niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrmetric.py

@@ -0,0 +1,525 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRMETRIC_METADATA = Metadata(
+    id="900f502c877db64aba337cc23f205ccc871706a3.boutiques",
+    name="mrmetric",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_MrmetricConfigParamsDictNoTag = typing.TypedDict('_MrmetricConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+MrmetricConfigParamsDictTagged = typing.TypedDict('MrmetricConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+MrmetricConfigParamsDict = _MrmetricConfigParamsDictNoTag | MrmetricConfigParamsDictTagged
+
+
+_MrmetricParamsDictNoTag = typing.TypedDict('_MrmetricParamsDictNoTag', {
+    "space": typing.NotRequired[str | None],
+    "interp": typing.NotRequired[str | None],
+    "metric": typing.NotRequired[str | None],
+    "mask1": typing.NotRequired[InputPathType | None],
+    "mask2": typing.NotRequired[InputPathType | None],
+    "nonormalisation": bool,
+    "overlap": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrmetricConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "image1": InputPathType,
+    "image2": InputPathType,
+})
+MrmetricParamsDictTagged = typing.TypedDict('MrmetricParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/mrmetric"],
+    "space": typing.NotRequired[str | None],
+    "interp": typing.NotRequired[str | None],
+    "metric": typing.NotRequired[str | None],
+    "mask1": typing.NotRequired[InputPathType | None],
+    "mask2": typing.NotRequired[InputPathType | None],
+    "nonormalisation": bool,
+    "overlap": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrmetricConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "image1": InputPathType,
+    "image2": InputPathType,
+})
+MrmetricParamsDict = _MrmetricParamsDictNoTag | MrmetricParamsDictTagged
+
+
+def mrmetric_config(
+    key: str,
+    value: str,
+) -> MrmetricConfigParamsDictTagged:
+    """
+    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 mrmetric_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrmetricConfigParamsDict` 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 mrmetric_config_cargs(
+    params: MrmetricConfigParamsDict,
+    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 MrmetricOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrmetricParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mrmetric_params(
+    image1: InputPathType,
+    image2: InputPathType,
+    space: str | None = None,
+    interp: str | None = None,
+    metric: str | None = None,
+    mask1: InputPathType | None = None,
+    mask2: InputPathType | None = None,
+    nonormalisation: bool = False,
+    overlap: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrmetricConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrmetricParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        image1: the first input image.
+        image2: the second input image.
+        space: voxel (default): per voxel image1: scanner space of image 1\
+            image2: scanner space of image 2 average: scanner space of the average\
+            affine transformation of image 1 and 2.
+        interp: set the interpolation method to use when reslicing (choices:\
+            nearest, linear, cubic, sinc. Default: linear).
+        metric: define the dissimilarity metric used to calculate the cost.\
+            Choices: diff (squared differences), cc (non-normalised negative cross\
+            correlation aka negative cross covariance). Default: diff). cc is only\
+            implemented for -space average and -interp linear and cubic.
+        mask1: mask for image 1.
+        mask2: mask for image 2.
+        nonormalisation: do not normalise the dissimilarity metric to the\
+            number of voxels.
+        overlap: output number of voxels that were used.
+        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/mrmetric",
+        "nonormalisation": nonormalisation,
+        "overlap": overlap,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "image1": image1,
+        "image2": image2,
+    }
+    if space is not None:
+        params["space"] = space
+    if interp is not None:
+        params["interp"] = interp
+    if metric is not None:
+        params["metric"] = metric
+    if mask1 is not None:
+        params["mask1"] = mask1
+    if mask2 is not None:
+        params["mask2"] = mask2
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mrmetric_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrmetricParamsDict` 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("space", None) is not None:
+        if not isinstance(params["space"], str):
+            raise StyxValidationError(f'`space` has the wrong type: Received `{type(params.get("space", None))}` expected `str | None`')
+    if params.get("interp", None) is not None:
+        if not isinstance(params["interp"], str):
+            raise StyxValidationError(f'`interp` has the wrong type: Received `{type(params.get("interp", None))}` expected `str | None`')
+    if params.get("metric", None) is not None:
+        if not isinstance(params["metric"], str):
+            raise StyxValidationError(f'`metric` has the wrong type: Received `{type(params.get("metric", None))}` expected `str | None`')
+    if params.get("mask1", None) is not None:
+        if not isinstance(params["mask1"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`mask1` has the wrong type: Received `{type(params.get("mask1", None))}` expected `InputPathType | None`')
+    if params.get("mask2", None) is not None:
+        if not isinstance(params["mask2"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`mask2` has the wrong type: Received `{type(params.get("mask2", None))}` expected `InputPathType | None`')
+    if params.get("nonormalisation", False) is None:
+        raise StyxValidationError("`nonormalisation` must not be None")
+    if not isinstance(params["nonormalisation"], bool):
+        raise StyxValidationError(f'`nonormalisation` has the wrong type: Received `{type(params.get("nonormalisation", False))}` expected `bool`')
+    if params.get("overlap", False) is None:
+        raise StyxValidationError("`overlap` must not be None")
+    if not isinstance(params["overlap"], bool):
+        raise StyxValidationError(f'`overlap` has the wrong type: Received `{type(params.get("overlap", False))}` expected `bool`')
+    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[MrmetricConfigParamsDict] | None`')
+        for e in params["config"]:
+            mrmetric_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("image1", None) is None:
+        raise StyxValidationError("`image1` must not be None")
+    if not isinstance(params["image1"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`image1` has the wrong type: Received `{type(params.get("image1", None))}` expected `InputPathType`')
+    if params.get("image2", None) is None:
+        raise StyxValidationError("`image2` must not be None")
+    if not isinstance(params["image2"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`image2` has the wrong type: Received `{type(params.get("image2", None))}` expected `InputPathType`')
+
+
+def mrmetric_cargs(
+    params: MrmetricParamsDict,
+    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("mrmetric")
+    if params.get("space", None) is not None:
+        cargs.extend([
+            "-space",
+            params.get("space", None)
+        ])
+    if params.get("interp", None) is not None:
+        cargs.extend([
+            "-interp",
+            params.get("interp", None)
+        ])
+    if params.get("metric", None) is not None:
+        cargs.extend([
+            "-metric",
+            params.get("metric", None)
+        ])
+    if params.get("mask1", None) is not None:
+        cargs.extend([
+            "-mask1",
+            execution.input_file(params.get("mask1", None))
+        ])
+    if params.get("mask2", None) is not None:
+        cargs.extend([
+            "-mask2",
+            execution.input_file(params.get("mask2", None))
+        ])
+    if params.get("nonormalisation", False):
+        cargs.append("-nonormalisation")
+    if params.get("overlap", False):
+        cargs.append("-overlap")
+    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 [mrmetric_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("image1", None)))
+    cargs.append(execution.input_file(params.get("image2", None)))
+    return cargs
+
+
+def mrmetric_outputs(
+    params: MrmetricParamsDict,
+    execution: Execution,
+) -> MrmetricOutputs:
+    """
+    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 = MrmetricOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mrmetric_execute(
+    params: MrmetricParamsDict,
+    runner: Runner | None = None,
+) -> MrmetricOutputs:
+    """
+    mrmetric
+    
+    Computes a dissimilarity metric between two images.
+    
+    Currently only the mean squared difference is fully implemented.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrmetricOutputs`).
+    """
+    mrmetric_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRMETRIC_METADATA)
+    params = execution.params(params)
+    cargs = mrmetric_cargs(params, execution)
+    ret = mrmetric_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrmetric(
+    image1: InputPathType,
+    image2: InputPathType,
+    space: str | None = None,
+    interp: str | None = None,
+    metric: str | None = None,
+    mask1: InputPathType | None = None,
+    mask2: InputPathType | None = None,
+    nonormalisation: bool = False,
+    overlap: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrmetricConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrmetricOutputs:
+    """
+    mrmetric
+    
+    Computes a dissimilarity metric between two images.
+    
+    Currently only the mean squared difference is fully implemented.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        image1: the first input image.
+        image2: the second input image.
+        space: voxel (default): per voxel image1: scanner space of image 1\
+            image2: scanner space of image 2 average: scanner space of the average\
+            affine transformation of image 1 and 2.
+        interp: set the interpolation method to use when reslicing (choices:\
+            nearest, linear, cubic, sinc. Default: linear).
+        metric: define the dissimilarity metric used to calculate the cost.\
+            Choices: diff (squared differences), cc (non-normalised negative cross\
+            correlation aka negative cross covariance). Default: diff). cc is only\
+            implemented for -space average and -interp linear and cubic.
+        mask1: mask for image 1.
+        mask2: mask for image 2.
+        nonormalisation: do not normalise the dissimilarity metric to the\
+            number of voxels.
+        overlap: output number of voxels that were used.
+        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 `MrmetricOutputs`).
+    """
+    params = mrmetric_params(
+        space=space,
+        interp=interp,
+        metric=metric,
+        mask1=mask1,
+        mask2=mask2,
+        nonormalisation=nonormalisation,
+        overlap=overlap,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        image1=image1,
+        image2=image2,
+    )
+    return mrmetric_execute(params, runner)
+
+
+__all__ = [
+    "MRMETRIC_METADATA",
+    "MrmetricConfigParamsDict",
+    "MrmetricConfigParamsDictTagged",
+    "MrmetricOutputs",
+    "MrmetricParamsDict",
+    "MrmetricParamsDictTagged",
+    "mrmetric",
+    "mrmetric_config",
+    "mrmetric_execute",
+    "mrmetric_params",
+]