def calibrate_chromatogram(self):
try:
self.cal_file = filedialog.askopenfilename(
title='Select Calibration File')
if not self.cal_file:
self.cal_file = None
self.reference = self.functions.read_peak_list(self.cal_file)
self.progress.reset_bar(self)
for index, self.chrom in enumerate(self.data):
progress = (float(index) / len(self.data)) * 100
self.counter.set(progress)
self.progress.update_progress_bar(self)
self.time_pairs = self.functions.find_peak(self)
self.function = self.functions.determine_calibration_function(
self)
self.functions.apply_calibration_function(self)
except Exception as e:
self.logger.error(e)
self.progress.fill_bar(self)
self.axes.clear()
for chrom in self.data:
chrom.plot_chrom(self)
finalize_plot(self)
def baseline_correction(self):
try:
self.axes.clear()
for chrom in self.data:
chrom.trace.baseline_correction(self)
chrom.plot_chrom(self)
finalize_plot(self)
except Exception as e:
self.logger.error(e)
def smooth_chromatogram(self):
try:
self.axes.clear()
for chrom in self.data:
chrom.trace.smooth_chrom(self)
chrom.plot_chrom(self)
finalize_plot(self)
except Exception as e:
self.logger.error(e)
def peak_detection(self):
try:
self.axes.clear()
for self.chrom in self.data:
self.detected_peaks = PeakDetection(self)
self.detected_peaks.detect_peaks()
self.detected_peaks.plot_peaks()
self.chrom.plot_chromatogram()
finalize_plot(self)
except Exception as e:
self.logger.error(e)
def open_chromatogram_window(self):
files = filedialog.askopenfilenames(title='Open Chromatogram File(s)')
data = []
if files:
for file in files:
foo = Chromatogram(Path(file))
data.append(foo)
self.data = data
self.axes.clear()
for chrom in self.data:
chrom.plot_chrom(self)
finalize_plot(self)
def baseline_correction(self):
try:
self.task_label.set('Baseline Correcting')
self.progress.reset_bar()
self.axes.clear()
for index, chrom in enumerate(self.data):
self.progress.counter.set((float(index) /
len(self.data))*100)
self.progress.update_progress_bar()
chrom.baseline_correction()
chrom.plot_chromatogram()
finalize_plot(self)
self.task_label.set('Idle')
self.progress.fill_bar()
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()
def open_chromatogram_window(self):
files = filedialog.askopenfilenames(title='Open Chromatogram File(s)')
data = []
if files:
self.task_label.set('Opening Chromatograms')
self.progress.reset_bar()
for index, filename in enumerate(files):
self.progress.counter.set((float(index) / len(files)) * 100)
self.progress.update_progress_bar()
self.filename = Path(filename)
chromatogram = Chromatogram(self)
chromatogram.open_chromatogram()
data.append(chromatogram)
self.data = data
self.task_label.set('Idle')
self.progress.fill_bar()
self.axes.clear()
for chrom in self.data:
chrom.plot_chromatogram()
finalize_plot(self)
