niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrcolour.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRCOLOUR_METADATA = Metadata(
+    id="5c34d1664fe214212552914265860aab8fddd651.boutiques",
+    name="mrcolour",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MrcolourConfigParameters = typing.TypedDict('MrcolourConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MrcolourParameters = typing.TypedDict('MrcolourParameters', {
+    "__STYX_TYPE__": typing.Literal["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[MrcolourConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "map": str,
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mrcolour": mrcolour_cargs,
+        "config": mrcolour_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 {
+        "mrcolour": mrcolour_outputs,
+    }.get(t)
+
+
+def mrcolour_config_params(
+    key: str,
+    value: str,
+) -> MrcolourConfigParameters:
+    """
+    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 mrcolour_config_cargs(
+    params: MrcolourConfigParameters,
+    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 MrcolourOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrcolour(...)`.
+    """
+    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[MrcolourConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrcolourParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "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_cargs(
+    params: MrcolourParameters,
+    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") is not None:
+        cargs.extend([
+            "-upper",
+            str(params.get("upper"))
+        ])
+    if params.get("lower") is not None:
+        cargs.extend([
+            "-lower",
+            str(params.get("lower"))
+        ])
+    if params.get("colour") is not None:
+        cargs.extend([
+            "-colour",
+            ",".join(map(str, params.get("colour")))
+        ])
+    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("input")))
+    cargs.append(params.get("map"))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def mrcolour_outputs(
+    params: MrcolourParameters,
+    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")),
+    )
+    return ret
+
+
+def mrcolour_execute(
+    params: MrcolourParameters,
+    execution: Execution,
+) -> MrcolourOutputs:
+    """
+    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.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrcolourOutputs`).
+    """
+    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[MrcolourConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrcolourOutputs:
+    """
+    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`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRCOLOUR_METADATA)
+    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, execution)
+
+
+__all__ = [
+    "MRCOLOUR_METADATA",
+    "MrcolourConfigParameters",
+    "MrcolourOutputs",
+    "MrcolourParameters",
+    "mrcolour",
+    "mrcolour_config_params",
+    "mrcolour_params",
+]