niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrhistmatch.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 *
+
+MRHISTMATCH_METADATA = Metadata(
+    id="82971ece0a248809e6ac4741b981b24094fbed5d.boutiques",
+    name="mrhistmatch",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MrhistmatchConfigParameters = typing.TypedDict('MrhistmatchConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MrhistmatchParameters = typing.TypedDict('MrhistmatchParameters', {
+    "__STYX_TYPE__": typing.Literal["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[MrhistmatchConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "type": str,
+    "input": InputPathType,
+    "target": InputPathType,
+    "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 {
+        "mrhistmatch": mrhistmatch_cargs,
+        "config": mrhistmatch_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 {
+        "mrhistmatch": mrhistmatch_outputs,
+    }.get(t)
+
+
+def mrhistmatch_config_params(
+    key: str,
+    value: str,
+) -> MrhistmatchConfigParameters:
+    """
+    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 mrhistmatch_config_cargs(
+    params: MrhistmatchConfigParameters,
+    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 MrhistmatchOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrhistmatch(...)`.
+    """
+    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[MrhistmatchConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrhistmatchParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "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_cargs(
+    params: MrhistmatchParameters,
+    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") is not None:
+        cargs.extend([
+            "-mask_input",
+            execution.input_file(params.get("mask_input"))
+        ])
+    if params.get("mask_target") is not None:
+        cargs.extend([
+            "-mask_target",
+            execution.input_file(params.get("mask_target"))
+        ])
+    if params.get("bins") is not None:
+        cargs.extend([
+            "-bins",
+            str(params.get("bins"))
+        ])
+    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(params.get("type"))
+    cargs.append(execution.input_file(params.get("input")))
+    cargs.append(execution.input_file(params.get("target")))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def mrhistmatch_outputs(
+    params: MrhistmatchParameters,
+    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")),
+    )
+    return ret
+
+
+def mrhistmatch_execute(
+    params: MrhistmatchParameters,
+    execution: Execution,
+) -> MrhistmatchOutputs:
+    """
+    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.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrhistmatchOutputs`).
+    """
+    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[MrhistmatchConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrhistmatchOutputs:
+    """
+    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`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRHISTMATCH_METADATA)
+    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, execution)
+
+
+__all__ = [
+    "MRHISTMATCH_METADATA",
+    "MrhistmatchConfigParameters",
+    "MrhistmatchOutputs",
+    "MrhistmatchParameters",
+    "mrhistmatch",
+    "mrhistmatch_config_params",
+    "mrhistmatch_params",
+]