf0bd92d56130cb.boutiques",
+    id="d0aea979aa7a9af4ee597051955d1bd0cc99a3b1.boutiques",
     name="3dAutomask",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V_3D_AUTOMASK_METADATA = Metadata(
 
 
 V3dAutomaskParameters = typing.TypedDict('V3dAutomaskParameters', {
-    "__STYXTYPE__": typing.Literal["3dAutomask"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAutomask"]],
+    "prefix": typing.NotRequired[str | None],
+    "apply_prefix": typing.NotRequired[str | None],
+    "clfrac": typing.NotRequired[float | None],
+    "dilate": typing.NotRequired[int | None],
+    "erode": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "in_file": InputPathType,
+})
+V3dAutomaskParametersTagged = typing.TypedDict('V3dAutomaskParametersTagged', {
+    "@type": typing.Literal["afni/3dAutomask"],
     "prefix": typing.NotRequired[str | None],
     "apply_prefix": typing.NotRequired[str | None],
     "clfrac": typing.NotRequired[float | None],
@@ -23,43 +33,11 @@ V3dAutomaskParameters = typing.TypedDict('V3dAutomaskParameters', {
     "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
     "in_file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dAutomask": v_3d_automask_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 {
-        "3dAutomask": v_3d_automask_outputs,
-    }.get(t)
 
 
 class V3dAutomaskOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_automask(...)`.
+    Output object returned when calling `V3dAutomaskParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +55,7 @@ def v_3d_automask_params(
     dilate: int | None = None,
     erode: int | None = None,
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
-) -> V3dAutomaskParameters:
+) -> V3dAutomaskParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +73,7 @@ def v_3d_automask_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAutomask",
+        "@type": "afni/3dAutomask",
         "in_file": in_file,
     }
     if prefix is not None:
@@ -128,34 +106,34 @@ def v_3d_automask_cargs(
     """
     cargs = []
     cargs.append("3dAutomask")
-    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("apply_prefix") is not None:
+    if params.get("apply_prefix", None) is not None:
         cargs.extend([
             "-apply_prefix",
-            params.get("apply_prefix")
+            params.get("apply_prefix", None)
         ])
-    if params.get("clfrac") is not None:
+    if params.get("clfrac", None) is not None:
         cargs.extend([
             "-clfrac",
-            str(params.get("clfrac"))
+            str(params.get("clfrac", None))
         ])
-    if params.get("dilate") is not None:
+    if params.get("dilate", None) is not None:
         cargs.extend([
             "-dilate",
-            str(params.get("dilate"))
+            str(params.get("dilate", None))
         ])
-    if params.get("erode") is not None:
+    if params.get("erode", None) is not None:
         cargs.extend([
             "-erode",
-            str(params.get("erode"))
+            str(params.get("erode", None))
         ])
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    cargs.append(execution.input_file(params.get("in_file")))
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
+    cargs.append(execution.input_file(params.get("in_file", None)))
     return cargs
 
 
@@ -174,17 +152,19 @@ def v_3d_automask_outputs(
     """
     ret = V3dAutomaskOutputs(
         root=execution.output_file("."),
-        brain_file=execution.output_file(params.get("apply_prefix")) if (params.get("apply_prefix") is not None) else None,
-        mask_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        brain_file=execution.output_file(params.get("apply_prefix", None)) if (params.get("apply_prefix") is not None) else None,
+        mask_file=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_automask_execute(
     params: V3dAutomaskParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAutomaskOutputs:
     """
+    3dAutomask
+    
     Create a brain-only mask of the image using AFNI 3dAutomask command.
     
     Author: AFNI Developers
@@ -193,10 +173,12 @@ def v_3d_automask_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAutomaskOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AUTOMASK_METADATA)
     params = execution.params(params)
     cargs = v_3d_automask_cargs(params, execution)
     ret = v_3d_automask_outputs(params, execution)
@@ -215,6 +197,8 @@ def v_3d_automask(
     runner: Runner | None = None,
 ) -> V3dAutomaskOutputs:
     """
+    3dAutomask
+    
     Create a brain-only mask of the image using AFNI 3dAutomask command.
     
     Author: AFNI Developers
@@ -235,8 +219,6 @@ def v_3d_automask(
     Returns:
         NamedTuple of outputs (described in `V3dAutomaskOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_AUTOMASK_METADATA)
     params = v_3d_automask_params(
         prefix=prefix,
         apply_prefix=apply_prefix,
@@ -246,13 +228,13 @@ def v_3d_automask(
         outputtype=outputtype,
         in_file=in_file,
     )
-    return v_3d_automask_execute(params, execution)
+    return v_3d_automask_execute(params, runner)
 
 
 __all__ = [
     "V3dAutomaskOutputs",
-    "V3dAutomaskParameters",
     "V_3D_AUTOMASK_METADATA",
     "v_3d_automask",
+    "v_3d_automask_execute",
     "v_3d_automask_params",
 ]

niwrap_afni/afni/v_3d_ball_match.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_BALL_MATCH_METADATA = Metadata(
-    id="e91bd8bca8af6f73af7781b32ec76cb4701697b9.boutiques",
+    id="12076e5b1959ea628a5005f966925a521c023965.boutiques",
     name="3dBallMatch",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V_3D_BALL_MATCH_METADATA = Metadata(
 
 
 V3dBallMatchParameters = typing.TypedDict('V3dBallMatchParameters', {
-    "__STYXTYPE__": typing.Literal["3dBallMatch"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dBallMatch"]],
+    "input_dataset": InputPathType,
+    "radius": typing.NotRequired[float | None],
+    "dataset_option": typing.NotRequired[str | None],
+    "ball_radius": typing.NotRequired[float | None],
+    "spheroid_axes": typing.NotRequired[list[float] | None],
+})
+V3dBallMatchParametersTagged = typing.TypedDict('V3dBallMatchParametersTagged', {
+    "@type": typing.Literal["afni/3dBallMatch"],
     "input_dataset": InputPathType,
     "radius": typing.NotRequired[float | None],
     "dataset_option": typing.NotRequired[str | None],
     "ball_radius": typing.NotRequired[float | None],
     "spheroid_axes": typing.NotRequired[list[float] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dBallMatch": v_3d_ball_match_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 {
-        "3dBallMatch": v_3d_ball_match_outputs,
-    }.get(t)
 
 
 class V3dBallMatchOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_ball_match(...)`.
+    Output object returned when calling `V3dBallMatchParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def v_3d_ball_match_params(
     dataset_option: str | None = None,
     ball_radius: float | None = None,
     spheroid_axes: list[float] | None = None,
-) -> V3dBallMatchParameters:
+) -> V3dBallMatchParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +62,7 @@ def v_3d_ball_match_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dBallMatch",
+        "@type": "afni/3dBallMatch",
         "input_dataset": input_dataset,
     }
     if radius is not None:
@@ -115,23 +91,23 @@ def v_3d_ball_match_cargs(
     """
     cargs = []
     cargs.append("3dBallMatch")
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    if params.get("radius") is not None:
-        cargs.append(str(params.get("radius")))
-    if params.get("dataset_option") is not None:
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
+    if params.get("radius", None) is not None:
+        cargs.append(str(params.get("radius", None)))
+    if params.get("dataset_option", None) is not None:
         cargs.extend([
             "-input",
-            params.get("dataset_option")
+            params.get("dataset_option", None)
         ])
-    if params.get("ball_radius") is not None:
+    if params.get("ball_radius", None) is not None:
         cargs.extend([
             "-ball",
-            str(params.get("ball_radius"))
+            str(params.get("ball_radius", None))
         ])
-    if params.get("spheroid_axes") is not None:
+    if params.get("spheroid_axes", None) is not None:
         cargs.extend([
             "-spheroid",
-            *map(str, params.get("spheroid_axes"))
+            *map(str, params.get("spheroid_axes", None))
         ])
     return cargs
 
@@ -158,11 +134,14 @@ def v_3d_ball_match_outputs(
 
 def v_3d_ball_match_execute(
     params: V3dBallMatchParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dBallMatchOutputs:
     """
-    A tool to find a good match between a ball (filled sphere) of the given radius
-    and a dataset to determine a crude approximate center of the brain quickly.
+    3dBallMatch
+    
+    A tool to find a good match between a ball (filled sphere) of the given
+    radius and a dataset to determine a crude approximate center of the brain
+    quickly.
     
     Author: AFNI Developers
     
@@ -170,10 +149,12 @@ def v_3d_ball_match_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dBallMatchOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BALL_MATCH_METADATA)
     params = execution.params(params)
     cargs = v_3d_ball_match_cargs(params, execution)
     ret = v_3d_ball_match_outputs(params, execution)
@@ -190,8 +171,11 @@ def v_3d_ball_match(
     runner: Runner | None = None,
 ) -> V3dBallMatchOutputs:
     """
-    A tool to find a good match between a ball (filled sphere) of the given radius
-    and a dataset to determine a crude approximate center of the brain quickly.
+    3dBallMatch
+    
+    A tool to find a good match between a ball (filled sphere) of the given
+    radius and a dataset to determine a crude approximate center of the brain
+    quickly.
     
     Author: AFNI Developers
     
@@ -208,8 +192,6 @@ def v_3d_ball_match(
     Returns:
         NamedTuple of outputs (described in `V3dBallMatchOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_BALL_MATCH_METADATA)
     params = v_3d_ball_match_params(
         input_dataset=input_dataset,
         radius=radius,
@@ -217,13 +199,13 @@ def v_3d_ball_match(
         ball_radius=ball_radius,
         spheroid_axes=spheroid_axes,
     )
-    return v_3d_ball_match_execute(params, execution)
+    return v_3d_ball_match_execute(params, runner)
 
 
 __all__ = [
     "V3dBallMatchOutputs",
-    "V3dBallMatchParameters",
     "V_3D_BALL_MATCH_METADATA",
     "v_3d_ball_match",
+    "v_3d_ball_match_execute",
     "v_3d_ball_match_params",
 ]

niwrap_afni/afni/v_3d_bandpass.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_BANDPASS_METADATA = Metadata(
-    id="85554b333e3bdcbc05fde6959f1cb444905c3dd7.boutiques",
+    id="f4449a76657f4e4efd9147021862a8773f7f451f.boutiques",
     name="3dBandpass",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,27 @@ V_3D_BANDPASS_METADATA = Metadata(
 
 
 V3dBandpassParameters = typing.TypedDict('V3dBandpassParameters', {
-    "__STYXTYPE__": typing.Literal["3dBandpass"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dBandpass"]],
+    "prefix": typing.NotRequired[str | None],
+    "automask": bool,
+    "blur": typing.NotRequired[float | None],
+    "despike": bool,
+    "highpass": float,
+    "lowpass": float,
+    "in_file": InputPathType,
+    "localPV": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "nfft": typing.NotRequired[int | None],
+    "no_detrend": bool,
+    "normalize": bool,
+    "notrans": bool,
+    "orthogonalize_dset": typing.NotRequired[InputPathType | None],
+    "orthogonalize_file": typing.NotRequired[list[InputPathType] | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "tr": typing.NotRequired[float | None],
+})
+V3dBandpassParametersTagged = typing.TypedDict('V3dBandpassParametersTagged', {
+    "@type": typing.Literal["afni/3dBandpass"],
     "prefix": typing.NotRequired[str | None],
     "automask": bool,
     "blur": typing.NotRequired[float | None],
@@ -33,43 +53,11 @@ V3dBandpassParameters = typing.TypedDict('V3dBandpassParameters', {
     "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
     "tr": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dBandpass": v_3d_bandpass_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 {
-        "3dBandpass": v_3d_bandpass_outputs,
-    }.get(t)
 
 
 class V3dBandpassOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_bandpass(...)`.
+    Output object returned when calling `V3dBandpassParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +83,7 @@ def v_3d_bandpass_params(
     orthogonalize_file: list[InputPathType] | None = None,
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
     tr: float | None = None,
-) -> V3dBandpassParameters:
+) -> V3dBandpassParametersTagged:
     """
     Build parameters.
     
@@ -135,7 +123,7 @@ def v_3d_bandpass_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dBandpass",
+        "@type": "afni/3dBandpass",
         "automask": automask,
         "despike": despike,
         "highpass": highpass,
@@ -181,60 +169,60 @@ def v_3d_bandpass_cargs(
     """
     cargs = []
     cargs.append("3dBandpass")
-    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("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("blur") is not None:
+    if params.get("blur", None) is not None:
         cargs.extend([
             "-blur",
-            str(params.get("blur"))
+            str(params.get("blur", None))
         ])
-    if params.get("despike"):
+    if params.get("despike", False):
         cargs.append("-despike")
-    cargs.append(str(params.get("highpass")))
-    cargs.append(str(params.get("lowpass")))
-    cargs.append(execution.input_file(params.get("in_file")))
-    if params.get("localPV") is not None:
+    cargs.append(str(params.get("highpass", None)))
+    cargs.append(str(params.get("lowpass", None)))
+    cargs.append(execution.input_file(params.get("in_file", None)))
+    if params.get("localPV", None) is not None:
         cargs.extend([
             "-localPV",
-            str(params.get("localPV"))
+            str(params.get("localPV", 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("nfft") is not None:
+    if params.get("nfft", None) is not None:
         cargs.extend([
             "-nfft",
-            str(params.get("nfft"))
+            str(params.get("nfft", None))
         ])
-    if params.get("no_detrend"):
+    if params.get("no_detrend", False):
         cargs.append("-nodetrend")
-    if params.get("normalize"):
+    if params.get("normalize", False):
         cargs.append("-norm")
-    if params.get("notrans"):
+    if params.get("notrans", False):
         cargs.append("-notrans")
-    if params.get("orthogonalize_dset") is not None:
+    if params.get("orthogonalize_dset", None) is not None:
         cargs.extend([
             "-dsort",
-            execution.input_file(params.get("orthogonalize_dset"))
+            execution.input_file(params.get("orthogonalize_dset", None))
         ])
-    if params.get("orthogonalize_file") is not None:
+    if params.get("orthogonalize_file", None) is not None:
         cargs.extend([
             "-ort",
-            *[execution.input_file(f) for f in params.get("orthogonalize_file")]
+            *[execution.input_file(f) for f in params.get("orthogonalize_file", None)]
         ])
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    if params.get("tr") is not None:
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
+    if params.get("tr", None) is not None:
         cargs.extend([
             "-dt",
-            str(params.get("tr"))
+            str(params.get("tr", None))
         ])
     return cargs
 
@@ -254,18 +242,20 @@ def v_3d_bandpass_outputs(
     """
     ret = V3dBandpassOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        out_file=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_bandpass_execute(
     params: V3dBandpassParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dBandpassOutputs:
     """
-    Program to lowpass and/or highpass each voxel time series in a dataset, offering
-    more/different options than Fourier.
+    3dBandpass
+    
+    Program to lowpass and/or highpass each voxel time series in a dataset,
+    offering more/different options than Fourier.
     
     Author: AFNI Developers
     
@@ -273,10 +263,12 @@ def v_3d_bandpass_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dBandpassOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BANDPASS_METADATA)
     params = execution.params(params)
     cargs = v_3d_bandpass_cargs(params, execution)
     ret = v_3d_bandpass_outputs(params, execution)
@@ -305,8 +297,10 @@ def v_3d_bandpass(
     runner: Runner | None = None,
 ) -> V3dBandpassOutputs:
     """
-    Program to lowpass and/or highpass each voxel time series in a dataset, offering
-    more/different options than Fourier.
+    3dBandpass
+    
+    Program to lowpass and/or highpass each voxel time series in a dataset,
+    offering more/different options than Fourier.
     
     Author: AFNI Developers
     
@@ -348,8 +342,6 @@ def v_3d_bandpass(
     Returns:
         NamedTuple of outputs (described in `V3dBandpassOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_BANDPASS_METADATA)
     params = v_3d_bandpass_params(
         prefix=prefix,
         automask=automask,
@@ -369,13 +361,13 @@ def v_3d_bandpass(
         outputtype=outputtype,
         tr=tr,
     )
-    return v_3d_bandpass_execute(params, execution)
+    return v_3d_bandpass_execute(params, runner)
 
 
 __all__ = [
     "V3dBandpassOutputs",
-    "V3dBandpassParameters",
     "V_3D_BANDPASS_METADATA",
     "v_3d_bandpass",
+    "v_3d_bandpass_execute",
     "v_3d_bandpass_params",
 ]