niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mtnormalise.py

@@ -0,0 +1,596 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MTNORMALISE_METADATA = Metadata(
+    id="3709b0ca1455372ea3dda75e22e31168270b187c.boutiques",
+    name="mtnormalise",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MtnormaliseConfigParameters = typing.TypedDict('MtnormaliseConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MtnormaliseInputOutputParameters = typing.TypedDict('MtnormaliseInputOutputParameters', {
+    "__STYX_TYPE__": typing.Literal["input_output"],
+    "input": InputPathType,
+    "output": str,
+})
+
+
+MtnormaliseParameters = typing.TypedDict('MtnormaliseParameters', {
+    "__STYX_TYPE__": typing.Literal["mtnormalise"],
+    "mask": InputPathType,
+    "order": typing.NotRequired[str | None],
+    "niter": typing.NotRequired[list[int] | None],
+    "reference": typing.NotRequired[float | None],
+    "balanced": bool,
+    "check_norm": typing.NotRequired[str | None],
+    "check_mask": typing.NotRequired[str | None],
+    "check_factors": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MtnormaliseConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input_output": list[MtnormaliseInputOutputParameters],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mtnormalise": mtnormalise_cargs,
+        "config": mtnormalise_config_cargs,
+        "input_output": mtnormalise_input_output_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 {
+        "mtnormalise": mtnormalise_outputs,
+        "input_output": mtnormalise_input_output_outputs,
+    }.get(t)
+
+
+def mtnormalise_config_params(
+    key: str,
+    value: str,
+) -> MtnormaliseConfigParameters:
+    """
+    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 mtnormalise_config_cargs(
+    params: MtnormaliseConfigParameters,
+    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 MtnormaliseInputOutputOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `list[MtnormaliseInputOutputParameters](...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """output normalised tissue compartment image."""
+
+
+def mtnormalise_input_output_params(
+    input_: InputPathType,
+    output: str,
+) -> MtnormaliseInputOutputParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: input tissue compartment image.
+        output: output normalised tissue compartment image.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "input_output",
+        "input": input_,
+        "output": output,
+    }
+    return params
+
+
+def mtnormalise_input_output_cargs(
+    params: MtnormaliseInputOutputParameters,
+    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(execution.input_file(params.get("input")))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def mtnormalise_input_output_outputs(
+    params: MtnormaliseInputOutputParameters,
+    execution: Execution,
+) -> MtnormaliseInputOutputOutputs:
+    """
+    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 = MtnormaliseInputOutputOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+class MtnormaliseOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mtnormalise(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    check_norm: OutputPathType | None
+    """output the final estimated spatially varying intensity level that is used
+    for normalisation. """
+    check_mask: OutputPathType | None
+    """output the final mask used to compute the normalisation. This mask
+    excludes regions identified as outliers by the optimisation process. """
+    check_factors: OutputPathType | None
+    """output the tissue balance factors computed during normalisation. """
+    input_output: list[MtnormaliseInputOutputOutputs]
+    """Outputs from `mtnormalise_input_output_outputs`.This is a list of outputs
+    with the same length and order as the inputs."""
+
+
+def mtnormalise_params(
+    mask: InputPathType,
+    input_output: list[MtnormaliseInputOutputParameters],
+    order: str | None = None,
+    niter: list[int] | None = None,
+    reference: float | None = None,
+    balanced: bool = False,
+    check_norm: str | None = None,
+    check_mask: str | None = None,
+    check_factors: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MtnormaliseConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MtnormaliseParameters:
+    """
+    Build parameters.
+    
+    Args:
+        mask: the mask defines the data used to compute the intensity\
+            normalisation. This option is mandatory.
+        input_output: list of all input and output tissue compartment files\
+            (see example usage).
+        order: the maximum order of the polynomial basis used to fit the\
+            normalisation field in the log-domain. An order of 0 is equivalent to\
+            not allowing spatial variance of the intensity normalisation factor.\
+            (default: 3).
+        niter: set the number of iterations. The first (and potentially only)\
+            entry applies to the main loop. If supplied as a comma-separated list\
+            of integers, the second entry applies to the inner loop to update the\
+            balance factors (default: 15,7).
+        reference: specify the (positive) reference value to which the summed\
+            tissue compartments will be normalised. (default: 0.282095, SH DC term\
+            for unit angular integral).
+        balanced: incorporate the per-tissue balancing factors into scaling of\
+            the output images (NOTE: use of this option has critical consequences\
+            for AFD intensity normalisation; should not be used unless these\
+            consequences are fully understood).
+        check_norm: output the final estimated spatially varying intensity\
+            level that is used for normalisation.
+        check_mask: output the final mask used to compute the normalisation.\
+            This mask excludes regions identified as outliers by the optimisation\
+            process.
+        check_factors: output the tissue balance factors computed during\
+            normalisation.
+        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__": "mtnormalise",
+        "mask": mask,
+        "balanced": balanced,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input_output": input_output,
+    }
+    if order is not None:
+        params["order"] = order
+    if niter is not None:
+        params["niter"] = niter
+    if reference is not None:
+        params["reference"] = reference
+    if check_norm is not None:
+        params["check_norm"] = check_norm
+    if check_mask is not None:
+        params["check_mask"] = check_mask
+    if check_factors is not None:
+        params["check_factors"] = check_factors
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def mtnormalise_cargs(
+    params: MtnormaliseParameters,
+    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("mtnormalise")
+    cargs.extend([
+        "-mask",
+        execution.input_file(params.get("mask"))
+    ])
+    if params.get("order") is not None:
+        cargs.extend([
+            "-order",
+            params.get("order")
+        ])
+    if params.get("niter") is not None:
+        cargs.extend([
+            "-niter",
+            ",".join(map(str, params.get("niter")))
+        ])
+    if params.get("reference") is not None:
+        cargs.extend([
+            "-reference",
+            str(params.get("reference"))
+        ])
+    if params.get("balanced"):
+        cargs.append("-balanced")
+    if params.get("check_norm") is not None:
+        cargs.extend([
+            "-check_norm",
+            params.get("check_norm")
+        ])
+    if params.get("check_mask") is not None:
+        cargs.extend([
+            "-check_mask",
+            params.get("check_mask")
+        ])
+    if params.get("check_factors") is not None:
+        cargs.extend([
+            "-check_factors",
+            params.get("check_factors")
+        ])
+    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.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("input_output")] for a in c])
+    return cargs
+
+
+def mtnormalise_outputs(
+    params: MtnormaliseParameters,
+    execution: Execution,
+) -> MtnormaliseOutputs:
+    """
+    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 = MtnormaliseOutputs(
+        root=execution.output_file("."),
+        check_norm=execution.output_file(params.get("check_norm")) if (params.get("check_norm") is not None) else None,
+        check_mask=execution.output_file(params.get("check_mask")) if (params.get("check_mask") is not None) else None,
+        check_factors=execution.output_file(params.get("check_factors")) if (params.get("check_factors") is not None) else None,
+        input_output=[dyn_outputs(i["__STYXTYPE__"])(i, execution) if dyn_outputs(i["__STYXTYPE__"]) else None for i in params.get("input_output")],
+    )
+    return ret
+
+
+def mtnormalise_execute(
+    params: MtnormaliseParameters,
+    execution: Execution,
+) -> MtnormaliseOutputs:
+    """
+    Multi-tissue informed log-domain intensity normalisation.
+    
+    This command takes as input any number of tissue components (e.g. from
+    multi-tissue CSD) and outputs corresponding normalised tissue components
+    corrected for the effects of (residual) intensity inhomogeneities. Intensity
+    normalisation is performed by optimising the voxel-wise sum of all tissue
+    compartments towards a constant value, under constraints of spatial
+    smoothness (polynomial basis of a given order). Different to the Raffelt et
+    al. 2017 abstract, this algorithm performs this task in the log-domain
+    instead, with added gradual outlier rejection, different handling of the
+    balancing factors between tissue compartments and a different iteration
+    structure.
+    
+    The -mask option is mandatory and is optimally provided with a brain mask
+    (such as the one obtained from dwi2mask earlier in the processing pipeline).
+    Outlier areas with exceptionally low or high combined tissue contributions
+    are accounted for and reoptimised as the intensity inhomogeneity estimation
+    becomes more accurate.
+    
+    References:
+    
+    Raffelt, D.; Dhollander, T.; Tournier, J.-D.; Tabbara, R.; Smith, R. E.;
+    Pierre, E. & Connelly, A. Bias Field Correction and Intensity Normalisation
+    for Quantitative Analysis of Apparent Fibre Density. In Proc. ISMRM, 2017,
+    26, 3541
+    
+    Dhollander, T.; Tabbara, R.; Rosnarho-Tornstrand, J.; Tournier, J.-D.;
+    Raffelt, D. & Connelly, A. Multi-tissue log-domain intensity and
+    inhomogeneity normalisation for quantitative apparent fibre density. In
+    Proc. ISMRM, 2021, 29, 2472.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MtnormaliseOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mtnormalise_cargs(params, execution)
+    ret = mtnormalise_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mtnormalise(
+    mask: InputPathType,
+    input_output: list[MtnormaliseInputOutputParameters],
+    order: str | None = None,
+    niter: list[int] | None = None,
+    reference: float | None = None,
+    balanced: bool = False,
+    check_norm: str | None = None,
+    check_mask: str | None = None,
+    check_factors: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MtnormaliseConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MtnormaliseOutputs:
+    """
+    Multi-tissue informed log-domain intensity normalisation.
+    
+    This command takes as input any number of tissue components (e.g. from
+    multi-tissue CSD) and outputs corresponding normalised tissue components
+    corrected for the effects of (residual) intensity inhomogeneities. Intensity
+    normalisation is performed by optimising the voxel-wise sum of all tissue
+    compartments towards a constant value, under constraints of spatial
+    smoothness (polynomial basis of a given order). Different to the Raffelt et
+    al. 2017 abstract, this algorithm performs this task in the log-domain
+    instead, with added gradual outlier rejection, different handling of the
+    balancing factors between tissue compartments and a different iteration
+    structure.
+    
+    The -mask option is mandatory and is optimally provided with a brain mask
+    (such as the one obtained from dwi2mask earlier in the processing pipeline).
+    Outlier areas with exceptionally low or high combined tissue contributions
+    are accounted for and reoptimised as the intensity inhomogeneity estimation
+    becomes more accurate.
+    
+    References:
+    
+    Raffelt, D.; Dhollander, T.; Tournier, J.-D.; Tabbara, R.; Smith, R. E.;
+    Pierre, E. & Connelly, A. Bias Field Correction and Intensity Normalisation
+    for Quantitative Analysis of Apparent Fibre Density. In Proc. ISMRM, 2017,
+    26, 3541
+    
+    Dhollander, T.; Tabbara, R.; Rosnarho-Tornstrand, J.; Tournier, J.-D.;
+    Raffelt, D. & Connelly, A. Multi-tissue log-domain intensity and
+    inhomogeneity normalisation for quantitative apparent fibre density. In
+    Proc. ISMRM, 2021, 29, 2472.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        mask: the mask defines the data used to compute the intensity\
+            normalisation. This option is mandatory.
+        input_output: list of all input and output tissue compartment files\
+            (see example usage).
+        order: the maximum order of the polynomial basis used to fit the\
+            normalisation field in the log-domain. An order of 0 is equivalent to\
+            not allowing spatial variance of the intensity normalisation factor.\
+            (default: 3).
+        niter: set the number of iterations. The first (and potentially only)\
+            entry applies to the main loop. If supplied as a comma-separated list\
+            of integers, the second entry applies to the inner loop to update the\
+            balance factors (default: 15,7).
+        reference: specify the (positive) reference value to which the summed\
+            tissue compartments will be normalised. (default: 0.282095, SH DC term\
+            for unit angular integral).
+        balanced: incorporate the per-tissue balancing factors into scaling of\
+            the output images (NOTE: use of this option has critical consequences\
+            for AFD intensity normalisation; should not be used unless these\
+            consequences are fully understood).
+        check_norm: output the final estimated spatially varying intensity\
+            level that is used for normalisation.
+        check_mask: output the final mask used to compute the normalisation.\
+            This mask excludes regions identified as outliers by the optimisation\
+            process.
+        check_factors: output the tissue balance factors computed during\
+            normalisation.
+        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 `MtnormaliseOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MTNORMALISE_METADATA)
+    params = mtnormalise_params(
+        mask=mask,
+        order=order,
+        niter=niter,
+        reference=reference,
+        balanced=balanced,
+        check_norm=check_norm,
+        check_mask=check_mask,
+        check_factors=check_factors,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_output=input_output,
+    )
+    return mtnormalise_execute(params, execution)
+
+
+__all__ = [
+    "MTNORMALISE_METADATA",
+    "MtnormaliseConfigParameters",
+    "MtnormaliseInputOutputOutputs",
+    "MtnormaliseInputOutputParameters",
+    "MtnormaliseOutputs",
+    "MtnormaliseParameters",
+    "mtnormalise",
+    "mtnormalise_config_params",
+    "mtnormalise_input_output_params",
+    "mtnormalise_params",
+]