prasopes.py

#!/usr/bin/env python3

from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from matplotlib.widgets import SpanSelector
from PyQt5 import QtCore
from PyQt5 import QtWidgets
from rawFin import load_raw
from scipy.signal import find_peaks
import sys
import matplotlib
import numpy as np
import logging
matplotlib.use("Qt5Agg")


def zoom_factory(ax, base_scale, plot=None, an=None):
    def zoom_fun(event, plot, an):
        if event.inaxes == ax:
            if event.button == 'up':
                #zoom in
                scale_factor = 1/base_scale
            elif event.button == 'down':
                #zoom out
                scale_factor = base_scale
            else:
                #should not happen
                scale_factor = 1
                print(event.button)

            if event.key == 'shift':
                data = event.ydata
                newtop = data + (ax.get_ylim()[1] - data)*scale_factor
                ax.set_ylim([newtop*-0.01,newtop])
            else:
                data = event.xdata
                xleft = data - ax.get_xlim()[0]
                xright = ax.get_xlim()[1] - data
                ax.set_xlim([data - xleft*scale_factor,
                            data + xright*scale_factor])
            if an != None:
                if type(plot['x']) != type(None):
                    annSpectr(event.inaxes,plot['x'], plot['y'], an)
            ax.figure.canvas.draw()

    fig = ax.get_figure()  # get the figure of interest
    # attach the call back
    fig.canvas.mpl_connect('scroll_event', lambda event: zoom_fun(event, plot, an))

    # return the function
    return zoom_fun


def pan_factory(ax, plot=None, an=None):
    def pan_fun(event):
        if event.button == 1 and event.inaxes == ax:
            ax.start_pan(event.x, event.y, event.button)
            id_drag = fig.canvas.mpl_connect('motion_notify_event', drag_fun)
            id_release = fig.canvas.mpl_connect('button_release_event',
                                                lambda action: drag_end(action, id_drag, id_release, plot, an))

    def drag_fun(event):
        ax.drag_pan(1, 'x', event.x, event.y)
        ax.figure.canvas.draw()

    def drag_end(event, id_drag, id_release, plot, an):
        if event.button == 1:
            fig.canvas.mpl_disconnect(id_drag)
            fig.canvas.mpl_disconnect(id_release)
            if an != None:
                if type(plot['x']) != type(None):
                    annSpectr(event.inaxes,plot['x'], plot['y'], an)
            ax.figure.canvas.draw()
    fig = ax.get_figure()
    fig.canvas.mpl_connect('button_press_event', pan_fun)


def picktimes(xmin, xmax, mplspectrum, dataset, mplchromatogram, an, ms_s):
    start_scan = 0
    end_scan = -1
    for i, j in enumerate(dataset['chromdat'][0, :]):
        if j > xmin and start_scan == 0:
            start_scan = i
        if j > xmax and end_scan == -1:
            end_scan = i
    mplspectrum.clear()
    an.clear()
    ms_s['x'] = dataset['masses']
    ms_s['y'] = np.mean(dataset['matrix'][start_scan:end_scan], axis=0) 
    spectrPlot(spectrum, ms['x'], ms['y'], an)
    mplchromatogram.clear()
    chromPlot(mplchromatogram, dataset['chromdat'][0, :], dataset['chromdat'][1, :])
    mplchromatogram.plot(dataset['chromdat'][0, start_scan:end_scan], dataset['chromdat'][1, start_scan:end_scan], 'b.')

def populate(mplchromatogram, mplspectrum, dataset, timeSel,an, ms_s):
    an.clear()
    def updateSpanSelector(chromatogram, spectrum, dataset, ms_s):
        timeselec = SpanSelector(chromatogram, lambda xmin, xmax: picktimes(xmin, xmax, spectrum, dataset, chromatogram, an, ms_s), 'horizontal', useblit=True, rectprops=dict(alpha=0.15, facecolor='purple'),button=3)
        return timeselec
    mplspectrum.clear()
    mplchromatogram.clear()
    ms_s['x'] = dataset['masses']
    ms_s['y'] = np.mean(dataset['matrix'], axis=0)
    spectrPlot(mplspectrum,ms_s['x'], ms_s['y'], an)
    chromPlot(mplchromatogram, dataset['chromdat'][0,:],dataset['chromdat'][1,:])
    timeSel[0] = updateSpanSelector(mplchromatogram, mplspectrum, ds, ms_s)
    mplchromatogram.figure.canvas.draw()
    mplspectrum.figure.canvas.draw()

def annSpectr(spectrum,mass,intensity,an):
    def sub_peaks(peakz,mass,intensity,x,y):
        gp=[]
        sp=[]
        for g in peakz:#[0]:
            if gp == [] or (abs(max(intensity[gp]) - intensity[g])*10 < y and abs(mass[gp[np.argmax(intensity[gp])]] - mass[g])*20 < x ):
                gp.append(g)
            else:
                sp.append(gp[np.argmax(intensity[gp])])
                gp = [g]
            if g == peakz[-1]:#[0][-1]:
                sp.append(gp[np.argmax(intensity[gp])])
        return sp

    borders=spectrum.get_xlim()
    start = np.argmax(mass>borders[0])
    end = np.argmax(mass>borders[1])
    if end == 0:
        end = np.argmax(mass)
    #peaks = find_peaks(intensity, height=spectrum.get_ylim()[1]/100)
    peaks = find_peaks(intensity[start:end], height=spectrum.get_ylim()[1]/100)
    peaks = peaks[0] + start
    sp = sub_peaks(peaks,mass,intensity,spectrum.get_xlim()[1]-spectrum.get_xlim()[0],spectrum.get_ylim()[1]-spectrum.get_ylim()[0])
    
    for j in an:
        j.remove()
    an.clear()

    for i in sp:
        an.append(spectrum.annotate('{0:.2f}'.format(mass[i]), xy=(mass[i],intensity[i]),textcoords='data'))

def spectrPlot(spetrum,mass,intensity, an):
    spectrum.plot(mass,intensity)
    spectrum.set_title("Spectrum:", loc = "right")
    spectrum.set_xlabel("m/z")
    spectrum.set_ylabel("ion count")
    spectrum.set_ylim(spectrum.get_ylim()[1]*-0.01,)
    spectrum.ticklabel_format(scilimits=(0,0),axis='y')
    annSpectr(spectrum, mass, intensity, an)

def chromPlot(chromatogram,times,tic):
    chromatogram.plot(times,tic)
    chromatogram.set_ylim(chromatogram.get_ylim()[1]*-0.011,chromatogram.get_ylim()[1]*1.1)
    chromatogram.set_title("Chromatogram:", loc = "right")
    chromatogram.set_xlabel("time (min)")
    chromatogram.set_ylabel("total ion count")
    chromatogram.ticklabel_format(scilimits=(0,0),axis='y')

def openFile(cromatogram, spectrum, ds, timeSel, an, ms_s):
    filename=QtWidgets.QFileDialog.getOpenFileName(caption = "Open spectrum", filter="Finnigan RAW files (*.raw, *.RAW)")[0]
    if filename is '':
        return
    ds['chromdat'],ds['masses'],ds['matrix'] = load_raw(filename)
    populate(chromatogram, spectrum, ds, timeSel, an, ms_s)


if __name__=="__main__":
    #ds for data_set
    ds = dict(chromdat=None,masses=None,matrix=None)
    #mass spectrometry set
    ms = dict(x=None,y=None)

    nlogger = logging.getLogger('parseLogger')
    logging.basicConfig()
    nlogger.setLevel("WARN")

    graph = Figure(figsize=(5,4),dpi=100)
    graph.patch.set_facecolor("None")

    chromatogram = graph.add_subplot(211,facecolor=(1,1,1,0.8))
    spectrum = graph.add_subplot(212,facecolor=(1,1,1,0.8))
    graph.tight_layout()

    mpl_canvas = FigureCanvas(graph)
    mpl_canvas.setStyleSheet("background-color:transparent;")
    mpl_canvas.setAutoFillBackground(False)
    mpl_canvas.setFocusPolicy( QtCore.Qt.ClickFocus )
    
    timeSelector=[None]
    annotation=[]

    pan_factory(chromatogram)
    zoom_factory(chromatogram, 1.15)
    pan_factory(spectrum, ms, annotation)
    zoom_factory(spectrum, 1.15, ms, annotation)

    app = QtWidgets.QApplication(sys.argv)
    main_window = QtWidgets.QMainWindow()

    file_menu = QtWidgets.QMenu('&File',main_window)
    main_window.menuBar().addMenu(file_menu)
    file_menu.addAction('&Open..', lambda: openFile(chromatogram,spectrum, ds, timeSelector,annotation, ms), QtCore.Qt.CTRL + QtCore.Qt.Key_O)
    file_menu.addAction('&Quit', main_window.close, QtCore.Qt.CTRL + QtCore.Qt.Key_Q)

    main_widget = QtWidgets.QWidget(main_window)
    main_window.setCentralWidget(main_widget)

    layout = QtWidgets.QVBoxLayout(main_widget)
    layout.addWidget(mpl_canvas)
    mpl_canvas.setFocus()

    try:
        rawfile=sys.argv[1]
        ds['chromdat'],ds['masses'],ds['matrix'] = load_raw(rawfile)
        populate(chromatogram, spectrum, ds, timeSelector,annotation, ms)
    except:
        spectrPlot(spectrum, [0], [0], annotation)
        chromPlot(chromatogram, [0], [0])

    main_window.show()
    sys.exit(app.exec_())