niwrap-freesurfer 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_freesurfer/freesurfer/epidewarp_fsl.py

@@ -1,439 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-EPIDEWARP_FSL_METADATA = Metadata(
-    id="0b6f576dc06a529efd6bb20065d0ee4307b24409.boutiques",
-    name="epidewarp.fsl",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-EpidewarpFslParameters = typing.TypedDict('EpidewarpFslParameters', {
-    "__STYX_TYPE__": typing.Literal["epidewarp.fsl"],
-    "mag": typing.NotRequired[InputPathType | None],
-    "dph": typing.NotRequired[InputPathType | None],
-    "ph": typing.NotRequired[InputPathType | None],
-    "complex": typing.NotRequired[list[float] | None],
-    "exf": typing.NotRequired[InputPathType | None],
-    "epi": typing.NotRequired[InputPathType | None],
-    "tediff": typing.NotRequired[float | None],
-    "esp": typing.NotRequired[float | None],
-    "perev": bool,
-    "sigma": typing.NotRequired[float | None],
-    "vsm_fwhm": typing.NotRequired[float | None],
-    "vsm": str,
-    "vsmmag": typing.NotRequired[str | None],
-    "exfdw": typing.NotRequired[str | None],
-    "epidw": typing.NotRequired[str | None],
-    "nomagexfreg": bool,
-    "head": bool,
-    "tmpdir": typing.NotRequired[str | None],
-    "log": typing.NotRequired[str | None],
-    "nocleanup": bool,
-    "cleanup": bool,
-    "debug": bool,
-})
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "epidewarp.fsl": epidewarp_fsl_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 {
-        "epidewarp.fsl": epidewarp_fsl_outputs,
-    }.get(t)
-
-
-class EpidewarpFslOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `epidewarp_fsl(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-    vsm_output: OutputPathType
-    """Voxel Shift Map output"""
-    exfdw_output: OutputPathType | None
-    """Dewarped example func volume"""
-    epidw_output: OutputPathType | None
-    """Dewarped EPI volume"""
-    vsmmag_output: OutputPathType | None
-    """Voxel shift map in mag space output"""
-
-
-def epidewarp_fsl_params(
-    vsm: str,
-    mag: InputPathType | None = None,
-    dph: InputPathType | None = None,
-    ph: InputPathType | None = None,
-    complex_: list[float] | None = None,
-    exf: InputPathType | None = None,
-    epi: InputPathType | None = None,
-    tediff: float | None = None,
-    esp: float | None = None,
-    perev: bool = False,
-    sigma: float | None = None,
-    vsm_fwhm: float | None = None,
-    vsmmag: str | None = None,
-    exfdw: str | None = None,
-    epidw: str | None = None,
-    nomagexfreg: bool = False,
-    head: bool = False,
-    tmpdir: str | None = None,
-    log: str | None = None,
-    nocleanup: bool = False,
-    cleanup: bool = False,
-    debug: bool = False,
-) -> EpidewarpFslParameters:
-    """
-    Build parameters.
-    
-    Args:
-        vsm: Voxel shift map (required).
-        mag: B0 magnitude volume.
-        dph: B0 phase difference volume.
-        ph: B0 phase volume.
-        complex_: B0 map in complex values: real1 imag1 real2 imag2.
-        exf: Example func volume.
-        epi: EPI volume to unwarp.
-        tediff: Difference in B0 field map TEs.
-        esp: EPI echo spacing.
-        perev: Assume reversed phase encode direction.
-        sigma: 2D spatial gaussian smoothing stddev (default 2mm).
-        vsm_fwhm: Allows VSM to be extended outside of the mask.
-        vsmmag: Voxel shift map in mag space.
-        exfdw: Dewarped example func volume.
-        epidw: Dewarped EPI volume.
-        nomagexfreg: Assume mag and exf are in register.
-        head: Mask to head instead of brain.
-        tmpdir: Save intermediate results here.
-        log: Use logfile instead of default.
-        nocleanup: Do not delete tmpdir.
-        cleanup: Force deletion of tmpdir.
-        debug: Prints copious amounts to the screen.
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "epidewarp.fsl",
-        "perev": perev,
-        "vsm": vsm,
-        "nomagexfreg": nomagexfreg,
-        "head": head,
-        "nocleanup": nocleanup,
-        "cleanup": cleanup,
-        "debug": debug,
-    }
-    if mag is not None:
-        params["mag"] = mag
-    if dph is not None:
-        params["dph"] = dph
-    if ph is not None:
-        params["ph"] = ph
-    if complex_ is not None:
-        params["complex"] = complex_
-    if exf is not None:
-        params["exf"] = exf
-    if epi is not None:
-        params["epi"] = epi
-    if tediff is not None:
-        params["tediff"] = tediff
-    if esp is not None:
-        params["esp"] = esp
-    if sigma is not None:
-        params["sigma"] = sigma
-    if vsm_fwhm is not None:
-        params["vsm_fwhm"] = vsm_fwhm
-    if vsmmag is not None:
-        params["vsmmag"] = vsmmag
-    if exfdw is not None:
-        params["exfdw"] = exfdw
-    if epidw is not None:
-        params["epidw"] = epidw
-    if tmpdir is not None:
-        params["tmpdir"] = tmpdir
-    if log is not None:
-        params["log"] = log
-    return params
-
-
-def epidewarp_fsl_cargs(
-    params: EpidewarpFslParameters,
-    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("epidewarp.fsl")
-    if params.get("mag") is not None:
-        cargs.extend([
-            "--mag",
-            execution.input_file(params.get("mag"))
-        ])
-    if params.get("dph") is not None:
-        cargs.extend([
-            "--dph",
-            execution.input_file(params.get("dph"))
-        ])
-    if params.get("ph") is not None:
-        cargs.extend([
-            "--ph",
-            execution.input_file(params.get("ph"))
-        ])
-    if params.get("complex") is not None:
-        cargs.extend([
-            "--complex",
-            *map(str, params.get("complex"))
-        ])
-    if params.get("exf") is not None:
-        cargs.extend([
-            "--exf",
-            execution.input_file(params.get("exf"))
-        ])
-    if params.get("epi") is not None:
-        cargs.extend([
-            "--epi",
-            execution.input_file(params.get("epi"))
-        ])
-    if params.get("tediff") is not None:
-        cargs.extend([
-            "--tediff",
-            str(params.get("tediff"))
-        ])
-    if params.get("esp") is not None:
-        cargs.extend([
-            "--esp",
-            str(params.get("esp"))
-        ])
-    if params.get("perev"):
-        cargs.append("--perev")
-    if params.get("sigma") is not None:
-        cargs.extend([
-            "--sigma",
-            str(params.get("sigma"))
-        ])
-    if params.get("vsm_fwhm") is not None:
-        cargs.extend([
-            "--vsm-fwhm",
-            str(params.get("vsm_fwhm"))
-        ])
-    cargs.extend([
-        "--vsm",
-        params.get("vsm")
-    ])
-    if params.get("vsmmag") is not None:
-        cargs.extend([
-            "--vsmmag",
-            params.get("vsmmag")
-        ])
-    if params.get("exfdw") is not None:
-        cargs.extend([
-            "--exfdw",
-            params.get("exfdw")
-        ])
-    if params.get("epidw") is not None:
-        cargs.extend([
-            "--epidw",
-            params.get("epidw")
-        ])
-    if params.get("nomagexfreg"):
-        cargs.append("--nomagexfreg")
-    if params.get("head"):
-        cargs.append("--head")
-    if params.get("tmpdir") is not None:
-        cargs.extend([
-            "--tmpdir",
-            params.get("tmpdir")
-        ])
-    if params.get("log") is not None:
-        cargs.extend([
-            "--log",
-            params.get("log")
-        ])
-    if params.get("nocleanup"):
-        cargs.append("--nocleanup")
-    if params.get("cleanup"):
-        cargs.append("--cleanup")
-    if params.get("debug"):
-        cargs.append("--debug")
-    return cargs
-
-
-def epidewarp_fsl_outputs(
-    params: EpidewarpFslParameters,
-    execution: Execution,
-) -> EpidewarpFslOutputs:
-    """
-    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 = EpidewarpFslOutputs(
-        root=execution.output_file("."),
-        vsm_output=execution.output_file(params.get("vsm") + ".nii.gz"),
-        exfdw_output=execution.output_file(params.get("exfdw") + ".nii.gz") if (params.get("exfdw") is not None) else None,
-        epidw_output=execution.output_file(params.get("epidw") + ".nii.gz") if (params.get("epidw") is not None) else None,
-        vsmmag_output=execution.output_file(params.get("vsmmag") + ".nii.gz") if (params.get("vsmmag") is not None) else None,
-    )
-    return ret
-
-
-def epidewarp_fsl_execute(
-    params: EpidewarpFslParameters,
-    execution: Execution,
-) -> EpidewarpFslOutputs:
-    """
-    Front end for FSL's PRELUDE and FUGUE programs to correct B0 distortion in EPI
-    scans.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `EpidewarpFslOutputs`).
-    """
-    params = execution.params(params)
-    cargs = epidewarp_fsl_cargs(params, execution)
-    ret = epidewarp_fsl_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def epidewarp_fsl(
-    vsm: str,
-    mag: InputPathType | None = None,
-    dph: InputPathType | None = None,
-    ph: InputPathType | None = None,
-    complex_: list[float] | None = None,
-    exf: InputPathType | None = None,
-    epi: InputPathType | None = None,
-    tediff: float | None = None,
-    esp: float | None = None,
-    perev: bool = False,
-    sigma: float | None = None,
-    vsm_fwhm: float | None = None,
-    vsmmag: str | None = None,
-    exfdw: str | None = None,
-    epidw: str | None = None,
-    nomagexfreg: bool = False,
-    head: bool = False,
-    tmpdir: str | None = None,
-    log: str | None = None,
-    nocleanup: bool = False,
-    cleanup: bool = False,
-    debug: bool = False,
-    runner: Runner | None = None,
-) -> EpidewarpFslOutputs:
-    """
-    Front end for FSL's PRELUDE and FUGUE programs to correct B0 distortion in EPI
-    scans.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        vsm: Voxel shift map (required).
-        mag: B0 magnitude volume.
-        dph: B0 phase difference volume.
-        ph: B0 phase volume.
-        complex_: B0 map in complex values: real1 imag1 real2 imag2.
-        exf: Example func volume.
-        epi: EPI volume to unwarp.
-        tediff: Difference in B0 field map TEs.
-        esp: EPI echo spacing.
-        perev: Assume reversed phase encode direction.
-        sigma: 2D spatial gaussian smoothing stddev (default 2mm).
-        vsm_fwhm: Allows VSM to be extended outside of the mask.
-        vsmmag: Voxel shift map in mag space.
-        exfdw: Dewarped example func volume.
-        epidw: Dewarped EPI volume.
-        nomagexfreg: Assume mag and exf are in register.
-        head: Mask to head instead of brain.
-        tmpdir: Save intermediate results here.
-        log: Use logfile instead of default.
-        nocleanup: Do not delete tmpdir.
-        cleanup: Force deletion of tmpdir.
-        debug: Prints copious amounts to the screen.
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `EpidewarpFslOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(EPIDEWARP_FSL_METADATA)
-    params = epidewarp_fsl_params(
-        mag=mag,
-        dph=dph,
-        ph=ph,
-        complex_=complex_,
-        exf=exf,
-        epi=epi,
-        tediff=tediff,
-        esp=esp,
-        perev=perev,
-        sigma=sigma,
-        vsm_fwhm=vsm_fwhm,
-        vsm=vsm,
-        vsmmag=vsmmag,
-        exfdw=exfdw,
-        epidw=epidw,
-        nomagexfreg=nomagexfreg,
-        head=head,
-        tmpdir=tmpdir,
-        log=log,
-        nocleanup=nocleanup,
-        cleanup=cleanup,
-        debug=debug,
-    )
-    return epidewarp_fsl_execute(params, execution)
-
-
-__all__ = [
-    "EPIDEWARP_FSL_METADATA",
-    "EpidewarpFslOutputs",
-    "EpidewarpFslParameters",
-    "epidewarp_fsl",
-    "epidewarp_fsl_params",
-]