niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_volsynth.py

@@ -0,0 +1,705 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_VOLSYNTH_METADATA = Metadata(
+    id="656047848a60982264a81504c030cd41366f6765.boutiques",
+    name="mri_volsynth",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriVolsynthParameters = typing.TypedDict('MriVolsynthParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_volsynth"],
+    "output_volid": str,
+    "template": typing.NotRequired[str | None],
+    "nframes": typing.NotRequired[float | None],
+    "offset_flag": bool,
+    "offset_mid_flag": bool,
+    "curv": typing.NotRequired[str | None],
+    "dim": typing.NotRequired[list[float] | None],
+    "res": typing.NotRequired[list[float] | None],
+    "vox_size": typing.NotRequired[list[float] | None],
+    "tr": typing.NotRequired[float | None],
+    "cdircos": typing.NotRequired[list[float] | None],
+    "rdircos": typing.NotRequired[list[float] | None],
+    "sdircos": typing.NotRequired[list[float] | None],
+    "c_ras": typing.NotRequired[list[float] | None],
+    "p0": typing.NotRequired[list[float] | None],
+    "precision": typing.NotRequired[str | None],
+    "seed": typing.NotRequired[float | None],
+    "seedfile": typing.NotRequired[InputPathType | None],
+    "pdf": typing.NotRequired[str | None],
+    "bb": typing.NotRequired[list[float] | None],
+    "gmean": typing.NotRequired[float | None],
+    "gstd": typing.NotRequired[float | None],
+    "delta_crsf": typing.NotRequired[list[float] | None],
+    "delta_val": typing.NotRequired[float | None],
+    "delta_val_off": typing.NotRequired[float | None],
+    "grid": typing.NotRequired[list[float] | None],
+    "dof": typing.NotRequired[float | None],
+    "dof_num": typing.NotRequired[float | None],
+    "dof_den": typing.NotRequired[float | None],
+    "rescale_flag": bool,
+    "val_a": typing.NotRequired[float | None],
+    "val_b": typing.NotRequired[float | None],
+    "vox_radius": typing.NotRequired[float | None],
+    "mm_radius": typing.NotRequired[float | None],
+    "sphere_center": typing.NotRequired[list[float] | None],
+    "hsc": typing.NotRequired[list[float] | None],
+    "abs_flag": bool,
+    "cp": typing.NotRequired[InputPathType | None],
+    "spike": typing.NotRequired[float | None],
+    "fwhm": typing.NotRequired[float | None],
+    "sum2": typing.NotRequired[InputPathType | None],
+    "dim_surf_flag": bool,
+    "ctab": 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 {
+        "mri_volsynth": mri_volsynth_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 MriVolsynthOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_volsynth(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mri_volsynth_params(
+    output_volid: str,
+    template: str | None = None,
+    nframes: float | None = None,
+    offset_flag: bool = False,
+    offset_mid_flag: bool = False,
+    curv: str | None = None,
+    dim: list[float] | None = None,
+    res: list[float] | None = None,
+    vox_size: list[float] | None = None,
+    tr: float | None = None,
+    cdircos: list[float] | None = None,
+    rdircos: list[float] | None = None,
+    sdircos: list[float] | None = None,
+    c_ras: list[float] | None = None,
+    p0: list[float] | None = None,
+    precision: str | None = None,
+    seed: float | None = None,
+    seedfile: InputPathType | None = None,
+    pdf: str | None = None,
+    bb: list[float] | None = None,
+    gmean: float | None = None,
+    gstd: float | None = None,
+    delta_crsf: list[float] | None = None,
+    delta_val: float | None = None,
+    delta_val_off: float | None = None,
+    grid: list[float] | None = None,
+    dof: float | None = None,
+    dof_num: float | None = None,
+    dof_den: float | None = None,
+    rescale_flag: bool = False,
+    val_a: float | None = None,
+    val_b: float | None = None,
+    vox_radius: float | None = None,
+    mm_radius: float | None = None,
+    sphere_center: list[float] | None = None,
+    hsc: list[float] | None = None,
+    abs_flag: bool = False,
+    cp: InputPathType | None = None,
+    spike: float | None = None,
+    fwhm: float | None = None,
+    sum2: InputPathType | None = None,
+    dim_surf_flag: bool = False,
+    ctab: InputPathType | None = None,
+) -> MriVolsynthParameters:
+    """
+    Build parameters.
+    
+    Args:
+        output_volid: Output volume path id and format.
+        template: Template volume id.
+        nframes: Override template number of frames.
+        offset_flag: Use template as intensity offset.
+        offset_mid_flag: Use middle frame of template as intensity offset.
+        curv: Save output as curvature, uses lh.thickness as template. Requires\
+            subject and hemisphere.
+        dim: Specify dimensionality nc nr ns nf.
+        res: Voxel resolution dc dr ds df (df is TR, in msec).
+        vox_size: Change template voxel resolution and dimension dc dr ds.
+        tr: Time between frames in msec.
+        cdircos: Column cosine direction x, y, z.
+        rdircos: Row cosine direction x, y, z.
+        sdircos: Slice cosine direction x, y, z.
+        c_ras: RAS coordinates of 'center' voxel c_r c_a c_s.
+        p0: First voxel coordinates p0r p0a p0s.
+        precision: Precision of the output (e.g., float).
+        seed: Seed for the random number generator.
+        seedfile: Write seed value to this file.
+        pdf: Probability distribution function (e.g., gaussian, uniform, const).
+        bb: Bounding box c r s dc dr ds (In=ValA, Out=ValB).
+        gmean: Mean for the gaussian distribution.
+        gstd: Standard deviation for the gaussian distribution.
+        delta_crsf: Delta's col, row, slice, and frame coordinates.
+        delta_val: Delta value.
+        delta_val_off: Delta background value.
+        grid: Grid dimensions dcol, drow, dslice.
+        dof: Degrees of freedom for t and chi2 distributions.
+        dof_num: Numerator degrees of freedom for F distribution.
+        dof_den: Denominator degrees of freedom for F distribution.
+        rescale_flag: Rescale z, t, F, or chi2 after smoothing.
+        val_a: Set ValA.
+        val_b: Set ValB.
+        vox_radius: Radius in voxels for sphere.
+        mm_radius: Radius in mm for sphere.
+        sphere_center: Sphere center coordinates column, row, slice.
+        hsc: Multiply each frame by a random number between min and max.
+        abs_flag: Compute absolute value.
+        cp: Set control point voxels to 1.
+        spike: Set all values at a given time point to 1e9.
+        fwhm: Smooth by Full Width at Half Maximum (FWHM) in mm.
+        sum2: Save sum of volume squared into specified file.
+        dim_surf_flag: Set dimension to nvertices x 1 x 1.
+        ctab: Embed color table.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_volsynth",
+        "output_volid": output_volid,
+        "offset_flag": offset_flag,
+        "offset_mid_flag": offset_mid_flag,
+        "rescale_flag": rescale_flag,
+        "abs_flag": abs_flag,
+        "dim_surf_flag": dim_surf_flag,
+    }
+    if template is not None:
+        params["template"] = template
+    if nframes is not None:
+        params["nframes"] = nframes
+    if curv is not None:
+        params["curv"] = curv
+    if dim is not None:
+        params["dim"] = dim
+    if res is not None:
+        params["res"] = res
+    if vox_size is not None:
+        params["vox_size"] = vox_size
+    if tr is not None:
+        params["tr"] = tr
+    if cdircos is not None:
+        params["cdircos"] = cdircos
+    if rdircos is not None:
+        params["rdircos"] = rdircos
+    if sdircos is not None:
+        params["sdircos"] = sdircos
+    if c_ras is not None:
+        params["c_ras"] = c_ras
+    if p0 is not None:
+        params["p0"] = p0
+    if precision is not None:
+        params["precision"] = precision
+    if seed is not None:
+        params["seed"] = seed
+    if seedfile is not None:
+        params["seedfile"] = seedfile
+    if pdf is not None:
+        params["pdf"] = pdf
+    if bb is not None:
+        params["bb"] = bb
+    if gmean is not None:
+        params["gmean"] = gmean
+    if gstd is not None:
+        params["gstd"] = gstd
+    if delta_crsf is not None:
+        params["delta_crsf"] = delta_crsf
+    if delta_val is not None:
+        params["delta_val"] = delta_val
+    if delta_val_off is not None:
+        params["delta_val_off"] = delta_val_off
+    if grid is not None:
+        params["grid"] = grid
+    if dof is not None:
+        params["dof"] = dof
+    if dof_num is not None:
+        params["dof_num"] = dof_num
+    if dof_den is not None:
+        params["dof_den"] = dof_den
+    if val_a is not None:
+        params["val_a"] = val_a
+    if val_b is not None:
+        params["val_b"] = val_b
+    if vox_radius is not None:
+        params["vox_radius"] = vox_radius
+    if mm_radius is not None:
+        params["mm_radius"] = mm_radius
+    if sphere_center is not None:
+        params["sphere_center"] = sphere_center
+    if hsc is not None:
+        params["hsc"] = hsc
+    if cp is not None:
+        params["cp"] = cp
+    if spike is not None:
+        params["spike"] = spike
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if sum2 is not None:
+        params["sum2"] = sum2
+    if ctab is not None:
+        params["ctab"] = ctab
+    return params
+
+
+def mri_volsynth_cargs(
+    params: MriVolsynthParameters,
+    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_volsynth")
+    cargs.extend([
+        "--o",
+        params.get("output_volid")
+    ])
+    if params.get("template") is not None:
+        cargs.extend([
+            "--template",
+            params.get("template")
+        ])
+    if params.get("nframes") is not None:
+        cargs.extend([
+            "--nframes",
+            str(params.get("nframes"))
+        ])
+    if params.get("offset_flag"):
+        cargs.append("--offset")
+    if params.get("offset_mid_flag"):
+        cargs.append("--offset-mid")
+    if params.get("curv") is not None:
+        cargs.extend([
+            "--curv",
+            params.get("curv")
+        ])
+    if params.get("dim") is not None:
+        cargs.extend([
+            "--dim",
+            *map(str, params.get("dim"))
+        ])
+    if params.get("res") is not None:
+        cargs.extend([
+            "--res",
+            *map(str, params.get("res"))
+        ])
+    if params.get("vox_size") is not None:
+        cargs.extend([
+            "--vox-size",
+            *map(str, params.get("vox_size"))
+        ])
+    if params.get("tr") is not None:
+        cargs.extend([
+            "--tr",
+            str(params.get("tr"))
+        ])
+    if params.get("cdircos") is not None:
+        cargs.extend([
+            "--cdircos",
+            *map(str, params.get("cdircos"))
+        ])
+    if params.get("rdircos") is not None:
+        cargs.extend([
+            "--rdircos",
+            *map(str, params.get("rdircos"))
+        ])
+    if params.get("sdircos") is not None:
+        cargs.extend([
+            "--sdircos",
+            *map(str, params.get("sdircos"))
+        ])
+    if params.get("c_ras") is not None:
+        cargs.extend([
+            "--c_ras",
+            *map(str, params.get("c_ras"))
+        ])
+    if params.get("p0") is not None:
+        cargs.extend([
+            "--p0",
+            *map(str, params.get("p0"))
+        ])
+    if params.get("precision") is not None:
+        cargs.extend([
+            "--precision",
+            params.get("precision")
+        ])
+    if params.get("seed") is not None:
+        cargs.extend([
+            "--seed",
+            str(params.get("seed"))
+        ])
+    if params.get("seedfile") is not None:
+        cargs.extend([
+            "--seedfile",
+            execution.input_file(params.get("seedfile"))
+        ])
+    if params.get("pdf") is not None:
+        cargs.extend([
+            "--pdf",
+            params.get("pdf")
+        ])
+    if params.get("bb") is not None:
+        cargs.extend([
+            "--bb",
+            *map(str, params.get("bb"))
+        ])
+    if params.get("gmean") is not None:
+        cargs.extend([
+            "--gmean",
+            str(params.get("gmean"))
+        ])
+    if params.get("gstd") is not None:
+        cargs.extend([
+            "--gstd",
+            str(params.get("gstd"))
+        ])
+    if params.get("delta_crsf") is not None:
+        cargs.extend([
+            "--delta-crsf",
+            *map(str, params.get("delta_crsf"))
+        ])
+    if params.get("delta_val") is not None:
+        cargs.extend([
+            "--delta-val",
+            str(params.get("delta_val"))
+        ])
+    if params.get("delta_val_off") is not None:
+        cargs.extend([
+            "--delta-val-off",
+            str(params.get("delta_val_off"))
+        ])
+    if params.get("grid") is not None:
+        cargs.extend([
+            "--grid",
+            *map(str, params.get("grid"))
+        ])
+    if params.get("dof") is not None:
+        cargs.extend([
+            "--dof",
+            str(params.get("dof"))
+        ])
+    if params.get("dof_num") is not None:
+        cargs.extend([
+            "--dof-num",
+            str(params.get("dof_num"))
+        ])
+    if params.get("dof_den") is not None:
+        cargs.extend([
+            "--dof-den",
+            str(params.get("dof_den"))
+        ])
+    if params.get("rescale_flag"):
+        cargs.append("--rescale")
+    if params.get("val_a") is not None:
+        cargs.extend([
+            "--val-a",
+            str(params.get("val_a"))
+        ])
+    if params.get("val_b") is not None:
+        cargs.extend([
+            "--val-b",
+            str(params.get("val_b"))
+        ])
+    if params.get("vox_radius") is not None:
+        cargs.extend([
+            "--vox-radius",
+            str(params.get("vox_radius"))
+        ])
+    if params.get("mm_radius") is not None:
+        cargs.extend([
+            "--mm-radius",
+            str(params.get("mm_radius"))
+        ])
+    if params.get("sphere_center") is not None:
+        cargs.extend([
+            "--sphere-center",
+            *map(str, params.get("sphere_center"))
+        ])
+    if params.get("hsc") is not None:
+        cargs.extend([
+            "--hsc",
+            *map(str, params.get("hsc"))
+        ])
+    if params.get("abs_flag"):
+        cargs.append("--abs")
+    if params.get("cp") is not None:
+        cargs.extend([
+            "--cp",
+            execution.input_file(params.get("cp"))
+        ])
+    if params.get("spike") is not None:
+        cargs.extend([
+            "--spike",
+            str(params.get("spike"))
+        ])
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "--fwhm",
+            str(params.get("fwhm"))
+        ])
+    if params.get("sum2") is not None:
+        cargs.extend([
+            "--sum2",
+            execution.input_file(params.get("sum2"))
+        ])
+    if params.get("dim_surf_flag"):
+        cargs.append("--dim-surf")
+    if params.get("ctab") is not None:
+        cargs.extend([
+            "--ctab",
+            execution.input_file(params.get("ctab"))
+        ])
+    return cargs
+
+
+def mri_volsynth_outputs(
+    params: MriVolsynthParameters,
+    execution: Execution,
+) -> MriVolsynthOutputs:
+    """
+    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 = MriVolsynthOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mri_volsynth_execute(
+    params: MriVolsynthParameters,
+    execution: Execution,
+) -> MriVolsynthOutputs:
+    """
+    Synthesizes a volume with specified geometry and probability distribution
+    function.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriVolsynthOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_volsynth_cargs(params, execution)
+    ret = mri_volsynth_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_volsynth(
+    output_volid: str,
+    template: str | None = None,
+    nframes: float | None = None,
+    offset_flag: bool = False,
+    offset_mid_flag: bool = False,
+    curv: str | None = None,
+    dim: list[float] | None = None,
+    res: list[float] | None = None,
+    vox_size: list[float] | None = None,
+    tr: float | None = None,
+    cdircos: list[float] | None = None,
+    rdircos: list[float] | None = None,
+    sdircos: list[float] | None = None,
+    c_ras: list[float] | None = None,
+    p0: list[float] | None = None,
+    precision: str | None = None,
+    seed: float | None = None,
+    seedfile: InputPathType | None = None,
+    pdf: str | None = None,
+    bb: list[float] | None = None,
+    gmean: float | None = None,
+    gstd: float | None = None,
+    delta_crsf: list[float] | None = None,
+    delta_val: float | None = None,
+    delta_val_off: float | None = None,
+    grid: list[float] | None = None,
+    dof: float | None = None,
+    dof_num: float | None = None,
+    dof_den: float | None = None,
+    rescale_flag: bool = False,
+    val_a: float | None = None,
+    val_b: float | None = None,
+    vox_radius: float | None = None,
+    mm_radius: float | None = None,
+    sphere_center: list[float] | None = None,
+    hsc: list[float] | None = None,
+    abs_flag: bool = False,
+    cp: InputPathType | None = None,
+    spike: float | None = None,
+    fwhm: float | None = None,
+    sum2: InputPathType | None = None,
+    dim_surf_flag: bool = False,
+    ctab: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> MriVolsynthOutputs:
+    """
+    Synthesizes a volume with specified geometry and probability distribution
+    function.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        output_volid: Output volume path id and format.
+        template: Template volume id.
+        nframes: Override template number of frames.
+        offset_flag: Use template as intensity offset.
+        offset_mid_flag: Use middle frame of template as intensity offset.
+        curv: Save output as curvature, uses lh.thickness as template. Requires\
+            subject and hemisphere.
+        dim: Specify dimensionality nc nr ns nf.
+        res: Voxel resolution dc dr ds df (df is TR, in msec).
+        vox_size: Change template voxel resolution and dimension dc dr ds.
+        tr: Time between frames in msec.
+        cdircos: Column cosine direction x, y, z.
+        rdircos: Row cosine direction x, y, z.
+        sdircos: Slice cosine direction x, y, z.
+        c_ras: RAS coordinates of 'center' voxel c_r c_a c_s.
+        p0: First voxel coordinates p0r p0a p0s.
+        precision: Precision of the output (e.g., float).
+        seed: Seed for the random number generator.
+        seedfile: Write seed value to this file.
+        pdf: Probability distribution function (e.g., gaussian, uniform, const).
+        bb: Bounding box c r s dc dr ds (In=ValA, Out=ValB).
+        gmean: Mean for the gaussian distribution.
+        gstd: Standard deviation for the gaussian distribution.
+        delta_crsf: Delta's col, row, slice, and frame coordinates.
+        delta_val: Delta value.
+        delta_val_off: Delta background value.
+        grid: Grid dimensions dcol, drow, dslice.
+        dof: Degrees of freedom for t and chi2 distributions.
+        dof_num: Numerator degrees of freedom for F distribution.
+        dof_den: Denominator degrees of freedom for F distribution.
+        rescale_flag: Rescale z, t, F, or chi2 after smoothing.
+        val_a: Set ValA.
+        val_b: Set ValB.
+        vox_radius: Radius in voxels for sphere.
+        mm_radius: Radius in mm for sphere.
+        sphere_center: Sphere center coordinates column, row, slice.
+        hsc: Multiply each frame by a random number between min and max.
+        abs_flag: Compute absolute value.
+        cp: Set control point voxels to 1.
+        spike: Set all values at a given time point to 1e9.
+        fwhm: Smooth by Full Width at Half Maximum (FWHM) in mm.
+        sum2: Save sum of volume squared into specified file.
+        dim_surf_flag: Set dimension to nvertices x 1 x 1.
+        ctab: Embed color table.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriVolsynthOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_VOLSYNTH_METADATA)
+    params = mri_volsynth_params(
+        output_volid=output_volid,
+        template=template,
+        nframes=nframes,
+        offset_flag=offset_flag,
+        offset_mid_flag=offset_mid_flag,
+        curv=curv,
+        dim=dim,
+        res=res,
+        vox_size=vox_size,
+        tr=tr,
+        cdircos=cdircos,
+        rdircos=rdircos,
+        sdircos=sdircos,
+        c_ras=c_ras,
+        p0=p0,
+        precision=precision,
+        seed=seed,
+        seedfile=seedfile,
+        pdf=pdf,
+        bb=bb,
+        gmean=gmean,
+        gstd=gstd,
+        delta_crsf=delta_crsf,
+        delta_val=delta_val,
+        delta_val_off=delta_val_off,
+        grid=grid,
+        dof=dof,
+        dof_num=dof_num,
+        dof_den=dof_den,
+        rescale_flag=rescale_flag,
+        val_a=val_a,
+        val_b=val_b,
+        vox_radius=vox_radius,
+        mm_radius=mm_radius,
+        sphere_center=sphere_center,
+        hsc=hsc,
+        abs_flag=abs_flag,
+        cp=cp,
+        spike=spike,
+        fwhm=fwhm,
+        sum2=sum2,
+        dim_surf_flag=dim_surf_flag,
+        ctab=ctab,
+    )
+    return mri_volsynth_execute(params, execution)
+
+
+__all__ = [
+    "MRI_VOLSYNTH_METADATA",
+    "MriVolsynthOutputs",
+    "MriVolsynthParameters",
+    "mri_volsynth",
+    "mri_volsynth_params",
+]