GUI_main.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
This script is the main script used to produce a GUI which should help for
cell segmentation. This script can only read .nd2 files containing the 
images of cells, especially it displays for each recorded positions (field
of view) the pictures in the time axis.

The script opens first a window which allows you to load an nd2 file and
to load or create an hdf file. The hdf file contains all the masks, so if
it is the first the user segments an nd2 file, a new one should be created.
And it can be then loaded for later use.  Along with new hdf file, created
by the name entered by the user (say filename), it creates three other hdf 
files (filename_predicted.h5, filename_thresholded.h5 and 
filename_segmented.h5) these contain all the steps of the NN to get to the 
segmented picture. 

After the first window is finished a second one opens, where at each time 
index, three pictures 
are displayed the t-1 picture, the t picture (current frame which can be
edited) and the t+1 picture. Using the arrows one can navigate through time.
On top of the picture, there is always a mask which is displayed, if no cells
are present in the mask then the mask is blank and the user does not see it. 
If one wants to hand anmotate the pictures, one can just start to draw on the
picture using the different functions (New Cell, Add Region, Brush, Eraser,
Save Mask,...) and the informations will be saved in the mask overlayed on 
top of the pictures. 

If one wants to segment using a neural network, one can press the
corresponding button (Launch CNN) and select the time range and 
the field of views on which the neural network is applied.

Once the neural network has finished predicting, there are still no visible
masks, but on the field of views and time indices where the NN has been
applied, the threshold and segment buttons are enabled. By checking these
two buttons one can either display the thresholded image of the prediction or
display the segmentation of the thresholded prediction.

At this stage, one can correct the segmentation of the prediction using
the functions (New Cell, Add Region, etc..) by selecting the Segment
checkbox and then save them using the Save Seg button.
If the user is happy with the segmentation, the Cell Correspondance button 
can be clicked. Until then, the cells get random numbers attributed by
the segmentation algorithm. In order to keep track of the cell through time,
the same cells should have the same number between two different time pictures.
This can be (with some errors) achieved by the Cell Correspondance button,
which tries to attribute the same number to corresponding cells in time.
After that, the final mask is saved and it is always visible when you go on
the corresponding picture. This mask can also be corrected using the 
usual buttons (because the Cell Correspondance makes also mistakes). 

"""

import sys
#append all the paths where the modules are stored. Such that this script
#looks into all of these folders when importing modules.
sys.path.append("./unet")
sys.path.append("./disk")
sys.path.append("./icons")
sys.path.append("./init")
sys.path.append("./misc")
import time
import os
import numpy as np


# Import everything for the Graphical User Interface from the PyQt5 library.
from PyQt5.QtWidgets import QApplication, QMainWindow, QDialog, QMenu, QVBoxLayout, QSizePolicy, QMessageBox, QWidget, QPushButton, QShortcut, QComboBox, QCheckBox, QLineEdit, QMenu, QAction, QStatusBar, QErrorMessage
from PyQt5 import QtGui
from PyQt5.QtCore import pyqtSignal, QObject, Qt

#Import from matplotlib to use it to display the pictures and masks.
from matplotlib.backends.qt_compat import QtCore, QtWidgets, is_pyqt5
from matplotlib.backends.backend_qt5agg import (FigureCanvasQTAgg as FigureCanvas, NavigationToolbar2QT as NavigationToolbar)
from matplotlib.figure import Figure
import matplotlib.pyplot as plt
#import the colormaps function to create a customed colormap scale with 10 
#colors only
from matplotlib import cm
from matplotlib.colors import ListedColormap, LinearSegmentedColormap
#import Path functions to handle the regions drawn by the user. ("add region
#and new cell")
from matplotlib.path import Path
 

#Import all the other python files
#this file handles the interaction with the disk, so loading/saving images
#and masks and it also runs the neural network.
import InteractionDisk_temp as nd


#this file contains a dialog window that takes two integers as entry to swap
#two cell values
import ExchangeCellValues as ecv
#this file contains a dialog window which is opened before the main program
#and allows to load the nd2 and hdf files by browsing through the computer.
import DialogFileBrowser as dfb
#this file contains a window that opens to change the value of one cell. It 
#is opened as soon as the user presses with the left click on a specific cell.
import ChangeOneCellValue as cocv
#this file contains a dialog window to browse for the excel file where
#all the extracted information on the fluoerscence is written. Or to create a 
#new excel file by typing a name in the text box. It is thought to have one 
#excel file per field of view.
import DialogDataBrowser as ddb
#this file contains a dialog window where a time range and the field of views
#can be selected to then launch a prediction of the neural network on
#a specific range of pictures.

import LaunchBatchPrediction as lbp

#this file initializes all the buttons present in the gui, sets the shortcuts
#to these buttons and also connect the buttons to the function that are 
#triggered when the buttons are pressed.
import InitButtons

#this file contains the layout of the main window so it justs puts the buttons
#and the pictures at the desired position in the main window.
import InitLayout


import random

#import everything needed to write and read excel files.
from openpyxl import load_workbook
from openpyxl import Workbook


#def show_error(msg):
#    error_dialog = QErrorMessage()
#    error_dialog.showMessage(msg)
#    error_dialog.exec_
    


class NavigationToolbar(NavigationToolbar):
    """This is the standard matplotlib toolbar but only the buttons
    that are of interest for this gui are loaded. These buttons allow 
    to zoom into the pictures/masks and to navigate in the zoomed picture. 
    A Home button can be used to set the view back to the original view.
    """
    toolitems = [t for t in NavigationToolbar.toolitems if
                 t[0] in ('Home', 'Pan', 'Zoom','Back', 'Forward')]
      
class App(QMainWindow):
    """This class creates the main window.

    """

    def __init__(self, nd2pathstr, hdfpathstr, newhdfstr):
        super().__init__()
#        initializes the window
#       set a title to the window
        self.title = 'YeaZ 1.0'

#        id is an integer that gives the id of the connection between the mouseclick method
#        and the activation of the button.

#       all these ids are integers which are used to set a connection between
#       the button and the function that this button calls.
#       There are three of them because it happens that one can trigger three 
#       different functions with one button.        
        self.id = 0
        self.id2 = 0
        self.id3 = 0 



#       it calls an object of the class Load Image from the InteractionDisk
#       file which is used to load images and masks from the nd2 file or tiff files. To
#       initialize this object it needs the path of the nd2 file, of an
#       existing hdf file and the name of a new hdf file. If the user has no
#       hdf file yet the hdfpathstr will be empty and vice versa if the user
#       selects an already existing hdf file.
#       It takes all the strings given by the first window 
#       (called before the main window opens) from the DialogFileBrowser.py 
#       file. (see at the end of this code)

        self.reader = nd.Reader(hdfpathstr, newhdfstr, nd2pathstr)
        
        
#       these variables are used to create/read/load the excel file used
#       to write the fluorescence values extracted. For each field of view,
#       the user will be asked each time to create a new xls file for the 
#       field of view or to load an existing field of view (this is the role
#       of the boolean variable)
        self.xlsfilename = ''
        self.nd2path = nd2pathstr
        self.FlagFluoExtraction = False

        
        
        
#        Set the indices for the time axis and the field of view index. These
#        indices represent everywhere the current picture (the one that can be
#        edited, i.e. the time t frame)
        self.Tindex = 0
        self.FOVindex = 0
        
#        loading the first images of the cells from the nd2 file