niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_label2label.py

@@ -0,0 +1,740 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_LABEL2LABEL_METADATA = Metadata(
+    id="17d5d1cd510c5a4c3d458511bf6609ccc3e1301b.boutiques",
+    name="mri_label2label",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriLabel2labelParameters = typing.TypedDict('MriLabel2labelParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_label2label"],
+    "src_label": InputPathType,
+    "trg_label": str,
+    "erode": typing.NotRequired[float | None],
+    "open": typing.NotRequired[float | None],
+    "close": typing.NotRequired[float | None],
+    "dilate": typing.NotRequired[float | None],
+    "ring": typing.NotRequired[float | None],
+    "src_subject": typing.NotRequired[str | None],
+    "trg_subject": typing.NotRequired[str | None],
+    "subject": typing.NotRequired[str | None],
+    "outmask": typing.NotRequired[str | None],
+    "outstat": typing.NotRequired[str | None],
+    "sample": typing.NotRequired[str | None],
+    "regmethod": typing.NotRequired[str | None],
+    "usepathfiles": bool,
+    "hemi": typing.NotRequired[str | None],
+    "src_hemi": typing.NotRequired[str | None],
+    "trg_hemi": typing.NotRequired[str | None],
+    "src_ico_order": typing.NotRequired[float | None],
+    "trg_ico_order": typing.NotRequired[float | None],
+    "direct": typing.NotRequired[str | None],
+    "trgsurf": typing.NotRequired[str | None],
+    "surfreg": typing.NotRequired[str | None],
+    "srcsurfreg": typing.NotRequired[str | None],
+    "trgsurfreg": typing.NotRequired[str | None],
+    "srcsurfreg_file": typing.NotRequired[str | None],
+    "trgsurfreg_file": typing.NotRequired[str | None],
+    "paint": typing.NotRequired[str | None],
+    "dmindmin": typing.NotRequired[str | None],
+    "baryfill": typing.NotRequired[str | None],
+    "label_cortex": typing.NotRequired[str | None],
+    "surf_label2mask": typing.NotRequired[str | None],
+    "srcmask": typing.NotRequired[str | None],
+    "srcmasksign": typing.NotRequired[str | None],
+    "srcmaskframe": typing.NotRequired[float | None],
+    "xfm": typing.NotRequired[str | None],
+    "reg": typing.NotRequired[str | None],
+    "xfm_invert": bool,
+    "projabs": typing.NotRequired[str | None],
+    "projfrac": typing.NotRequired[str | None],
+    "sd": typing.NotRequired[str | None],
+    "nohash": bool,
+    "norevmap": bool,
+    "to_scanner": typing.NotRequired[str | None],
+    "to_tkr": typing.NotRequired[str | None],
+    "scanner": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_label2label": mri_label2label_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 MriLabel2labelOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_label2label(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mri_label2label_params(
+    src_label: InputPathType,
+    trg_label: str,
+    erode: float | None = None,
+    open_: float | None = None,
+    close: float | None = None,
+    dilate: float | None = None,
+    ring: float | None = None,
+    src_subject: str | None = None,
+    trg_subject: str | None = None,
+    subject: str | None = None,
+    outmask: str | None = None,
+    outstat: str | None = None,
+    sample: str | None = None,
+    regmethod: str | None = None,
+    usepathfiles: bool = False,
+    hemi: str | None = None,
+    src_hemi: str | None = None,
+    trg_hemi: str | None = None,
+    src_ico_order: float | None = None,
+    trg_ico_order: float | None = None,
+    direct: str | None = None,
+    trgsurf: str | None = None,
+    surfreg: str | None = None,
+    srcsurfreg: str | None = None,
+    trgsurfreg: str | None = None,
+    srcsurfreg_file: str | None = None,
+    trgsurfreg_file: str | None = None,
+    paint: str | None = None,
+    dmindmin: str | None = None,
+    baryfill: str | None = None,
+    label_cortex: str | None = None,
+    surf_label2mask: str | None = None,
+    srcmask: str | None = None,
+    srcmasksign: str | None = None,
+    srcmaskframe: float | None = None,
+    xfm: str | None = None,
+    reg: str | None = None,
+    xfm_invert: bool = False,
+    projabs: str | None = None,
+    projfrac: str | None = None,
+    sd: str | None = None,
+    nohash: bool = False,
+    norevmap: bool = False,
+    to_scanner: str | None = None,
+    to_tkr: str | None = None,
+    scanner: bool = False,
+) -> MriLabel2labelParameters:
+    """
+    Build parameters.
+    
+    Args:
+        src_label: Input label file.
+        trg_label: Output label file.
+        erode: Erode the label N times before writing.
+        open_: Open the label N times before writing.
+        close: Close the label N times before writing.
+        dilate: Dilate the label N times before writing.
+        ring: Dilate the label N times then remove the original before writing.
+        src_subject: Source subject.
+        trg_subject: Target subject.
+        subject: Use for both target and source.
+        outmask: Save output label as a binary mask (surf only).
+        outstat: Save output label stat as a mask (surf only).
+        sample: Sample label onto surface.
+        regmethod: Registration method (surface, volume).
+        usepathfiles: Read from and write to a path file.
+        hemi: Hemisphere (lh or rh) (with surface).
+        src_hemi: Source Hemisphere (lh or rh).
+        trg_hemi: Target Hemisphere (lh or rh).
+        src_ico_order: When srcsubject=ico.
+        trg_ico_order: When trgsubject=ico.
+        direct: Use the [xyz] coords for src and trg surfaces to do direct\
+            lookup.
+        trgsurf: Get xyz from this surface (white).
+        surfreg: Surface registration (sphere.reg).
+        srcsurfreg: Source surface registration (sphere.reg).
+        trgsurfreg: Target surface registration (sphere.reg).
+        srcsurfreg_file: Specify full path to source reg.
+        trgsurfreg_file: Specify full path to target reg.
+        paint: Map to closest vertex on source surfname if d < dmax.
+        dmindmin: Bin mask with vertex of closest label point when painting.
+        baryfill: Fill with barycentric interpolation.
+        label_cortex: Create a label like ?h.cortex.label.
+        surf_label2mask: Convert a label to a binary mask.
+        srcmask: Source mask surfvalfile thresh <format>.
+        srcmasksign: Source mask sign (<abs>, pos, neg).
+        srcmaskframe: Source mask frame number (0-based).
+        xfm: Use xfm file instead of computing tal xfm.
+        reg: Use register.dat file instead of computing tal xfm.
+        xfm_invert: Invert xfm, or reg.
+        projabs: Project dist mm along surf normal.
+        projfrac: Project frac of thickness along surf normal.
+        sd: Use specified subjects directory.
+        nohash: Don't use hash table when regmethod is surface.
+        norevmap: Don't use reverse mapping when regmethod is surface.
+        to_scanner: Convert coords to scanner RAS prior to other operations.
+        to_tkr: Convert coords to tkregister RAS prior to other operations.
+        scanner: Set output coordinate type to scanner.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_label2label",
+        "src_label": src_label,
+        "trg_label": trg_label,
+        "usepathfiles": usepathfiles,
+        "xfm_invert": xfm_invert,
+        "nohash": nohash,
+        "norevmap": norevmap,
+        "scanner": scanner,
+    }
+    if erode is not None:
+        params["erode"] = erode
+    if open_ is not None:
+        params["open"] = open_
+    if close is not None:
+        params["close"] = close
+    if dilate is not None:
+        params["dilate"] = dilate
+    if ring is not None:
+        params["ring"] = ring
+    if src_subject is not None:
+        params["src_subject"] = src_subject
+    if trg_subject is not None:
+        params["trg_subject"] = trg_subject
+    if subject is not None:
+        params["subject"] = subject
+    if outmask is not None:
+        params["outmask"] = outmask
+    if outstat is not None:
+        params["outstat"] = outstat
+    if sample is not None:
+        params["sample"] = sample
+    if regmethod is not None:
+        params["regmethod"] = regmethod
+    if hemi is not None:
+        params["hemi"] = hemi
+    if src_hemi is not None:
+        params["src_hemi"] = src_hemi
+    if trg_hemi is not None:
+        params["trg_hemi"] = trg_hemi
+    if src_ico_order is not None:
+        params["src_ico_order"] = src_ico_order
+    if trg_ico_order is not None:
+        params["trg_ico_order"] = trg_ico_order
+    if direct is not None:
+        params["direct"] = direct
+    if trgsurf is not None:
+        params["trgsurf"] = trgsurf
+    if surfreg is not None:
+        params["surfreg"] = surfreg
+    if srcsurfreg is not None:
+        params["srcsurfreg"] = srcsurfreg
+    if trgsurfreg is not None:
+        params["trgsurfreg"] = trgsurfreg
+    if srcsurfreg_file is not None:
+        params["srcsurfreg_file"] = srcsurfreg_file
+    if trgsurfreg_file is not None:
+        params["trgsurfreg_file"] = trgsurfreg_file
+    if paint is not None:
+        params["paint"] = paint
+    if dmindmin is not None:
+        params["dmindmin"] = dmindmin
+    if baryfill is not None:
+        params["baryfill"] = baryfill
+    if label_cortex is not None:
+        params["label_cortex"] = label_cortex
+    if surf_label2mask is not None:
+        params["surf_label2mask"] = surf_label2mask
+    if srcmask is not None:
+        params["srcmask"] = srcmask
+    if srcmasksign is not None:
+        params["srcmasksign"] = srcmasksign
+    if srcmaskframe is not None:
+        params["srcmaskframe"] = srcmaskframe
+    if xfm is not None:
+        params["xfm"] = xfm
+    if reg is not None:
+        params["reg"] = reg
+    if projabs is not None:
+        params["projabs"] = projabs
+    if projfrac is not None:
+        params["projfrac"] = projfrac
+    if sd is not None:
+        params["sd"] = sd
+    if to_scanner is not None:
+        params["to_scanner"] = to_scanner
+    if to_tkr is not None:
+        params["to_tkr"] = to_tkr
+    return params
+
+
+def mri_label2label_cargs(
+    params: MriLabel2labelParameters,
+    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("mri_label2label")
+    cargs.extend([
+        "--srclabel",
+        execution.input_file(params.get("src_label"))
+    ])
+    cargs.extend([
+        "--trglabel",
+        params.get("trg_label")
+    ])
+    if params.get("erode") is not None:
+        cargs.extend([
+            "--erode",
+            str(params.get("erode"))
+        ])
+    if params.get("open") is not None:
+        cargs.extend([
+            "--open",
+            str(params.get("open"))
+        ])
+    if params.get("close") is not None:
+        cargs.extend([
+            "--close",
+            str(params.get("close"))
+        ])
+    if params.get("dilate") is not None:
+        cargs.extend([
+            "--dilate",
+            str(params.get("dilate"))
+        ])
+    if params.get("ring") is not None:
+        cargs.extend([
+            "--ring",
+            str(params.get("ring"))
+        ])
+    if params.get("src_subject") is not None:
+        cargs.extend([
+            "--srcsubject",
+            params.get("src_subject")
+        ])
+    if params.get("trg_subject") is not None:
+        cargs.extend([
+            "--trgsubject",
+            params.get("trg_subject")
+        ])
+    if params.get("subject") is not None:
+        cargs.extend([
+            "--s",
+            params.get("subject")
+        ])
+    if params.get("outmask") is not None:
+        cargs.extend([
+            "--outmask",
+            params.get("outmask")
+        ])
+    if params.get("outstat") is not None:
+        cargs.extend([
+            "--outstat",
+            params.get("outstat")
+        ])
+    if params.get("sample") is not None:
+        cargs.extend([
+            "--sample",
+            params.get("sample")
+        ])
+    if params.get("regmethod") is not None:
+        cargs.extend([
+            "--regmethod",
+            params.get("regmethod")
+        ])
+    if params.get("usepathfiles"):
+        cargs.append("--usepathfiles")
+    if params.get("hemi") is not None:
+        cargs.extend([
+            "--hemi",
+            params.get("hemi")
+        ])
+    if params.get("src_hemi") is not None:
+        cargs.extend([
+            "--srchemi",
+            params.get("src_hemi")
+        ])
+    if params.get("trg_hemi") is not None:
+        cargs.extend([
+            "--trghemi",
+            params.get("trg_hemi")
+        ])
+    if params.get("src_ico_order") is not None:
+        cargs.extend([
+            "--srcicoorder",
+            str(params.get("src_ico_order"))
+        ])
+    if params.get("trg_ico_order") is not None:
+        cargs.extend([
+            "--trgicoorder",
+            str(params.get("trg_ico_order"))
+        ])
+    if params.get("direct") is not None:
+        cargs.extend([
+            "--direct",
+            params.get("direct")
+        ])
+    if params.get("trgsurf") is not None:
+        cargs.extend([
+            "--trgsurf",
+            params.get("trgsurf")
+        ])
+    if params.get("surfreg") is not None:
+        cargs.extend([
+            "--surfreg",
+            params.get("surfreg")
+        ])
+    if params.get("srcsurfreg") is not None:
+        cargs.extend([
+            "--srcsurfreg",
+            params.get("srcsurfreg")
+        ])
+    if params.get("trgsurfreg") is not None:
+        cargs.extend([
+            "--trgsurfreg",
+            params.get("trgsurfreg")
+        ])
+    if params.get("srcsurfreg_file") is not None:
+        cargs.extend([
+            "--srcsurfreg-file",
+            params.get("srcsurfreg_file")
+        ])
+    if params.get("trgsurfreg_file") is not None:
+        cargs.extend([
+            "--trgsurfreg-file",
+            params.get("trgsurfreg_file")
+        ])
+    if params.get("paint") is not None:
+        cargs.extend([
+            "--paint",
+            params.get("paint")
+        ])
+    if params.get("dmindmin") is not None:
+        cargs.extend([
+            "--dmindmin",
+            params.get("dmindmin")
+        ])
+    if params.get("baryfill") is not None:
+        cargs.extend([
+            "--baryfill",
+            params.get("baryfill")
+        ])
+    if params.get("label_cortex") is not None:
+        cargs.extend([
+            "--label-cortex",
+            params.get("label_cortex")
+        ])
+    if params.get("surf_label2mask") is not None:
+        cargs.extend([
+            "--surf-label2mask",
+            params.get("surf_label2mask")
+        ])
+    if params.get("srcmask") is not None:
+        cargs.extend([
+            "--srcmask",
+            params.get("srcmask")
+        ])
+    if params.get("srcmasksign") is not None:
+        cargs.extend([
+            "--srcmasksign",
+            params.get("srcmasksign")
+        ])
+    if params.get("srcmaskframe") is not None:
+        cargs.extend([
+            "--srcmaskframe",
+            str(params.get("srcmaskframe"))
+        ])
+    if params.get("xfm") is not None:
+        cargs.extend([
+            "--xfm",
+            params.get("xfm")
+        ])
+    if params.get("reg") is not None:
+        cargs.extend([
+            "--reg",
+            params.get("reg")
+        ])
+    if params.get("xfm_invert"):
+        cargs.append("--xfm-invert")
+    if params.get("projabs") is not None:
+        cargs.extend([
+            "--projabs",
+            params.get("projabs")
+        ])
+    if params.get("projfrac") is not None:
+        cargs.extend([
+            "--projfrac",
+            params.get("projfrac")
+        ])
+    if params.get("sd") is not None:
+        cargs.extend([
+            "--sd",
+            params.get("sd")
+        ])
+    if params.get("nohash"):
+        cargs.append("--nohash")
+    if params.get("norevmap"):
+        cargs.append("--norevmap")
+    if params.get("to_scanner") is not None:
+        cargs.extend([
+            "--to-scanner",
+            params.get("to_scanner")
+        ])
+    if params.get("to_tkr") is not None:
+        cargs.extend([
+            "--to-tkr",
+            params.get("to_tkr")
+        ])
+    if params.get("scanner"):
+        cargs.append("--scanner")
+    return cargs
+
+
+def mri_label2label_outputs(
+    params: MriLabel2labelParameters,
+    execution: Execution,
+) -> MriLabel2labelOutputs:
+    """
+    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 = MriLabel2labelOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mri_label2label_execute(
+    params: MriLabel2labelParameters,
+    execution: Execution,
+) -> MriLabel2labelOutputs:
+    """
+    No description.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriLabel2labelOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_label2label_cargs(params, execution)
+    ret = mri_label2label_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_label2label(
+    src_label: InputPathType,
+    trg_label: str,
+    erode: float | None = None,
+    open_: float | None = None,
+    close: float | None = None,
+    dilate: float | None = None,
+    ring: float | None = None,
+    src_subject: str | None = None,
+    trg_subject: str | None = None,
+    subject: str | None = None,
+    outmask: str | None = None,
+    outstat: str | None = None,
+    sample: str | None = None,
+    regmethod: str | None = None,
+    usepathfiles: bool = False,
+    hemi: str | None = None,
+    src_hemi: str | None = None,
+    trg_hemi: str | None = None,
+    src_ico_order: float | None = None,
+    trg_ico_order: float | None = None,
+    direct: str | None = None,
+    trgsurf: str | None = None,
+    surfreg: str | None = None,
+    srcsurfreg: str | None = None,
+    trgsurfreg: str | None = None,
+    srcsurfreg_file: str | None = None,
+    trgsurfreg_file: str | None = None,
+    paint: str | None = None,
+    dmindmin: str | None = None,
+    baryfill: str | None = None,
+    label_cortex: str | None = None,
+    surf_label2mask: str | None = None,
+    srcmask: str | None = None,
+    srcmasksign: str | None = None,
+    srcmaskframe: float | None = None,
+    xfm: str | None = None,
+    reg: str | None = None,
+    xfm_invert: bool = False,
+    projabs: str | None = None,
+    projfrac: str | None = None,
+    sd: str | None = None,
+    nohash: bool = False,
+    norevmap: bool = False,
+    to_scanner: str | None = None,
+    to_tkr: str | None = None,
+    scanner: bool = False,
+    runner: Runner | None = None,
+) -> MriLabel2labelOutputs:
+    """
+    No description.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        src_label: Input label file.
+        trg_label: Output label file.
+        erode: Erode the label N times before writing.
+        open_: Open the label N times before writing.
+        close: Close the label N times before writing.
+        dilate: Dilate the label N times before writing.
+        ring: Dilate the label N times then remove the original before writing.
+        src_subject: Source subject.
+        trg_subject: Target subject.
+        subject: Use for both target and source.
+        outmask: Save output label as a binary mask (surf only).
+        outstat: Save output label stat as a mask (surf only).
+        sample: Sample label onto surface.
+        regmethod: Registration method (surface, volume).
+        usepathfiles: Read from and write to a path file.
+        hemi: Hemisphere (lh or rh) (with surface).
+        src_hemi: Source Hemisphere (lh or rh).
+        trg_hemi: Target Hemisphere (lh or rh).
+        src_ico_order: When srcsubject=ico.
+        trg_ico_order: When trgsubject=ico.
+        direct: Use the [xyz] coords for src and trg surfaces to do direct\
+            lookup.
+        trgsurf: Get xyz from this surface (white).
+        surfreg: Surface registration (sphere.reg).
+        srcsurfreg: Source surface registration (sphere.reg).
+        trgsurfreg: Target surface registration (sphere.reg).
+        srcsurfreg_file: Specify full path to source reg.
+        trgsurfreg_file: Specify full path to target reg.
+        paint: Map to closest vertex on source surfname if d < dmax.
+        dmindmin: Bin mask with vertex of closest label point when painting.
+        baryfill: Fill with barycentric interpolation.
+        label_cortex: Create a label like ?h.cortex.label.
+        surf_label2mask: Convert a label to a binary mask.
+        srcmask: Source mask surfvalfile thresh <format>.
+        srcmasksign: Source mask sign (<abs>, pos, neg).
+        srcmaskframe: Source mask frame number (0-based).
+        xfm: Use xfm file instead of computing tal xfm.
+        reg: Use register.dat file instead of computing tal xfm.
+        xfm_invert: Invert xfm, or reg.
+        projabs: Project dist mm along surf normal.
+        projfrac: Project frac of thickness along surf normal.
+        sd: Use specified subjects directory.
+        nohash: Don't use hash table when regmethod is surface.
+        norevmap: Don't use reverse mapping when regmethod is surface.
+        to_scanner: Convert coords to scanner RAS prior to other operations.
+        to_tkr: Convert coords to tkregister RAS prior to other operations.
+        scanner: Set output coordinate type to scanner.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriLabel2labelOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_LABEL2LABEL_METADATA)
+    params = mri_label2label_params(
+        src_label=src_label,
+        trg_label=trg_label,
+        erode=erode,
+        open_=open_,
+        close=close,
+        dilate=dilate,
+        ring=ring,
+        src_subject=src_subject,
+        trg_subject=trg_subject,
+        subject=subject,
+        outmask=outmask,
+        outstat=outstat,
+        sample=sample,
+        regmethod=regmethod,
+        usepathfiles=usepathfiles,
+        hemi=hemi,
+        src_hemi=src_hemi,
+        trg_hemi=trg_hemi,
+        src_ico_order=src_ico_order,
+        trg_ico_order=trg_ico_order,
+        direct=direct,
+        trgsurf=trgsurf,
+        surfreg=surfreg,
+        srcsurfreg=srcsurfreg,
+        trgsurfreg=trgsurfreg,
+        srcsurfreg_file=srcsurfreg_file,
+        trgsurfreg_file=trgsurfreg_file,
+        paint=paint,
+        dmindmin=dmindmin,
+        baryfill=baryfill,
+        label_cortex=label_cortex,
+        surf_label2mask=surf_label2mask,
+        srcmask=srcmask,
+        srcmasksign=srcmasksign,
+        srcmaskframe=srcmaskframe,
+        xfm=xfm,
+        reg=reg,
+        xfm_invert=xfm_invert,
+        projabs=projabs,
+        projfrac=projfrac,
+        sd=sd,
+        nohash=nohash,
+        norevmap=norevmap,
+        to_scanner=to_scanner,
+        to_tkr=to_tkr,
+        scanner=scanner,
+    )
+    return mri_label2label_execute(params, execution)
+
+
+__all__ = [
+    "MRI_LABEL2LABEL_METADATA",
+    "MriLabel2labelOutputs",
+    "MriLabel2labelParameters",
+    "mri_label2label",
+    "mri_label2label_params",
+]