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 quantify_chromatogram(self):
try:
self.results = []
self.functions.batch_folder = self.batch_folder
self.quant_file = filedialog.askopenfilename(
title='Select Quantitation File')
if not self.quant_file:
self.quant_file = None
self.reference = self.functions.read_peak_list(self.quant_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.results.append({
'file':
Path(self.chrom.filename).name,
'results':
self.functions.quantify_chrom(self)
})
self.output = Output(self)
self.output.init_output_file(self)
self.output.build_output_file(self)
self.progress.fill_bar(self)
except Exception as e:
self.logger.error(e)
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()
class HappyToolsGui(object):
@classmethod
def run(cls):
root = tk.Tk()
HappyToolsGui(root)
root.mainloop()
def __init__(self, master):
# Inherit Tk() root object
self.master = master
# Define task_label for progress bar functionality
task_label = tk.StringVar()
task_label.set('Idle')
# LOGGING
logging.basicConfig(filename='HappyTools.log',
format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
datefmt='%Y-%m-%d %H:%M', filemode='a',
level=logging.WARNING)
# ACCESS CHECK
self.directories = directories
if not check_disk_access(self):
messagebox.showinfo(
'Access Error', 'HappyTools does ' +
'not have sufficient disk access rights. Please close ' +
'HappyTools and check if the current user has read/' +
'write access to all folders in the Happytools folder.')
# CANVAS
fig = figure.Figure(figsize=(12,6))
axes = fig.add_subplot(111)
axes.axis('off')
canvas = FigureCanvasTkAgg(fig, master=master)
CustomToolbar(canvas, master)
canvas.get_tk_widget().pack(fill=tk.BOTH, expand=tk.YES)
canvas.draw()
# FRAME
tk.Frame(master)
master.title('HappyTools '+str(version.version) +
' (Build '+str(version.build)+')')
iconbitmap = Path.cwd() / 'HappyTools' / 'gui' / 'assets' / 'Icon.ico'
backgroundimage = Path.cwd() / 'HappyTools' / 'gui' / 'assets' / 'UI.png'
try:
master.iconbitmap(default=iconbitmap)
except tk.TclError as e:
logging.getLogger(__name__).warn(e)
if backgroundimage.is_file():
img = image.imread(str(backgroundimage))
axes.imshow(img)
axes.set_aspect('auto')
task = tk.Label(master, textvariable=task_label, width=20)
task.pack()
progress = ProgressBar(self.master)
progress.bar.pack(fill=tk.X)
# QUIT
master.protocol('WM_DELETE_WINDOW', self.close)
# MENU
menu = tk.Menu(master)
master.config(menu=menu)
filemenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='File', menu=filemenu)
filemenu.add_command(label='Open Chromatogram',
command=self.open_chromatogram_window)
filemenu.add_command(label='Smooth Chromatogram',
command=self.smooth_chromatogram)
filemenu.add_command(label='Baseline Correction',
command=self.baseline_correction)
filemenu.add_command(label='Normalize chromatogram',
command=self.normalize_chromatogram)
filemenu.add_command(label='Save Chromatogram',
command=self.save_chromatogram)
processmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='Process', menu=processmenu)
processmenu.add_command(label='Calibrate Chromatogram',
command=self.calibrate_chromatogram)
processmenu.add_command(label='Quantify Chromatogram',
command=self.quantify_chromatogram)
processmenu.add_command(label='Select Outputs',
command=self.open_output_window)
advancedmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='Advanced', menu=advancedmenu)
advancedmenu.add_command(label='Peak Detection',
command=self.peak_detection)
advancedmenu.add_command(label='Save Calibrants',
command=self.save_calibrants)
advancedmenu.add_command(label='Save Annotation',
command=self.save_annotation)
batchmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='Batch', menu=batchmenu)
batchmenu.add_command(label='Batch Process',
command=self.open_batch_window)
settingsmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='Settings', menu=settingsmenu)
settingsmenu.add_command(label='Settings',
command=self.settings_window)
aboutmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='About', menu=aboutmenu)
aboutmenu.add_command(label='About HappyTools',
command=self.open_about_window)
if (Path.cwd() / 'HappyTools' / 'plugins').glob("*.py"):
pluginsmenu = tk.Menu(menu,tearoff=0)
menu.add_cascade(label="Plugins", menu=pluginsmenu)
for file in(Path.cwd() / 'HappyTools' / 'plugins').glob('*.py'):
if '__' in str(file):
continue
module_name = PurePath(file).stem
module = "HappyTools.plugins."+str(module_name)
module = importlib.import_module(module)
try:
module_name = module.name
except Exception as e:
logging.getLogger(__name__).error(e)
pluginsmenu.add_command(label=module_name,
command=self.make_function(module))
# INHERITANCE
self.logger = logging.getLogger(__name__)
self.settings = Settings(self)
self.output_parameters = OutputParameters(self)
self.process_parameters = ProcessParameters(self)
self.axes = axes
self.canvas = canvas
self.progress = progress
self.task_label = task_label
def make_function(self, module):
try:
def x():
return module.start(self)
except AttributeError as e:
self.logger.error('Problem with the plugin: '+str(e))
return x
@classmethod
def open_about_window(cls):
AboutWindow()
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)
def open_output_window(self):
OutputWindow(self)
def open_settings_window(self):
self.settings.settings_popup(self.settings)
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 close(self):
self.master.destroy()
self.master.quit()
def generate_pdf_reports(self):
self.progress.reset_bar()
self.task_label.set('Generating PDF reports')
for index, chrom in enumerate(self.data):
self.progress.counter.set((float(index) /
len(self.data))*100)
self.progress.update_progress_bar()
chrom.generate_pdf_report()
self.task_label.set('Idle')
self.progress.fill_bar()
def open_batch_window(self):
batchWindow(self)
def normalize_chromatogram(self):
try:
self.task_label.set('Normalizing Chromatograms')
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.normalize_chromatogram()
chrom.plot_chromatogram()
finalize_plot(self)
self.task_label.set('Idle')
self.progress.fill_bar()
except Exception as e:
self.logger.error(e)
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 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 save_annotation(self):
try:
for self.chrom in self.data:
self.detected_peaks.write_peaks()
except Exception as e:
self.logger.error(e)
def save_calibrants(self):
save_calibrants(self)
def smooth_chromatogram(self):
try:
self.task_label.set('Smoothing Chromatograms')
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.smooth_chromatogram()
chrom.plot_chromatogram()
finalize_plot(self)
self.task_label.set('Idle')
self.progress.fill_bar()
except Exception as e:
self.logger.error(e)
def save_chromatogram(self):
try:
for chrom in self.data:
chrom.save_chromatogram(self)
except Exception as e:
self.logger.error(e)
def settings_window(self):
try:
SettingsWindow(self)
except Exception as e:
self.logger.error(e)
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)
class HappyToolsGui(object):
@classmethod
def run(cls):
root = tk.Tk()
HappyToolsGui(root)
root.mainloop()
def __init__(self, master):
self.output_window_open = tk.IntVar(value=0)
self.batch_folder = tk.StringVar(value=Path.cwd())
self.abs_int = tk.IntVar(value=1)
self.rel_int = tk.IntVar(value=1)
self.gauss_int = tk.IntVar(value=1)
self.bck_sub = tk.IntVar(value=1)
self.bck_noise = tk.IntVar(value=1)
self.peak_qual = tk.IntVar(value=1)
self.create_figure = 'True'
self.master = master
self.counter = tk.IntVar(value=0)
logging.basicConfig(
filename='HappyTools.log',
format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
datefmt='%Y-%m-%d %H:%M',
filemode='a',
level=logging.WARNING)
self.logger = logging.getLogger(__name__)
self.functions = Functions(self) # Change functions from class to non
# ACCESS CHECK
self.directories = directories
if not self.functions.check_disk_access(self):
messagebox.showinfo(
'Access Error', 'HappyTools does ' +
'not have sufficient disk access rights. Please close ' +
'HappyTools and check if the current user has read/' +
'write access to all folders in the Happytools folder.')
# SETTINGS
self.settings = Settings(self)
if (Path.cwd() / self.settings.settings).is_file():
self.settings.read_settings(self.settings)
# CANVAS
self.fig = figure.Figure(figsize=(12, 6))
self.fig.subplots_adjust(left=0.05, bottom=0.05, right=0.95, top=0.95)
self.axes = self.fig.add_subplot(111)
self.axes.axis('off')
self.canvas = FigureCanvasTkAgg(self.fig, master=master)
self.toolbar = CustomToolbar(self.canvas, master)
self.canvas.get_tk_widget().pack(fill=tk.BOTH, expand=tk.YES)
self.canvas.draw()
# FRAME
tk.Frame(master)
master.title('HappyTools ' + str(version.version) + ' (Build ' +
str(version.build) + ')')
iconbitmap = Path.cwd() / 'HappyTools' / 'gui' / 'assets' / 'Icon.ico'
backgroundimage = Path.cwd(
) / 'HappyTools' / 'gui' / 'assets' / 'UI.png'
if iconbitmap.is_file():
master.iconbitmap(default=iconbitmap)
if backgroundimage.is_file():
img = image.imread(str(backgroundimage))
self.axes.imshow(img)
self.axes.set_aspect('auto')
self.progress = progressbar.SimpleProgressBar(self)
self.progress.bar.pack(fill=tk.X)
# QUIT
master.protocol('WM_DELETE_WINDOW', self.close)
# MENU
menu = tk.Menu(master)
master.config(menu=menu)
filemenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='File', menu=filemenu)
filemenu.add_command(label='Open Chromatogram',
command=self.open_chromatogram_window)
filemenu.add_command(label='Smooth Chromatogram',
command=self.smooth_chromatogram)
filemenu.add_command(label='Baseline Correction',
command=self.baseline_correction)
filemenu.add_command(label='Normalize chromatogram',
command=self.normalize_chromatogram)
filemenu.add_command(label='Save Chromatogram',
command=self.save_chromatogram)
processmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='Process', menu=processmenu)
processmenu.add_command(label='Calibrate Chromatogram',
command=self.calibrate_chromatogram)
processmenu.add_command(label='Quantify Chromatogram',
command=self.quantify_chromatogram)
processmenu.add_command(label='Select Outputs',
command=self.open_output_window)
advancedmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='Advanced', menu=advancedmenu)
advancedmenu.add_command(label='Peak Detection',
command=self.peak_detection)
advancedmenu.add_command(label='Save Calibrants',
command=self.save_calibrants)
advancedmenu.add_command(label='Save Annotation',
command=self.save_annotation)
batchmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='Batch', menu=batchmenu)
batchmenu.add_command(label='Batch Process',
command=self.open_batch_window)
settingsmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='Settings', menu=settingsmenu)
settingsmenu.add_command(label='Settings',
command=self.open_settings_window)
aboutmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label='About', menu=aboutmenu)
aboutmenu.add_command(label='About HappyTools',
command=self.open_about_window)
if (Path.cwd() / 'HappyTools' / 'plugins').glob("*.py"):
pluginsmenu = tk.Menu(menu, tearoff=0)
menu.add_cascade(label="Plugins", menu=pluginsmenu)
for file in (Path.cwd() / 'HappyTools' / 'plugins').glob('*.py'):
if '__' in str(file):
continue
module_name = PurePath(file).stem
module = "HappyTools.plugins." + str(module_name)
module = importlib.import_module(module)
try:
module_name = module.name
except Exception as e:
self.logger.error(e)
pluginsmenu.add_command(label=module_name,
command=self.make_function(module))
def make_function(self, module):
try:
def x():
return module.start(self)
except AttributeError as e:
self.logger.error('Problem with the plugin: ' + str(e))
return x
@classmethod
def open_about_window(cls):
AboutWindow()
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 open_output_window(self):
OutputWindow(self)
def open_settings_window(self):
self.settings.settings_popup(self.settings)
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 close(self):
self.master.destroy()
self.master.quit()
def open_batch_window(self):
batchWindow(self)
def normalize_chromatogram(self):
try:
self.axes.clear()
for chrom in self.data:
chrom.trace.norm_chrom(self)
chrom.plot_chrom(self)
finalize_plot(self)
except Exception as e:
self.logger.error(e)
def quantify_chromatogram(self):
try:
self.results = []
self.functions.batch_folder = self.batch_folder
self.quant_file = filedialog.askopenfilename(
title='Select Quantitation File')
if not self.quant_file:
self.quant_file = None
self.reference = self.functions.read_peak_list(self.quant_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.results.append({
'file':
Path(self.chrom.filename).name,
'results':
self.functions.quantify_chrom(self)
})
self.output = Output(self)
self.output.init_output_file(self)
self.output.build_output_file(self)
self.progress.fill_bar(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)
self.detected_peaks.plot_peaks(self)
self.chrom.plot_chrom(self)
finalize_plot(self)
except Exception as e:
self.logger.error(e)
def save_annotation(self):
try:
for self.chrom in self.data:
self.detected_peaks.write_peaks(self)
except Exception as e:
self.logger.error(e)
def save_calibrants(self):
self.functions.save_calibrants(self)
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 save_chromatogram(self):
try:
for chrom in self.data:
chrom.save_chrom(self)
except Exception as e:
self.logger.error(e)
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)