niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__retino_proc.py

@@ -0,0 +1,670 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__RETINO_PROC_METADATA = Metadata(
+    id="0836ad099b5ae0ebd794fce9bafc7b29723fb572.boutiques",
+    name="@RetinoProc",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VRetinoProcParameters = typing.TypedDict('VRetinoProcParameters', {
+    "__STYX_TYPE__": typing.Literal["@RetinoProc"],
+    "ccw": typing.NotRequired[list[InputPathType] | None],
+    "clw": typing.NotRequired[list[InputPathType] | None],
+    "exp": typing.NotRequired[list[InputPathType] | None],
+    "con": typing.NotRequired[list[InputPathType] | None],
+    "epi_ref": typing.NotRequired[InputPathType | None],
+    "epi_anat_ref": typing.NotRequired[InputPathType | None],
+    "anat_vol": typing.NotRequired[InputPathType | None],
+    "anat_vol_epi": typing.NotRequired[InputPathType | None],
+    "surf_vol": typing.NotRequired[InputPathType | None],
+    "surf_vol_epi": typing.NotRequired[InputPathType | None],
+    "phase": bool,
+    "delay": bool,
+    "tr": float,
+    "period_ecc": float,
+    "period_pol": float,
+    "pre_ecc": typing.NotRequired[float | None],
+    "pre_pol": typing.NotRequired[float | None],
+    "on_ecc": typing.NotRequired[str | None],
+    "on_pol": typing.NotRequired[str | None],
+    "var_on_ecc": typing.NotRequired[str | None],
+    "var_on_pol": typing.NotRequired[str | None],
+    "nwedges": typing.NotRequired[float | None],
+    "nrings": typing.NotRequired[float | None],
+    "fwhm_pol": typing.NotRequired[float | None],
+    "fwhm_ecc": typing.NotRequired[float | None],
+    "ignore": typing.NotRequired[float | None],
+    "no_tshift": bool,
+    "spec_left": typing.NotRequired[InputPathType | None],
+    "spec_right": typing.NotRequired[InputPathType | None],
+    "dorts": typing.NotRequired[InputPathType | None],
+    "ccw_orts": typing.NotRequired[list[InputPathType] | None],
+    "clw_orts": typing.NotRequired[list[InputPathType] | None],
+    "exp_orts": typing.NotRequired[list[InputPathType] | None],
+    "con_orts": typing.NotRequired[list[InputPathType] | None],
+    "sid": typing.NotRequired[str | None],
+    "out_dir": typing.NotRequired[str | None],
+    "echo": bool,
+    "echo_edu": bool,
+    "a2e_opts": typing.NotRequired[str | None],
+    "aea_opts": 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 {
+        "@RetinoProc": v__retino_proc_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 {
+    }.get(t)
+
+
+class VRetinoProcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__retino_proc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__retino_proc_params(
+    tr: float,
+    period_ecc: float,
+    period_pol: float,
+    ccw: list[InputPathType] | None = None,
+    clw: list[InputPathType] | None = None,
+    exp: list[InputPathType] | None = None,
+    con: list[InputPathType] | None = None,
+    epi_ref: InputPathType | None = None,
+    epi_anat_ref: InputPathType | None = None,
+    anat_vol: InputPathType | None = None,
+    anat_vol_epi: InputPathType | None = None,
+    surf_vol: InputPathType | None = None,
+    surf_vol_epi: InputPathType | None = None,
+    phase: bool = False,
+    delay: bool = False,
+    pre_ecc: float | None = None,
+    pre_pol: float | None = None,
+    on_ecc: str | None = None,
+    on_pol: str | None = None,
+    var_on_ecc: str | None = None,
+    var_on_pol: str | None = None,
+    nwedges: float | None = None,
+    nrings: float | None = None,
+    fwhm_pol: float | None = None,
+    fwhm_ecc: float | None = None,
+    ignore: float | None = None,
+    no_tshift: bool = False,
+    spec_left: InputPathType | None = None,
+    spec_right: InputPathType | None = None,
+    dorts: InputPathType | None = None,
+    ccw_orts: list[InputPathType] | None = None,
+    clw_orts: list[InputPathType] | None = None,
+    exp_orts: list[InputPathType] | None = None,
+    con_orts: list[InputPathType] | None = None,
+    sid: str | None = None,
+    out_dir: str | None = None,
+    echo: bool = False,
+    echo_edu: bool = False,
+    a2e_opts: str | None = None,
+    aea_opts: str | None = None,
+) -> VRetinoProcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        tr: TR, in seconds, of retinotopic scans.
+        period_ecc: Period, in seconds, of eccentricity stimuli.
+        period_pol: Period, in seconds, of polar angle stimuli.
+        ccw: Input time series dataset for counterclockwise stimulus.
+        clw: Input time series dataset for clockwise stimulus.
+        exp: Input time series dataset for expanding stimulus.
+        con: Input time series dataset for contracting stimulus.
+        epi_ref: Specify a volume from the EPI time series to which all EPI\
+            volumes are aligned.
+        epi_anat_ref: Specify a volume from the EPI time series that is better\
+            suited for aligning the T1 to it than EpiRef might be.
+        anat_vol: T1 volume acquired during the same session as the retinotopic\
+            scans.
+        anat_vol_epi: Anatomical volume aligned to EPI reference.
+        surf_vol: Surface Volume for the cortical surfaces.
+        surf_vol_epi: Surface volume aligned to experiment's EPI data.
+        phase: Use phase of fundamental frequency to estimate latency.
+        delay: Use delay relative to reference time series to estimate latency.
+        pre_ecc: Duration, in seconds, before eccentricity stimulus.
+        pre_pol: Duration, in seconds, before polar angle stimulus.
+        on_ecc: Number of stimulation blocks and duration of stimulation for\
+            eccentricity stimulus.
+        on_pol: Number of stimulation blocks and duration of stimulation for\
+            polar angle stimulus.
+        var_on_ecc: Multiple on durations for eccentricity stimulus.
+        var_on_pol: Multiple on durations for polar angle stimulus.
+        nwedges: Number of wedges in polar stimulus.
+        nrings: Number of rings in eccentricity stimulus.
+        fwhm_pol: Target smoothness for polar stimulus.
+        fwhm_ecc: Target smoothness for eccentricity stimulus.
+        ignore: Ignore volumes from the beginning of each time series.
+        no_tshift: Do not correct for slice timing.
+        spec_left: Spec file for left hemisphere.
+        spec_right: Spec file for right hemisphere.
+        dorts: Detrend time series using columns in ORT1D file.
+        ccw_orts: Detrend time series for counterclockwise stimulus.
+        clw_orts: Detrend time series for clockwise stimulus.
+        exp_orts: Detrend time series for expanding stimulus.
+        con_orts: Detrend time series for contracting stimulus.
+        sid: SID is a flag identifying the subject.
+        out_dir: Directory where processing results are to be stored.
+        echo: Turn on the command echoing to help with debugging script failure.
+        echo_edu: Turn on command echoing for certain programs only.
+        a2e_opts: Pass options to @SUMA_AlignToExperiment script.
+        aea_opts: Pass options to align_epi_anat.py.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@RetinoProc",
+        "phase": phase,
+        "delay": delay,
+        "tr": tr,
+        "period_ecc": period_ecc,
+        "period_pol": period_pol,
+        "no_tshift": no_tshift,
+        "echo": echo,
+        "echo_edu": echo_edu,
+    }
+    if ccw is not None:
+        params["ccw"] = ccw
+    if clw is not None:
+        params["clw"] = clw
+    if exp is not None:
+        params["exp"] = exp
+    if con is not None:
+        params["con"] = con
+    if epi_ref is not None:
+        params["epi_ref"] = epi_ref
+    if epi_anat_ref is not None:
+        params["epi_anat_ref"] = epi_anat_ref
+    if anat_vol is not None:
+        params["anat_vol"] = anat_vol
+    if anat_vol_epi is not None:
+        params["anat_vol_epi"] = anat_vol_epi
+    if surf_vol is not None:
+        params["surf_vol"] = surf_vol
+    if surf_vol_epi is not None:
+        params["surf_vol_epi"] = surf_vol_epi
+    if pre_ecc is not None:
+        params["pre_ecc"] = pre_ecc
+    if pre_pol is not None:
+        params["pre_pol"] = pre_pol
+    if on_ecc is not None:
+        params["on_ecc"] = on_ecc
+    if on_pol is not None:
+        params["on_pol"] = on_pol
+    if var_on_ecc is not None:
+        params["var_on_ecc"] = var_on_ecc
+    if var_on_pol is not None:
+        params["var_on_pol"] = var_on_pol
+    if nwedges is not None:
+        params["nwedges"] = nwedges
+    if nrings is not None:
+        params["nrings"] = nrings
+    if fwhm_pol is not None:
+        params["fwhm_pol"] = fwhm_pol
+    if fwhm_ecc is not None:
+        params["fwhm_ecc"] = fwhm_ecc
+    if ignore is not None:
+        params["ignore"] = ignore
+    if spec_left is not None:
+        params["spec_left"] = spec_left
+    if spec_right is not None:
+        params["spec_right"] = spec_right
+    if dorts is not None:
+        params["dorts"] = dorts
+    if ccw_orts is not None:
+        params["ccw_orts"] = ccw_orts
+    if clw_orts is not None:
+        params["clw_orts"] = clw_orts
+    if exp_orts is not None:
+        params["exp_orts"] = exp_orts
+    if con_orts is not None:
+        params["con_orts"] = con_orts
+    if sid is not None:
+        params["sid"] = sid
+    if out_dir is not None:
+        params["out_dir"] = out_dir
+    if a2e_opts is not None:
+        params["a2e_opts"] = a2e_opts
+    if aea_opts is not None:
+        params["aea_opts"] = aea_opts
+    return params
+
+
+def v__retino_proc_cargs(
+    params: VRetinoProcParameters,
+    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("@RetinoProc")
+    if params.get("ccw") is not None:
+        cargs.extend([
+            "-ccw",
+            *[execution.input_file(f) for f in params.get("ccw")]
+        ])
+    if params.get("clw") is not None:
+        cargs.extend([
+            "-clw",
+            *[execution.input_file(f) for f in params.get("clw")]
+        ])
+    if params.get("exp") is not None:
+        cargs.extend([
+            "-exp",
+            *[execution.input_file(f) for f in params.get("exp")]
+        ])
+    if params.get("con") is not None:
+        cargs.extend([
+            "-con",
+            *[execution.input_file(f) for f in params.get("con")]
+        ])
+    if params.get("epi_ref") is not None:
+        cargs.extend([
+            "-epi_ref",
+            execution.input_file(params.get("epi_ref"))
+        ])
+    if params.get("epi_anat_ref") is not None:
+        cargs.extend([
+            "-epi_anat_ref",
+            execution.input_file(params.get("epi_anat_ref"))
+        ])
+    if params.get("anat_vol") is not None:
+        cargs.extend([
+            "-anat_vol",
+            execution.input_file(params.get("anat_vol"))
+        ])
+    if params.get("anat_vol_epi") is not None:
+        cargs.extend([
+            "-anat_vol@epi",
+            execution.input_file(params.get("anat_vol_epi"))
+        ])
+    if params.get("surf_vol") is not None:
+        cargs.extend([
+            "-surf_vol",
+            execution.input_file(params.get("surf_vol"))
+        ])
+    if params.get("surf_vol_epi") is not None:
+        cargs.extend([
+            "-surf_vol@epi",
+            execution.input_file(params.get("surf_vol_epi"))
+        ])
+    if params.get("phase"):
+        cargs.append("-phase")
+    if params.get("delay"):
+        cargs.append("-delay")
+    cargs.extend([
+        "-TR",
+        str(params.get("tr"))
+    ])
+    cargs.extend([
+        "-period_ecc",
+        str(params.get("period_ecc"))
+    ])
+    cargs.extend([
+        "-period_pol",
+        str(params.get("period_pol"))
+    ])
+    if params.get("pre_ecc") is not None:
+        cargs.extend([
+            "-pre_ecc",
+            str(params.get("pre_ecc"))
+        ])
+    if params.get("pre_pol") is not None:
+        cargs.extend([
+            "-pre_pol",
+            str(params.get("pre_pol"))
+        ])
+    if params.get("on_ecc") is not None:
+        cargs.extend([
+            "-on_ecc",
+            params.get("on_ecc")
+        ])
+    if params.get("on_pol") is not None:
+        cargs.extend([
+            "-on_pol",
+            params.get("on_pol")
+        ])
+    if params.get("var_on_ecc") is not None:
+        cargs.extend([
+            "-var_on_ecc",
+            params.get("var_on_ecc")
+        ])
+    if params.get("var_on_pol") is not None:
+        cargs.extend([
+            "-var_on_pol",
+            params.get("var_on_pol")
+        ])
+    if params.get("nwedges") is not None:
+        cargs.extend([
+            "-nwedges",
+            str(params.get("nwedges"))
+        ])
+    if params.get("nrings") is not None:
+        cargs.extend([
+            "-nrings",
+            str(params.get("nrings"))
+        ])
+    if params.get("fwhm_pol") is not None:
+        cargs.extend([
+            "-fwhm_pol",
+            str(params.get("fwhm_pol"))
+        ])
+    if params.get("fwhm_ecc") is not None:
+        cargs.extend([
+            "-fwhm_ecc",
+            str(params.get("fwhm_ecc"))
+        ])
+    if params.get("ignore") is not None:
+        cargs.extend([
+            "-ignore",
+            str(params.get("ignore"))
+        ])
+    if params.get("no_tshift"):
+        cargs.append("-no_tshift")
+    if params.get("spec_left") is not None:
+        cargs.extend([
+            "-spec_left",
+            execution.input_file(params.get("spec_left"))
+        ])
+    if params.get("spec_right") is not None:
+        cargs.extend([
+            "-spec_right",
+            execution.input_file(params.get("spec_right"))
+        ])
+    if params.get("dorts") is not None:
+        cargs.extend([
+            "-dorts",
+            execution.input_file(params.get("dorts"))
+        ])
+    if params.get("ccw_orts") is not None:
+        cargs.extend([
+            "-ccw_orts",
+            *[execution.input_file(f) for f in params.get("ccw_orts")]
+        ])
+    if params.get("clw_orts") is not None:
+        cargs.extend([
+            "-clw_orts",
+            *[execution.input_file(f) for f in params.get("clw_orts")]
+        ])
+    if params.get("exp_orts") is not None:
+        cargs.extend([
+            "-exp_orts",
+            *[execution.input_file(f) for f in params.get("exp_orts")]
+        ])
+    if params.get("con_orts") is not None:
+        cargs.extend([
+            "-con_orts",
+            *[execution.input_file(f) for f in params.get("con_orts")]
+        ])
+    if params.get("sid") is not None:
+        cargs.extend([
+            "-sid",
+            params.get("sid")
+        ])
+    if params.get("out_dir") is not None:
+        cargs.extend([
+            "-out_dir",
+            params.get("out_dir")
+        ])
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("echo_edu"):
+        cargs.append("-echo_edu")
+    if params.get("a2e_opts") is not None:
+        cargs.extend([
+            "-A2E_opts",
+            params.get("a2e_opts")
+        ])
+    if params.get("aea_opts") is not None:
+        cargs.extend([
+            "-AEA_opts",
+            params.get("aea_opts")
+        ])
+    return cargs
+
+
+def v__retino_proc_outputs(
+    params: VRetinoProcParameters,
+    execution: Execution,
+) -> VRetinoProcOutputs:
+    """
+    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 = VRetinoProcOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__retino_proc_execute(
+    params: VRetinoProcParameters,
+    execution: Execution,
+) -> VRetinoProcOutputs:
+    """
+    A script to process retinotopic FMRI data, using AFNI's 3dRetinoPhase and
+    SurfRetinMap.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VRetinoProcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__retino_proc_cargs(params, execution)
+    ret = v__retino_proc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__retino_proc(
+    tr: float,
+    period_ecc: float,
+    period_pol: float,
+    ccw: list[InputPathType] | None = None,
+    clw: list[InputPathType] | None = None,
+    exp: list[InputPathType] | None = None,
+    con: list[InputPathType] | None = None,
+    epi_ref: InputPathType | None = None,
+    epi_anat_ref: InputPathType | None = None,
+    anat_vol: InputPathType | None = None,
+    anat_vol_epi: InputPathType | None = None,
+    surf_vol: InputPathType | None = None,
+    surf_vol_epi: InputPathType | None = None,
+    phase: bool = False,
+    delay: bool = False,
+    pre_ecc: float | None = None,
+    pre_pol: float | None = None,
+    on_ecc: str | None = None,
+    on_pol: str | None = None,
+    var_on_ecc: str | None = None,
+    var_on_pol: str | None = None,
+    nwedges: float | None = None,
+    nrings: float | None = None,
+    fwhm_pol: float | None = None,
+    fwhm_ecc: float | None = None,
+    ignore: float | None = None,
+    no_tshift: bool = False,
+    spec_left: InputPathType | None = None,
+    spec_right: InputPathType | None = None,
+    dorts: InputPathType | None = None,
+    ccw_orts: list[InputPathType] | None = None,
+    clw_orts: list[InputPathType] | None = None,
+    exp_orts: list[InputPathType] | None = None,
+    con_orts: list[InputPathType] | None = None,
+    sid: str | None = None,
+    out_dir: str | None = None,
+    echo: bool = False,
+    echo_edu: bool = False,
+    a2e_opts: str | None = None,
+    aea_opts: str | None = None,
+    runner: Runner | None = None,
+) -> VRetinoProcOutputs:
+    """
+    A script to process retinotopic FMRI data, using AFNI's 3dRetinoPhase and
+    SurfRetinMap.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        tr: TR, in seconds, of retinotopic scans.
+        period_ecc: Period, in seconds, of eccentricity stimuli.
+        period_pol: Period, in seconds, of polar angle stimuli.
+        ccw: Input time series dataset for counterclockwise stimulus.
+        clw: Input time series dataset for clockwise stimulus.
+        exp: Input time series dataset for expanding stimulus.
+        con: Input time series dataset for contracting stimulus.
+        epi_ref: Specify a volume from the EPI time series to which all EPI\
+            volumes are aligned.
+        epi_anat_ref: Specify a volume from the EPI time series that is better\
+            suited for aligning the T1 to it than EpiRef might be.
+        anat_vol: T1 volume acquired during the same session as the retinotopic\
+            scans.
+        anat_vol_epi: Anatomical volume aligned to EPI reference.
+        surf_vol: Surface Volume for the cortical surfaces.
+        surf_vol_epi: Surface volume aligned to experiment's EPI data.
+        phase: Use phase of fundamental frequency to estimate latency.
+        delay: Use delay relative to reference time series to estimate latency.
+        pre_ecc: Duration, in seconds, before eccentricity stimulus.
+        pre_pol: Duration, in seconds, before polar angle stimulus.
+        on_ecc: Number of stimulation blocks and duration of stimulation for\
+            eccentricity stimulus.
+        on_pol: Number of stimulation blocks and duration of stimulation for\
+            polar angle stimulus.
+        var_on_ecc: Multiple on durations for eccentricity stimulus.
+        var_on_pol: Multiple on durations for polar angle stimulus.
+        nwedges: Number of wedges in polar stimulus.
+        nrings: Number of rings in eccentricity stimulus.
+        fwhm_pol: Target smoothness for polar stimulus.
+        fwhm_ecc: Target smoothness for eccentricity stimulus.
+        ignore: Ignore volumes from the beginning of each time series.
+        no_tshift: Do not correct for slice timing.
+        spec_left: Spec file for left hemisphere.
+        spec_right: Spec file for right hemisphere.
+        dorts: Detrend time series using columns in ORT1D file.
+        ccw_orts: Detrend time series for counterclockwise stimulus.
+        clw_orts: Detrend time series for clockwise stimulus.
+        exp_orts: Detrend time series for expanding stimulus.
+        con_orts: Detrend time series for contracting stimulus.
+        sid: SID is a flag identifying the subject.
+        out_dir: Directory where processing results are to be stored.
+        echo: Turn on the command echoing to help with debugging script failure.
+        echo_edu: Turn on command echoing for certain programs only.
+        a2e_opts: Pass options to @SUMA_AlignToExperiment script.
+        aea_opts: Pass options to align_epi_anat.py.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VRetinoProcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__RETINO_PROC_METADATA)
+    params = v__retino_proc_params(
+        ccw=ccw,
+        clw=clw,
+        exp=exp,
+        con=con,
+        epi_ref=epi_ref,
+        epi_anat_ref=epi_anat_ref,
+        anat_vol=anat_vol,
+        anat_vol_epi=anat_vol_epi,
+        surf_vol=surf_vol,
+        surf_vol_epi=surf_vol_epi,
+        phase=phase,
+        delay=delay,
+        tr=tr,
+        period_ecc=period_ecc,
+        period_pol=period_pol,
+        pre_ecc=pre_ecc,
+        pre_pol=pre_pol,
+        on_ecc=on_ecc,
+        on_pol=on_pol,
+        var_on_ecc=var_on_ecc,
+        var_on_pol=var_on_pol,
+        nwedges=nwedges,
+        nrings=nrings,
+        fwhm_pol=fwhm_pol,
+        fwhm_ecc=fwhm_ecc,
+        ignore=ignore,
+        no_tshift=no_tshift,
+        spec_left=spec_left,
+        spec_right=spec_right,
+        dorts=dorts,
+        ccw_orts=ccw_orts,
+        clw_orts=clw_orts,
+        exp_orts=exp_orts,
+        con_orts=con_orts,
+        sid=sid,
+        out_dir=out_dir,
+        echo=echo,
+        echo_edu=echo_edu,
+        a2e_opts=a2e_opts,
+        aea_opts=aea_opts,
+    )
+    return v__retino_proc_execute(params, execution)
+
+
+__all__ = [
+    "VRetinoProcOutputs",
+    "VRetinoProcParameters",
+    "V__RETINO_PROC_METADATA",
+    "v__retino_proc",
+    "v__retino_proc_params",
+]