niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fod2fixel.py

@@ -0,0 +1,530 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FOD2FIXEL_METADATA = Metadata(
+    id="4748cd2237541a5061a51ecd86840055b92d34ff.boutiques",
+    name="fod2fixel",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Fod2fixelConfigParameters = typing.TypedDict('Fod2fixelConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Fod2fixelParameters = typing.TypedDict('Fod2fixelParameters', {
+    "__STYX_TYPE__": typing.Literal["fod2fixel"],
+    "afd": typing.NotRequired[str | None],
+    "peak_amp": typing.NotRequired[str | None],
+    "disp": typing.NotRequired[str | None],
+    "fmls_integral": typing.NotRequired[float | None],
+    "fmls_peak_value": typing.NotRequired[float | None],
+    "fmls_no_thresholds": bool,
+    "fmls_lobe_merge_ratio": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "maxnum": typing.NotRequired[int | None],
+    "nii": bool,
+    "dirpeak": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fod2fixelConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "fod": InputPathType,
+    "fixel_directory": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fod2fixel": fod2fixel_cargs,
+        "config": fod2fixel_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 {
+        "fod2fixel": fod2fixel_outputs,
+    }.get(t)
+
+
+def fod2fixel_config_params(
+    key: str,
+    value: str,
+) -> Fod2fixelConfigParameters:
+    """
+    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 fod2fixel_config_cargs(
+    params: Fod2fixelConfigParameters,
+    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 Fod2fixelOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fod2fixel(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    fixel_directory: OutputPathType
+    """the output fixel directory"""
+    afd: OutputPathType | None
+    """output the total Apparent Fibre Density per fixel (integral of FOD lobe)
+    """
+    peak_amp: OutputPathType | None
+    """output the amplitude of the FOD at the maximal peak per fixel """
+    disp: OutputPathType | None
+    """output a measure of dispersion per fixel as the ratio between FOD lobe
+    integral and maximal peak amplitude """
+
+
+def fod2fixel_params(
+    fod: InputPathType,
+    fixel_directory: str,
+    afd: str | None = None,
+    peak_amp: str | None = None,
+    disp: str | None = None,
+    fmls_integral: float | None = None,
+    fmls_peak_value: float | None = None,
+    fmls_no_thresholds: bool = False,
+    fmls_lobe_merge_ratio: float | None = None,
+    mask: InputPathType | None = None,
+    maxnum: int | None = None,
+    nii: bool = False,
+    dirpeak: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fod2fixelConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Fod2fixelParameters:
+    """
+    Build parameters.
+    
+    Args:
+        fod: the input fod image.
+        fixel_directory: the output fixel directory.
+        afd: output the total Apparent Fibre Density per fixel (integral of FOD\
+            lobe).
+        peak_amp: output the amplitude of the FOD at the maximal peak per fixel.
+        disp: output a measure of dispersion per fixel as the ratio between FOD\
+            lobe integral and maximal peak amplitude.
+        fmls_integral: threshold absolute numerical integral of positive FOD\
+            lobes. Any lobe for which the integral is smaller than this threshold\
+            will be discarded. Default: 0.
+        fmls_peak_value: threshold peak amplitude of positive FOD lobes. Any\
+            lobe for which the maximal peak amplitude is smaller than this\
+            threshold will be discarded. Default: 0.1.
+        fmls_no_thresholds: disable all FOD lobe thresholding; every lobe where\
+            the FOD is positive will be retained.
+        fmls_lobe_merge_ratio: Specify the ratio between a given FOD amplitude\
+            sample between two lobes, and the smallest peak amplitude of the\
+            adjacent lobes, above which those lobes will be merged. This is the\
+            amplitude of the FOD at the 'bridge' point between the two lobes,\
+            divided by the peak amplitude of the smaller of the two adjoining\
+            lobes. A value of 1.0 will never merge two lobes into one; a value of\
+            0.0 will always merge lobes unless they are bisected by a zero-valued\
+            crossing. Default: 1.
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        maxnum: maximum number of fixels to output for any particular voxel\
+            (default: no limit).
+        nii: output the directions and index file in nii format (instead of the\
+            default mif).
+        dirpeak: define the fixel direction as that of the lobe's maximal peak\
+            as opposed to its weighted mean direction (the default).
+        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__": "fod2fixel",
+        "fmls_no_thresholds": fmls_no_thresholds,
+        "nii": nii,
+        "dirpeak": dirpeak,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "fod": fod,
+        "fixel_directory": fixel_directory,
+    }
+    if afd is not None:
+        params["afd"] = afd
+    if peak_amp is not None:
+        params["peak_amp"] = peak_amp
+    if disp is not None:
+        params["disp"] = disp
+    if fmls_integral is not None:
+        params["fmls_integral"] = fmls_integral
+    if fmls_peak_value is not None:
+        params["fmls_peak_value"] = fmls_peak_value
+    if fmls_lobe_merge_ratio is not None:
+        params["fmls_lobe_merge_ratio"] = fmls_lobe_merge_ratio
+    if mask is not None:
+        params["mask"] = mask
+    if maxnum is not None:
+        params["maxnum"] = maxnum
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fod2fixel_cargs(
+    params: Fod2fixelParameters,
+    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("fod2fixel")
+    if params.get("afd") is not None:
+        cargs.extend([
+            "-afd",
+            params.get("afd")
+        ])
+    if params.get("peak_amp") is not None:
+        cargs.extend([
+            "-peak_amp",
+            params.get("peak_amp")
+        ])
+    if params.get("disp") is not None:
+        cargs.extend([
+            "-disp",
+            params.get("disp")
+        ])
+    if params.get("fmls_integral") is not None:
+        cargs.extend([
+            "-fmls_integral",
+            str(params.get("fmls_integral"))
+        ])
+    if params.get("fmls_peak_value") is not None:
+        cargs.extend([
+            "-fmls_peak_value",
+            str(params.get("fmls_peak_value"))
+        ])
+    if params.get("fmls_no_thresholds"):
+        cargs.append("-fmls_no_thresholds")
+    if params.get("fmls_lobe_merge_ratio") is not None:
+        cargs.extend([
+            "-fmls_lobe_merge_ratio",
+            str(params.get("fmls_lobe_merge_ratio"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("maxnum") is not None:
+        cargs.extend([
+            "-maxnum",
+            str(params.get("maxnum"))
+        ])
+    if params.get("nii"):
+        cargs.append("-nii")
+    if params.get("dirpeak"):
+        cargs.append("-dirpeak")
+    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(execution.input_file(params.get("fod")))
+    cargs.append(params.get("fixel_directory"))
+    return cargs
+
+
+def fod2fixel_outputs(
+    params: Fod2fixelParameters,
+    execution: Execution,
+) -> Fod2fixelOutputs:
+    """
+    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 = Fod2fixelOutputs(
+        root=execution.output_file("."),
+        fixel_directory=execution.output_file(params.get("fixel_directory")),
+        afd=execution.output_file(params.get("afd")) if (params.get("afd") is not None) else None,
+        peak_amp=execution.output_file(params.get("peak_amp")) if (params.get("peak_amp") is not None) else None,
+        disp=execution.output_file(params.get("disp")) if (params.get("disp") is not None) else None,
+    )
+    return ret
+
+
+def fod2fixel_execute(
+    params: Fod2fixelParameters,
+    execution: Execution,
+) -> Fod2fixelOutputs:
+    """
+    Perform segmentation of continuous Fibre Orientation Distributions (FODs) to
+    produce discrete fixels.
+    
+    
+    
+    References:
+    
+    * Reference for the FOD segmentation method:
+    Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT:
+    Spherical-deconvolution informed filtering of tractograms. NeuroImage, 2013,
+    67, 298-312 (Appendix 2)
+    
+    * Reference for Apparent Fibre Density (AFD):
+    Raffelt, D.; Tournier, J.-D.; Rose, S.; Ridgway, G.R.; Henderson, R.;
+    Crozier, S.; Salvado, O.; Connelly, A. Apparent Fibre Density: a novel
+    measure for the analysis of diffusion-weighted magnetic resonance
+    images.Neuroimage, 2012, 15;59(4), 3976-94.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Fod2fixelOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fod2fixel_cargs(params, execution)
+    ret = fod2fixel_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fod2fixel(
+    fod: InputPathType,
+    fixel_directory: str,
+    afd: str | None = None,
+    peak_amp: str | None = None,
+    disp: str | None = None,
+    fmls_integral: float | None = None,
+    fmls_peak_value: float | None = None,
+    fmls_no_thresholds: bool = False,
+    fmls_lobe_merge_ratio: float | None = None,
+    mask: InputPathType | None = None,
+    maxnum: int | None = None,
+    nii: bool = False,
+    dirpeak: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fod2fixelConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Fod2fixelOutputs:
+    """
+    Perform segmentation of continuous Fibre Orientation Distributions (FODs) to
+    produce discrete fixels.
+    
+    
+    
+    References:
+    
+    * Reference for the FOD segmentation method:
+    Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT:
+    Spherical-deconvolution informed filtering of tractograms. NeuroImage, 2013,
+    67, 298-312 (Appendix 2)
+    
+    * Reference for Apparent Fibre Density (AFD):
+    Raffelt, D.; Tournier, J.-D.; Rose, S.; Ridgway, G.R.; Henderson, R.;
+    Crozier, S.; Salvado, O.; Connelly, A. Apparent Fibre Density: a novel
+    measure for the analysis of diffusion-weighted magnetic resonance
+    images.Neuroimage, 2012, 15;59(4), 3976-94.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        fod: the input fod image.
+        fixel_directory: the output fixel directory.
+        afd: output the total Apparent Fibre Density per fixel (integral of FOD\
+            lobe).
+        peak_amp: output the amplitude of the FOD at the maximal peak per fixel.
+        disp: output a measure of dispersion per fixel as the ratio between FOD\
+            lobe integral and maximal peak amplitude.
+        fmls_integral: threshold absolute numerical integral of positive FOD\
+            lobes. Any lobe for which the integral is smaller than this threshold\
+            will be discarded. Default: 0.
+        fmls_peak_value: threshold peak amplitude of positive FOD lobes. Any\
+            lobe for which the maximal peak amplitude is smaller than this\
+            threshold will be discarded. Default: 0.1.
+        fmls_no_thresholds: disable all FOD lobe thresholding; every lobe where\
+            the FOD is positive will be retained.
+        fmls_lobe_merge_ratio: Specify the ratio between a given FOD amplitude\
+            sample between two lobes, and the smallest peak amplitude of the\
+            adjacent lobes, above which those lobes will be merged. This is the\
+            amplitude of the FOD at the 'bridge' point between the two lobes,\
+            divided by the peak amplitude of the smaller of the two adjoining\
+            lobes. A value of 1.0 will never merge two lobes into one; a value of\
+            0.0 will always merge lobes unless they are bisected by a zero-valued\
+            crossing. Default: 1.
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        maxnum: maximum number of fixels to output for any particular voxel\
+            (default: no limit).
+        nii: output the directions and index file in nii format (instead of the\
+            default mif).
+        dirpeak: define the fixel direction as that of the lobe's maximal peak\
+            as opposed to its weighted mean direction (the default).
+        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 `Fod2fixelOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FOD2FIXEL_METADATA)
+    params = fod2fixel_params(
+        afd=afd,
+        peak_amp=peak_amp,
+        disp=disp,
+        fmls_integral=fmls_integral,
+        fmls_peak_value=fmls_peak_value,
+        fmls_no_thresholds=fmls_no_thresholds,
+        fmls_lobe_merge_ratio=fmls_lobe_merge_ratio,
+        mask=mask,
+        maxnum=maxnum,
+        nii=nii,
+        dirpeak=dirpeak,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        fod=fod,
+        fixel_directory=fixel_directory,
+    )
+    return fod2fixel_execute(params, execution)
+
+
+__all__ = [
+    "FOD2FIXEL_METADATA",
+    "Fod2fixelConfigParameters",
+    "Fod2fixelOutputs",
+    "Fod2fixelParameters",
+    "fod2fixel",
+    "fod2fixel_config_params",
+    "fod2fixel_params",
+]