niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrhistmatch.py

@@ -0,0 +1,494 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRHISTMATCH_METADATA = Metadata(
+    id="1798cd7ea1a79d9523cf1fd1a7ec35b94aa4a5ab.boutiques",
+    name="mrhistmatch",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_MrhistmatchConfigParamsDictNoTag = typing.TypedDict('_MrhistmatchConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+MrhistmatchConfigParamsDictTagged = typing.TypedDict('MrhistmatchConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+MrhistmatchConfigParamsDict = _MrhistmatchConfigParamsDictNoTag | MrhistmatchConfigParamsDictTagged
+
+
+_MrhistmatchParamsDictNoTag = typing.TypedDict('_MrhistmatchParamsDictNoTag', {
+    "mask_input": typing.NotRequired[InputPathType | None],
+    "mask_target": typing.NotRequired[InputPathType | None],
+    "bins": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrhistmatchConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "type": str,
+    "input": InputPathType,
+    "target": InputPathType,
+    "output": str,
+})
+MrhistmatchParamsDictTagged = typing.TypedDict('MrhistmatchParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/mrhistmatch"],
+    "mask_input": typing.NotRequired[InputPathType | None],
+    "mask_target": typing.NotRequired[InputPathType | None],
+    "bins": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrhistmatchConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "type": str,
+    "input": InputPathType,
+    "target": InputPathType,
+    "output": str,
+})
+MrhistmatchParamsDict = _MrhistmatchParamsDictNoTag | MrhistmatchParamsDictTagged
+
+
+def mrhistmatch_config(
+    key: str,
+    value: str,
+) -> MrhistmatchConfigParamsDictTagged:
+    """
+    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 mrhistmatch_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrhistmatchConfigParamsDict` 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 mrhistmatch_config_cargs(
+    params: MrhistmatchConfigParamsDict,
+    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 MrhistmatchOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrhistmatchParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image"""
+
+
+def mrhistmatch_params(
+    type_: str,
+    input_: InputPathType,
+    target: InputPathType,
+    output: str,
+    mask_input: InputPathType | None = None,
+    mask_target: InputPathType | None = None,
+    bins: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrhistmatchConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrhistmatchParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        type_: type of histogram matching to perform; options are:\
+            scale,linear,nonlinear.
+        input_: the input image to be modified.
+        target: the input image from which to derive the target histogram.
+        output: the output image.
+        mask_input: only generate input histogram based on a specified binary\
+            mask image.
+        mask_target: only generate target histogram based on a specified binary\
+            mask image.
+        bins: the number of bins to use to generate the histograms.
+        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/mrhistmatch",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "type": type_,
+        "input": input_,
+        "target": target,
+        "output": output,
+    }
+    if mask_input is not None:
+        params["mask_input"] = mask_input
+    if mask_target is not None:
+        params["mask_target"] = mask_target
+    if bins is not None:
+        params["bins"] = bins
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrhistmatch_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrhistmatchParamsDict` 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("mask_input", None) is not None:
+        if not isinstance(params["mask_input"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`mask_input` has the wrong type: Received `{type(params.get("mask_input", None))}` expected `InputPathType | None`')
+    if params.get("mask_target", None) is not None:
+        if not isinstance(params["mask_target"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`mask_target` has the wrong type: Received `{type(params.get("mask_target", None))}` expected `InputPathType | None`')
+    if params.get("bins", None) is not None:
+        if not isinstance(params["bins"], int):
+            raise StyxValidationError(f'`bins` has the wrong type: Received `{type(params.get("bins", None))}` expected `int | 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[MrhistmatchConfigParamsDict] | None`')
+        for e in params["config"]:
+            mrhistmatch_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("type", None) is None:
+        raise StyxValidationError("`type` must not be None")
+    if not isinstance(params["type"], str):
+        raise StyxValidationError(f'`type` has the wrong type: Received `{type(params.get("type", None))}` expected `str`')
+    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("target", None) is None:
+        raise StyxValidationError("`target` must not be None")
+    if not isinstance(params["target"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`target` has the wrong type: Received `{type(params.get("target", None))}` expected `InputPathType`')
+    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 mrhistmatch_cargs(
+    params: MrhistmatchParamsDict,
+    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("mrhistmatch")
+    if params.get("mask_input", None) is not None:
+        cargs.extend([
+            "-mask_input",
+            execution.input_file(params.get("mask_input", None))
+        ])
+    if params.get("mask_target", None) is not None:
+        cargs.extend([
+            "-mask_target",
+            execution.input_file(params.get("mask_target", None))
+        ])
+    if params.get("bins", None) is not None:
+        cargs.extend([
+            "-bins",
+            str(params.get("bins", 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 [mrhistmatch_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(params.get("type", None))
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(execution.input_file(params.get("target", None)))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def mrhistmatch_outputs(
+    params: MrhistmatchParamsDict,
+    execution: Execution,
+) -> MrhistmatchOutputs:
+    """
+    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 = MrhistmatchOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+def mrhistmatch_execute(
+    params: MrhistmatchParamsDict,
+    runner: Runner | None = None,
+) -> MrhistmatchOutputs:
+    """
+    mrhistmatch
+    
+    Modify the intensities of one image to match the histogram of another.
+    
+    
+    
+    References:
+    
+    * If using inverse contrast normalization for inter-modal (DWI - T1)
+    registration:
+    Bhushan, C.; Haldar, J. P.; Choi, S.; Joshi, A. A.; Shattuck, D. W. & Leahy,
+    R. M. Co-registration and distortion correction of diffusion and anatomical
+    images based on inverse contrast normalization. NeuroImage, 2015, 115,
+    269-280.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrhistmatchOutputs`).
+    """
+    mrhistmatch_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRHISTMATCH_METADATA)
+    params = execution.params(params)
+    cargs = mrhistmatch_cargs(params, execution)
+    ret = mrhistmatch_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrhistmatch(
+    type_: str,
+    input_: InputPathType,
+    target: InputPathType,
+    output: str,
+    mask_input: InputPathType | None = None,
+    mask_target: InputPathType | None = None,
+    bins: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrhistmatchConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrhistmatchOutputs:
+    """
+    mrhistmatch
+    
+    Modify the intensities of one image to match the histogram of another.
+    
+    
+    
+    References:
+    
+    * If using inverse contrast normalization for inter-modal (DWI - T1)
+    registration:
+    Bhushan, C.; Haldar, J. P.; Choi, S.; Joshi, A. A.; Shattuck, D. W. & Leahy,
+    R. M. Co-registration and distortion correction of diffusion and anatomical
+    images based on inverse contrast normalization. NeuroImage, 2015, 115,
+    269-280.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        type_: type of histogram matching to perform; options are:\
+            scale,linear,nonlinear.
+        input_: the input image to be modified.
+        target: the input image from which to derive the target histogram.
+        output: the output image.
+        mask_input: only generate input histogram based on a specified binary\
+            mask image.
+        mask_target: only generate target histogram based on a specified binary\
+            mask image.
+        bins: the number of bins to use to generate the histograms.
+        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 `MrhistmatchOutputs`).
+    """
+    params = mrhistmatch_params(
+        mask_input=mask_input,
+        mask_target=mask_target,
+        bins=bins,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        type_=type_,
+        input_=input_,
+        target=target,
+        output=output,
+    )
+    return mrhistmatch_execute(params, runner)
+
+
+__all__ = [
+    "MRHISTMATCH_METADATA",
+    "MrhistmatchConfigParamsDict",
+    "MrhistmatchConfigParamsDictTagged",
+    "MrhistmatchOutputs",
+    "MrhistmatchParamsDict",
+    "MrhistmatchParamsDictTagged",
+    "mrhistmatch",
+    "mrhistmatch_config",
+    "mrhistmatch_execute",
+    "mrhistmatch_params",
+]