def export(self):
path = self.test_path
if self.test_path == 'none':
path = get_save_directory_name()
logger.info('Exporting files to %s' % path)
for data in data_manager.get_growth_data_files():
filename = data.label + '.csv'
if self.rename.isChecked():
filename = path + '/' + data.profile + '_ada.csv'
else:
filename = path + '/' + \
filename.split('/')[-1].split('.')[0] + '_ada.csv'
logger.debug('Exporting file %s' % filename)
# Get the condition data if that option is checked
conditions = None
if self.conditions.isChecked():
for cond_data in data_manager.get_condition_data_files():
if data.reactor != cond_data.reactor:
continue
if data.date != cond_data.date:
continue
if data.time != cond_data.time:
continue
conditions = cond_data
with open(filename, 'w', newline='') as csvfile:
writer = csv.writer(csvfile)
name_header = [
'Name', data.label, 'Title', data.title, 'Reactor',
data.reactor, 'Profile', data.profile
]
writer.writerow(name_header)
date_header = ['Date', data.date, 'Time', data.time]
writer.writerow(date_header)
measurement_header = [
data.xaxis.name + ' [' + data.xaxis.unit + ']'
]
for sig in data.signals:
measurement_header.append(sig.name + ' [' + sig.unit + ']')
if conditions is not None:
measurement_header.append('Conditions')
for sig in conditions.signals:
measurement_header.append(sig.name + ' [' + sig.unit +
']')
writer.writerow(measurement_header)
for i, xdat in enumerate(data.xaxis.data):
row = [xdat]
for sig in data.signals:
row.append(sig.data[i])
# Find closest signal time
if conditions is not None:
row.append('')
cond_ind = (np.abs(conditions.xaxis.data -
xdat)).argmin()
for sig in conditions.signals:
row.append(sig.data[cond_ind])
writer.writerow(row)
self.close()
def load_algem_pro(self, file_name):
logger.info('Loading an Algem-Pro file %s' % file_name)
# Read in files from Algem Pro
algem_data = read_algem_pro(file_name)
if self.row == -1:
data_manager.growth_data.add_data(algem_data)
else:
data_manager.growth_data.add_replicate(algem_data, self.row)
def load_algem_pro_conditions(self, file_name, downsample):
logger.info('Loading Algem-Pro condition file %s, downsample %i' %
(file_name, downsample))
# Read in conditions files from Algem Pro
algem_conditions = read_algem_pro(file_name, downsample)
if self.row == -1:
data_manager.condition_data.add_data(algem_conditions)
else:
data_manager.condition_data.add_replicate(algem_conditions,
self.row)
def load_ada(self, file_name):
logger.info('Loading ADA file %s' % file_name)
ada_data, condition_data = read_ada(file_name)
if self.row == -1:
data_manager.growth_data.add_data(ada_data)
if condition_data is not None:
data_manager.condition_data.add_data(condition_data)
else:
data_manager.growth_data.add_replicate(ada_data, self.row)
if condition_data is not None:
data_manager.condition_data.add_replicate(
condition_data, self.row)
def load_psi(self, file_name):
logger.info('Loading PSI file %s' % file_name)
# Read in files from Photon System Instruments photobioreactor
try:
psi_data, condition_data = read_psi(file_name)
except Exception as e:
raise RuntimeError('Error reading file ' + file_name + '\n' +
str(e))
if self.row == -1:
data_manager.growth_data.add_data(psi_data)
data_manager.condition_data.add_data(condition_data)
else:
data_manager.growth_data.add_replicate(psi_data, self.row)
data_manager.condition_data.add_replicate(condition_data, self.row)
def load_ip(self, file_name):
logger.info('Loading IP file %s' % file_name)
# Read in files from Industrial Plankton
try:
ip_data, condition_data = read_ip(file_name)
except Exception as e:
raise RuntimeError('Error reading file ' + file_name + '\n' +
str(e))
if self.row == -1:
data_manager.growth_data.add_data(ip_data)
data_manager.condition_data.add_data(condition_data)
else:
data_manager.growth_data.add_replicate(ip_data, self.row)
data_manager.condition_data.add_replicate(condition_data, self.row)
def load_microbemeter(self, file_name):
logger.info('Loading MicrobeMeter file %s' % file_name)
data_list, condition_data = read_microbemeter(file_name)
if self.row == -1:
data_manager.growth_data.add_data(data_list[0])
n_files = len(data_manager.growth_data.data_files)
for data in data_list[1:]:
if self.merge_replicates.isChecked():
data_manager.growth_data.add_replicate(data, n_files - 1)
else:
data_manager.growth_data.add_data(data)
if condition_data is not None:
data_manager.condition_data.add_data(condition_data)
else:
for data in data_list:
data_manager.growth_data.add_replicate(data, self.row)
def load_algem_ht24(self, file_name):
logger.info('Loading HT-24 file %s' % file_name)
# Read in files from Algem HT24 if no details file is provided
if len(self.details) == 0:
algem_data_list = read_algem_ht24(file_name)
for algem_data in algem_data_list:
data_manager.growth_data.add_data(algem_data)
# Read in files from Algem HT24 with details file
else:
algem_data_list, replicate_data_list = read_algem_ht24_details(
file_name, self.details[0])
for algem_data in algem_data_list:
data_manager.growth_data.add_data(algem_data)
for replicate in replicate_data_list:
if self.merge_replicates.isChecked():
data_manager.growth_data.add_replicate(
replicate[0], replicate[1])
else:
data_manager.growth_data.add_data(replicate[0])
def load_algem_ht24_conditions(self, file_name, downsample):
logger.info('Loading HT-24 condition file %s, downsample %i' %
(file_name, downsample))
# Read in files from Algem HT24 if details file is provided
if len(self.details) == 0:
algem_conditions_list = read_algem_ht24(file_name, downsample)
for algem_conditions in algem_conditions_list:
data_manager.condition_data.add_data(algem_conditions)
# Read in files from Algem HT24 without details file
else:
algem_conditions_list, replicate_conditions_list = \
read_algem_ht24_details(file_name, self.details[0],
downsample)
for algem_conditions in algem_conditions_list:
data_manager.condition_data.add_data(algem_conditions)
for replicate in replicate_conditions_list:
if self.merge_replicates.isChecked():
data_manager.condition_data.add_replicate(
replicate[0], replicate[1])
else:
data_manager.condition_data.add_data(replicate[0])
def load_algem_ht24_txt(self, file_name):
downsample = self.downsample.get_int()
logger.info('Loading a partial HT-24 file %s, downsample: %i' %
(file_name, downsample))
algem_data_list, rep_algem_data_list, cond_data_list,\
rep_cond_data_list = read_algem_ht24_txt(file_name, downsample)
for algem_data in algem_data_list:
data_manager.growth_data.add_data(algem_data)
for replicate in rep_algem_data_list:
if self.merge_replicates.isChecked():
data_manager.growth_data.add_replicate(replicate[0],
replicate[1])
else:
data_manager.growth_data.add_data(replicate[0])
for condition_data in cond_data_list:
data_manager.condition_data.add_data(condition_data)
for replicate in rep_cond_data_list:
if self.merge_replicates.isChecked():
data_manager.condition_data.add_replicate(
replicate[0], replicate[1])
else:
data_manager.condition_data.add_data(replicate[0])
def _createMenuBar(self):
logger.info('Creating menu')
menu_bar = self.menuBar()
menu_bar.setNativeMenuBar(False)
file_menu = menu_bar.addMenu("&File")
self.save_action = QAction('Save plot', self)
self.save_action.triggered.connect(self.save_plot)
file_menu.addAction(self.save_action)
self.export_action = QAction('Export data', self)
self.export_action.triggered.connect(self.export_files)
file_menu.addAction(self.export_action)
help_menu = menu_bar.addMenu("&Help")
self.docs_action = QAction('Documentation', self)
self.docs_action.triggered.connect(self.open_docs)
help_menu.addAction(self.docs_action)
self.video_action = QAction('Tutorials', self)
self.video_action.triggered.connect(self.open_video)
help_menu.addAction(self.video_action)
self.issues_action = QAction('Issues', self)
self.issues_action.triggered.connect(self.open_issues)
help_menu.addAction(self.issues_action)
def save_plot(self):
logger.info('Saving the correlation plot')
self.plot.save()
def save_plot(self):
logger.info('Saving the plot')
self.plot.save()
# Local imports
from ada.gui.main_window import App
import ada.configuration as config
from ada.logger import logger
# Standard imports
import sys
# pyqt5 imports
from PyQt5.QtWidgets import QApplication
if __name__ == '__main__':
app = QApplication(sys.argv)
screen = app.primaryScreen()
size = screen.availableGeometry()
config.wr = size.width() / 1280.
config.hr = size.width() / 1280.
logger.info('Configuring screen dimensions width = %.2f, height = %.2f' %
(size.width(), size.height()))
logger.info('Starting application')
ex = App()
sys.exit(app.exec_())
