niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3ddelay.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DDELAY_METADATA = Metadata(
+    id="d876295ae5d31352ba81e14a366aedff6fceb582.boutiques",
+    name="3ddelay",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3ddelayParameters = typing.TypedDict('V3ddelayParameters', {
+    "__STYX_TYPE__": typing.Literal["3ddelay"],
+    "input_file": InputPathType,
+    "reference_file": InputPathType,
+    "sampling_freq": float,
+    "stim_period": float,
+    "prefix": typing.NotRequired[str | None],
+    "polort": typing.NotRequired[float | None],
+    "nodtrnd": bool,
+    "units_seconds": bool,
+    "units_degrees": bool,
+    "units_radians": bool,
+    "phzwrp": bool,
+    "nophzwrp": bool,
+    "phzreverse": bool,
+    "phzscale": typing.NotRequired[float | None],
+    "bias": bool,
+    "nobias": bool,
+    "dsamp": bool,
+    "nodsamp": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "nfirst": typing.NotRequired[float | None],
+    "nlast": typing.NotRequired[float | None],
+    "co": typing.NotRequired[float | None],
+    "asc": typing.NotRequired[str | None],
+    "ascts": 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 {
+        "3ddelay": v_3ddelay_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 {
+        "3ddelay": v_3ddelay_outputs,
+    }.get(t)
+
+
+class V3ddelayOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3ddelay(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_brick: OutputPathType | None
+    """Primary output results Brick for Delay"""
+    output_asc: OutputPathType | None
+    """Output ASCII file for results"""
+    output_asc_log: OutputPathType | None
+    """Log file containing parameter settings and warnings"""
+    output_asc_ts: OutputPathType | None
+    """Output ASCII file with time series"""
+
+
+def v_3ddelay_params(
+    input_file: InputPathType,
+    reference_file: InputPathType,
+    sampling_freq: float,
+    stim_period: float,
+    prefix: str | None = None,
+    polort: float | None = None,
+    nodtrnd: bool = False,
+    units_seconds: bool = False,
+    units_degrees: bool = False,
+    units_radians: bool = False,
+    phzwrp: bool = False,
+    nophzwrp: bool = False,
+    phzreverse: bool = False,
+    phzscale: float | None = None,
+    bias: bool = False,
+    nobias: bool = False,
+    dsamp: bool = False,
+    nodsamp: bool = False,
+    mask: InputPathType | None = None,
+    nfirst: float | None = None,
+    nlast: float | None = None,
+    co: float | None = None,
+    asc: str | None = None,
+    ascts: str | None = None,
+) -> V3ddelayParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Filename of the input 3D+time dataset.
+        reference_file: Input ideal time series file name.
+        sampling_freq: Sampling frequency in Hz. of data time series (1/TR).
+        stim_period: Stimulus period in seconds. Set to 0 if stimulus is not\
+            periodic.
+        prefix: The prefix for the results Brick.
+        polort: Detrend input time series with polynomial of specified order.\
+            Default is -1 for auto selection.
+        nodtrnd: Remove only the mean (equivalent to polort 0).
+        units_seconds: Units for delay estimates in seconds.
+        units_degrees: Units for delay estimates in degrees. Requires Tstim > 0.
+        units_radians: Units for delay estimates in radians. Requires Tstim > 0.
+        phzwrp: Wrap delay (or phase) values.
+        nophzwrp: Do not wrap phase (default).
+        phzreverse: Reverse phase such that phase -> (T-phase).
+        phzscale: Scale phase: phase -> phase*SC (default no scaling).
+        bias: Do not correct for the bias in the estimates.
+        nobias: Correct for the bias in the estimates (default).
+        dsamp: Correct for slice timing differences (default).
+        nodsamp: Do not correct for slice timing differences.
+        mask: Filename of mask dataset. Only voxels with non-zero values in the\
+            mask will be considered.
+        nfirst: Number of first dataset image to use in the delay estimate.
+        nlast: Number of last dataset image to use in the delay estimate.
+        co: Cross Correlation Coefficient threshold value to limit ascii output.
+        asc: Write the results to an ascii file for voxels with cross\
+            correlation coefficients larger than CCT.
+        ascts: Write the results and time series to an ascii file for voxels\
+            with cross correlation coefficients larger than CCT.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3ddelay",
+        "input_file": input_file,
+        "reference_file": reference_file,
+        "sampling_freq": sampling_freq,
+        "stim_period": stim_period,
+        "nodtrnd": nodtrnd,
+        "units_seconds": units_seconds,
+        "units_degrees": units_degrees,
+        "units_radians": units_radians,
+        "phzwrp": phzwrp,
+        "nophzwrp": nophzwrp,
+        "phzreverse": phzreverse,
+        "bias": bias,
+        "nobias": nobias,
+        "dsamp": dsamp,
+        "nodsamp": nodsamp,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if polort is not None:
+        params["polort"] = polort
+    if phzscale is not None:
+        params["phzscale"] = phzscale
+    if mask is not None:
+        params["mask"] = mask
+    if nfirst is not None:
+        params["nfirst"] = nfirst
+    if nlast is not None:
+        params["nlast"] = nlast
+    if co is not None:
+        params["co"] = co
+    if asc is not None:
+        params["asc"] = asc
+    if ascts is not None:
+        params["ascts"] = ascts
+    return params
+
+
+def v_3ddelay_cargs(
+    params: V3ddelayParameters,
+    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("3ddelay")
+    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(execution.input_file(params.get("reference_file")))
+    cargs.extend([
+        "-fs",
+        str(params.get("sampling_freq"))
+    ])
+    cargs.extend([
+        "-T",
+        str(params.get("stim_period"))
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    if params.get("nodtrnd"):
+        cargs.append("-nodtrnd")
+    if params.get("units_seconds"):
+        cargs.append("-uS")
+    if params.get("units_degrees"):
+        cargs.append("-uD")
+    if params.get("units_radians"):
+        cargs.append("-uR")
+    if params.get("phzwrp"):
+        cargs.append("-phzwrp")
+    if params.get("nophzwrp"):
+        cargs.append("-nophzwrp")
+    if params.get("phzreverse"):
+        cargs.append("-phzreverse")
+    if params.get("phzscale") is not None:
+        cargs.extend([
+            "-phzscale",
+            str(params.get("phzscale"))
+        ])
+    if params.get("bias"):
+        cargs.append("-bias")
+    if params.get("nobias"):
+        cargs.append("-nobias")
+    if params.get("dsamp"):
+        cargs.append("-dsamp")
+    if params.get("nodsamp"):
+        cargs.append("-nodsamp")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("nfirst") is not None:
+        cargs.extend([
+            "-nfirst",
+            str(params.get("nfirst"))
+        ])
+    if params.get("nlast") is not None:
+        cargs.extend([
+            "-nlast",
+            str(params.get("nlast"))
+        ])
+    if params.get("co") is not None:
+        cargs.extend([
+            "-co",
+            str(params.get("co"))
+        ])
+    if params.get("asc") is not None:
+        cargs.extend([
+            "-asc",
+            params.get("asc")
+        ])
+    if params.get("ascts") is not None:
+        cargs.extend([
+            "-ascts",
+            params.get("ascts")
+        ])
+    return cargs
+
+
+def v_3ddelay_outputs(
+    params: V3ddelayParameters,
+    execution: Execution,
+) -> V3ddelayOutputs:
+    """
+    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 = V3ddelayOutputs(
+        root=execution.output_file("."),
+        output_brick=execution.output_file(params.get("prefix") + ".DEL+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_asc=execution.output_file(params.get("prefix") + ".ASC") if (params.get("prefix") is not None) else None,
+        output_asc_log=execution.output_file(params.get("prefix") + ".ASC.log") if (params.get("prefix") is not None) else None,
+        output_asc_ts=execution.output_file(params.get("prefix") + ".ASC.ts") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3ddelay_execute(
+    params: V3ddelayParameters,
+    execution: Execution,
+) -> V3ddelayOutputs:
+    """
+    Estimates the time delay between each voxel time series in a 3D+time dataset and
+    a reference time series.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3ddelayOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3ddelay_cargs(params, execution)
+    ret = v_3ddelay_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3ddelay(
+    input_file: InputPathType,
+    reference_file: InputPathType,
+    sampling_freq: float,
+    stim_period: float,
+    prefix: str | None = None,
+    polort: float | None = None,
+    nodtrnd: bool = False,
+    units_seconds: bool = False,
+    units_degrees: bool = False,
+    units_radians: bool = False,
+    phzwrp: bool = False,
+    nophzwrp: bool = False,
+    phzreverse: bool = False,
+    phzscale: float | None = None,
+    bias: bool = False,
+    nobias: bool = False,
+    dsamp: bool = False,
+    nodsamp: bool = False,
+    mask: InputPathType | None = None,
+    nfirst: float | None = None,
+    nlast: float | None = None,
+    co: float | None = None,
+    asc: str | None = None,
+    ascts: str | None = None,
+    runner: Runner | None = None,
+) -> V3ddelayOutputs:
+    """
+    Estimates the time delay between each voxel time series in a 3D+time dataset and
+    a reference time series.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Filename of the input 3D+time dataset.
+        reference_file: Input ideal time series file name.
+        sampling_freq: Sampling frequency in Hz. of data time series (1/TR).
+        stim_period: Stimulus period in seconds. Set to 0 if stimulus is not\
+            periodic.
+        prefix: The prefix for the results Brick.
+        polort: Detrend input time series with polynomial of specified order.\
+            Default is -1 for auto selection.
+        nodtrnd: Remove only the mean (equivalent to polort 0).
+        units_seconds: Units for delay estimates in seconds.
+        units_degrees: Units for delay estimates in degrees. Requires Tstim > 0.
+        units_radians: Units for delay estimates in radians. Requires Tstim > 0.
+        phzwrp: Wrap delay (or phase) values.
+        nophzwrp: Do not wrap phase (default).
+        phzreverse: Reverse phase such that phase -> (T-phase).
+        phzscale: Scale phase: phase -> phase*SC (default no scaling).
+        bias: Do not correct for the bias in the estimates.
+        nobias: Correct for the bias in the estimates (default).
+        dsamp: Correct for slice timing differences (default).
+        nodsamp: Do not correct for slice timing differences.
+        mask: Filename of mask dataset. Only voxels with non-zero values in the\
+            mask will be considered.
+        nfirst: Number of first dataset image to use in the delay estimate.
+        nlast: Number of last dataset image to use in the delay estimate.
+        co: Cross Correlation Coefficient threshold value to limit ascii output.
+        asc: Write the results to an ascii file for voxels with cross\
+            correlation coefficients larger than CCT.
+        ascts: Write the results and time series to an ascii file for voxels\
+            with cross correlation coefficients larger than CCT.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3ddelayOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DDELAY_METADATA)
+    params = v_3ddelay_params(
+        input_file=input_file,
+        reference_file=reference_file,
+        sampling_freq=sampling_freq,
+        stim_period=stim_period,
+        prefix=prefix,
+        polort=polort,
+        nodtrnd=nodtrnd,
+        units_seconds=units_seconds,
+        units_degrees=units_degrees,
+        units_radians=units_radians,
+        phzwrp=phzwrp,
+        nophzwrp=nophzwrp,
+        phzreverse=phzreverse,
+        phzscale=phzscale,
+        bias=bias,
+        nobias=nobias,
+        dsamp=dsamp,
+        nodsamp=nodsamp,
+        mask=mask,
+        nfirst=nfirst,
+        nlast=nlast,
+        co=co,
+        asc=asc,
+        ascts=ascts,
+    )
+    return v_3ddelay_execute(params, execution)
+
+
+__all__ = [
+    "V3ddelayOutputs",
+    "V3ddelayParameters",
+    "V_3DDELAY_METADATA",
+    "v_3ddelay",
+    "v_3ddelay_params",
+]