removeBackgroundGUI.py

"""
Remove background from dataset
      
* Import data (.csv): 
*     File > Load File
*         OR
*     Ctrl+L
* Set Order and Threshold parameters
* Calculate Background
*     File > Calculate Background
*         OR
*     Ctrl+B
*         OR
*     Click "Background"
* Export data
*     File > Export (.csv)
*         OR
*     Ctrl+E

Colin Brosseau (colin@erzatz.info)
License: 
Last modified: 2016/11/29
"""

"""
TODO

grey calculate background, save image of export data if not possible
display error message if background absent while saving
add options for reading the csv file (header, etc)
add generic interface for custom cost function
"""

#import sys, os, random
import sys
from PyQt4.QtCore import *
from PyQt4.QtGui import *

import numpy as np

import matplotlib

from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
#from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
from matplotlib.figure import Figure

import backcor
from importCsvGui import importCsv

class AppForm(QMainWindow):
    def __init__(self, parent=None):
        QMainWindow.__init__(self, parent)
        self.showMaximized()
        self.x = 0
        self.y = 0
        self.setWindowTitle('Background removal')

        self.create_menu()
        self.create_main_frame()
        self.create_status_bar()

        self.order.setText('6')
        self.threshold.setText('50')
        self.has_background = False
        self.background_removed = False
        #self.plot_data()

    def export_csv(self):
        header = ''
        if self.background_removed:
            header = header + ' > Background removed'

        file_choices = "CSV (*.csv)|*.csv"
        
        path = str(QFileDialog.getSaveFileName(self, 
                        'Save file', '', 
                        file_choices))
        if path:
#            self.canvas.print_figure(path, dpi=self.dpi)
            self.statusBar().showMessage('Saved to %s' % path, 2000)

            np.savetxt(path, np.array([self.x, self.y-self.background]).transpose(), fmt='%1.7e', delimiter=',', header=header)
        
    def save_plot(self):
        file_choices = "PNG (*.png)|*.png"
        
        path = str(QFileDialog.getSaveFileName(self, 
                        'Save file', '', 
                        file_choices))
        if path:
            self.canvas.print_figure(path, dpi=self.dpi)
            self.statusBar().showMessage('Saved to %s' % path, 2000)
    
    def load_csv(self):
        self.x, self.y, parameters, ok = importCsv.getData()
        if ok:
            print(parameters)
            self.draw_button.setEnabled(True)
            self.has_background = False
            self.background_removed = False
            self.plot_data()
            
    def on_about(self):
        msg = """ 
         Remove background from dataset
        
         * Import data (.csv): 
         *     File > Load File
         * Set Order and Threshold parameters
         * Calculate Background
         *     File > Calculate Background
         * Export data
         *     File > Export (.csv)
        """
        QMessageBox.about(self, "Basic usage", msg.strip())
    
    def plot_data(self):
        """ Redraws the figure
        """
        self.axes.clear()        
        self.axes.grid(self.grid_cb.isChecked())

        self.axes.plot(self.x, self.y, '.', label='data')
        self.axes.set_xlim([np.min(self.x), np.max(self.x)])
        self.axes.set_ylim([np.min(self.y), np.max(self.y)])
        self.axes.set_title('Data')
        self.axes.set_xticklabels([])
        
        self.axes2.clear()        
        if self.has_background:
            self.axes.set_title('Data & Background')
            self.axes.plot(self.x,self.background,'', label='background')

            z = self.y - self.background
            self.axes2.grid(self.grid_cb.isChecked())
            
            self.axes2.plot(self.x, z, '.', label='data - background')
            self.axes2.set_xlim([np.min(self.x), np.max(self.x)])
            self.axes2.set_ylim([np.min(z), np.max(z)])
            self.axes2.set_title('Difference')
            self.axes2.legend()
            
        self.axes.legend()
        self.canvas.draw()
    
    def calculate_background(self):
        """ Calculate the background
        """
        # fit method
        text = str(self.fit_method.currentText())
        if text == "symmetric Huber function":
            method = 'sh'
        elif text == "asymmetric Huber function":
            method = 'ah'
        elif text == "symmetric truncated quadratic":
            method = 'stq'
        elif text == "asymmetric truncated quadratic":
            method = 'atq'
            
        self.statusBar().showMessage('Calculating background...')  # problem here: it just make status bar to blink. Like it print this line after it make calculation
        order = int(self.order.text())
        threshold = float(self.threshold.text())
        z, a, it = backcor.backcor(self.x, self.y, order, threshold, method)
        self.statusBar().showMessage('')
        self.has_background = True
        self.background = z
        self.plot_data()
    
    def create_main_frame(self):
        self.main_frame = QWidget()
        
        self.dpi = 100
#        self.fig = Figure((5.0, 4.0), dpi=self.dpi)
        self.fig = Figure(dpi=self.dpi, tight_layout=True)
        self.canvas = FigureCanvas(self.fig)
        self.canvas.setParent(self.main_frame)
        
        self.axes = self.fig.add_subplot(211)
        self.axes2 = self.fig.add_subplot(212)
        
        # Create the navigation toolbar, tied to the canvas
        self.mpl_toolbar = NavigationToolbar(self.canvas, self.main_frame)
        
        # Other GUI controls

        # Order of the polynomial
        order_label = QLabel('Order')
        self.order = QLineEdit()
        self.order.setValidator(QIntValidator(0, 101, self))
        self.order.setMinimumWidth(3)
        self.order.setMaxLength(3)
        order = QVBoxLayout()
        order.addWidget(order_label)
        order.addWidget(self.order)

        # Threshold (peak detection)
        threshold_label = QLabel('Threshold')
        self.threshold = QLineEdit()
        self.threshold.setMinimumWidth(3)
        self.threshold.setValidator(QDoubleValidator(bottom=0))
        threshold = QVBoxLayout()
        threshold.addWidget(threshold_label)
        threshold.addWidget(self.threshold)
        
        # Fit method
        fit_method_label = QLabel('Fit Method')

        self.fit_method = QComboBox(self)
        self.fit_method.addItem("symmetric Huber function")
        self.fit_method.addItem("asymmetric Huber function")
        self.fit_method.addItem("symmetric truncated quadratic")
        self.fit_method.addItem("asymmetric truncated quadratic")
        index = self.fit_method.findText('asymmetric truncated quadratic')
        if index >= 0:
            self.fit_method.setCurrentIndex(index)
        fit_method = QVBoxLayout()
        fit_method.addWidget(fit_method_label)
        fit_method.addWidget(self.fit_method)
        
        self.draw_button = QPushButton("&Background")
        self.draw_button.setEnabled(False)
        self.connect(self.draw_button, SIGNAL('clicked()'), self.calculate_background)

        self.grid_cb = QCheckBox("Show &Grid")
        self.grid_cb.setChecked(False)
        self.connect(self.grid_cb, SIGNAL('stateChanged(int)'), self.plot_data)
        
        # Layout with box sizers
        hbox = QHBoxLayout()

        hbox.addLayout(order)
        hbox.setAlignment(order, Qt.AlignVCenter)
        hbox.addLayout(threshold)
        hbox.setAlignment(threshold, Qt.AlignVCenter)
        hbox.addLayout(fit_method)
        hbox.setAlignment(fit_method, Qt.AlignVCenter)
#        for w in [  self.order, self.threshold, self.draw_button, self.remove_button, self.grid_cb,
        for w in [ self.draw_button, self.grid_cb,]:
            hbox.addWidget(w)
            hbox.setAlignment(w, Qt.AlignVCenter)

        # Main window (everything together)
        vbox = QVBoxLayout()
        vbox.addWidget(self.canvas)
        vbox.addWidget(self.mpl_toolbar)
        vbox.addLayout(hbox)
        
        self.main_frame.setLayout(vbox)
        self.setCentralWidget(self.main_frame)
    
    def create_status_bar(self):
        self.status_text = QLabel("")
        self.statusBar().addWidget(self.status_text, 1)
        
    def create_menu(self):        
        self.file_menu = self.menuBar().addMenu("&File")
        
        load_file_action = self.create_action("&Load file",
            shortcut="Ctrl+O", slot=self.load_csv, 
            tip="Load data")
        calculate_action = self.create_action("Calculate &Background",
            shortcut="Ctrl+B", slot=self.calculate_background, 
            tip="Calculate Background")
        save_file_action = self.create_action("&Save plot",
            shortcut="Ctrl+S", slot=self.save_plot, 
            tip="Save the plot")
        export_csv_action = self.create_action("&Export (.csv)",
            shortcut="Ctrl+E", slot=self.export_csv, 
            tip="Export to csv")
        quit_action = self.create_action("&Quit", slot=self.close, 
            shortcut="Ctrl+Q", tip="Close the application")
        
        self.add_actions(self.file_menu, 
            (load_file_action, calculate_action, save_file_action, export_csv_action, None, quit_action))
        
        self.help_menu = self.menuBar().addMenu("&Help")
        about_action = self.create_action("&About", 
            shortcut='F1', slot=self.on_about, 
            tip='About this program')
        
        self.add_actions(self.help_menu, (about_action,))

    def add_actions(self, target, actions):
        for action in actions:
            if action is None:
                target.addSeparator()
            else:
                target.addAction(action)

    def create_action(  self, text, slot=None, shortcut=None, 
                        icon=None, tip=None, checkable=False, 
                        signal="triggered()"):
        action = QAction(text, self)
        if icon is not None:
            action.setIcon(QIcon(":/%s.png" % icon))
        if shortcut is not None:
            action.setShortcut(shortcut)
        if tip is not None:
            action.setToolTip(tip)
            action.setStatusTip(tip)
        if slot is not None:
            self.connect(action, SIGNAL(signal), slot)
        if checkable:
            action.setCheckable(True)
        return action

def main():
    app = QApplication(sys.argv)
    form = AppForm()
    form.show()
    app.exec_()

if __name__ == "__main__":
    main()