def rereaddata(self):
filetype = self.analysistype.currentText()
if self.itemselectedboolean == 1:
selectedfile = str(self.datafiles.currentItem().text())
if filetype == 'CTD':
self.initctd = InitialiseCTDData.initCTDdata(selectedfile, self.db, self.currpath, self.currproject,
self.interactive, True)
if filetype == 'Nutrients':
self.initnutrientdata = processingNutrientsWindow(selectedfile, self.db, self.currpath,
self.currproject, self.interactive, True)
if filetype == 'Salinity':
self.initsaltdata = processingSalinityWindow(selectedfile, self.db, self.currpath, self.currproject,
self.interactive, True)
if filetype == 'Oxygen':
self.initoxydata = processingOxygenWindow(selectedfile, self.db, self.currpath, self.currproject,
self.interactive, True)
if filetype == 'Sampling':
self.initsampledata = InitialiseSampleSheet.initSampleSheet(selectedfile, self.currproject, self.db,
self.currpath, self.interactive, True)
else:
messagebox = hyproMessageBoxTemplate('Error',
'Please select a file to reread... ',
'information')
def open_processing(self):
try:
if self.currproject == 'No active project':
message_box = hyproMessageBoxTemplate(
'Error',
'There is no active project currently selected, please create or import one.',
'information')
else:
self.project = self.currprojectdisp.text()
with open('C:/HyPro/hyprosettings.json', 'r') as file:
params = json.loads(file.read())
path = params['projects'][self.project]['path']
self.proccing = Processingmenu(self.project, path)
self.proccing.show()
sleep(0.3)
self.hide()
self.proccing.backToMain.connect(self.show)
#self.proccing.backToMain.connect(self.proccing.output_box.close)
self.proccing.backToMain.connect(
lambda: self.proccing.output_box.widget.close())
self.proccing.backToMain.connect(lambda: logging.shutdown())
self.proccing.backToMain.connect(self.proccing.hide)
except Exception as e:
print(e)
def save_output_window(self):
filedialog = QFileDialog.getSaveFileName(self, 'Save File', '', '.txt')
if filedialog[0]:
outputfile = open(filedialog[0] + filedialog[1], 'w')
outputtext = self.output_box.gettext()
outputfile.write(outputtext)
outputfile.close()
message_box = hyproMessageBoxTemplate(
'Saving Success', 'Output log was successfully saved.',
'success')
def savefunction(self):
try:
surveyname = str(self.surveyName.text())
with open(self.currpath + '/' + '%sParams.json' % self.currproject,
'r') as file:
params = json.loads(file.read())
newsurvey = {'%s' % surveyname: {}}
if self.nuts_active:
newsurvey[surveyname]['seal'] = {
'activated': self.activate_nutrient.isChecked(),
'ctdsurvey': self.ctd_survey_nutrient.isChecked(),
'usesampleid': self.sample_id_nutrient.isChecked(),
'surveyprefix': self.survey_prefix_nutrient.text(),
'decodedepfromid':
self.decode_deployment_nutrient.isChecked(),
'depformat': self.dep_rp_format_nutrient.text(),
'decodesampleid': self.decode_nutrient.isChecked()
}
if self.salt_active:
newsurvey[surveyname]['guildline'] = {
'activated': self.activate_salt.isChecked(),
'ctdsurvey': self.ctd_survey_salt.isChecked(),
'decodesampleid': self.decode_salt.isChecked(),
'surveyprefix': self.survey_number_station.text(),
'decodedepfromid': self.decode_salt_deployment.isChecked(),
'usesampleid': self.sample_salt_id.isChecked(),
'depformat': self.dep_rp_format_salt.text()
}
if self.oxy_active:
newsurvey[surveyname]['scripps'] = {
'activated': self.activate_oxygen.isChecked(),
'ctdsurvey': self.ctd_survey_oxygen.isChecked(),
'decodesampleid': self.decode_oxygen.isChecked(),
'surveyprefix': self.survey_number_station.text(),
'decodedepfromid':
self.decode_oxygen_deployment.isChecked(),
'usesampleid': self.sample_oxygen_id.isChecked()
}
params['surveyparams'].update(newsurvey)
with open(self.currpath + '/' + '%sParams.json' % self.currproject,
'w') as file:
json.dump(params, file)
message_box = hyproMessageBoxTemplate(
'Settings Saved', 'Survey settings were successfully saved',
'success')
except Exception as e:
print('Error: ' + e)
def createProj(self):
try:
self.project_directorystr = str(self.project_directory.text())
self.project_prefix_str = str(self.project_prefix.text())
self.project_type_str = str(self.project_type.currentText())
if (self.project_directorystr != '') & (self.project_prefix_str != ''):
if os.path.exists(self.project_directory.text()):
project_directorystr = str(self.project_directory.text())
with open('C:/HyPro/hyprosettings.json', 'r') as f:
self.params = json.load(f)
continuecreateproj = True
for x in self.params['projects'].keys():
if self.project_prefix_str == x:
messagebox = hyproMessageBoxTemplate('Error',
'There is already a project with that name, please '
'choose a different name for the project.', 'error')
continuecreateproj = False
if continuecreateproj:
newproj = {'%s' % self.project_prefix_str: {'path': project_directorystr, 'type': self.project_type_str}}
self.params['projects'].update(newproj)
#self.params['activeproject'] = project_prefixstr
# Write project info back to disk
with open('C:/HyPro/hyprosettings.json', 'w') as file:
json.dump(self.params, file)
# Create directories for the project
if not os.path.exists((project_directorystr + "/Nutrients")):
os.makedirs((project_directorystr + "/Nutrients"))
if not os.path.exists((project_directorystr + "/Salinity")):
os.makedirs((project_directorystr + "/Salinity"))
if not os.path.exists((project_directorystr + "/Oxygen")):
os.makedirs((project_directorystr + "/Oxygen"))
if not os.path.exists((project_directorystr + "/CTD")):
os.makedirs((project_directorystr + "/CTD"))
if not os.path.exists((project_directorystr + "/Sampling")):
os.makedirs((project_directorystr + "/Sampling"))
# Make weird little hack 'hypro' file, used for when a project needs to be imported
filebuffer = open(project_directorystr + '/' + self.project_prefix_str + '.hypro', 'w')
filebuffer.write(self.project_prefix_str + '\n')
filebuffer.write(self.project_type_str + '\n')
filebuffer.write(project_directorystr + '\n')
filebuffer.close()
messagebox = hyproMessageBoxTemplate('Success', 'A new project was successfully created.',
'success')
sleep(0.4)
self.close()
sleep(0.5)
self.new_project_created.emit()
else:
messagebox = hyproMessageBoxTemplate('Error',
'There is already a project with that name, please choose '
'a different name for the project.', 'error')
else:
messagebox = hyproMessageBoxTemplate('Error', 'Provided path does not exist', 'error')
else:
messagebox = hyproMessageBoxTemplate('Error', 'Fields are empty, please fill them in.', 'information')
except Exception as e:
logging.error(traceback.print_exc())
def delete_data(self):
try:
filetype = self.analysis_type.currentText()
selectedfile = self.data_files.currentItem()
if selectedfile:
selectedfile = str(selectedfile.text())
conn = sqlite3.connect(self.db)
c = conn.cursor()
filename = [selectedfile]
# Different statement for each analysis as the database structure for each is different
if filetype == 'CTD':
deploymentnumber = [selectedfile[-7:-4]]
print(deploymentnumber)
c.execute('DELETE from ctdData where deployment=?',
deploymentnumber)
conn.commit()
c.execute('DELETE from ctdFilesProcessed where filename=?',
filename)
conn.commit()
conn.close()
if self.deletefilescheckbox.isChecked():
print('Deleting data files as well')
file = self.currpath + '/' + 'CTD' + '/' + selectedfile
os.remove(file)
logging.info('CTD data - ' + str(selectedfile) +
' deleted, the file was also deleted')
else:
logging.info('CTD data - ' + str(selectedfile) +
' deleted')
if filetype == 'Nutrients':
pass
# TODO: complete the section for nutrients
if filetype == 'Salinity':
runnumber = [selectedfile[-8:-5]]
c.execute('DELETE from salinityData where runNumber=?',
runnumber)
conn.commit()
c.execute(
'DELETE from salinityFilesProcessed where filename=?',
filename)
conn.commit()
conn.close()
if self.delete_files_checkbox.isChecked():
print('Deleting data files as well')
file = self.currpath + '/' + 'Salinity' + '/' + selectedfile
os.remove(file)
logging.info('Salinity data - ' + str(selectedfile) +
' deleted, the file was also deleted')
else:
logging.info('Salinity data - ' + str(selectedfile) +
' deleted')
if filetype == 'Oxygen':
runnumber = [selectedfile[-7:-4]]
c.execute('DELETE from oxygenData where runNumber=?',
runnumber)
conn.commit()
c.execute(
'DELETE from oxygenFilesProcessed where filename=?',
filename)
conn.commit()
conn.close()
if self.delete_files_checkbox.isChecked():
print('Deleting data files as well')
file = self.currpath + '/' + 'Oxygen' + '/' + selectedfile
os.remove(file)
logging.info('Oxygen data - ' + str(selectedfile) +
' deleted, the file was also deleted')
else:
logging.info('Oxygen data - ' + str(selectedfile) +
' deleted')
if filetype == 'Sampling':
runnumber = [selectedfile[-11:-8]]
print(runnumber)
c.execute('DELETE from logsheetData where deployment=?',
runnumber)
conn.commit()
c.execute(
'DELETE from logsheetFilesProcessed where filename=?',
filename)
conn.commit()
conn.close()
if self.delete_files_checkbox.isChecked():
print('Deleting data files as well')
file = self.currpath + '/' + 'Sampling' + '/' + selectedfile
os.remove(file)
logging.info('Sample logsheet data - ' +
str(selectedfile) +
' deleted, the file was also deleted')
else:
logging.info('Sample logsheet data - ' +
str(selectedfile) + ' deleted')
messagebox = hyproMessageBoxTemplate(
'Deleted successfully',
'Data was deleted from the database file', 'delete')
else:
messagebox = hyproMessageBoxTemplate(
'Error', 'Please select a file to delete ',
'error')
except Exception:
logging.error(traceback.print_exc())
def about_information(self):
message_box = hyproMessageBoxTemplate(
'About Hypro',
'This is an experimental version of HyPro built using Python.',
'about')
def call_plot(self, sample_ids, deployments, rosette_positions, salinity):
# Pull out relevant CTD data based on the samples that were analysed
deps_set = tuple(set(sample_ids))
queryq = '?'
queryplace = ', '.join(queryq for unused in deps_set)
conn = sqlite3.connect(self.database)
c = conn.cursor()
q = 'SELECT * FROM ctdData WHERE deployment IN (%s)' % queryplace
c.execute(q, deps_set)
conn.commit()
ctd_data = list(c.fetchall())
conn.close()
if not ctd_data:
logging.info(
f'<b>The salinity file {self.file} contains CTD samples - however there is no CTD sensor data in HyPro. The file'
' is processed but no error plot appears because of this error. Once CTD data is imported, '
'reprocess this file to see the error plot. </b>')
time.sleep(0.3)
message_box = hyproMessageBoxTemplate('HyPro - Oxygen Processing Anomaly',
f'CTD data matching results in the file {self.file} are not in HyPro.',
'information',
long_text=f'The salinity file {self.file} contains CTD samples, '
f'however there is no matching CTD sensor data in HyPro. '
f'The file is processed but no error plot appears because '
f'of this error. Once CTD data is imported, reprocess '
f'this file to see the error plot.')
time.sleep(0.2)
self.proceed_processing()
else:
ctd_salt1 = [x[8] for x in ctd_data]
ctd_salt2 = [x[9] for x in ctd_data]
ctd_deployment = [x[0] for x in ctd_data]
ctd_rp = [x[11] for x in ctd_data]
ctd_depths = [x[7] for x in ctd_data]
ctd_data_to_plot = {'primary_sal': [], 'secondary_sal': [], 'dep_rosette_postion': [],
'rosette_position_to_plot': [], 'deployment': [], 'depths': [], 'bottle_sal': []}
reference_indexes = []
for i, bottle_dep in enumerate(deployments):
for l, ctd_dep in enumerate(ctd_deployment):
if bottle_dep == ctd_dep:
if rosette_positions[i] == ctd_rp[l]:
reference_indexes.append(i)
ctd_data_to_plot['bottle_sal'].append(salinity[i])
ctd_data_to_plot['deployment'].append(bottle_dep)
ctd_data_to_plot['depths'].append(ctd_depths[l])
ctd_data_to_plot['rosette_position_to_plot'].append(rosette_positions[i])
ctd_data_to_plot['primary_sal'].append(ctd_salt1[l])
ctd_data_to_plot['secondary_sal'].append(ctd_salt2[l])
if max(ctd_data_to_plot['rosette_position_to_plot']) > 24:
max_rp = 36
else:
max_rp = 24
# Create the X data for the plot - x data is calculated as RP times Deployment, meaning x data will
# go up continually from 1. i.e. deployment 2 RP 5 will equal x data of 41
ctd_data_to_plot['dep_rosette_position'] = [(((x - 1) * max_rp) + ctd_data_to_plot['rosette_position_to_plot'][i])
for i, x in enumerate(ctd_data_to_plot['deployment'])]
time.sleep(0.2)
self.salinity_error_plot = salinityDifferencesPlot(ctd_data_to_plot['deployment'],
ctd_data_to_plot['dep_rosette_position'],
ctd_data_to_plot['bottle_sal'],
ctd_data_to_plot['primary_sal'],
ctd_data_to_plot['secondary_sal'],
ctd_data_to_plot['depths'],
max_rp,
reference_indexes,
self.salinity_data)
self.salinity_error_plot.proceed.clicked.connect(self.proceed_processing)