def _connect_fired(self):
try:
connection = SerialManager(device=self.serial_device,
baudrate=self.baudrate,
sleep_after_connect=self.sleep_after_connect,
timeout=self.timeout)
connection.open()
print ArduinoApi(connection=connection).millis()
except Exception as e:
traceback.print_exc()
message(traceback.format_exc(), buttons=['OK'])
return
a = self.tree = ArduinoTree(connection=connection)
d = a.define.as_dict
s = [GuiDefine(name=k, value=str(v)) for k, v in d.items()]
s.sort(key=lambda x: x.name)
self.defines = s
self.digital_pins = [PinWrapper(pin=a.pin.get(x))
for x in a.pin.names_digital]
self.analog_pins = [PinWrapper(pin=a.pin.get(x))
for x in a.pin.names_analog]
self.pins = self.digital_pins + self.analog_pins
fw = a.firmware_info
self.arduino_version = fw.get('arduino_version')
self.firmware_build_time = str(fw.get('compile_datetime'))
self.avr_name = fw.get('avr_name')
self.gcc_version = fw.get('gcc_version')
self.libc_version = fw.get('libc_version')
self.libc_date = str(fw.get('libc_date'))
self.connected = True
def _info_button_fired(self):
"""Open dialog with description of statistics."""
if self.statistics_name in GLOBAL_STATS:
stat_func = GLOBAL_STATS[self.statistics_name]
else:
stat_func = PAIRWISE_STATS[self.statistics_name]
message(message = stat_func.__doc__, title='Statistics info')
def _info_button_fired(self):
"""Open dialog with description of statistics."""
if self.statistics_name in GLOBAL_STATS:
stat_func = GLOBAL_STATS[self.statistics_name]
else:
stat_func = PAIRWISE_STATS[self.statistics_name]
message(message=stat_func.__doc__, title='Statistics info')
def log(self, msg, alert=False):
"""Log a message to the console and, optionally, to terminal and/or pop-up dialog."""
_msg = msg.strip()
txt = "\n[{}]: {}\n".format(datetime.now(), _msg)
self._log += txt
if self.debug:
print(txt)
if alert:
message(_msg, "PyAMI Alert")
def _gcuts_fired(self):
sp = os.path.join(self.project_surface_directory,self.subject_id)
if os.path.exists(os.path.join(sp,'mri','brainmask.braincuts.mgz')):
message(message='gcuts has already been run for subject %s'%self.subject_id)
else:
if not os.path.isfile(os.path.join(sp,'mri','brainmask_backup_%s.mgz'%self.date)):
copy(os.path.join(sp,'mri','brainmask.mgz'),os.path.join(sp,'mri','brainmask_backup_%s.mgz'%self.date))
os.system('recon-all -skullstrip -clean-bm -gcut -subjid %s'%self.subject_id)
os.system('echo "gcuts was run on %s" >> %s' %(time.strftime("%Y_%b_%d_%H%M",time.localtime()),os.path.join(sp,'edit.log')))
def _check_for_subjects_surfaces_fired(self):
project_surface_directory=self.project_surface_directory
subject_id=self.subject_id
os.environ['SUBJECTS_DIR']=self.project_surface_directory
if os.path.isfile(os.path.join(project_surface_directory,subject_id,
'mri','aparc+aseg.mgz')):
self.subjects_existence=True
message(message='Subject %s was successfully found at %s.'%(subject_id,os.path.join(project_surface_directory,subject_id)),title='Subject successfully found', buttons=['OK'])
else:
self.subjects_existence=False
error(message='Subject %s was not found at %s. Please check your subject directory and subject id'%(subject_id,os.path.join(project_surface_directory,subject_id)), title='Subject not found', buttons=['OK'])
def _delete_fired(self):
assert self.measurement
res = message(
'Delete "%s" ?' % self.measurement, buttons=['OK', 'Cancel'])
if res:
# path
(self.project.result_dir / self.measurement).remove()
self.update_available_measurements()
def _delete_fired(self):
assert self.measurement
res = message('Delete "%s" ?' % self.measurement,
buttons=['OK', 'Cancel'])
if res:
# path
(self.project.result_dir / self.measurement).remove()
self.update_available_measurements()
def _delete_action(self):
# open dialog asking are you sure
msg = 'Remove selected result from database?'
result = message(message=msg,
title='Delete result from database',
buttons=['OK', 'Cancel'])
if result:
# remove from results_table
self.results_table.remove(self.current_selection)
self.current_selection = None
def _delete_action(self):
# open dialog asking are you sure
msg = 'Remove selected result from database?'
result = message(message=msg,
title='Delete result from database',
buttons = ['OK', 'Cancel'])
if result:
# remove from results_table
self.results_table.remove(self.current_selection)
self.current_selection = None
def _get_info_on_model_fired(self):
"""Open dialog with model description."""
model_class = self._model_name_to_class[self.model_name]
message(message = model_class.__doc__, title='Model info')
def _check_on_jobs_fired(self):
user=getuser()
recon_jobs=subprocess.check_output("qstat -u %s | grep 'recon'"%user,shell = True)
message(message='%s'%recon_jobs)
def _get_info_on_model_fired(self):
"""Open dialog with model description."""
model_class = self._model_name_to_class[self.model_name]
message(message=model_class.__doc__, title='Model info')
def _fire_event_fired():
message("Button clicked!")
def _fire_event_fired():
message("Button clicked!")
