class Aditi(QMainWindow):
def __init__(self):
QMainWindow.__init__(self)
# title
self.setWindowTitle("Aditi")
self.setDockOptions(QMainWindow.VerticalTabs | QMainWindow.AnimatedDocks)
#self.showMaximized()
# model
self.rawfiles_by_short_path = {}
self.xic_by_rawfile_short_path = {}
self.tic_by_rawfile_short_path = {}
self.spec_by_rawfile_short_path = {}
self.inf_line_tic_item = None
self.curr_scan_id_by_short_path = {}
# menu
self.file_menu = self.menuBar().addMenu('&File')
#self.file_menu.setTearOffEnabled(False)
open_action = QAction("&Open...", self)
open_action.setToolTip("Open a rawfile")
open_action.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_O))
self.file_menu.addAction(open_action)
open_action.triggered.connect(self.show_open_dialog)
exit_action = QAction("&Exit", self)
exit_action.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_Q))
self.file_menu.addAction(exit_action)
exit_action.triggered.connect(self.quit)
self.tab_widget = QTabWidget(self)
# spectrum plot Widget
self.graphics_layout_widget = GraphicsLayoutWidget(parent=self.tab_widget)
self.graphics_layout_widget.keyPressEvent = self.handle_key_press_event
self.graphics_layout_widget.useOpenGL(False)
self.graphics_layout_widget.setAntialiasing(False)
self.plot_widget_tic = self.graphics_layout_widget.addPlot(title="TIC(s)",
labels={'left': "Intensity",
'bottom': "Retention Time (sec)"})
self.plot_widget_tic.showGrid(x=True, y=True)
self.graphics_layout_widget.nextRow()
self.plot_widget_spectrum = self.graphics_layout_widget.addPlot(title="Spectrum", labels={'left': "Intensity",
'bottom': "m/z"})
self.plot_widget_spectrum.showGrid(x=True, y=True)
# finally add tab
self.tab_widget.addTab(self.graphics_layout_widget, "Spectrum")
# Xic plotWidget
self.plot_widget_xic = PlotWidget(name="MainPlot", labels={'left': "Intensity",
'bottom': "Retention Time (sec)"})
self.plot_widget_xic.showGrid(x=True, y=True)
self.tab_widget.addTab(self.plot_widget_xic, "Xic extraction")
self.setCentralWidget(self.tab_widget)
self.statusBar().showMessage("Ready")
# dock 1
self.rawfile_dock_widget = QDockWidget("Rawfiles")
self.rawfile_table_view = QTableView()
self.rawfile_table_view.horizontalHeader().setVisible(False)
self.rawfile_table_view.horizontalHeader().setResizeMode(QHeaderView.ResizeToContents)
self.rawfile_dock_widget.setWidget(self.rawfile_table_view)
self.rawfile_model = QStandardItemModel()
self.rawfile_model.setHorizontalHeaderLabels(["Rawfiles"])
self.rawfile_table_view.setModel(self.rawfile_model)
self.rawfile_model.itemChanged.connect(self.item_changed)
self.addDockWidget(0x2, self.rawfile_dock_widget)
# xic dock widget extraction parameter
self.xic_dock_widget = QDockWidget("Xic extraction")
self.xic_widget = XicWidget()
self.xic_widget.plotButton.clicked.connect(self.plot)
self.xic_dock_widget.setWidget(self.xic_widget)
self.addDockWidget(0x2, self.xic_dock_widget)
def handle_key_press_event(self, evt):
if self.inf_line_tic_item is None:
return
times = []
if evt.key() == Qt.Key_Left:
for rawfile in self.rawfiles_by_short_path.values()[:1]:
if not rawfile.is_checked:
continue
curr_scan_id = self.curr_scan_id_by_short_path[rawfile.short_path]
scan_ids = rawfile.reader.rt_by_scan_id_by_ms_level[1].keys()
idx = scan_ids.index(curr_scan_id)
times.append(rawfile.reader.rt_by_scan_id_by_ms_level[1][scan_ids[idx - 1]])
self.curr_scan_id_by_short_path[rawfile.short_path] = scan_ids[idx - 1]
elif evt.key() == Qt.Key_Right:
for rawfile in self.rawfiles_by_short_path.values()[:1]:
if not rawfile.is_checked:
continue
curr_scan_id = self.curr_scan_id_by_short_path[rawfile.short_path]
scan_ids = rawfile.reader.rt_by_scan_id_by_ms_level[1].keys()
idx = scan_ids.index(curr_scan_id)
times.append(rawfile.reader.rt_by_scan_id_by_ms_level[1][scan_ids[idx + 1]])
self.curr_scan_id_by_short_path[rawfile.short_path] = scan_ids[idx + 1]
self._plot_spectrum()
if times:
self.inf_line_tic_item.setPos(sum(times) / float(len(times)))
def _plot_spectrum(self):
self.plot_widget_spectrum.clear()
min_mz, max_mz = 1e9, 0
min_int, max_int = 1e10, 0
for rawfile in self.rawfiles_by_short_path.values():
if not rawfile.is_checked:
continue
scan_id, mzs, intensities = rawfile.reader.get_scan(self.curr_scan_id_by_short_path[rawfile.short_path])
min_mz = min(min_mz, mzs[0])
max_mz = max(max_mz, mzs[-1])
min_int = min(min_int, min(intensities))
max_int = max(max_int, max(intensities))
item = BarGraphItem(x=mzs, height=intensities, width=0.01, pen=rawfile.qcolor, brush=rawfile.qcolor)
self.plot_widget_spectrum.addItem(item)
self.plot_widget_spectrum.setLimits(xMin=min_mz, xMax=max_mz, yMin=min_int, yMax=max_int)
def plot_spectrum(self, ev):
#clear
if ev.button() == Qt.RightButton:
return
self.plot_widget_spectrum.clear()
vb = self.plot_widget_tic.vb
mouse_point = vb.mapSceneToView(ev.scenePos())
t = mouse_point.x()
if self.inf_line_tic_item is None:
self.inf_line_tic_item = InfiniteLine(pos=t, angle=90)
self.plot_widget_tic.addItem(self.inf_line_tic_item)
self.inf_line_tic_item.setMovable(True)
else:
self.inf_line_tic_item.setPos(t)
min_mz, max_mz = 1e9, 0
min_int, max_int = 1e10, 0
for rawfile in self.rawfiles_by_short_path.values():
if not rawfile.is_checked:
continue
scan_id, mzs, intensities = rawfile.reader.get_scan_for_time(t)
self.curr_scan_id_by_short_path[rawfile.short_path] = scan_id
min_mz = min(min_mz, mzs[0])
max_mz = max(max_mz, mzs[-1])
min_int = min(min_int, min(intensities))
max_int = max(max_int, max(intensities))
item = BarGraphItem(x=mzs, height=intensities, width=0.01, pen=rawfile.qcolor, brush=rawfile.qcolor)
self.plot_widget_spectrum.addItem(item)
self.plot_widget_spectrum.setLimits(xMin=min_mz, xMax=max_mz, yMin=min_int, yMax=max_int)
def item_changed(self, item):
print "item changed", item.text()
s = item.text()
if item.checkState():
self.rawfiles_by_short_path[s].is_checked = True
else:
self.rawfiles_by_short_path[s].is_checked = False
#self.qApp.emit(SIGNAL('redraw()'))
self.update_plot_()
def show_open_dialog(self):
files = QFileDialog(self).getOpenFileNames()
if files:
preload = Preloader(files, self)
preload.loaded.connect(self.update_rawfile_model)
preload.start()
def update_rawfile_model(self, obj):
files, r = obj[0], obj[1]
n = len(files)
not_database = []
min_time, max_time = 1e9, 0
min_int, max_int = 1e9, 0
for i, f in enumerate(files):
i_f = float(i)
c = WithoutBlank.get_color(i_f / n, asQColor=True)
c_ = WithoutBlank.get_color(i_f / n, asQColor=True)
filename = f.split("\\")[-1]
abs_path = str(f.replace("\\", "\\\\"))
if r[i]:
rawfile = Rawfile(abs_path, c, filename)
self.rawfiles_by_short_path[filename] = rawfile #[MzDBReader(abs_path), c, True]
self.rawfile_model.appendRow(Aditi.get_coloured_root_item(filename, c, c_))
times, intensities = rawfile.reader.get_tic()
min_time = min(min_time, min(times))
max_time = max(max_time, max(times))
min_int = min(min_int, min(intensities))
max_int = max(max_int, max(intensities))
self.plot_widget_tic.plot(times, intensities, pen=mkPen(color=rawfile.qcolor, width=1.3))
else:
not_database.append(str(filename))
self.plot_widget_tic.setLimits(xMin=min_time, xMax=max_time, yMin=min_int, yMax=max_int)
self.plot_widget_tic.scene().sigMouseClicked.connect(self.plot_spectrum)
if not_database:
v = "\n".join(not_database)
QMessageBox.information(self, "Error",
"The following files are not valid sqlite database:\n" + v)
@staticmethod
def get_coloured_root_item(filepath, color, colorr):
root = QStandardItem(filepath)
gradient = QLinearGradient(-100, -100, 100, 100)
gradient.setColorAt(0.7, colorr)
gradient.setColorAt(1, color)
root.setBackground(QBrush(gradient))
root.setEditable(False)
root.setCheckState(Qt.Checked)
root.setCheckable(True)
return root
def quit(self):
res = QMessageBox.warning(self, "Exiting...", "Are you sure ?", QMessageBox.Ok | QMessageBox.Cancel)
if res == QMessageBox.Cancel:
return
QtGui.qApp.quit()
def plot(self):
#clear pw
self.plot_widget_xic.clear()
# check sample checked
checked_files = [rawfile for rawfile in self.rawfiles_by_short_path.values() if rawfile.is_checked]
mz = self.xic_widget.mzSpinBox.value()
mz_tol = self.xic_widget.mzTolSpinBox.value()
mz_diff = mz * mz_tol / 1e6
min_mz, max_mz = mz - mz_diff, mz + mz_diff
#Thread implementation not as fast
# args = [(data[0], min_mz, max_mz, data[2]) for data in checked_files]
# extractor_thread = Extractor(args, self)
# extractor_thread.extracted.connect(self._plot)
# extractor_thread.start()
min_time_val, max_time_val = 10000, 0
min_int_val, max_int_val = 1e9, 0
for rawfile in checked_files:
t1 = time.clock()
times, intensities = rawfile.reader.get_xic(min_mz, max_mz)
print "elapsed: ", time.clock() - t1
# min_time_val = min(min_time_val, times[0])
# max_time_val = max(max_time_val, times[-1])
# min_int_val = min(min_int_val, min(intensities))
# max_int_val = max(max_int_val, max(intensities))
item = self.plot_widget_xic.plot(times, intensities, pen=mkPen(color=rawfile.qcolor, width=1.3))
item.curve.setClickable(True)
def on_curve_clicked():
if not rawfile.is_highlighted:
item.setPen(mkPen(color=rawfile.qcolor, width=4))
rawfile.is_highlighted = True
else:
item.setPen(mkPen(color=rawfile.qcolor, width=2))
rawfile.is_highlighted = False
item.sigClicked.connect(on_curve_clicked)
#item.sigHovered = on_curve_clicked
self.xic_by_rawfile_short_path[rawfile.short_path] = item
self.plot_widget_xic.setTitle(title="Xic@" + str(mz))
#self.plot_widget_xic.setLimits(xMin=min_time_val, xMax=max_time_val, yMin=min_int_val, yMax=max_int_val)
def update_plot_(self):
for rawfile in self.rawfiles_by_short_path.viewvalues():
if rawfile.is_checked:
try:
self.plot_widget_xic.addItem(self.xic_by_rawfile_short_path[rawfile.short_path])
except KeyError:
mz = self.xic_widget.mzSpinBox.value()
mz_tol = self.xic_widget.mzTolSpinBox.value()
mz_diff = mz * mz_tol / 1e6
min_mz, max_mz = mz - mz_diff, mz + mz_diff
times, intensities = rawfile.reader.get_xic(min_mz, max_mz)
item = self.plot_widget_xic.plot(times, intensities, pen=mkPen(color=rawfile.qcolor, width=2))
self.xic_by_rawfile_short_path[rawfile.short_path] = item
else:
try:
#self.plot_widget_xic.removeItem(self.xic_by_rawfile_short_path[rawfile.short_path])
self.xic_by_rawfile_short_path[rawfile.short_path].hide()
except KeyError:
pass
