QSpaceConverter.py 59.9 KB
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# coding: utf-8
# /*##########################################################################
#
# 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"]
__license__ = "MIT"
__date__ = "01/03/2016"


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import logging
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import os
import time
import ctypes
from threading import Thread
import multiprocessing as mp
import multiprocessing.sharedctypes as mp_sharedctypes

import numpy as np
import xrayutilities as xu

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from ...util.medianfilter import medfilt2d
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from ...util.histogramnd_lut import histogramnd_get_lut, histogramnd_from_lut
# from silx.math import histogramnd
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from ...io import XsocsH5, QSpaceH5, ShiftH5
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logger = logging.getLogger(__name__)


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disp_times = False


class QSpaceConverter(object):
    (READY, RUNNING, DONE,
     ERROR, CANCELED, UNKNOWN) = __STATUSES = range(6)
    """ Available status codes """

    status = property(lambda self: self.__status)
    """ Current status code of this instance """

    status_msg = property(lambda self: self.__status_msg)
    """ Status message if any, or None """

    results = property(lambda self: self.__results)
    """ Parse results. KmapParseResults instance. """

    xsocsH5_f = property(lambda self: self.__xsocsH5_f)
    """ Input file name. """

    output_f = property(lambda self: self.__output_f)
    """ Output file name. """

    qspace_dims = property(lambda self: self.__params['qspace_dims'])
    """ dimensions of the Q Space (i.e : number of bins). """

    image_binning = property(lambda self: self.__params['image_binning'])
    """ Binning applied to the images before conversion. """

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    medfilt_dims = property(lambda self: self.__params['medfilt_dims'])
    """ Median filter applied to the images after binning (if any)
        and before conversion. """

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    beam_energy = property(lambda self: self.__params['beam_energy'])
    """Beam energy or None to read it from entries"""

    direct_beam = property(lambda self: self.__params['direct_beam'])
    """Direct beam calibration position or None to read it from entries"""

    channels_per_degree = property(lambda self: self.__params['channels_per_degree'])
    """Channels per degree calibration or None to read it from entries"""

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    sample_indices = property(lambda self: self.__params['sample_indices'])
    """ Indices of sample positions that will be converted. """

    n_proc = property(lambda self: self.__n_proc)
    """ Number of processes to use. Will use cpu_count() if None or 0. """

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    roi = property(lambda self: self.__params['roi'])
    """ Selected ROI in sample coordinates : [xmin, xmax, ymin, ymax] """
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    normalizer = property(lambda self: self.__params['normalizer'])
    """ Selected normalizer name in measurement group (str) or None """

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    mask = property(lambda self: self.__params['mask'])
    """ Mask to apply on images (2D numpy.ndarray) or None.

    A non-zero value means that the pixel is masked.
    """

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    def __init__(self,
                 xsocsH5_f,
                 qspace_dims=None,
                 img_binning=None,
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                 medfilt_dims=None,
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                 output_f=None,
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                 roi=None,
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                 entries=None,
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                 callback=None,
                 shiftH5_f=None):
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        """
        Merger for the Kmap SPEC and EDF files. This loads a spech5 file,
             converts it to HDF5 and then tries to match scans and edf image
             files.
        :param xsocsH5_f: path to the input XsocsH5 file.
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        :param qspace_dims: dimensions of the qspace volume
        :param img_binning: binning to apply to the images before conversion.
            Default : (1, 1)
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        :param medfilt_dims: dimensions of the median filter kernel
            to apply to the images before conversion. The filter is not
            applied if this keyword is set to None (this is the default).
            The median filter is always applied AFTER the binning (if any).
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        :param output_f: path to the output file that will be created.
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        :param roi: Roi in sample coordinates (xMin, xMax, yMin, yMax)
        :param entries: a list of entry names to convert to qspace. If None,
            all entries found in the xsocsH5File will be used.
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        :param callback: callback to call when the parsing is done.
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        :param shiftH5_f: a ShiftH5 file name to use if applying shift.
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        """
        super(QSpaceConverter, self).__init__()

        self.__status = None

        self.__set_status(self.UNKNOWN, 'Init')

        self.__xsocsH5_f = xsocsH5_f
        self.__output_f = output_f

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        if shiftH5_f:
            shiftH5 = ShiftH5.ShiftH5(shiftH5_f)
        else:
            shiftH5 = None

        self.__shiftH5 = shiftH5

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        xsocsH5 = XsocsH5.XsocsH5(xsocsH5_f)
        # checking entries
        if entries is None:
            entries = xsocsH5.entries()
        else:
            diff = set(entries) - set(xsocsH5.entries())
            if len(diff) > 0:
                raise ValueError('The following entries were not found in '
                                 'the input file :\n - {0}'
                                 ''.format('\n -'.join(diff)))

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        self.__params = {'qspace_dims': None,
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                         'mask': None,
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                         'normalizer': None,
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                         'image_binning': None,
                         'sample_indices': None,
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                         'roi': None,
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                         'entries': sorted(entries),
                         'beam_energy': None,
                         'direct_beam': None,
                         'channels_per_degree': None}
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        self.__callback = callback
        self.__n_proc = None
        self.__overwrite = False

        self.__shared_progress = None
        self.__results = None
        self.__term_evt = None

        self.__thread = None

        self.image_binning = img_binning
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        self.medfilt_dims = medfilt_dims
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        self.qspace_dims = qspace_dims
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        self.roi = roi
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        self.__set_status(self.READY)

    def __get_scans(self):
        """
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        Returns the entries that will be converted.
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        """
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        return self.__params['entries']
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    scans = property(__get_scans)
    """ Returns the scans found in the input file. """

    def __set_status(self, status, msg=None):
        """
        Sets the status of this instance.
        :param status:
        :param msg:
        :return:
        """
        assert status in self.__STATUSES
        self.__status = status
        self.__status_msg = msg

    def convert(self,
                overwrite=False,
                blocking=True,
                callback=None,
                check_consistency=True):
        """
        Starts the conversion.
        :param overwrite: if False raises an exception if some files already
        exist.
        :param blocking: if False, the merge will be done in a separate
         thread and this method will return immediately.
        :param callback: callback that will be called when the merging is done.
        It overwrites the one passed the constructor.
        :param check_consistency: set to False to ignore any incensitencies
        in the input entries (e.g : different counters, ...).
        :return:
        """

        if self.is_running():
            raise RuntimeError('This QSpaceConverter instance is already '
                               'parsing.')

        self.__set_status(self.RUNNING)

        errors = self.check_parameters()

        if len(errors) > 0:
            msg = 'Invalid parameters.\n{0}'.format('\n'.join(errors))
            raise ValueError(msg)

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        errors = self.check_consistency(
            beam_energy_check=self.beam_energy is None,
            direct_beam_check=self.direct_beam is None,
            channels_per_degree_check=self.channels_per_degree is None)
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        if len(errors) > 0:
            msg = 'Inconsistent input data.\n{0}'.format('\n'.join(errors))

            if check_consistency:
                raise ValueError(msg)
            else:
                print('==============.')
                print('==============.')
                print('WARNING.')
                print(msg)

        output_f = self.__output_f
        if output_f is None:
            self.__set_status(self.ERROR)
            raise ValueError('Output file name (output_f) has not been set.')

        output_dir = os.path.dirname(output_f)
        if not os.path.exists(output_dir):
            os.makedirs(output_dir)

        if not overwrite:
            if len(self.check_overwrite()):
                    self.__set_status(self.ERROR)
                    raise RuntimeError('Some files already exist. Use the '
                                       'overwrite keyword to ignore this '
                                       'warning.')

        self.__results = None
        self.__overwrite = overwrite

        if callback is not None:
            self.__callback = callback

        if blocking:
            self.__run_convert()
        else:
            thread = self.__thread = Thread(target=self.__run_convert)
            thread.start()

    @qspace_dims.setter
    def qspace_dims(self, qspace_dims):
        """
        Sets the dimensions of the qspace volume (i.e. number of bins).
        """

        if qspace_dims is None or None in qspace_dims:
            self.__params['qspace_dims'] = None
            return

        qspace_dims = np.array(qspace_dims, ndmin=1).astype(np.int32)

        if qspace_dims.ndim != 1 or qspace_dims.size != 3:
            raise ValueError('qspace_dims must be a three elements array.')

        if not np.all(qspace_dims > 1):
            raise ValueError('<qspace_dims> values must be strictly'
                             ' greater than one.')
        self.__params['qspace_dims'] = qspace_dims

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    @normalizer.setter
    def normalizer(self, normalizer):
        """Name of dataset in measurement to use for normalization"""
        if normalizer is not None:
             normalizer = str(normalizer)

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             # Check for valid input in all entries
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             with XsocsH5.XsocsH5(self.__xsocsH5_f) as xsocsH5:
                 for entry in xsocsH5.entries():
                     if xsocsH5.measurement(
                             entry=entry, measurement=normalizer) is None:
                         raise ValueError(
                             'normalizer %s is not available in measurement group of entry %s' %
                             normalizer, entry)
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        self.__params['normalizer'] = normalizer

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    @mask.setter
    def mask(self, mask):
        """Mask array or None to mask pixels in input images"""
        if mask is not None:
            mask = np.array(mask)
            if mask.ndim != 2:
                raise ValueError('Mask is not an image')

            # TODO this might be a problem when saving a subset of the images
            with XsocsH5.XsocsH5(self.__xsocsH5_f) as xsocsH5:
                image_size = xsocsH5.image_size()
            if image_size != mask.shape:
                raise ValueError('Mask has not the size of the images')

        self.__params['mask'] = mask

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    @image_binning.setter
    def image_binning(self, image_binning):
        """
        Binning applied to the image before converting to qspace
        """
        err = False
        if image_binning is None:
            self.__params['image_binning'] = (1, 1)
            return

        image_binning_int = None
        if len(image_binning) != 2:
            raise ValueError('image_binning must be a two elements array.')
        if None in image_binning:
            err = True
        else:
            image_binning_int = [int(image_binning[0]), int(image_binning[1])]
            if min(image_binning_int) <= 0:
                err = True
        if err:
            raise ValueError('<image_binning> values must be strictly'
                             ' positive integers.')
        self.__params['image_binning'] = np.array(image_binning_int,
                                                  dtype=np.int32)

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    @medfilt_dims.setter
    def medfilt_dims(self, medfilt_dims):
        """
        Median filter applied to the image after binning (if any) and
        before converting to qspace.
        """
        err = False
        if medfilt_dims is None:
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            self.__params['medfilt_dims'] = (1, 1)
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            return

        medfilt_dims_int = None
        if len(medfilt_dims) != 2:
            raise ValueError('medfilt_dims must be a two elements array.')
        if None in medfilt_dims:
            err = True
        else:
            medfilt_dims_int = [int(medfilt_dims[0]), int(medfilt_dims[1])]
            if min(medfilt_dims_int) <= 0:
                err = True
        if err:
            raise ValueError('<medfilt_dims> values must be strictly'
                             ' positive integers.')
        self.__params['medfilt_dims'] = np.array(medfilt_dims_int,
                                                 dtype=np.int32)

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    @beam_energy.setter
    def beam_energy(self, beam_energy):
        """Beam energy setter"""
        beam_energy = float(beam_energy) if beam_energy is not None else None
        self.__params['beam_energy'] = beam_energy

    @direct_beam.setter
    def direct_beam(self, direct_beam):
        """Direct beam calibration position"""
        if direct_beam is not None:
            direct_beam = float(direct_beam[0]), float(direct_beam[1])
        self.__params['direct_beam'] = direct_beam

    @channels_per_degree.setter
    def channels_per_degree(self, channels_per_degree):
        """Channels per degree calibration"""
        if channels_per_degree is not None:
            channels_per_degree = (float(channels_per_degree[0]),
                                   float(channels_per_degree[1]))
        self.__params['channels_per_degree'] = channels_per_degree

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    # @sample_indices.setter
    # def sample_indices(self, sample_indices):
    #     """
    #     Binning applied to the image before converting to qspace
    #     """
    #     if sample_indices is None:
    #         self.__params['sample_indices'] = None
    #         return
    #
    #     sample_indices = np.array(sample_indices, ndmin=1).astype(np.long)
    #
    #     if sample_indices.ndim != 1:
    #         raise ValueError('sample_indices must be a 1D array.')
    #
    #     if len(sample_indices) == 0:
    #         self.__params['sample_indices'] = None
    #         return
    #
    #     # TODO : check values
    #     self.__params['sample_indices'] = np.array(sample_indices,
    #                                                dtype=np.int32)
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    @roi.setter
    def roi(self, roi):
        """
        Sets the roi. Set to None to unset it. To change an already set roi
        the previous one has to be unset first.
        :param roi: roi coordinates in sample coordinates.
            Four elements array : (xmin, xmax, ymin, ymax)
        :return:
        """
        if self.roi is False:
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            raise ValueError('Cannot set a rectangular ROI, pos_indices are '
                             'already set, remove them first.')
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        self.__params['roi'] = roi
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        self.__params['sample_indices'] = self.__indices_from_roi()

    def __indices_from_roi(self):
        # TODO : check all positions
        # at the moment using only the first scan's positions
        with XsocsH5.XsocsH5(self.__xsocsH5_f) as xsocsH5:
            entries = xsocsH5.entries()
            positions = xsocsH5.scan_positions(entries[0])
            x_pos = positions.pos_0
            y_pos = positions.pos_1

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        if self.__shiftH5:
            with self.__shiftH5:
                shifted_idx = self.__shiftH5.shifted_indices(entries[0])
        else:
            shifted_idx = None

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        roi = self.roi
        if self.roi is None:
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            if shifted_idx is not None and shifted_idx.size != 0:
                return np.arange(shifted_idx.size)
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            return np.arange(len(x_pos))

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        if shifted_idx is not None and shifted_idx.size != 0:
            x_pos = x_pos[shifted_idx]
            y_pos = y_pos[shifted_idx]

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        x_min = roi[0]
        x_max = roi[1]
        y_min = roi[2]
        y_max = roi[3]
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        # we cant do this because the points arent perfectly aligned!
        # we could end up with non rectangular rois
        pos_indices = np.where((x_pos >= x_min) & (x_pos <= x_max) &
                               (y_pos >= y_min) & (y_pos <= y_max))[0]
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        # # TODO : rework this
        # n_x = scan_params['motor_0_steps']
        # n_y = scan_params['motor_1_steps']
        # steps_0 = scan_params['motor_0_steps']
        # steps_1 = scan_params['motor_1_steps']
        # x = np.linspace(scan_params['motor_0_start'],
        #                 scan_params['motor_0_end'], steps_0, endpoint=False)
        # y = np.linspace(scan_params['motor_1_start'],
        #                 scan_params['motor_1_end'], steps_1, endpoint=False)


        # x_pos = x_pos[]
        #
        # x_pos.shape = (n_y, n_x)
        # y_pos.shape = (n_y, n_x)
        # pos_indices_2d = np.where((x_pos >= x_min) & (x_pos <= x_max) &
        #                           (y_pos >= y_min) & (y_pos <= y_max))[0]
        return pos_indices  # pos_indices_2d.shape

    def check_overwrite(self):
        """
        Checks if the output file(s) already exist(s).
        """
        output_f = self.__output_f
        if output_f is not None and os.path.exists(output_f):
            return [self.__output_f]
        return []

    def summary(self):
        """
        Gives an summary of what will be done.
        """
        # TODO : finish
        files = [self.output_f]
        return files

    def check_parameters(self):
        """
        Checks if the RecipSpaceConverter parameters are valid.
        Returns a list of strings describing those errors, if any,
        or an empty list.
        """
        errors = []

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        image_binning = self.image_binning
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        if (image_binning is None
                or None in image_binning
                or len(image_binning) != 2
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                or min(image_binning) <= 0):
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            errors.append('- "image binning" : must be an array of two'
                          ' strictly positive integers.')

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        qspace_dims = self.qspace_dims
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        if (qspace_dims is None
                or None in qspace_dims
                or len(qspace_dims) != 3
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                or min(qspace_dims) <= 0):
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            errors.append('- "qspace size" must be an array of three'
                          ' strictly positive integers.')
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        return errors

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    def check_consistency(self,
                          beam_energy_check=True,
                          direct_beam_check=True,
                          channels_per_degree_check=True):
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        """
        Check if all entries have the same values plus some other
        MINIMAL checks.
        This does not check if the parameter values are valid.
        Returns a list of strings describing those errors, if any,
        or an empty list.
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        :param bool beam_energy_check: Toggle beam_energy check
        :param bool direct_beam_check: Toggle direct_beam check
        :param bool channels_per_degree_check: Toggle channels_per_degree check
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        """
        errors = []

        params = _get_all_params(self.__xsocsH5_f)

        def check_values(dic, key, description):
            values = [dic[scan][key] for scan in sorted(dic.keys())]
            if isinstance(values[0], (list, tuple)):
                values = [tuple(val) for val in values]
            values_set = set(values)
            if len(values_set) != 1:
                errors.append('Parameter inconsistency : '
                              '"{0}" : {1}.'
                              ''.format(description, '; '.join(str(m)
                                        for m in values_set)))

        check_values(params, 'n_images', 'Number of images')
        check_values(params, 'n_positions', 'Number of X/Y positions')
        check_values(params, 'img_size', 'Images size')
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        if beam_energy_check:
            check_values(params, 'beam_energy', 'Beam energy')
        if channels_per_degree_check:
            check_values(params, 'chan_per_deg', 'Chan. per deg.')
        if direct_beam_check:
            check_values(params, 'center_chan', 'Center channel')
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        keys = list(params.keys())
        n_images = params[keys[0]]['n_images']
        n_positions = params[keys[0]]['n_positions']
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        if n_images != n_positions:
            errors.append('number of images != number of X/Y coordinates '
                          'on sample : '
                          '{0} != {1}'.format(n_images, n_positions))

        return errors

    def scan_params(self, scan):
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        """ Returns the scan parameters (filled during acquisition). """
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        params = _get_all_params(self.__xsocsH5_f)
        return params[scan]

    def __run_convert(self):
        """
        Performs the conversion.
        :return:
        """

        self.__set_status(self.RUNNING)

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        normalizer = self.normalizer
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        image_binning = self.image_binning
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        medfilt_dims = self.medfilt_dims
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        qspace_dims = self.qspace_dims
        xsocsH5_f = self.xsocsH5_f
        output_f = self.output_f
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        sample_roi = self.__params['roi']
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        beam_energy = self.__params['beam_energy']
        center_chan = self.__params['direct_beam']
        chan_per_deg = self.__params['channels_per_degree']
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        try:
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            # checking image_binning
            if image_binning is not None:
                image_binning = np.array(image_binning, ndmin=1)
                if image_binning.ndim != 1:
                    raise ValueError('image_binning must be a 1D array.')
                if image_binning.size > 2:
                    raise ValueError(
                        'image_binning must be a one or two elements'
                        ' array.')
                if image_binning.size == 1:
                    image_binning = np.repeat(image_binning, 2)
                if np.any(np.less(image_binning, [1, 1])):
                    raise ValueError('image_binnng values must be >= 1.')

            # setting medfilt_dims to None if it is equal to [1, 1]
            if medfilt_dims is not None:
                medfilt_dims = np.array(medfilt_dims, ndmin=1)
                if medfilt_dims.ndim != 1:
                    raise ValueError('medfilt_dims must be a 1D array.')
                if medfilt_dims.size > 2:
                    raise ValueError(
                        'medfilt_dims must be a one or two elements'
                        ' array.')
                if medfilt_dims.size == 1:
                    medfilt_dims = np.repeat(medfilt_dims, 2)
                if np.any(np.less(medfilt_dims, [1, 1])):
                    raise ValueError('medfilt_dims values must be >= 1.')

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            ta = time.time()

            params = _get_all_params(xsocsH5_f)

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            entries = self.__get_scans()
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            n_entries = len(entries)

            first_param = params[entries[0]]

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            if beam_energy is None:  # Load it from first entry
                beam_energy = first_param['beam_energy']
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            if beam_energy is None:
                raise ValueError('Invalid/missing beam energy : {0}.'
                                 ''.format(beam_energy))

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            if chan_per_deg is None:  # Load it from first entry
                chan_per_deg = first_param['chan_per_deg']
            if chan_per_deg is None or len(chan_per_deg) != 2:
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                raise ValueError('Invalid/missing chan_per_deg value : {0}.'
                                 ''.format(chan_per_deg))

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            if center_chan is None:  # Load it from first entry
                center_chan = first_param['center_chan']
            if center_chan is None or len(center_chan) != 2:
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                raise ValueError('Invalid/missing center_chan value : {0}.'
                                 ''.format(center_chan))

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            # Load image ROI from first entry
            image_roi_offset = first_param['image_roi_offset']

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            n_images = first_param['n_images']
            if n_images is None or n_images == 0:
                raise ValueError(
                    'Data does not contain any images (n_images={0}).'
                    ''.format(n_images))

            img_size = first_param['img_size']
            if img_size is None or 0 in img_size:
                raise ValueError('Invalid image size (img_size={0}).'
                                 ''.format(img_size))

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            mask = self.mask
            if mask is not None:
                if np.count_nonzero(mask) == mask.size:
                    # Mask is empty, disable mask
                    mask = None
                else:
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                    if (image_roi_offset is not None and
                            image_roi_offset != (0, 0)):
                        # Apply image ROI to mask
                        row, column = image_roi_offset
                        mask = mask[row[0]:row[0]+img_size[0],
                                    column[1]:column[1]+img_size[1]]
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                    if mask.shape != img_size:
                        raise ValueError('Invalid mask size')
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                    if (image_binning is not None and
                            not np.all(np.equal(image_binning, (1, 1)))):
                        raise ValueError(
                            'Image binning is not implemented with mask')

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            shiftH5 = self.__shiftH5

            if shiftH5:
                shifted_idx = shiftH5.shifted_indices(entries[0])
                if shifted_idx is not None and shifted_idx.size > 0:
                    n_images = shifted_idx.size
                else:
                    shifted_idx = None
            else:
                shifted_idx = None

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            # TODO value testing
            sample_indices = self.sample_indices
            if sample_indices is None:
                sample_indices = np.arange(n_images)
            else:
                n_images = len(sample_indices)

            n_xy = len(sample_indices)

            print('Parameters :')
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            print('\t- beam energy        : {0}'.format(beam_energy))
            print('\t- center channel     : {0}'.format(center_chan))
            print('\t- image roi offset   : {0}'.format(image_roi_offset))
            print('\t- channel per degree : {0}'.format(chan_per_deg))
            print('\t- mask               : {0}'.format(
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                'Yes' if mask is not None else 'No'))
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            print('\t- normalizer         : {0}'.format(normalizer))
            print('\t- img binning        : {0}'.format(image_binning))
            print('\t- medfilt dims       : {0}'.format(medfilt_dims))
            print('\t- qspace size        : {0}'.format(qspace_dims))

            # Offset center_chan with image roi offset if any
            if image_roi_offset is not None:
                center_chan = (center_chan[0] - image_roi_offset[0],
                               center_chan[1] - image_roi_offset[1])
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            # TODO : make this editable?
            nx, ny, nz = qspace_dims
            qconv = xu.experiment.QConversion(['y-', 'z-'],
                                              ['z-', 'y-'],
                                              [1, 0, 0])

            # convention for coordinate system:
            # x downstream
            # z upwards
            # y to the "outside"
            # (righthanded)
            hxrd = xu.HXRD([1, 0, 0],
                           [0, 0, 1],
                           en=beam_energy,
                           qconv=qconv)

            hxrd.Ang2Q.init_area('z-',
                                 'y+',
                                 cch1=center_chan[0],
                                 cch2=center_chan[1],
                                 Nch1=img_size[0],
                                 Nch2=img_size[1],
                                 chpdeg1=chan_per_deg[0],
                                 chpdeg2=chan_per_deg[1],
                                 Nav=image_binning)

            # shape of the array that will store the qx/qy/qz for all
            # rocking angles
            q_shape = (n_entries,
                       (img_size[0] // image_binning[0]) * (
                           img_size[1] // image_binning[1]),
                       3)

            # then the array
            q_ar = np.zeros(q_shape, dtype=np.float64)

            img_dtype = None

            with XsocsH5.XsocsH5(xsocsH5_f, mode='r') as master_h5:

                entry_files = []

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                all_entries = set(master_h5.entries())

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                positions = master_h5.scan_positions(entries[0])
                sample_x = positions.pos_0
                sample_y = positions.pos_1

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                if shifted_idx is not None:
                    sample_x = sample_x[shifted_idx]
                    sample_y = sample_y[shifted_idx]

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                for entry_idx, entry in enumerate(entries):
                    entry_file = master_h5.entry_filename(entry)
                    if not os.path.isabs(entry_file):
                        base_dir = os.path.dirname(xsocsH5_f)
                        entry_file = os.path.abspath(os.path.join(base_dir,
                                                                  entry_file))
                    entry_files.append(entry_file)

                    phi = np.float64(master_h5.positioner(entry, 'phi'))
                    eta = np.float64(master_h5.positioner(entry, 'eta'))
                    nu = np.float64(master_h5.positioner(entry, 'nu'))
                    delta = np.float64(master_h5.positioner(entry, 'del'))

                    qx, qy, qz = hxrd.Ang2Q.area(eta, phi, nu, delta)
                    q_ar[entry_idx, :, 0] = qx.reshape(-1)
                    q_ar[entry_idx, :, 1] = qy.reshape(-1)
                    q_ar[entry_idx, :, 2] = qz.reshape(-1)

                    entry_dtype = master_h5.image_dtype(entry=entry)

                    if img_dtype is None:
                        img_dtype = entry_dtype
                    elif img_dtype != entry_dtype:
                        raise TypeError(
                            'All images in the input HDF5 files should '
                            'be of the same type. Found {0} and {1}.'
                            ''.format(img_dtype, entry_dtype))

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            if mask is not None:
                # Mark masked pixels (i.e., non zero in the mask) with NaN
                q_ar[:, mask.reshape(-1) != 0, :] = np.nan
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            # custom bins range to have the same histo as
            # xrayutilities.gridder3d
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            # bins centered around the qx, qy, qz
            # bins will be like :
            # bin_1 = [min - step/2, min + step/2[
            # bin_2 = [min - step/2, min + 3*step/2]
            # ...
            # bin_N = [max - step/2, max + step/2]
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            qx_min = np.nanmin(q_ar[:, :, 0])
            qy_min = np.nanmin(q_ar[:, :, 1])
            qz_min = np.nanmin(q_ar[:, :, 2])
            qx_max = np.nanmax(q_ar[:, :, 0])
            qy_max = np.nanmax(q_ar[:, :, 1])
            qz_max = np.nanmax(q_ar[:, :, 2])
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            step_x = (qx_max - qx_min) / (nx - 1.)
            step_y = (qy_max - qy_min) / (ny - 1.)
            step_z = (qz_max - qz_min) / (nz - 1.)

            bins_rng_x = ([qx_min - step_x / 2., qx_min +
                           (qx_max - qx_min + step_x) - step_x / 2.])
            bins_rng_y = ([qy_min - step_y / 2., qy_min +
                           (qy_max - qy_min + step_y) - step_y / 2.])
            bins_rng_z = ([qz_min - step_z / 2., qz_min +
                           (qz_max - qz_min + step_z) - step_z / 2.])
            bins_rng = [bins_rng_x, bins_rng_y, bins_rng_z]

            qx_idx = qx_min + step_x * np.arange(0, nx, dtype=np.float64)
            qy_idx = qy_min + step_y * np.arange(0, ny, dtype=np.float64)
            qz_idx = qz_min + step_z * np.arange(0, nz, dtype=np.float64)

            # TODO : on windows we may be forced to use shared memory
            # TODO : find why we use more memory when using shared arrays
            #        this shouldnt be the case
            #        (use the same amount as non shared mem)
            # on linux apparently we dont because when fork() is called data is
            # only copied on write.
            # shared histo used by all processes
            # histo_shared = mp_sharedctypes.RawArray(ctypes.c_int32,
            #                                         nx * ny * nz)
            # histo = np.frombuffer(histo_shared, dtype='int32')
            # histo.shape = nx, ny, nz
            # histo[:] = 0
            histo = np.zeros(qspace_dims, dtype=np.int32)

            # shared LUT used by all processes
            # h_lut = None
            # h_lut_shared = None
            h_lut = []
            lut = None
            for h_idx in range(n_entries):
                lut = histogramnd_get_lut(q_ar[h_idx, ...],
                                          bins_rng,
                                          [nx, ny, nz],
                                          last_bin_closed=True)

                # if h_lut_shared is None:
                #     lut_dtype = lut[0].dtype
                #     if lut_dtype == np.int16:
                #         lut_ctype = ctypes.c_int16
                #     elif lut_dtype == np.int32:
                #         lut_ctype = ctypes.c_int32
                #     elif lut_dtype == np.int64:
                #         lut_ctype == ctypes.c_int64
                #     else:
                #         raise TypeError('Unknown type returned by '
                #                         'histogramnd_get_lut : {0}.'
                #                         ''.format(lut.dtype))
                #     h_lut_shared = mp_sharedctypes.RawArray(lut_ctype,
                #                                       n_images * lut[0].size)
                #     h_lut = np.frombuffer(h_lut_shared, dtype=lut_dtype)
                #     h_lut.shape = (n_images, -1)
                #
                # h_lut[h_idx, ...] = lut[0]
                h_lut.append(lut[0])
                histo += lut[1]

            del lut
            del q_ar

            # TODO : split the output file into several files? speedup?
            output_shape = histo.shape

            chunks = (1,
                      max(output_shape[0] // 4, 1),
                      max(output_shape[1] // 4, 1),
                      max(output_shape[2] // 4, 1),)
            qspace_sum_chunks = max(n_images // 10, 1),

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            discarded_entries = sorted(all_entries - set(entries))

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            _create_result_file(output_f,
                                output_shape,
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                                image_binning,
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                                medfilt_dims,
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                                sample_roi,
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                                sample_x[sample_indices],
                                sample_y[sample_indices],
                                qx_idx,
                                qy_idx,
                                qz_idx,
                                histo,
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                                selected_entries=entries,
                                discarded_entries=discarded_entries,
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                                compression='lzf',
                                qspace_chunks=chunks,
                                qspace_sum_chunks=qspace_sum_chunks,
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                                overwrite=self.__overwrite,
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                                shiftH5=shiftH5,
                                beam_energy=beam_energy,
                                direct_beam=center_chan,
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                                channels_per_degree=chan_per_deg,
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                                normalizer=normalizer,
                                mask=mask)
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            manager = mp.Manager()
            self.__term_evt = term_evt = manager.Event()

            write_lock = manager.Lock()
            idx_queue = manager.Queue()

            n_proc = self.n_proc
            if n_proc is None or n_proc <= 0:
                n_proc = mp.cpu_count()

            self.__shared_progress = mp_sharedctypes.RawArray(ctypes.c_int32,
                                                              n_proc)
            np.frombuffer(self.__shared_progress, dtype='int32')[:] = 0

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            if shiftH5 is not None and shifted_idx is not None:
                n_shifted = n_entries * shifted_idx.size
                shared_shifted = mp_sharedctypes.RawArray(ctypes.c_int32,
                                                          n_shifted)
                shifted_np = np.frombuffer(shared_shifted, dtype='int32')
                shifted_np.shape = n_entries, shifted_idx.size
                shared_shifted_shape = shifted_np.shape

                for i_entry, entry in enumerate(entries):
                    shifted_indices = shiftH5.shifted_indices(entry)
                    shifted_np[i_entry, :] = shifted_indices
            else:
                shared_shifted = None
                shared_shifted_shape = None

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            pool = mp.Pool(n_proc,
                           initializer=_init_thread,
                           initargs=(idx_queue,
                                     write_lock,
                                     bins_rng,
                                     qspace_dims,
                                     h_lut,  # _shared,
                                     None,  # lut_dtype,
                                     n_xy,
                                     histo,  # _shared,))
                                     self.__shared_progress,
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                                     term_evt,
                                     shared_shifted,
                                     shared_shifted_shape,))
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            if disp_times:
                class myTimes(object):
                    def __init__(self):
                        self.t_histo = 0.
                        self.t_sum = 0.
                        self.t_mask = 0.
                        self.t_read = 0.
                        self.t_context = 0.
                        self.t_dnsamp = 0.
                        self.t_medfilt = 0.
                        self.t_write = 0.
                        self.t_w_lock = 0.

                    def update(self, arg):
                        (t_read_, t_context_, t_dnsamp_, t_medfilt_, t_histo_,
                         t_mask_, t_sum_, t_write_, t_w_lock_) = arg[2]
                        self.t_histo += t_histo_
                        self.t_sum += t_sum_
                        self.t_mask += t_mask_
                        self.t_read += t_read_
                        self.t_context += t_context_
                        self.t_dnsamp += t_dnsamp_
                        self.t_medfilt += t_medfilt_
                        self.t_write += t_write_
                        self.t_w_lock += t_w_lock_

                res_times = myTimes()
                callback = res_times.update
            else:
                callback = None

            # creating the processes
            results = []
            for th_idx in range(n_proc):
                arg_list = (th_idx,
                            entry_files,
                            entries,
                            img_size,
                            output_f,
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                            normalizer,
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                            image_binning,
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                            medfilt_dims,
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                            img_dtype)
                res = pool.apply_async(_to_qspace, args=arg_list,
                                       callback=callback)
                results.append(res)
            # sending the image indices
            for result_idx, pos_idx in enumerate(sample_indices):
                idx_queue.put((result_idx, pos_idx))

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            # sending the None value to let the threads know that they
            # should return
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            for th_idx in range(n_proc):
                idx_queue.put(None)

            pool.close()
            pool.join()

            tb = time.time()

            if disp_times:
                print('TOTAL {0}'.format(tb - ta))
                print('Read {0}'.format(res_times.t_read))
                print('Context {0}'.format(res_times.t_context))
                print('Dn Sample {0}'.format(res_times.t_dnsamp))
                print('Medfilt {0}'.format(res_times.t_medfilt))
                print('Histo {0}'.format(res_times.t_histo))
                print('Mask {0}'.format(res_times.t_mask))
                print('Sum {0}'.format(res_times.t_sum))
                print('Write {0}'.format(res_times.t_write))
                print('(lock : {0})'.format(res_times.t_w_lock))

            proc_results = [result.get() for result in results]
            proc_codes = np.array([proc_result[0]
                                   for proc_result in proc_results])

            rc = self.DONE
            if not np.all(proc_codes == self.DONE):
                if self.ERROR in proc_codes:
                    rc = self.ERROR
                elif self.CANCELED in proc_codes:
                    rc = self.CANCELED
                else:
                    raise ValueError('Unknown return code.')

            if rc != self.DONE:
                errMsg = 'Conversion failed. Process status :'
                for th_idx, result in enumerate(proc_results):
                    errMsg += ('\n- Proc {0} : rc={1}; {2}'
                               ''.format(th_idx, result[0], result[1]))
                self.__set_status(rc, errMsg)
            else:
                self.__set_status(rc)

        except Exception as ex:
            self.__set_status(self.ERROR, str(ex))
        else:
            self.__results = self.output_f

        # TODO : catch exception?
        if self.__callback:
            self.__callback()

        return self.__results

    def wait(self):
        """
        Waits until parsing is done, or returns if it is not running.
        :return:
        """
        if self.__thread:
            self.__thread.join()

    def __running_exception(self):
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        """ Raises an exception if a conversion is in progress. """
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        if self.is_running():
            raise RuntimeError('Operation not permitted while '
                               'a parse or merge in running.')

    def is_running(self):
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        """ Returns True if a conversion is in progress. """
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        return self.status == QSpaceConverter.RUNNING
        #self.__thread and self.__thread.is_alive()

    @output_f.setter
    def output_f(self, output_f):
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        """ Sets the output file. """
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        if not isinstance(output_f, str):
            raise TypeError('output_f must be a string. Received {0}'
                            ''.format(type(output_f)))
        self.__output_f = output_f

    @n_proc.setter
    def n_proc(self, n_proc):
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        """ Sets the number of processes to use. If None or 0 the number of
            processes used will be the number returned by
            multiprocessing.cpu_count.
        """
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        if n_proc is None:
            self.__n_proc = None
            return

        n_proc = int(n_proc)
        if n_proc <= 0:
            self.__n_proc = None
        else:
            self.__n_proc = n_proc

    def abort(self, wait=True):
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        """
        Aborts the current conversion, if any.
        :param wait: set to False to return immediatly without waiting for the
        processes to return.
        :return:
        """
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        if self.is_running():
            self.__term_evt.set()
            if wait:
                self.wait()

    def progress(self):
        """
        Returns the progress of the conversion.
        :return:
        """
        if self.__shared_progress:
            progress = np.frombuffer(self.__shared_progress, dtype='int32')
            return progress.max()
        return 0


def _init_thread(idx_queue_,
                 write_lock_,
                 bins_rng_,
                 qspace_size_,
                 h_lut_shared_,
                 h_lut_dtype_,
                 n_xy_,
                 histo_shared_,
                 shared_progress_,
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                 term_evt_,
                 shared_shifted_,
                 shared_shifted_shape_):
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    global idx_queue, \
        write_lock, \
        bins_rng, \
        qspace_size, \
        h_lut_shared, \
        h_lut_dtype, \
        n_xy, \
        histo_shared, \
        shared_progress, \
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        term_evt, \
        shared_shifted, \
        shared_shifted_shape
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    idx_queue = idx_queue_
    write_lock = write_lock_
    bins_rng = bins_rng_
    qspace_size = qspace_size_
    h_lut_shared = h_lut_shared_
    h_lut_dtype = h_lut_dtype_
    n_xy = n_xy_
    histo_shared = histo_shared_
    shared_progress = shared_progress_
    term_evt = term_evt_
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    shared_shifted = shared_shifted_
    shared_shifted_shape = shared_shifted_shape_
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def _create_result_file(h5_fn,
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                        qspace_dims,
                        image_binning,
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                        medfilt_dims,
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                        sample_roi,
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                        pos_x,
                        pos_y,
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                        q_x,
                        q_y,
                        q_z,
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                        histo,
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                        selected_entries,
                        discarded_entries=None,
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                        compression='lzf',
                        qspace_chunks=None,
                        qspace_sum_chunks=None,
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                        overwrite=False,
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                        shiftH5=None,
                        beam_energy=None,
                        direct_beam=None,
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                        channels_per_degree=None,
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                        normalizer='',
                        mask=None):
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    """
    Initializes the output file.
    :param h5_fn: name of the file to initialize
    :param qspace_dims: dimensions of the q space
    :param image_binning: binning applied to the images
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    :param medfilt_dims: dimensions of the median filter applied to the image
        after binning (if any).
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    :param pos_x: sample X positions (one for each qspace cube)
    :param pos_y: sample Y positions (one for each qspace cube)
    :param q_x: X coordinates of the qspace cube
    :param q_y: Y coordinates of the qspace cube
    :param q_z: Z coordinates of the qspace cube
    :param histo: histogram (number of hits per element of the qspace elements)
    :param selected_entries: list of input entries used for the conversion
    :param discarded_entries: list of input entries discarded, or None
    :param compression: datasets compression
    :param qspace_chunks: qspace chunking
    :param qspace_sum_chunks:
    :param overwrite: True to force overwriting the file if it already exists.
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    :param shiftH5: file containing the shifts applied to the selected entries
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    :param beam_energy: Beam energy in eV
    :param direct_beam: Direct beam calibration position
    :param channels_per_degree: Channels per degree calibration
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    :param str normalizer:
        Name of measurement group dataset used for normalization
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    :param Union[numpy.ndarray, None] mask:
        Mask used to discard pixels in images
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    """

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    if not overwrite:
        mode = 'w-'
    else:
        mode = 'w'

    dir_name = os.path.dirname(h5_fn)
    if len(dir_name) > 0 and not os.path.exists(dir_name):
        os.makedirs(dir_name)

    qspace_h5 = QSpaceH5.QSpaceH5Writer(h5_fn, mode=mode)
    qspace_h5.init_file(len(pos_x),
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                        qspace_dims,
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                        qspace_chunks=qspace_chunks,
                        qspace_sum_chunks=qspace_sum_chunks,
                        compression=compression)
    qspace_h5.set_histo(histo)
    qspace_h5.set_sample_x(pos_x)
    qspace_h5.set_sample_y(pos_y)
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    qspace_h5.set_qx(q_x)
    qspace_h5.set_qy(q_y)
    qspace_h5.set_qz(q_z)
    qspace_h5.set_image_binning(image_binning)
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    qspace_h5.set_medfilt_dims(medfilt_dims)
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    qspace_h5.set_sample_roi(sample_roi)
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    qspace_h5.set_beam_energy(beam_energy)
    qspace_h5.set_direct_beam(direct_beam)
    qspace_h5.set_channels_per_degree(channels_per_degree)
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    if normalizer is None:
        normalizer = ''
    qspace_h5.set_image_normalizer(normalizer)

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    if mask is not None:
        qspace_h5.set_image_mask(mask)

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    if shiftH5:
        sample_shifts = []
        grid_shifts = []
        with shiftH5:
            for entry in selected_entries:
                shift = shiftH5.shift(entry)

                if shift is not None:
                    sample_shifts.append([shift['shift_x'], shift['shift_y']])
                    if shiftH5.is_snapped_to_grid():
                        grid_shifts.append(shift['grid_shift'])

        if len(grid_shifts) == 0:
            grid_shifts = None
    else:
        sample_shifts = None
        grid_shifts = None

    qspace_h5.set_entries(selected_entries,
                          discarded=discarded_entries,
                          sample_shifts=sample_shifts,
                          grid_shifts=grid_shifts)

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def _to_qspace(th_idx,
               entry_files,
               entries,
               img_size,
               output_fn,
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               normalizer,
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               image_binning,
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               medfilt_dims,
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               img_dtype):
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    """
    Fonction running in a process. Performs the conversion.
    :param th_idx:
    :param entry_files:
    :param entries:
    :param img_size:
    :param output_fn:
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    :param str normalizer:
       Name of measurement group dataset to use for normalization
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    :param image_binning:
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    :param medfilt_dims:
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    :param img_dtype:
    :return:
    """
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    print('Process {0} started.'.format(th_idx))
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    t_histo = 0.
    t_mask = 0.
    t_sum = 0.
    t_read = 0.
    t_dnsamp = 0.
    t_medfilt = 0.
    t_write = 0.
    t_w_lock = 0.
    t_context = 0.

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    write_lock.acquire()
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    output_h5 = QSpaceH5.QSpaceH5Writer(output_fn, mode='r+')
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    write_lock.release()
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    if shared_progress is not None:
        progress_np = np.frombuffer(shared_progress, dtype='int32')
        progress_np[th_idx] = 0
    else:
        progress_np = None

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    if shared_shifted is not None:
        shifted_np = np.frombuffer(shared_shifted, dtype='int32')
        shifted_np.shape = shared_shifted_shape
    else:
        shifted_np = None

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    # histo = np.frombuffer(histo_shared, dtype='int32')
    # histo.shape = qspace_size
    histo = histo_shared
    mask = histo > 0

    # h_lut = np.frombuffer(h_lut_shared, dtype=h_lut_dtype)
    # h_lut.shape = (n_xy, -1)
    h_lut = h_lut_shared

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    if normalizer and img_dtype.kind != 'f':
        # Force the type to float64
        logger.info('Using float64 to perform normalization')
        img_dtype = np.float64

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    img = np.ascontiguousarray(np.zeros(img_size), dtype=img_dtype)

    # TODO : handle case when nav is not a multiple of img_size!!
    # TODO : find why the first version is faster than the second one
    img_shape_1 = img_size[0] // image_binning[0], image_binning[0], img_size[1]
    img_shape_2 = (img_shape_1[0], img_shape_1[2] // image_binning[1],
                   image_binning[1])
    sum_axis_1 = 1
    sum_axis_2 = 2
    # img_shape_1 = img_size[0], img_size[1]/nav[1], nav[1]
    # img_shape_2 = img_size[0]//nav[0], nav[0], img_shape_1[1]
    # sum_axis_1 = 2
    # sum_axis_2 = 1
    avg_weight = 1. / (image_binning[0] * image_binning[1])

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    # Set OpenMP to use a single thread (for median filter)
    os.environ["OMP_NUM_THREADS"] = "1"

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    rc = None
    errMsg = None
    try:
        while True:
            if term_evt.is_set():  # noqa
                rc = QSpaceConverter.CANCELED
                raise Exception('conversion aborted')

            next_data = idx_queue.get()
            if next_data is None:
                rc = QSpaceConverter.DONE
                break

            result_idx, image_idx = next_data
            if result_idx % 100 == 0:
                print('#{0}/{1}'.format(result_idx, n_xy))

            cumul = None
            # histo = None

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            if shifted_np is not None:
                image_indices = shifted_np[:, image_idx]
            else:
                image_indices = None

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            for entry_idx, entry in enumerate(entries):
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                xsocsH5 = XsocsH5.XsocsH5(entry_files[entry_idx], mode='r')
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                t0 = time.time()

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                if image_indices is not None:
                    image_idx = image_indices[entry_idx]

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                try:
                    # TODO : there s room for improvement here maybe
                    # (recreating a XsocsH5 instance each time slows down
                    # slows down things a big, not much tho)
                    # TODO : add a lock on the files if there is no SWMR
                    # test if it slows down things much
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                    with xsocsH5.image_dset_ctx() as img_data:
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                        t1 = time.time()
                        img_data.read_direct(img,
                                             source_sel=np.s_[image_idx],
                                             dest_sel=None)
                        t_context = time.time() - t1
                        # img = img_data[image_idx].astype(np.float64)
                except Exception as ex:
                    raise RuntimeError('Error in proc {0} while reading '
                                       'img {1} from entry {2} ({3}) : {4}.'
                                       ''.format(th_idx, image_idx, entry_idx,
                                                 entry, ex))

                t_read += time.time() - t0
                t0 = time.time()

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                # Apply normalization

                if normalizer:
                    normalization = xsocsH5.measurement(entry, normalizer)
                    # Make sure to use float to perform division
                    assert img.dtype.kind == 'f'
                    img /= normalization[image_idx]

                # Perform binning

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                if image_binning[0] != 1 or image_binning[1] != 1:
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                    # Increase type size for (u)int8|16
                    if img.dtype.kind == 'u' and img.dtype.itemsize < 4:
                        binning_dtype = np.uint32
                    elif img.dtype.kind == 'i' and img.dtype.itemsize < 4:
                        binning_dtype = np.int32
                    else:  # Keep same dtype for (u)int32|64 and float
                        binning_dtype = img.dtype

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                    intensity = (img.reshape(img_shape_1).
                                 sum(axis=sum_axis_1,
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                                     dtype=binning_dtype).reshape(img_shape_2).
                                 sum(axis=sum_axis_2, dtype=binning_dtype) *
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                                 avg_weight)
                    # intensity = xu.blockAverage2D(img, nav[0],
                    #                               nav[1], roi=roi)
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                else:
                    intensity = img

                t_dnsamp += time.time() - t0
                t0 = time.time()

                # intensity = medfilt2d(intensity, 3)
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                if medfilt_dims[0] != 1 or medfilt_dims[1] != 1:
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                    intensity = medfilt2d(intensity,
                                          medfilt_dims,
                                          mode='constant',
                                          cval=0)
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