niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_retino_phase.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_3D_RETINO_PHASE_METADATA = Metadata(
+    id="3db78d8b872cbcd25d2278819aa85d3e6ecbba57.boutiques",
+    name="3dRetinoPhase",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dRetinoPhaseParameters = typing.TypedDict('V3dRetinoPhaseParameters', {
+    "__STYX_TYPE__": typing.Literal["3dRetinoPhase"],
+    "prefix": str,
+    "dataset": InputPathType,
+    "exp": typing.NotRequired[str | None],
+    "con": typing.NotRequired[str | None],
+    "clw": typing.NotRequired[str | None],
+    "ccw": typing.NotRequired[str | None],
+    "spectra": bool,
+    "tstim": typing.NotRequired[float | None],
+    "nrings": typing.NotRequired[float | None],
+    "nwedges": typing.NotRequired[float | None],
+    "ort_adjust": typing.NotRequired[float | None],
+    "pre_stim": typing.NotRequired[float | None],
+    "sum_adjust": typing.NotRequired[str | None],
+    "phase_estimate": typing.NotRequired[str | None],
+    "ref_ts": typing.NotRequired[InputPathType | None],
+    "multi_ref_ts": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dRetinoPhase": v_3d_retino_phase_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 {
+        "3dRetinoPhase": v_3d_retino_phase_outputs,
+    }.get(t)
+
+
+class V3dRetinoPhaseOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_retino_phase(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    ecc_plus: OutputPathType
+    """Output file for positive (expanding) eccentricity"""
+    ecc_minus: OutputPathType
+    """Output file for negative (contracting) eccentricity"""
+    pol_plus: OutputPathType
+    """Output file for clockwise polar angle mapping"""
+    pol_minus: OutputPathType
+    """Output file for counterclockwise polar angle mapping"""
+
+
+def v_3d_retino_phase_params(
+    prefix: str,
+    dataset: InputPathType,
+    exp: str | None = None,
+    con: str | None = None,
+    clw: str | None = None,
+    ccw: str | None = None,
+    spectra: bool = False,
+    tstim: float | None = None,
+    nrings: float | None = None,
+    nwedges: float | None = None,
+    ort_adjust: float | None = None,
+    pre_stim: float | None = None,
+    sum_adjust: str | None = None,
+    phase_estimate: str | None = None,
+    ref_ts: InputPathType | None = None,
+    multi_ref_ts: InputPathType | None = None,
+) -> V3dRetinoPhaseParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix of output datasets.
+        dataset: Time series from a retinotopy stimulus.
+        exp: Expanding rings stimulus.
+        con: Contracting rings stimulus.
+        clw: Clockwise moving polar angle mapping stimulus.
+        ccw: Counterclockwise moving polar angle mapping stimulus.
+        spectra: Output amplitude and phase spectra datasets.
+        tstim: Period of stimulus in seconds.
+        nrings: Number of rings in the stimulus. Default is 1.
+        nwedges: Number of wedges in the stimulus. Default is 1.
+        ort_adjust: Number of DOF lost in detrending outside of this program.
+        pre_stim: Blank period, in seconds, before stimulus began.
+        sum_adjust: Adjust sum of angles for wrapping based on the angle\
+            difference. Default is 'y'.
+        phase_estimate: Method of phase estimation.
+        ref_ts: 0 lag reference time series of response for DELAY phase\
+            estimation method.
+        multi_ref_ts: Multiple 0 lag reference time series. This allows you to\
+            test multiple regressors.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dRetinoPhase",
+        "prefix": prefix,
+        "dataset": dataset,
+        "spectra": spectra,
+    }
+    if exp is not None:
+        params["exp"] = exp
+    if con is not None:
+        params["con"] = con
+    if clw is not None:
+        params["clw"] = clw
+    if ccw is not None:
+        params["ccw"] = ccw
+    if tstim is not None:
+        params["tstim"] = tstim
+    if nrings is not None:
+        params["nrings"] = nrings
+    if nwedges is not None:
+        params["nwedges"] = nwedges
+    if ort_adjust is not None:
+        params["ort_adjust"] = ort_adjust
+    if pre_stim is not None:
+        params["pre_stim"] = pre_stim
+    if sum_adjust is not None:
+        params["sum_adjust"] = sum_adjust
+    if phase_estimate is not None:
+        params["phase_estimate"] = phase_estimate
+    if ref_ts is not None:
+        params["ref_ts"] = ref_ts
+    if multi_ref_ts is not None:
+        params["multi_ref_ts"] = multi_ref_ts
+    return params
+
+
+def v_3d_retino_phase_cargs(
+    params: V3dRetinoPhaseParameters,
+    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("3dRetinoPhase")
+    cargs.append(params.get("prefix"))
+    cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("exp") is not None:
+        cargs.extend([
+            "-exp",
+            params.get("exp")
+        ])
+    if params.get("con") is not None:
+        cargs.extend([
+            "-con",
+            params.get("con")
+        ])
+    if params.get("clw") is not None:
+        cargs.extend([
+            "-clw",
+            params.get("clw")
+        ])
+    if params.get("ccw") is not None:
+        cargs.extend([
+            "-ccw",
+            params.get("ccw")
+        ])
+    if params.get("spectra"):
+        cargs.append("-spectra")
+    if params.get("tstim") is not None:
+        cargs.extend([
+            "-Tstim",
+            str(params.get("tstim"))
+        ])
+    if params.get("nrings") is not None:
+        cargs.extend([
+            "-nrings",
+            str(params.get("nrings"))
+        ])
+    if params.get("nwedges") is not None:
+        cargs.extend([
+            "-nwedges",
+            str(params.get("nwedges"))
+        ])
+    if params.get("ort_adjust") is not None:
+        cargs.extend([
+            "-ort_adjust",
+            str(params.get("ort_adjust"))
+        ])
+    if params.get("pre_stim") is not None:
+        cargs.extend([
+            "-pre_stim",
+            str(params.get("pre_stim"))
+        ])
+    if params.get("sum_adjust") is not None:
+        cargs.extend([
+            "-sum_adjust",
+            params.get("sum_adjust")
+        ])
+    if params.get("phase_estimate") is not None:
+        cargs.extend([
+            "-phase_estimate",
+            params.get("phase_estimate")
+        ])
+    if params.get("ref_ts") is not None:
+        cargs.extend([
+            "-ref_ts",
+            execution.input_file(params.get("ref_ts"))
+        ])
+    if params.get("multi_ref_ts") is not None:
+        cargs.extend([
+            "-multi_ref_ts",
+            execution.input_file(params.get("multi_ref_ts"))
+        ])
+    return cargs
+
+
+def v_3d_retino_phase_outputs(
+    params: V3dRetinoPhaseParameters,
+    execution: Execution,
+) -> V3dRetinoPhaseOutputs:
+    """
+    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 = V3dRetinoPhaseOutputs(
+        root=execution.output_file("."),
+        ecc_plus=execution.output_file(params.get("prefix") + ".ecc+"),
+        ecc_minus=execution.output_file(params.get("prefix") + ".ecc-"),
+        pol_plus=execution.output_file(params.get("prefix") + ".pol+"),
+        pol_minus=execution.output_file(params.get("prefix") + ".pol-"),
+    )
+    return ret
+
+
+def v_3d_retino_phase_execute(
+    params: V3dRetinoPhaseParameters,
+    execution: Execution,
+) -> V3dRetinoPhaseOutputs:
+    """
+    Process time series from retinotopy stimuli to create phase datasets and visual
+    field angle datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dRetinoPhaseOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_retino_phase_cargs(params, execution)
+    ret = v_3d_retino_phase_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_retino_phase(
+    prefix: str,
+    dataset: InputPathType,
+    exp: str | None = None,
+    con: str | None = None,
+    clw: str | None = None,
+    ccw: str | None = None,
+    spectra: bool = False,
+    tstim: float | None = None,
+    nrings: float | None = None,
+    nwedges: float | None = None,
+    ort_adjust: float | None = None,
+    pre_stim: float | None = None,
+    sum_adjust: str | None = None,
+    phase_estimate: str | None = None,
+    ref_ts: InputPathType | None = None,
+    multi_ref_ts: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> V3dRetinoPhaseOutputs:
+    """
+    Process time series from retinotopy stimuli to create phase datasets and visual
+    field angle datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix of output datasets.
+        dataset: Time series from a retinotopy stimulus.
+        exp: Expanding rings stimulus.
+        con: Contracting rings stimulus.
+        clw: Clockwise moving polar angle mapping stimulus.
+        ccw: Counterclockwise moving polar angle mapping stimulus.
+        spectra: Output amplitude and phase spectra datasets.
+        tstim: Period of stimulus in seconds.
+        nrings: Number of rings in the stimulus. Default is 1.
+        nwedges: Number of wedges in the stimulus. Default is 1.
+        ort_adjust: Number of DOF lost in detrending outside of this program.
+        pre_stim: Blank period, in seconds, before stimulus began.
+        sum_adjust: Adjust sum of angles for wrapping based on the angle\
+            difference. Default is 'y'.
+        phase_estimate: Method of phase estimation.
+        ref_ts: 0 lag reference time series of response for DELAY phase\
+            estimation method.
+        multi_ref_ts: Multiple 0 lag reference time series. This allows you to\
+            test multiple regressors.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dRetinoPhaseOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RETINO_PHASE_METADATA)
+    params = v_3d_retino_phase_params(
+        prefix=prefix,
+        dataset=dataset,
+        exp=exp,
+        con=con,
+        clw=clw,
+        ccw=ccw,
+        spectra=spectra,
+        tstim=tstim,
+        nrings=nrings,
+        nwedges=nwedges,
+        ort_adjust=ort_adjust,
+        pre_stim=pre_stim,
+        sum_adjust=sum_adjust,
+        phase_estimate=phase_estimate,
+        ref_ts=ref_ts,
+        multi_ref_ts=multi_ref_ts,
+    )
+    return v_3d_retino_phase_execute(params, execution)
+
+
+__all__ = [
+    "V3dRetinoPhaseOutputs",
+    "V3dRetinoPhaseParameters",
+    "V_3D_RETINO_PHASE_METADATA",
+    "v_3d_retino_phase",
+    "v_3d_retino_phase_params",
+]