import matplotlib.pyplot as plt
from functools import partial
from PyQt5 import QtWidgets, QtCore
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
from processing_utils.roi import construct_tic, construct_eic
from gui_utils.auxilary_utils import ProgressBarsList, ProgressBarsListItem, FileListWidget, FeatureListWidget
from gui_utils.threading import Worker
class AbtractMainWindow(QtWidgets.QMainWindow):
def __init__(self):
super().__init__()
self._thread_pool = QtCore.QThreadPool()
self._pb_list = ProgressBarsList(self)
self._list_of_files = FileListWidget()
self._list_of_features = FeatureListWidget()
self._feature_parameters = None
self._figure = plt.figure()
self._ax = self._figure.add_subplot(111) # plot here
self._ax.set_xlabel('Retention time [min]')
self._ax.set_ylabel('Intensity')
self._ax.ticklabel_format(axis='y', scilimits=(0, 0))
self._label2line = dict() # a label (aka line name) to plotted line
self._canvas = FigureCanvas(self._figure)
self._toolbar = NavigationToolbar(self._canvas, self)
def run_thread(self, caption: str, worker: Worker, text=None, icon=None):
pb = ProgressBarsListItem(caption, parent=self._pb_list)
self._pb_list.addItem(pb)
worker.signals.progress.connect(pb.setValue)
worker.signals.operation.connect(pb.setLabel)
worker.signals.finished.connect(partial(self._threads_finisher,
text=text, icon=icon, pb=pb))
self._thread_pool.start(worker)
def _threads_finisher(self, text=None, icon=None, pb=None):
if pb is not None:
self._pb_list.removeItem(pb)
pb.setParent(None)
if text is not None:
msg = QtWidgets.QMessageBox(self)
msg.setText(text)
msg.setIcon(icon)
msg.exec_()
def set_features(self, obj):
features, parameters = obj
self._list_of_features.clear()
for feature in sorted(features, key=lambda x: x.mz):
self._list_of_features.add_feature(feature)
self._feature_parameters = parameters
def plotter(self, obj):
if not self._label2line: # in case if 'feature' was plotted
self._figure.clear()
self._ax = self._figure.add_subplot(111)
self._ax.set_xlabel('Retention time [min]')
self._ax.set_ylabel('Intensity')
self._ax.ticklabel_format(axis='y', scilimits=(0, 0))
line = self._ax.plot(obj['x'], obj['y'], label=obj['label'])
self._label2line[obj['label']] = line[0] # save line
self._ax.legend(loc='best')
self._figure.tight_layout()
self._canvas.draw()
def close_file(self, item):
self._list_of_files.deleteFile(item)
def get_selected_files(self):
return self._list_of_files.selectedItems()
def get_selected_features(self):
return self._list_of_features.selectedItems()
def get_plotted_lines(self):
return list(self._label2line.keys())
def plot_feature(self, item, shifted=True):
feature = self._list_of_features.get_feature(item)
self._label2line = dict() # empty plotted TIC and EIC
self._figure.clear()
self._ax = self._figure.add_subplot(111)
feature.plot(self._ax, shifted=shifted)
self._ax.set_title(item.text())
self._ax.set_xlabel('Retention time')
self._ax.set_ylabel('Intensity')
self._ax.ticklabel_format(axis='y', scilimits=(0, 0))
self._figure.tight_layout()
self._canvas.draw() # refresh canvas
def plot_tic(self, file):
label = f'TIC: {file[:file.rfind(".")]}'
plotted = False
if label not in self._label2line:
path = self._list_of_files.file2path[file]
pb = ProgressBarsListItem(f'Plotting TIC: {file}', parent=self._pb_list)
self._pb_list.addItem(pb)
worker = Worker(construct_tic, path, label)
worker.signals.progress.connect(pb.setValue)
worker.signals.result.connect(self.plotter)
worker.signals.finished.connect(partial(self._threads_finisher, pb=pb))
self._thread_pool.start(worker)
plotted = True
return plotted, label
def plot_eic(self, file, mz, delta):
label = f'EIC {mz:.4f} ± {delta:.4f}: {file[:file.rfind(".")]}'
plotted = False
if label not in self._label2line:
path = self._list_of_files.file2path[file]
pb = ProgressBarsListItem(f'Plotting EIC (mz={mz:.4f}): {file}', parent=self._pb_list)
self._pb_list.addItem(pb)
worker = Worker(construct_eic, path, label, mz, delta)
worker.signals.progress.connect(pb.setValue)
worker.signals.result.connect(self.plotter)
worker.signals.finished.connect(partial(self._threads_finisher, pb=pb))
self._thread_pool.start(worker)
plotted = True
return plotted, label
def delete_line(self, label):
self._ax.lines.remove(self._label2line[label])
del self._label2line[label]
def refresh_canvas(self):
if self._label2line:
self._ax.legend(loc='best')
self._ax.relim() # recompute the ax.dataLim
self._ax.autoscale_view() # update ax.viewLim using the new dataLim
else:
self._figure.clear()
self._ax = self._figure.add_subplot(111)
self._ax.set_xlabel('Retention time [min]')
self._ax.set_ylabel('Intensity')
self._ax.ticklabel_format(axis='y', scilimits=(0, 0))
self._canvas.draw()
