__main__.py 7.77 KB
Newer Older
Yan's avatar
Yan committed
1
2
3
4
5
6
7
#!/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
Yan's avatar
Yan committed
8
from PyQt5 import QtGui
Yan's avatar
Yan committed
9
10
11
from rawprasslib import load_raw
import prasopes.graphtools as gt
import prasopes.filetools as ft
Yan's avatar
Yan committed
12
import prasopes.zcetools as zce
Yan's avatar
Yan committed
13
import prasopes.drltools as drl
Yan's avatar
Yan committed
14
import prasopes.config as cf
Yan's avatar
Yan committed
15
import prasopes.tangoicons
Yan's avatar
Yan committed
16
17
18
import sys
import matplotlib
import logging
3Yan's avatar
3Yan committed
19
import os.path
Yan's avatar
Yan committed
20
21
22
matplotlib.use("Qt5Agg")


23
24
def load_file(parent, chrom_plot, spc, d_set, ms_s, fn, chrom_s,
              settings, filename=None):
Yan's avatar
Yan committed
25
    """populates dataset and plots it"""
3Yan's avatar
3Yan committed
26
27
28
    directory=settings.value("open_folder")
    if fn[0] is not None:
        directory=fn[0]
Yan's avatar
Yan committed
29
30
    if filename == None:
        filename = QtWidgets.QFileDialog.getOpenFileName(
3Yan's avatar
3Yan committed
31
32
33
34
35
36
            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"))
Yan's avatar
Yan committed
37
        gt.populate(chrom_plot, spc, d_set, ms_s, chrom_s)
3Yan's avatar
3Yan committed
38
        fn[0] = filename
39
40
        parent.setWindowTitle("Prasopes - {}".format(
            os.path.basename(filename)))
3Yan's avatar
3Yan committed
41

Yan's avatar
Yan committed
42

Yan's avatar
Yan committed
43
44
45
46
47
48
49
50
51
52
53
54
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()


55
56
def dropped(event, parent, chromatogram, spectrum, ds, ms, filename,
            chrom, config):
57
    dropurl = event.mimeData().urls()[0].toLocalFile()
58
59
    load_file(parent, chromatogram, spectrum, ds, ms, filename,
              chrom, config, filename=dropurl)
Yan's avatar
Yan committed
60
61
62
63


def drag_entered(event):
    if event.mimeData().hasUrls() and event.mimeData().urls()[0]\
64
        .toLocalFile().lower().endswith('.raw'):
Yan's avatar
Yan committed
65
66
67
        event.accept()


Yan's avatar
Yan committed
68
def main():
Yan's avatar
Yan committed
69
70
71
    # 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=[],
Yan's avatar
Yan committed
72
              name="Spectrum", xlabel="m/z", ylabel="ion count",
Yan's avatar
Yan committed
73
              xtics=20, autoy=True)
Yan's avatar
Yan committed
74
75
    chrom = dict(x=[0], y=[0], line=None, t_start=None, t_end=None,
                 name="Chromatogram", xlabel="time(min)",
76
                 ylabel="total ion count", timesarg=None)
Yan's avatar
Yan committed
77
    filename = [None]
3Yan's avatar
3Yan committed
78
    drlcache = [None, None]
Yan's avatar
Yan committed
79

Yan's avatar
Yan committed
80
81
    config = cf.settings()

Yan's avatar
Yan committed
82
    p_logger = logging.getLogger('parseLogger')
Yan's avatar
Yan committed
83
    drl_logger = logging.getLogger('drlLogger')
Yan's avatar
Yan committed
84
85
    logging.basicConfig()
    p_logger.setLevel("WARN")
Yan's avatar
Yan committed
86
    drl_logger.setLevel("INFO")
Yan's avatar
Yan committed
87

Yan's avatar
Yan committed
88
    graph = Figure(figsize=(5, 4), dpi=100, facecolor="None")
Yan's avatar
Yan committed
89
90
91
92
93
94
95
96
97
98
99
100

    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)
101
    gt.arrow_factory(spectrum, chromatogram, ds, ms, chrom)
Yan's avatar
Yan committed
102
103
    gt.pan_factory(spectrum, ms)
    gt.zoom_factory(spectrum, 1.15, ms)
104
    mass_selector = SpanSelector(
Yan's avatar
Yan committed
105
        spectrum, lambda x_min, x_max: gt.pick_masses(
106
107
108
            x_min, x_max, spectrum, ms), 'horizontal', minspan=0.01,
        useblit=True, rectprops=dict(alpha=0.15, facecolor='purple'),
        button=3)
109
    time_selector = SpanSelector(
Yan's avatar
Yan committed
110
111
112
113
114
115
         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)
Yan's avatar
Yan committed
116
    main_window = QtWidgets.QMainWindow(windowTitle="Prasopes")
Yan's avatar
Yan committed
117

Yan's avatar
Yan committed
118
119
120
    if QtGui.QIcon.themeName() is "":
        QtGui.QIcon.setThemeName("TangoMFK")

Yan's avatar
Yan committed
121
    openact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
122
        "document-open"), "&Open...", None)
Yan's avatar
Yan committed
123
124
    openact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_O)
    openact.triggered.connect(lambda: load_file(
125
126
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
        config))
Yan's avatar
Yan committed
127
    exportact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
128
        "document-save-as"), "&Export...", None)
Yan's avatar
Yan committed
129
130
131
132
    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(
Yan's avatar
Yan committed
133
        "preferences-system"), "&Settings...", None)
Yan's avatar
Yan committed
134
135
    settingsact.triggered.connect(lambda: cf.dial(main_window))
    quitact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
136
        "application-exit"), "&Quit", None)
Yan's avatar
Yan committed
137
138
139
    quitact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_Q)
    quitact.triggered.connect(main_window.close)
    zceact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
140
        "applications-utilities"), "&TSQ zce...", None)
Yan's avatar
Yan committed
141
142
143
144
    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(
Yan's avatar
Yan committed
145
        "applications-utilities"), "&DRL...", None)
Yan's avatar
Yan committed
146
147
148
    drlact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_D)
    drlact.triggered.connect(lambda: drl.main_window(
        main_window, ds, filename, drlcache))
Yan's avatar
Yan committed
149
    autozoomy = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
150
        "zoom-original"), "Auto Zoom Y", None)
Yan's avatar
Yan committed
151
152
153
154
    autozoomy.setCheckable(True)
    autozoomy.setChecked(True)
    autozoomy.triggered.connect(lambda: gt.autozoomy(
        autozoomy.isChecked(), spectrum, ms))
Yan's avatar
Yan committed
155

Yan's avatar
Yan committed
156
157
    file_menu = QtWidgets.QMenu('&File', main_window)
    main_window.menuBar().addMenu(file_menu)
Yan's avatar
Yan committed
158
159
160
161
162
163
    file_menu.addAction(openact)
    file_menu.addAction(exportact)
    file_menu.addSeparator()
    file_menu.addAction(settingsact)
    file_menu.addSeparator()
    file_menu.addAction(quitact)
Yan's avatar
Yan committed
164
165
    tools_menu = QtWidgets.QMenu('&Tools', main_window)
    main_window.menuBar().addMenu(tools_menu)
Yan's avatar
Yan committed
166
167
    tools_menu.addAction(zceact)
    tools_menu.addAction(drlact)
Yan's avatar
Yan committed
168
169
170
171

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

Yan's avatar
Yan committed
172
173
174
175
176
    toolBar = QtWidgets.QToolBar(main_window)
    toolBar.setAllowedAreas(QtCore.Qt.TopToolBarArea)
    toolBar.setFloatable(False)
    toolBar.setMovable(False)
    toolBar.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
Yan's avatar
Yan committed
177

Yan's avatar
Yan committed
178
179
180
181
182
    toolBar.addAction(openact)
    toolBar.addAction(exportact)
    toolBar.addSeparator()
    toolBar.addAction(zceact)
    toolBar.addAction(drlact)
Yan's avatar
Yan committed
183
184
    toolBar.addSeparator()
    toolBar.addAction(autozoomy)
Yan's avatar
Yan committed
185

Yan's avatar
Yan committed
186
    layout = QtWidgets.QVBoxLayout(main_widget)
Yan's avatar
Yan committed
187
    layout.addWidget(toolBar)
Yan's avatar
Yan committed
188
189
190
    layout.addWidget(mpl_canvas)
    mpl_canvas.setFocus()

191
    mpl_canvas.mpl_connect('key_press_event', lambda event:
Yan's avatar
Yan committed
192
193
        update_spectrum(event, chromatogram, spectrum, ds, ms,
                        filename, chrom, config))
Yan's avatar
Yan committed
194
195
    main_window.dragEnterEvent = lambda event: drag_entered(event)
    main_window.dropEvent = lambda event: dropped(
196
197
        event, main_window, chromatogram, spectrum, ds, ms, filename,
        chrom, config)
Yan's avatar
Yan committed
198
    main_window.setAcceptDrops(True)
Yan's avatar
Yan committed
199

Yan's avatar
Yan committed
200
    if len(sys.argv) == 2:
201
202
        load_file(main_window, chromatogram, spectrum, ds, ms,
                  filename, chrom, config, filename=sys.argv[1])
Yan's avatar
Yan committed
203
204
205
206
207
208
    else:
        gt.pop_plot(spectrum, ms)
        gt.pop_plot(chromatogram, chrom)

    main_window.show()
    sys.exit(app.exec_())
Yan's avatar
Yan committed
209

210

Yan's avatar
Yan committed
211
212
if __name__ == "__main__":
    main()