__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
try:
    from rawautoparams import load_params
    autoparams = True
except:
    autoparams = False
import numpy as np
import prasopes.config as cf
import prasopes.datatools as dt
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()


class QStatusBarLogger(logging.Handler):
    def __init__(self, parent=None):
        super().__init__()
        self.statusBar = QtWidgets.QStatusBar(parent)

    def emit(self, record):
        msg = self.format(record)
        self.statusBar.showMessage(msg)


def load_file(parent, chrom_plot, spc, d_set, ms_s, fn, chrom_s,
              update, settings, loadthread, 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)\
                          and not os.path.isdir(filename):
        error = update_signal()
        errormsg = []
        def runfnc():
            try:
                [i.clear() for i in (
                    d_set, chrom_s['timesarg'], ms_s['params'],ms_s['headers'])]
                [d_set.append(dict(chrom_dat=i[0], masses=i[1], matrix=i[2]))
                    for i in load_raw(filename, settings.value("tmp_location"))]
            except rawprasslib.ParsingException as pex:
                errormsg.append("Opening of the file has failed!")
                errormsg.append(
                    "File is incompatible with the rawprasslib, "
                    "canceling request!\n\n"
                    "Error message:\n{}".format(pex.args[0]))
                error.signal.emit()
                return
            if autoparams == True:
                try:
                    ms_s['params'], rawheaders = load_params(filename)
                    segments = [len(subset['chrom_dat'][0]) for subset in d_set]
                    indicies = [sum(segments[:i+1]) for i in range(len(segments))]
                    ms_s['headers'] = np.split(rawheaders, indicies)[:-1]
                except Exception as pex:
                    errormsg.append("File is incompatible with the rawautoparams,")
                    errormsg.append(
                            "no parameters loaded!\n\n"
                            "Error message:\n{}".format(pex.args[0]))
                    error.signal.emit()
                    print("panoc baby")
            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()
        error.signal.connect(lambda:
            QtWidgets.QMessageBox.critical(parent, errormsg[0], errormsg[1]))
        loadthread.run = runfnc
        loadthread.start()


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.clear()
        [ds.append(dict(chrom_dat=i[0], masses=i[1], matrix=i[2])) for i
                in 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 update_paramstable(table, ms, chrom):
    if len(ms['params']) == 0:
        table.setRowCount(0)
        return
    table.setRowCount(len(ms['params'][0]))
    validator = QtGui.QDoubleValidator()
    for row, paramname in enumerate(ms['params'][0]):
        [table.setItem(row,col, QtWidgets.QTableWidgetItem())
                for col in range(2)]
        table.item(row,0).setText(paramname)
        vals = [param[row] for param in ms['params'][1]]
        if all([type(val) in [np.float32, np.float64] for val in vals]):
            aver = np.average(vals)
            minim = min(vals)
            maxim = max(vals)
            text = "{:.2f} (from {:.2f} to {:.2f})".format(aver, minim, maxim)
        else:
            values = [str(i) for i in np.unique(np.array(vals), axis=0)]
            text = " or ".join(values)
        table.item(row,1).setText(text)


def dropped(event, parent, chromatogram, spectrum, ds, ms, filename,
            chrom, update, config, loadthread):
    dropurl = event.mimeData().urls()[0].toLocalFile()
    load_file(parent, chromatogram, spectrum, ds, ms, filename,
              chrom, update, config, loadthread, 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 oddeven_changed(chromatogram, spectrum, ds, ms, filename, chrom, config,
        oddevenact):
    config.setValue("view/oddeven", oddevenact.isChecked())
    update_spectrum(chromatogram, spectrum, ds, ms, filename, chrom, config)


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:
        if event.modifiers().__int__() == QtCore.Qt.ControlModifier:
            imgt.clip_spect_img(ms_ds, spect)
        if event.modifiers().__int__() == QtCore.Qt.ControlModifier+\
                                          QtCore.Qt.ShiftModifier:
            dt.clip_spectstr(spect, chrom_ds, fn)
    if event.key() in (QtCore.Qt.Key_Left, QtCore.Qt.Key_Right):
        gt.shift_times(event, spect, chrom, ds, ms_ds, chrom_ds)


def about(parent):
    """constructs window with "about" info"""
    QtWidgets.QMessageBox.information(
            parent, "About Prasopes",
            "Prasopes Finnigan raw file viewer\n\n"
            "Version: 0.0.12 (alpha)")


def main():
    app = QtWidgets.QApplication(sys.argv)
    loadthread = QtCore.QThread()

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

    config = cf.settings()

    barHandler = QStatusBarLogger()

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

    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, loadthread))
    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(
        spectrum, 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:
        oddeven_changed(chromatogram, spectrum, ds, ms, filename, chrom,
            config, oddevenact))
    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_window.setCentralWidget(mpl_canvas)

    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)

    paramsdock = QtWidgets.QDockWidget()
    paramstable = dt.table(["name","value"], 100)
    update.signal.connect(lambda: update_paramstable(paramstable, ms, chrom))
    paramsdock.setWidget(paramstable)

    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()
    def scrolltoonce():
        fileModel.directoryLoaded.disconnect(scrolltoonce)
        treeview.scrollTo(fileModel.index(config.value("open_folder")), 1)
    fileModel.directoryLoaded.connect(scrolltoonce)
    fileModel.directoryLoaded.connect(
            lambda: treeview.resizeColumnToContents(0))
    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])))))
    clickload = lambda index: load_file(
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
        update, config, loadthread, filename=fileModel.filePath(index))
    for i in [treeview.doubleClicked, dirview.doubleClicked, dirview.clicked]:
        i.connect(clickload)
    #fileModel gots stuck sometimes, better give it a separate thread
    #it complains at the start, but still works later 
    #and I did not found better solution
    treedockThread = QtCore.QThread()
    treedockThread.start()
    fileModel.moveToThread(treedockThread)
    def closeOverride(event, dock, action):
        action.setChecked(False)
        dock.hide()
        event.ignore()
    treedock.closeEvent = lambda event: closeOverride(
            event, treedock, filebrowseract)

    main_window.closeEvent = lambda event: treedockThread.quit()
    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)

    main_window.addToolBar(QtCore.Qt.TopToolBarArea, toolBar)
    main_window.addDockWidget(QtCore.Qt.LeftDockWidgetArea, treedock)
    main_window.addDockWidget(QtCore.Qt.RightDockWidgetArea, paramsdock)
    main_window.setStatusBar(barHandler.statusBar)

    main_window.setFocus()

    if len(sys.argv) == 2:
        load_file(main_window, chromatogram, spectrum, ds, ms,
                  filename, chrom, update, config, loadthread,
                  filename=sys.argv[1])
    else:
        gt.pop_plot(0, 0, spectrum, ms)
        gt.pop_plot(0, 0, chromatogram, chrom)

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


if __name__ == "__main__":
    main()