niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixelcrop.py

@@ -0,0 +1,422 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXELCROP_METADATA = Metadata(
+    id="d70da385bb1143b77638a918a070ee631393b7f4.boutiques",
+    name="fixelcrop",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_FixelcropConfigParamsDictNoTag = typing.TypedDict('_FixelcropConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+FixelcropConfigParamsDictTagged = typing.TypedDict('FixelcropConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+FixelcropConfigParamsDict = _FixelcropConfigParamsDictNoTag | FixelcropConfigParamsDictTagged
+
+
+_FixelcropParamsDictNoTag = typing.TypedDict('_FixelcropParamsDictNoTag', {
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelcropConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input_fixel_directory": InputPathType,
+    "input_fixel_mask": InputPathType,
+    "output_fixel_directory": str,
+})
+FixelcropParamsDictTagged = typing.TypedDict('FixelcropParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/fixelcrop"],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelcropConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input_fixel_directory": InputPathType,
+    "input_fixel_mask": InputPathType,
+    "output_fixel_directory": str,
+})
+FixelcropParamsDict = _FixelcropParamsDictNoTag | FixelcropParamsDictTagged
+
+
+def fixelcrop_config(
+    key: str,
+    value: str,
+) -> FixelcropConfigParamsDictTagged:
+    """
+    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 fixelcrop_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelcropConfigParamsDict` 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 fixelcrop_config_cargs(
+    params: FixelcropConfigParamsDict,
+    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 FixelcropOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `FixelcropParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_fixel_directory: OutputPathType
+    """the output directory to store the cropped directions and data files"""
+
+
+def fixelcrop_params(
+    input_fixel_directory: InputPathType,
+    input_fixel_mask: InputPathType,
+    output_fixel_directory: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelcropConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> FixelcropParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_fixel_directory: input fixel directory, all data files and\
+            directions file will be cropped and saved in the output fixel directory.
+        input_fixel_mask: the input fixel data file defining which fixels to\
+            crop. Fixels with zero values will be removed.
+        output_fixel_directory: the output directory to store the cropped\
+            directions and data files.
+        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/fixelcrop",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input_fixel_directory": input_fixel_directory,
+        "input_fixel_mask": input_fixel_mask,
+        "output_fixel_directory": output_fixel_directory,
+    }
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixelcrop_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelcropParamsDict` 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("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[FixelcropConfigParamsDict] | None`')
+        for e in params["config"]:
+            fixelcrop_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("input_fixel_directory", None) is None:
+        raise StyxValidationError("`input_fixel_directory` must not be None")
+    if not isinstance(params["input_fixel_directory"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`input_fixel_directory` has the wrong type: Received `{type(params.get("input_fixel_directory", None))}` expected `InputPathType`')
+    if params.get("input_fixel_mask", None) is None:
+        raise StyxValidationError("`input_fixel_mask` must not be None")
+    if not isinstance(params["input_fixel_mask"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`input_fixel_mask` has the wrong type: Received `{type(params.get("input_fixel_mask", None))}` expected `InputPathType`')
+    if params.get("output_fixel_directory", None) is None:
+        raise StyxValidationError("`output_fixel_directory` must not be None")
+    if not isinstance(params["output_fixel_directory"], str):
+        raise StyxValidationError(f'`output_fixel_directory` has the wrong type: Received `{type(params.get("output_fixel_directory", None))}` expected `str`')
+
+
+def fixelcrop_cargs(
+    params: FixelcropParamsDict,
+    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("fixelcrop")
+    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 [fixelcrop_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("input_fixel_directory", None)))
+    cargs.append(execution.input_file(params.get("input_fixel_mask", None)))
+    cargs.append(params.get("output_fixel_directory", None))
+    return cargs
+
+
+def fixelcrop_outputs(
+    params: FixelcropParamsDict,
+    execution: Execution,
+) -> FixelcropOutputs:
+    """
+    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 = FixelcropOutputs(
+        root=execution.output_file("."),
+        output_fixel_directory=execution.output_file(params.get("output_fixel_directory", None)),
+    )
+    return ret
+
+
+def fixelcrop_execute(
+    params: FixelcropParamsDict,
+    runner: Runner | None = None,
+) -> FixelcropOutputs:
+    """
+    fixelcrop
+    
+    Crop/remove fixels from sparse fixel image using a binary fixel mask.
+    
+    The mask must be input as a fixel data file the same dimensions as the fixel
+    data file(s) to be cropped.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FixelcropOutputs`).
+    """
+    fixelcrop_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELCROP_METADATA)
+    params = execution.params(params)
+    cargs = fixelcrop_cargs(params, execution)
+    ret = fixelcrop_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixelcrop(
+    input_fixel_directory: InputPathType,
+    input_fixel_mask: InputPathType,
+    output_fixel_directory: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelcropConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> FixelcropOutputs:
+    """
+    fixelcrop
+    
+    Crop/remove fixels from sparse fixel image using a binary fixel mask.
+    
+    The mask must be input as a fixel data file the same dimensions as the fixel
+    data file(s) to be cropped.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_fixel_directory: input fixel directory, all data files and\
+            directions file will be cropped and saved in the output fixel directory.
+        input_fixel_mask: the input fixel data file defining which fixels to\
+            crop. Fixels with zero values will be removed.
+        output_fixel_directory: the output directory to store the cropped\
+            directions and data files.
+        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 `FixelcropOutputs`).
+    """
+    params = fixelcrop_params(
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_fixel_directory=input_fixel_directory,
+        input_fixel_mask=input_fixel_mask,
+        output_fixel_directory=output_fixel_directory,
+    )
+    return fixelcrop_execute(params, runner)
+
+
+__all__ = [
+    "FIXELCROP_METADATA",
+    "FixelcropConfigParamsDict",
+    "FixelcropConfigParamsDictTagged",
+    "FixelcropOutputs",
+    "FixelcropParamsDict",
+    "FixelcropParamsDictTagged",
+    "fixelcrop",
+    "fixelcrop_config",
+    "fixelcrop_execute",
+    "fixelcrop_params",
+]