def __init__(self, page_url, key=None):
BackgroundTask.__init__(self, name="download video")
if key is None:
self.key = int(math.ceil(time.time() * 1000))
else:
self.key = int(key)
self.page_url = page_url
def __init__(self,
url,
filename,
progress_callback=lambda value: None,
block_size=1024 * 1024):
BackgroundTask.__init__(self, name="download:" + filename)
self.set_parent_progress = progress_callback
self.target_url = url
self.save_file = filename
self.block_size = block_size
def queryDatabaseImages(self, session_name):
'''
'''
username = self.ui.dbUsernameLineEdit.text()
password = self.ui.dbPasswordLineEdit.text()
#targetuser = self.ui.usernameLineEdit.text()
#targetpass = self.ui.passwordLineEdit.text()
prjhost = self.ui.projectHostnameLineEdit.text() if self.ui.projectHostnameLineEdit.text() != "" else self.ui.leginonHostnameLineEdit.text()
leginonDB = self.ui.leginonHostnameLineEdit.text()+'/'+self.ui.leginonDBNameLineEdit.text()
projectDB = prjhost+'/'+self.ui.projectDBNameLineEdit.text()
try:
session = leginondb.query_session_info(username, password, leginonDB, projectDB, session_name)#, alternteUser)
except:
_logger.exception("Error accessing images")
messagebox.exception_message(self, "Error accessing images")
self.ui.loginStackedWidget.setCurrentIndex(1)
else:
if len(session)==0:
_logger.error("Error accessing images")
return
self.taskFinished.connect(self.imageLoadFinished)
self.taskError.connect(self.imageLoadError)
self.task = BackgroundTask.launch_mp(self, load_images_iter, session)
self.ui.progressDialog.show()
self.ui.progressDialog.setValue(0)
def queryDatabaseImages(self, session_name):
'''
'''
username = self.ui.dbUsernameLineEdit.text()
password = self.ui.dbPasswordLineEdit.text()
#targetuser = self.ui.usernameLineEdit.text()
#targetpass = self.ui.passwordLineEdit.text()
prjhost = self.ui.projectHostnameLineEdit.text(
) if self.ui.projectHostnameLineEdit.text(
) != "" else self.ui.leginonHostnameLineEdit.text()
leginonDB = self.ui.leginonHostnameLineEdit.text(
) + '/' + self.ui.leginonDBNameLineEdit.text()
projectDB = prjhost + '/' + self.ui.projectDBNameLineEdit.text()
try:
session = leginondb.query_session_info(
username, password, leginonDB, projectDB,
session_name) #, alternteUser)
except:
_logger.exception("Error accessing images")
messagebox.exception_message(self, "Error accessing images")
self.ui.loginStackedWidget.setCurrentIndex(1)
else:
if len(session) == 0:
_logger.error("Error accessing images")
return
self.taskFinished.connect(self.imageLoadFinished)
self.taskError.connect(self.imageLoadError)
self.task = BackgroundTask.launch_mp(self, load_images_iter,
session)
self.ui.progressDialog.show()
self.ui.progressDialog.setValue(0)
def queryDatabaseForProjects(self, dummy=None):
'''
'''
targetuser = self.ui.usernameLineEdit.text()
targetpass = hashlib.md5(self.ui.passwordLineEdit.text()).hexdigest()
username = self.ui.dbUsernameLineEdit.text()
password = self.ui.dbPasswordLineEdit.text()
prjhost = self.ui.projectHostnameLineEdit.text(
) if self.ui.projectHostnameLineEdit.text(
) != "" else self.ui.leginonHostnameLineEdit.text()
leginonDB = self.ui.leginonHostnameLineEdit.text(
) + '/' + self.ui.leginonDBNameLineEdit.text()
projectDB = prjhost + '/' + self.ui.projectDBNameLineEdit.text()
limit = self.ui.entryLimitSpinBox.value()
if self.login.get('username', None) == username and \
self.login.get('leginonDB', None) == leginonDB and \
self.login.get('projectDB', None) == projectDB and \
self.login.get('password', None) == password and \
self.login.get('targetpass', None) == targetpass and \
self.login.get('targetuser', None) == targetuser and \
self.login.get('limit', None) == limit:
return
#alternteUser = self.ui.alternateUserLineEdit.text()
try:
user, experiments = leginondb.query_user_info(
username, password, leginonDB, projectDB, targetuser,
targetpass) #, alternteUser)
except leginondb.AuthenticationError:
messagebox.error_message(self, "Username or password incorrect!")
#self.ui.loginStackedWidget.setCurrentIndex(1)
self.startTabIndex = 1
except:
_logger.exception("Error accessing project")
messagebox.exception_message(self, "Error accessing project")
#self.ui.loginStackedWidget.setCurrentIndex(1)
self.startTabIndex = 1
else:
self.login['username'] = username
self.login['leginonDB'] = leginonDB
self.login['projectDB'] = projectDB
self.login['password'] = password
self.login['limit'] = limit
self.login['targetuser'] = targetuser
self.login['targetpass'] = targetpass
self.ui.progressDialog.show()
self.ui.label.setText("Welcome " + str(user.fullname))
self.taskFinished.connect(self.projectFinished)
self.taskError.connect(self.projectLoadError)
experiment_list = []
cnt = 0
for i in xrange(len(experiments)):
if len(experiments[i].session.exposures) == 0: continue
experiment_list.append(experiments[i])
cnt += 1
if cnt >= limit: break
self.task = BackgroundTask.launch_mp(self, load_projects_iter,
experiment_list)
def on_runPushButton_clicked(self, index=None):
'''
'''
if index is None:
extra = self.controlOptionValueDict()
else:
#model = self.ui.autopickHistoryTableView.model()
extra = dict([v for v in zip(self.options, index.data(QtCore.Qt.UserRole)[2:])])
#disk_mult, mask_mult, overlap_mult = index.data(QtCore.Qt.UserRole)[2:]
# Get list of micrographs
files = self.parent_control.currentFileList()
# Update parameters
if len(files) == 0:
return
self.micrograph_files = files
self.setEnabled(False)
'''
self.ui.diskDoubleSpinBox.setEnabled(False)
self.ui.maskDoubleSpinBox.setEnabled(False)
self.ui.overlapDoubleSpinBox.setEnabled(False)
self.ui.runPushButton.setEnabled(False)
'''
bin_factor = float(self.parent_control.micrographDecimationFactor())
output, base = os.path.split(self.output_base)
output+="-%.2f-%.2f-%.2f"%(extra['disk_mult'], extra['mask_mult'], extra['overlap_mult'])
output = output.replace(".", "_")
output = os.path.join(output, base)
self.autopick_program.update(dict(input_files=self.autopick_program.values.input_files.__class__(files),
#mask_mult=mask_mult,
#disk_mult=disk_mult,
#overlap_mult=overlap_mult,
bin_factor=bin_factor,
disable_bin=True,
selection_file="",
output=output,
**extra))
self.taskFinished.connect(self.programFinished)
self.taskError.connect(self.programError)
def _run_worker(prog):
yield 1
yield 0
_logger.info("Running "+str(prog.name()))
prog.check_options_validity()
prog.launch()
yield 1
self.output = output
self.task = BackgroundTask.launch_mp(self, _run_worker, self.autopick_program)
def queryDatabaseForProjects(self, dummy=None):
'''
'''
targetuser = self.ui.usernameLineEdit.text()
targetpass = hashlib.md5(self.ui.passwordLineEdit.text()).hexdigest()
username = self.ui.dbUsernameLineEdit.text()
password = self.ui.dbPasswordLineEdit.text()
prjhost = self.ui.projectHostnameLineEdit.text() if self.ui.projectHostnameLineEdit.text() != "" else self.ui.leginonHostnameLineEdit.text()
leginonDB = self.ui.leginonHostnameLineEdit.text()+'/'+self.ui.leginonDBNameLineEdit.text()
projectDB = prjhost+'/'+self.ui.projectDBNameLineEdit.text()
limit = self.ui.entryLimitSpinBox.value()
if self.login.get('username', None) == username and \
self.login.get('leginonDB', None) == leginonDB and \
self.login.get('projectDB', None) == projectDB and \
self.login.get('password', None) == password and \
self.login.get('targetpass', None) == targetpass and \
self.login.get('targetuser', None) == targetuser and \
self.login.get('limit', None) == limit: return
#alternteUser = self.ui.alternateUserLineEdit.text()
try:
user, experiments = leginondb.query_user_info(username, password, leginonDB, projectDB, targetuser, targetpass)#, alternteUser)
except leginondb.AuthenticationError:
messagebox.error_message(self, "Username or password incorrect!")
#self.ui.loginStackedWidget.setCurrentIndex(1)
self.startTabIndex=1
except:
_logger.exception("Error accessing project")
messagebox.exception_message(self, "Error accessing project")
#self.ui.loginStackedWidget.setCurrentIndex(1)
self.startTabIndex=1
else:
self.login['username']=username
self.login['leginonDB']=leginonDB
self.login['projectDB']=projectDB
self.login['password']=password
self.login['limit']=limit
self.login['targetuser']=targetuser
self.login['targetpass']=targetpass
self.ui.progressDialog.show()
self.ui.label.setText("Welcome "+str(user.fullname))
self.taskFinished.connect(self.projectFinished)
self.taskError.connect(self.projectLoadError)
experiment_list = []
cnt = 0
for i in xrange(len(experiments)):
if len(experiments[i].session.exposures) == 0: continue
experiment_list.append(experiments[i])
cnt += 1
if cnt >= limit: break
self.task = BackgroundTask.launch_mp(self, load_projects_iter, experiment_list)
def on_emdbDownloadPushButton_clicked(self):
'''Called when the user clicks the download button
'''
num = self.ui.emdbNumberLineEdit.text()
if num == "":
QtGui.QMessageBox.warning(self, "Warning",
"Empty Accession Number")
return
url = "ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-%s/map/emd_%s.map.gz" % (
num, num)
self.setEnabled(False)
if not os.path.exists('data/rawmap/'):
try:
os.makedirs('data/rawmap/')
except:
pass
self.task = BackgroundTask.launch(self, download_gunzip_task, url,
'data/rawmap/')
def on_runPushButton_clicked(self, index=None):
'''
'''
if index is None:
extra = self.controlOptionValueDict()
else:
#model = self.ui.autopickHistoryTableView.model()
extra = dict([
v for v in zip(self.options,
index.data(QtCore.Qt.UserRole)[2:])
])
#disk_mult, mask_mult, overlap_mult = index.data(QtCore.Qt.UserRole)[2:]
# Get list of micrographs
files = self.parent_control.currentFileList()
# Update parameters
if len(files) == 0:
return
self.micrograph_files = files
self.setEnabled(False)
'''
self.ui.diskDoubleSpinBox.setEnabled(False)
self.ui.maskDoubleSpinBox.setEnabled(False)
self.ui.overlapDoubleSpinBox.setEnabled(False)
self.ui.runPushButton.setEnabled(False)
'''
bin_factor = float(self.parent_control.micrographDecimationFactor())
output, base = os.path.split(self.output_base)
output += "-%.2f-%.2f-%.2f" % (extra['disk_mult'], extra['mask_mult'],
extra['overlap_mult'])
output = output.replace(".", "_")
output = os.path.join(output, base)
self.autopick_program.update(
dict(
input_files=self.autopick_program.values.input_files.__class__(
files),
#mask_mult=mask_mult,
#disk_mult=disk_mult,
#overlap_mult=overlap_mult,
bin_factor=bin_factor,
disable_bin=True,
selection_file="",
output=output,
**extra))
self.taskFinished.connect(self.programFinished)
self.taskError.connect(self.programError)
def _run_worker(prog):
yield 1
yield 0
_logger.info("Running " + str(prog.name()))
prog.check_options_validity()
prog.launch()
yield 1
self.output = output
self.task = BackgroundTask.launch_mp(self, _run_worker,
self.autopick_program)