def calibrate_mass_spectrum(self): try: self.progress.reset_bar() self.process_parameters.calibration = True peak_list = functions.get_peak_list( self.process_parameters.calibration_file) self.peak_list = peak_list self.process_mass_spectrum() self.task_label.set('Calibrating Mass Spectra') for index, mass_spectrum in enumerate(self.mass_spectra): mass_spectrum.calibrate() self.progress.counter.set( (float(index) / len(self.mass_spectra)) * 100) self.progress.update_progress_bar() self.task_label.set('Idle') self.progress.fill_bar() self.axes.clear() for mass_spectrum in self.mass_spectra: mass_spectrum.plot_mass_spectrum() finalize_plot(self) self.process_parameters.calibration = False if not self.process_parameters.calibration_file: messagebox.showinfo('Warning', 'No Calibration File ' + 'Selected') except Exception as e: self.logger.error(e)
def open_mass_spectrum(self): try: self.progress.reset_bar() data_buffer = [] files = filedialog.askopenfilenames(title='Select Mass ' + 'Spectrum File(s)') self.task_label.set('Opening Mass Spectra') for index, file in enumerate(files): self.progress.counter.set((float(index) / len(files)) * 100) self.progress.update_progress_bar() self.filename = file mass_spec_buffer = MassSpectrum(self) mass_spec_buffer.open_mass_spectrum() data_buffer.append(mass_spec_buffer) self.mass_spectra = data_buffer self.task_label.set('Idle') self.progress.fill_bar() self.task_label.set('Plotting Mass Spectra') if self.mass_spectra: self.axes.clear() for index, mass_spectrum in enumerate(self.mass_spectra): self.progress.counter.set( (float(index) / len(files)) * 100) self.progress.update_progress_bar() mass_spectrum.plot_mass_spectrum() finalize_plot(self) self.task_label.set('Idle') self.progress.fill_bar() except Exception as e: messagebox.showinfo('Warning', 'The selected files could ' + 'not be opened.') self.logger.error(e)
def open_mass_spectrum(self): try: self.progress.reset_bar() data_buffer = [] files = filedialog.askopenfilenames(title='Select Mass '+ 'Spectrum File(s)') self.task_label.set('Opening Mass Spectra') for index, file in enumerate(files): self.progress.counter.set((float(index) / len(files))*100) self.progress.update_progress_bar() self.filename = file mass_spec_buffer = MassSpectrum(self) mass_spec_buffer.open_mass_spectrum() data_buffer.append(mass_spec_buffer) self.mass_spectra = data_buffer self.task_label.set('Idle') self.progress.fill_bar() self.task_label.set('Plotting Mass Spectra') if self.mass_spectra: self.axes.clear() for index, mass_spectrum in enumerate(self.mass_spectra): self.progress.counter.set((float(index) / len(files))*100) self.progress.update_progress_bar() mass_spectrum.plot_mass_spectrum() finalize_plot(self) self.task_label.set('Idle') self.progress.fill_bar() except Exception as e: messagebox.showinfo('Warning','The selected files could '+ 'not be opened.') self.logger.error(e)
def calibrate_mass_spectrum(self): try: self.progress.reset_bar() self.process_parameters.calibration = True peak_list = functions.get_peak_list( self.process_parameters.calibration_file) self.peak_list = peak_list self.process_mass_spectrum() self.task_label.set('Calibrating Mass Spectra') for index, mass_spectrum in enumerate(self.mass_spectra): mass_spectrum.calibrate() self.progress.counter.set((float(index) / len(self.mass_spectra))*100) self.progress.update_progress_bar() self.task_label.set('Idle') self.progress.fill_bar() self.axes.clear() for mass_spectrum in self.mass_spectra: mass_spectrum.plot_mass_spectrum() finalize_plot(self) self.process_parameters.calibration = False if not self.process_parameters.calibration_file: messagebox.showinfo('Warning','No Calibration File '+ 'Selected') except Exception as e: self.logger.error(e)
def baseline_correct(self): try: self.axes.clear() for mass_spectrum in self.mass_spectra: mass_spectrum.baseline_correct() mass_spectrum.plot_mass_spectrum() finalize_plot(self) except Exception as e: self.logger.error(e)
def baseline_correct(self): try: self.axes.clear() for mass_spectrum in self.mass_spectra: mass_spectrum.baseline_correct() mass_spectrum.plot_mass_spectrum() finalize_plot(self) except Exception as e: self.logger.error(e)
def classify_mass_spectra(self): try: classification.classify_mass_spectra(self.mass_spectra) self.axes.clear() for mass_spectrum in self.mass_spectra: mass_spectrum.plot_mass_spectrum() finalize_plot(self) except Exception as e: self.logger.error(e)
def normalize_mass_spectrum(self): try: for mass_spectrum in self.mass_spectra: mass_spectrum.normalize_mass_spectrum() if self.mass_spectra: self.axes.clear() for mass_spectrum in self.mass_spectra: mass_spectrum.plot_mass_spectrum() finalize_plot(self) except Exception as e: self.logger.error(e)
def normalize_mass_spectrum(self): try: for mass_spectrum in self.mass_spectra: mass_spectrum.normalize_mass_spectrum() if self.mass_spectra: self.axes.clear() for mass_spectrum in self.mass_spectra: mass_spectrum.plot_mass_spectrum() finalize_plot(self) except Exception as e: self.logger.error(e)