def _connect(self):
self._check_host_url()
success = False
msg = 'Error on connecting to cluster control service on %s' % self._host_url
try:
client = RemotingService(self._host_url)
self.dlg = waitingProgressDialog('Please wait for the cluster...',
self)
self.dlg.setTarget(client.getService, 'clustercontrol')
self.dlg.exec_()
self._service = self.dlg.getTargetResult()
except:
exception(self, msg)
else:
try:
self.dlg.setTarget(self._service.get_cecog_versions)
self.dlg.exec_()
cluster_versions = self.dlg.getTargetResult()
except:
exception(self, msg)
else:
if not VERSION in set(cluster_versions):
warning(self, 'Cecog version %s not supported by the cluster' %
VERSION, 'Valid versions are: %s' \
% ', '.join(cluster_versions))
else:
success = True
return success
def _connect(self):
self._check_host_url()
success = False
msg = 'Error on connecting to cluster control service on %s' % self._host_url
try:
client = RemotingService(self._host_url)
self.dlg = waitingProgressDialog('Please wait for the cluster...', self)
self.dlg.setTarget(client.getService, 'clustercontrol')
self.dlg.exec_()
self._service = self.dlg.getTargetResult()
except:
exception(self, msg)
else:
try:
self.dlg.setTarget(self._service.get_cecog_versions)
self.dlg.exec_()
cluster_versions = self.dlg.getTargetResult()
except:
exception(self, msg)
else:
if not VERSION in set(cluster_versions):
warning(self, 'Cecog version %s not supported by the cluster' %
VERSION, 'Valid versions are: %s' \
% ', '.join(cluster_versions))
else:
success = True
return success
def _abort_processing(self):
self.setCursor(Qt.BusyCursor)
self._is_abort = True
self.dlg = waitingProgressDialog('Please wait until the processing has been terminated...', self)
self.dlg.setTarget(self._analyzer.abort, wait=True)
self.dlg.exec_()
self.setCursor(Qt.ArrowCursor)
def _abort_processing(self):
self.setCursor(Qt.BusyCursor)
self._is_abort = True
self.dlg = waitingProgressDialog(
'Please wait until the processing has been terminated...', self)
self.dlg.setTarget(self._analyzer.abort, wait=True)
self.dlg.exec_()
self.setCursor(Qt.ArrowCursor)
def _update_job_status(self):
try:
self.dlg = waitingProgressDialog('Please wait for the cluster update...', self)
self.dlg.setTarget(self._service.get_job_status, self._jobid)
self.dlg.exec_()
txt = self.dlg.getTargetResult()
except:
exception(self, 'Error on retrieve job status')
else:
self._label_jobstatus.setText(txt)
return txt
def _on_terminate_job(self):
try:
self.dlg = waitingProgressDialog("Please wait until the job has been terminated...", self)
self.dlg.setTarget(self._service.control_job, self._jobid, JOB_CONTROL_TERMINATE)
self.dlg.exec_()
except:
exception(self, 'Error on job termination')
else:
self._btn_toogle.setChecked(False)
self._toggle_state = JOB_CONTROL_SUSPEND
self._btn_toogle.setText(self._toggle_state)
self._update_job_status()
def _update_job_status(self):
try:
self.dlg = waitingProgressDialog(
'Please wait for the cluster update...', self)
self.dlg.setTarget(self._service.get_job_status, self._jobid)
self.dlg.exec_()
txt = self.dlg.getTargetResult()
except:
exception(self, 'Error on retrieve job status')
else:
self._label_jobstatus.setText(txt)
return txt
def _on_terminate_job(self):
try:
self.dlg = waitingProgressDialog(
"Please wait until the job has been terminated...", self)
self.dlg.setTarget(self._service.control_job, self._jobid,
JOB_CONTROL_TERMINATE)
self.dlg.exec_()
except:
exception(self, 'Error on job termination')
else:
self._btn_toogle.setChecked(False)
self._toggle_state = JOB_CONTROL_SUSPEND
self._btn_toogle.setText(self._toggle_state)
self._update_job_status()
def _on_toggle_job(self):
try:
self.dlg = waitingProgressDialog("Please wait until the job has been suspended/resumed...", self)
self.dlg.setTarget(self._service.control_job, self._jobid, self._toggle_state)
self.dlg.exec_()
except:
self._toggle_state = JOB_CONTROL_SUSPEND
self._btn_toogle.setChecked(False)
exception(self, 'Error on toggle job status')
else:
if self._toggle_state == JOB_CONTROL_SUSPEND:
self._toggle_state = JOB_CONTROL_RESUME
else:
self._toggle_state = JOB_CONTROL_SUSPEND
self._update_job_status()
self._btn_toogle.setText(self._toggle_state)
def _on_submit_job(self):
self._submit_settings.set_section(SECTION_NAME_GENERAL)
if not self._submit_settings.get2('constrain_positions'):
positions = []
for plate_id in self.imagecontainer.plates:
self.imagecontainer.set_plate(plate_id)
meta_data = self.imagecontainer.get_meta_data()
positions += [
'%s___%s' % (plate_id, p) for p in meta_data.positions
]
self._submit_settings.set2('positions', ','.join(positions))
nr_items = len(positions)
else:
positions = self._submit_settings.get2('positions')
nr_items = len(positions.split(','))
# FIXME: we need to get the current value for 'position_granularity'
settings_dummy = ProcessingFrame.get_special_settings(self._settings)
position_granularity = settings_dummy.get(SECTION_NAME_CLUSTER,
'position_granularity')
path_out = self._submit_settings.get2('pathout')
emails = str(self._txt_mail.text()).split(',')
try:
self.dlg = waitingProgressDialog(
'Please wait until the job has been submitted...', self)
self.dlg.setTarget(self._service.submit_job, 'cecog_batch',
self._submit_settings.to_string(), path_out,
emails, nr_items, position_granularity, VERSION)
self.dlg.exec_()
jobid = self.dlg.getTargetResult()
except:
exception(self, 'Error on job submission')
else:
# FIXME: no idea how DRMAA 1.0 compatible this is
if type(jobid) == types.ListType:
self._jobid = ','.join(jobid)
main_jobid = jobid[0].split('.')[0]
else:
self._jobid = str(jobid)
main_jobid = jobid
self._txt_jobid.setText(self._jobid)
self._update_job_status()
information(
self, 'Job submitted successfully',
"Job successfully submitted to the cluster.\nJob ID: %s, items: %d"
% (main_jobid, nr_items))
def _on_submit_job(self):
self._submit_settings.set_section(SECTION_NAME_GENERAL)
if not self._submit_settings.get2('constrain_positions'):
# FIXME:
imagecontainer = qApp._main_window._imagecontainer
positions = []
for plate_id in imagecontainer.plates:
imagecontainer.set_plate(plate_id)
meta_data = imagecontainer.get_meta_data()
positions += ['%s___%s' % (plate_id, p) for p in meta_data.positions]
self._submit_settings.set2('positions', ','.join(positions))
nr_items = len(positions)
else:
positions = self._submit_settings.get2('positions')
nr_items = len(positions.split(','))
# FIXME: we need to get the current value for 'position_granularity'
settings_dummy = ProcessingFrame.get_special_settings(self._settings)
position_granularity = settings_dummy.get(SECTION_NAME_CLUSTER, 'position_granularity')
path_out = self._submit_settings.get2('pathout')
emails = str(self._txt_mail.text()).split(',')
try:
self.dlg = waitingProgressDialog('Please wait until the job has been submitted...', self)
self.dlg.setTarget(self._service.submit_job,
'cecog_batch', self._submit_settings.to_string(), path_out, emails, nr_items,
position_granularity, VERSION)
self.dlg.exec_()
jobid = self.dlg.getTargetResult()
except:
exception(self, 'Error on job submission')
else:
# FIXME: no idea how DRMAA 1.0 compatible this is
if type(jobid) == types.ListType:
self._jobid = ','.join(jobid)
main_jobid = jobid[0].split('.')[0]
else:
self._jobid = str(jobid)
main_jobid = jobid
self._txt_jobid.setText(self._jobid)
self._update_job_status()
information(self, 'Job submitted successfully',
"Job successfully submitted to the cluster.\nJob ID: %s, items: %d" % (main_jobid, nr_items))
def _on_toggle_job(self):
try:
self.dlg = waitingProgressDialog(
"Please wait until the job has been suspended/resumed...",
self)
self.dlg.setTarget(self._service.control_job, self._jobid,
self._toggle_state)
self.dlg.exec_()
except:
self._toggle_state = JOB_CONTROL_SUSPEND
self._btn_toogle.setChecked(False)
exception(self, 'Error on toggle job status')
else:
if self._toggle_state == JOB_CONTROL_SUSPEND:
self._toggle_state = JOB_CONTROL_RESUME
else:
self._toggle_state = JOB_CONTROL_SUSPEND
self._update_job_status()
self._btn_toogle.setText(self._toggle_state)
def _set_plate(self, coordinate_new, set_current=False):
coordinate_old = self.browser.get_coordinate()
plate = coordinate_new.plate
self.dlg = waitingProgressDialog(\
"Please wait until the plate has been loaded...", self)
self.dlg.setTarget(self._imagecontainer.set_plate, plate)
self.dlg.exec_()
meta_data = self._imagecontainer.get_meta_data()
if set_current:
self._set_current_plate(plate)
self._update_position_table(meta_data)
self._get_closeby_position(coordinate_old, coordinate_new)
self._set_current_position(coordinate_new.position)
if self._imagecontainer.has_timelapse:
self._update_time_table(meta_data, coordinate_new)
self._get_closeby_time(coordinate_old, coordinate_new)
self._set_current_time(coordinate_new.time)
self._update_info_frame(meta_data)
self.coordinate_changed.emit(coordinate_new)
def _set_plate(self, coordinate_new, set_current=False):
coordinate_old = self.browser.get_coordinate()
plate = coordinate_new.plate
self.dlg = waitingProgressDialog(\
"Please wait until the plate has been loaded...", self)
self.dlg.setTarget(self._imagecontainer.set_plate, plate)
self.dlg.exec_()
meta_data = self._imagecontainer.get_meta_data()
if set_current:
self._set_current_plate(plate)
self._update_position_table(meta_data)
self._get_closeby_position(coordinate_old, coordinate_new)
self._set_current_position(coordinate_new.position)
if self._imagecontainer.has_timelapse:
self._update_time_table(meta_data, coordinate_new)
self._get_closeby_time(coordinate_old, coordinate_new)
self._set_current_time(coordinate_new.time)
self._update_info_frame(meta_data)
self.coordinate_changed.emit(coordinate_new)
def _load_image_container(self, plate_infos, scan_plates=None, show_dlg=True):
self._clear_browser()
imagecontainer = ImageContainer()
self._imagecontainer = imagecontainer
if scan_plates is None:
scan_plates = dict((info[0], False) for info in plate_infos)
def load(dlg):
iter = imagecontainer.iter_import_from_settings(self._settings, scan_plates)
for idx, info in enumerate(iter):
dlg.targetSetValue.emit(idx + 1)
if len(imagecontainer.plates) > 0:
plate = imagecontainer.plates[0]
imagecontainer.set_plate(plate)
self.dlg = waitingProgressDialog('Please wait until the input structure is scanned\n'
'or the structure data loaded...', self, load, (0, len(scan_plates)))
self.dlg.exec_(passDialog=True)
if len(imagecontainer.plates) > 0:
imagecontainer.check_dimensions()
channels = imagecontainer.channels
# do not report value changes to the main window
self._settings.set_notify_change(False)
self.set_image_crop_size()
problems = []
for prefix in ['primary', 'secondary', 'tertiary']:
trait = self._settings.get_trait(SECTION_NAME_OBJECTDETECTION,
'%s_channelid' % prefix)
if trait.set_list_data(channels) is None:
problems.append(prefix)
self._tabs[1].get_widget('%s_channelid' % prefix).update()
# report problems about a mismatch between channel IDs found in the data and specified by the user
if len(problems) > 0:
critical(self, "Selected channel IDs not valid",
"The selected channel IDs for %s are not valid.\nValid IDs are %s." %
(", ".join(["'%s Channel'" % s.capitalize() for s in problems]),
", ".join(["'%s'" % s for s in channels])))
# a mismatch between settings and data will cause changed settings
self.settings_changed(True)
trait = self._settings.get_trait(SECTION_NAME_TRACKING,
'tracking_duration_unit')
# allow time-base tracking durations only if time-stamp
# information is present
meta_data = imagecontainer.get_meta_data()
if meta_data.has_timestamp_info:
result = trait.set_list_data(TRACKING_DURATION_UNITS_TIMELAPSE)
else:
result = trait.set_list_data(TRACKING_DURATION_UNITS_DEFAULT)
if result is None:
critical(self, "Could not set tracking duration units",
"The tracking duration units selected to match the load data. Please check your settings.")
# a mismatch between settings and data will cause changed settings
self.settings_changed(True)
# activate change notification again
self._settings.set_notify_change(True)
self.set_modules_active(state=True)
if show_dlg:
information(self, "Plate(s) successfully loaded",
"%d plates loaded successfully." % len(imagecontainer.plates))
else:
critical(self, "No valid image data found",
"The naming schema provided might not fit your image data"
"or the coordinate file is not correct.\n\nPlease modify "
"the values and scan the structure again.")