niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tckstats.py

@@ -0,0 +1,550 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TCKSTATS_METADATA = Metadata(
+    id="1c376e03915b6fa825105cf6a3a1f00bd7cafd03.boutiques",
+    name="tckstats",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_TckstatsOutputParamsDictNoTag = typing.TypedDict('_TckstatsOutputParamsDictNoTag', {
+    "field": str,
+})
+TckstatsOutputParamsDictTagged = typing.TypedDict('TckstatsOutputParamsDictTagged', {
+    "@type": typing.Literal["output"],
+    "field": str,
+})
+TckstatsOutputParamsDict = _TckstatsOutputParamsDictNoTag | TckstatsOutputParamsDictTagged
+
+
+_TckstatsConfigParamsDictNoTag = typing.TypedDict('_TckstatsConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+TckstatsConfigParamsDictTagged = typing.TypedDict('TckstatsConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+TckstatsConfigParamsDict = _TckstatsConfigParamsDictNoTag | TckstatsConfigParamsDictTagged
+
+
+_TckstatsParamsDictNoTag = typing.TypedDict('_TckstatsParamsDictNoTag', {
+    "output": typing.NotRequired[list[TckstatsOutputParamsDict] | None],
+    "histogram": typing.NotRequired[str | None],
+    "dump": typing.NotRequired[str | None],
+    "ignorezero": bool,
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckstatsConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "tracks_in": InputPathType,
+})
+TckstatsParamsDictTagged = typing.TypedDict('TckstatsParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/tckstats"],
+    "output": typing.NotRequired[list[TckstatsOutputParamsDict] | None],
+    "histogram": typing.NotRequired[str | None],
+    "dump": typing.NotRequired[str | None],
+    "ignorezero": bool,
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckstatsConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "tracks_in": InputPathType,
+})
+TckstatsParamsDict = _TckstatsParamsDictNoTag | TckstatsParamsDictTagged
+
+
+def tckstats_output(
+    field: str,
+) -> TckstatsOutputParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        field: output only the field specified. Multiple such options can be\
+            supplied if required. Choices are: mean, median, std, min, max, count.\
+            Useful for use in scripts.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "output",
+        "field": field,
+    }
+    return params
+
+
+def tckstats_output_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TckstatsOutputParamsDict` 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("field", None) is None:
+        raise StyxValidationError("`field` must not be None")
+    if not isinstance(params["field"], str):
+        raise StyxValidationError(f'`field` has the wrong type: Received `{type(params.get("field", None))}` expected `str`')
+
+
+def tckstats_output_cargs(
+    params: TckstatsOutputParamsDict,
+    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("-output")
+    cargs.append(params.get("field", None))
+    return cargs
+
+
+def tckstats_config(
+    key: str,
+    value: str,
+) -> TckstatsConfigParamsDictTagged:
+    """
+    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 tckstats_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TckstatsConfigParamsDict` 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 tckstats_config_cargs(
+    params: TckstatsConfigParamsDict,
+    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 TckstatsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `TckstatsParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    histogram: OutputPathType | None
+    """output a histogram of streamline lengths """
+    dump: OutputPathType | None
+    """dump the streamlines lengths to a text file """
+
+
+def tckstats_params(
+    tracks_in: InputPathType,
+    output: list[TckstatsOutputParamsDict] | None = None,
+    histogram: str | None = None,
+    dump: str | None = None,
+    ignorezero: bool = False,
+    tck_weights_in: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckstatsConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TckstatsParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        tracks_in: the input track file.
+        output: output only the field specified. Multiple such options can be\
+            supplied if required. Choices are: mean, median, std, min, max, count.\
+            Useful for use in scripts.
+        histogram: output a histogram of streamline lengths.
+        dump: dump the streamlines lengths to a text file.
+        ignorezero: do not generate a warning if the track file contains\
+            streamlines with zero length.
+        tck_weights_in: specify a text scalar file containing the streamline\
+            weights.
+        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/tckstats",
+        "ignorezero": ignorezero,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "tracks_in": tracks_in,
+    }
+    if output is not None:
+        params["output"] = output
+    if histogram is not None:
+        params["histogram"] = histogram
+    if dump is not None:
+        params["dump"] = dump
+    if tck_weights_in is not None:
+        params["tck_weights_in"] = tck_weights_in
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tckstats_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TckstatsParamsDict` 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("output", None) is not None:
+        if not isinstance(params["output"], list):
+            raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `list[TckstatsOutputParamsDict] | None`')
+        for e in params["output"]:
+            tckstats_output_validate(e)
+    if params.get("histogram", None) is not None:
+        if not isinstance(params["histogram"], str):
+            raise StyxValidationError(f'`histogram` has the wrong type: Received `{type(params.get("histogram", None))}` expected `str | None`')
+    if params.get("dump", None) is not None:
+        if not isinstance(params["dump"], str):
+            raise StyxValidationError(f'`dump` has the wrong type: Received `{type(params.get("dump", None))}` expected `str | None`')
+    if params.get("ignorezero", False) is None:
+        raise StyxValidationError("`ignorezero` must not be None")
+    if not isinstance(params["ignorezero"], bool):
+        raise StyxValidationError(f'`ignorezero` has the wrong type: Received `{type(params.get("ignorezero", 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("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[TckstatsConfigParamsDict] | None`')
+        for e in params["config"]:
+            tckstats_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`')
+
+
+def tckstats_cargs(
+    params: TckstatsParamsDict,
+    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("tckstats")
+    if params.get("output", None) is not None:
+        cargs.extend([a for c in [tckstats_output_cargs(s, execution) for s in params.get("output", None)] for a in c])
+    if params.get("histogram", None) is not None:
+        cargs.extend([
+            "-histogram",
+            params.get("histogram", None)
+        ])
+    if params.get("dump", None) is not None:
+        cargs.extend([
+            "-dump",
+            params.get("dump", None)
+        ])
+    if params.get("ignorezero", False):
+        cargs.append("-ignorezero")
+    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("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 [tckstats_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)))
+    return cargs
+
+
+def tckstats_outputs(
+    params: TckstatsParamsDict,
+    execution: Execution,
+) -> TckstatsOutputs:
+    """
+    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 = TckstatsOutputs(
+        root=execution.output_file("."),
+        histogram=execution.output_file(params.get("histogram", None)) if (params.get("histogram") is not None) else None,
+        dump=execution.output_file(params.get("dump", None)) if (params.get("dump") is not None) else None,
+    )
+    return ret
+
+
+def tckstats_execute(
+    params: TckstatsParamsDict,
+    runner: Runner | None = None,
+) -> TckstatsOutputs:
+    """
+    tckstats
+    
+    Calculate statistics on streamlines lengths.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TckstatsOutputs`).
+    """
+    tckstats_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKSTATS_METADATA)
+    params = execution.params(params)
+    cargs = tckstats_cargs(params, execution)
+    ret = tckstats_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tckstats(
+    tracks_in: InputPathType,
+    output: list[TckstatsOutputParamsDict] | None = None,
+    histogram: str | None = None,
+    dump: str | None = None,
+    ignorezero: bool = False,
+    tck_weights_in: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckstatsConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TckstatsOutputs:
+    """
+    tckstats
+    
+    Calculate statistics on streamlines lengths.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        tracks_in: the input track file.
+        output: output only the field specified. Multiple such options can be\
+            supplied if required. Choices are: mean, median, std, min, max, count.\
+            Useful for use in scripts.
+        histogram: output a histogram of streamline lengths.
+        dump: dump the streamlines lengths to a text file.
+        ignorezero: do not generate a warning if the track file contains\
+            streamlines with zero length.
+        tck_weights_in: specify a text scalar file containing the streamline\
+            weights.
+        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 `TckstatsOutputs`).
+    """
+    params = tckstats_params(
+        output=output,
+        histogram=histogram,
+        dump=dump,
+        ignorezero=ignorezero,
+        tck_weights_in=tck_weights_in,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        tracks_in=tracks_in,
+    )
+    return tckstats_execute(params, runner)
+
+
+__all__ = [
+    "TCKSTATS_METADATA",
+    "TckstatsConfigParamsDict",
+    "TckstatsConfigParamsDictTagged",
+    "TckstatsOutputParamsDict",
+    "TckstatsOutputParamsDictTagged",
+    "TckstatsOutputs",
+    "TckstatsParamsDict",
+    "TckstatsParamsDictTagged",
+    "tckstats",
+    "tckstats_config",
+    "tckstats_execute",
+    "tckstats_output",
+    "tckstats_params",
+]