niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dirmerge.py

@@ -0,0 +1,446 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DIRMERGE_METADATA = Metadata(
+    id="40d07b2a5fb8d4016b42c7968c68cb8ea4d70a1a.boutiques",
+    name="dirmerge",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_DirmergeConfigParamsDictNoTag = typing.TypedDict('_DirmergeConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+DirmergeConfigParamsDictTagged = typing.TypedDict('DirmergeConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+DirmergeConfigParamsDict = _DirmergeConfigParamsDictNoTag | DirmergeConfigParamsDictTagged
+
+
+_DirmergeParamsDictNoTag = typing.TypedDict('_DirmergeParamsDictNoTag', {
+    "unipolar_weight": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DirmergeConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "subsets": int,
+    "bvalue_files": list[str],
+    "out": str,
+})
+DirmergeParamsDictTagged = typing.TypedDict('DirmergeParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/dirmerge"],
+    "unipolar_weight": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DirmergeConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "subsets": int,
+    "bvalue_files": list[str],
+    "out": str,
+})
+DirmergeParamsDict = _DirmergeParamsDictNoTag | DirmergeParamsDictTagged
+
+
+def dirmerge_config(
+    key: str,
+    value: str,
+) -> DirmergeConfigParamsDictTagged:
+    """
+    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 dirmerge_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DirmergeConfigParamsDict` 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 dirmerge_config_cargs(
+    params: DirmergeConfigParamsDict,
+    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 DirmergeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `DirmergeParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out: OutputPathType
+    """the output directions file, with each row listing the X Y Z gradient
+    directions, the b-value, and an index representing the phase encode
+    direction"""
+
+
+def dirmerge_params(
+    subsets: int,
+    bvalue_files: list[str],
+    out: str,
+    unipolar_weight: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DirmergeConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> DirmergeParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        subsets: the number of subsets (eg. phase encoding directions) per\
+            b-value.
+        bvalue_files: the b-value and sets of corresponding files, in order.
+        out: the output directions file, with each row listing the X Y Z\
+            gradient directions, the b-value, and an index representing the phase\
+            encode direction.
+        unipolar_weight: set the weight given to the unipolar electrostatic\
+            repulsion model compared to the bipolar model (default: 0.2).
+        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/dirmerge",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "subsets": subsets,
+        "bvalue_files": bvalue_files,
+        "out": out,
+    }
+    if unipolar_weight is not None:
+        params["unipolar_weight"] = unipolar_weight
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def dirmerge_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `DirmergeParamsDict` 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("unipolar_weight", None) is not None:
+        if not isinstance(params["unipolar_weight"], (float, int)):
+            raise StyxValidationError(f'`unipolar_weight` has the wrong type: Received `{type(params.get("unipolar_weight", None))}` expected `float | 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[DirmergeConfigParamsDict] | None`')
+        for e in params["config"]:
+            dirmerge_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("subsets", None) is None:
+        raise StyxValidationError("`subsets` must not be None")
+    if not isinstance(params["subsets"], int):
+        raise StyxValidationError(f'`subsets` has the wrong type: Received `{type(params.get("subsets", None))}` expected `int`')
+    if params.get("bvalue_files", None) is None:
+        raise StyxValidationError("`bvalue_files` must not be None")
+    if not isinstance(params["bvalue_files"], list):
+        raise StyxValidationError(f'`bvalue_files` has the wrong type: Received `{type(params.get("bvalue_files", None))}` expected `list[str]`')
+    for e in params["bvalue_files"]:
+        if not isinstance(e, str):
+            raise StyxValidationError(f'`bvalue_files` has the wrong type: Received `{type(params.get("bvalue_files", None))}` expected `list[str]`')
+    if params.get("out", None) is None:
+        raise StyxValidationError("`out` must not be None")
+    if not isinstance(params["out"], str):
+        raise StyxValidationError(f'`out` has the wrong type: Received `{type(params.get("out", None))}` expected `str`')
+
+
+def dirmerge_cargs(
+    params: DirmergeParamsDict,
+    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("dirmerge")
+    if params.get("unipolar_weight", None) is not None:
+        cargs.extend([
+            "-unipolar_weight",
+            str(params.get("unipolar_weight", 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 [dirmerge_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(str(params.get("subsets", None)))
+    cargs.extend(params.get("bvalue_files", None))
+    cargs.append(params.get("out", None))
+    return cargs
+
+
+def dirmerge_outputs(
+    params: DirmergeParamsDict,
+    execution: Execution,
+) -> DirmergeOutputs:
+    """
+    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 = DirmergeOutputs(
+        root=execution.output_file("."),
+        out=execution.output_file(params.get("out", None)),
+    )
+    return ret
+
+
+def dirmerge_execute(
+    params: DirmergeParamsDict,
+    runner: Runner | None = None,
+) -> DirmergeOutputs:
+    """
+    dirmerge
+    
+    Splice / merge multiple sets of directions in such a way as to maintain
+    near-optimality upon truncation.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DirmergeOutputs`).
+    """
+    dirmerge_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DIRMERGE_METADATA)
+    params = execution.params(params)
+    cargs = dirmerge_cargs(params, execution)
+    ret = dirmerge_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dirmerge(
+    subsets: int,
+    bvalue_files: list[str],
+    out: str,
+    unipolar_weight: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DirmergeConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> DirmergeOutputs:
+    """
+    dirmerge
+    
+    Splice / merge multiple sets of directions in such a way as to maintain
+    near-optimality upon truncation.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        subsets: the number of subsets (eg. phase encoding directions) per\
+            b-value.
+        bvalue_files: the b-value and sets of corresponding files, in order.
+        out: the output directions file, with each row listing the X Y Z\
+            gradient directions, the b-value, and an index representing the phase\
+            encode direction.
+        unipolar_weight: set the weight given to the unipolar electrostatic\
+            repulsion model compared to the bipolar model (default: 0.2).
+        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 `DirmergeOutputs`).
+    """
+    params = dirmerge_params(
+        unipolar_weight=unipolar_weight,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        subsets=subsets,
+        bvalue_files=bvalue_files,
+        out=out,
+    )
+    return dirmerge_execute(params, runner)
+
+
+__all__ = [
+    "DIRMERGE_METADATA",
+    "DirmergeConfigParamsDict",
+    "DirmergeConfigParamsDictTagged",
+    "DirmergeOutputs",
+    "DirmergeParamsDict",
+    "DirmergeParamsDictTagged",
+    "dirmerge",
+    "dirmerge_config",
+    "dirmerge_execute",
+    "dirmerge_params",
+]