niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fod2dec.py

@@ -0,0 +1,571 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FOD2DEC_METADATA = Metadata(
+    id="56fd41eb31bb1240fd6341ac5abf21815b0e9dac.boutiques",
+    name="fod2dec",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Fod2decConfigParamsDictNoTag = typing.TypedDict('_Fod2decConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Fod2decConfigParamsDictTagged = typing.TypedDict('Fod2decConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Fod2decConfigParamsDict = _Fod2decConfigParamsDictNoTag | Fod2decConfigParamsDictTagged
+
+
+_Fod2decParamsDictNoTag = typing.TypedDict('_Fod2decParamsDictNoTag', {
+    "mask": typing.NotRequired[InputPathType | None],
+    "contrast": typing.NotRequired[InputPathType | None],
+    "lum": bool,
+    "lum_coefs": typing.NotRequired[list[float] | None],
+    "lum_gamma": typing.NotRequired[float | None],
+    "threshold": typing.NotRequired[float | None],
+    "no_weight": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fod2decConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+Fod2decParamsDictTagged = typing.TypedDict('Fod2decParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/fod2dec"],
+    "mask": typing.NotRequired[InputPathType | None],
+    "contrast": typing.NotRequired[InputPathType | None],
+    "lum": bool,
+    "lum_coefs": typing.NotRequired[list[float] | None],
+    "lum_gamma": typing.NotRequired[float | None],
+    "threshold": typing.NotRequired[float | None],
+    "no_weight": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fod2decConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+Fod2decParamsDict = _Fod2decParamsDictNoTag | Fod2decParamsDictTagged
+
+
+def fod2dec_config(
+    key: str,
+    value: str,
+) -> Fod2decConfigParamsDictTagged:
+    """
+    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 fod2dec_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Fod2decConfigParamsDict` 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 fod2dec_config_cargs(
+    params: Fod2decConfigParamsDict,
+    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 Fod2decOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Fod2decParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """The output DEC image (weighted RGB triplets)."""
+
+
+def fod2dec_params(
+    input_: InputPathType,
+    output: str,
+    mask: InputPathType | None = None,
+    contrast: InputPathType | None = None,
+    lum: bool = False,
+    lum_coefs: list[float] | None = None,
+    lum_gamma: float | None = None,
+    threshold: float | None = None,
+    no_weight: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fod2decConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Fod2decParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: The input FOD image (spherical harmonic coefficients).
+        output: The output DEC image (weighted RGB triplets).
+        mask: Only perform DEC computation within the specified mask image.
+        contrast: Weight the computed DEC map by the provided image contrast.\
+            If the contrast has a different image grid, the DEC map is first\
+            resliced and renormalised. To achieve panchromatic sharpening, provide\
+            an image with a higher spatial resolution than the input FOD image;\
+            e.g., a T1 anatomical volume. Only the DEC is subject to the mask, so\
+            as to allow for partial colouring of the contrast image.\
+            Default when this option is *not* provided: integral of input FOD,\
+            subject to the same mask/threshold as used for DEC computation.
+        lum: Correct for luminance/perception, using default values Cr,Cg,Cb =\
+            0.3,0.5,0.2 and gamma = 2.2 (*not* correcting is the theoretical\
+            equivalent of Cr,Cg,Cb = 1,1,1 and gamma = 2).
+        lum_coefs: The coefficients Cr,Cg,Cb to correct for\
+            luminance/perception.\
+            Note: this implicitly switches on luminance/perception correction,\
+            using a default gamma = 2.2 unless specified otherwise.
+        lum_gamma: The gamma value to correct for luminance/perception.\
+            Note: this implicitly switches on luminance/perception correction,\
+            using a default Cr,Cg,Cb = 0.3,0.5,0.2 unless specified otherwise.
+        threshold: FOD amplitudes below the threshold value are considered\
+            zero.
+        no_weight: Do not weight the DEC map; just output the unweighted\
+            colours. Reslicing and renormalising of colours will still happen when\
+            providing the -contrast option as a template.
+        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/fod2dec",
+        "lum": lum,
+        "no_weight": no_weight,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if contrast is not None:
+        params["contrast"] = contrast
+    if lum_coefs is not None:
+        params["lum_coefs"] = lum_coefs
+    if lum_gamma is not None:
+        params["lum_gamma"] = lum_gamma
+    if threshold is not None:
+        params["threshold"] = threshold
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fod2dec_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Fod2decParamsDict` 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", None) is not None:
+        if not isinstance(params["mask"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`mask` has the wrong type: Received `{type(params.get("mask", None))}` expected `InputPathType | None`')
+    if params.get("contrast", None) is not None:
+        if not isinstance(params["contrast"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`contrast` has the wrong type: Received `{type(params.get("contrast", None))}` expected `InputPathType | None`')
+    if params.get("lum", False) is None:
+        raise StyxValidationError("`lum` must not be None")
+    if not isinstance(params["lum"], bool):
+        raise StyxValidationError(f'`lum` has the wrong type: Received `{type(params.get("lum", False))}` expected `bool`')
+    if params.get("lum_coefs", None) is not None:
+        if not isinstance(params["lum_coefs"], list):
+            raise StyxValidationError(f'`lum_coefs` has the wrong type: Received `{type(params.get("lum_coefs", None))}` expected `list[float] | None`')
+        for e in params["lum_coefs"]:
+            if not isinstance(e, (float, int)):
+                raise StyxValidationError(f'`lum_coefs` has the wrong type: Received `{type(params.get("lum_coefs", None))}` expected `list[float] | None`')
+    if params.get("lum_gamma", None) is not None:
+        if not isinstance(params["lum_gamma"], (float, int)):
+            raise StyxValidationError(f'`lum_gamma` has the wrong type: Received `{type(params.get("lum_gamma", None))}` expected `float | None`')
+    if params.get("threshold", None) is not None:
+        if not isinstance(params["threshold"], (float, int)):
+            raise StyxValidationError(f'`threshold` has the wrong type: Received `{type(params.get("threshold", None))}` expected `float | None`')
+    if params.get("no_weight", False) is None:
+        raise StyxValidationError("`no_weight` must not be None")
+    if not isinstance(params["no_weight"], bool):
+        raise StyxValidationError(f'`no_weight` has the wrong type: Received `{type(params.get("no_weight", 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[Fod2decConfigParamsDict] | None`')
+        for e in params["config"]:
+            fod2dec_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("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 fod2dec_cargs(
+    params: Fod2decParamsDict,
+    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("fod2dec")
+    if params.get("mask", None) is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask", None))
+        ])
+    if params.get("contrast", None) is not None:
+        cargs.extend([
+            "-contrast",
+            execution.input_file(params.get("contrast", None))
+        ])
+    if params.get("lum", False):
+        cargs.append("-lum")
+    if params.get("lum_coefs", None) is not None:
+        cargs.extend([
+            "-lum_coefs",
+            *map(str, params.get("lum_coefs", None))
+        ])
+    if params.get("lum_gamma", None) is not None:
+        cargs.extend([
+            "-lum_gamma",
+            str(params.get("lum_gamma", None))
+        ])
+    if params.get("threshold", None) is not None:
+        cargs.extend([
+            "-threshold",
+            str(params.get("threshold", None))
+        ])
+    if params.get("no_weight", False):
+        cargs.append("-no_weight")
+    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 [fod2dec_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("output", None))
+    return cargs
+
+
+def fod2dec_outputs(
+    params: Fod2decParamsDict,
+    execution: Execution,
+) -> Fod2decOutputs:
+    """
+    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 = Fod2decOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+def fod2dec_execute(
+    params: Fod2decParamsDict,
+    runner: Runner | None = None,
+) -> Fod2decOutputs:
+    """
+    fod2dec
+    
+    Generate FOD-based DEC maps, with optional panchromatic sharpening and/or
+    luminance/perception correction.
+    
+    By default, the FOD-based DEC is weighted by the integral of the FOD. To
+    weight by another scalar map, use the -contrast option. This option can also
+    be used for panchromatic sharpening, e.g., by supplying a T1 (or other
+    sensible) anatomical volume with a higher spatial resolution.
+    
+    References:
+    
+    Dhollander T, Smith RE, Tournier JD, Jeurissen B, Connelly A. Time to move
+    on: an FOD-based DEC map to replace DTI's trademark DEC FA. Proc Intl Soc
+    Mag Reson Med, 2015, 23, 1027
+    
+    Dhollander T, Raffelt D, Smith RE, Connelly A. Panchromatic sharpening of
+    FOD-based DEC maps by structural T1 information. Proc Intl Soc Mag Reson
+    Med, 2015, 23, 566.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Fod2decOutputs`).
+    """
+    fod2dec_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FOD2DEC_METADATA)
+    params = execution.params(params)
+    cargs = fod2dec_cargs(params, execution)
+    ret = fod2dec_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fod2dec(
+    input_: InputPathType,
+    output: str,
+    mask: InputPathType | None = None,
+    contrast: InputPathType | None = None,
+    lum: bool = False,
+    lum_coefs: list[float] | None = None,
+    lum_gamma: float | None = None,
+    threshold: float | None = None,
+    no_weight: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fod2decConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Fod2decOutputs:
+    """
+    fod2dec
+    
+    Generate FOD-based DEC maps, with optional panchromatic sharpening and/or
+    luminance/perception correction.
+    
+    By default, the FOD-based DEC is weighted by the integral of the FOD. To
+    weight by another scalar map, use the -contrast option. This option can also
+    be used for panchromatic sharpening, e.g., by supplying a T1 (or other
+    sensible) anatomical volume with a higher spatial resolution.
+    
+    References:
+    
+    Dhollander T, Smith RE, Tournier JD, Jeurissen B, Connelly A. Time to move
+    on: an FOD-based DEC map to replace DTI's trademark DEC FA. Proc Intl Soc
+    Mag Reson Med, 2015, 23, 1027
+    
+    Dhollander T, Raffelt D, Smith RE, Connelly A. Panchromatic sharpening of
+    FOD-based DEC maps by structural T1 information. Proc Intl Soc Mag Reson
+    Med, 2015, 23, 566.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: The input FOD image (spherical harmonic coefficients).
+        output: The output DEC image (weighted RGB triplets).
+        mask: Only perform DEC computation within the specified mask image.
+        contrast: Weight the computed DEC map by the provided image contrast.\
+            If the contrast has a different image grid, the DEC map is first\
+            resliced and renormalised. To achieve panchromatic sharpening, provide\
+            an image with a higher spatial resolution than the input FOD image;\
+            e.g., a T1 anatomical volume. Only the DEC is subject to the mask, so\
+            as to allow for partial colouring of the contrast image.\
+            Default when this option is *not* provided: integral of input FOD,\
+            subject to the same mask/threshold as used for DEC computation.
+        lum: Correct for luminance/perception, using default values Cr,Cg,Cb =\
+            0.3,0.5,0.2 and gamma = 2.2 (*not* correcting is the theoretical\
+            equivalent of Cr,Cg,Cb = 1,1,1 and gamma = 2).
+        lum_coefs: The coefficients Cr,Cg,Cb to correct for\
+            luminance/perception.\
+            Note: this implicitly switches on luminance/perception correction,\
+            using a default gamma = 2.2 unless specified otherwise.
+        lum_gamma: The gamma value to correct for luminance/perception.\
+            Note: this implicitly switches on luminance/perception correction,\
+            using a default Cr,Cg,Cb = 0.3,0.5,0.2 unless specified otherwise.
+        threshold: FOD amplitudes below the threshold value are considered\
+            zero.
+        no_weight: Do not weight the DEC map; just output the unweighted\
+            colours. Reslicing and renormalising of colours will still happen when\
+            providing the -contrast option as a template.
+        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 `Fod2decOutputs`).
+    """
+    params = fod2dec_params(
+        mask=mask,
+        contrast=contrast,
+        lum=lum,
+        lum_coefs=lum_coefs,
+        lum_gamma=lum_gamma,
+        threshold=threshold,
+        no_weight=no_weight,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return fod2dec_execute(params, runner)
+
+
+__all__ = [
+    "FOD2DEC_METADATA",
+    "Fod2decConfigParamsDict",
+    "Fod2decConfigParamsDictTagged",
+    "Fod2decOutputs",
+    "Fod2decParamsDict",
+    "Fod2decParamsDictTagged",
+    "fod2dec",
+    "fod2dec_config",
+    "fod2dec_execute",
+    "fod2dec_params",
+]