dpc_gui.py

#!/usr/bin/env python
"""
Created on May 23, 2013
@author: Cheng Chang (cheng.chang.ece@gmail.com)
         Computer Science Group, Computational Science Center
         Brookhaven National Laboratory

This code is for Differential Phase Contrast (DPC) imaging based on
Fourier-shift fitting implementation.

Reference: Yan, H. et al. Quantitative x-ray phase imaging at the nanoscale by
           multilayer Laue lenses. Sci. Rep. 3, 1307; DOI:10.1038/srep01307
           (2013).

Test data is available at:
https://docs.google.com/file/d/0B3v6W1bQwN_AdjZwWmE3WTNqVnc/edit?usp=sharing
"""
from __future__ import print_function, division

import os
import sys
import csv

import time
import logging
from datetime import datetime
from functools import wraps
import multiprocessing as mp
import subprocess

from PyQt5 import QtCore
from PyQt5.QtCore import Qt
from PyQt5.QtWidgets import (
    QApplication,
    QMainWindow,
    QInputDialog,
    QFileDialog,
    QLabel,
    QLineEdit,
    QDoubleSpinBox,
    QSpinBox,
    QComboBox,
    QPushButton,
    QSizePolicy,
    QGroupBox,
    QGridLayout,
    QListWidget,
    QWidget,
    QCheckBox,
    QTextEdit,
    QFrame,
    QHBoxLayout,
    QSlider,
    QAction,
    QStyleFactory,
    QRubberBand,
    QMessageBox,
    QMenu,
)
from PyQt5.QtGui import QPalette, QPixmap, QIcon, QPen, QPainter, QTextCursor
import matplotlib.cm as cm
from PIL import Image
import PIL
from skimage import exposure
import numpy as np
import matplotlib as mpl

from matplotlib.backends.backend_qt4agg import (
    FigureCanvasQTAgg as FigureCanvas,
    NavigationToolbar2QT as NavigationToolbar,
)

from matplotlib.figure import Figure
from matplotlib.patches import Rectangle
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import psutil

try:
    from tifffile import imsave

    havetiff = True
except ImportError as ex:
    print("[!] Import error - tifffile not available. Tif files will not be saved")
    print("[!] (import error: {})".format(ex))
    havetiff = False

import load_timepix
import h5py
import dpc_kernel as dpc
import pyspecfile

from db_config.db_config import db

try:
    import hxntools
    from hxntools.scan_info import ScanInfo
    from hxntools.scan_monitor import HxnScanMonitor

    # from databroker import DataBroker
except ImportError as ex:
    print("[!] Unable to import hxntools-related packages some features will " "be unavailable")
    print("[!] (import error: {})".format(ex))
    hxntools = None


logger = logging.getLogger(__name__)
get_save_filename = QFileDialog.getSaveFileName
get_open_filename = QFileDialog.getOpenFileName

version = "1.1.0"


SOLVERS = [
    "Nelder-Mead",
    "Powell",
    "CG",
    "BFGS",
    "Newton-CG",
    "Anneal",
    "L-BFGS-B",
    "TNC",
    "COBYLA",
    "SLS-QP",
    "dogleg",
    "trust-ncg",
]

TYPES = [
    "TIFF",
    "Timepix TIFF",
    "ASCII",
    "HDF5",
    "FileStore",
]

roi_x1 = 0
roi_x2 = 0
roi_y1 = 0
roi_y2 = 0
a = None
gx = None
gy = None
phi = None
rx = None
ry = None

CMAP_PREVIEW_PATH = os.path.join(os.path.dirname(__file__), ".cmap_previews")


def load_image_pil(path):
    """
    Read images using the PIL lib
    """
    f = Image.open(str(path))  # 'I;16B'
    return np.array(f.getdata()).reshape(f.size[::-1])


def load_data_hdf5(file_path):
    """
    Read images using the h5py lib
    """
    f = h5py.File(str(file_path), "r")
    entry = f["entry"]
    instrument = entry["instrument"]
    detector = instrument["detector"]
    dsdata = detector["data"]
    data = dsdata[...]
    f.close()

    return np.array(data)


def load_image_hdf5(file_path):

    data = load_data_hdf5(file_path)

    return data[0, :, :]


def load_image_ascii(path):
    """
    Read ASCII images using the csv lib
    """
    delimiter = "\t"
    data = []
    for row in csv.reader(open(path), delimiter=delimiter):
        data.append(row[:-1])
    img = np.array(data).astype(np.double)
    return img


def brush_to_color_tuple(brush):
    r, g, b, a = brush.color().getRgbF()
    return (r, g, b)


class MyStream(QtCore.QObject):
    message = QtCore.pyqtSignal(str)

    def __init__(self, parent=None):
        super(MyStream, self).__init__(parent)

    def write(self, message):
        self.message.emit(str(message))

    def flush(self):
        pass


class DPCThread(QtCore.QThread):
    def __init__(self, canvas, pool=None, parent=None):
        QtCore.QThread.__init__(self, parent)
        self.canvas = canvas
        self.pool = pool

    update_signal = QtCore.pyqtSignal(object, object, object, object, object, object)

    def run(self):
        print("DPC thread started")
        main = DPCWindow.instance
        try:
            ret = dpc.main(
                pool=self.pool,
                display_fcn=self.update_signal.emit,
                load_image=main.load_image,
                **self.dpc_settings,
            )
            print("DPC finished")
            global a
            global gx
            global gy
            global phi
            global rx
            global ry
            a, gx, gy, phi, rx, ry = ret

            main.a, main.gx, main.gy, main.phi, main.rx, main.ry = a, gx, gy, phi, rx, ry
            main.line_btn.setEnabled(True)
            main.reverse_x.setEnabled(True)
            main.reverse_y.setEnabled(True)
            main.swap_xy.setEnabled(True)
            main.save_result_tiff.setEnabled(True)
            main.save_result_txt.setEnabled(True)
            main.hanging_opt.setEnabled(True)
            main.random_processing_opt.setEnabled(True)
            main.pyramid_scan.setEnabled(True)
            main.pad_recon.setEnabled(True)
            # main.direction_btn.setEnabled(True)
            # main.removal_btn.setEnabled(True)
            # main.confirm_btn.setEnabled(True)
        finally:
            main.set_running(False)


class MplCanvas(FigureCanvas):
    """
    Canvas which allows us to use matplotlib with pyqt4
    """

    def __init__(self, fig=None, parent=None, width=5, height=4, dpi=100):
        fig = Figure(figsize=(width, height), dpi=dpi)

        # We want the axes cleared every time plot() is called
        self.axes = fig.add_subplot(1, 1, 1)
        # self.axes.hold(False)
        self.axes.cla()

        FigureCanvas.__init__(self, fig)

        # self.figure
        self.setParent(parent)

        FigureCanvas.setSizePolicy(self, QSizePolicy.Expanding, QSizePolicy.Expanding)
        FigureCanvas.updateGeometry(self)

        self._title = ""
        self.title_font = {"family": "serif", "fontsize": 10}
        self._title_size = 0
        self.figure.subplots_adjust(top=0.95, bottom=0.15)

        window_brush = self.window().palette().window()
        fig.set_facecolor(brush_to_color_tuple(window_brush))
        fig.set_edgecolor(brush_to_color_tuple(window_brush))
        self._active = False

    def _get_title(self):
        return self._title

    def _set_title(self, title):
        self._title = title
        if self.axes:
            self.axes.set_title(title, fontdict=self.title_font)
            # bbox = t.get_window_extent()
            # bbox = bbox.inverse_transformed(self.figure.transFigure)
            # self._title_size = bbox.height
            # self.figure.subplots_adjust(top=1.0 - self._title_size)

    title = property(_get_title, _set_title)


class Label(QLabel):
    def __init__(self, parent=None):
        super(Label, self).__init__(parent)
        self.rubberBand = QRubberBand(QRubberBand.Rectangle, self)
        self.origin = QtCore.QPoint()

    def mousePressEvent(self, event):
        global roi_x1
        global roi_y1
        self.rubberBand.hide()
        if event.button() == Qt.LeftButton:
            self.origin = QtCore.QPoint(event.pos())
            self.rubberBand.setGeometry(QtCore.QRect(self.origin, QtCore.QSize()))
            self.rubberBand.show()
            roi_x1 = event.pos().x()
            roi_y1 = event.pos().y()

    def mouseMoveEvent(self, event):
        # if event.buttons() == QtCore.Qt.NoButton:
        #     pos = event.pos()
        if not self.origin.isNull():
            self.rubberBand.setGeometry(QtCore.QRect(self.origin, event.pos()).normalized())

    def mouseReleaseEvent(self, event):
        global roi_x2
        global roi_y2
        roi_x2 = event.pos().x()
        roi_y2 = event.pos().y()
        main = DPCWindow.instance
        if (roi_x1, roi_y1) != (roi_x2, roi_y2):
            main.roi_x1_widget.setValue(roi_x1)
            main.roi_y1_widget.setValue(roi_y1)
            main.roi_x2_widget.setValue(roi_x2)
            main.roi_y2_widget.setValue(roi_y2)
        else:
            if main.bad_flag != 0:
                main.bad_pixels_widget.addItem("%d, %d" % (event.pos().x(), event.pos().y()))
                for i in range(len(main.bad_pixels)):
                    main.roi_img_masked[main.bad_pixels[i][1], main.bad_pixels[i][0]] = 0
                main.ax.imshow(
                    main.roi_img_masked, interpolation="nearest", origin="upper", cmap=main._ref_color_map
                )
                main.ref_canvas.draw()
                self.rubberBand.show()


class paintLabel(QLabel):
    def __init__(self, parent=None):
        super(paintLabel, self).__init__(parent)

    def paintEvent(self, event):
        super(paintLabel, self).paintEvent(event)
        qp = QPainter()
        qp.begin(self)
        self.drawLine(event, qp)
        qp.end()

    def drawLine(self, event, qp):
        size = self.size()
        pen = QPen(QtCore.Qt.red)
        qp.setPen(pen)
        qp.drawLine(size.width() / 2, 0, size.width() / 2, size.height() - 1)
        qp.drawLine(size.width() / 2 - 1, 0, size.width() / 2 - 1, size.height() - 1)
        qp.drawLine(0, size.height() / 2, size.width() - 1, size.height() / 2)
        qp.drawLine(0, size.height() / 2 - 1, size.width() - 1, size.height() / 2 - 1)

        pen.setStyle(QtCore.Qt.DashLine)
        pen.setColor(QtCore.Qt.black)
        qp.setPen(pen)
        qp.drawLine(0, 0, size.width() - 1, 0)
        qp.drawLine(0, size.height() - 1, size.width() - 1, size.height() - 1)
        qp.drawLine(0, 0, 0, size.height() - 1)
        qp.drawLine(size.width() - 1, 0, size.width() - 1, size.height() - 1)


class DPCWindow(QMainWindow):
    CM_DEFAULT = "gray"

    def __init__(self, parent=None):
        QMainWindow.__init__(self, parent)
        DPCWindow.instance = self

        self.bin_num = 2 ** 16
        self._thread = None
        self.ion_data = None
        self.bad_flag = 0
        self.direction = -1  # 1 for horizontal and -1 for vertical
        self.crop_x0 = None
        self.crop_x1 = None
        self.crop_y0 = None
        self.crop_y1 = None
        self.set_roi_enabled = False
        self.his_enabled = False
        self.scan = None
        self.contrastval = 0
        self.histequalization = False
        self.showresiduals = False
        self.running = False

        self.gx, self.gy, self.phi, self.a, self.rx, self.ry = None, None, None, None, None, None
        self.file_widget = QLineEdit("Chromosome_9_%05d.tif")
        self.file_widget.setFixedWidth(350)
        self.save_path_widget = QLineEdit("/home")
        self.focus_widget = QDoubleSpinBox()

        self.dx_widget = QDoubleSpinBox()
        self.dy_widget = QDoubleSpinBox()
        self.pixel_widget = QDoubleSpinBox()
        self.energy_widget = QDoubleSpinBox()
        self.rows_widget = QSpinBox()
        self.cols_widget = QSpinBox()
        self.mosaic_x_widget = QSpinBox()
        self.mosaic_y_widget = QSpinBox()
        self.roi_x1_widget = QSpinBox()
        self.roi_x2_widget = QSpinBox()
        self.roi_y1_widget = QSpinBox()
        self.roi_y2_widget = QSpinBox()
        self.strap_start = QSpinBox()
        self.strap_end = QSpinBox()
        self.first_widget = QSpinBox()
        self.first_widget.valueChanged.connect(self._first_changed)

        self.processes_widget = QSpinBox()
        self.processes_widget.setMinimum(1)
        self.processes_widget.setValue(psutil.cpu_count())
        self.processes_widget.setMaximum(psutil.cpu_count())

        self.solver_widget = QComboBox()
        for solver in SOLVERS:
            self.solver_widget.addItem(solver)

        self.start_widget = QPushButton("Start")
        self.stop_widget = QPushButton("Stop")
        self.save_widget = QPushButton("Save")
        self.scan_button = QPushButton("Load")

        self.color_map = QComboBox()
        self.update_color_maps()
        self.color_map.currentIndexChanged.connect(self._set_color_map)
        self._color_map = mpl.cm.get_cmap(self.CM_DEFAULT)

        self.ref_color_map = QComboBox()
        self.update_ref_color_maps()
        self.ref_color_map.currentIndexChanged.connect(self._set_ref_color_map)
        self._ref_color_map = mpl.cm.get_cmap(self.CM_DEFAULT)

        self.start_widget.clicked.connect(self.start)
        self.stop_widget.clicked.connect(self.stop)
        self.save_widget.clicked.connect(self.save)
        self.scan_button.clicked.connect(self.load_from_spec_scan)

        self.load_image = load_timepix.load

        def format_coord(x, y):
            col = int(x + 0.5)
            row = int(y + 0.5)
            if row >= 0 and row < self.roi_img.shape[0] and col >= 0 and col < self.roi_img.shape[1]:
                z = self.roi_img[row, col]
                return "x=%1.4f   y=%1.4f   v=%1.4f" % (x, y, z)
            else:
                return "x=%1.4f   y=%1.4f" % (x, y)

        self.rect = Rectangle((0, 0), 0, 0, alpha=0.3, facecolor="gray", edgecolor="red", linewidth=2)
        self.ref_fig = plt.figure()
        # self.ref_canvas = MplCanvas(self.ref_fig, width=8, height=10, dpi=50)
        self.ref_canvas = FigureCanvas(self.ref_fig)
        self.ref_fig.subplots_adjust(top=0.99, left=0.01, right=0.99, bottom=0.04)
        self.ref_fig.canvas.mpl_connect("button_press_event", self.on_press)
        self.ref_fig.canvas.mpl_connect("button_release_event", self.on_release)
        self.ref_fig.canvas.mpl_connect("motion_notify_event", self.on_motion)
        self.ax = self.ref_fig.add_subplot(111)
        self.ax.format_coord = format_coord
        self.ax.add_patch(self.rect)
        self.ax.figure.canvas.draw()
        self.ref_toolbar = NavigationToolbar(self.ref_canvas, self)

        self.his_btn = QPushButton("Equalize")
        self.his_btn.setCheckable(True)
        self.his_btn.clicked[bool].connect(self.histgramEqua)
        self.roi_btn = QPushButton("Set ROI")
        self.roi_btn.setCheckable(True)
        self.roi_btn.clicked[bool].connect(self.set_roi_enable)
        self.bri_btn = QPushButton("Brightest")
        self.bri_btn.clicked.connect(self.select_bri_pixels)
        self.bad_btn = QPushButton("Pick")
        self.bad_btn.setCheckable(True)
        self.bad_btn.clicked[bool].connect(self.bad_enable)

        self.line_btn = QPushButton("Add")
        self.line_btn.setEnabled(False)
        self.line_btn.clicked.connect(self.add_strap)
        direction_text = "\N{CLOCKWISE OPEN CIRCLE ARROW} 90\N{DEGREE SIGN}"
        self.direction_btn = QPushButton(direction_text)
        self.direction_btn.clicked.connect(self.change_direction)
        self.direction_btn.setEnabled(False)
        self.removal_btn = QPushButton("Remove")
        self.removal_btn.clicked.connect(self.remove_background)
        self.removal_btn.setEnabled(False)
        self.confirm_btn = QPushButton("Apply")
        self.confirm_btn.clicked.connect(self.confirm)
        self.confirm_btn.setEnabled(False)
        self.hide_btn = QPushButton("View && set")
        self.hide_btn.setCheckable(True)
        self.hide_btn.clicked.connect(self.hide_ref)

        self.ok_btn = QPushButton("OK")
        self.ok_btn.clicked.connect(self.crop_ok)
        self.cancel_btn = QPushButton("Cancel")
        self.cancel_btn.clicked.connect(self.crop_cancel)

        # Setting widget (QGridLayout) in the bottom of reference image
        self.min_lbl = QLabel("Min")
        self.max_lbl = QLabel("Max")
        self.min_box = QSpinBox()
        self.max_box = QSpinBox()
        self.min_box.setMaximum(self.bin_num)
        self.min_box.setMinimum(0)
        self.max_box.setMaximum(self.bin_num)
        self.max_box.setMinimum(0)
        self.rescale_intensity_btn = QPushButton("Apply")
        self.rescale_intensity_btn.clicked.connect(self.rescale_intensity)

        self.badPixelGbox = QGroupBox("Bad pixels")
        self.badPixelGridLayout = QGridLayout()
        self.badPixelGbox.setLayout(self.badPixelGridLayout)
        bpw = self.bad_pixels_widget = QListWidget()
        # Set the minimum height of the qlistwidget as 1 so that the
        # qlistwidget is always as as high as its two side buttons
        bpw.setMinimumHeight(1)
        bpw.setContextMenuPolicy(Qt.CustomContextMenu)
        bpw.customContextMenuRequested.connect(self._bad_pixels_menu)

        self.badPixelGridLayout.addWidget(self.bri_btn, 0, 0)
        self.badPixelGridLayout.addWidget(self.bad_btn, 1, 0)
        self.badPixelGridLayout.addWidget(self.bad_pixels_widget, 0, 1, 2, 1)

        def ref_close(event):
            self.hide_btn.setChecked(False)

        self.ref_grid = QGridLayout()
        self.ref_widget = QWidget()
        self.ref_widget.closeEvent = ref_close
        self.ref_widget.setLayout(self.ref_grid)
        self.ref_grid.addWidget(self.ref_canvas, 0, 0, 1, 6)
        self.ref_grid.addWidget(self.ref_toolbar, 1, 0, 1, 6)
        self.ref_grid.addWidget(self.badPixelGbox, 2, 0, 3, 1)
        self.ref_grid.addWidget(self.ref_color_map, 2, 1, 1, 5)
        self.ref_grid.addWidget(self.his_btn, 3, 1, 1, 2)
        self.ref_grid.addWidget(self.roi_btn, 3, 3, 1, 2)
        self.ref_grid.addWidget(self.min_lbl, 4, 1)
        self.ref_grid.addWidget(self.min_box, 4, 2)
        self.ref_grid.addWidget(self.max_lbl, 4, 3)
        self.ref_grid.addWidget(self.max_box, 4, 4)
        self.ref_grid.addWidget(self.rescale_intensity_btn, 4, 5)

        self.file_format_btn = QPushButton("Select")
        # self.file_format_btn.setStyle(WinLayout)
        self.file_format_btn.clicked.connect(self.select_path)

        """
        QGroupBox implementation for image settings
        """
        self.imageSettingGbox = QGroupBox("Image settings")
        self.imageSettingGridLayout = QGridLayout()
        self.imageSettingGbox.setLayout(self.imageSettingGridLayout)
        self.scan_number_lbl = QLabel("Scan number")
        self.roi_x1_lbl = QLabel("ROI X1")
        self.roi_x2_lbl = QLabel("ROI X2")
        self.roi_y1_lbl = QLabel("ROI Y1")
        self.roi_y2_lbl = QLabel("ROI Y2")
        self.img_type_lbl = QLabel("Image type")
        self.pixel_size_lbl = QLabel("Pixel size (um)")
        self.file_name_lbl = QLabel("File name")
        self.first_img_num_lbl = QLabel("First image number")
        self.scan_info_lbl = QLabel("")
        self.scan_info_lbl.setWordWrap(True)
        self.select_ref_btn = QPushButton("Select the reference")
        self.select_ref_btn.clicked.connect(self.select_ref_img)
        self.img_type_combobox = itc = QComboBox()
        for types in TYPES:
            itc.addItem(types)
        itc.currentIndexChanged.connect(self.load_img_method)

        self.first_ref_cbox = QCheckBox("Use as the reference image")
        self.first_ref_cbox.stateChanged.connect(self.first_equal_ref)

        self.use_scan_number_cb = QCheckBox("Read from metadatastore")
        self.use_scan_number_cb.toggled.connect(self._use_scan_number_clicked)
        fs_key_cbox = self.fs_key_cbox = QComboBox()
        fs_key_cbox.currentIndexChanged.connect(self._filestore_key_changed)

        self.load_scan_btn = QPushButton("Load")
        self.load_scan_btn.clicked.connect(self.load_scan_from_mds)

        self.ref_image_path_QLineEdit = QLineEdit("reference image")
        self.ref_image_path_QLineEdit.setFixedWidth(350)
        self.scan_number_text = QLineEdit("3449")

        row = 0

        layout = self.imageSettingGridLayout
        if hxntools is not None:
            layout.addWidget(self.scan_number_lbl, row, 0)
            layout.addWidget(self.scan_number_text, row, 1)
            layout.addWidget(self.load_scan_btn, row, 2)
            layout.addWidget(self.use_scan_number_cb, row, 3)
            row += 1

            layout.addWidget(self.fs_key_cbox, row, 0)
            layout.addWidget(self.scan_info_lbl, row, 1, 1, 3)
            row += 1

        layout.addWidget(self.img_type_lbl, row, 0)
        layout.addWidget(self.img_type_combobox, row, 1)
        layout.addWidget(self.pixel_size_lbl, row, 2)
        layout.addWidget(self.pixel_widget, row, 3)

        row += 1
        layout.addWidget(self.file_name_lbl, row, 0)
        layout.addWidget(self.file_widget, row, 1, 1, 3)
        layout.addWidget(self.file_format_btn, row, 4)

        row += 1
        layout.addWidget(self.first_img_num_lbl, row, 0)
        layout.addWidget(self.first_widget, row, 1)
        layout.addWidget(self.first_ref_cbox, row, 2, 1, 2)

        row += 1
        layout.addWidget(self.select_ref_btn, row, 0)
        layout.addWidget(self.ref_image_path_QLineEdit, row, 1, 1, 3)

        row += 1
        layout.addWidget(self.roi_x1_lbl, row, 0)
        layout.addWidget(self.roi_x1_widget, row, 1)
        layout.addWidget(self.roi_x2_lbl, row, 2)
        layout.addWidget(self.roi_x2_widget, row, 3)
        layout.addWidget(self.hide_btn, row, 4)

        row += 1
        layout.addWidget(self.roi_y1_lbl, row, 0)
        layout.addWidget(self.roi_y1_widget, row, 1)
        layout.addWidget(self.roi_y2_lbl, row, 2)
        layout.addWidget(self.roi_y2_widget, row, 3)

        # QGroupBox implementation for experiment parameters
        self.experimentParaGbox = QGroupBox("Experiment parameters")
        self.experimentParaGridLayout = QGridLayout()
        self.experimentParaGbox.setLayout(self.experimentParaGridLayout)
        self.energy_lbl = QLabel("Energy (keV)")
        self.detector_sample_lbl = QLabel("Detector-sample distance (m)")
        self.x_step_size_lbl = QLabel("X step size (um)")
        self.y_step_size_lbl = QLabel("Y step size (um)")
        self.x_steps_number_lbl = QLabel("Columns (x)")
        self.y_steps_number_lbl = QLabel("Rows (y)")
        self.mosaic_x_size_lbl = QLabel("Mosaic column number")
        self.mosaic_y_size_lbl = QLabel("Mosaic row number")
        self.experimentParaGridLayout.addWidget(self.energy_lbl, 0, 0)
        self.experimentParaGridLayout.addWidget(self.energy_widget, 0, 1)
        self.experimentParaGridLayout.addWidget(self.detector_sample_lbl, 0, 2)
        self.experimentParaGridLayout.addWidget(self.focus_widget, 0, 3)
        self.experimentParaGridLayout.addWidget(self.x_step_size_lbl, 1, 0)
        self.experimentParaGridLayout.addWidget(self.dx_widget, 1, 1)
        self.experimentParaGridLayout.addWidget(self.y_step_size_lbl, 1, 2)
        self.experimentParaGridLayout.addWidget(self.dy_widget, 1, 3)
        self.experimentParaGridLayout.addWidget(self.x_steps_number_lbl, 2, 0)
        self.experimentParaGridLayout.addWidget(self.cols_widget, 2, 1)
        self.experimentParaGridLayout.addWidget(self.y_steps_number_lbl, 2, 2)
        self.experimentParaGridLayout.addWidget(self.rows_widget, 2, 3)
        self.experimentParaGridLayout.addWidget(self.mosaic_x_size_lbl, 3, 0)
        self.experimentParaGridLayout.addWidget(self.mosaic_x_widget, 3, 1)
        self.experimentParaGridLayout.addWidget(self.mosaic_y_size_lbl, 3, 2)
        self.experimentParaGridLayout.addWidget(self.mosaic_y_widget, 3, 3)

        """
        QGroupBox implementation for computation parameters
        """
        self.computationParaGbox = QGroupBox("Computation parameters")
        self.computationParaGridLayout = QGridLayout()
        self.computationParaGbox.setLayout(self.computationParaGridLayout)
        self.solver_method_lbl = QLabel("Solver method")
        self.processes_lbl = QLabel("Processes")
        self.random_processing_checkbox = QCheckBox("Random mode")
        self.hanging_checkbox = QCheckBox("Hanging mode")

        layout = self.computationParaGridLayout
        layout.addWidget(self.solver_method_lbl, 0, 0)
        layout.addWidget(self.solver_widget, 0, 1)
        layout.addWidget(self.processes_lbl, 0, 2)
        layout.addWidget(self.processes_widget, 0, 3)
        # layout.addWidget(self.random_processing_checkbox, 1, 0)
        # layout.addWidget(self.hanging_checkbox, 1, 1)
        layout.addWidget(self.start_widget, 0, 4)
        layout.addWidget(self.stop_widget, 0, 5)

        """
        QGroupBox implementation for console information
        """
        self.consoleInfoGbox = QGroupBox("Console information")
        self.consoleInfoGridLayout = QGridLayout()
        self.consoleInfoGbox.setLayout(self.consoleInfoGridLayout)
        self.console_info = QTextEdit(self)
        self.console_info.setReadOnly(True)
        self.consoleInfoGridLayout.addWidget(self.console_info)

        self.background_remove_qbox = QGroupBox("Remove background")
        self.background_remove_layout = QGridLayout()
        self.background_remove_qbox.setLayout(self.background_remove_layout)
        self.strap_start_label = QLabel("Start")
        self.strap_end_label = QLabel("End")
        self.background_remove_layout.addWidget(self.strap_start_label, 0, 0)
        self.background_remove_layout.addWidget(self.strap_start, 0, 1)
        self.background_remove_layout.addWidget(self.strap_end_label, 0, 2)
        self.background_remove_layout.addWidget(self.strap_end, 0, 3)
        self.background_remove_layout.addWidget(self.line_btn, 0, 4)
        self.background_remove_layout.addWidget(self.direction_btn, 0, 5)
        self.background_remove_layout.addWidget(self.removal_btn, 0, 6)
        self.background_remove_layout.addWidget(self.confirm_btn, 0, 7)

        self.canvas = MplCanvas(width=10, height=12, dpi=50)
        self.toolbar = NavigationToolbar(self.canvas, self)
        self.image_vis_qbox = QGroupBox("Image visualization")
        self.image_vis_layout = QGridLayout()
        self.image_vis_qbox.setLayout(self.image_vis_layout)
        self.image_vis_layout.addWidget(self.toolbar, 0, 0)
        self.image_vis_layout.addWidget(self.color_map, 0, 1)

        line = QFrame()
        line.setFrameShape(QFrame.HLine)
        line.setFrameShadow(QFrame.Sunken)
        self.image_vis_layout.addWidget(line, 1, 0)
        line = QFrame()
        line.setFrameShape(QFrame.HLine)
        line.setFrameShadow(QFrame.Sunken)
        self.image_vis_layout.addWidget(line, 1, 1)

        hboxcb = QHBoxLayout()
        self.cb_histeq = QCheckBox("Histogram Equalization", self)
        self.cb_histeq.setChecked(False)
        self.cb_histeq.stateChanged.connect(self.OnCBHistEqualization)
        hboxcb.addWidget(self.cb_histeq)

        self.cb_resid = QCheckBox("Show Residuals", self)
        self.cb_resid.setChecked(False)
        self.cb_resid.stateChanged.connect(self.OnCBShowResiduals)
        hboxcb.addWidget(self.cb_resid)

        self.image_vis_layout.addLayout(hboxcb, 2, 1)

        hboxslider = QHBoxLayout()
        hboxslider.addWidget(QLabel("Contrast"))
        self.slider_constrast = QSlider(QtCore.Qt.Horizontal)
        self.slider_constrast.setFocusPolicy(QtCore.Qt.StrongFocus)
        self.slider_constrast.setRange(0, 25)
        self.slider_constrast.setValue(0)
        self.slider_constrast.setTickPosition(QSlider.TicksBelow)
        self.slider_constrast.setTickInterval(5)
        hboxslider.addWidget(self.slider_constrast)
        self.slider_constrast.valueChanged[int].connect(self.OnContrastSlider)
        self.image_vis_layout.addLayout(hboxslider, 2, 0)

        self.canvas_QGridLayout = QGridLayout()
        self.canvas_widget = QWidget()
        self.canvas_widget.setLayout(self.canvas_QGridLayout)
        self.canvas_QGridLayout.addWidget(self.canvas, 0, 0, 1, 2)
        self.canvas_QGridLayout.addWidget(self.image_vis_qbox, 1, 0)
        self.canvas_QGridLayout.addWidget(self.background_remove_qbox, 1, 1)

        self.crop_widget = QWidget()
        self.crop_layout = QGridLayout()
        self.crop_widget.setLayout(self.crop_layout)
        self.crop_canvas = MplCanvas(width=8, height=8, dpi=50)
        self.crop_fig = self.crop_canvas.figure
        self.crop_fig.subplots_adjust(top=0.95, left=0.05, right=0.95, bottom=0.05)
        self.crop_ax = self.crop_fig.add_subplot(111)
        # self.crop_ax.hold(False)
        self.crop_ax.cla()
        self.crop_layout.addWidget(self.crop_canvas, 0, 0, 1, 2)
        self.crop_layout.addWidget(self.ok_btn, 1, 0)
        self.crop_layout.addWidget(self.cancel_btn, 1, 1)

        self.last_path = ""

        self.main_grid = QGridLayout()
        self.main_widget = QWidget()
        self.main_widget.setLayout(self.main_grid)
        self.main_grid.addWidget(self.imageSettingGbox, 0, 0)
        self.main_grid.addWidget(self.experimentParaGbox, 1, 0)
        self.main_grid.addWidget(self.computationParaGbox, 2, 0)
        self.main_grid.addWidget(self.consoleInfoGbox, 3, 0)

        # Add menu
        self.menu = self.menuBar()
        self.save_result_tiff = QAction("Export to .tiff", self)
        self.save_result_tiff.setEnabled(False)
        self.save_result_tiff.triggered.connect(self.save_file_tiff)
        self.save_result_txt = QAction("Export to .txt", self)
        self.save_result_txt.setEnabled(False)
        self.save_result_txt.triggered.connect(self.save_file_txt)
        self.save_scan_params = QAction("Save scan parameters", self)
        self.save_scan_params.triggered.connect(self.save_params_to_file)
        self.load_scan_params = QAction("Load scan parameters", self)
        self.load_scan_params.triggered.connect(self.load_params_from_file)
        self.start_batch_gui = QAction("Launch DPC Batch GUI", self)
        self.start_batch_gui.triggered.connect(self.launch_batch_gui)
        self.reverse_x = QAction("Reverse gx", self, checkable=True)
        self.reverse_x.triggered.connect(self.reverse_gx)
        self.reverse_x.setEnabled(False)
        self.reverse_y = QAction("Reverse gy", self, checkable=True)
        self.reverse_y.triggered.connect(self.reverse_gy)
        self.reverse_y.setEnabled(False)
        self.swap_xy = QAction("Swap x/y", self, checkable=True)
        self.swap_xy.triggered.connect(self.swap_x_y)
        self.swap_xy.setEnabled(False)
        self.random_processing_opt = QAction("Random mode", self, checkable=True)
        self.hanging_opt = QAction("Hanging mode", self, checkable=True)
        self.pyramid_scan = QAction("Pyramid scan", self, checkable=True)
        self.pad_recon = QAction("Padding mode", self, checkable=True)
        self.pad_recon.triggered.connect(self.padding_recon)

        file_menu = self.menu.addMenu("File")
        file_menu.addAction(self.save_result_tiff)
        file_menu.addAction(self.save_result_txt)
        file_menu.addAction(self.save_scan_params)
        file_menu.addAction(self.load_scan_params)
        file_menu.addAction(self.start_batch_gui)
        option_menu = self.menu.addMenu("Option")
        option_menu.addAction(self.reverse_x)
        option_menu.addAction(self.reverse_y)
        option_menu.addAction(self.swap_xy)
        option_menu.addAction(self.random_processing_opt)
        option_menu.addAction(self.hanging_opt)
        option_menu.addAction(self.pyramid_scan)
        option_menu.addAction(self.pad_recon)

        if hxntools is not None:
            self.monitor_scans = QAction("Monitor acquired scans", self, checkable=True)
            self.monitor_scans.triggered.connect(self.monitor_toggled)
            self.scan_monitor = HxnScanMonitor(uid_pv, db)
            self.scan_monitor.connect("start", self.bs_scan_started)
            self.scan_monitor.connect("stop", self.bs_scan_finished)
            option_menu.addAction(self.monitor_scans)

        self.setCentralWidget(self.main_widget)
        self.setWindowTitle("DPC v.{0}".format(version))

        # QApplication.setStyle(QStyleFactory.create('Cleanlooks'))
        QApplication.setStyle(QStyleFactory.create("Plastique"))
        # QApplication.setStyle(QStyleFactory.create('cde'))

        self._init_settings()

        for w in [
            self.pixel_widget,
            self.focus_widget,
            self.energy_widget,
            self.dx_widget,
            self.dy_widget,
            self.rows_widget,
            self.cols_widget,
            self.roi_x1_widget,
            self.roi_x2_widget,
            self.roi_y1_widget,
            self.roi_y2_widget,
            self.first_widget,
            self.mosaic_x_widget,
            self.mosaic_y_widget,
            self.strap_start,
            self.strap_end,
        ]:
            w.setMinimum(0)
            w.setMaximum(int(2 ** 31 - 1))
            try:
                w.setDecimals(3)
            except Exception:
                pass

        for w in [self.strap_start, self.strap_end]:
            w.setMinimum(0)
            w.setMaximum(9999)

        self.load_settings()

    def monitor_toggled(self):
        pass

    def bs_scan_started(self, uid, hxn_info=None, **hdr):
        if not self.monitoring:
            return

        print("Scan started")
        self.set_scan_from_scaninfo(ScanInfo(hdr), load_config=True)

    def bs_scan_finished(self, uid, hxn_info=None, **hdr):
        if not self.monitoring:
            return

        print("Scan finished")
        self.stop()
        self.set_scan_from_scaninfo(ScanInfo(hdr), load_config=True)

    def _init_settings(self):
        def typed_setter(fcn, type_):
            @wraps(fcn)
            def wrapped(value):
                return fcn(type_(value))

            return wrapped

        def checked_setter(widget, offset=1):
            @wraps(widget.setChecked)
            def wrapped(value):
                widget.setChecked(int(value) + offset)

            return wrapped

        def getter(attr):
            def wrapped():
                return getattr(self, attr)

            return wrapped

        def setter(attr):
            def wrapped(value):
                return setattr(self, attr, value)

            return wrapped

        self._settings = {
            "file_format": [getter("file_format"), self.file_widget.setText],
            "save_path": [getter("save_path"), self.save_path_widget.setText],
            "dx": [getter("dx"), setter("dx")],
            "dy": [getter("dy"), setter("dy")],
            "x1": [getter("roi_x1"), typed_setter(self.roi_x1_widget.setValue, int)],
            "y1": [getter("roi_y1"), typed_setter(self.roi_y1_widget.setValue, int)],
            "x2": [getter("roi_x2"), typed_setter(self.roi_x2_widget.setValue, int)],
            "y2": [getter("roi_y2"), typed_setter(self.roi_y2_widget.setValue, int)],
            "pixel_size": [getter("pixel_size"), typed_setter(self.pixel_widget.setValue, float)],
            "focus_to_det": [getter("focus"), typed_setter(self.focus_widget.setValue, float)],
            "energy": [getter("energy"), typed_setter(self.energy_widget.setValue, float)],
            "rows": [getter("rows"), typed_setter(self.rows_widget.setValue, int)],
            "cols": [getter("cols"), typed_setter(self.cols_widget.setValue, int)],
            "mosaic_y": [getter("mosaic_y"), typed_setter(self.mosaic_y_widget.setValue, int)],
            "mosaic_x": [getter("mosaic_x"), typed_setter(self.mosaic_x_widget.setValue, int)],
            "swap": [getter("swap"), checked_setter(self.swap_xy, 1)],
            "reverse_x": [getter("re_x"), checked_setter(self.reverse_x, -1)],
            "reverse_y": [getter("re_y"), checked_setter(self.reverse_y, -1)],
            "random": [getter("random"), checked_setter(self.random_processing_opt, 1)],
            "pyramid": [getter("pyramid"), checked_setter(self.pyramid_scan, 1)],
            "pad": [getter("pad"), checked_setter(self.pad_recon, True)],
            "hang": [getter("hang"), checked_setter(self.hanging_opt, 1)],
            "ref_image": [getter("ref_image"), self.ref_image_path_QLineEdit.setText],
            "first_image": [getter("first_image"), typed_setter(self.first_widget.setValue, int)],
            "processes": [getter("processes"), typed_setter(self.processes_widget.setValue, int)],
            "bad_pixels": [getter("bad_pixels"), self.set_bad_pixels],
            "solver": [getter("solver"), setter("solver")],
            "last_path": [getter("last_path"), setter("last_path")],
            "scan_number": [getter("scan_number"), setter("scan_number")],
            "use_mds": [getter("use_mds"), setter("use_mds")],
            "filestore_key": [getter("filestore_key"), setter("filestore_key")],
            # 'color_map': [lambda: self._color_map,
            #               setter('last_path')],
        }

    def _use_scan_number_clicked(self, checked):
        self.use_mds = checked
        self.file_widget.setEnabled(not self.use_mds)
        self.fs_key_cbox.setVisible(self.use_mds)
        self.scan_info_lbl.setVisible(self.use_mds)
        self.select_ref_btn.setEnabled(not self.use_mds)
        self.ref_image_path_QLineEdit.setEnabled(not self.use_mds)

        if self.use_mds:
            self.img_type_combobox.setCurrentIndex(TYPES.index("FileStore"))
            self.first_ref_cbox.setChecked(True)

        self.img_type_combobox.setEnabled(not self.use_mds)

    @property
    def use_mds(self):
        if hxntools is None:
            return False

        return bool(self.use_scan_number_cb.isChecked())

    @use_mds.setter
    def use_mds(self, checked):
        self.use_scan_number_cb.setChecked(bool(checked))

    @property
    def filestore_key(self):
        return str(self.fs_key_cbox.currentText())

    @filestore_key.setter
    def filestore_key(self, key):
        keys = list(sorted(self.scan.filestore_keys))
        self.fs_key_cbox.setCurrentIndex(keys.index(key))

    def _load_scan_from_mds(self, scan_id, load_config=True):

        hdrs = list(db(scan_id=scan_id))

        if len(hdrs) == 1:
            hdr = hdrs[0]

        else:

            def get_ts(hdr):
                return datetime.fromtimestamp(hdr["start"]["time"])

            scans = ["{} ({})".format(get_ts(hdr), hdr["start"]["uid"]) for hdr in hdrs]
            print("Multiple headers found...")
            s, ok = QInputDialog.getItem(self, "Multiple scans", "Which scan?", scans, 0, False)
            if ok:
                index = scans.index(str(s))
                hdr = hdrs[index]
            else:
                return

        self.set_scan_from_scaninfo(ScanInfo(hdr), load_config=load_config)

    def set_scan_from_scaninfo(self, scan, load_config=True):
        self.scan = scan
        selected = self.filestore_key
        self.fs_key_cbox.clear()
        if load_config:
            self.ref_image_path_QLineEdit.setText("")

        for i, key in enumerate(sorted(self.scan.filestore_keys)):
            self.fs_key_cbox.addItem(key)
            if key == selected:
                self.fs_key_cbox.setCurrentIndex(i)

        self.scan.key = self.filestore_key
        self.use_mds = True

        if self.scan.dimensions is None or len(self.scan.dimensions) == 0:
            return
        elif not load_config:
            return

        scan_range = self.scan.range
        print("Scan dimensions", self.scan.dimensions)
        print("Scan range:", scan_range)

        self.pyramid_scan.setChecked(self.scan.pyramid)

        if isinstance(scan_range, dict):
            scan_range = [scan_range[mtr] for mtr in self.scan.motors]

        if len(self.scan.dimensions) == 1:
            nx, ny = self.scan.dimensions[0], 1
            if scan_range is not None:
                self.dx = np.diff(scan_range[0]) / nx
                self.dy = 0.0
        else:
            nx, ny = self.scan.dimensions
            if scan_range is not None:
                self.dx = np.diff(scan_range[0]) / nx
                self.dy = np.diff(scan_range[1]) / ny

        self.cols = nx
        self.rows = ny

        self.scan_info_lbl.setText("Range: {}".format(scan_range))

    def load_scan_from_mds(self, **kwargs):
        return self._load_scan_from_mds(self.scan_number, **kwargs)

    @property
    def scan_number(self):
        try:
            return int(self.scan_number_text.text())
        except ValueError:
            return None

    @scan_number.setter
    def scan_number(self, value):
        self.scan_number_text.setText(str(value))

    def _first_changed(self, event):
        if self.use_mds:
            self.get_ref_from_mds()

    def get_ref_from_mds(self):
        if self.scan is None:
            return

        iter_ = iter(self.scan)

        first_image = max((1, self.first_image + 1))
        ref_image = None

        try:
            for i in range(first_image):
                ref_image = next(iter_)
        except StopIteration:
            print("Reference image #{} does not exist with data key {}" "".format(first_image, self.scan.key))

        if ref_image is not None:
            self.ref_image_path_QLineEdit.setText(ref_image)

    def _filestore_key_changed(self, event):
        key = self.filestore_key
        if self.scan is not None:
            self.scan.key = key
            print("MDS key set:", key)
            self.get_ref_from_mds()

    def on_press(self, event):
        if event.inaxes:
            self.crop_x0 = event.xdata
            self.crop_y0 = event.ydata

    def on_release(self, event):
        self.crop_x1 = event.xdata
        self.crop_y1 = event.ydata
        if event.inaxes:
            if (self.crop_x0, self.crop_y0) == (self.crop_x1, self.crop_y1):
                if self.bad_flag:
                    self.bad_pixels_widget.addItem("%d, %d" % (int(round(self.crop_x1)), int(round(self.crop_y1))))
                    for i in range(len(self.bad_pixels)):
                        self.roi_img_masked[self.bad_pixels[i][1], self.bad_pixels[i][0]] = 0
                    self.ax.imshow(
                        self.roi_img_masked, interpolation="nearest", origin="upper", cmap=self._ref_color_map
                    )
                    self.ref_canvas.draw()

            elif self.set_roi_enabled:
                if self.his_enabled:
                    roi_crop = self.roi_img_equ[
                        int(round(self.crop_y0)) : int(round(self.crop_y1)),
                        int(round(self.crop_x0)) : int(round(self.crop_x1)),
                    ]
                else:
                    roi_crop = self.roi_img[
                        int(round(self.crop_y0)) : int(round(self.crop_y1)),
                        int(round(self.crop_x0)) : int(round(self.crop_x1)),
                    ]
                self.crop_ax.imshow(
                    roi_crop,
                    interpolation="nearest",
                    origin="upper",
                    cmap=self._ref_color_map,
                    extent=[
                        int(round(self.crop_x0)),
                        int(round(self.crop_x1)),
                        int(round(self.crop_y0)),
                        int(round(self.crop_y1)),
                    ],
                )

                tfont = {"size": "22", "weight": "semibold"}

                msg = "ROI will be set as (%d, %d) - (%d, %d)" % (
                    int(round(self.crop_x0)),
                    int(round(self.crop_y0)),
                    int(round(self.crop_x1)),
                    int(round(self.crop_y1)),
                )
                self.crop_ax.set_title(msg, **tfont)
                self.crop_canvas.draw()
                self.crop_widget.show()

    def on_motion(self, event):
        if self.set_roi_enabled and event.button == 1 and event.inaxes:
            self.rect.set_width(event.xdata - self.crop_x0)
            self.rect.set_height(event.ydata - self.crop_y0)
            self.rect.set_xy((self.crop_x0, self.crop_y0))
            self.ax.figure.canvas.draw()

    def crop_ok(self):
        self.roi_x1_widget.setValue(int(round(self.crop_x0)))
        self.roi_y1_widget.setValue(int(round(self.crop_y0)))
        self.roi_x2_widget.setValue(int(round(self.crop_x1)))
        self.roi_y2_widget.setValue(int(round(self.crop_y1)))
        self.crop_widget.hide()

    def crop_cancel(self):
        self.crop_widget.hide()

    def set_roi_enable(self, pressed):
        if pressed:
            self.rect.set_visible(True)
            self.ax.figure.canvas.draw()
            self.set_roi_enabled = True
        else:
            self.rect.set_visible(False)
            self.ax.figure.canvas.draw()
            self.set_roi_enabled = False

    def update_display(self, a, gx, gy, phi, rx, ry, flag=None):

        # ax is a pyplot object

        def show_line(ax, line):
            ax.plot(line, "-*")
            # return mpl.pyplot.show()

        # def show_line_T(ax, line):
        #     ax.plot(line)

        def show_image(ax, image):
            # return ax.imshow(np.flipud(image.T), interpolation='nearest',
            #                  origin='upper', cmap=cm.Greys_r)

            if image is None:
                print("image is none")
                return

            if self.histequalization:
                return ax.imshow(
                    exposure.equalize_hist(image), interpolation="nearest", origin="upper", cmap=cm.Greys_r
                )
            elif self.contrastval > 0:

                adjustedimage = (image - image.min()) * 255.0 / image.ptp()
                return ax.imshow(
                    adjustedimage,
                    interpolation="nearest",
                    vmax=255 - self.contrastval * 10,
                    origin="upper",
                    cmap=cm.Greys_r,
                )
            else:
                return ax.imshow(image, interpolation="nearest", origin="upper", cmap=cm.Greys_r)

        def show_image_line(ax, image, start, end, direction=1):
            if direction == 1:
                ax.axhspan(start, end, facecolor="0.5", alpha=0.5)
                return ax.imshow(image, interpolation="nearest", origin="upper", cmap=cm.Greys_r)
            if direction == -1:
                ax.axvspan(start, end, facecolor="0.5", alpha=0.5)
                return ax.imshow(image, interpolation="nearest", origin="upper", cmap=cm.Greys_r)

        tfont = {"size": "28", "weight": "semibold"}

        # plt.hold(True)
        main = DPCWindow.instance
        canvas = self.canvas
        fig = canvas.figure
        fig.clear()
        fig.subplots_adjust(top=0.95, left=0.05, right=0.95, bottom=0.03)

        # Check 2D or 1D mode
        cols_num = main.cols_widget.value()
        rows_num = main.rows_widget.value()
        oned = (cols_num == 1) or (rows_num == 1)

        if oned is True:

            if cols_num == 1:
                gs = gridspec.GridSpec(3, 1)

                canvas.a_ax = a_ax = fig.add_subplot(gs[0, 0])
                a_ax.set_title("Intensity", **tfont)
                canvas.ima = ima = show_line(a_ax, a)

                canvas.gx_ax = gx_ax = fig.add_subplot(gs[1, 0])
                gx_ax.set_title("Phase gradient (x)", **tfont)
                # canvas.imx = imx = show_image(gx_ax, gx)
                canvas.imx = imx = show_line(gx_ax, gx)
                # fig.colorbar(imx)

                canvas.gy_ax = gy_ax = fig.add_subplot(gs[2, 0])
                gy_ax.set_title("Phase gradient (y)", **tfont)
                # canvas.imy = imy = show_image(gy_ax, gy)
                canvas.imy = imy = show_line(gy_ax, gy)
                # fig.colorbar(imy)

            else:
                gs = gridspec.GridSpec(3, 1)

                canvas.a_ax = a_ax = fig.add_subplot(gs[0, 0])
                a_ax.set_title("Intensity", **tfont)
                canvas.ima = ima = show_line(a_ax, a.T)

                canvas.gx_ax = gx_ax = fig.add_subplot(gs[1, 0])
                gx_ax.set_title("Phase gradient (x)", **tfont)
                canvas.imx = imx = show_line(gx_ax, gx.T)

                canvas.gy_ax = gy_ax = fig.add_subplot(gs[2, 0])
                gy_ax.set_title("Phase gradient (y)", **tfont)
                canvas.imy = imy = show_line(gy_ax, gy.T)

        else:
            if self.showresiduals:
                gs = gridspec.GridSpec(2, 3)
            else:
                gs = gridspec.GridSpec(2, 2)

            """
            if main.ion_data is not None:
                pixels = a.shape[0] * a.shape[1]
                ion_data = np.zeros(pixels)
                ion_data[:len(main.ion_data)] = main.ion_data
                ion_data[len(main.ion_data):] = ion_data[0]
                ion_data = ion_data.reshape(a.shape)

                min_ = np.min(a[np.where(a > 0)])
                a[np.where(a == 0)] = min_

                canvas.a_ax = a_ax = fig.add_subplot(gs[0, 1])
                a_ax.set_title('a')
                a_data = a / ion_data * ion_data[0]
                canvas.ima = ima = show_image(a_ax, a_data)
                fig.colorbar(ima)
            """

            canvas.a_ax = a_ax = fig.add_subplot(gs[1, 0])
            a_ax.set_title("Intensity", **tfont)
            # a_data = a / ion_data * ion_data[0]
            canvas.ima = ima = show_image(a_ax, a)
            fig.colorbar(ima)
            ima.set_cmap(main._color_map)

            if flag is None:
                canvas.gx_ax = gx_ax = fig.add_subplot(gs[0, 0])
                gx_ax.set_title("Phase gradient (x)", **tfont)
                canvas.imx = imx = show_image(gx_ax, gx)
                # canvas.imx = imx = show_line(gx_ax, gx)
                fig.colorbar(imx)
                imx.set_cmap(main._color_map)

                canvas.gy_ax = gy_ax = fig.add_subplot(gs[0, 1])
                gy_ax.set_title("Phase gradient (y)", **tfont)
                canvas.imy = imy = show_image(gy_ax, gy)
                # canvas.imy = imy = show_line(gy_ax, gy)
                fig.colorbar(imy)
                imy.set_cmap(main._color_map)

                if self.showresiduals:
                    canvas.rx_ax = rx_ax = fig.add_subplot(gs[0, 2])
                    rx_ax.set_title("Residual error (x)", **tfont)
                    canvas.imrx = imrx = show_image(rx_ax, rx)
                    fig.colorbar(imrx)
                    imrx.set_cmap(main._color_map)

                    canvas.ry_ax = ry_ax = fig.add_subplot(gs[1, 2])
                    ry_ax.set_title("Residual error (y)", **tfont)
                    canvas.imry = imry = show_image(ry_ax, ry)
                    fig.colorbar(imry)
                    imry.set_cmap(main._color_map)
            else:
                canvas.gx_ax = gx_ax = fig.add_subplot(gs[0, 0])
                gx_ax.set_title("Phase gradient (x)", **tfont)
                main = DPCWindow.instance
                canvas.imx = imx = show_image_line(
                    gx_ax, gx, main.strap_start.value(), main.strap_end.value(), main.direction
                )
                fig.colorbar(imx)
                imx.set_cmap(main._color_map)

                canvas.gy_ax = gy_ax = fig.add_subplot(gs[0, 1])
                gy_ax.set_title("Phase gradient (y)", **tfont)
                canvas.imy = imy = show_image_line(
                    gy_ax, gy, main.strap_start.value(), main.strap_end.value(), main.direction
                )
                fig.colorbar(imy)
                imy.set_cmap(main._color_map)

                if self.showresiduals:
                    canvas.rx_ax = rx_ax = fig.add_subplot(gs[0, 2])
                    rx_ax.set_title("Residual error (x)", **tfont)
                    main = DPCWindow.instance
                    canvas.imrx = imrx = show_image_line(
                        rx_ax, rx, main.strap_start.value(), main.strap_end.value(), main.direction
                    )
                    fig.colorbar(imrx)
                    imrx.set_cmap(main._color_map)

                    canvas.ry_ax = ry_ax = fig.add_subplot(gs[1, 2])
                    ry_ax.set_title("Residual error (y)", **tfont)
                    canvas.imry = imry = show_image_line(
                        ry_ax, ry, main.strap_start.value(), main.strap_end.value(), main.direction
                    )
                    fig.colorbar(imry)
                    imry.set_cmap(main._color_map)

            if phi is not None:
                phi_ax = fig.add_subplot(gs[1, 1])

                canvas.phi_ax = phi_ax
                phi_ax.set_title("Phase", **tfont)
                canvas.imphi = imphi = show_image(phi_ax, phi)
                fig.colorbar(imphi)
                imphi.set_cmap(main._color_map)

        for splot in fig.axes:
            splot.tick_params(axis="both", which="major", labelsize=21)

        canvas.draw()

    def add_strap(self, pressed):
        """
        Add two lines in the gx and gy
        """
        self.confirm_btn.setEnabled(False)
        self.direction_btn.setEnabled(True)
        self.removal_btn.setEnabled(True)
        self.update_display(a, gx, gy, phi, rx, ry, "strap")

    def change_direction(self, pressed):
        """
        Change the orientation of the strap
        """
        self.direction = -self.direction
        self.update_display(a, gx, gy, phi, rx, ry, "strap")

    def OnContrastSlider(self, pressed):
        """
        Change the contrast of the images
        """
        self.contrastval = self.slider_constrast.value()
        if not self.running:
            self.update_display(a, gx, gy, phi, rx, ry)

    def OnCBHistEqualization(self, state):
        """
        Image histogram equalization
        """
        if state == QtCore.Qt.Checked:
            self.histequalization = True
        else:
            self.histequalization = False

        if not self.running:
            self.update_display(a, gx, gy, phi, rx, ry)

    def OnCBShowResiduals(self, state):
        """
        Show residual images
        """
        if state == QtCore.Qt.Checked:
            self.showresiduals = True
        else:
            self.showresiduals = False

        if not self.running:
            self.update_display(a, gx, gy, phi, rx, ry)

    def remove_background(self, pressed):
        """
        Remove the background of the phase image
        """
        global gx, gy, phi, rx, ry
        self.confirm_btn.setEnabled(True)
        self.direction_btn.setEnabled(False)
        if self.direction == 1:
            strap_gx = gx[self.strap_start.value() : self.strap_end.value(), :]
            line_gx = np.mean(strap_gx, axis=0)
            self.gx_r = gx - line_gx
            strap_gy = gy[self.strap_start.value() : self.strap_end.value(), :]
            line_gy = np.mean(strap_gy, axis=0)
            self.gy_r = gy - line_gy
            self.phi_r = dpc.recon(self.gx_r, self.gy_r, self.dx_widget.value(), self.dy_widget.value())
            self.update_display(a, self.gx_r, self.gy_r, self.phi_r, rx, ry)

        if self.direction == -1:
            strap_gx = gx[:, self.strap_start.value() : self.strap_end.value()]
            line_gx = np.mean(strap_gx, axis=1)
            self.gx_r = np.transpose(gx)
            self.gx_r = self.gx_r - line_gx
            self.gx_r = np.transpose(self.gx_r)

            strap_gy = gy[:, self.strap_start.value() : self.strap_end.value()]
            line_gy = np.mean(strap_gy, axis=1)
            self.gy_r = np.transpose(gy)
            self.gy_r = self.gy_r - line_gy
            self.gy_r = np.transpose(self.gy_r)
            self.phi_r = dpc.recon(self.gx_r, self.gy_r, self.dx_widget.value(), self.dy_widget.value())
            self.update_display(a, self.gx_r, self.gy_r, self.phi_r, rx, ry)

    def confirm(self, pressed):
        """
        Confirm the background removal
        """
        global phi, gx, gy, rx, ry

        phi = self.phi_r
        imsave("phi.jpg", phi)
        np.savetxt("phi.txt", phi)

        gx = self.gx_r
        imsave("gx.jpg", gx)
        np.savetxt("gx.txt", gx)

        gy = self.gy_r
        imsave("gy.jpg", gy)
        np.savetxt("gy.txt", gy)

        self.confirm_btn.setEnabled(False)
        self.direction_btn.setEnabled(False)
        self.removal_btn.setEnabled(False)

    def bad_enable(self, pressed):
        """
        Enable or disable bad pixels selection by changing the bad_flag value
        """
        self.bad_flag = 1 if pressed else 0

    def histgramEqua(self, pressed):
        """
        Histogram equalization for the reference image
        """
        if pressed:
            self.his_enabled = True
            im = self.ax.imshow(self.roi_img_equ, interpolation="nearest", origin="upper", cmap=cm.Greys_r)

        else:
            self.his_enabled = False
            im = self.ax.imshow(self.roi_img, interpolation="nearest", origin="upper", cmap=cm.Greys_r)
        im.set_cmap(self._ref_color_map)
        self.ref_canvas.ref_im = im
        self.ref_canvas.draw()

    """
    def preContrast(self):
        self.contrastImage = self.roi_img.convert('L')
        # self.contrastImage = self.roi_img
        self.enh = ImageEnhance.Contrast(self.contrastImage)
    """

    def rescale_intensity(self):
        """
        Stretch or shrink ROI image intensity levels
        """
        min_ = self.min_box.value()
        max_ = self.max_box.value()
        roi_array = exposure.rescale_intensity(self.roi_img, in_range=(min_, max_))
        self.ax.imshow(roi_array, interpolation="nearest", origin="upper", cmap=self._ref_color_map)
        self.ref_canvas.draw()

    def calHist(self):
        """
        Calculate the histogram of the image used to select ROI
        """
        imhist, bins = np.histogram(self.roi_img, bins=self.bin_num, range=(0, self.bin_num), density=True)
        cdf = imhist.cumsum()
        cdf = (self.bin_num - 1) * cdf / cdf[-1]
        # cdf = (self.roi_img_max-self.roi_img_min) * cdf / cdf[-1]
        equalizedImg = np.floor(np.interp(self.roi_img, bins[:-1], cdf))
        self.roi_img_equ = np.reshape(equalizedImg, self.roi_img.shape, order="C")

        # skimage histgram equalization
        # img = np.array(self.roi_img.getdata(),
        #                dtype=np.uint16).reshape(self.roi_img.size[1],
        #                                         self.roi_img.size[0])
        # equalizedImg = exposure.equalize_hist(img)
        # scipy.misc.imsave('equalizedImg.tif', equalizedImg)

    def select_bri_pixels(self):
        """
        Select the bad pixels (pixels with the maximum pixel value)
        """
        indices = np.where(self.roi_img == self.roi_img.max())
        indices_num = indices[0].size
        for i in range(indices_num):
            item = "%d, %d" % (indices[1][i], indices[0][i])
            self.bad_pixels_widget.addItem(item)

        for i in range(len(self.bad_pixels)):
            self.roi_img_masked[self.bad_pixels[i][1], self.bad_pixels[i][0]] = 0

        self.ax.imshow(self.roi_img_masked, interpolation="nearest", origin="upper", cmap=self._ref_color_map)
        self.ref_canvas.draw()

    """
    def change_contrast(self, value):
        '''
        Change the contrast of the ROI image by slider bar
        '''
        delta = value / 10.0
        self.enh.enhance(delta).save('change_contrast.tif')
        contrastImageTemp = QPixmap('change_contrast.tif')
        self.img_lbl.setPixmap(contrastImageTemp)
    """

    """
    def eventFilter(self, source, event):
        '''
        Event filter to enable cursor coordinates tracking on the ROI image
        '''
        if (event.type() == QtCore.QEvent.MouseMove and
            source is self.ref_canvas):
            if event.buttons() == QtCore.Qt.NoButton:
                pos = event.pos()
                self.txt_lbl.setText('min=%d, max=%d, x=%d, y=%d, value=%d ' %
                                     (self.roi_img_min, self.roi_img_max,
                                      pos.x(), pos.y(),
                                      self.roi_img.getpixel((pos.x(),
                                                             pos.y()))))

                top_left_x = pos.x()-10 if pos.x()-10>=0 else 0
                top_left_y = pos.y()-10 if pos.y()-10>=0 else 0
                bottom_right_x = (pos.x()+10 if pos.x()+10<self.roi_img.size[0]
                                  else self.roi_img.size[0]-1)
                bottom_right_y = (pos.y()+10 if pos.y()+10<self.roi_img.size[1]
                                  else self.roi_img.size[1]-1)

                if (pos.y()-10)<0:
                    self.temp_lbl.setAlignment(QtCore.Qt.AlignBottom)
                if (pos.x()+10)>=self.roi_img.size[0]:
                    self.temp_lbl.setAlignment(QtCore.Qt.AlignLeft)
                if (pos.x()-10)<0:
                    self.temp_lbl.setAlignment(QtCore.Qt.AlignRight)
                if (pos.y()+10)>=self.roi_img.size[1]:
                    self.temp_lbl.setAlignment(QtCore.Qt.AlignTop)

                width = bottom_right_x - top_left_x + 1
                height = bottom_right_y - top_left_y+ 1
                img_fraction = self.img_lbl.pixmap().copy(top_left_x,
                                                          top_left_y, width,
                                                          height)
                scaled_img_fraction = img_fraction.scaled(width*8, height*8)
                self.temp_lbl.setPixmap(scaled_img_fraction)

        if (event.type() == QtCore.QEvent.MouseMove and
            source is not self.img_lbl):
            if event.buttons() == QtCore.Qt.NoButton:
                self.txt_lbl.setText('min=%d, max=%d' % (self.roi_img_min,
                                                         self.roi_img_max))
                self.temp_lbl.clear()

        return QDialog.eventFilter(self, source, event)
    """

    def select_path(self):
        """
        Select path and initiate file format for the data

        """
        fname = get_open_filename(self, "Open file", "/home")[0]
        fname = str(fname)
        basename, extension = os.path.splitext(fname)
        if extension == ".h5":
            self.file_widget.setText(fname)
        else:
            if fname != "":
                index1 = fname.rfind(".")
                index2 = fname.rfind("_")
                digits = index1 - index2 - 1
                if digits == 1:
                    format_str = "%d"
                else:
                    format_str = "%" + "0%dd" % digits
                modified = fname.replace(fname[index2 + 1 : index1], format_str)
                self.file_widget.setText(modified)

    def save_file_tiff(self):

        self.save_file(save_txt=False, save_tif=True)

    def save_file_txt(self):

        self.save_file(save_txt=True, save_tif=False)

    def save_file(self, save_txt=True, save_tif=True):
        """
        Select the path where the results will be saved

        """
        global a, gx, gy, phi, rx, ry
        default_path = str(self.save_path_widget.text())
        path = get_save_filename(self, "Select path", default_path)[0]
        path = str(path)
        self.save_path_widget.setText(path)
        if path != "":
            if save_txt:
                a_path = path + "_a.txt"
                # print(a_path)
                np.savetxt(a_path, a)
                gx_path = path + "_gx.txt"
                np.savetxt(gx_path, gx)
                gy_path = path + "_gy.txt"
                np.savetxt(gy_path, gy)
                rx_path = path + "_rx.txt"
                np.savetxt(rx_path, rx)
                ry_path = path + "_ry.txt"
                np.savetxt(ry_path, ry)
                if phi is not None:
                    phi_path = path + "_phi.txt"
                    np.savetxt(phi_path, phi)

            if havetiff and save_tif:
                if phi is not None:
                    imgs = np.stack((a, gx, gy, rx, ry, phi))
                    imsave(path + ".tif", imgs.astype(np.float32))
                else:
                    imgs = np.stack((a, gx, gy, rx, ry))
                    imsave(path + ".tif", imgs.astype(np.float32))

    def save_params_to_file(self):
        self.save_settings()
        path = get_save_filename(self, "Select path", "", ".txt")[0]
        path = str(path)
        if path != "":
            print("Saving parameters to {0}".format(path))
            settings = self.dpc_settings

            # Save parameters to the parameter text file
            param_file = open(path, "w")
            param_file.write("step_size_dx_um = {0}\n".format(settings["dx"]))
            param_file.write("step_size_dy_um = {0}\n".format(settings["dy"]))
            param_file.write("cols_x = {0}\n".format(settings["cols"]))
            param_file.write("rows_y = {0}\n".format(settings["rows"]))
            param_file.write("pixel_size_um = {0}\n".format(settings["pixel_size"]))
            param_file.write("detector_sample_distance = {0}\n".format(settings["focus_to_det"]))
            param_file.write("energy_keV = {0}\n".format(settings["energy"]))
            param_file.write("roi_x1 = {0}\n".format(settings["x1"]))
            param_file.write("roi_x2 = {0}\n".format(settings["x2"]))
            param_file.write("roi_y1 = {0}\n".format(settings["y1"]))
            param_file.write("roi_y2 = {0}\n".format(settings["y2"]))
            param_file.write("mosaic_column_number_x = {0}\n".format(settings["mosaic_x"]))
            param_file.write("mosaic_column_number_y = {0}\n".format(settings["mosaic_y"]))
            param_file.write("solver = {0}\n".format(settings["solver"]))
            param_file.write("random = {0}\n".format(settings["random"]))
            param_file.write("pyramid = {0}\n".format(settings["pyramid"]))
            param_file.write("hang = {0}\n".format(settings["hang"]))
            param_file.write("swap = {0}\n".format(settings["swap"]))
            param_file.write("reverse_x = {0}\n".format(settings["reverse_x"]))
            param_file.write("reverse_y = {0}\n".format(settings["reverse_y"]))
            param_file.write("pad = {0}\n".format(1 if settings["pad"] else 0))

            param_file.close()

    def load_params_from_file(self):

        path = get_open_filename(self, "Select path", "", "Parameter files (*.txt);;")[0]
        path = str(path)
        if path != "":
            print("Loading parameters from {0}".format(path))
            settings = self.settings

            # Save parameters to the parameter text file
            param_file = open(path, "r")

            for line in param_file:

                if line.startswith("#"):
                    continue

                elif "step_size_dx_um" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("dx", float(slist[1]))

                elif "step_size_dy_um" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("dy", float(slist[1]))

                elif "cols_x" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("cols", int(slist[1]))

                elif "rows_y" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("rows", int(slist[1]))

                elif "pixel_size_um" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("pixel_size", float(slist[1]))

                elif "detector_sample_distance" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("focus_to_det", float(slist[1]))

                elif "energy_keV" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("energy", float(slist[1]))

                elif "roi_x1" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("x1", int(slist[1]))

                elif "roi_x2" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("x2", int(slist[1]))

                elif "roi_y1" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("y1", int(slist[1]))

                elif "roi_y2" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("y2", int(slist[1]))

                elif "mosaic_column_number_x" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("mosaic_x", int(slist[1]))

                elif "mosaic_column_number_y" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("mosaic_y", int(slist[1]))

                elif "solver" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("solver", "{0}".format(slist[1].strip()))

                elif "random" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("random", int(slist[1]))

                elif "pyramid" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("pyramid", int(slist[1]))

                elif "hang" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("hang", int(slist[1]))

                elif "swap" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("swap", int(slist[1]))

                elif "reverse_x" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("reverse_x", int(slist[1]))

                elif "reverse_y" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("reverse_y", int(slist[1]))

                elif "pad" in line.lower():
                    slist = line.strip().split("=")
                    settings.setValue("pad", int(slist[1]))

            param_file.close()

        loaded = {}
        for key, (getter, setter) in self._settings.items():
            value = settings.value(key)
            try:
                value = value.toPyObject()
            except AttributeError:
                pass

            if value is not None:
                try:
                    setter(value)
                except Exception as ex:
                    print("Unable to set value for %s=%s (%s) %s" "" % (key, value, ex.__class__.__name__, ex))
                else:
                    loaded[key] = value

        try:
            self.setGeometry(loaded["geometry"])
        except Exception as ex:
            pass

        try:
            self.ref_widget.setGeometry(loaded["ref_geo"])
        except Exception as ex:
            pass

        try:
            self.img_type_combobox.setCurrentIndex(loaded["image_type"])
        except Exception as ex:
            pass

        try:
            self.ref_image_path_QLineEdit.setText(loaded["ref_image"])
        except Exception as ex:
            pass

        try:
            self.first_ref_cbox.setChecked(loaded["first_as_ref"])
        except Exception as ex:
            pass

        try:
            self.use_mds.setChecked(loaded["use_mds"])
        except Exception as ex:
            pass

    def launch_batch_gui(self):
        dir_name, _ = os.path.split(__file__)
        fln = os.path.join(dir_name, "dpc_batch_gui.py")
        subprocess.Popen(["python", fln])

    def swap_x_y(self):
        global a, gx, gy, phi, rx, ry
        gx, gy = gy, gx
        phi = dpc.recon(gx, gy, self.dx_widget.value(), self.dy_widget.value())
        self.update_display(a, gx, gy, phi, rx, ry)

    def reverse_gx(self):
        global a, gx, gy, phi, rx, ry
        gx = -gx
        phi = dpc.recon(gx, gy, self.dx_widget.value(), self.dy_widget.value())
        self.update_display(a, gx, gy, phi, rx, ry)

    def reverse_gy(self):
        global a, gx, gy, phi, rx, ry
        gy = -gy
        phi = dpc.recon(gx, gy, self.dx_widget.value(), self.dy_widget.value())
        self.update_display(a, gx, gy, phi, rx, ry)

    def padding_recon(self):
        global a, gx, gy, phi, rx, ry
        if self.pad_recon.isChecked():
            phi = dpc.recon(gx, gy, self.dx_widget.value(), self.dy_widget.value(), 3)
            print("Padding mode enabled!")
        else:
            phi = dpc.recon(gx, gy, self.dx_widget.value(), self.dy_widget.value())
            print("Padding mode disabled!")
        self.update_display(a, gx, gy, phi, rx, ry)

    def select_ref_img(self):
        """
        Select the reference image and record its location and name

        """
        fname = get_open_filename(self, "Open file", "/home")[0]
        fname = str(fname)
        if fname != "":
            self.ref_image_path_QLineEdit.setText(fname)

    def hide_ref(self, pressed):
        """
        Hide/Show the reference image related widgets

        """
        if pressed:
            self.load_img_method()
            not_ref = self.first_ref_cbox.checkState() == Qt.Unchecked
            if not_ref or self.use_mds:
                ref_path = str(self.ref_image_path_QLineEdit.text())
            else:
                if self.file_widget.text()[-3:] == ".h5":
                    ref_path = str(self.file_widget.text())
                else:
                    ref_path = str(self.file_widget.text()) % self.first_widget.value()

            try:
                self.roi_img = self.load_image(ref_path)

                self.roi_img_masked = self.roi_img.copy()

                self.calHist()
                ref_im = self.ax.imshow(
                    self.roi_img_masked, interpolation="nearest", origin="upper", cmap=cm.Greys_r
                )
                ref_im.set_cmap(self._ref_color_map)
                self.ref_canvas.ref_im = ref_im
                self.ref_widget.show()
                self.ref_canvas.draw()
            except Exception as ex:
                logger.error("Reference image read failed", exc_info=ex)
                msg = "Could not read the reference image! \r (%s) %s" "" % (ex.__class__.__name__, ex)
                QMessageBox.information(self, "Read error", msg, QMessageBox.Ok)
                self.hide_btn.setChecked(False)

        else:
            self.ref_widget.hide()

    def first_equal_ref(self, state):
        """
        First image ?= reference image
        """

        if state == QtCore.Qt.Checked:
            palette = QPalette()
            palette.setColor(QPalette.Base, QtCore.Qt.lightGray)
            self.ref_image_path_QLineEdit.setPalette(palette)
            self.select_ref_btn.setEnabled(False)
            self.ref_image_path_QLineEdit.setEnabled(False)
        else:
            self.select_ref_btn.setEnabled(True)
            self.ref_image_path_QLineEdit.setEnabled(True)
            palette = QPalette()
            palette.setColor(QPalette.Base, QtCore.Qt.white)
            self.ref_image_path_QLineEdit.setPalette(palette)

    def load_img_method(self):
        method = str(self.img_type_combobox.currentText())

        if method == "Timepix TIFF":
            self.load_image = load_timepix.load
        elif method == "TIFF":
            self.load_image = load_image_pil
        elif method == "ASCII":
            self.load_image = load_image_ascii
        elif method == "HDF5":
            self.load_image = load_image_hdf5
        elif method == "FileStore":
            self.load_image = dpc.load_image_filestore

    def _set_color_map(self, index):
        """
        User changed color map callback.
        """
        cm_ = str(self.color_map.itemText(index))
        print("Color map set to: %s" % cm_)
        self._color_map = mpl.cm.get_cmap(cm_)
        for im in ["imphi", "imx", "imy", "ima"]:
            try:
                im = getattr(self.canvas, im)
                im.set_cmap(self._color_map)
            except Exception as ex:
                print("failed to set color map: (%s) %s" "" % (ex.__class__.__name__, ex))

        self.canvas.draw()

    def _set_ref_color_map(self, index):
        """
        User changed color map callback.
        """
        cm_ = str(self.ref_color_map.itemText(index))
        self._ref_color_map = mpl.cm.get_cmap(cm_)
        try:
            for im in [
                self.ref_canvas.ref_im,
            ]:
                im.set_cmap(self._ref_color_map)
        except Exception as ex:
            print("failed to set color map: (%s) %s" % (ex.__class__.__name__, ex))
        finally:
            self.ref_canvas.draw()

    def create_cmap_previews(self):
        """
        Create the color map previews for the combobox
        """
        cm_names = sorted(_cm for _cm in mpl.cm.datad.keys() if not _cm.endswith("_r"))
        cm_filenames = [os.path.join(CMAP_PREVIEW_PATH, "%s.png" % cm_name) for cm_name in cm_names]

        ret = zip(cm_names, cm_filenames)
        points = np.outer(np.ones(10), np.arange(0, 1, 0.01))
        if not os.path.exists(CMAP_PREVIEW_PATH):
            try:
                os.mkdir(CMAP_PREVIEW_PATH)
            except Exception as ex:
                print("Unable to create preview path: %s" % ex)

            return ret

        for cm_name, fn in zip(cm_names, cm_filenames):
            if not os.path.exists(fn):
                print("Generating colormap preview: %s" % fn)
                canvas = MplCanvas(width=2, height=0.25, dpi=50)
                fig = canvas.figure
                fig.clear()

                ax = fig.add_subplot(1, 1, 1)
                ax.axis("off")
                fig.subplots_adjust(top=1, left=0, right=1, bottom=0)
                _cm = mpl.cm.get_cmap(cm_name)
                ax.imshow(points, aspect="auto", cmap=_cm, origin="upper")
                try:
                    fig.savefig(fn)
                except Exception as ex:
                    print('Unable to create color map preview "%s"' % fn, file=sys.stderr)
                    break

        return ret

    def update_color_maps(self):
        size = None
        for i, (cm_name, fn) in enumerate(self.create_cmap_previews()):
            if os.path.exists(fn):
                self.color_map.addItem(QIcon(fn), cm_name)
                if size is None:
                    size = QPixmap(fn).size()
                    self.color_map.setIconSize(size)
            else:
                self.color_map.addItem(cm_name)

            if cm_name == self.CM_DEFAULT:
                self.color_map.setCurrentIndex(i)

    def update_ref_color_maps(self):
        size = None
        for i, (cm_name, fn) in enumerate(self.create_cmap_previews()):
            if os.path.exists(fn):
                self.ref_color_map.addItem(QIcon(fn), cm_name)
                if size is None:
                    size = QPixmap(fn).size()
                    self.ref_color_map.setIconSize(size)
            else:
                self.ref_color_map.addItem(cm_name)

            if cm_name == self.CM_DEFAULT:
                self.ref_color_map.setCurrentIndex(i)

    @property
    def settings(self):
        return QtCore.QSettings("BNL", "DPC-GUI")

    def save_settings(self):
        settings = self.settings
        for key, (getter, setter) in self._settings.items():
            settings.setValue(key, getter())

        settings.setValue("geometry", self.geometry())
        settings.setValue("ref_geo", self.ref_widget.geometry())
        settings.setValue("image_type", self.img_type_combobox.currentIndex())
        settings.setValue("ref_image", self.ref_image_path_QLineEdit.text())
        settings.setValue("first_as_ref", self.first_ref_cbox.isChecked())

    def load_settings(self):
        settings = self.settings
        loaded = {}
        for key, (getter, setter) in self._settings.items():
            value = settings.value(key)
            try:
                value = value.toPyObject()
            except AttributeError:
                pass

            if value is not None:
                try:
                    setter(value)
                except Exception as ex:
                    print("Unable to set value for %s=%s (%s) %s" "" % (key, value, ex.__class__.__name__, ex))
                else:
                    loaded[key] = value

        try:
            self.setGeometry(loaded["geometry"])
        except Exception as ex:
            pass

        try:
            self.ref_widget.setGeometry(loaded["ref_geo"])
        except Exception as ex:
            pass

        try:
            self.img_type_combobox.setCurrentIndex(loaded["image_type"])
        except Exception as ex:
            pass

        try:
            self.ref_image_path_QLineEdit.setText(loaded["ref_image"])
        except Exception as ex:
            pass

        try:
            self.first_ref_cbox.setChecked(loaded["first_as_ref"])
        except Exception as ex:
            pass

        try:
            self.use_mds.setChecked(loaded["use_mds"])
        except Exception as ex:
            pass

    def closeEvent(self, event=None):
        self.save_settings()
        sys.exit()

    @property
    def dx(self):
        return float(self.dx_widget.text())

    @dx.setter
    def dx(self, dx):
        self.dx_widget.setValue(float(dx))

    @property
    def dy(self):
        return float(self.dy_widget.text())

    @dy.setter
    def dy(self, dy):
        self.dy_widget.setValue(float(dy))

    @property
    def processes(self):
        return int(self.processes_widget.text())

    @property
    def file_format(self):
        return str(self.file_widget.text())

    @property
    def save_path(self):
        return str(self.save_path_widget.text())

    @property
    def pixel_size(self):
        return self.pixel_widget.value()

    @property
    def focus(self):
        return self.focus_widget.value()

    @property
    def energy(self):
        return self.energy_widget.value()

    @property
    def rows(self):
        return self.rows_widget.value()

    @rows.setter
    def rows(self, rows):
        self.rows_widget.setValue(rows)

    @property
    def cols(self):
        return self.cols_widget.value()

    @cols.setter
    def cols(self, cols):
        self.cols_widget.setValue(cols)

    @property
    def mosaic_x(self):
        return self.mosaic_x_widget.value()

    @property
    def mosaic_y(self):
        return self.mosaic_y_widget.value()

    @property
    def monitoring(self):
        return self.monitor_scans.isChecked()

    @property
    def random(self):
        if self.random_processing_opt.isChecked():
            return 1
        else:
            return -1

    @property
    def pad(self):
        if self.pad_recon.isChecked():
            return True
        else:
            return False

    @property
    def pyramid(self):
        if self.pyramid_scan.isChecked():
            return 1
        else:
            return -1

    @property
    def swap(self):
        if self.swap_xy.isChecked():
            return 1
        else:
            return -1

    @property
    def re_x(self):
        if self.reverse_x.isChecked():
            return -1
        else:
            return 1

    @property
    def re_y(self):
        if self.reverse_y.isChecked():
            return -1
        else:
            return 1

    @property
    def hang(self):
        if self.hanging_opt.isChecked():
            return 1
        else:
            return -1

    @property
    def first_image(self):
        return self.first_widget.value()

    @property
    def ref_image(self):
        if self.first_ref_cbox.checkState() == Qt.Unchecked or self.use_mds:
            return str(self.ref_image_path_QLineEdit.text())
        else:
            if self.file_widget.text()[-3:] == ".h5":
                return str(self.file_widget.text())
            else:
                return str(self.file_widget.text()) % self.first_widget.value()

    @property
    def roi_x1(self):
        return self.roi_x1_widget.value()

    @property
    def roi_x2(self):
        return self.roi_x2_widget.value()

    @property
    def roi_y1(self):
        return self.roi_y1_widget.value()

    @property
    def roi_y2(self):
        return self.roi_y2_widget.value()

    @property
    def bad_pixels(self):
        w = self.bad_pixels_widget

        def fix_tuple(item):
            item = str(item.text())
            return [int(x) for x in item.split(",")]

        return [fix_tuple(w.item(i)) for i in range(w.count())]

    def _bad_pixels_menu(self, pos):
        def add():
            msg = "Position in the format: x, y"
            s, ok = QInputDialog.getText(self, "Position?", msg)
            if ok:
                s = str(s)
                x, y = s.split(",")
                x = int(x)
                y = int(y)
                self.bad_pixels_widget.addItem("%d, %d" % (x, y))
                for i in range(len(self.bad_pixels)):
                    self.roi_img_masked[self.bad_pixels[i][1], self.bad_pixels[i][0]] = 0
                self.ax.imshow(
                    self.roi_img_masked, interpolation="nearest", origin="upper", cmap=self._ref_color_map
                )
                self.ref_canvas.draw()

        def remove():
            rows = [index.row() for index in self.bad_pixels_widget.selectedIndexes()]
            for row in reversed(sorted(rows)):
                self.bad_pixels_widget.takeItem(row)
            self.roi_img_masked = self.roi_img.copy()
            for i in range(len(self.bad_pixels)):
                self.roi_img_masked[self.bad_pixels[i][1], self.bad_pixels[i][0]] = 0
            self.ax.imshow(self.roi_img_masked, interpolation="nearest", origin="upper", cmap=self._ref_color_map)
            self.ref_canvas.draw()

        def clear():
            self.bad_pixels_widget.clear()
            self.roi_img_masked = self.roi_img.copy()
            self.ax.imshow(self.roi_img_masked, interpolation="nearest", origin="upper", cmap=self._ref_color_map)
            self.ref_canvas.draw()

        self.menu = menu = QMenu()
        menu.addAction("&Add", add)
        menu.addAction("&Remove", remove)
        menu.addAction("&Clear", clear)

        menu.popup(self.bad_pixels_widget.mapToGlobal(pos))

    def load_from_spec_scan(self):
        filename = get_open_filename(self, "Scan filename", self.last_path, "*.spec")[0]
        if not filename:
            return

        self.last_path = filename

        print("Loading %s" % filename)
        with pyspecfile.SPECFileReader(filename, parse_data=False) as f:
            scans = dict((int(scan["number"]), scan) for scan in f.scans)
            scan_info = [
                "%04d - %s" % (number, scan["command"])
                for number, scan in scans.items()
                if "mesh" in scan["command"]
            ]

            scan_info.sort()
            print("\n".join(scan_info))

            s, ok = QInputDialog.getItem(self, "Scan selection", "Scan number?", scan_info, 0, False)
            if ok:
                print("Selected scan", s)
                number = int(s.split(" ")[0])
                sd = scans[number]
                f.parse_data(sd)

                timepix_index = sd["columns"].index("tpx_image")
                line0 = sd["lines"][0]
                timepix_first_image = int(line0[timepix_index])

                try:
                    ion1_index = sd["columns"].index("Ion1")
                    self.ion_data = np.array([line[ion1_index] for line in sd["lines"]])
                except Exception as ex:
                    print("Failed loading Ion1 data (%s) %s" "" % (ex, ex.__class__.__name__))
                    self.ion_data = None

                print("First timepix image:", timepix_first_image)

                self.first_widget.setValue(timepix_first_image - 1)

                command = sd["command"].replace("  ", " ")

                x = [2, 3, 4]  # x start, end, points
                y = [6, 7, 8]  # y start, end, points
                info = command.split(" ")

                x_info = [float(info[i]) for i in x]
                y_info = [float(info[i]) for i in y]

                dx = (x_info[1] - x_info[0]) / (x_info[2] - 1)
                dy = (y_info[1] - y_info[0]) / (y_info[2] - 1)

                self.rows_widget.setValue(int(y_info[-1]))
                self.cols_widget.setValue(int(x_info[-1]))

                self.dx_widget.setValue(float(dx))
                self.dy_widget.setValue(float(dy))

    @property
    def solver(self):
        return SOLVERS[self.solver_widget.currentIndex()]

    @solver.setter
    def solver(self, solver):
        self.solver_widget.setCurrentIndex(SOLVERS.index(solver))

    def set_bad_pixels(self, pixels):
        w = self.bad_pixels_widget
        w.clear()
        for item in pixels:
            x, y = item
            w.addItem(
                "%d, %d"
                % (
                    x,
                    y,
                )
            )

    @property
    def dpc_settings(self):
        ret = {}
        for key, (getter, setter) in self._settings.items():
            if key not in ("last_path", "scan_number", "filestore_key", "processes"):
                ret[key] = getter()
        return ret

    def start(self):
        self.load_img_method()
        self.save_settings()

        if self.use_mds and self.scan is None:
            if self.scan_number is not None:
                self.load_scan_from_mds(load_config=False)

            if self.scan is None:
                not_loaded = "Scan not loaded from metadatastore"
                QMessageBox.information(self, "Load scan", not_loaded, QMessageBox.Ok)
                return

        self.reverse_x.setEnabled(False)
        self.reverse_y.setEnabled(False)
        self.swap_xy.setEnabled(False)
        self.hanging_opt.setEnabled(False)
        self.random_processing_opt.setEnabled(False)
        self.pyramid_scan.setEnabled(False)
        self.pad_recon.setEnabled(False)
        self.save_result_tiff.setEnabled(False)
        self.save_result_txt.setEnabled(False)
        self.canvas_widget.show()
        self.line_btn.setEnabled(False)
        self.direction_btn.setEnabled(False)
        self.removal_btn.setEnabled(False)
        self.confirm_btn.setEnabled(False)

        if self._thread is not None and self._thread.isFinished():
            self._thread = None

        if self._thread is None:
            if self.processes == 0:
                pool = None
            else:
                pool = mp.Pool(processes=self.processes)

            thread = self._thread = DPCThread(self.canvas, pool=pool)
            thread.update_signal.connect(self.update_display)

            thread.dpc_settings = self.dpc_settings
            if self.use_mds:
                thread.dpc_settings["scan"] = self.scan

            if self.load_image == load_image_hdf5:
                thread.dpc_settings["use_hdf5"] = True
            else:
                thread.dpc_settings["use_hdf5"] = False

            thread.start()
            self.set_running(True)

    def set_running(self, running):
        self.start_widget.setEnabled(not running)
        self.stop_widget.setEnabled(running)
        self.running = running

    def stop(self):
        if self._thread is not None:
            pool = self._thread.pool
            if pool is not None:
                pool.terminate()
                self._thread.pool = None

            time.sleep(0.2)
            self._thread.terminate()
            self._thread = None
            self.set_running(False)

    def save(self):
        filename = get_save_filename(self, "Save filename prefix", "", "")[0]
        if not filename:
            return

        arrays = [
            ("gx", self.gx),
            ("gy", self.gy),
            ("phi", self.phi),
            ("a", self.a),
            ("rx", self.rx),
            ("ry", self.ry),
        ]

        for name, arr in arrays:
            im = PIL.Image.fromarray(arr)
            im.save("%s_%s.tif" % (filename, name))
            np.savetxt("%s_%s.txt" % (filename, name), im)

    @QtCore.pyqtSlot(str)
    def on_myStream_message(self, message):
        self.console_info.moveCursor(QTextCursor.End)
        self.console_info.insertPlainText(message)


if __name__ == "__main__":
    try:
        uid_pv = sys.argv[1]
    except IndexError:
        uid_pv = "XF:03IDC-ES{BS-Scan}UID-I"

    logging.basicConfig(level=logging.INFO)
    app = QApplication(sys.argv)
    # app.setAttribute(Qt.AA_X11InitThreads)

    window = DPCWindow()
    window.show()
    app.installEventFilter(window)

    myStream = MyStream()
    myStream.message.connect(window.on_myStream_message)

    sys.stdout = myStream
    sys.exit(app.exec_())