niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_convert.py

@@ -0,0 +1,597 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_CONVERT_METADATA = Metadata(
+    id="2935cffb17b5edbbc239ffbc0efa59b1c070ffca.boutiques",
+    name="mris_convert",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisConvertParameters = typing.TypedDict('MrisConvertParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_convert"],
+    "input_file": InputPathType,
+    "second_input_file": typing.NotRequired[InputPathType | None],
+    "output_file": str,
+    "patch": bool,
+    "curv_overlay_files": typing.NotRequired[list[str] | None],
+    "functional_data_file": typing.NotRequired[InputPathType | None],
+    "orig_positions": typing.NotRequired[str | None],
+    "scale": typing.NotRequired[float | None],
+    "rescale": bool,
+    "talairach_xfm": typing.NotRequired[str | None],
+    "normals": bool,
+    "neighbors": bool,
+    "xyz": bool,
+    "annotation_file": typing.NotRequired[InputPathType | None],
+    "parcstats_file": typing.NotRequired[InputPathType | None],
+    "gifti_dataarray_num": typing.NotRequired[float | None],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "label_stats_file": typing.NotRequired[str | None],
+    "combine_surfs": bool,
+    "merge_gifti": bool,
+    "split_gifti": bool,
+    "gifti_outdir": typing.NotRequired[str | None],
+    "delete_cmds": bool,
+    "center": bool,
+    "vol_geom": typing.NotRequired[str | None],
+    "remove_vol_geom": bool,
+    "to_surf": typing.NotRequired[str | None],
+    "to_scanner": bool,
+    "to_tkr": bool,
+    "userealras": bool,
+    "usesurfras": bool,
+    "upsample": typing.NotRequired[str | None],
+    "volume": typing.NotRequired[str | None],
+    "area": typing.NotRequired[str | None],
+    "angle": typing.NotRequired[str | None],
+    "label_to_mask": typing.NotRequired[str | None],
+    "cras_add": bool,
+    "cras_subtract": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_convert": mris_convert_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 {
+        "mris_convert": mris_convert_outputs,
+    }.get(t)
+
+
+class MrisConvertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_convert(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    converted_surface: OutputPathType
+    """Output converted surface file"""
+
+
+def mris_convert_params(
+    input_file: InputPathType,
+    output_file: str,
+    second_input_file: InputPathType | None = None,
+    patch: bool = False,
+    curv_overlay_files: list[str] | None = None,
+    functional_data_file: InputPathType | None = None,
+    orig_positions: str | None = None,
+    scale: float | None = None,
+    rescale: bool = False,
+    talairach_xfm: str | None = None,
+    normals: bool = False,
+    neighbors: bool = False,
+    xyz: bool = False,
+    annotation_file: InputPathType | None = None,
+    parcstats_file: InputPathType | None = None,
+    gifti_dataarray_num: float | None = None,
+    label_file: InputPathType | None = None,
+    label_stats_file: str | None = None,
+    combine_surfs: bool = False,
+    merge_gifti: bool = False,
+    split_gifti: bool = False,
+    gifti_outdir: str | None = None,
+    delete_cmds: bool = False,
+    center: bool = False,
+    vol_geom: str | None = None,
+    remove_vol_geom: bool = False,
+    to_surf: str | None = None,
+    to_scanner: bool = False,
+    to_tkr: bool = False,
+    userealras: bool = False,
+    usesurfras: bool = False,
+    upsample: str | None = None,
+    volume: str | None = None,
+    area: str | None = None,
+    angle: str | None = None,
+    label_to_mask: str | None = None,
+    cras_add: bool = False,
+    cras_subtract: bool = False,
+) -> MrisConvertParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input filename.
+        output_file: Output filename.
+        second_input_file: Second input filename to be combined, required for\
+            --combinesurfs.
+        patch: Input file is a patch file, not a full surface.
+        curv_overlay_files: Input scalar curv overlay files.
+        functional_data_file: Input functional time-series or other multi-frame\
+            data.
+        orig_positions: Read orig positions.
+        scale: Scale vertex xyz by scale.
+        rescale: Rescale vertex xyz so total area is same as group average.
+        talairach_xfm: Apply talairach xfm of subject to vertex xyz.
+        normals: Output ascii file where vertex data is the surface normal\
+            vector.
+        neighbors: Write out neighbors of a vertex in each row.
+        xyz: Print only surface xyz to ascii file.
+        annotation_file: Input annotation or gifti label data.
+        parcstats_file: Input text file containing label/val pairs for\
+            parcellation.
+        gifti_dataarray_num: Input gifti dataarray number to use.
+        label_file: Input .label file and name for this label.
+        label_stats_file: Output gifti file to which label stats will be\
+            written.
+        combine_surfs: Combine surface files, two input surface files required.
+        merge_gifti: Generate combined gifti file with surface and multiple\
+            curvature data.
+        split_gifti: Separate surface and data array from combined gifti file.
+        gifti_outdir: Output directory for generated gifti files.
+        delete_cmds: Delete command lines in surface.
+        center: Put center of surface at (0,0,0).
+        vol_geom: Use MRIVol to set the volume geometry.
+        remove_vol_geom: Set the valid flag in vg to 0.
+        to_surf: Copy coordinates from surfcoords to output (good for patches).
+        to_scanner: Convert coordinates from native FS (tkr) coords to scanner\
+            coords.
+        to_tkr: Convert coordinates from scanner coords to native FS (tkr)\
+            coords.
+        userealras: Same as --to-scanner.
+        usesurfras: Same as --to-tkr.
+        upsample: Upsample N times by splitting edges/faces.
+        volume: Compute vertex-wise volume.
+        area: Compute vertex-wise area.
+        angle: Compute cortical orientation angles.
+        label_to_mask: Convert a surface-based label to a binary mask.
+        cras_add: Shift center to scanner coordinate center.
+        cras_subtract: Shift center from scanner coordinate center.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_convert",
+        "input_file": input_file,
+        "output_file": output_file,
+        "patch": patch,
+        "rescale": rescale,
+        "normals": normals,
+        "neighbors": neighbors,
+        "xyz": xyz,
+        "combine_surfs": combine_surfs,
+        "merge_gifti": merge_gifti,
+        "split_gifti": split_gifti,
+        "delete_cmds": delete_cmds,
+        "center": center,
+        "remove_vol_geom": remove_vol_geom,
+        "to_scanner": to_scanner,
+        "to_tkr": to_tkr,
+        "userealras": userealras,
+        "usesurfras": usesurfras,
+        "cras_add": cras_add,
+        "cras_subtract": cras_subtract,
+    }
+    if second_input_file is not None:
+        params["second_input_file"] = second_input_file
+    if curv_overlay_files is not None:
+        params["curv_overlay_files"] = curv_overlay_files
+    if functional_data_file is not None:
+        params["functional_data_file"] = functional_data_file
+    if orig_positions is not None:
+        params["orig_positions"] = orig_positions
+    if scale is not None:
+        params["scale"] = scale
+    if talairach_xfm is not None:
+        params["talairach_xfm"] = talairach_xfm
+    if annotation_file is not None:
+        params["annotation_file"] = annotation_file
+    if parcstats_file is not None:
+        params["parcstats_file"] = parcstats_file
+    if gifti_dataarray_num is not None:
+        params["gifti_dataarray_num"] = gifti_dataarray_num
+    if label_file is not None:
+        params["label_file"] = label_file
+    if label_stats_file is not None:
+        params["label_stats_file"] = label_stats_file
+    if gifti_outdir is not None:
+        params["gifti_outdir"] = gifti_outdir
+    if vol_geom is not None:
+        params["vol_geom"] = vol_geom
+    if to_surf is not None:
+        params["to_surf"] = to_surf
+    if upsample is not None:
+        params["upsample"] = upsample
+    if volume is not None:
+        params["volume"] = volume
+    if area is not None:
+        params["area"] = area
+    if angle is not None:
+        params["angle"] = angle
+    if label_to_mask is not None:
+        params["label_to_mask"] = label_to_mask
+    return params
+
+
+def mris_convert_cargs(
+    params: MrisConvertParameters,
+    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("mris_convert")
+    cargs.append(execution.input_file(params.get("input_file")))
+    if params.get("second_input_file") is not None:
+        cargs.append(execution.input_file(params.get("second_input_file")))
+    cargs.append(params.get("output_file"))
+    if params.get("patch"):
+        cargs.append("-p")
+    if params.get("curv_overlay_files") is not None:
+        cargs.extend([
+            "-c",
+            *params.get("curv_overlay_files")
+        ])
+    if params.get("functional_data_file") is not None:
+        cargs.extend([
+            "-f",
+            execution.input_file(params.get("functional_data_file"))
+        ])
+    if params.get("orig_positions") is not None:
+        cargs.extend([
+            "-o",
+            params.get("orig_positions")
+        ])
+    if params.get("scale") is not None:
+        cargs.extend([
+            "-s",
+            str(params.get("scale"))
+        ])
+    if params.get("rescale"):
+        cargs.append("-r")
+    if params.get("talairach_xfm") is not None:
+        cargs.extend([
+            "-t",
+            params.get("talairach_xfm")
+        ])
+    if params.get("normals"):
+        cargs.append("-n")
+    if params.get("neighbors"):
+        cargs.append("-v")
+    if params.get("xyz"):
+        cargs.append("-a")
+    if params.get("annotation_file") is not None:
+        cargs.extend([
+            "--annot",
+            execution.input_file(params.get("annotation_file"))
+        ])
+    if params.get("parcstats_file") is not None:
+        cargs.extend([
+            "--parcstats",
+            execution.input_file(params.get("parcstats_file"))
+        ])
+    if params.get("gifti_dataarray_num") is not None:
+        cargs.extend([
+            "--da_num",
+            str(params.get("gifti_dataarray_num"))
+        ])
+    if params.get("label_file") is not None:
+        cargs.extend([
+            "--label",
+            execution.input_file(params.get("label_file"))
+        ])
+    if params.get("label_stats_file") is not None:
+        cargs.extend([
+            "--labelstats",
+            params.get("label_stats_file")
+        ])
+    if params.get("combine_surfs"):
+        cargs.append("--combinesurfs")
+    if params.get("merge_gifti"):
+        cargs.append("--mergegifti")
+    if params.get("split_gifti"):
+        cargs.append("--splitgifti")
+    if params.get("gifti_outdir") is not None:
+        cargs.extend([
+            "--giftioutdir",
+            params.get("gifti_outdir")
+        ])
+    if params.get("delete_cmds"):
+        cargs.append("--delete-cmds")
+    if params.get("center"):
+        cargs.append("--center")
+    if params.get("vol_geom") is not None:
+        cargs.extend([
+            "--vol-geom",
+            params.get("vol_geom")
+        ])
+    if params.get("remove_vol_geom"):
+        cargs.append("--remove-vol-geom")
+    if params.get("to_surf") is not None:
+        cargs.extend([
+            "--to-surf",
+            params.get("to_surf")
+        ])
+    if params.get("to_scanner"):
+        cargs.append("--to-scanner")
+    if params.get("to_tkr"):
+        cargs.append("--to-tkr")
+    if params.get("userealras"):
+        cargs.append("--userealras")
+    if params.get("usesurfras"):
+        cargs.append("--usesurfras")
+    if params.get("upsample") is not None:
+        cargs.extend([
+            "--upsample",
+            params.get("upsample")
+        ])
+    if params.get("volume") is not None:
+        cargs.extend([
+            "--volume",
+            params.get("volume")
+        ])
+    if params.get("area") is not None:
+        cargs.extend([
+            "--area",
+            params.get("area")
+        ])
+    if params.get("angle") is not None:
+        cargs.extend([
+            "--angle",
+            params.get("angle")
+        ])
+    if params.get("label_to_mask") is not None:
+        cargs.extend([
+            "--label2mask",
+            params.get("label_to_mask")
+        ])
+    if params.get("cras_add"):
+        cargs.append("--cras_add")
+    if params.get("cras_subtract"):
+        cargs.append("--cras_subtract")
+    return cargs
+
+
+def mris_convert_outputs(
+    params: MrisConvertParameters,
+    execution: Execution,
+) -> MrisConvertOutputs:
+    """
+    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 = MrisConvertOutputs(
+        root=execution.output_file("."),
+        converted_surface=execution.output_file(params.get("output_file")),
+    )
+    return ret
+
+
+def mris_convert_execute(
+    params: MrisConvertParameters,
+    execution: Execution,
+) -> MrisConvertOutputs:
+    """
+    This program will convert MRI-surface data formats.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisConvertOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_convert_cargs(params, execution)
+    ret = mris_convert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_convert(
+    input_file: InputPathType,
+    output_file: str,
+    second_input_file: InputPathType | None = None,
+    patch: bool = False,
+    curv_overlay_files: list[str] | None = None,
+    functional_data_file: InputPathType | None = None,
+    orig_positions: str | None = None,
+    scale: float | None = None,
+    rescale: bool = False,
+    talairach_xfm: str | None = None,
+    normals: bool = False,
+    neighbors: bool = False,
+    xyz: bool = False,
+    annotation_file: InputPathType | None = None,
+    parcstats_file: InputPathType | None = None,
+    gifti_dataarray_num: float | None = None,
+    label_file: InputPathType | None = None,
+    label_stats_file: str | None = None,
+    combine_surfs: bool = False,
+    merge_gifti: bool = False,
+    split_gifti: bool = False,
+    gifti_outdir: str | None = None,
+    delete_cmds: bool = False,
+    center: bool = False,
+    vol_geom: str | None = None,
+    remove_vol_geom: bool = False,
+    to_surf: str | None = None,
+    to_scanner: bool = False,
+    to_tkr: bool = False,
+    userealras: bool = False,
+    usesurfras: bool = False,
+    upsample: str | None = None,
+    volume: str | None = None,
+    area: str | None = None,
+    angle: str | None = None,
+    label_to_mask: str | None = None,
+    cras_add: bool = False,
+    cras_subtract: bool = False,
+    runner: Runner | None = None,
+) -> MrisConvertOutputs:
+    """
+    This program will convert MRI-surface data formats.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_file: Input filename.
+        output_file: Output filename.
+        second_input_file: Second input filename to be combined, required for\
+            --combinesurfs.
+        patch: Input file is a patch file, not a full surface.
+        curv_overlay_files: Input scalar curv overlay files.
+        functional_data_file: Input functional time-series or other multi-frame\
+            data.
+        orig_positions: Read orig positions.
+        scale: Scale vertex xyz by scale.
+        rescale: Rescale vertex xyz so total area is same as group average.
+        talairach_xfm: Apply talairach xfm of subject to vertex xyz.
+        normals: Output ascii file where vertex data is the surface normal\
+            vector.
+        neighbors: Write out neighbors of a vertex in each row.
+        xyz: Print only surface xyz to ascii file.
+        annotation_file: Input annotation or gifti label data.
+        parcstats_file: Input text file containing label/val pairs for\
+            parcellation.
+        gifti_dataarray_num: Input gifti dataarray number to use.
+        label_file: Input .label file and name for this label.
+        label_stats_file: Output gifti file to which label stats will be\
+            written.
+        combine_surfs: Combine surface files, two input surface files required.
+        merge_gifti: Generate combined gifti file with surface and multiple\
+            curvature data.
+        split_gifti: Separate surface and data array from combined gifti file.
+        gifti_outdir: Output directory for generated gifti files.
+        delete_cmds: Delete command lines in surface.
+        center: Put center of surface at (0,0,0).
+        vol_geom: Use MRIVol to set the volume geometry.
+        remove_vol_geom: Set the valid flag in vg to 0.
+        to_surf: Copy coordinates from surfcoords to output (good for patches).
+        to_scanner: Convert coordinates from native FS (tkr) coords to scanner\
+            coords.
+        to_tkr: Convert coordinates from scanner coords to native FS (tkr)\
+            coords.
+        userealras: Same as --to-scanner.
+        usesurfras: Same as --to-tkr.
+        upsample: Upsample N times by splitting edges/faces.
+        volume: Compute vertex-wise volume.
+        area: Compute vertex-wise area.
+        angle: Compute cortical orientation angles.
+        label_to_mask: Convert a surface-based label to a binary mask.
+        cras_add: Shift center to scanner coordinate center.
+        cras_subtract: Shift center from scanner coordinate center.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisConvertOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_CONVERT_METADATA)
+    params = mris_convert_params(
+        input_file=input_file,
+        second_input_file=second_input_file,
+        output_file=output_file,
+        patch=patch,
+        curv_overlay_files=curv_overlay_files,
+        functional_data_file=functional_data_file,
+        orig_positions=orig_positions,
+        scale=scale,
+        rescale=rescale,
+        talairach_xfm=talairach_xfm,
+        normals=normals,
+        neighbors=neighbors,
+        xyz=xyz,
+        annotation_file=annotation_file,
+        parcstats_file=parcstats_file,
+        gifti_dataarray_num=gifti_dataarray_num,
+        label_file=label_file,
+        label_stats_file=label_stats_file,
+        combine_surfs=combine_surfs,
+        merge_gifti=merge_gifti,
+        split_gifti=split_gifti,
+        gifti_outdir=gifti_outdir,
+        delete_cmds=delete_cmds,
+        center=center,
+        vol_geom=vol_geom,
+        remove_vol_geom=remove_vol_geom,
+        to_surf=to_surf,
+        to_scanner=to_scanner,
+        to_tkr=to_tkr,
+        userealras=userealras,
+        usesurfras=usesurfras,
+        upsample=upsample,
+        volume=volume,
+        area=area,
+        angle=angle,
+        label_to_mask=label_to_mask,
+        cras_add=cras_add,
+        cras_subtract=cras_subtract,
+    )
+    return mris_convert_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_CONVERT_METADATA",
+    "MrisConvertOutputs",
+    "MrisConvertParameters",
+    "mris_convert",
+    "mris_convert_params",
+]