__main__.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 PyQt5 import QtGui
from rawprasslib import load_raw
import prasopes.graphtools as gt
import prasopes.filetools as ft
import prasopes.zcetools as zce
import prasopes.drltools as drl
import prasopes.config as cf
import prasopes.tangoicons
import sys
import matplotlib
import logging
import os.path
matplotlib.use("Qt5Agg")


def load_file(chrom_plot, spc, d_set, ms_s, fn, chrom_s, settings):
    """populates dataset and plots it"""
    directory=settings.value("open_folder")
    if fn[0] is not None:
        directory=fn[0]
    filename = QtWidgets.QFileDialog.getOpenFileName(
            caption="Open spectrum",
            directory=directory,
            filter="Finnigan RAW files (*.raw, *.RAW)")[0]
    if filename is not '':
        d_set['chrom_dat'], d_set['masses'], d_set['matrix'] \
             = load_raw(filename, settings.value("tmp_location"))
        gt.populate(chrom_plot, spc, d_set, ms_s, chrom_s)
        fn[0] = filename


def update_spectrum(event, chromatogram, spect, ds,
                    ms, fn, chrom, config):
    if fn[0] is not None and event.key is "f5":
        slims = [spect.get_xlim(), spect.get_ylim()]
        ds['chrom_dat'], ds['masses'], ds['matrix'] \
            = load_raw(fn[0], config.value("tmp_location"))
        gt.populate(chromatogram, spect, ds, ms, chrom)
        spect.set_xlim(slims[0])
        spect.set_ylim(slims[1])
        spect.get_figure().canvas.draw()


def main():
    # ds for data_set, ms for mass_spec_dataset, chrom for chrom_dataset
    ds = dict(chrom_dat=None, masses=None, matrix=None)
    ms = dict(x=[0], y=[0], line=None, annotation=[],
              name="Spectrum", xlabel="m/z", ylabel="ion count",
              xtics=20)
    chrom = dict(x=[0], y=[0], line=None, t_start=None, t_end=None,
                 name="Chromatogram", xlabel="time(min)",
                 ylabel="total ion count", timesarg=None)
    filename = [None]
    drlcache = [None, None, None]

    config = cf.settings()

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

    graph = Figure(figsize=(5, 4), dpi=100, 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)
    
    gt.pan_factory(chromatogram)
    gt.zoom_factory(chromatogram, 1.15)
    gt.arrow_factory(spectrum, chromatogram, ds, ms, chrom)
    gt.pan_factory(spectrum, ms)
    gt.zoom_factory(spectrum, 1.15, ms)
    mass_selector = SpanSelector(
        spectrum, lambda x_min, x_max: gt.pick_masses(
            x_min, x_max, spectrum, ms), 'horizontal', minspan=0.01,
        useblit=True, rectprops=dict(alpha=0.15, facecolor='purple'),
        button=3)
    time_selector = SpanSelector(
         chromatogram, lambda x_min, x_max: gt.pick_times(
             x_min, x_max, spectrum, ds, chromatogram, ms, chrom), 
         'horizontal', useblit=True, rectprops=dict(
             alpha=0.15, facecolor='purple'), button=3)

    app = QtWidgets.QApplication(sys.argv)
    main_window = QtWidgets.QMainWindow(windowTitle="Prasopes")

    if QtGui.QIcon.themeName() is "":
        QtGui.QIcon.setThemeName("TangoMFK")

    openact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "document-open"), "&Open...")
    openact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_O)
    openact.triggered.connect(lambda: load_file(
        chromatogram, spectrum, ds, ms, filename, chrom, config))
    exportact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "document-save-as"), "&Export...")
    exportact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_E)
    exportact.triggered.connect(lambda: ft.export_dial(
        ms, chrom, filename, main_window))
    settingsact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "preferences-system"), "&Settings...")
    settingsact.triggered.connect(lambda: cf.dial(main_window))
    quitact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "application-exit"), "&Quit")
    quitact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_Q)
    quitact.triggered.connect(main_window.close)
    zceact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "applications-utilities"), "&TSQ zce...")
    zceact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_T)
    zceact.triggered.connect(lambda: zce.dialog(
        main_window, ds, filename))
    drlact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "applications-utilities"), "&DRL...")
    drlact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_D)
    drlact.triggered.connect(lambda: drl.main_window(
        main_window, ds, filename, drlcache))




    file_menu = QtWidgets.QMenu('&File', main_window)
    main_window.menuBar().addMenu(file_menu)
    file_menu.addAction(openact)
    file_menu.addAction(exportact)
    file_menu.addSeparator()
    file_menu.addAction(settingsact)
    file_menu.addSeparator()
    file_menu.addAction(quitact)
    tools_menu = QtWidgets.QMenu('&Tools', main_window)
    main_window.menuBar().addMenu(tools_menu)
    tools_menu.addAction(zceact)
    tools_menu.addAction(drlact)
    """tools_menu.addAction('&TSQ zce', lambda: zce.dialog(
        main_window, ds, filename), QtCore.Qt.CTRL + QtCore.Qt.Key_T)
    tools_menu.addAction('&DRL..', lambda: drl.main_window(
        main_window, ds, filename, drlcache),
        QtCore.Qt.CTRL + QtCore.Qt.Key_D)"""

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

    toolBar = QtWidgets.QToolBar(main_window)
    toolBar.setAllowedAreas(QtCore.Qt.TopToolBarArea)
    toolBar.setFloatable(False)
    toolBar.setMovable(False)
    toolBar.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
    toolBar.addAction(openact)
    toolBar.addAction(exportact)
    toolBar.addSeparator()
    toolBar.addAction(zceact)
    toolBar.addAction(drlact)

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

    mpl_canvas.mpl_connect('key_press_event', lambda event:
        update_spectrum(event, chromatogram, spectrum, ds, ms,
                        filename, chrom, config))


    if len(sys.argv) == 2:
        raw_file = sys.argv[1]
        filename[0] = raw_file
        ds['chrom_dat'], ds['masses'], ds['matrix'] = load_raw(
                raw_file, config.value("tmp_location"))
        gt.populate(chromatogram, spectrum, ds, ms, chrom)
    else:
        gt.pop_plot(spectrum, ms)
        gt.pop_plot(chromatogram, chrom)

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


if __name__ == "__main__":
    main()