niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_tshift.py

@@ -0,0 +1,342 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TSHIFT_METADATA = Metadata(
+    id="1e963c8aacff12ed5089324cd001cc9158093823.boutiques",
+    name="3dTshift",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTshiftParameters = typing.TypedDict('V3dTshiftParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTshift"],
+    "prefix": typing.NotRequired[str | None],
+    "ignore": typing.NotRequired[int | None],
+    "in_file": InputPathType,
+    "interp": typing.NotRequired[typing.Literal["Fourier", "linear", "cubic", "quintic", "heptic"] | None],
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "rlt": bool,
+    "rltplus": bool,
+    "slice_encoding_direction": typing.NotRequired[typing.Literal["k", "k-"] | None],
+    "tpattern": typing.NotRequired[typing.Literal["alt+z", "altplus", "alt+z2", "alt-z", "altminus", "alt-z2", "seq+z", "seqplus", "seq-z", "seqminus"] | None],
+    "tr": typing.NotRequired[float | None],
+    "tslice": typing.NotRequired[int | None],
+    "tzero": 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 {
+        "3dTshift": v_3d_tshift_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 {
+        "3dTshift": v_3d_tshift_outputs,
+    }.get(t)
+
+
+class V3dTshiftOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tshift(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Output image file name."""
+    timing_file: OutputPathType
+    """Afni formatted timing file, if ``slice_timing`` is a list."""
+
+
+def v_3d_tshift_params(
+    in_file: InputPathType,
+    prefix: str | None = None,
+    ignore: int | None = None,
+    interp: typing.Literal["Fourier", "linear", "cubic", "quintic", "heptic"] | None = None,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    rlt: bool = False,
+    rltplus: bool = False,
+    slice_encoding_direction: typing.Literal["k", "k-"] | None = None,
+    tpattern: typing.Literal["alt+z", "altplus", "alt+z2", "alt-z", "altminus", "alt-z2", "seq+z", "seqplus", "seq-z", "seqminus"] | None = None,
+    tr: float | None = None,
+    tslice: int | None = None,
+    tzero: float | None = None,
+) -> V3dTshiftParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3dtshift.
+        prefix: Prefix for output image file name.
+        ignore: Ignore the first set of points specified.
+        interp: 'fourier' or 'linear' or 'cubic' or 'quintic' or 'heptic'.\
+            Different interpolation methods (see 3dtshift for details) default =\
+            fourier.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        rlt: Before shifting, remove the mean and linear trend.
+        rltplus: Before shifting, remove the mean and linear trend and later\
+            put back the mean.
+        slice_encoding_direction: 'k' or 'k-'. Direction in which slice_timing\
+            is specified (default: k). if negative,slice_timing is defined in\
+            reverse order, that is, the first entry corresponds to the slice with\
+            the largest index, and the final entry corresponds to slice index zero.\
+            only in effect when slice_timing is passed as list, not when it is\
+            passed as file.
+        tpattern: 'alt+z' or 'altplus' or 'alt+z2' or 'alt-z' or 'altminus' or\
+            'alt-z2' or 'seq+z' or 'seqplus' or 'seq-z' or 'seqminus' or a string.\
+            Use specified slice time pattern rather than one in header.
+        tr: Manually set the tr. you can attach suffix "s" for seconds or "ms"\
+            for milliseconds.
+        tslice: Align each slice to time offset of given slice.
+        tzero: Align each slice to given time offset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTshift",
+        "in_file": in_file,
+        "rlt": rlt,
+        "rltplus": rltplus,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if ignore is not None:
+        params["ignore"] = ignore
+    if interp is not None:
+        params["interp"] = interp
+    if num_threads is not None:
+        params["num_threads"] = num_threads
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    if slice_encoding_direction is not None:
+        params["slice_encoding_direction"] = slice_encoding_direction
+    if tpattern is not None:
+        params["tpattern"] = tpattern
+    if tr is not None:
+        params["tr"] = tr
+    if tslice is not None:
+        params["tslice"] = tslice
+    if tzero is not None:
+        params["tzero"] = tzero
+    return params
+
+
+def v_3d_tshift_cargs(
+    params: V3dTshiftParameters,
+    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("3dTshift")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("ignore") is not None:
+        cargs.extend([
+            "-ignore",
+            str(params.get("ignore"))
+        ])
+    cargs.append(execution.input_file(params.get("in_file")))
+    if params.get("interp") is not None:
+        cargs.extend([
+            "-",
+            params.get("interp")
+        ])
+    if params.get("num_threads") is not None:
+        cargs.append(str(params.get("num_threads")))
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    if params.get("rlt"):
+        cargs.append("-rlt")
+    if params.get("rltplus"):
+        cargs.append("-rlt+")
+    if params.get("slice_encoding_direction") is not None:
+        cargs.append(params.get("slice_encoding_direction"))
+    if params.get("tpattern") is not None:
+        cargs.extend([
+            "-tpattern",
+            params.get("tpattern")
+        ])
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-TR",
+            str(params.get("tr"))
+        ])
+    if params.get("tslice") is not None:
+        cargs.extend([
+            "-slice",
+            str(params.get("tslice"))
+        ])
+    if params.get("tzero") is not None:
+        cargs.extend([
+            "-tzero",
+            str(params.get("tzero"))
+        ])
+    return cargs
+
+
+def v_3d_tshift_outputs(
+    params: V3dTshiftParameters,
+    execution: Execution,
+) -> V3dTshiftOutputs:
+    """
+    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 = V3dTshiftOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        timing_file=execution.output_file("timing_file"),
+    )
+    return ret
+
+
+def v_3d_tshift_execute(
+    params: V3dTshiftParameters,
+    execution: Execution,
+) -> V3dTshiftOutputs:
+    """
+    Shifts voxel time series from input so that separate slices are aligned to the
+    same temporal origin.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTshiftOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tshift_cargs(params, execution)
+    ret = v_3d_tshift_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tshift(
+    in_file: InputPathType,
+    prefix: str | None = None,
+    ignore: int | None = None,
+    interp: typing.Literal["Fourier", "linear", "cubic", "quintic", "heptic"] | None = None,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    rlt: bool = False,
+    rltplus: bool = False,
+    slice_encoding_direction: typing.Literal["k", "k-"] | None = None,
+    tpattern: typing.Literal["alt+z", "altplus", "alt+z2", "alt-z", "altminus", "alt-z2", "seq+z", "seqplus", "seq-z", "seqminus"] | None = None,
+    tr: float | None = None,
+    tslice: int | None = None,
+    tzero: float | None = None,
+    runner: Runner | None = None,
+) -> V3dTshiftOutputs:
+    """
+    Shifts voxel time series from input so that separate slices are aligned to the
+    same temporal origin.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3dtshift.
+        prefix: Prefix for output image file name.
+        ignore: Ignore the first set of points specified.
+        interp: 'fourier' or 'linear' or 'cubic' or 'quintic' or 'heptic'.\
+            Different interpolation methods (see 3dtshift for details) default =\
+            fourier.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        rlt: Before shifting, remove the mean and linear trend.
+        rltplus: Before shifting, remove the mean and linear trend and later\
+            put back the mean.
+        slice_encoding_direction: 'k' or 'k-'. Direction in which slice_timing\
+            is specified (default: k). if negative,slice_timing is defined in\
+            reverse order, that is, the first entry corresponds to the slice with\
+            the largest index, and the final entry corresponds to slice index zero.\
+            only in effect when slice_timing is passed as list, not when it is\
+            passed as file.
+        tpattern: 'alt+z' or 'altplus' or 'alt+z2' or 'alt-z' or 'altminus' or\
+            'alt-z2' or 'seq+z' or 'seqplus' or 'seq-z' or 'seqminus' or a string.\
+            Use specified slice time pattern rather than one in header.
+        tr: Manually set the tr. you can attach suffix "s" for seconds or "ms"\
+            for milliseconds.
+        tslice: Align each slice to time offset of given slice.
+        tzero: Align each slice to given time offset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTshiftOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TSHIFT_METADATA)
+    params = v_3d_tshift_params(
+        prefix=prefix,
+        ignore=ignore,
+        in_file=in_file,
+        interp=interp,
+        num_threads=num_threads,
+        outputtype=outputtype,
+        rlt=rlt,
+        rltplus=rltplus,
+        slice_encoding_direction=slice_encoding_direction,
+        tpattern=tpattern,
+        tr=tr,
+        tslice=tslice,
+        tzero=tzero,
+    )
+    return v_3d_tshift_execute(params, execution)
+
+
+__all__ = [
+    "V3dTshiftOutputs",
+    "V3dTshiftParameters",
+    "V_3D_TSHIFT_METADATA",
+    "v_3d_tshift",
+    "v_3d_tshift_params",
+]

niwrap_afni/afni/v_3d_tsmooth.py

@@ -0,0 +1,331 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TSMOOTH_METADATA = Metadata(
+    id="b237186199e1da14b990e2891bc27f1f59ceede0.boutiques",
+    name="3dTsmooth",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTsmoothParameters = typing.TypedDict('V3dTsmoothParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTsmooth"],
+    "input_dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "datum_type": typing.NotRequired[str | None],
+    "lin_filter": bool,
+    "med_filter": bool,
+    "osf_filter": bool,
+    "lin_filter_custom": typing.NotRequired[float | None],
+    "hamming": typing.NotRequired[int | None],
+    "blackman": typing.NotRequired[int | None],
+    "custom_filter": typing.NotRequired[InputPathType | None],
+    "extend": bool,
+    "zero": bool,
+    "trend": bool,
+    "adaptive": typing.NotRequired[int | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dTsmooth": v_3d_tsmooth_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 {
+        "3dTsmooth": v_3d_tsmooth_outputs,
+    }.get(t)
+
+
+class V3dTsmoothOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tsmooth(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType | None
+    """Smoothed 3D+time dataset"""
+
+
+def v_3d_tsmooth_params(
+    input_dataset: InputPathType,
+    prefix: str | None = None,
+    datum_type: str | None = None,
+    lin_filter: bool = False,
+    med_filter: bool = False,
+    osf_filter: bool = False,
+    lin_filter_custom: float | None = None,
+    hamming: int | None = None,
+    blackman: int | None = None,
+    custom_filter: InputPathType | None = None,
+    extend: bool = False,
+    zero: bool = False,
+    trend: bool = False,
+    adaptive: int | None = None,
+) -> V3dTsmoothParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: The input 3D+time dataset.
+        prefix: Sets the prefix of the output dataset.
+        datum_type: Coerce output dataset to be stored as the given type.
+        lin_filter: 3 point linear filter: 0.15*a + 0.70*b + 0.15*c.
+        med_filter: 3 point median filter: median(a,b,c).
+        osf_filter: 3 point order statistics filter: 0.15*min(a,b,c) +\
+            0.70*median(a,b,c) + 0.15*max(a,b,c).
+        lin_filter_custom: 3 point linear filter with custom weight:\
+            0.5*(1-m)*a + m*b + 0.5*(1-m)*c.
+        hamming: Use N point Hamming window filter.
+        blackman: Use N point Blackman window filter.
+        custom_filter: Use custom filter with coefficients from a specified\
+            file.
+        extend: BEFORE: use the first value; AFTER: use the last value.
+        zero: BEFORE and AFTER: use zero.
+        trend: Compute a linear trend, and extrapolate BEFORE and AFTER.
+        adaptive: Use adaptive mean filtering of width N (N must be odd and\
+            bigger than 3).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTsmooth",
+        "input_dataset": input_dataset,
+        "lin_filter": lin_filter,
+        "med_filter": med_filter,
+        "osf_filter": osf_filter,
+        "extend": extend,
+        "zero": zero,
+        "trend": trend,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if datum_type is not None:
+        params["datum_type"] = datum_type
+    if lin_filter_custom is not None:
+        params["lin_filter_custom"] = lin_filter_custom
+    if hamming is not None:
+        params["hamming"] = hamming
+    if blackman is not None:
+        params["blackman"] = blackman
+    if custom_filter is not None:
+        params["custom_filter"] = custom_filter
+    if adaptive is not None:
+        params["adaptive"] = adaptive
+    return params
+
+
+def v_3d_tsmooth_cargs(
+    params: V3dTsmoothParameters,
+    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("3dTsmooth")
+    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("datum_type") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum_type")
+        ])
+    if params.get("lin_filter"):
+        cargs.append("-lin")
+    if params.get("med_filter"):
+        cargs.append("-med")
+    if params.get("osf_filter"):
+        cargs.append("-osf")
+    if params.get("lin_filter_custom") is not None:
+        cargs.extend([
+            "-3lin",
+            str(params.get("lin_filter_custom"))
+        ])
+    if params.get("hamming") is not None:
+        cargs.extend([
+            "-hamming",
+            str(params.get("hamming"))
+        ])
+    if params.get("blackman") is not None:
+        cargs.extend([
+            "-blackman",
+            str(params.get("blackman"))
+        ])
+    if params.get("custom_filter") is not None:
+        cargs.extend([
+            "-custom",
+            execution.input_file(params.get("custom_filter"))
+        ])
+    if params.get("extend"):
+        cargs.append("-EXTEND")
+    if params.get("zero"):
+        cargs.append("-ZERO")
+    if params.get("trend"):
+        cargs.append("-TREND")
+    if params.get("adaptive") is not None:
+        cargs.extend([
+            "-adaptive",
+            str(params.get("adaptive"))
+        ])
+    return cargs
+
+
+def v_3d_tsmooth_outputs(
+    params: V3dTsmoothParameters,
+    execution: Execution,
+) -> V3dTsmoothOutputs:
+    """
+    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 = V3dTsmoothOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_tsmooth_execute(
+    params: V3dTsmoothParameters,
+    execution: Execution,
+) -> V3dTsmoothOutputs:
+    """
+    Smooths each voxel time series in a 3D+time dataset and produces as output a new
+    3D+time dataset (e.g., lowpass filter in time).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTsmoothOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tsmooth_cargs(params, execution)
+    ret = v_3d_tsmooth_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tsmooth(
+    input_dataset: InputPathType,
+    prefix: str | None = None,
+    datum_type: str | None = None,
+    lin_filter: bool = False,
+    med_filter: bool = False,
+    osf_filter: bool = False,
+    lin_filter_custom: float | None = None,
+    hamming: int | None = None,
+    blackman: int | None = None,
+    custom_filter: InputPathType | None = None,
+    extend: bool = False,
+    zero: bool = False,
+    trend: bool = False,
+    adaptive: int | None = None,
+    runner: Runner | None = None,
+) -> V3dTsmoothOutputs:
+    """
+    Smooths each voxel time series in a 3D+time dataset and produces as output a new
+    3D+time dataset (e.g., lowpass filter in time).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: The input 3D+time dataset.
+        prefix: Sets the prefix of the output dataset.
+        datum_type: Coerce output dataset to be stored as the given type.
+        lin_filter: 3 point linear filter: 0.15*a + 0.70*b + 0.15*c.
+        med_filter: 3 point median filter: median(a,b,c).
+        osf_filter: 3 point order statistics filter: 0.15*min(a,b,c) +\
+            0.70*median(a,b,c) + 0.15*max(a,b,c).
+        lin_filter_custom: 3 point linear filter with custom weight:\
+            0.5*(1-m)*a + m*b + 0.5*(1-m)*c.
+        hamming: Use N point Hamming window filter.
+        blackman: Use N point Blackman window filter.
+        custom_filter: Use custom filter with coefficients from a specified\
+            file.
+        extend: BEFORE: use the first value; AFTER: use the last value.
+        zero: BEFORE and AFTER: use zero.
+        trend: Compute a linear trend, and extrapolate BEFORE and AFTER.
+        adaptive: Use adaptive mean filtering of width N (N must be odd and\
+            bigger than 3).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTsmoothOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TSMOOTH_METADATA)
+    params = v_3d_tsmooth_params(
+        input_dataset=input_dataset,
+        prefix=prefix,
+        datum_type=datum_type,
+        lin_filter=lin_filter,
+        med_filter=med_filter,
+        osf_filter=osf_filter,
+        lin_filter_custom=lin_filter_custom,
+        hamming=hamming,
+        blackman=blackman,
+        custom_filter=custom_filter,
+        extend=extend,
+        zero=zero,
+        trend=trend,
+        adaptive=adaptive,
+    )
+    return v_3d_tsmooth_execute(params, execution)
+
+
+__all__ = [
+    "V3dTsmoothOutputs",
+    "V3dTsmoothParameters",
+    "V_3D_TSMOOTH_METADATA",
+    "v_3d_tsmooth",
+    "v_3d_tsmooth_params",
+]