niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrcolour.py

@@ -0,0 +1,490 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRCOLOUR_METADATA = Metadata(
+    id="9cd4b4f06262529bb32fb59ee13631275aef99fa.boutiques",
+    name="mrcolour",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_MrcolourConfigParamsDictNoTag = typing.TypedDict('_MrcolourConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+MrcolourConfigParamsDictTagged = typing.TypedDict('MrcolourConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+MrcolourConfigParamsDict = _MrcolourConfigParamsDictNoTag | MrcolourConfigParamsDictTagged
+
+
+_MrcolourParamsDictNoTag = typing.TypedDict('_MrcolourParamsDictNoTag', {
+    "upper": typing.NotRequired[float | None],
+    "lower": typing.NotRequired[float | None],
+    "colour": typing.NotRequired[list[float] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrcolourConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "map": str,
+    "output": str,
+})
+MrcolourParamsDictTagged = typing.TypedDict('MrcolourParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/mrcolour"],
+    "upper": typing.NotRequired[float | None],
+    "lower": typing.NotRequired[float | None],
+    "colour": typing.NotRequired[list[float] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrcolourConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "map": str,
+    "output": str,
+})
+MrcolourParamsDict = _MrcolourParamsDictNoTag | MrcolourParamsDictTagged
+
+
+def mrcolour_config(
+    key: str,
+    value: str,
+) -> MrcolourConfigParamsDictTagged:
+    """
+    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 mrcolour_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrcolourConfigParamsDict` 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 mrcolour_config_cargs(
+    params: MrcolourConfigParamsDict,
+    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 MrcolourOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrcolourParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image"""
+
+
+def mrcolour_params(
+    input_: InputPathType,
+    map_: str,
+    output: str,
+    upper: float | None = None,
+    lower: float | None = None,
+    colour: list[float] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrcolourConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrcolourParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input image.
+        map_: the colourmap to apply; choices are:\
+            gray,hot,cool,jet,inferno,viridis,pet,colour,rgb.
+        output: the output image.
+        upper: manually set the upper intensity of the colour mapping.
+        lower: manually set the lower intensity of the colour mapping.
+        colour: set the target colour for use of the 'colour' map (three\
+            comma-separated floating-point values).
+        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/mrcolour",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "map": map_,
+        "output": output,
+    }
+    if upper is not None:
+        params["upper"] = upper
+    if lower is not None:
+        params["lower"] = lower
+    if colour is not None:
+        params["colour"] = colour
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrcolour_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrcolourParamsDict` 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("upper", None) is not None:
+        if not isinstance(params["upper"], (float, int)):
+            raise StyxValidationError(f'`upper` has the wrong type: Received `{type(params.get("upper", None))}` expected `float | None`')
+    if params.get("lower", None) is not None:
+        if not isinstance(params["lower"], (float, int)):
+            raise StyxValidationError(f'`lower` has the wrong type: Received `{type(params.get("lower", None))}` expected `float | None`')
+    if params.get("colour", None) is not None:
+        if not isinstance(params["colour"], list):
+            raise StyxValidationError(f'`colour` has the wrong type: Received `{type(params.get("colour", None))}` expected `list[float] | None`')
+        for e in params["colour"]:
+            if not isinstance(e, (float, int)):
+                raise StyxValidationError(f'`colour` has the wrong type: Received `{type(params.get("colour", None))}` expected `list[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[MrcolourConfigParamsDict] | None`')
+        for e in params["config"]:
+            mrcolour_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", None) is None:
+        raise StyxValidationError("`input` must not be None")
+    if not isinstance(params["input"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`input` has the wrong type: Received `{type(params.get("input", None))}` expected `InputPathType`')
+    if params.get("map", None) is None:
+        raise StyxValidationError("`map` must not be None")
+    if not isinstance(params["map"], str):
+        raise StyxValidationError(f'`map` has the wrong type: Received `{type(params.get("map", None))}` expected `str`')
+    if params.get("output", None) is None:
+        raise StyxValidationError("`output` must not be None")
+    if not isinstance(params["output"], str):
+        raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `str`')
+
+
+def mrcolour_cargs(
+    params: MrcolourParamsDict,
+    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("mrcolour")
+    if params.get("upper", None) is not None:
+        cargs.extend([
+            "-upper",
+            str(params.get("upper", None))
+        ])
+    if params.get("lower", None) is not None:
+        cargs.extend([
+            "-lower",
+            str(params.get("lower", None))
+        ])
+    if params.get("colour", None) is not None:
+        cargs.extend([
+            "-colour",
+            ",".join(map(str, params.get("colour", 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 [mrcolour_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", None)))
+    cargs.append(params.get("map", None))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def mrcolour_outputs(
+    params: MrcolourParamsDict,
+    execution: Execution,
+) -> MrcolourOutputs:
+    """
+    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 = MrcolourOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+def mrcolour_execute(
+    params: MrcolourParamsDict,
+    runner: Runner | None = None,
+) -> MrcolourOutputs:
+    """
+    mrcolour
+    
+    Apply a colour map to an image.
+    
+    Under typical usage, this command will receive as input ad 3D greyscale
+    image, and output a 4D image with 3 volumes corresponding to red-green-blue
+    components; other use cases are possible, and are described in more detail
+    below.
+    
+    By default, the command will automatically determine the maximum and minimum
+    intensities of the input image, and use that information to set the upper
+    and lower bounds of the applied colourmap. This behaviour can be overridden
+    by manually specifying these bounds using the -upper and -lower options
+    respectively.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrcolourOutputs`).
+    """
+    mrcolour_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRCOLOUR_METADATA)
+    params = execution.params(params)
+    cargs = mrcolour_cargs(params, execution)
+    ret = mrcolour_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrcolour(
+    input_: InputPathType,
+    map_: str,
+    output: str,
+    upper: float | None = None,
+    lower: float | None = None,
+    colour: list[float] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrcolourConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrcolourOutputs:
+    """
+    mrcolour
+    
+    Apply a colour map to an image.
+    
+    Under typical usage, this command will receive as input ad 3D greyscale
+    image, and output a 4D image with 3 volumes corresponding to red-green-blue
+    components; other use cases are possible, and are described in more detail
+    below.
+    
+    By default, the command will automatically determine the maximum and minimum
+    intensities of the input image, and use that information to set the upper
+    and lower bounds of the applied colourmap. This behaviour can be overridden
+    by manually specifying these bounds using the -upper and -lower options
+    respectively.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input image.
+        map_: the colourmap to apply; choices are:\
+            gray,hot,cool,jet,inferno,viridis,pet,colour,rgb.
+        output: the output image.
+        upper: manually set the upper intensity of the colour mapping.
+        lower: manually set the lower intensity of the colour mapping.
+        colour: set the target colour for use of the 'colour' map (three\
+            comma-separated floating-point values).
+        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 `MrcolourOutputs`).
+    """
+    params = mrcolour_params(
+        upper=upper,
+        lower=lower,
+        colour=colour,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        map_=map_,
+        output=output,
+    )
+    return mrcolour_execute(params, runner)
+
+
+__all__ = [
+    "MRCOLOUR_METADATA",
+    "MrcolourConfigParamsDict",
+    "MrcolourConfigParamsDictTagged",
+    "MrcolourOutputs",
+    "MrcolourParamsDict",
+    "MrcolourParamsDictTagged",
+    "mrcolour",
+    "mrcolour_config",
+    "mrcolour_execute",
+    "mrcolour_params",
+]