niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/connectome2tck.py

@@ -0,0 +1,583 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CONNECTOME2TCK_METADATA = Metadata(
+    id="ae2ef98104119bc0342c1596e2bea3d807ec75ef.boutiques",
+    name="connectome2tck",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Connectome2tckConfigParamsDictNoTag = typing.TypedDict('_Connectome2tckConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Connectome2tckConfigParamsDictTagged = typing.TypedDict('Connectome2tckConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Connectome2tckConfigParamsDict = _Connectome2tckConfigParamsDictNoTag | Connectome2tckConfigParamsDictTagged
+
+
+_Connectome2tckParamsDictNoTag = typing.TypedDict('_Connectome2tckParamsDictNoTag', {
+    "nodes": typing.NotRequired[list[int] | None],
+    "exclusive": bool,
+    "files": typing.NotRequired[str | None],
+    "exemplars": typing.NotRequired[InputPathType | None],
+    "keep_unassigned": bool,
+    "keep_self": bool,
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "prefix_tck_weights_out": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Connectome2tckConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "tracks_in": InputPathType,
+    "assignments_in": InputPathType,
+    "prefix_out": str,
+})
+Connectome2tckParamsDictTagged = typing.TypedDict('Connectome2tckParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/connectome2tck"],
+    "nodes": typing.NotRequired[list[int] | None],
+    "exclusive": bool,
+    "files": typing.NotRequired[str | None],
+    "exemplars": typing.NotRequired[InputPathType | None],
+    "keep_unassigned": bool,
+    "keep_self": bool,
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "prefix_tck_weights_out": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Connectome2tckConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "tracks_in": InputPathType,
+    "assignments_in": InputPathType,
+    "prefix_out": str,
+})
+Connectome2tckParamsDict = _Connectome2tckParamsDictNoTag | Connectome2tckParamsDictTagged
+
+
+def connectome2tck_config(
+    key: str,
+    value: str,
+) -> Connectome2tckConfigParamsDictTagged:
+    """
+    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 connectome2tck_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Connectome2tckConfigParamsDict` 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 connectome2tck_config_cargs(
+    params: Connectome2tckConfigParamsDict,
+    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 Connectome2tckOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Connectome2tckParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def connectome2tck_params(
+    tracks_in: InputPathType,
+    assignments_in: InputPathType,
+    prefix_out: str,
+    nodes: list[int] | None = None,
+    exclusive: bool = False,
+    files: str | None = None,
+    exemplars: InputPathType | None = None,
+    keep_unassigned: bool = False,
+    keep_self: bool = False,
+    tck_weights_in: InputPathType | None = None,
+    prefix_tck_weights_out: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Connectome2tckConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Connectome2tckParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        tracks_in: the input track file.
+        assignments_in: input text file containing the node assignments for\
+            each streamline.
+        prefix_out: the output file / prefix.
+        nodes: only select tracks that involve a set of nodes of interest\
+            (provide as a comma-separated list of integers).
+        exclusive: only select tracks that exclusively connect nodes from\
+            within the list of nodes of interest.
+        files: select how the resulting streamlines will be grouped in output\
+            files. Options are: per_edge, per_node, single (default: per_edge).
+        exemplars: generate a mean connection exemplar per edge, rather than\
+            keeping all streamlines (the parcellation node image must be provided\
+            in order to constrain the exemplar endpoints).
+        keep_unassigned: by default, the program discards those streamlines\
+            that are not successfully assigned to a node. Set this option to\
+            generate corresponding outputs containing these streamlines (labelled\
+            as node index 0).
+        keep_self: by default, the program will not output streamlines that\
+            connect to the same node at both ends. Set this option to instead keep\
+            these self-connections.
+        tck_weights_in: specify a text scalar file containing the streamline\
+            weights.
+        prefix_tck_weights_out: provide a prefix for outputting a text file\
+            corresponding to each output file, each containing only the streamline\
+            weights relevant for that track 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 = {
+        "@type": "mrtrix/connectome2tck",
+        "exclusive": exclusive,
+        "keep_unassigned": keep_unassigned,
+        "keep_self": keep_self,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "tracks_in": tracks_in,
+        "assignments_in": assignments_in,
+        "prefix_out": prefix_out,
+    }
+    if nodes is not None:
+        params["nodes"] = nodes
+    if files is not None:
+        params["files"] = files
+    if exemplars is not None:
+        params["exemplars"] = exemplars
+    if tck_weights_in is not None:
+        params["tck_weights_in"] = tck_weights_in
+    if prefix_tck_weights_out is not None:
+        params["prefix_tck_weights_out"] = prefix_tck_weights_out
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def connectome2tck_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Connectome2tckParamsDict` 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("nodes", None) is not None:
+        if not isinstance(params["nodes"], list):
+            raise StyxValidationError(f'`nodes` has the wrong type: Received `{type(params.get("nodes", None))}` expected `list[int] | None`')
+        for e in params["nodes"]:
+            if not isinstance(e, int):
+                raise StyxValidationError(f'`nodes` has the wrong type: Received `{type(params.get("nodes", None))}` expected `list[int] | None`')
+    if params.get("exclusive", False) is None:
+        raise StyxValidationError("`exclusive` must not be None")
+    if not isinstance(params["exclusive"], bool):
+        raise StyxValidationError(f'`exclusive` has the wrong type: Received `{type(params.get("exclusive", False))}` expected `bool`')
+    if params.get("files", None) is not None:
+        if not isinstance(params["files"], str):
+            raise StyxValidationError(f'`files` has the wrong type: Received `{type(params.get("files", None))}` expected `str | None`')
+    if params.get("exemplars", None) is not None:
+        if not isinstance(params["exemplars"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`exemplars` has the wrong type: Received `{type(params.get("exemplars", None))}` expected `InputPathType | None`')
+    if params.get("keep_unassigned", False) is None:
+        raise StyxValidationError("`keep_unassigned` must not be None")
+    if not isinstance(params["keep_unassigned"], bool):
+        raise StyxValidationError(f'`keep_unassigned` has the wrong type: Received `{type(params.get("keep_unassigned", False))}` expected `bool`')
+    if params.get("keep_self", False) is None:
+        raise StyxValidationError("`keep_self` must not be None")
+    if not isinstance(params["keep_self"], bool):
+        raise StyxValidationError(f'`keep_self` has the wrong type: Received `{type(params.get("keep_self", False))}` expected `bool`')
+    if params.get("tck_weights_in", None) is not None:
+        if not isinstance(params["tck_weights_in"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`tck_weights_in` has the wrong type: Received `{type(params.get("tck_weights_in", None))}` expected `InputPathType | None`')
+    if params.get("prefix_tck_weights_out", None) is not None:
+        if not isinstance(params["prefix_tck_weights_out"], str):
+            raise StyxValidationError(f'`prefix_tck_weights_out` has the wrong type: Received `{type(params.get("prefix_tck_weights_out", None))}` expected `str | None`')
+    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[Connectome2tckConfigParamsDict] | None`')
+        for e in params["config"]:
+            connectome2tck_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_in", None) is None:
+        raise StyxValidationError("`tracks_in` must not be None")
+    if not isinstance(params["tracks_in"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`tracks_in` has the wrong type: Received `{type(params.get("tracks_in", None))}` expected `InputPathType`')
+    if params.get("assignments_in", None) is None:
+        raise StyxValidationError("`assignments_in` must not be None")
+    if not isinstance(params["assignments_in"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`assignments_in` has the wrong type: Received `{type(params.get("assignments_in", None))}` expected `InputPathType`')
+    if params.get("prefix_out", None) is None:
+        raise StyxValidationError("`prefix_out` must not be None")
+    if not isinstance(params["prefix_out"], str):
+        raise StyxValidationError(f'`prefix_out` has the wrong type: Received `{type(params.get("prefix_out", None))}` expected `str`')
+
+
+def connectome2tck_cargs(
+    params: Connectome2tckParamsDict,
+    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("connectome2tck")
+    if params.get("nodes", None) is not None:
+        cargs.extend([
+            "-nodes",
+            ",".join(map(str, params.get("nodes", None)))
+        ])
+    if params.get("exclusive", False):
+        cargs.append("-exclusive")
+    if params.get("files", None) is not None:
+        cargs.extend([
+            "-files",
+            params.get("files", None)
+        ])
+    if params.get("exemplars", None) is not None:
+        cargs.extend([
+            "-exemplars",
+            execution.input_file(params.get("exemplars", None))
+        ])
+    if params.get("keep_unassigned", False):
+        cargs.append("-keep_unassigned")
+    if params.get("keep_self", False):
+        cargs.append("-keep_self")
+    if params.get("tck_weights_in", None) is not None:
+        cargs.extend([
+            "-tck_weights_in",
+            execution.input_file(params.get("tck_weights_in", None))
+        ])
+    if params.get("prefix_tck_weights_out", None) is not None:
+        cargs.extend([
+            "-prefix_tck_weights_out",
+            params.get("prefix_tck_weights_out", None)
+        ])
+    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 [connectome2tck_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_in", None)))
+    cargs.append(execution.input_file(params.get("assignments_in", None)))
+    cargs.append(params.get("prefix_out", None))
+    return cargs
+
+
+def connectome2tck_outputs(
+    params: Connectome2tckParamsDict,
+    execution: Execution,
+) -> Connectome2tckOutputs:
+    """
+    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 = Connectome2tckOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def connectome2tck_execute(
+    params: Connectome2tckParamsDict,
+    runner: Runner | None = None,
+) -> Connectome2tckOutputs:
+    """
+    connectome2tck
+    
+    Extract streamlines from a tractogram based on their assignment to
+    parcellated nodes.
+    
+    The compulsory input file "assignments_in" should contain a text file where
+    there is one row for each streamline, and each row contains a list of
+    numbers corresponding to the parcels to which that streamline was assigned
+    (most typically there will be two entries per streamline, one for each
+    endpoint; but this is not strictly a requirement). This file will most
+    typically be generated using the tck2connectome command with the
+    -out_assignments option.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Connectome2tckOutputs`).
+    """
+    connectome2tck_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONNECTOME2TCK_METADATA)
+    params = execution.params(params)
+    cargs = connectome2tck_cargs(params, execution)
+    ret = connectome2tck_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def connectome2tck(
+    tracks_in: InputPathType,
+    assignments_in: InputPathType,
+    prefix_out: str,
+    nodes: list[int] | None = None,
+    exclusive: bool = False,
+    files: str | None = None,
+    exemplars: InputPathType | None = None,
+    keep_unassigned: bool = False,
+    keep_self: bool = False,
+    tck_weights_in: InputPathType | None = None,
+    prefix_tck_weights_out: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Connectome2tckConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Connectome2tckOutputs:
+    """
+    connectome2tck
+    
+    Extract streamlines from a tractogram based on their assignment to
+    parcellated nodes.
+    
+    The compulsory input file "assignments_in" should contain a text file where
+    there is one row for each streamline, and each row contains a list of
+    numbers corresponding to the parcels to which that streamline was assigned
+    (most typically there will be two entries per streamline, one for each
+    endpoint; but this is not strictly a requirement). This file will most
+    typically be generated using the tck2connectome command with the
+    -out_assignments option.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        tracks_in: the input track file.
+        assignments_in: input text file containing the node assignments for\
+            each streamline.
+        prefix_out: the output file / prefix.
+        nodes: only select tracks that involve a set of nodes of interest\
+            (provide as a comma-separated list of integers).
+        exclusive: only select tracks that exclusively connect nodes from\
+            within the list of nodes of interest.
+        files: select how the resulting streamlines will be grouped in output\
+            files. Options are: per_edge, per_node, single (default: per_edge).
+        exemplars: generate a mean connection exemplar per edge, rather than\
+            keeping all streamlines (the parcellation node image must be provided\
+            in order to constrain the exemplar endpoints).
+        keep_unassigned: by default, the program discards those streamlines\
+            that are not successfully assigned to a node. Set this option to\
+            generate corresponding outputs containing these streamlines (labelled\
+            as node index 0).
+        keep_self: by default, the program will not output streamlines that\
+            connect to the same node at both ends. Set this option to instead keep\
+            these self-connections.
+        tck_weights_in: specify a text scalar file containing the streamline\
+            weights.
+        prefix_tck_weights_out: provide a prefix for outputting a text file\
+            corresponding to each output file, each containing only the streamline\
+            weights relevant for that track 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 `Connectome2tckOutputs`).
+    """
+    params = connectome2tck_params(
+        nodes=nodes,
+        exclusive=exclusive,
+        files=files,
+        exemplars=exemplars,
+        keep_unassigned=keep_unassigned,
+        keep_self=keep_self,
+        tck_weights_in=tck_weights_in,
+        prefix_tck_weights_out=prefix_tck_weights_out,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        tracks_in=tracks_in,
+        assignments_in=assignments_in,
+        prefix_out=prefix_out,
+    )
+    return connectome2tck_execute(params, runner)
+
+
+__all__ = [
+    "CONNECTOME2TCK_METADATA",
+    "Connectome2tckConfigParamsDict",
+    "Connectome2tckConfigParamsDictTagged",
+    "Connectome2tckOutputs",
+    "Connectome2tckParamsDict",
+    "Connectome2tckParamsDictTagged",
+    "connectome2tck",
+    "connectome2tck_config",
+    "connectome2tck_execute",
+    "connectome2tck_params",
+]