peak_fit.py 13.5 KB
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#!/usr/bin/python
# coding: utf8
# /*##########################################################################
#
# Copyright (c) 2015-2016 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ###########################################################################*/

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from __future__ import absolute_import

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__authors__ = ["D. Naudet"]
__date__ = "01/06/2016"
__license__ = "MIT"

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import logging
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import ctypes
import multiprocessing as mp
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from threading import Thread
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import multiprocessing.sharedctypes as mp_sharedctypes
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from silx.math.fit import snip1d
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import numpy as np
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from scipy.optimize import leastsq
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from ... import config
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from ...io import QSpaceH5
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from ...io.FitH5 import BackgroundTypes
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from ...util import gaussian
from .fitresults import FitResult
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_logger = logging.getLogger(__name__)


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def background_estimation(mode, data):
    """Estimates a background of mode kind for data

    :param BackgroundTypes mode: The kind of background to compute
    :param numpy.ndarray data: The data array to process
    :return: The estimated background as an array with same shape as input
    :rtype: numpy.ndarray
    :raises ValueError: In case mode is not known
    """
    # Background subtraction
    if mode == BackgroundTypes.CONSTANT:
        # Shift data so that smallest value is 0
        return np.ones_like(data) * np.nanmin(data)

    elif mode == BackgroundTypes.LINEAR:
        # Simple linear background
        return np.linspace(data[0], data[-1], num=len(data), endpoint=True)

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    elif mode == BackgroundTypes.SNIP:
        # Using snip background
        return snip1d(data, snip_width=len(data))

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    elif mode == BackgroundTypes.NONE:
        return np.zeros_like(data)

    else:
        raise ValueError("Unsupported background mode")


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class FitTypes(object):
    """Kind of fit available"""
    ALLOWED = range(2)
    GAUSSIAN, CENTROID = ALLOWED


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class PeakFitter(Thread):
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    """
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    :param str qspace_f: path to the HDF5 file containing the qspace cubes
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    :param FitTypes fit_type:
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    :param indices: indices of the cubes (in the input HDF5 dataset) for which
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        the dim0/dim1/dim2 peaks coordinates will be computed. E.g : if the array
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        [1, 2, 3] is provided, only those cubes will be fitted.
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    :type indices: *optional* `array_like`
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    :param Union[int,None] n_proc:
        Number of process to use. If None, the config value is used.
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    :param BackgroundTypes background: The background subtraction to perform
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    """
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    READY, RUNNING, DONE, ERROR, CANCELED = __STATUSES = range(5)

    def __init__(self,
                 qspace_f,
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                 fit_type=FitTypes.GAUSSIAN,
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                 indices=None,
                 n_proc=None,
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                 roi_indices=None,
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                 background=BackgroundTypes.NONE):
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        super(PeakFitter, self).__init__()

        self.__results = None
        self.__thread = None
        self.__progress = 0
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        self.__callback = None
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        self.__status = self.READY

        self.__indices = None

        self.__qspace_f = qspace_f
        self.__fit_type = fit_type
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        self.__background = background
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        self.__n_proc = n_proc if n_proc else config.DEFAULT_PROCESS_NUMBER
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        self.__shared_progress = mp_sharedctypes.RawArray(ctypes.c_int32,
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                                                          self.__n_proc)
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        if roi_indices is not None:
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            self.__roi_indices = np.array(roi_indices[:])
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        else:
            self.__roi_indices = None

        if fit_type not in FitTypes.ALLOWED:
            self.__set_status(self.ERROR)
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            raise ValueError('Unknown fit type: {0}'.format(fit_type))

        if background not in BackgroundTypes.ALLOWED:
            self.__set_status(self.ERROR)
            raise ValueError('Unknown background type: {}'.format(background))
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        try:
            with QSpaceH5.QSpaceH5(qspace_f) as qspace_h5:
                with qspace_h5.qspace_dset_ctx() as dset:
                    qdata_shape = dset.shape
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                n_points = qdata_shape[0]
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                if indices is None:
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                    indices = list(range(n_points))
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                else:
                    indices = indices[:]
        except IOError:
            self.__set_status(self.ERROR)
            raise
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        self.__indices = np.array(indices)
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    def __set_status(self, status):
        assert status in self.__STATUSES
        self.__status = status

    status = property(lambda self: self.__status)

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    results = property(lambda self: self.__results)

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    def peak_fit(self, blocking=True, callback=None):
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        if self.__thread and self.__thread.is_alive():
            raise RuntimeError('A fit is already in progress.')

        self.__results = None

        if blocking:
            return self.__peak_fit()
        else:
            thread = self.__thread = Thread(target=self.__peak_fit)
            self.__callback = callback
            thread.start()

    def progress(self):
        return (100.0 *
                np.frombuffer(self.__shared_progress, dtype='int32').max() /
                (len(self.__indices) - 1))

    def __peak_fit(self):
        self.__set_status(self.RUNNING)

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        # TODO
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        progress = np.frombuffer(self.__shared_progress, dtype='int32')
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        progress[:] = 0
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        # TODO check file exists and can be opened

        import functools
        pool = mp.Pool(self.__n_proc)
        fit_results = pool.map(
            functools.partial(_fit_process,
                              qspace_f=self.__qspace_f,
                              fit_type=self.__fit_type,
                              background_type=self.__background,
                              roiIndices=self.__roi_indices),
            self.__indices)
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        pool.close()
        pool.join()

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        # Prepare FitResult object
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        with QSpaceH5.QSpaceH5(self.__qspace_f) as qspace_h5:
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            x_pos = qspace_h5.sample_x[self.__indices]
            y_pos = qspace_h5.sample_y[self.__indices]
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            q_dim0, q_dim1, q_dim2 = qspace_h5.qspace_dimension_values
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        if self.__roi_indices is not None:
            q_dim0 = q_dim0[self.__roi_indices[0][0]:self.__roi_indices[0][1]]
            q_dim1 = q_dim1[self.__roi_indices[1][0]:self.__roi_indices[1][1]]
            q_dim2 = q_dim2[self.__roi_indices[2][0]:self.__roi_indices[2][1]]
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        if self.__fit_type == FitTypes.GAUSSIAN:
            fit_name = 'Gaussian'
            result_name = 'gauss_0'
            result_dtype = [('Area', np.float64),
                            ('Center', np.float64),
                            ('Sigma', np.float64),
                            ('Status', np.bool_)]

        elif self.__fit_type == FitTypes.CENTROID:
            fit_name = 'Centroid'
            result_name = 'centroid'
            result_dtype = [('COM', np.float64),
                            ('I_sum', np.float64),
                            ('I_max', np.float64),
                            ('Pos_max', np.float64),
                            ('Status', np.bool_)]

        else:
            raise RuntimeError('Unknown Fit Type')
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        results = FitResult(entry=fit_name,
                            sample_x=x_pos,
                            sample_y=y_pos,
                            q_x=q_dim0,
                            q_y=q_dim1,
                            q_z=q_dim2,
                            background_mode=self.__background)
        fit_results = np.array(fit_results, dtype=result_dtype)
        # From points x axes to axes x points
        fit_results = np.transpose(fit_results)
        for axis_index, array in enumerate(fit_results):
            for name, _ in result_dtype[:-1]:
                results._add_axis_result(result_name, axis_index, name, array[name])
            results._set_axis_status(axis_index, array['Status'])

        self.__results = results
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        self.__set_status(self.DONE)

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        if self.__callback:
            self.__callback()

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        return results


def _fit_process(index,
                 qspace_f,
                 fit_type=FitTypes.GAUSSIAN,
                 background_type=BackgroundTypes.NONE,
                 roiIndices=None):
    """Run fit processing.

    It loads a QSpace, extracts a ROI from it, project to axes,
    and then for each axis, it subtracts a background and performs a fit/COM.

    This function is run through a multiprocessing.Pool

    :param int index: The index of the QSpace to process
    :param str qspace_f: Filename of the hdf5 file containing QSpace
    :param FitTypes fit_type: The kind of fit to perform
    :param BackgroundTypes background_type:
        The kind of background subtraction to perform
    :param Union[List[List[int]],None] roiIndices:
        Optional QSpace ROI start:end in the 3 dimensions
    :return: Fit results as a list of results for dim0, dim1 and dim2
    :rtype: List[List[Union[float,bool]]]
    """
    # Read data from file
    with QSpaceH5.QSpaceH5(qspace_f) as qspace_h5:
        axes = qspace_h5.qspace_dimension_values
        hits = qspace_h5.histo
        qspace = qspace_h5.qspace_slice(index)

    # apply Qspace ROI
    if roiIndices is not None:
        dim0Slice = slice(roiIndices[0][0], roiIndices[0][1], 1)
        dim1Slice = slice(roiIndices[1][0], roiIndices[1][1], 1)
        dim2Slice = slice(roiIndices[2][0], roiIndices[2][1], 1)

        axes = [axis[roi] for axis, roi in
                zip(axes, (dim0Slice, dim1Slice, dim2Slice))]
        hits = hits[dim0Slice, dim1Slice, dim2Slice]
        qspace = qspace[dim0Slice, dim1Slice, dim2Slice]

    # Normalize with hits and project to axes
    projections = project(qspace, hits)
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    # Background subtraction
    if background_type != BackgroundTypes.NONE:
        for array in projections:
            array -= background_estimation(background_type, array)
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    # Fit/COM
    fit = {FitTypes.CENTROID: centroid,
           FitTypes.GAUSSIAN: gaussian_fit}[fit_type]
    result = [fit(axis, values) for axis, values in zip(axes, projections)]
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    return result
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def project(data, hits=None):
    """Sum data along each axis
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    :param numpy.ndarray data: 3D histogram
    :param Union[numpy.ndarray,None] hits:
        Number of bin count of the histogram or None to ignore
    :return: Projections on each axis of the dataset
    :rtype: List[numpy.ndarray]
    """
    if hits is not None:
        data /= hits
        data[hits <= 0] = 0
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    dim2_sum = data.sum(axis=0).sum(axis=0)
    data_sum_dim2 = data.sum(axis=2)
    dim1_sum = data_sum_dim2.sum(axis=0)
    dim0_sum = data_sum_dim2.sum(axis=1)
    return dim0_sum, dim1_sum, dim2_sum
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# Center of mass
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def centroid(axis, signal):
    """Returns Center of mass and maximum information
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    :param numpy.ndarray axis: 1D x data
    :param numpy.ndarray signal: 1D y data
    :return: Center of mass, sum of signal, max of signal, position of max and status
        ('COM', 'I_sum', 'I_max', 'Pos_max', 'status')
    :rtype: List[Union[float,bool]]
    """
    signal_sum = signal.sum()
    if signal_sum == 0:
        return float('nan'), float('nan'), float('nan'), float('nan'), False
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    else:
        max_idx = signal.argmax()
        return (float(np.dot(axis, signal) / signal_sum),
                float(signal_sum),
                float(signal[max_idx]),
                float(axis[max_idx]),
                True)
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# Gaussian fit
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def _gaussian_err(parameters, axis, signal):
    """Returns difference between signal and given gaussian
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    :param List[float] parameters: area, center, sigma
    :param numpy.ndarray axis: 1D x data
    :param numpy.ndarray signal: 1D y data
    :return:
    """
    area, center, sigma = parameters
    return gaussian(axis, area, center, sigma) - signal
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_SQRT_2_PI = np.sqrt(2 * np.pi)
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# TODO double check
def gaussian_fit(axis, signal):
    """Returns gaussian fitting information
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    parameters: (a, c, s)
    and f(x) = (a / (sqrt(2 * pi) * s)) * exp(- 0.5 * ((x - c) / s)^2)
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    :param axis: 1D x data
    :param signal: 1D y data
    :return: Area, center, sigma, status
        ('Area', 'Center', 'Sigma', 'status)
    :rtype: List[Union[float,bool]]
    """
    # compute guess
    area = signal.sum() * (axis[-1] - axis[0]) / len(axis)
    center = axis[signal.argmax()]
    sigma = area / (signal.max() * _SQRT_2_PI)

    # Fit a gaussian
    result = leastsq(_gaussian_err,
                     x0=(area, center, sigma),
                     args=(axis, signal),
                     maxfev=100000,
                     full_output=True)

    if result[4] not in [1, 2, 3, 4]:
        return float('nan'), float('nan'), float('nan'), False

    else:
        area, center, sigma = result[0]
        return float(area), float(center), float(sigma), True