niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/connectome2tck.py

@@ -0,0 +1,470 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CONNECTOME2TCK_METADATA = Metadata(
+    id="68591f4f9a13309e07f97bb4a65436101f61042f.boutiques",
+    name="connectome2tck",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Connectome2tckConfigParameters = typing.TypedDict('Connectome2tckConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Connectome2tckParameters = typing.TypedDict('Connectome2tckParameters', {
+    "__STYX_TYPE__": typing.Literal["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[Connectome2tckConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "tracks_in": InputPathType,
+    "assignments_in": InputPathType,
+    "prefix_out": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "connectome2tck": connectome2tck_cargs,
+        "config": connectome2tck_config_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)
+
+
+def connectome2tck_config_params(
+    key: str,
+    value: str,
+) -> Connectome2tckConfigParameters:
+    """
+    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 connectome2tck_config_cargs(
+    params: Connectome2tckConfigParameters,
+    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
+
+
+class Connectome2tckOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `connectome2tck(...)`.
+    """
+    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[Connectome2tckConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Connectome2tckParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "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_cargs(
+    params: Connectome2tckParameters,
+    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") is not None:
+        cargs.extend([
+            "-nodes",
+            ",".join(map(str, params.get("nodes")))
+        ])
+    if params.get("exclusive"):
+        cargs.append("-exclusive")
+    if params.get("files") is not None:
+        cargs.extend([
+            "-files",
+            params.get("files")
+        ])
+    if params.get("exemplars") is not None:
+        cargs.extend([
+            "-exemplars",
+            execution.input_file(params.get("exemplars"))
+        ])
+    if params.get("keep_unassigned"):
+        cargs.append("-keep_unassigned")
+    if params.get("keep_self"):
+        cargs.append("-keep_self")
+    if params.get("tck_weights_in") is not None:
+        cargs.extend([
+            "-tck_weights_in",
+            execution.input_file(params.get("tck_weights_in"))
+        ])
+    if params.get("prefix_tck_weights_out") is not None:
+        cargs.extend([
+            "-prefix_tck_weights_out",
+            params.get("prefix_tck_weights_out")
+        ])
+    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.append(execution.input_file(params.get("tracks_in")))
+    cargs.append(execution.input_file(params.get("assignments_in")))
+    cargs.append(params.get("prefix_out"))
+    return cargs
+
+
+def connectome2tck_outputs(
+    params: Connectome2tckParameters,
+    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: Connectome2tckParameters,
+    execution: Execution,
+) -> Connectome2tckOutputs:
+    """
+    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.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Connectome2tckOutputs`).
+    """
+    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[Connectome2tckConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Connectome2tckOutputs:
+    """
+    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`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONNECTOME2TCK_METADATA)
+    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, execution)
+
+
+__all__ = [
+    "CONNECTOME2TCK_METADATA",
+    "Connectome2tckConfigParameters",
+    "Connectome2tckOutputs",
+    "Connectome2tckParameters",
+    "connectome2tck",
+    "connectome2tck_config_params",
+    "connectome2tck_params",
+]