niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_info.py

@@ -0,0 +1,646 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_INFO_METADATA = Metadata(
+    id="fea16b2c0cef821a4d6928c8ea143c9f2909ad1b.boutiques",
+    name="mri_info",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriInfoParameters = typing.TypedDict('MriInfoParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_info"],
+    "input1": InputPathType,
+    "input2": typing.NotRequired[InputPathType | None],
+    "conformed": bool,
+    "conformed_to_min": bool,
+    "is_1mm_iso": bool,
+    "type": bool,
+    "tr": bool,
+    "te": bool,
+    "ti": bool,
+    "fa": bool,
+    "pedir": bool,
+    "res": bool,
+    "cres": bool,
+    "rres": bool,
+    "sres": bool,
+    "voxvol": bool,
+    "voxvolsum": bool,
+    "ncols": bool,
+    "nrows": bool,
+    "nslices": bool,
+    "dim": bool,
+    "cdc": bool,
+    "rdc": bool,
+    "sdc": bool,
+    "vox2ras": bool,
+    "ras2vox": bool,
+    "vox2ras_tkr": bool,
+    "ras2vox_tkr": bool,
+    "vox2ras_fsl": bool,
+    "tkr2scanner": bool,
+    "scanner2tkr": bool,
+    "ras_good": bool,
+    "cras": bool,
+    "center": bool,
+    "zero_cras": bool,
+    "p0": bool,
+    "det": bool,
+    "dof": bool,
+    "nframes": bool,
+    "mid_frame": bool,
+    "format": bool,
+    "orientation": bool,
+    "slicedirection": bool,
+    "autoalign": bool,
+    "ctab": bool,
+    "cmds": bool,
+    "dump": bool,
+    "voxel_crs": typing.NotRequired[list[str] | None],
+    "entropy": bool,
+    "output_file": typing.NotRequired[InputPathType | None],
+    "orig_ras2vox": bool,
+    "in_type": 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 {
+        "mri_info": mri_info_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 MriInfoOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_info(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mri_info_params(
+    input1: InputPathType,
+    input2: InputPathType | None = None,
+    conformed: bool = False,
+    conformed_to_min: bool = False,
+    is_1mm_iso: bool = False,
+    type_: bool = False,
+    tr: bool = False,
+    te: bool = False,
+    ti: bool = False,
+    fa: bool = False,
+    pedir: bool = False,
+    res: bool = False,
+    cres: bool = False,
+    rres: bool = False,
+    sres: bool = False,
+    voxvol: bool = False,
+    voxvolsum: bool = False,
+    ncols: bool = False,
+    nrows: bool = False,
+    nslices: bool = False,
+    dim: bool = False,
+    cdc: bool = False,
+    rdc: bool = False,
+    sdc: bool = False,
+    vox2ras: bool = False,
+    ras2vox: bool = False,
+    vox2ras_tkr: bool = False,
+    ras2vox_tkr: bool = False,
+    vox2ras_fsl: bool = False,
+    tkr2scanner: bool = False,
+    scanner2tkr: bool = False,
+    ras_good: bool = False,
+    cras: bool = False,
+    center: bool = False,
+    zero_cras: bool = False,
+    p0: bool = False,
+    det: bool = False,
+    dof: bool = False,
+    nframes: bool = False,
+    mid_frame: bool = False,
+    format_: bool = False,
+    orientation: bool = False,
+    slicedirection: bool = False,
+    autoalign: bool = False,
+    ctab: bool = False,
+    cmds: bool = False,
+    dump: bool = False,
+    voxel_crs: list[str] | None = None,
+    entropy: bool = False,
+    output_file: InputPathType | None = None,
+    orig_ras2vox: bool = False,
+    in_type: str | None = None,
+) -> MriInfoParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input1: Primary input file.
+        input2: Secondary input file (optional).
+        conformed: Print whether a volume is conformed.
+        conformed_to_min: Print whether a volume is conformed-to-min.
+        is_1mm_iso: Print whether the voxel size is 1mm isotropic.
+        type_: Print the voxel type/precision.
+        tr: Print TR.
+        te: Print TE.
+        ti: Print TI.
+        fa: Print flip angle.
+        pedir: Print phase encode direction.
+        res: Print column, row, slice, and frame resolution.
+        cres: Print column voxel size.
+        rres: Print row voxel size.
+        sres: Print slice voxel size.
+        voxvol: Print voxel volume.
+        voxvolsum: Compute sum of all voxels times the voxel volume.
+        ncols: Print number of columns.
+        nrows: Print number of rows.
+        nslices: Print number of slices.
+        dim: Print number of columns, rows, slices, and frames.
+        cdc: Print column direction cosine (x_{r,a,s}).
+        rdc: Print row direction cosine (y_{r,a,s}).
+        sdc: Print slice direction cosine (z_{r,a,s}).
+        vox2ras: Print the native/qform vox2ras matrix.
+        ras2vox: Print the native/qform ras2vox matrix.
+        vox2ras_tkr: Print the tkregister vox2ras matrix.
+        ras2vox_tkr: Print the tkregister ras2vox matrix.
+        vox2ras_fsl: Print the FSL/FLIRT vox2ras matrix.
+        tkr2scanner: Print tkrRAS-to-scannerRAS matrix.
+        scanner2tkr: Print scannerRAS-to-tkrRAS matrix.
+        ras_good: Print the ras_good_flag.
+        cras: Print the RAS near the center of the volume.
+        center: Print the RAS at the actual center of the volume.
+        zero_cras: Zero the center ras.
+        p0: Print the RAS at voxel (0,0,0).
+        det: Print the determinant of the vox2ras matrix.
+        dof: Print the degrees of freedom stored in the header.
+        nframes: Print the number of frames.
+        mid_frame: Print the middle frame.
+        format_: Print file format.
+        orientation: Print orientation string (e.g., LPS, RAS, RPI).
+        slicedirection: Print primary slice direction (e.g., axial).
+        autoalign: Print auto align matrix (if it exists).
+        ctab: Print embedded color lookup table.
+        cmds: Print command-line provenance info.
+        dump: Print FA, TR, TE, TI, etc.
+        voxel_crs: Dump voxel value from column, row, slice (0-based, all\
+            frames).
+        entropy: Compute and print entropy.
+        output_file: Print flagged results to file.
+        orig_ras2vox: Print orig Ras2Vox matrix if present.
+        in_type: Explicitly specify file type.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_info",
+        "input1": input1,
+        "conformed": conformed,
+        "conformed_to_min": conformed_to_min,
+        "is_1mm_iso": is_1mm_iso,
+        "type": type_,
+        "tr": tr,
+        "te": te,
+        "ti": ti,
+        "fa": fa,
+        "pedir": pedir,
+        "res": res,
+        "cres": cres,
+        "rres": rres,
+        "sres": sres,
+        "voxvol": voxvol,
+        "voxvolsum": voxvolsum,
+        "ncols": ncols,
+        "nrows": nrows,
+        "nslices": nslices,
+        "dim": dim,
+        "cdc": cdc,
+        "rdc": rdc,
+        "sdc": sdc,
+        "vox2ras": vox2ras,
+        "ras2vox": ras2vox,
+        "vox2ras_tkr": vox2ras_tkr,
+        "ras2vox_tkr": ras2vox_tkr,
+        "vox2ras_fsl": vox2ras_fsl,
+        "tkr2scanner": tkr2scanner,
+        "scanner2tkr": scanner2tkr,
+        "ras_good": ras_good,
+        "cras": cras,
+        "center": center,
+        "zero_cras": zero_cras,
+        "p0": p0,
+        "det": det,
+        "dof": dof,
+        "nframes": nframes,
+        "mid_frame": mid_frame,
+        "format": format_,
+        "orientation": orientation,
+        "slicedirection": slicedirection,
+        "autoalign": autoalign,
+        "ctab": ctab,
+        "cmds": cmds,
+        "dump": dump,
+        "entropy": entropy,
+        "orig_ras2vox": orig_ras2vox,
+    }
+    if input2 is not None:
+        params["input2"] = input2
+    if voxel_crs is not None:
+        params["voxel_crs"] = voxel_crs
+    if output_file is not None:
+        params["output_file"] = output_file
+    if in_type is not None:
+        params["in_type"] = in_type
+    return params
+
+
+def mri_info_cargs(
+    params: MriInfoParameters,
+    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_info")
+    cargs.append(execution.input_file(params.get("input1")))
+    if params.get("input2") is not None:
+        cargs.append(execution.input_file(params.get("input2")))
+    if params.get("conformed"):
+        cargs.append("--conformed")
+    if params.get("conformed_to_min"):
+        cargs.append("--conformed-to-min")
+    if params.get("is_1mm_iso"):
+        cargs.append("--is-1mm-iso")
+    if params.get("type"):
+        cargs.append("--type")
+    if params.get("tr"):
+        cargs.append("--tr")
+    if params.get("te"):
+        cargs.append("--te")
+    if params.get("ti"):
+        cargs.append("--ti")
+    if params.get("fa"):
+        cargs.append("--fa")
+    if params.get("pedir"):
+        cargs.append("--pedir")
+    if params.get("res"):
+        cargs.append("--res")
+    if params.get("cres"):
+        cargs.append("--cres")
+    if params.get("rres"):
+        cargs.append("--rres")
+    if params.get("sres"):
+        cargs.append("--sres")
+    if params.get("voxvol"):
+        cargs.append("--voxvol")
+    if params.get("voxvolsum"):
+        cargs.append("--voxvolsum")
+    if params.get("ncols"):
+        cargs.append("--ncols")
+    if params.get("nrows"):
+        cargs.append("--nrows")
+    if params.get("nslices"):
+        cargs.append("--nslices")
+    if params.get("dim"):
+        cargs.append("--dim")
+    if params.get("cdc"):
+        cargs.append("--cdc")
+    if params.get("rdc"):
+        cargs.append("--rdc")
+    if params.get("sdc"):
+        cargs.append("--sdc")
+    if params.get("vox2ras"):
+        cargs.append("--vox2ras")
+    if params.get("ras2vox"):
+        cargs.append("--ras2vox")
+    if params.get("vox2ras_tkr"):
+        cargs.append("--vox2ras-tkr")
+    if params.get("ras2vox_tkr"):
+        cargs.append("--ras2vox-tkr")
+    if params.get("vox2ras_fsl"):
+        cargs.append("--vox2ras-fsl")
+    if params.get("tkr2scanner"):
+        cargs.append("--tkr2scanner")
+    if params.get("scanner2tkr"):
+        cargs.append("--scanner2tkr")
+    if params.get("ras_good"):
+        cargs.append("--ras_good")
+    if params.get("cras"):
+        cargs.append("--cras")
+    if params.get("center"):
+        cargs.append("--center")
+    if params.get("zero_cras"):
+        cargs.append("--zero-cras")
+    if params.get("p0"):
+        cargs.append("--p0")
+    if params.get("det"):
+        cargs.append("--det")
+    if params.get("dof"):
+        cargs.append("--dof")
+    if params.get("nframes"):
+        cargs.append("--nframes")
+    if params.get("mid_frame"):
+        cargs.append("--mid-frame")
+    if params.get("format"):
+        cargs.append("--format")
+    if params.get("orientation"):
+        cargs.append("--orientation")
+    if params.get("slicedirection"):
+        cargs.append("--slicedirection")
+    if params.get("autoalign"):
+        cargs.append("--autoalign")
+    if params.get("ctab"):
+        cargs.append("--ctab")
+    if params.get("cmds"):
+        cargs.append("--cmds")
+    if params.get("dump"):
+        cargs.append("--dump")
+    if params.get("voxel_crs") is not None:
+        cargs.extend([
+            "--voxel",
+            *params.get("voxel_crs")
+        ])
+    if params.get("entropy"):
+        cargs.append("--entropy")
+    if params.get("output_file") is not None:
+        cargs.extend([
+            "--o",
+            execution.input_file(params.get("output_file"))
+        ])
+    if params.get("orig_ras2vox"):
+        cargs.append("--orig_ras2vox")
+    if params.get("in_type") is not None:
+        cargs.extend([
+            "--in_type",
+            params.get("in_type")
+        ])
+    return cargs
+
+
+def mri_info_outputs(
+    params: MriInfoParameters,
+    execution: Execution,
+) -> MriInfoOutputs:
+    """
+    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 = MriInfoOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mri_info_execute(
+    params: MriInfoParameters,
+    execution: Execution,
+) -> MriInfoOutputs:
+    """
+    Tool to extract metadata from MRI volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriInfoOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_info_cargs(params, execution)
+    ret = mri_info_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_info(
+    input1: InputPathType,
+    input2: InputPathType | None = None,
+    conformed: bool = False,
+    conformed_to_min: bool = False,
+    is_1mm_iso: bool = False,
+    type_: bool = False,
+    tr: bool = False,
+    te: bool = False,
+    ti: bool = False,
+    fa: bool = False,
+    pedir: bool = False,
+    res: bool = False,
+    cres: bool = False,
+    rres: bool = False,
+    sres: bool = False,
+    voxvol: bool = False,
+    voxvolsum: bool = False,
+    ncols: bool = False,
+    nrows: bool = False,
+    nslices: bool = False,
+    dim: bool = False,
+    cdc: bool = False,
+    rdc: bool = False,
+    sdc: bool = False,
+    vox2ras: bool = False,
+    ras2vox: bool = False,
+    vox2ras_tkr: bool = False,
+    ras2vox_tkr: bool = False,
+    vox2ras_fsl: bool = False,
+    tkr2scanner: bool = False,
+    scanner2tkr: bool = False,
+    ras_good: bool = False,
+    cras: bool = False,
+    center: bool = False,
+    zero_cras: bool = False,
+    p0: bool = False,
+    det: bool = False,
+    dof: bool = False,
+    nframes: bool = False,
+    mid_frame: bool = False,
+    format_: bool = False,
+    orientation: bool = False,
+    slicedirection: bool = False,
+    autoalign: bool = False,
+    ctab: bool = False,
+    cmds: bool = False,
+    dump: bool = False,
+    voxel_crs: list[str] | None = None,
+    entropy: bool = False,
+    output_file: InputPathType | None = None,
+    orig_ras2vox: bool = False,
+    in_type: str | None = None,
+    runner: Runner | None = None,
+) -> MriInfoOutputs:
+    """
+    Tool to extract metadata from MRI volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input1: Primary input file.
+        input2: Secondary input file (optional).
+        conformed: Print whether a volume is conformed.
+        conformed_to_min: Print whether a volume is conformed-to-min.
+        is_1mm_iso: Print whether the voxel size is 1mm isotropic.
+        type_: Print the voxel type/precision.
+        tr: Print TR.
+        te: Print TE.
+        ti: Print TI.
+        fa: Print flip angle.
+        pedir: Print phase encode direction.
+        res: Print column, row, slice, and frame resolution.
+        cres: Print column voxel size.
+        rres: Print row voxel size.
+        sres: Print slice voxel size.
+        voxvol: Print voxel volume.
+        voxvolsum: Compute sum of all voxels times the voxel volume.
+        ncols: Print number of columns.
+        nrows: Print number of rows.
+        nslices: Print number of slices.
+        dim: Print number of columns, rows, slices, and frames.
+        cdc: Print column direction cosine (x_{r,a,s}).
+        rdc: Print row direction cosine (y_{r,a,s}).
+        sdc: Print slice direction cosine (z_{r,a,s}).
+        vox2ras: Print the native/qform vox2ras matrix.
+        ras2vox: Print the native/qform ras2vox matrix.
+        vox2ras_tkr: Print the tkregister vox2ras matrix.
+        ras2vox_tkr: Print the tkregister ras2vox matrix.
+        vox2ras_fsl: Print the FSL/FLIRT vox2ras matrix.
+        tkr2scanner: Print tkrRAS-to-scannerRAS matrix.
+        scanner2tkr: Print scannerRAS-to-tkrRAS matrix.
+        ras_good: Print the ras_good_flag.
+        cras: Print the RAS near the center of the volume.
+        center: Print the RAS at the actual center of the volume.
+        zero_cras: Zero the center ras.
+        p0: Print the RAS at voxel (0,0,0).
+        det: Print the determinant of the vox2ras matrix.
+        dof: Print the degrees of freedom stored in the header.
+        nframes: Print the number of frames.
+        mid_frame: Print the middle frame.
+        format_: Print file format.
+        orientation: Print orientation string (e.g., LPS, RAS, RPI).
+        slicedirection: Print primary slice direction (e.g., axial).
+        autoalign: Print auto align matrix (if it exists).
+        ctab: Print embedded color lookup table.
+        cmds: Print command-line provenance info.
+        dump: Print FA, TR, TE, TI, etc.
+        voxel_crs: Dump voxel value from column, row, slice (0-based, all\
+            frames).
+        entropy: Compute and print entropy.
+        output_file: Print flagged results to file.
+        orig_ras2vox: Print orig Ras2Vox matrix if present.
+        in_type: Explicitly specify file type.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriInfoOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_INFO_METADATA)
+    params = mri_info_params(
+        input1=input1,
+        input2=input2,
+        conformed=conformed,
+        conformed_to_min=conformed_to_min,
+        is_1mm_iso=is_1mm_iso,
+        type_=type_,
+        tr=tr,
+        te=te,
+        ti=ti,
+        fa=fa,
+        pedir=pedir,
+        res=res,
+        cres=cres,
+        rres=rres,
+        sres=sres,
+        voxvol=voxvol,
+        voxvolsum=voxvolsum,
+        ncols=ncols,
+        nrows=nrows,
+        nslices=nslices,
+        dim=dim,
+        cdc=cdc,
+        rdc=rdc,
+        sdc=sdc,
+        vox2ras=vox2ras,
+        ras2vox=ras2vox,
+        vox2ras_tkr=vox2ras_tkr,
+        ras2vox_tkr=ras2vox_tkr,
+        vox2ras_fsl=vox2ras_fsl,
+        tkr2scanner=tkr2scanner,
+        scanner2tkr=scanner2tkr,
+        ras_good=ras_good,
+        cras=cras,
+        center=center,
+        zero_cras=zero_cras,
+        p0=p0,
+        det=det,
+        dof=dof,
+        nframes=nframes,
+        mid_frame=mid_frame,
+        format_=format_,
+        orientation=orientation,
+        slicedirection=slicedirection,
+        autoalign=autoalign,
+        ctab=ctab,
+        cmds=cmds,
+        dump=dump,
+        voxel_crs=voxel_crs,
+        entropy=entropy,
+        output_file=output_file,
+        orig_ras2vox=orig_ras2vox,
+        in_type=in_type,
+    )
+    return mri_info_execute(params, execution)
+
+
+__all__ = [
+    "MRI_INFO_METADATA",
+    "MriInfoOutputs",
+    "MriInfoParameters",
+    "mri_info",
+    "mri_info_params",
+]