niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tcksample.py

@@ -0,0 +1,497 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TCKSAMPLE_METADATA = Metadata(
+    id="274c00456de615fd846529a52bdcb4684c1c52eb.boutiques",
+    name="tcksample",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_TcksampleConfigParamsDictNoTag = typing.TypedDict('_TcksampleConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+TcksampleConfigParamsDictTagged = typing.TypedDict('TcksampleConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+TcksampleConfigParamsDict = _TcksampleConfigParamsDictNoTag | TcksampleConfigParamsDictTagged
+
+
+_TcksampleParamsDictNoTag = typing.TypedDict('_TcksampleParamsDictNoTag', {
+    "stat_tck": typing.NotRequired[str | None],
+    "nointerp": bool,
+    "precise": bool,
+    "use_tdi_fraction": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TcksampleConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "tracks": InputPathType,
+    "image": InputPathType,
+    "values": str,
+})
+TcksampleParamsDictTagged = typing.TypedDict('TcksampleParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/tcksample"],
+    "stat_tck": typing.NotRequired[str | None],
+    "nointerp": bool,
+    "precise": bool,
+    "use_tdi_fraction": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TcksampleConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "tracks": InputPathType,
+    "image": InputPathType,
+    "values": str,
+})
+TcksampleParamsDict = _TcksampleParamsDictNoTag | TcksampleParamsDictTagged
+
+
+def tcksample_config(
+    key: str,
+    value: str,
+) -> TcksampleConfigParamsDictTagged:
+    """
+    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 = {
+        "@type": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def tcksample_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TcksampleConfigParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("key", None) is None:
+        raise StyxValidationError("`key` must not be None")
+    if not isinstance(params["key"], str):
+        raise StyxValidationError(f'`key` has the wrong type: Received `{type(params.get("key", None))}` expected `str`')
+    if params.get("value", None) is None:
+        raise StyxValidationError("`value` must not be None")
+    if not isinstance(params["value"], str):
+        raise StyxValidationError(f'`value` has the wrong type: Received `{type(params.get("value", None))}` expected `str`')
+
+
+def tcksample_config_cargs(
+    params: TcksampleConfigParamsDict,
+    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", None))
+    cargs.append(params.get("value", None))
+    return cargs
+
+
+class TcksampleOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `TcksampleParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    values_: OutputPathType
+    """the output sampled values"""
+
+
+def tcksample_params(
+    tracks: InputPathType,
+    image: InputPathType,
+    values_: str,
+    stat_tck: str | None = None,
+    nointerp: bool = False,
+    precise: bool = False,
+    use_tdi_fraction: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TcksampleConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TcksampleParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        tracks: the input track file.
+        image: the image to be sampled.
+        values_: the output sampled values.
+        stat_tck: compute some statistic from the values along each streamline\
+            (options are: mean,median,min,max).
+        nointerp: do not use trilinear interpolation when sampling image values.
+        precise: use the precise mechanism for mapping streamlines to voxels\
+            (obviates the need for trilinear interpolation) (only applicable if\
+            some per-streamline statistic is requested).
+        use_tdi_fraction: each streamline is assigned a fraction of the image\
+            intensity in each voxel based on the fraction of the track density\
+            contributed by that streamline (this is only appropriate for processing\
+            a whole-brain tractogram, and images for which the quantiative\
+            parameter is additive).
+        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 = {
+        "@type": "mrtrix/tcksample",
+        "nointerp": nointerp,
+        "precise": precise,
+        "use_tdi_fraction": use_tdi_fraction,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "tracks": tracks,
+        "image": image,
+        "values": values_,
+    }
+    if stat_tck is not None:
+        params["stat_tck"] = stat_tck
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tcksample_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TcksampleParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("stat_tck", None) is not None:
+        if not isinstance(params["stat_tck"], str):
+            raise StyxValidationError(f'`stat_tck` has the wrong type: Received `{type(params.get("stat_tck", None))}` expected `str | None`')
+    if params.get("nointerp", False) is None:
+        raise StyxValidationError("`nointerp` must not be None")
+    if not isinstance(params["nointerp"], bool):
+        raise StyxValidationError(f'`nointerp` has the wrong type: Received `{type(params.get("nointerp", False))}` expected `bool`')
+    if params.get("precise", False) is None:
+        raise StyxValidationError("`precise` must not be None")
+    if not isinstance(params["precise"], bool):
+        raise StyxValidationError(f'`precise` has the wrong type: Received `{type(params.get("precise", False))}` expected `bool`')
+    if params.get("use_tdi_fraction", False) is None:
+        raise StyxValidationError("`use_tdi_fraction` must not be None")
+    if not isinstance(params["use_tdi_fraction"], bool):
+        raise StyxValidationError(f'`use_tdi_fraction` has the wrong type: Received `{type(params.get("use_tdi_fraction", False))}` expected `bool`')
+    if params.get("info", False) is None:
+        raise StyxValidationError("`info` must not be None")
+    if not isinstance(params["info"], bool):
+        raise StyxValidationError(f'`info` has the wrong type: Received `{type(params.get("info", False))}` expected `bool`')
+    if params.get("quiet", False) is None:
+        raise StyxValidationError("`quiet` must not be None")
+    if not isinstance(params["quiet"], bool):
+        raise StyxValidationError(f'`quiet` has the wrong type: Received `{type(params.get("quiet", False))}` expected `bool`')
+    if params.get("debug", False) is None:
+        raise StyxValidationError("`debug` must not be None")
+    if not isinstance(params["debug"], bool):
+        raise StyxValidationError(f'`debug` has the wrong type: Received `{type(params.get("debug", False))}` expected `bool`')
+    if params.get("force", False) is None:
+        raise StyxValidationError("`force` must not be None")
+    if not isinstance(params["force"], bool):
+        raise StyxValidationError(f'`force` has the wrong type: Received `{type(params.get("force", False))}` expected `bool`')
+    if params.get("nthreads", None) is not None:
+        if not isinstance(params["nthreads"], int):
+            raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `int | None`')
+    if params.get("config", None) is not None:
+        if not isinstance(params["config"], list):
+            raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[TcksampleConfigParamsDict] | None`')
+        for e in params["config"]:
+            tcksample_config_validate(e)
+    if params.get("help", False) is None:
+        raise StyxValidationError("`help` must not be None")
+    if not isinstance(params["help"], bool):
+        raise StyxValidationError(f'`help` has the wrong type: Received `{type(params.get("help", False))}` expected `bool`')
+    if params.get("version", False) is None:
+        raise StyxValidationError("`version` must not be None")
+    if not isinstance(params["version"], bool):
+        raise StyxValidationError(f'`version` has the wrong type: Received `{type(params.get("version", False))}` expected `bool`')
+    if params.get("tracks", None) is None:
+        raise StyxValidationError("`tracks` must not be None")
+    if not isinstance(params["tracks"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`tracks` has the wrong type: Received `{type(params.get("tracks", None))}` expected `InputPathType`')
+    if params.get("image", None) is None:
+        raise StyxValidationError("`image` must not be None")
+    if not isinstance(params["image"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`image` has the wrong type: Received `{type(params.get("image", None))}` expected `InputPathType`')
+    if params.get("values", None) is None:
+        raise StyxValidationError("`values` must not be None")
+    if not isinstance(params["values"], str):
+        raise StyxValidationError(f'`values` has the wrong type: Received `{type(params.get("values", None))}` expected `str`')
+
+
+def tcksample_cargs(
+    params: TcksampleParamsDict,
+    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("tcksample")
+    if params.get("stat_tck", None) is not None:
+        cargs.extend([
+            "-stat_tck",
+            params.get("stat_tck", None)
+        ])
+    if params.get("nointerp", False):
+        cargs.append("-nointerp")
+    if params.get("precise", False):
+        cargs.append("-precise")
+    if params.get("use_tdi_fraction", False):
+        cargs.append("-use_tdi_fraction")
+    if params.get("info", False):
+        cargs.append("-info")
+    if params.get("quiet", False):
+        cargs.append("-quiet")
+    if params.get("debug", False):
+        cargs.append("-debug")
+    if params.get("force", False):
+        cargs.append("-force")
+    if params.get("nthreads", None) is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads", None))
+        ])
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [tcksample_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
+        cargs.append("-help")
+    if params.get("version", False):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("tracks", None)))
+    cargs.append(execution.input_file(params.get("image", None)))
+    cargs.append(params.get("values", None))
+    return cargs
+
+
+def tcksample_outputs(
+    params: TcksampleParamsDict,
+    execution: Execution,
+) -> TcksampleOutputs:
+    """
+    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 = TcksampleOutputs(
+        root=execution.output_file("."),
+        values_=execution.output_file(params.get("values", None)),
+    )
+    return ret
+
+
+def tcksample_execute(
+    params: TcksampleParamsDict,
+    runner: Runner | None = None,
+) -> TcksampleOutputs:
+    """
+    tcksample
+    
+    Sample values of an associated image along tracks.
+    
+    By default, the value of the underlying image at each point along the track
+    is written to either an ASCII file (with all values for each track on the
+    same line), or a track scalar file (.tsf). Alternatively, some statistic can
+    be taken from the values along each streamline and written to a vector file.
+    
+    References:
+    
+    * If using -precise option: Smith, R. E.; Tournier, J.-D.; Calamante, F. &
+    Connelly, A. SIFT: Spherical-deconvolution informed filtering of
+    tractograms. NeuroImage, 2013, 67, 298-312.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TcksampleOutputs`).
+    """
+    tcksample_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKSAMPLE_METADATA)
+    params = execution.params(params)
+    cargs = tcksample_cargs(params, execution)
+    ret = tcksample_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tcksample(
+    tracks: InputPathType,
+    image: InputPathType,
+    values_: str,
+    stat_tck: str | None = None,
+    nointerp: bool = False,
+    precise: bool = False,
+    use_tdi_fraction: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TcksampleConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TcksampleOutputs:
+    """
+    tcksample
+    
+    Sample values of an associated image along tracks.
+    
+    By default, the value of the underlying image at each point along the track
+    is written to either an ASCII file (with all values for each track on the
+    same line), or a track scalar file (.tsf). Alternatively, some statistic can
+    be taken from the values along each streamline and written to a vector file.
+    
+    References:
+    
+    * If using -precise option: Smith, R. E.; Tournier, J.-D.; Calamante, F. &
+    Connelly, A. SIFT: Spherical-deconvolution informed filtering of
+    tractograms. NeuroImage, 2013, 67, 298-312.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        tracks: the input track file.
+        image: the image to be sampled.
+        values_: the output sampled values.
+        stat_tck: compute some statistic from the values along each streamline\
+            (options are: mean,median,min,max).
+        nointerp: do not use trilinear interpolation when sampling image values.
+        precise: use the precise mechanism for mapping streamlines to voxels\
+            (obviates the need for trilinear interpolation) (only applicable if\
+            some per-streamline statistic is requested).
+        use_tdi_fraction: each streamline is assigned a fraction of the image\
+            intensity in each voxel based on the fraction of the track density\
+            contributed by that streamline (this is only appropriate for processing\
+            a whole-brain tractogram, and images for which the quantiative\
+            parameter is additive).
+        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 `TcksampleOutputs`).
+    """
+    params = tcksample_params(
+        stat_tck=stat_tck,
+        nointerp=nointerp,
+        precise=precise,
+        use_tdi_fraction=use_tdi_fraction,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        tracks=tracks,
+        image=image,
+        values_=values_,
+    )
+    return tcksample_execute(params, runner)
+
+
+__all__ = [
+    "TCKSAMPLE_METADATA",
+    "TcksampleConfigParamsDict",
+    "TcksampleConfigParamsDictTagged",
+    "TcksampleOutputs",
+    "TcksampleParamsDict",
+    "TcksampleParamsDictTagged",
+    "tcksample",
+    "tcksample_config",
+    "tcksample_execute",
+    "tcksample_params",
+]