niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_bandpass.py

@@ -0,0 +1,381 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_BANDPASS_METADATA = Metadata(
+    id="cff0fd5c98147d66e1386a8d92bd67c38c9b9fa7.boutiques",
+    name="3dBandpass",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dBandpassParameters = typing.TypedDict('V3dBandpassParameters', {
+    "__STYX_TYPE__": typing.Literal["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],
+})
+
+
+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(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Output file from 3dbandpass."""
+
+
+def v_3d_bandpass_params(
+    highpass: float,
+    lowpass: float,
+    in_file: InputPathType,
+    prefix: str | None = None,
+    automask: bool = False,
+    blur: float | None = None,
+    despike: bool = False,
+    local_pv: float | None = None,
+    mask: InputPathType | None = None,
+    nfft: int | None = None,
+    no_detrend: bool = False,
+    normalize: bool = False,
+    notrans: bool = False,
+    orthogonalize_dset: InputPathType | None = None,
+    orthogonalize_file: list[InputPathType] | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    tr: float | None = None,
+) -> V3dBandpassParameters:
+    """
+    Build parameters.
+    
+    Args:
+        highpass: Highpass.
+        lowpass: Lowpass.
+        in_file: Input file to 3dbandpass.
+        prefix: Prefix for output file.
+        automask: Create a mask from the input dataset.
+        blur: Blur (inside the mask only) with a filter width (fwhm) of 'fff'\
+            millimeters.
+        despike: Despike each time series before other processing. hopefully,\
+            you don't actually need to do this, which is why it is optional.
+        local_pv: Replace each vector by the local principal vector (aka first\
+            singular vector) from a neighborhood of radius 'rrr' millimeters. note\
+            that the pv time series is l2 normalized. this option is mostly for bob\
+            cox to have fun with.
+        mask: Mask file.
+        nfft: Set the fft length [must be a legal value].
+        no_detrend: Skip the quadratic detrending of the input that occurs\
+            before the fft-based bandpassing. you would only want to do this if the\
+            dataset had been detrended already in some other program.
+        normalize: Make all output time series have l2 norm = 1 (i.e., sum of\
+            squares = 1).
+        notrans: Don't check for initial positive transients in the data. the\
+            test is a little slow, so skipping it is ok, if you know the data time\
+            series are transient-free.
+        orthogonalize_dset: Orthogonalize each voxel to the corresponding voxel\
+            time series in dataset 'fset', which must have the same spatial and\
+            temporal grid structure as the main input dataset. at present, only one\
+            '-dsort' option is allowed.
+        orthogonalize_file: Also orthogonalize input to columns in f.1d.\
+            multiple '-ort' options are allowed.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        tr: Set time step (tr) in sec [default=from dataset header].
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dBandpass",
+        "automask": automask,
+        "despike": despike,
+        "highpass": highpass,
+        "lowpass": lowpass,
+        "in_file": in_file,
+        "no_detrend": no_detrend,
+        "normalize": normalize,
+        "notrans": notrans,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if blur is not None:
+        params["blur"] = blur
+    if local_pv is not None:
+        params["localPV"] = local_pv
+    if mask is not None:
+        params["mask"] = mask
+    if nfft is not None:
+        params["nfft"] = nfft
+    if orthogonalize_dset is not None:
+        params["orthogonalize_dset"] = orthogonalize_dset
+    if orthogonalize_file is not None:
+        params["orthogonalize_file"] = orthogonalize_file
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    if tr is not None:
+        params["tr"] = tr
+    return params
+
+
+def v_3d_bandpass_cargs(
+    params: V3dBandpassParameters,
+    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("3dBandpass")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("blur") is not None:
+        cargs.extend([
+            "-blur",
+            str(params.get("blur"))
+        ])
+    if params.get("despike"):
+        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.extend([
+            "-localPV",
+            str(params.get("localPV"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("nfft") is not None:
+        cargs.extend([
+            "-nfft",
+            str(params.get("nfft"))
+        ])
+    if params.get("no_detrend"):
+        cargs.append("-nodetrend")
+    if params.get("normalize"):
+        cargs.append("-norm")
+    if params.get("notrans"):
+        cargs.append("-notrans")
+    if params.get("orthogonalize_dset") is not None:
+        cargs.extend([
+            "-dsort",
+            execution.input_file(params.get("orthogonalize_dset"))
+        ])
+    if params.get("orthogonalize_file") is not None:
+        cargs.extend([
+            "-ort",
+            *[execution.input_file(f) for f in params.get("orthogonalize_file")]
+        ])
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-dt",
+            str(params.get("tr"))
+        ])
+    return cargs
+
+
+def v_3d_bandpass_outputs(
+    params: V3dBandpassParameters,
+    execution: Execution,
+) -> V3dBandpassOutputs:
+    """
+    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 = V3dBandpassOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_bandpass_execute(
+    params: V3dBandpassParameters,
+    execution: Execution,
+) -> V3dBandpassOutputs:
+    """
+    Program to lowpass and/or highpass each voxel time series in a dataset, offering
+    more/different options than Fourier.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dBandpassOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_bandpass_cargs(params, execution)
+    ret = v_3d_bandpass_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_bandpass(
+    highpass: float,
+    lowpass: float,
+    in_file: InputPathType,
+    prefix: str | None = None,
+    automask: bool = False,
+    blur: float | None = None,
+    despike: bool = False,
+    local_pv: float | None = None,
+    mask: InputPathType | None = None,
+    nfft: int | None = None,
+    no_detrend: bool = False,
+    normalize: bool = False,
+    notrans: bool = False,
+    orthogonalize_dset: InputPathType | None = None,
+    orthogonalize_file: list[InputPathType] | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    tr: float | None = None,
+    runner: Runner | None = None,
+) -> V3dBandpassOutputs:
+    """
+    Program to lowpass and/or highpass each voxel time series in a dataset, offering
+    more/different options than Fourier.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        highpass: Highpass.
+        lowpass: Lowpass.
+        in_file: Input file to 3dbandpass.
+        prefix: Prefix for output file.
+        automask: Create a mask from the input dataset.
+        blur: Blur (inside the mask only) with a filter width (fwhm) of 'fff'\
+            millimeters.
+        despike: Despike each time series before other processing. hopefully,\
+            you don't actually need to do this, which is why it is optional.
+        local_pv: Replace each vector by the local principal vector (aka first\
+            singular vector) from a neighborhood of radius 'rrr' millimeters. note\
+            that the pv time series is l2 normalized. this option is mostly for bob\
+            cox to have fun with.
+        mask: Mask file.
+        nfft: Set the fft length [must be a legal value].
+        no_detrend: Skip the quadratic detrending of the input that occurs\
+            before the fft-based bandpassing. you would only want to do this if the\
+            dataset had been detrended already in some other program.
+        normalize: Make all output time series have l2 norm = 1 (i.e., sum of\
+            squares = 1).
+        notrans: Don't check for initial positive transients in the data. the\
+            test is a little slow, so skipping it is ok, if you know the data time\
+            series are transient-free.
+        orthogonalize_dset: Orthogonalize each voxel to the corresponding voxel\
+            time series in dataset 'fset', which must have the same spatial and\
+            temporal grid structure as the main input dataset. at present, only one\
+            '-dsort' option is allowed.
+        orthogonalize_file: Also orthogonalize input to columns in f.1d.\
+            multiple '-ort' options are allowed.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        tr: Set time step (tr) in sec [default=from dataset header].
+        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 = v_3d_bandpass_params(
+        prefix=prefix,
+        automask=automask,
+        blur=blur,
+        despike=despike,
+        highpass=highpass,
+        lowpass=lowpass,
+        in_file=in_file,
+        local_pv=local_pv,
+        mask=mask,
+        nfft=nfft,
+        no_detrend=no_detrend,
+        normalize=normalize,
+        notrans=notrans,
+        orthogonalize_dset=orthogonalize_dset,
+        orthogonalize_file=orthogonalize_file,
+        outputtype=outputtype,
+        tr=tr,
+    )
+    return v_3d_bandpass_execute(params, execution)
+
+
+__all__ = [
+    "V3dBandpassOutputs",
+    "V3dBandpassParameters",
+    "V_3D_BANDPASS_METADATA",
+    "v_3d_bandpass",
+    "v_3d_bandpass_params",
+]

niwrap_afni/afni/v_3d_blur_in_mask.py

@@ -0,0 +1,291 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_BLUR_IN_MASK_METADATA = Metadata(
+    id="2020eccbab2609356d0e3ab2fdd84a54c25cb900.boutiques",
+    name="3dBlurInMask",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dBlurInMaskParameters = typing.TypedDict('V3dBlurInMaskParameters', {
+    "__STYX_TYPE__": typing.Literal["3dBlurInMask"],
+    "input_file": InputPathType,
+    "output_prefix": str,
+    "fwhm": float,
+    "fwhm_dataset": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "multi_mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "preserve": bool,
+    "quiet": bool,
+    "float": bool,
+    "fwhm_xyz": 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 {
+        "3dBlurInMask": v_3d_blur_in_mask_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 {
+        "3dBlurInMask": v_3d_blur_in_mask_outputs,
+    }.get(t)
+
+
+class V3dBlurInMaskOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_blur_in_mask(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output dataset"""
+
+
+def v_3d_blur_in_mask_params(
+    input_file: InputPathType,
+    output_prefix: str,
+    fwhm: float,
+    fwhm_dataset: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    multi_mask: InputPathType | None = None,
+    automask: bool = False,
+    preserve: bool = False,
+    quiet: bool = False,
+    float_: bool = False,
+    fwhm_xyz: list[float] | None = None,
+) -> V3dBlurInMaskParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Dataset to be smoothed and output.
+        output_prefix: Prefix for output dataset.
+        fwhm: Amount of smoothness to add to the dataset (in mm).
+        fwhm_dataset: Dataset containing the amount of smoothness for each\
+            voxel.
+        mask: Mask dataset for blurring; voxels NOT in the mask will be zeroed\
+            in the output.
+        multi_mask: Multi-mask dataset; each distinct nonzero value is treated\
+            as a separate mask.
+        automask: Create an automask from the input dataset.
+        preserve: Preserve original values in the dataset outside the mask.
+        quiet: Don't be verbose with progress reports.
+        float_: Save dataset as floats.
+        fwhm_xyz: Add different amounts of smoothness in the 3 spatial\
+            directions.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dBlurInMask",
+        "input_file": input_file,
+        "output_prefix": output_prefix,
+        "fwhm": fwhm,
+        "automask": automask,
+        "preserve": preserve,
+        "quiet": quiet,
+        "float": float_,
+    }
+    if fwhm_dataset is not None:
+        params["fwhm_dataset"] = fwhm_dataset
+    if mask is not None:
+        params["mask"] = mask
+    if multi_mask is not None:
+        params["multi_mask"] = multi_mask
+    if fwhm_xyz is not None:
+        params["fwhm_xyz"] = fwhm_xyz
+    return params
+
+
+def v_3d_blur_in_mask_cargs(
+    params: V3dBlurInMaskParameters,
+    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("3dBlurInMask")
+    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(params.get("output_prefix"))
+    cargs.extend([
+        "-FWHM",
+        str(params.get("fwhm"))
+    ])
+    if params.get("fwhm_dataset") is not None:
+        cargs.extend([
+            "-FWHMdset",
+            execution.input_file(params.get("fwhm_dataset"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("multi_mask") is not None:
+        cargs.extend([
+            "-Mmask",
+            execution.input_file(params.get("multi_mask"))
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("preserve"):
+        cargs.append("-preserve")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("float"):
+        cargs.append("-float")
+    if params.get("fwhm_xyz") is not None:
+        cargs.extend([
+            "-FWHMxyz",
+            *map(str, params.get("fwhm_xyz"))
+        ])
+    return cargs
+
+
+def v_3d_blur_in_mask_outputs(
+    params: V3dBlurInMaskParameters,
+    execution: Execution,
+) -> V3dBlurInMaskOutputs:
+    """
+    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 = V3dBlurInMaskOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_prefix")),
+    )
+    return ret
+
+
+def v_3d_blur_in_mask_execute(
+    params: V3dBlurInMaskParameters,
+    execution: Execution,
+) -> V3dBlurInMaskOutputs:
+    """
+    Blurs a dataset spatially inside a mask.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dBlurInMaskOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_blur_in_mask_cargs(params, execution)
+    ret = v_3d_blur_in_mask_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_blur_in_mask(
+    input_file: InputPathType,
+    output_prefix: str,
+    fwhm: float,
+    fwhm_dataset: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    multi_mask: InputPathType | None = None,
+    automask: bool = False,
+    preserve: bool = False,
+    quiet: bool = False,
+    float_: bool = False,
+    fwhm_xyz: list[float] | None = None,
+    runner: Runner | None = None,
+) -> V3dBlurInMaskOutputs:
+    """
+    Blurs a dataset spatially inside a mask.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Dataset to be smoothed and output.
+        output_prefix: Prefix for output dataset.
+        fwhm: Amount of smoothness to add to the dataset (in mm).
+        fwhm_dataset: Dataset containing the amount of smoothness for each\
+            voxel.
+        mask: Mask dataset for blurring; voxels NOT in the mask will be zeroed\
+            in the output.
+        multi_mask: Multi-mask dataset; each distinct nonzero value is treated\
+            as a separate mask.
+        automask: Create an automask from the input dataset.
+        preserve: Preserve original values in the dataset outside the mask.
+        quiet: Don't be verbose with progress reports.
+        float_: Save dataset as floats.
+        fwhm_xyz: Add different amounts of smoothness in the 3 spatial\
+            directions.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dBlurInMaskOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BLUR_IN_MASK_METADATA)
+    params = v_3d_blur_in_mask_params(
+        input_file=input_file,
+        output_prefix=output_prefix,
+        fwhm=fwhm,
+        fwhm_dataset=fwhm_dataset,
+        mask=mask,
+        multi_mask=multi_mask,
+        automask=automask,
+        preserve=preserve,
+        quiet=quiet,
+        float_=float_,
+        fwhm_xyz=fwhm_xyz,
+    )
+    return v_3d_blur_in_mask_execute(params, execution)
+
+
+__all__ = [
+    "V3dBlurInMaskOutputs",
+    "V3dBlurInMaskParameters",
+    "V_3D_BLUR_IN_MASK_METADATA",
+    "v_3d_blur_in_mask",
+    "v_3d_blur_in_mask_params",
+]