niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tckconvert.py

@@ -0,0 +1,580 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TCKCONVERT_METADATA = Metadata(
+    id="e099f163628c4f4e1f744a964fec71d2c4cd255c.boutiques",
+    name="tckconvert",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+TckconvertConfigParameters = typing.TypedDict('TckconvertConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+TckconvertVariousStringParameters = typing.TypedDict('TckconvertVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+TckconvertVariousFileParameters = typing.TypedDict('TckconvertVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+TckconvertParameters = typing.TypedDict('TckconvertParameters', {
+    "__STYX_TYPE__": typing.Literal["tckconvert"],
+    "scanner2voxel": typing.NotRequired[InputPathType | None],
+    "scanner2image": typing.NotRequired[InputPathType | None],
+    "voxel2scanner": typing.NotRequired[InputPathType | None],
+    "image2scanner": typing.NotRequired[InputPathType | None],
+    "sides": typing.NotRequired[int | None],
+    "increment": typing.NotRequired[int | None],
+    "dec": bool,
+    "radius": typing.NotRequired[float | None],
+    "ascii": bool,
+    "binary": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckconvertConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": typing.Union[TckconvertVariousStringParameters, TckconvertVariousFileParameters],
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "tckconvert": tckconvert_cargs,
+        "config": tckconvert_config_cargs,
+        "VariousString": tckconvert_various_string_cargs,
+        "VariousFile": tckconvert_various_file_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 {
+        "tckconvert": tckconvert_outputs,
+    }.get(t)
+
+
+def tckconvert_config_params(
+    key: str,
+    value: str,
+) -> TckconvertConfigParameters:
+    """
+    Build parameters.
+    
+    Args:
+        key: temporarily set the value of an MRtrix config file entry.
+        value: temporarily set the value of an MRtrix config file entry.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def tckconvert_config_cargs(
+    params: TckconvertConfigParameters,
+    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("-config")
+    cargs.append(params.get("key"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+def tckconvert_various_string_params(
+    obj: str,
+) -> TckconvertVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def tckconvert_various_string_cargs(
+    params: TckconvertVariousStringParameters,
+    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(params.get("obj"))
+    return cargs
+
+
+def tckconvert_various_file_params(
+    obj: InputPathType,
+) -> TckconvertVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def tckconvert_various_file_cargs(
+    params: TckconvertVariousFileParameters,
+    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(execution.input_file(params.get("obj")))
+    return cargs
+
+
+class TckconvertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `tckconvert(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output track file."""
+
+
+def tckconvert_params(
+    input_: typing.Union[TckconvertVariousStringParameters, TckconvertVariousFileParameters],
+    output: str,
+    scanner2voxel: InputPathType | None = None,
+    scanner2image: InputPathType | None = None,
+    voxel2scanner: InputPathType | None = None,
+    image2scanner: InputPathType | None = None,
+    sides: int | None = None,
+    increment: int | None = None,
+    dec: bool = False,
+    radius: float | None = None,
+    ascii_: bool = False,
+    binary: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckconvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TckconvertParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input track file.
+        output: the output track file.
+        scanner2voxel: if specified, the properties of this image will be used\
+            to convert track point positions from real (scanner) coordinates into\
+            voxel coordinates.
+        scanner2image: if specified, the properties of this image will be used\
+            to convert track point positions from real (scanner) coordinates into\
+            image coordinates (in mm).
+        voxel2scanner: if specified, the properties of this image will be used\
+            to convert track point positions from voxel coordinates into real\
+            (scanner) coordinates.
+        image2scanner: if specified, the properties of this image will be used\
+            to convert track point positions from image coordinates (in mm) into\
+            real (scanner) coordinates.
+        sides: number of sides for streamlines.
+        increment: generate streamline points at every (increment) points.
+        dec: add DEC as a primvar.
+        radius: radius of the streamlines.
+        ascii_: write an ASCII VTK file (this is the default).
+        binary: write a binary VTK file.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "tckconvert",
+        "dec": dec,
+        "ascii": ascii_,
+        "binary": binary,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if scanner2voxel is not None:
+        params["scanner2voxel"] = scanner2voxel
+    if scanner2image is not None:
+        params["scanner2image"] = scanner2image
+    if voxel2scanner is not None:
+        params["voxel2scanner"] = voxel2scanner
+    if image2scanner is not None:
+        params["image2scanner"] = image2scanner
+    if sides is not None:
+        params["sides"] = sides
+    if increment is not None:
+        params["increment"] = increment
+    if radius is not None:
+        params["radius"] = radius
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tckconvert_cargs(
+    params: TckconvertParameters,
+    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("tckconvert")
+    if params.get("scanner2voxel") is not None:
+        cargs.extend([
+            "-scanner2voxel",
+            execution.input_file(params.get("scanner2voxel"))
+        ])
+    if params.get("scanner2image") is not None:
+        cargs.extend([
+            "-scanner2image",
+            execution.input_file(params.get("scanner2image"))
+        ])
+    if params.get("voxel2scanner") is not None:
+        cargs.extend([
+            "-voxel2scanner",
+            execution.input_file(params.get("voxel2scanner"))
+        ])
+    if params.get("image2scanner") is not None:
+        cargs.extend([
+            "-image2scanner",
+            execution.input_file(params.get("image2scanner"))
+        ])
+    if params.get("sides") is not None:
+        cargs.extend([
+            "-sides",
+            str(params.get("sides"))
+        ])
+    if params.get("increment") is not None:
+        cargs.extend([
+            "-increment",
+            str(params.get("increment"))
+        ])
+    if params.get("dec"):
+        cargs.append("-dec")
+    if params.get("radius") is not None:
+        cargs.extend([
+            "-radius",
+            str(params.get("radius"))
+        ])
+    if params.get("ascii"):
+        cargs.append("-ascii")
+    if params.get("binary"):
+        cargs.append("-binary")
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.extend(dyn_cargs(params.get("input")["__STYXTYPE__"])(params.get("input"), execution))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def tckconvert_outputs(
+    params: TckconvertParameters,
+    execution: Execution,
+) -> TckconvertOutputs:
+    """
+    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 = TckconvertOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def tckconvert_execute(
+    params: TckconvertParameters,
+    execution: Execution,
+) -> TckconvertOutputs:
+    """
+    Convert between different track file formats.
+    
+    The program currently supports MRtrix .tck files (input/output), ascii text
+    files (input/output), VTK polydata files (input/output), and RenderMan RIB
+    (export only).
+    
+    Note that ascii files will be stored with one streamline per numbered file.
+    To support this, the command will use the multi-file numbering syntax, where
+    square brackets denote the position of the numbering for the files, for
+    example:
+    
+    $ tckconvert input.tck output-'[]'.txt
+    
+    will produce files named output-0000.txt, output-0001.txt, output-0002.txt,
+    ...
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `TckconvertOutputs`).
+    """
+    params = execution.params(params)
+    cargs = tckconvert_cargs(params, execution)
+    ret = tckconvert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tckconvert(
+    input_: typing.Union[TckconvertVariousStringParameters, TckconvertVariousFileParameters],
+    output: str,
+    scanner2voxel: InputPathType | None = None,
+    scanner2image: InputPathType | None = None,
+    voxel2scanner: InputPathType | None = None,
+    image2scanner: InputPathType | None = None,
+    sides: int | None = None,
+    increment: int | None = None,
+    dec: bool = False,
+    radius: float | None = None,
+    ascii_: bool = False,
+    binary: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckconvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TckconvertOutputs:
+    """
+    Convert between different track file formats.
+    
+    The program currently supports MRtrix .tck files (input/output), ascii text
+    files (input/output), VTK polydata files (input/output), and RenderMan RIB
+    (export only).
+    
+    Note that ascii files will be stored with one streamline per numbered file.
+    To support this, the command will use the multi-file numbering syntax, where
+    square brackets denote the position of the numbering for the files, for
+    example:
+    
+    $ tckconvert input.tck output-'[]'.txt
+    
+    will produce files named output-0000.txt, output-0001.txt, output-0002.txt,
+    ...
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input track file.
+        output: the output track file.
+        scanner2voxel: if specified, the properties of this image will be used\
+            to convert track point positions from real (scanner) coordinates into\
+            voxel coordinates.
+        scanner2image: if specified, the properties of this image will be used\
+            to convert track point positions from real (scanner) coordinates into\
+            image coordinates (in mm).
+        voxel2scanner: if specified, the properties of this image will be used\
+            to convert track point positions from voxel coordinates into real\
+            (scanner) coordinates.
+        image2scanner: if specified, the properties of this image will be used\
+            to convert track point positions from image coordinates (in mm) into\
+            real (scanner) coordinates.
+        sides: number of sides for streamlines.
+        increment: generate streamline points at every (increment) points.
+        dec: add DEC as a primvar.
+        radius: radius of the streamlines.
+        ascii_: write an ASCII VTK file (this is the default).
+        binary: write a binary VTK file.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TckconvertOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKCONVERT_METADATA)
+    params = tckconvert_params(
+        scanner2voxel=scanner2voxel,
+        scanner2image=scanner2image,
+        voxel2scanner=voxel2scanner,
+        image2scanner=image2scanner,
+        sides=sides,
+        increment=increment,
+        dec=dec,
+        radius=radius,
+        ascii_=ascii_,
+        binary=binary,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return tckconvert_execute(params, execution)
+
+
+__all__ = [
+    "TCKCONVERT_METADATA",
+    "TckconvertConfigParameters",
+    "TckconvertOutputs",
+    "TckconvertParameters",
+    "TckconvertVariousFileParameters",
+    "TckconvertVariousStringParameters",
+    "tckconvert",
+    "tckconvert_config_params",
+    "tckconvert_params",
+    "tckconvert_various_file_params",
+    "tckconvert_various_string_params",
+]