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)