def batch_process(self):
if self.process_parameters.data_folder:
self.process_window = BatchProcessProgressWindow(self)
self.process_window.create_window()
# Calibration
if self.process_parameters.calibration_file:
self.reference = read_peak_list(
self.process_parameters.calibration_file)
self.files = self.get_calibration_files()
# Read data
self.read_data()
# Perform calibration
progress = self.process_window.calibration_progress_bar
for index, self.chrom in enumerate(self.data):
progress.counter.set((float(index) / len(self.data)) * 100)
progress.update_progress_bar()
self.chrom.determine_calibration_timepairs()
# Still need to include a check against number of calibrants
self.chrom.determine_calibration_function()
self.chrom.calibrate_chromatogram()
progress.fill_bar()
# Quantitation
if self.process_parameters.quantitation_file:
self.reference = read_peak_list(
self.process_parameters.quantitation_file)
self.files = self.get_quantitation_files()
# Read data
if not self.data:
self.data = self.read_data()
# Perform quantitation
progress = self.process_window.quantitation_progress_bar
for index, self.chrom in enumerate(self.data):
progress.counter.set((float(index) / len(self.data)) * 100)
progress.update_progress_bar()
self.chrom.quantify_chromatogram()
progress.fill_bar()
# Generate summary file
output = Output(self)
output.init_output_file()
output.build_output_file()
# Report generation
if self.output_parameters.pdf_report.get() == True:
progress = self.process_window.report_progress_bar
for index, self.chrom in enumerate(self.data):
progress.counter.set((float(index) / len(self.data)) * 100)
progress.update_progress_bar()
self.chrom.generate_pdf_report()
progress.fill_bar()
def quantify_chromatogram(self):
try:
self.process_parameters.quantitation = True
self.process_parameters.quanititation_file = filedialog.askopenfilename(
title='Select Quantitation File')
if not self.process_parameters.quanititation_file:
self.process_parameters.quantitation = False
return
self.reference = read_peak_list(
self.process_parameters.quanititation_file)
self.progress.reset_bar()
self.task_label.set('Quantifying Chromatograms')
for index, chrom in enumerate(self.data):
self.progress.counter.set((float(index) /
len(self.data))*100)
self.progress.update_progress_bar()
chrom.quantify_chromatogram()
self.task_label.set('Idle')
self.progress.fill_bar()
if self.output_parameters.pdf_report.get() == True:
self.generate_pdf_reports()
self.output = Output(self)
self.output.init_output_file()
self.output.build_output_file()
self.process_parameters.quantitation = False
except Exception as e:
self.logger.error(e)
def calibrate_chromatogram(self):
try:
self.process_parameters.calibration = True
self.process_parameters.calibration_file = filedialog.askopenfilename(
title='Select Calibration File')
if not self.process_parameters.calibration_file:
self.process_parameters.quantitation = False
return
self.reference = read_peak_list(
self.process_parameters.calibration_file)
self.progress.reset_bar()
self.task_label.set('Calibrating Chromatograms')
for index, self.chrom in enumerate(self.data):
self.progress.counter.set((float(index) /
len(self.data))*100)
self.progress.update_progress_bar()
self.chrom.determine_calibration_timepairs()
# Still need to include a check against number of calibrants
self.chrom.determine_calibration_function()
self.chrom.calibrate_chromatogram()
self.task_label.set('Idle')
self.progress.fill_bar()
self.process_parameters.quantitation = False
except Exception as e:
self.logger.error(e)
self.progress.fill_bar()
self.axes.clear()
self.progress.reset_bar()
self.task_label.set('Plotting Chromatograms')
for index, chrom in enumerate(self.data):
self.progress.counter.set((float(index) /
len(self.data))*100)
self.progress.update_progress_bar()
chrom.plot_chromatogram()
finalize_plot(self)
self.task_label.set('Idle')
self.progress.fill_bar()