niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3danisosmooth.py

@@ -0,0 +1,436 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DANISOSMOOTH_METADATA = Metadata(
+    id="0f940845485d0f2e6aa4a1bbafdccc58018a21a2.boutiques",
+    name="3danisosmooth",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3danisosmoothParameters = typing.TypedDict('V3danisosmoothParameters', {
+    "__STYX_TYPE__": typing.Literal["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,
+})
+
+
+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(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType | None
+    """Output dataset after anisotropic smoothing"""
+    gradient_data: OutputPathType
+    """Gradient dataset saved at each iteration"""
+    eigens_data: OutputPathType
+    """Eigens dataset saved at each iteration"""
+    phi_data: OutputPathType
+    """Phi dataset saved at each iteration"""
+    dtensor_data: OutputPathType
+    """Dtensor dataset saved at each iteration"""
+    ematrix_data: OutputPathType
+    """Ematrix dataset saved at the first sub-brick iteration"""
+    flux_data: OutputPathType
+    """Flux dataset saved at the first sub-brick iteration"""
+    gmatrix_data: OutputPathType
+    """Gmatrix dataset saved at the first sub-brick iteration"""
+    diff_measures_data: OutputPathType
+    """Dataset containing FA, MD, Cl, Cp, and Cs values saved at each
+    iteration"""
+
+
+def v_3danisosmooth_params(
+    input_dataset: InputPathType,
+    prefix: str | None = None,
+    iterations: float | None = None,
+    v_2d_flag: bool = False,
+    v_3d_flag: bool = False,
+    mask_dataset: InputPathType | None = None,
+    automask_flag: bool = False,
+    viewer_flag: bool = False,
+    nosmooth_flag: bool = False,
+    sigma1: float | None = None,
+    sigma2: float | None = None,
+    deltat: float | None = None,
+    savetempdata_flag: bool = False,
+    save_temp_with_diff_measures_flag: bool = False,
+    phiding_flag: bool = False,
+    phiexp_flag: bool = False,
+    noneg_flag: bool = False,
+    setneg_value: float | None = None,
+    edgefraction: float | None = None,
+    datum_type: str | None = None,
+    matchorig_flag: bool = False,
+    help_flag: bool = False,
+) -> V3danisosmoothParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset to be smoothed.
+        prefix: Output dataset prefix name.
+        iterations: Number of iterations (default=10).
+        v_2d_flag: Smooth a slice at a time (default).
+        v_3d_flag: Smooth through slices.
+        mask_dataset: Use specified dataset as mask to include/exclude voxels.
+        automask_flag: Automatically compute mask for dataset.
+        viewer_flag: Show central axial slice image every iteration.
+        nosmooth_flag: Do not do intermediate smoothing of gradients.
+        sigma1: Gaussian smoothing sigma before gradient computation\
+            (default=0.5).
+        sigma2: Gaussian smoothing sigma after gradient computation\
+            (default=1.0).
+        deltat: Pseudo-time step (default=0.25).
+        savetempdata_flag: Save temporary datasets each iteration.
+        save_temp_with_diff_measures_flag: Save temporary datasets with\
+            different measures in a dataset.
+        phiding_flag: Use Ding method for computing phi (default).
+        phiexp_flag: Use exponential method for computing phi.
+        noneg_flag: Set negative voxels to 0.
+        setneg_value: Set negative voxels to specified value.
+        edgefraction: Adjust the fraction of the anisotropic component added (0\
+            to 1, default=0.5).
+        datum_type: Specify type for output data (byte, short, float)\
+            [default=float].
+        matchorig_flag: Match datum type and clip min/max to input data.
+        help_flag: Print help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3danisosmooth",
+        "input_dataset": input_dataset,
+        "2d_flag": v_2d_flag,
+        "3d_flag": v_3d_flag,
+        "automask_flag": automask_flag,
+        "viewer_flag": viewer_flag,
+        "nosmooth_flag": nosmooth_flag,
+        "savetempdata_flag": savetempdata_flag,
+        "save_temp_with_diff_measures_flag": save_temp_with_diff_measures_flag,
+        "phiding_flag": phiding_flag,
+        "phiexp_flag": phiexp_flag,
+        "noneg_flag": noneg_flag,
+        "matchorig_flag": matchorig_flag,
+        "help_flag": help_flag,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if iterations is not None:
+        params["iterations"] = iterations
+    if mask_dataset is not None:
+        params["mask_dataset"] = mask_dataset
+    if sigma1 is not None:
+        params["sigma1"] = sigma1
+    if sigma2 is not None:
+        params["sigma2"] = sigma2
+    if deltat is not None:
+        params["deltat"] = deltat
+    if setneg_value is not None:
+        params["setneg_value"] = setneg_value
+    if edgefraction is not None:
+        params["edgefraction"] = edgefraction
+    if datum_type is not None:
+        params["datum_type"] = datum_type
+    return params
+
+
+def v_3danisosmooth_cargs(
+    params: V3danisosmoothParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3danisosmooth")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("iterations") is not None:
+        cargs.extend([
+            "-iters",
+            str(params.get("iterations"))
+        ])
+    if params.get("2d_flag"):
+        cargs.append("-2D")
+    if params.get("3d_flag"):
+        cargs.append("-3D")
+    if params.get("mask_dataset") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_dataset"))
+        ])
+    if params.get("automask_flag"):
+        cargs.append("-automask")
+    if params.get("viewer_flag"):
+        cargs.append("-viewer")
+    if params.get("nosmooth_flag"):
+        cargs.append("-nosmooth")
+    if params.get("sigma1") is not None:
+        cargs.extend([
+            "-sigma1",
+            str(params.get("sigma1"))
+        ])
+    if params.get("sigma2") is not None:
+        cargs.extend([
+            "-sigma2",
+            str(params.get("sigma2"))
+        ])
+    if params.get("deltat") is not None:
+        cargs.extend([
+            "-deltat",
+            str(params.get("deltat"))
+        ])
+    if params.get("savetempdata_flag"):
+        cargs.append("-savetempdata")
+    if params.get("save_temp_with_diff_measures_flag"):
+        cargs.append("-save_temp_with_diff_measures")
+    if params.get("phiding_flag"):
+        cargs.append("-phiding")
+    if params.get("phiexp_flag"):
+        cargs.append("-phiexp")
+    if params.get("noneg_flag"):
+        cargs.append("-noneg")
+    if params.get("setneg_value") is not None:
+        cargs.extend([
+            "-setneg",
+            str(params.get("setneg_value"))
+        ])
+    if params.get("edgefraction") is not None:
+        cargs.extend([
+            "-edgefraction",
+            str(params.get("edgefraction"))
+        ])
+    if params.get("datum_type") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum_type")
+        ])
+    if params.get("matchorig_flag"):
+        cargs.append("-matchorig")
+    if params.get("help_flag"):
+        cargs.append("-help")
+    return cargs
+
+
+def v_3danisosmooth_outputs(
+    params: V3danisosmoothParameters,
+    execution: Execution,
+) -> V3danisosmoothOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3danisosmoothOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + "+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"),
+        dtensor_data=execution.output_file("Dtensor.ITER"),
+        ematrix_data=execution.output_file("Ematrix.ITER"),
+        flux_data=execution.output_file("Flux.ITER"),
+        gmatrix_data=execution.output_file("Gmatrix.ITER"),
+        diff_measures_data=execution.output_file("Diff_measures.ITER"),
+    )
+    return ret
+
+
+def v_3danisosmooth_execute(
+    params: V3danisosmoothParameters,
+    execution: Execution,
+) -> V3danisosmoothOutputs:
+    """
+    Smooths a dataset using an anisotropic smoothing technique.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3danisosmoothOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3danisosmooth_cargs(params, execution)
+    ret = v_3danisosmooth_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3danisosmooth(
+    input_dataset: InputPathType,
+    prefix: str | None = None,
+    iterations: float | None = None,
+    v_2d_flag: bool = False,
+    v_3d_flag: bool = False,
+    mask_dataset: InputPathType | None = None,
+    automask_flag: bool = False,
+    viewer_flag: bool = False,
+    nosmooth_flag: bool = False,
+    sigma1: float | None = None,
+    sigma2: float | None = None,
+    deltat: float | None = None,
+    savetempdata_flag: bool = False,
+    save_temp_with_diff_measures_flag: bool = False,
+    phiding_flag: bool = False,
+    phiexp_flag: bool = False,
+    noneg_flag: bool = False,
+    setneg_value: float | None = None,
+    edgefraction: float | None = None,
+    datum_type: str | None = None,
+    matchorig_flag: bool = False,
+    help_flag: bool = False,
+    runner: Runner | None = None,
+) -> V3danisosmoothOutputs:
+    """
+    Smooths a dataset using an anisotropic smoothing technique.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset to be smoothed.
+        prefix: Output dataset prefix name.
+        iterations: Number of iterations (default=10).
+        v_2d_flag: Smooth a slice at a time (default).
+        v_3d_flag: Smooth through slices.
+        mask_dataset: Use specified dataset as mask to include/exclude voxels.
+        automask_flag: Automatically compute mask for dataset.
+        viewer_flag: Show central axial slice image every iteration.
+        nosmooth_flag: Do not do intermediate smoothing of gradients.
+        sigma1: Gaussian smoothing sigma before gradient computation\
+            (default=0.5).
+        sigma2: Gaussian smoothing sigma after gradient computation\
+            (default=1.0).
+        deltat: Pseudo-time step (default=0.25).
+        savetempdata_flag: Save temporary datasets each iteration.
+        save_temp_with_diff_measures_flag: Save temporary datasets with\
+            different measures in a dataset.
+        phiding_flag: Use Ding method for computing phi (default).
+        phiexp_flag: Use exponential method for computing phi.
+        noneg_flag: Set negative voxels to 0.
+        setneg_value: Set negative voxels to specified value.
+        edgefraction: Adjust the fraction of the anisotropic component added (0\
+            to 1, default=0.5).
+        datum_type: Specify type for output data (byte, short, float)\
+            [default=float].
+        matchorig_flag: Match datum type and clip min/max to input data.
+        help_flag: Print help message.
+        runner: Command runner.
+    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,
+        iterations=iterations,
+        v_2d_flag=v_2d_flag,
+        v_3d_flag=v_3d_flag,
+        mask_dataset=mask_dataset,
+        automask_flag=automask_flag,
+        viewer_flag=viewer_flag,
+        nosmooth_flag=nosmooth_flag,
+        sigma1=sigma1,
+        sigma2=sigma2,
+        deltat=deltat,
+        savetempdata_flag=savetempdata_flag,
+        save_temp_with_diff_measures_flag=save_temp_with_diff_measures_flag,
+        phiding_flag=phiding_flag,
+        phiexp_flag=phiexp_flag,
+        noneg_flag=noneg_flag,
+        setneg_value=setneg_value,
+        edgefraction=edgefraction,
+        datum_type=datum_type,
+        matchorig_flag=matchorig_flag,
+        help_flag=help_flag,
+    )
+    return v_3danisosmooth_execute(params, execution)
+
+
+__all__ = [
+    "V3danisosmoothOutputs",
+    "V3danisosmoothParameters",
+    "V_3DANISOSMOOTH_METADATA",
+    "v_3danisosmooth",
+    "v_3danisosmooth_params",
+]

niwrap_afni/afni/v_3daxialize.py

@@ -0,0 +1,253 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DAXIALIZE_METADATA = Metadata(
+    id="bcc8e30177064f95c8a4e5b95029e8dd46cb1692.boutiques",
+    name="3daxialize",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3daxializeParameters = typing.TypedDict('V3daxializeParameters', {
+    "__STYX_TYPE__": typing.Literal["3daxialize"],
+    "infile": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "verb": bool,
+    "sagittal": bool,
+    "coronal": bool,
+    "axial": bool,
+    "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(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType | None
+    """Output dataset with axial slices orientation"""
+
+
+def v_3daxialize_params(
+    infile: InputPathType,
+    prefix: str | None = None,
+    verb: bool = False,
+    sagittal: bool = False,
+    coronal: bool = False,
+    axial: bool = False,
+    orient_code: str | None = None,
+    frugal: bool = False,
+) -> V3daxializeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Dataset to be axially oriented.
+        prefix: Use specified prefix for the new dataset. Default is\
+            'axialize'.
+        verb: Print out a progress report.
+        sagittal: Write dataset in sagittal slice order.
+        coronal: Write dataset in coronal slice order.
+        axial: Write dataset in axial slice order, the default orientation.
+        orient_code: Orientation code for output. 3 letters: one from {R,L},\
+            {A,P}, {I,S}.
+        frugal: Write data as it is rotated, saving memory. Not available with\
+            NIFTI datasets.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3daxialize",
+        "infile": infile,
+        "verb": verb,
+        "sagittal": sagittal,
+        "coronal": coronal,
+        "axial": axial,
+        "frugal": frugal,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if orient_code is not None:
+        params["orient_code"] = orient_code
+    return params
+
+
+def v_3daxialize_cargs(
+    params: V3daxializeParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3daxialize")
+    cargs.append(execution.input_file(params.get("infile")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("verb"):
+        cargs.append("-verb")
+    if params.get("sagittal"):
+        cargs.append("-sagittal")
+    if params.get("coronal"):
+        cargs.append("-coronal")
+    if params.get("axial"):
+        cargs.append("-axial")
+    if params.get("orient_code") is not None:
+        cargs.extend([
+            "-orient",
+            params.get("orient_code")
+        ])
+    if params.get("frugal"):
+        cargs.append("-frugal")
+    return cargs
+
+
+def v_3daxialize_outputs(
+    params: V3daxializeParameters,
+    execution: Execution,
+) -> V3daxializeOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3daxializeOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("prefix") + "+orig") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3daxialize_execute(
+    params: V3daxializeParameters,
+    execution: Execution,
+) -> V3daxializeOutputs:
+    """
+    Read and write dataset as new dataset with data brick oriented as axial slices.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3daxializeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3daxialize_cargs(params, execution)
+    ret = v_3daxialize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3daxialize(
+    infile: InputPathType,
+    prefix: str | None = None,
+    verb: bool = False,
+    sagittal: bool = False,
+    coronal: bool = False,
+    axial: bool = False,
+    orient_code: str | None = None,
+    frugal: bool = False,
+    runner: Runner | None = None,
+) -> V3daxializeOutputs:
+    """
+    Read and write dataset as new dataset with data brick oriented as axial slices.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Dataset to be axially oriented.
+        prefix: Use specified prefix for the new dataset. Default is\
+            'axialize'.
+        verb: Print out a progress report.
+        sagittal: Write dataset in sagittal slice order.
+        coronal: Write dataset in coronal slice order.
+        axial: Write dataset in axial slice order, the default orientation.
+        orient_code: Orientation code for output. 3 letters: one from {R,L},\
+            {A,P}, {I,S}.
+        frugal: Write data as it is rotated, saving memory. Not available with\
+            NIFTI datasets.
+        runner: Command runner.
+    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,
+        verb=verb,
+        sagittal=sagittal,
+        coronal=coronal,
+        axial=axial,
+        orient_code=orient_code,
+        frugal=frugal,
+    )
+    return v_3daxialize_execute(params, execution)
+
+
+__all__ = [
+    "V3daxializeOutputs",
+    "V3daxializeParameters",
+    "V_3DAXIALIZE_METADATA",
+    "v_3daxialize",
+    "v_3daxialize_params",
+]