__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 matplotlib.gridspec import GridSpec
from PyQt5 import QtCore
from PyQt5 import QtWidgets
from PyQt5 import QtGui
from PyQt5 import QtPrintSupport
from rawprasslib import load_raw
from rawprasslib import rawprasslib
from prasopes.predictmz import predict as getmzpattern
import numpy as np
import prasopes.config as cf
import prasopes.drltools as drl
import prasopes.filetools as ft
import prasopes.graphtools as gt
import prasopes.imagetools as imgt
import prasopes.zcetools as zce
import prasopes.tangoicons
import sys
import matplotlib
import logging
import os.path
matplotlib.use("Qt5Agg")


class update_signal(QtCore.QObject):
    signal = QtCore.pyqtSignal()


def load_file(parent, chrom_plot, spc, d_set, ms_s, fn, chrom_s,
              update, settings, filename=None):
    """populates dataset and plots it"""
    directory=settings.value("open_folder")
    if fn[0] is not None:
        directory=fn[0]
    if filename == None:
        filename = QtWidgets.QFileDialog.getOpenFileName(
            caption="Open spectrum",
            directory=directory,
            filter="Finnigan RAW files (*.raw, *.RAW)")[0]
    if filename is not '' and os.path.isfile(filename):
        try:
            d_set['chrom_dat'], d_set['masses'], d_set['matrix'] \
                = load_raw(filename, settings.value("tmp_location"))
        except rawprasslib.ParsingException as pex:
            QtWidgets.QMessageBox.critical(
                parent, "Opening of the file has failed!",
                "File is incompatible with the rawprasslib, "
                "canceling request!\n\n"
                "Error message:\n{}".format(pex.args[0]))
            return

        gt.populate(chrom_plot, spc, d_set, ms_s, chrom_s)
        fn[0] = filename
        parent.setWindowTitle("Prasopes - {}".format(
            os.path.basename(filename)))
        update.signal.emit()


def print_graph(data_set, mass_spec, chrom_spec, spect, fn):
    def printimage(printdevice, img):
        printer.setResolution(600)
        painter = QtGui.QPainter(printdevice)
        painter.drawImage(0,0,img)
        painter.end()
    #TODO: substitute the QPrintPreviewDialog with QPrintPreviewWidget
    printPreview = QtPrintSupport.QPrintPreviewDialog()
    printer = printPreview.printer()
    printer.setPageSize(printer.A5)
    printer.setDuplex(printer.DuplexNone)
    image = imgt.paint_image(mass_spec, spect, printer)
    printPreview.paintRequested.connect(lambda:
                                        printimage(printer, image))
    printPreview.exec()


def update_spectrum(chromatogram, spect, ds, ms, fn, chrom, config):
    if fn[0] is not None:
        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])
        gt.ann_spec(spect, ms)
        spect.get_figure().canvas.draw()


def dropped(event, parent, chromatogram, spectrum, ds, ms, filename,
            chrom, update, config):
    dropurl = event.mimeData().urls()[0].toLocalFile()
    load_file(parent, chromatogram, spectrum, ds, ms, filename,
              chrom, update, config, filename=dropurl)


def drag_entered(event):
    if event.mimeData().hasUrls() and event.mimeData().urls()[0]\
        .toLocalFile().lower().endswith('.raw'):
        event.accept()


def predictmz(form, chromatogram, spect, ds, ms, chrom):
    text = form.text()
    if text == "":
        ms["predict"] = None
        return
    slims = [spect.get_xlim(), spect.get_ylim()]
    ms["predict"] = getmzpattern(text)
    gt.populate(chromatogram, spect, ds, ms, chrom)
    spect.set_xlim(slims[0])
    spect.set_ylim(slims[1])
    spect.get_figure().canvas.draw()


def key_pressed(event, chrom, spect, ds, ms_ds, fn, chrom_ds, config):
    if event.key() == QtCore.Qt.Key_F5:
        update_spectrum(chrom, spect, ds, ms_ds, fn, chrom_ds, config)
    if event.key() == QtCore.Qt.Key_C\
        and event.modifiers().__int__() == QtCore.Qt.ControlModifier:
        imgt.clip_spect_img(ms_ds, spect)


def about(parent):
    """constructs window with "about" info"""
    QtWidgets.QMessageBox.information(
            parent, "About Prasopes",
            "Prasopes Finnigan raw file viewer\n\n"
            "Version: 0.0.11 (alpha)")


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], annotation=[],
              name="Spectrum", xlabel="m/z", ylabel="ion count",
              xtics=20, predict=None)
    chrom = dict(x=[0], y=[0], t_start=None, t_end=None,
                 name="Chromatogram", xlabel="time(min)",
                 ylabel="total ion count", timesarg=None)
    filename = [None]
    drlcache = [None, None]
    update = update_signal()

    config = cf.settings()

    p_logger = logging.getLogger('parseLogger')
    drl_logger = logging.getLogger('drlLogger')
    zce_logger = logging.getLogger('zceLogger')
    logging.basicConfig()
    p_logger.setLevel("WARN")
    #drl_logger.setLevel("INFO")
    drl_logger.setLevel("DEBUG")
    zce_logger.setLevel("DEBUG")

    graph = Figure(figsize=(5, 4), dpi=100, facecolor="None")
    grid = graph.add_gridspec(2, 1)
    chromatogram = graph.add_subplot(grid[0,0], facecolor=(1, 1, 1, 0.8))
    spectrum = graph.add_subplot(grid[1,0], facecolor=(1, 1, 1, 0.8))
    graph.tight_layout()
    mpl_canvas = FigureCanvas(graph)
    mpl_canvas.setStyleSheet("background-color:transparent;")
    mpl_canvas.setAutoFillBackground(False)
    
    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...", None)
    openact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_O)
    openact.triggered.connect(lambda: load_file(
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
        update, config))
    exportact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "document-save-as"), "&Export...", None)
    exportact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_E)
    exportact.triggered.connect(lambda: ft.export_dial(
        ms, chrom, filename, main_window))
    printact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "document-print"), "&Print", None)
    printact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_P)
    printact.triggered.connect(lambda: print_graph(
        ds, ms, chrom, spectrum, filename))
    settingsact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "preferences-system"), "&Settings...", None)
    settingsact.triggered.connect(lambda: cf.dial(main_window))
    quitact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "application-exit"), "&Quit", None)
    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...", None)
    zceact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_T)
    zceact.triggered.connect(lambda: zce.dialog(
        main_window, ds, filename, update))
    drlact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "applications-utilities"), "&DRL...", None)
    drlact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_D)
    drlact.triggered.connect(lambda: drl.main_window(
        main_window, ds, filename, drlcache, update))
    aboutact = QtWidgets.QAction("&About Prasopes", None)
    aboutact.triggered.connect(lambda: about(main_window))
    autozoomy = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "zoom-original"), "Auto Zoom Y", None, checkable=True,
        checked=config.value("view/autozoomy", type=bool))
    autozoomy.triggered.connect(lambda: config.setValue(
                                "view/autozoomy", autozoomy.isChecked()))
    autozoomy.triggered.connect(lambda: gt.autozoomy(spectrum))
    intensitiesact = QtWidgets.QAction("&Show intensities", None,
            checkable=True, checked=config.value("view/intensities",
                type=bool))
    intensitiesact.triggered.connect(lambda: config.setValue(
        "view/intensities", intensitiesact.isChecked()))
    intensitiesact.triggered.connect(lambda: gt.ann_spec(spectrum, ms))
    intensitiesact.triggered.connect(lambda: spectrum.figure.canvas.draw())
    oddevenact = QtWidgets.QAction("&Odd / even", None, checkable=True,
            checked=config.value("view/oddeven", type=bool))
    oddevenact.triggered.connect(lambda: config.setValue(
        "view/oddeven", oddevenact.isChecked()))
    oddevenact.triggered.connect(lambda:
        update_spectrum(chromatogram, spectrum, ds, ms, filename, chrom,
            config))
    filebrowseract = QtWidgets.QAction(
            "&File browser", None, checkable=True,
            checked=config.value("view/filebrowservisible", type=bool))
    filebrowseract.triggered.connect(lambda: config.setValue(
        "view/filebrowservisible", filebrowseract.isChecked()))
    filebrowseract.triggered.connect(
        lambda: treedock.show() if filebrowseract.isChecked() == True
                else treedock.hide())

    predictform = QtWidgets.QLineEdit(maximumWidth=150)
    predictform.editingFinished.connect(lambda: predictmz(
        predictform, chromatogram, spectrum, ds, ms, chrom))

    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(printact)
    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.addSeparator()
    view_menu = QtWidgets.QMenu('&View', main_window)
    view_menu.addAction(filebrowseract)
    view_menu.addAction(autozoomy)
    view_menu.addAction(intensitiesact)
    view_menu.addSeparator()
    view_menu.addAction(oddevenact)
    main_window.menuBar().addMenu(view_menu)
    help_menu = QtWidgets.QMenu('&Help', main_window)
    main_window.menuBar().addMenu(help_menu)
    help_menu.addAction(aboutact)

    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.addWidget(QtWidgets.QLabel("Predict Formula:"))
    toolBar.addWidget(predictform)
    toolBar.addSeparator()
    toolBar.addAction(zceact)
    toolBar.addAction(drlact)
    toolBar.addSeparator()
    toolBar.addAction(autozoomy)


    fileModel = QtWidgets.QFileSystemModel()
    fileModel.setRootPath('')
    activeDir = fileModel.index(config.value("open_folder"))
    treeview = QtWidgets.QTreeView()
    treeview.setModel(fileModel)
    treeview.setCurrentIndex(activeDir)
    treeview.expand(activeDir)
    dirview = QtWidgets.QListView()
    dirview.setModel(fileModel)
    treedock = QtWidgets.QDockWidget()
    if not config.value("view/filebrowservisible",type=bool):
        treedock.hide()
    treedock.setWidget(QtWidgets.QWidget())
    treedock_layout = QtWidgets.QVBoxLayout(treedock.widget())
    treedock_layout.addWidget(treeview)
    treedock_layout.addWidget(dirview)
    update.signal.connect(
        lambda: treeview.setCurrentIndex(fileModel.index(filename[0])))
    update.signal.connect(
        lambda: dirview.setRootIndex(fileModel.index(
            os.path.dirname(os.path.realpath(filename[0])))))
    treeview.doubleClicked.connect(lambda index: load_file(
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
        update, config, filename=fileModel.filePath(index)))
    dirview.doubleClicked.connect(lambda index: load_file(
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
        update, config, filename=fileModel.filePath(index)))
    dirview.clicked.connect(lambda index: load_file(
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
        update, config, filename=fileModel.filePath(index)))
    def closeOverride(event, dock, action):
        action.setChecked(False)
        dock.hide()
        event.ignore()
    treedock.closeEvent = lambda event: closeOverride(
            event, treedock, filebrowseract)
    main_window.addDockWidget(QtCore.Qt.LeftDockWidgetArea, treedock)

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


    main_window.setFocus()
    main_window.dragEnterEvent = lambda event: drag_entered(event)
    main_window.dropEvent = lambda event: dropped(
        event, main_window, chromatogram, spectrum, ds, ms, filename,
        chrom, update, config)
    main_window.setAcceptDrops(True)
    main_window.keyPressEvent = lambda event: key_pressed(event, chromatogram,
            spectrum, ds, ms, filename, chrom, config)

    if len(sys.argv) == 2:
        load_file(main_window, chromatogram, spectrum, ds, ms,
                  filename, chrom, update, config, filename=sys.argv[1])
    else:
        gt.pop_plot(spectrum, ms)
        gt.pop_plot(chromatogram, chrom)

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


if __name__ == "__main__":
    main()