def _start_tracking(self, camera, result_writer, rois, M, TrackerClass,
tracker_kwargs, hardware_connection, StimulatorClass,
stimulator_kwargs):
#Here the stimulator passes args. Hardware connection was previously open as thread.
stimulators = [
StimulatorClass(hardware_connection, **stimulator_kwargs)
for _ in rois
]
kwargs = self._monit_kwargs.copy()
kwargs.update(tracker_kwargs)
# todo: pickle hardware connection, camera, rois, tracker class, stimulator class,.
# then rerun stimulators and Monitor(......)
self._monit = Monitor(camera,
TrackerClass,
rois,
stimulators=stimulators,
*self._monit_args,
**self._monit_kwargs)
self._info["status"] = "running"
logging.info("Setting monitor status as running: '%s'" %
self._info["status"])
quality_controller = QualityControl(result_writer)
self._monit.run(result_writer, self._drawer, quality_controller, M)
def test_stimulator(StimulatorClass,
InterfaceClass,
remove_db_file=True,
*args,
**kwargs):
tmp = tempfile.mkstemp(suffix="_ethoscope_test.db")[1]
print("Making a tmp db: " + tmp)
cam = MovieVirtualCamera(VIDEO, drop_each=15)
rb = SleepMonitorWithTargetROIBuilder()
rois = rb.build(cam)
cam.restart()
connection = HardwareConnection(InterfaceClass)
try:
# stimulators = [MockSDStimulator(connection,min_inactive_time= 10) for _ in rois ]
stimulators = [
StimulatorClass(connection, *args, **kwargs) for _ in rois
]
mon = Monitor(cam, AdaptiveBGModel, rois, stimulators=stimulators)
drawer = DefaultDrawer(draw_frames=DRAW_FRAMES)
with SQLiteResultWriter(tmp, rois) as rw:
mon.run(result_writer=rw, drawer=drawer)
# cred = {"name": "ethoscope_db",
# "user": "******",
# "password": "******"}
# with ResultWriter( cred , rois) as rw:
# mon.run(result_writer=rw, drawer=drawer)
finally:
if remove_db_file:
print("Removing temp db (" + tmp + ")")
os.remove(tmp)
else:
print("db file lives in (" + tmp + ")")
connection.stop()
def test_API(self):
random.seed(1)
cam = MovieVirtualCamera(VIDEO)
rb = SleepMonitorWithTargetROIBuilder()
rois = rb.build(cam)
hc = HardwareConnection(MockInterface)
stimulators = [MockStimulator(hc) for _ in rois]
cam.restart()
mon = Monitor(cam, AdaptiveBGModel, rois, stimulators)
drawer = DefaultDrawer(draw_frames=DRAW_FRAMES)
tmp = tempfile.mkstemp(suffix="_ethoscope_test.db")[1]
try:
print("Making a tmp db: " + tmp)
with SQLiteResultWriter(tmp, rois) as rw:
mon.run(result_writer=rw, drawer=drawer)
except:
self.fail("testAPI raised ExceptionType unexpectedly!")
finally:
hc.stop()
cam._close()
print("Removing temp db (" + tmp + ")")
os.remove(tmp)
class ControlThread(Thread):
"""
The versatile control thread
From this thread, the PI passes option to the node.
Note: Options are passed and shown only if the remote class contains a "_description" field!
"""
_evanescent = False
_option_dict = {
"roi_builder": {
"possible_classes": [
FSLSleepMonitorWithTargetROIBuilder,
SleepMonitorWithTargetROIBuilder, HighContrastTargetROIBuilder,
ManualROIBuilder, DefaultROIBuilder, TargetGridROIBuilder,
OlfactionAssayROIBuilder, ElectricShockAssayROIBuilder
],
},
"tracker": {
"possible_classes": [AdaptiveBGModel, RichAdaptiveBGModel],
},
"interactor": {
"possible_classes": [
DefaultStimulator,
SleepDepStimulator,
OptomotorSleepDepriver,
GearOptomotorSleepDepriver,
RobustSleepDepriver,
MiddleCrossingStimulator,
#SystematicSleepDepInteractor,
ExperimentalSleepDepStimulator,
#GearMotorSleepDepStimulator,
#DynamicOdourDeliverer,
DynamicOdourSleepDepriver,
OptoMidlineCrossStimulator,
MotoMidlineCrossStimulator,
RobustMotoMidlineCrossStimulator,
OptomotorSleepDepriverSystematic,
MiddleCrossingOdourStimulator,
MiddleCrossingOdourStimulatorFlushed,
SegmentedStimulator
],
},
"drawer": {
"possible_classes": [DefaultDrawer, NullDrawer],
},
"camera": {
"possible_classes": [
FSLPiCameraAsync, OurPiCameraAsync, MovieVirtualCamera,
DummyPiCameraAsync, V4L2Camera, FSLVirtualCamera
],
},
"result_writer": {
"possible_classes":
[ResultWriter, DebugResultWriter, SQLiteResultWriter],
},
"experimental_info": {
"possible_classes": [ExperimentalInformation],
}
}
#some classes do not need to be offered as choices to the user in normal conditions
#these are shown only if the machine is not a PI
_is_a_rPi = isMachinePI() and hasPiCamera() and not isExperimental()
_hidden_options = {} #{'result_writer'}
for k in _option_dict:
_option_dict[k]["class"] = _option_dict[k]["possible_classes"][0]
_option_dict[k]["kwargs"] = {}
_tmp_last_img_file = "last_img.jpg"
_dbg_img_file = "dbg_img.png"
_log_file = "ethoscope.log"
#give the database an ethoscope specific name
#future proof in case we want to use a remote server
_db_credentials = {
"name": "%s_db" % get_machine_name(),
"user": "******",
"password": "******"
}
_default_monitor_info = {
#fixme, not needed
"last_positions": None,
"last_time_stamp": 0,
"fps": 0
}
_persistent_state_file = "/var/cache/ethoscope/persistent_state.pkl"
def __init__(self,
machine_id,
name,
version,
ethoscope_dir,
data=None,
*args,
**kwargs):
self._monit_args = args
self._monit_kwargs = kwargs
self._metadata = None
# for FPS computation
self._last_info_t_stamp = 0
self._last_info_frame_idx = 0
# We wipe off previous logs and debug images
try:
os.remove(os.path.join(ethoscope_dir, self._log_file))
except OSError:
pass
try:
os.remove(os.path.join(ethoscope_dir, self._dbg_img_file))
except OSError:
pass
try:
os.makedirs(ethoscope_dir)
except OSError:
pass
self._tmp_dir = tempfile.mkdtemp(prefix="ethoscope_")
#todo add 'data' -> how monitor was started to metadata
self._info = {
"status": "stopped",
"time": time.time(),
"error": None,
"log_file": os.path.join(ethoscope_dir, self._log_file),
"dbg_img": os.path.join(ethoscope_dir, self._dbg_img_file),
"last_drawn_img": os.path.join(self._tmp_dir,
self._tmp_last_img_file),
"id": machine_id,
"name": name,
"version": version,
"db_name": self._db_credentials["name"],
"monitor_info": self._default_monitor_info,
#"user_options": self._get_user_options(),
"experimental_info": {}
}
self._monit = None
self._parse_user_options(data)
DrawerClass = self._option_dict["drawer"]["class"]
drawer_kwargs = self._option_dict["drawer"]["kwargs"]
self._drawer = DrawerClass(**drawer_kwargs)
super(ControlThread, self).__init__()
@property
def info(self):
self._update_info()
return self._info
@property
def was_interrupted(self):
return os.path.exists(self._persistent_state_file)
@classmethod
def user_options(self):
out = {}
for key, value in list(self._option_dict.items()):
# check if the options for the remote class will be visible
# they will be visible only if they have a description, and if we are on a PC or they are not hidden
if (self._is_a_rPi
and key not in self._hidden_options) or not self._is_a_rPi:
out[key] = []
for p in value["possible_classes"]:
try:
d = p.__dict__["_description"]
except KeyError:
continue
d["name"] = p.__name__
out[key].append(d)
out_curated = {}
for key, value in list(out.items()):
if len(value) > 0:
out_curated[key] = value
return out_curated
def _parse_one_user_option(self, field, data):
logging.warning(field)
logging.warning(data)
try:
subdata = data[field]
except KeyError:
logging.warning("No field %s, using default" % field)
return None, (), {}
Class = eval(subdata["name"])
try:
args = subdata["args"]
except KeyError:
args = ()
try:
kwargs = subdata["kwargs"]
except KeyError:
try:
kwargs = subdata["arguments"]
except KeyError:
kwargs = {}
logging.warning("Parsing %s", Class)
logging.warning("args:")
logging.warning(args)
logging.warning("kwargs:")
logging.warning(kwargs)
logging.warning("subdata")
logging.warning(subdata)
return Class, args, kwargs
def _parse_user_options(self, data):
if data is None:
return
#FIXME DEBUG
logging.warning("Starting control thread with data:")
logging.warning(str(data))
for key in list(self._option_dict.keys()):
x = self._parse_one_user_option(key, data)
if len(x) == 3:
Class, args, kwargs = x
else:
Class, args = x
kwargs = {}
# when no field is present in the JSON config, we get the default class
if Class is None:
self._option_dict[key]["class"] = self._option_dict[key][
"possible_classes"][0]
self._option_dict[key]["args"] = ()
self._option_dict[key]["kwargs"] = {}
continue
self._option_dict[key]["class"] = Class
self._option_dict[key]["args"] = args
self._option_dict[key]["kwargs"] = kwargs
def _update_info(self):
if self._monit is None:
return
t = self._monit.last_time_stamp
frame_idx = self._monit.last_frame_idx
wall_time = time.time()
dt = wall_time - self._last_info_t_stamp
df = float(frame_idx - self._last_info_frame_idx)
if self._last_info_t_stamp == 0 or dt > 0:
f = round(df / dt, 2)
else:
f = "NaN"
if t is not None: # and p is not None:
self._info["monitor_info"] = {
# "last_positions":pos,
"last_time_stamp": t,
"fps": f
}
frame = self._drawer.last_drawn_frame
if frame is not None:
tempdir = os.path.dirname(self._info["last_drawn_img"])
os.makedirs(tempdir, exist_ok=True)
cv2.imwrite(self._info["last_drawn_img"], frame,
[int(cv2.IMWRITE_JPEG_QUALITY), 50])
self._last_info_t_stamp = wall_time
self._last_info_frame_idx = frame_idx
def _start_tracking(self, camera, result_writer, rois, M, TrackerClass,
tracker_kwargs, hardware_connection, StimulatorClass,
stimulator_kwargs):
#Here the stimulator passes args. Hardware connection was previously open as thread.
stimulators = [
StimulatorClass(hardware_connection, **stimulator_kwargs)
for _ in rois
]
kwargs = self._monit_kwargs.copy()
kwargs.update(tracker_kwargs)
# todo: pickle hardware connection, camera, rois, tracker class, stimulator class,.
# then rerun stimulators and Monitor(......)
self._monit = Monitor(camera,
TrackerClass,
rois,
stimulators=stimulators,
*self._monit_args,
**self._monit_kwargs)
self._info["status"] = "running"
logging.info("Setting monitor status as running: '%s'" %
self._info["status"])
quality_controller = QualityControl(result_writer)
self._monit.run(result_writer, self._drawer, quality_controller, M)
def _has_pickle_file(self):
"""
"""
return os.path.exists(self._persistent_state_file)
def _set_tracking_from_pickled(self):
"""
"""
with open(self._persistent_state_file, "rb") as f:
time.sleep(15)
return pickle.load(f)
def _save_pickled_state(self, camera, result_writer, rois, M, TrackerClass,
tracker_kwargs, hardware_connection,
StimulatorClass, stimulator_kwargs, running_info):
"""
note that cv2.videocapture is not a serializable object and cannot be pickled
"""
tpl = (camera, result_writer, rois, M, TrackerClass, tracker_kwargs,
hardware_connection, StimulatorClass, stimulator_kwargs,
running_info)
if not os.path.exists(os.path.dirname(self._persistent_state_file)):
logging.warning("No cache dir detected. making one")
os.makedirs(os.path.dirname(self._persistent_state_file))
with open(self._persistent_state_file, "wb") as f:
return pickle.dump(tpl, f)
def _set_tracking_from_scratch(self):
"""
"""
CameraClass = self._option_dict["camera"]["class"]
camera_args = self._option_dict["camera"]["args"]
camera_kwargs = self._option_dict["camera"]["kwargs"]
ROIBuilderClass = self._option_dict["roi_builder"]["class"]
roi_builder_kwargs = self._option_dict["roi_builder"]["kwargs"]
StimulatorClass = self._option_dict["interactor"]["class"]
stimulator_kwargs = self._option_dict["interactor"]["kwargs"]
logging.warning(StimulatorClass)
logging.warning(StimulatorClass.__dict__)
HardWareInterfaceClass = StimulatorClass.__dict__[
"_HardwareInterfaceClass"]
TrackerClass = self._option_dict["tracker"]["class"]
tracker_kwargs = self._option_dict["tracker"]["kwargs"]
ResultWriterClass = self._option_dict["result_writer"]["class"]
result_writer_kwargs = self._option_dict["result_writer"]["kwargs"]
print("camera_args")
print(camera_args)
print("camera_kwargs")
print(camera_kwargs)
cam = CameraClass(*camera_args, **camera_kwargs)
if isinstance(cam, OurPiCameraAsync):
for i, (t, frame) in cam:
cv2.imwrite(os.path.join(os.environ["HOME"], 'last_img.png'),
frame)
break
logging.info(ROIBuilderClass)
logging.info(roi_builder_kwargs)
roi_builder = ROIBuilderClass(args=(), kwargs=roi_builder_kwargs)
try:
if roi_builder.__class__.__name__ == "HighContrastTargetROIBuilder":
img, M, rois = roi_builder.build(cam)
else:
rois = roi_builder.build(cam)
M = None
except EthoscopeException as e:
cam._close()
raise e
logging.info(f"PID {os.getpid()}: Initialising monitor")
cam.restart()
# the camera start time is the reference 0
ExpInfoClass = self._option_dict["experimental_info"]["class"]
exp_info_kwargs = self._option_dict["experimental_info"]["kwargs"]
self._info["experimental_info"] = ExpInfoClass(
**exp_info_kwargs).info_dic
self._info["time"] = cam.start_time
#here the hardwareconnection call the interface class without passing any argument!
hardware_connection = HardwareConnection(HardWareInterfaceClass)
#creates a unique tracking id to label this tracking run
self._info["experimental_info"]["run_id"] = secrets.token_hex(8)
if self._info["experimental_info"]["sensor"]:
#if is URL:
sensor = EthoscopeSensor(self._info["experimental_info"]["sensor"])
logging.info("Using sensor with URL %s" %
self._info["experimental_info"]["sensor"])
else:
sensor = None
logging.info("Generating metadata of this run")
logging.info(self._info)
self._metadata = {
"machine_id": self._info["id"],
"machine_name": self._info["name"],
"date_time":
cam.start_time, # the camera start time is the reference 0
"frame_width": cam.width,
"frame_height": cam.height,
"version": self._info["version"]["id"],
"experimental_info": str(self._info["experimental_info"]),
"selected_options": str(self._option_dict),
}
logging.warning("Detected camera start time is %d", cam.start_time)
# hardware_interface is a running thread
rw = ResultWriterClass(self._db_credentials,
rois,
metadata=self._metadata,
sensor=sensor,
**result_writer_kwargs)
return (cam, rw, rois, M, TrackerClass, tracker_kwargs,
hardware_connection, StimulatorClass, stimulator_kwargs)
def run(self):
cam = None
hardware_connection = None
try:
self._info["status"] = "initialising"
logging.info("Starting Monitor thread")
self._info["error"] = None
self._last_info_t_stamp = 0
self._last_info_frame_idx = 0
if self._has_pickle_file():
try:
cam, rw, rois, M, TrackerClass, tracker_kwargs, hardware_connection, StimulatorClass, stimulator_kwargs, self._info = self._set_tracking_from_pickled(
)
except Exception as e:
logging.error(
"Could not load previous state for unexpected reason:")
raise e
else:
cam, rw, rois, M, TrackerClass, tracker_kwargs, hardware_connection, StimulatorClass, stimulator_kwargs = self._set_tracking_from_scratch(
)
# return (cam, rw, rois, M, TrackerClass, tracker_kwargs,
# hardware_connection, StimulatorClass, stimulator_kwargs)
with rw as result_writer:
if cam.canbepickled:
self._save_pickled_state(cam, rw, rois, M, TrackerClass,
tracker_kwargs,
hardware_connection,
StimulatorClass,
stimulator_kwargs, self._info)
if M is not None:
logging.info(type(M))
logging.info(M.shape)
else:
logging.info('M is None!')
self._start_tracking(cam, result_writer, rois, M, TrackerClass,
tracker_kwargs, hardware_connection,
StimulatorClass, stimulator_kwargs)
self.stop()
except EthoscopeException as e:
if e.img is not None:
cv2.imwrite(self._info["dbg_img"], e.img)
self.stop(traceback.format_exc())
except Exception as e:
self.stop(traceback.format_exc())
finally:
try:
os.remove(self._persistent_state_file)
except:
logging.warning("Failed to remove persistent file")
try:
if cam is not None:
cam._close()
except:
logging.warning("Could not close camera properly")
pass
try:
if hardware_connection is not None:
hardware_connection.stop()
except:
logging.warning("Could not close hardware connection properly")
pass
#for testing purposes
if self._evanescent:
del self._drawer
self.stop()
os._exit(0)
def stop(self, error=None):
self._info["status"] = "stopping"
self._info["time"] = time.time()
# we reset all the user data of the latest experiment except the run_id
# a new run_id will be created when we start another experiment
if "experimental_info" in self._info and "run_id" in self._info[
"experimental_info"]:
self._info["experimental_info"] = {
"run_id": self._info["experimental_info"]["run_id"]
}
logging.info("Stopping monitor")
if not self._monit is None:
self._monit.stop()
self._monit = None
self._info["status"] = "stopped"
self._info["time"] = time.time()
self._info["error"] = error
self._info["monitor_info"] = self._default_monitor_info
if error is not None:
logging.error("Monitor closed with an error:")
logging.error(error)
else:
logging.info("Monitor closed all right")
def __del__(self):
self.stop()
shutil.rmtree(self._tmp_dir, ignore_errors=True)
shutil.rmtree(self._persistent_state_file, ignore_errors=True)
def set_evanescent(self, value=True):
self._evanescent = value
class ControlThread(Thread):
"""
The versatile control thread
From this thread, the PI passes option to the node.
Note: Options are passed and shown only if the remote class contains a "_description" field!
"""
_evanescent = False
_option_dict = {
"roi_builder": {
"possible_classes": [
DefaultROIBuilder, SleepMonitorWithTargetROIBuilder,
TargetGridROIBuilder, OlfactionAssayROIBuilder,
ElectricShockAssayROIBuilder
],
},
"tracker": {
"possible_classes": [AdaptiveBGModel],
},
"interactor": {
"possible_classes": [
DefaultStimulator,
SleepDepStimulator,
OptomotorSleepDepriver,
MiddleCrossingStimulator,
#SystematicSleepDepInteractor,
ExperimentalSleepDepStimulator,
#GearMotorSleepDepStimulator,
#DynamicOdourDeliverer,
DynamicOdourSleepDepriver,
OptoMidlineCrossStimulator,
OptomotorSleepDepriverSystematic,
MiddleCrossingOdourStimulator,
MiddleCrossingOdourStimulatorFlushed
],
},
"drawer": {
"possible_classes": [DefaultDrawer, NullDrawer],
},
"camera": {
"possible_classes": [
OurPiCameraAsync, MovieVirtualCamera, DummyPiCameraAsync,
V4L2Camera
],
},
"result_writer": {
"possible_classes": [ResultWriter, SQLiteResultWriter],
},
"experimental_info": {
"possible_classes": [ExperimentalInformations],
}
}
#some classes do not need to be offered as choices to the user in normal conditions
#these are shown only if the machine is not a PI
_is_a_rPi = isMachinePI() and hasPiCamera() and not isExperimental()
_hidden_options = {'camera', 'result_writer'}
for k in _option_dict:
_option_dict[k]["class"] = _option_dict[k]["possible_classes"][0]
_option_dict[k]["kwargs"] = {}
_tmp_last_img_file = "last_img.jpg"
_dbg_img_file = "dbg_img.png"
_log_file = "ethoscope.log"
_db_credentials = {
"name": "ethoscope_db",
"user": "******",
"password": "******"
}
_default_monitor_info = {
#fixme, not needed
"last_positions": None,
"last_time_stamp": 0,
"fps": 0
}
_persistent_state_file = "/var/cache/ethoscope/persistent_state.pkl"
def __init__(self,
machine_id,
name,
version,
ethoscope_dir,
data=None,
*args,
**kwargs):
self._monit_args = args
self._monit_kwargs = kwargs
self._metadata = None
# for FPS computation
self._last_info_t_stamp = 0
self._last_info_frame_idx = 0
# We wipe off previous data
# DOES THIS MAKE SENSE? WE LOST LOTS OF DATA DOING THIS in THE PAST!! [TODO]
try:
os.remove(os.path.join(ethoscope_dir, self._log_file))
except OSError:
pass
try:
os.remove(os.path.join(ethoscope_dir, self._dbg_img_file))
except OSError:
pass
try:
os.makedirs(ethoscope_dir)
except OSError:
pass
self._tmp_dir = tempfile.mkdtemp(prefix="ethoscope_")
#todo add 'data' -> how monitor was started to metadata
self._info = {
"status": "stopped",
"time": time.time(),
"error": None,
"log_file": os.path.join(ethoscope_dir, self._log_file),
"dbg_img": os.path.join(ethoscope_dir, self._dbg_img_file),
"last_drawn_img": os.path.join(self._tmp_dir,
self._tmp_last_img_file),
"id": machine_id,
"name": name,
"version": version,
"db_name": self._db_credentials["name"],
"monitor_info": self._default_monitor_info,
#"user_options": self._get_user_options(),
"experimental_info": {}
}
self._monit = None
self._parse_user_options(data)
DrawerClass = self._option_dict["drawer"]["class"]
drawer_kwargs = self._option_dict["drawer"]["kwargs"]
self._drawer = DrawerClass(**drawer_kwargs)
super(ControlThread, self).__init__()
@property
def info(self):
self._update_info()
return self._info
@property
def was_interrupted(self):
return os.path.exists(self._persistent_state_file)
@classmethod
def user_options(self):
out = {}
for key, value in list(self._option_dict.items()):
# check if the options for the remote class will be visible
# they will be visible only if they have a description, and if we are on a PC or they are not hidden
if (self._is_a_rPi
and key not in self._hidden_options) or not self._is_a_rPi:
out[key] = []
for p in value["possible_classes"]:
try:
d = p.__dict__["_description"]
except KeyError:
continue
d["name"] = p.__name__
out[key].append(d)
out_curated = {}
for key, value in list(out.items()):
if len(value) > 0:
out_curated[key] = value
return out_curated
def _parse_one_user_option(self, field, data):
try:
subdata = data[field]
except KeyError:
logging.warning("No field %s, using default" % field)
return None, {}
Class = eval(subdata["name"])
kwargs = subdata["arguments"]
return Class, kwargs
def _parse_user_options(self, data):
if data is None:
return
#FIXME DEBUG
logging.warning("Starting control thread with data:")
logging.warning(str(data))
for key in list(self._option_dict.keys()):
Class, kwargs = self._parse_one_user_option(key, data)
# when no field is present in the JSON config, we get the default class
if Class is None:
self._option_dict[key]["class"] = self._option_dict[key][
"possible_classes"][0]
self._option_dict[key]["kwargs"] = {}
continue
self._option_dict[key]["class"] = Class
self._option_dict[key]["kwargs"] = kwargs
def _update_info(self):
if self._monit is None:
return
t = self._monit.last_time_stamp
frame_idx = self._monit.last_frame_idx
wall_time = time.time()
dt = wall_time - self._last_info_t_stamp
df = float(frame_idx - self._last_info_frame_idx)
if self._last_info_t_stamp == 0 or dt > 0:
f = round(df / dt, 2)
else:
f = "NaN"
if t is not None: # and p is not None:
self._info["monitor_info"] = {
# "last_positions":pos,
"last_time_stamp": t,
"fps": f
}
frame = self._drawer.last_drawn_frame
if frame is not None:
cv2.imwrite(self._info["last_drawn_img"], frame,
[int(cv2.IMWRITE_JPEG_QUALITY), 50])
self._last_info_t_stamp = wall_time
self._last_info_frame_idx = frame_idx
def _start_tracking(self, camera, result_writer, rois, TrackerClass,
tracker_kwargs, hardware_connection, StimulatorClass,
stimulator_kwargs):
#Here the stimulator passes args. Hardware connection was previously open as thread.
stimulators = [
StimulatorClass(hardware_connection, **stimulator_kwargs)
for _ in rois
]
kwargs = self._monit_kwargs.copy()
kwargs.update(tracker_kwargs)
# todo: pickle hardware connection, camera, rois, tracker class, stimulator class,.
# then rerun stimulators and Monitor(......)
self._monit = Monitor(camera,
TrackerClass,
rois,
stimulators=stimulators,
*self._monit_args)
self._info["status"] = "running"
logging.info("Setting monitor status as running: '%s'" %
self._info["status"])
self._monit.run(result_writer, self._drawer)
def _set_tracking_from_pickled(self):
"""
"""
with open(self._persistent_state_file, "rb") as f:
time.sleep(15)
return pickle.load(f)
def _save_pickled_state(self, camera, result_writer, rois, TrackerClass,
tracker_kwargs, hardware_connection,
StimulatorClass, stimulator_kwargs):
"""
note that cv2.videocapture is not a serializable object and cannot be pickled
"""
tpl = (camera, result_writer, rois, TrackerClass, tracker_kwargs,
hardware_connection, StimulatorClass, stimulator_kwargs)
if not os.path.exists(os.path.dirname(self._persistent_state_file)):
logging.warning("No cache dir detected. making one")
os.makedirs(os.path.dirname(self._persistent_state_file))
with open(self._persistent_state_file, "wb") as f:
return pickle.dump(tpl, f)
def _set_tracking_from_scratch(self):
CameraClass = self._option_dict["camera"]["class"]
camera_kwargs = self._option_dict["camera"]["kwargs"]
ROIBuilderClass = self._option_dict["roi_builder"]["class"]
roi_builder_kwargs = self._option_dict["roi_builder"]["kwargs"]
StimulatorClass = self._option_dict["interactor"]["class"]
stimulator_kwargs = self._option_dict["interactor"]["kwargs"]
HardWareInterfaceClass = StimulatorClass.__dict__[
"_HardwareInterfaceClass"]
TrackerClass = self._option_dict["tracker"]["class"]
tracker_kwargs = self._option_dict["tracker"]["kwargs"]
ResultWriterClass = self._option_dict["result_writer"]["class"]
result_writer_kwargs = self._option_dict["result_writer"]["kwargs"]
cam = CameraClass(**camera_kwargs)
roi_builder = ROIBuilderClass(**roi_builder_kwargs)
try:
rois = roi_builder.build(cam)
except EthoscopeException as e:
cam._close()
raise e
logging.info("Initialising monitor")
cam.restart()
# the camera start time is the reference 0
ExpInfoClass = self._option_dict["experimental_info"]["class"]
exp_info_kwargs = self._option_dict["experimental_info"]["kwargs"]
self._info["experimental_info"] = ExpInfoClass(
**exp_info_kwargs).info_dic
self._info["time"] = cam.start_time
#here the hardwareconnection call the interface class without passing any argument!
hardware_connection = HardwareConnection(HardWareInterfaceClass)
self._metadata = {
"machine_id": self._info["id"],
"machine_name": self._info["name"],
"date_time":
cam.start_time, # the camera start time is the reference 0
"frame_width": cam.width,
"frame_height": cam.height,
"version": self._info["version"]["id"],
"experimental_info": str(self._info["experimental_info"]),
"selected_options": str(self._option_dict),
}
# hardware_interface is a running thread
rw = ResultWriter(self._db_credentials,
rois,
self._metadata,
take_frame_shots=True)
return (cam, rw, rois, TrackerClass, tracker_kwargs,
hardware_connection, StimulatorClass, stimulator_kwargs)
def run(self):
cam = None
hardware_connection = None
try:
self._info["status"] = "initialising"
logging.info("Starting Monitor thread")
self._info["error"] = None
self._last_info_t_stamp = 0
self._last_info_frame_idx = 0
try:
cam, rw, rois, TrackerClass, tracker_kwargs, hardware_connection, StimulatorClass, stimulator_kwargs = self._set_tracking_from_pickled(
)
except FileNotFoundError:
cam, rw, rois, TrackerClass, tracker_kwargs, hardware_connection, StimulatorClass, stimulator_kwargs = self._set_tracking_from_scratch(
)
except Exception as e:
logging.error(
"Could not load previous state for unexpected reason:")
raise e
with rw as result_writer:
if cam.canbepickled:
self._save_pickled_state(cam, rw, rois, TrackerClass,
tracker_kwargs,
hardware_connection,
StimulatorClass,
stimulator_kwargs)
self._start_tracking(cam, result_writer, rois, TrackerClass,
tracker_kwargs, hardware_connection,
StimulatorClass, stimulator_kwargs)
self.stop()
except EthoscopeException as e:
if e.img is not None:
cv2.imwrite(self._info["dbg_img"], e.img)
self.stop(traceback.format_exc())
except Exception as e:
self.stop(traceback.format_exc())
finally:
try:
os.remove(self._persistent_state_file)
except:
logging.warning("Failed to remove persistent file")
try:
if cam is not None:
cam._close()
except:
logging.warning("Could not close camera properly")
pass
try:
if hardware_connection is not None:
hardware_connection.stop()
except:
logging.warning("Could not close hardware connection properly")
pass
#for testing purposes
if self._evanescent:
del self._drawer
self.stop()
os._exit(0)
def stop(self, error=None):
self._info["status"] = "stopping"
self._info["time"] = time.time()
self._info["experimental_info"] = {}
logging.info("Stopping monitor")
if not self._monit is None:
self._monit.stop()
self._monit = None
self._info["status"] = "stopped"
self._info["time"] = time.time()
self._info["error"] = error
self._info["monitor_info"] = self._default_monitor_info
if error is not None:
logging.error("Monitor closed with an error:")
logging.error(error)
else:
logging.info("Monitor closed all right")
def __del__(self):
self.stop()
shutil.rmtree(self._tmp_dir, ignore_errors=True)
shutil.rmtree(self._persistent_state_file, ignore_errors=True)
def set_evanescent(self, value=True):
self._evanescent = value
parser.add_option("-p",
"--prefix",
dest="prefix",
help="The prefix for result dir")
(options, args) = parser.parse_args()
option_dict = vars(options)
INPUT = option_dict["input"]
OUTPUT = os.path.splitext(INPUT)[0] + ".db"
OUTPUT = option_dict["prefix"] + "/" + OUTPUT
try:
os.makedirs(os.path.dirname(OUTPUT))
except OSError:
pass
print INPUT + " ===> " + OUTPUT
cam = MovieVirtualCamera(INPUT)
rois = SleepMonitorWithTargetROIBuilder().build(cam)
drawer = DefaultDrawer(draw_frames=True)
mon = Monitor(cam, AdaptiveBGModel, rois)
#fixme
date = datetime.datetime.strptime("2016-05-03_08-25-02",
"%Y-%m-%d_%H-%M-%S")
ts = int(calendar.timegm(date.timetuple()))
#todo parse metadata from filename
# metadata = {}
with SQLiteResultWriter(OUTPUT, rois) as rw:
mon.run(rw, drawer)
class ABGMImageSaver(AdaptiveBGModel):
fg_model = ObjectModelImageSaver()
# change these three variables according to how you name your input/output files
INPUT_VIDEO = "/home/quentin/comput/ethoscope-git/src/ethoscope/tests/integration_server_tests/test_video.mp4"
OUTPUT_VIDEO = "/tmp/my_output.avi"
OUTPUT_DB = "/tmp/results.db"
# We use a video input file as if it was a "camera"
cam = MovieVirtualCamera(INPUT_VIDEO)
# here, we generate ROIs automatically from the targets in the images
roi_builder = SleepMonitorWithTargetROIBuilder()
rois = roi_builder.build(cam)
# Then, we go back to the first frame of the video
cam.restart()
# we use a drawer to show inferred position for each animal, display frames and save them as a video
drawer = DefaultDrawer(OUTPUT_VIDEO, draw_frames=True)
# We build our monitor
monitor = Monitor(cam, ABGMImageSaver, rois)
# Now everything ius ready, we run the monitor with a result writer and a drawer
with SQLiteResultWriter(OUTPUT_DB, rois) as rw:
monitor.run(rw, drawer)
def run(self):
try:
self._info["status"] = "initialising"
logging.info("Starting Monitor thread")
self._info["error"] = None
self._last_info_t_stamp = 0
self._last_info_frame_idx = 0
try:
CameraClass = self._option_dict["camera"]["class"]
camera_kwargs = self._option_dict["camera"]["kwargs"]
ROIBuilderClass = self._option_dict["roi_builder"]["class"]
roi_builder_kwargs = self._option_dict["roi_builder"]["kwargs"]
InteractorClass = self._option_dict["interactor"]["class"]
interactor_kwargs = self._option_dict["interactor"]["kwargs"]
HardWareInterfaceClass = InteractorClass.__dict__[
"_hardwareInterfaceClass"]
TrackerClass = self._option_dict["tracker"]["class"]
tracker_kwargs = self._option_dict["tracker"]["kwargs"]
ResultWriterClass = self._option_dict["result_writer"]["class"]
result_writer_kwargs = self._option_dict["result_writer"][
"kwargs"]
cam = CameraClass(**camera_kwargs)
roi_builder = ROIBuilderClass(**roi_builder_kwargs)
rois = roi_builder.build(cam)
logging.info("Initialising monitor")
cam.restart()
#the camera start time is the reference 0
ExpInfoClass = self._option_dict["experimental_info"]["class"]
exp_info_kwargs = self._option_dict["experimental_info"][
"kwargs"]
self._info["experimental_info"] = ExpInfoClass(
**exp_info_kwargs).info_dic
self._info["time"] = cam.start_time
self._metadata = {
"machine_id": self._info["id"],
"machine_name": self._info["name"],
"date_time":
cam.start_time, #the camera start time is the reference 0
"frame_width": cam.width,
"frame_height": cam.height,
"version": self._info["version"]["id"],
"experimental_info": str(self._info["experimental_info"]),
"selected_options": str(self._option_dict)
}
hardware_interface = HardWareInterfaceClass()
interactors = [
InteractorClass(hardware_interface, **interactor_kwargs)
for _ in rois
]
kwargs = self._monit_kwargs.copy()
kwargs.update(tracker_kwargs)
self._monit = Monitor(cam,
TrackerClass,
rois,
interactors=interactors,
*self._monit_args,
**kwargs)
logging.info("Starting monitor")
#fixme
with ResultWriter(self._db_credentials,
rois,
self._metadata,
take_frame_shots=True) as rw:
self._info["status"] = "running"
logging.info("Setting monitor status as running: '%s'" %
self._info["status"])
self._monit.run(rw, self._drawer)
logging.info("Stopping Monitor thread")
self.stop()
finally:
try:
cam._close()
except:
logging.warning("Could not close camera properly")
pass
except EthoscopeException as e:
if e.img is not None:
cv2.imwrite(self._info["dbg_img"], e.img)
self.stop(traceback.format_exc(e))
except Exception as e:
self.stop(traceback.format_exc(e))
#for testing purposes
if self._evanescent:
import os
del self._drawer
self.stop()
os._exit(0)
def main(argv):
parser = ArgumentParser(
description='Runs an Ethoscope machinery on the given video file,' +
' which is meant to be a recording of single daphnia moving' +
' in a bunch of wells.' +
' The area of each well is determined by non-black regions' +
' in the supplied regions of interest (ROI) image file.' +
' Optionally an output video may be produced, documenting the ' +
' detection of animals.')
parser.add_argument("-i",
"--input-video",
dest="inp_video_filename",
required=True,
help="The video file to be processed.",
metavar='<input video filename>')
parser.add_argument("-o",
"--output-db",
dest="db_filename",
required=True,
help="Create Sqlite DB file for storing results.",
metavar='<output DB filename>')
parser.add_argument(
"-r",
"--roi_image",
dest="roi_filename",
required=True,
help="Create Sqlite DB file DB_FILENAME for storing results.",
metavar='<roi image>')
parser.add_argument("-a",
"--output-video",
dest="outp_video_filename",
help="The annotated output video file.",
metavar='<output video filename>')
parser.add_argument(
"-b",
"--single-roi-video",
dest="single_roi_video_filename",
help=
"For debugging purpose a video file of a single roi may be produced.",
metavar='<single roi video filename>')
parser.add_argument(
"-n",
"--single-roi-video-roi-nbr",
dest="single_roi_video_roi_nbr",
type=int,
default=0,
help="Select the number of the roi to produce a debugging video from."
+ " If not specified, roi 0 is the default.",
metavar='<single roi video roi number>')
args = parser.parse_args()
# change these variables according to how you name your input/output files
INPUT_DATA_DIR = "/home/lukas/tmp/AAA-Video/"
OUTPUT_DATA_DIR = "/home/lukas/tmp/ethoscope/"
#ROI_IMAGE = INPUT_DATA_DIR + "irbacklit_20200109_1525_4x4x6_squaremask_valued.png"
ROI_IMAGE = INPUT_DATA_DIR + "4xWellplates4x6_registred_squaremask_tight.png"
#INPUT_VIDEO = INPUT_DATA_DIR + "Basler_acA5472-17um__23065142__20200109_152536071.mp4"
INPUT_VIDEO = INPUT_DATA_DIR + "Basler_acA5472-17um__23065142__20200205_172106124.mp4"
logfile = OUTPUT_DATA_DIR + '20200205.log'
OUTPUT_VIDEO = OUTPUT_DATA_DIR + "20200205.avi"
OUTPUT_DB = OUTPUT_DATA_DIR + "results20200205.db"
#logfile = OUTPUT_DATA_DIR + 'results.log'
#OUTPUT_VIDEO = OUTPUT_DATA_DIR + "output.avi"
#OUTPUT_DB = OUTPUT_DATA_DIR + "output.db"
dbgImgWinSizeX = 2200
dbgImgWinSizeY = 1500
# setup logging
logging.basicConfig(filename=logfile, level=logging.INFO)
#logging.basicConfig(filename=logfile, level=logging.DEBUG)
# define a Handler which writes INFO messages or higher to the sys.stderr
console = logging.StreamHandler()
console.setLevel(logging.INFO)
# add the handler to the root logger
logging.getLogger('').addHandler(console)
# Make the ethoscope packages accessible
package_path = os.path.join(os.path.dirname(sys.path[0]), '')
logging.info("path of ethoscope package: %s" % package_path)
sys.path.insert(0, package_path)
import cv2
# import the bricks from ethoscope package
# Use a mask image to define rois. Mask image must have black background, every non-black
# region defines a roi.
from ethoscope.roi_builders.img_roi_builder import ImgMaskROIBuilder
from ethoscope.core.monitor import Monitor
from ethoscope.trackers.adaptive_bg_tracker import AdaptiveBGModel
from ethoscope.utils.io import SQLiteResultWriter
from ethoscope.hardware.input.cameras import MovieVirtualCamera
from ethoscope.drawers.drawers import DefaultDrawer
# Generate ROIs from the mask image
logging.info("reading roi mask")
roi_builder = ImgMaskROIBuilder(args.roi_filename)
logging.info("building rois from \"%s\"" % args.roi_filename)
roi_builder.build(
None) # use image already loaded by ImgMaskROIBuilder instance
rois = roi_builder.gridSort(50, 50)
#for r in rois:
# print("Roi %d: value: %d, (%d,%d)" % (r.idx, r._value, r._rectangle[0], r._rectangle[1]))
# We use a video input file as if it were a camera
cam = MovieVirtualCamera(args.inp_video_filename)
logging.info("Loading \"%s\"-encoded movie with %d FPS of duration %d s." %
(cam.fourcc, cam.frames_per_sec,
cam._total_n_frames / cam.frames_per_sec))
# we use a drawer to show inferred position for each animal, display frames and save them as a video
do_draw_frames = False
if args.outp_video_filename is not None:
do_draw_frames = True
drawer = DefaultDrawer(args.outp_video_filename,
draw_frames=do_draw_frames,
framesWinSizeX=dbgImgWinSizeX,
framesWinSizeY=dbgImgWinSizeY)
# We build our monitor
#monitor = Monitor(cam, AdaptiveBGModel, rois)
if args.single_roi_video_filename is not None:
monitor = Monitor(
cam,
AdaptiveBGModel,
rois,
dbg_roi_value=args.single_roi_video_roi_nbr,
dbg_roi_video_filename=args.single_roi_video_filename)
else:
monitor = Monitor(cam, AdaptiveBGModel, rois)
# Now everything is ready, we run the monitor with a result writer and a drawer
logging.info("run monitor with drawer")
with SQLiteResultWriter(args.db_filename, rois) as rw:
monitor.run(rw, drawer)
class ControlThread(Thread):
"""
The versatile control thread
From this thread, the PI passes option to the node.
Note: Options are passed and shown only if the remote class contains a "_description" field!
"""
_auto_SQL_backup_at_stop = False
_option_dict = {
"roi_builder": {
"possible_classes": [
DefaultROIBuilder, SleepMonitorWithTargetROIBuilder,
TargetGridROIBuilder, OlfactionAssayROIBuilder,
ElectricShockAssayROIBuilder
],
},
"tracker": {
"possible_classes": [AdaptiveBGModel],
},
"interactor": {
"possible_classes": [
DefaultStimulator,
SleepDepStimulator,
OptomotorSleepDepriver,
MiddleCrossingStimulator,
#SystematicSleepDepInteractor,
ExperimentalSleepDepStimulator,
#GearMotorSleepDepStimulator,
#DynamicOdourDeliverer,
DynamicOdourSleepDepriver,
OptoMidlineCrossStimulator,
OptomotorSleepDepriverSystematic,
MiddleCrossingOdourStimulator,
MiddleCrossingOdourStimulatorFlushed,
mAGO
],
},
"drawer": {
"possible_classes": [DefaultDrawer, NullDrawer],
},
"camera": {
"possible_classes": [
OurPiCameraAsync, MovieVirtualCamera, DummyPiCameraAsync,
V4L2Camera
],
},
"result_writer": {
"possible_classes": [ResultWriter, SQLiteResultWriter],
},
"experimental_info": {
"possible_classes": [ExperimentalInformation],
}
}
#some classes do not need to be offered as choices to the user in normal conditions
#these are shown only if the machine is not a PI
_is_a_rPi = isMachinePI() and hasPiCamera() and not isExperimental()
_hidden_options = {'camera', 'result_writer', 'tracker'}
for k in _option_dict:
_option_dict[k]["class"] = _option_dict[k]["possible_classes"][0]
_option_dict[k]["kwargs"] = {}
_tmp_last_img_file = "last_img.jpg"
_dbg_img_file = "dbg_img.png"
_log_file = "ethoscope.log"
#give the database an ethoscope specific name
#future proof in case we want to use a remote server
_db_credentials = {
"name": "%s_db" % get_machine_name(),
"user": "******",
"password": "******"
}
_default_monitor_info = {
#fixme, not needed
"last_positions": None,
"last_time_stamp": 0,
"fps": 0
}
_persistent_state_file = PERSISTENT_STATE
def __init__(self,
machine_id,
name,
version,
ethoscope_dir,
data=None,
*args,
**kwargs):
self._monit_args = args
self._monit_kwargs = kwargs
self._metadata = None
# for FPS computation
self._last_info_t_stamp = 0
self._last_info_frame_idx = 0
# We wipe off previous logs and debug images
try:
os.remove(os.path.join(ethoscope_dir, self._log_file))
except OSError:
pass
try:
os.remove(os.path.join(ethoscope_dir, self._dbg_img_file))
except OSError:
pass
try:
os.remove("/tmp/ethoscope_*")
except OSError:
pass
try:
os.makedirs(ethoscope_dir)
except OSError:
pass
self._tmp_dir = tempfile.mkdtemp(prefix="ethoscope_")
#todo add 'data' -> how monitor was started to metadata
self._info = {
"status": "stopped",
"time": time.time(),
"error": None,
"log_file": os.path.join(ethoscope_dir, self._log_file),
"dbg_img": os.path.join(ethoscope_dir, self._dbg_img_file),
"last_drawn_img": os.path.join(self._tmp_dir,
self._tmp_last_img_file),
"db_name": self._db_credentials["name"],
"monitor_info": self._default_monitor_info,
#"user_options": self._get_user_options(),
"experimental_info": {},
"id": machine_id,
"name": name,
"version": version
}
self._monit = None
self._parse_user_options(data)
DrawerClass = self._option_dict["drawer"]["class"]
drawer_kwargs = self._option_dict["drawer"]["kwargs"]
self._drawer = DrawerClass(**drawer_kwargs)
logging.info('Starting a new monitor control thread')
super(ControlThread, self).__init__()
@property
def hw_info(self):
"""
This is information about the ethoscope that is not changing in time such as hardware specs and configuration parameters
"""
_hw_info = {}
_hw_info['kernel'] = os.uname()[2]
_hw_info['pi_version'] = pi_version()
_hw_info['camera'] = getPiCameraVersion()
_hw_info['SD_CARD_AGE'] = get_SD_CARD_AGE()
_hw_info['partitions'] = get_partition_infos()
_hw_info['SD_CARD_NAME'] = get_SD_CARD_NAME()
return _hw_info
@property
def info(self):
self._update_info()
return self._info
@property
def was_interrupted(self):
return os.path.exists(self._persistent_state_file)
@classmethod
def user_options(self):
out = {}
for key, value in list(self._option_dict.items()):
# check if the options for the remote class will be visible
# they will be visible only if they have a description, and if we are on a PC or they are not hidden
if (self._is_a_rPi
and key not in self._hidden_options) or not self._is_a_rPi:
out[key] = []
for p in value["possible_classes"]:
try:
d = p.__dict__["_description"]
except KeyError:
continue
d["name"] = p.__name__
out[key].append(d)
out_curated = {}
for key, value in list(out.items()):
if len(value) > 0:
out_curated[key] = value
return out_curated
def _parse_one_user_option(self, field, data):
try:
subdata = data[field]
except KeyError:
logging.warning("No field %s, using default" % field)
return None, {}
Class = eval(subdata["name"])
kwargs = subdata["arguments"]
return Class, kwargs
def _parse_user_options(self, data):
if data is None:
return
for key in list(self._option_dict.keys()):
Class, kwargs = self._parse_one_user_option(key, data)
# when no field is present in the JSON config, we get the default class
if Class is None:
self._option_dict[key]["class"] = self._option_dict[key][
"possible_classes"][0]
self._option_dict[key]["kwargs"] = {}
continue
self._option_dict[key]["class"] = Class
self._option_dict[key]["kwargs"] = kwargs
def _update_info(self):
'''
Updates a dictionary with information that relates to the current status of the machine, ie data linked for instance to data acquisition
Information that is not related to control and it is not experiment-dependent will come from elsewhere
'''
if self._monit is None:
return
t = self._monit.last_time_stamp
frame_idx = self._monit.last_frame_idx
wall_time = time.time()
dt = wall_time - self._last_info_t_stamp
df = float(frame_idx - self._last_info_frame_idx)
if self._last_info_t_stamp == 0 or dt > 0:
f = round(df / dt, 2)
else:
f = "NaN"
if t is not None: # and p is not None:
self._info["monitor_info"] = {
# "last_positions":pos,
"last_time_stamp": t,
"fps": f
}
frame = self._drawer.last_drawn_frame
if frame is not None:
cv2.imwrite(self._info["last_drawn_img"], frame,
[int(cv2.IMWRITE_JPEG_QUALITY), 50])
self._last_info_t_stamp = wall_time
self._last_info_frame_idx = frame_idx
def _start_tracking(self, camera, result_writer, rois, reference_points,
TrackerClass, tracker_kwargs, hardware_connection,
StimulatorClass, stimulator_kwargs):
#Here the stimulator passes args. Hardware connection was previously open as thread.
stimulators = [
StimulatorClass(hardware_connection, **stimulator_kwargs)
for _ in rois
]
kwargs = self._monit_kwargs.copy()
kwargs.update(tracker_kwargs)
# todo: pickle hardware connection, camera, rois, tracker class, stimulator class,.
# then rerun stimulators and Monitor(......)
self._monit = Monitor(camera,
TrackerClass,
rois,
reference_points=reference_points,
stimulators=stimulators,
*self._monit_args)
self._info["status"] = "running"
logging.info("Setting monitor status as running: '%s'" %
self._info["status"])
self._monit.run(result_writer, self._drawer)
def _has_pickle_file(self):
"""
"""
return os.path.exists(self._persistent_state_file)
def _set_tracking_from_pickled(self):
"""
"""
with open(self._persistent_state_file, "rb") as f:
time.sleep(15)
return pickle.load(f)
def _save_pickled_state(self, camera, result_writer, rois,
reference_points, TrackerClass, tracker_kwargs,
hardware_connection, StimulatorClass,
stimulator_kwargs, running_info):
"""
note that cv2.videocapture is not a serializable object and cannot be pickled
"""
tpl = (camera, result_writer, rois, reference_points, TrackerClass,
tracker_kwargs, hardware_connection, StimulatorClass,
stimulator_kwargs, running_info)
if not os.path.exists(os.path.dirname(self._persistent_state_file)):
logging.warning("No cache dir detected. making one")
os.makedirs(os.path.dirname(self._persistent_state_file))
with open(self._persistent_state_file, "wb") as f:
return pickle.dump(tpl, f)
def _set_tracking_from_scratch(self):
"""
"""
CameraClass = self._option_dict["camera"]["class"]
camera_kwargs = self._option_dict["camera"]["kwargs"]
ROIBuilderClass = self._option_dict["roi_builder"]["class"]
roi_builder_kwargs = self._option_dict["roi_builder"]["kwargs"]
StimulatorClass = self._option_dict["interactor"]["class"]
stimulator_kwargs = self._option_dict["interactor"]["kwargs"]
HardWareInterfaceClass = StimulatorClass.__dict__[
"_HardwareInterfaceClass"]
TrackerClass = self._option_dict["tracker"]["class"]
tracker_kwargs = self._option_dict["tracker"]["kwargs"]
ResultWriterClass = self._option_dict["result_writer"]["class"]
result_writer_kwargs = self._option_dict["result_writer"]["kwargs"]
cam = CameraClass(**camera_kwargs)
roi_builder = ROIBuilderClass(**roi_builder_kwargs)
try:
reference_points, rois = roi_builder.build(cam)
except EthoscopeException as e:
cam._close()
raise e
logging.info("Initialising monitor")
cam.restart()
# the camera start time is the reference 0
ExpInfoClass = self._option_dict["experimental_info"]["class"]
exp_info_kwargs = self._option_dict["experimental_info"]["kwargs"]
self._info["experimental_info"] = ExpInfoClass(
**exp_info_kwargs).info_dic
self._info["time"] = cam.start_time
#here the hardwareconnection call the interface class without passing any argument!
hardware_connection = HardwareConnection(HardWareInterfaceClass)
#creates a unique tracking id to label this tracking run
self._info["experimental_info"]["run_id"] = secrets.token_hex(8)
if self._info["experimental_info"]["sensor"]:
#if is URL:
sensor = EthoscopeSensor(self._info["experimental_info"]["sensor"])
logging.info("Using sensor with URL %s" %
self._info["experimental_info"]["sensor"])
else:
sensor = None
if "append" in self._info["experimental_info"]:
append_to_db = self._info["experimental_info"]["append"]
logging.info([
"Recreating a new database",
"Appending tracking data to the existing database"
][append_to_db])
else:
append_to_db = False
#this will be saved in the metadata table
self._metadata = {
"machine_id": self._info["id"],
"machine_name": self._info["name"],
"date_time":
cam.start_time, # the camera start time is the reference 0
"frame_width": cam.width,
"frame_height": cam.height,
"version": self._info["version"]["id"],
"experimental_info": str(self._info["experimental_info"]),
"selected_options": str(self._option_dict),
"hardware_info": str(self.hw_info),
"reference_points": str([(p[0], p[1]) for p in reference_points])
}
# hardware_interface is a running thread
rw = ResultWriter(
self._db_credentials,
rois,
self._metadata,
take_frame_shots=True,
erase_old_db=(not append_to_db),
sensor=sensor,
)
return (cam, rw, rois, reference_points, TrackerClass, tracker_kwargs,
hardware_connection, StimulatorClass, stimulator_kwargs)
def run(self):
cam = None
hardware_connection = None
try:
self._info["status"] = "initialising"
logging.info("Starting Monitor thread")
self._info["error"] = None
self._last_info_t_stamp = 0
self._last_info_frame_idx = 0
#check if a previous instance exist and if it does attempts to start from there
if self._has_pickle_file():
logging.warning(
"Attempting to resume a previously interrupted state")
try:
cam, rw, rois, reference_points, TrackerClass, tracker_kwargs, hardware_connection, StimulatorClass, stimulator_kwargs, self._info = self._set_tracking_from_pickled(
)
except Exception as e:
logging.error(
"Could not load previous state for unexpected reason:")
raise e
#a previous instance does not exist, hence we create a new one
else:
cam, rw, rois, reference_points, TrackerClass, tracker_kwargs, hardware_connection, StimulatorClass, stimulator_kwargs = self._set_tracking_from_scratch(
)
with rw as result_writer:
# and we save it if we can
if cam.canbepickled:
self._save_pickled_state(cam, rw, rois, reference_points,
TrackerClass, tracker_kwargs,
hardware_connection,
StimulatorClass,
stimulator_kwargs, self._info)
# then we start tracking
self._start_tracking(cam, result_writer, rois,
reference_points, TrackerClass,
tracker_kwargs, hardware_connection,
StimulatorClass, stimulator_kwargs)
#self.stop()
except EthoscopeException as e:
if e.img is not None:
cv2.imwrite(self._info["dbg_img"], e.img)
self.stop(traceback.format_exc())
except Exception as e:
self.stop(traceback.format_exc())
finally:
if os.path.exists(self._persistent_state_file):
try:
os.remove(self._persistent_state_file)
except:
logging.warning("Failed to remove persistent file")
try:
if cam is not None:
cam._close()
except:
logging.warning("Could not close camera properly")
pass
try:
if hardware_connection is not None:
hardware_connection.stop()
except:
logging.warning("Could not close hardware connection properly")
pass
def stop(self, error=None):
"""
"""
self._info["status"] = "stopping"
self._info["time"] = time.time()
# we reset all the user data of the latest experiment except the run_id
# a new run_id will be created when we start another experiment
if "experimental_info" in self._info and "run_id" in self._info[
"experimental_info"]:
self._info["experimental_info"] = {
"run_id": self._info["experimental_info"]["run_id"]
}
logging.info("Stopping monitor")
if not self._monit is None:
self._monit.stop()
self._monit = None
if self._auto_SQL_backup_at_stop:
logging.info("Performing a SQL dump of the database.")
t = Thread(target=SQL_dump)
t.start()
self._info["status"] = "stopped"
self._info["time"] = time.time()
self._info["error"] = error
self._info["monitor_info"] = self._default_monitor_info
if error is not None:
logging.error("Monitor closed with an error:")
logging.error(error)
else:
logging.info("Monitor closed all right")
def __del__(self):
"""
"""
self.stop()
shutil.rmtree(self._tmp_dir, ignore_errors=True)
shutil.rmtree(self._persistent_state_file, ignore_errors=True)
# We use the npy tracker to save data in a npy file
rdw = rawdatawriter(basename=input_video + ".npy",
n_rois=len(rois),
entities=entities)
#rdw = None
#for multifly tracking using BS subtraction
if ttype == "multi":
monit = Monitor(camera,
MultiFlyTracker,
rois,
stimulators=None,
data={
'maxN': 50,
'visualise': False,
'fg_data': {
'sample_size': 400,
'normal_limits': (50, 200),
'tolerance': 0.8
}
})
#For the haar tracking
if ttype == "haar":
monit = Monitor(camera,
HaarTracker,
rois,
stimulators=None,
data={
'maxN': entities,
def _start_tracking(self, camera, result_writer, rois, TrackerClass,
tracker_kwargs, hardware_connection, StimulatorClass,
stimulator_kwargs):
#Here the stimulator passes args. Hardware connection was previously open as thread.
stimulators = [
StimulatorClass(hardware_connection, **stimulator_kwargs)
for _ in rois
]
kwargs = self._monit_kwargs.copy()
kwargs.update(tracker_kwargs)
# todo: pickle hardware connection, camera, rois, tracker class, stimulator class,.
# then rerun stimulators and Monitor(......)
self._monit = Monitor(camera,
TrackerClass,
rois,
stimulators=stimulators,
*self._monit_args)
conditionVariables = []
try:
variable = camera.metadata(
"analog_gain"
) # This might fail depending on the type of camera
conditionVariables.append(
ConditionVariable(variable, "camera_gain"))
except KeyError as error:
# analog_gain is not part of the meta data for this camera
logging.warning(
"Unable to get the camera gain to add to the condition database"
)
try:
sensorChip = BufferedHIH6130()
conditionVariables.append(
ConditionVariableFunction(sensorChip.humidity, "humidity"))
conditionVariables.append(
ConditionVariableFunction(sensorChip.temperature,
"temperature"))
except Exception as error:
logging.warning(
"Unable to get the temperature or humidity sensor to add to the conditions database because: "
+ str(error))
try:
lightSensorChip = TSL2591()
lightSensorChip.powerOn()
conditionVariables.append(
ConditionVariableFunction(lightSensorChip.lux, "illuminance"))
except Exception as error:
logging.warning(
"Unable to get the light sensor to add to the conditions database because: "
+ str(error))
self._conditionsMonitor = ConditionsMonitor(conditionVariables)
dbConnectionString = "mysql://" + self._db_credentials[
"user"] + ":" + self._db_credentials[
"password"] + "@localhost/" + self._db_credentials["name"]
self._info["status"] = "running"
logging.info("Setting monitor status as running: '%s'" %
self._info["status"])
# Set all times in the database to be relative to the start of the run. Usually this means setting
# to zero, unless continuing a previous run (e.g. after power failure). self._monit handles this
# internally. The "1000" is so that everything is in milliseconds.
self._conditionsMonitor.setTime(
(time.time() - camera.start_time) * 1000, 1000)
self._conditionsMonitor.run(
dbConnectionString) # This runs asynchronously
self._monit.run(result_writer, self._drawer) # This blocks
class ControlThread(Thread):
_evanescent = False
_option_dict = {
"roi_builder": {
"possible_classes": [
DefaultROIBuilder, SleepMonitorWithTargetROIBuilder,
TargetGridROIBuilder, OlfactionAssayROIBuilder
],
},
"tracker": {
"possible_classes": [AdaptiveBGModel],
},
"interactor": {
"possible_classes": [
DefaultInteractor, SleepDepInteractor,
SystematicSleepDepInteractor, ExperimentalSleepDepInteractor,
FakeSystematicSleepDepInteractor
],
},
"drawer": {
"possible_classes": [DefaultDrawer, NullDrawer],
},
"camera": {
"possible_classes": [OurPiCameraAsync, MovieVirtualCamera],
},
"result_writer": {
"possible_classes": [ResultWriter, SQLiteResultWriter],
},
"experimental_info": {
"possible_classes": [ExperimentalInformations],
}
}
for k in _option_dict:
_option_dict[k]["class"] = _option_dict[k]["possible_classes"][0]
_option_dict[k]["kwargs"] = {}
_tmp_last_img_file = "last_img.jpg"
_dbg_img_file = "dbg_img.png"
_log_file = "ethoscope.log"
_db_credentials = {
"name": "ethoscope_db",
"user": "******",
"password": "******"
}
_default_monitor_info = {
#fixme, not needed
"last_positions": None,
"last_time_stamp": 0,
"fps": 0
}
def __init__(self,
machine_id,
name,
version,
ethoscope_dir,
data=None,
*args,
**kwargs):
self._monit_args = args
self._monit_kwargs = kwargs
self._metadata = None
# for FPS computation
self._last_info_t_stamp = 0
self._last_info_frame_idx = 0
# We wipe off previous data
shutil.rmtree(ethoscope_dir, ignore_errors=True)
try:
os.makedirs(ethoscope_dir)
except OSError:
pass
self._tmp_dir = tempfile.mkdtemp(prefix="ethoscope_")
#todo add 'data' -> how monitor was started to metadata
self._info = {
"status": "stopped",
"time": time.time(),
"error": None,
"log_file": os.path.join(ethoscope_dir, self._log_file),
"dbg_img": os.path.join(ethoscope_dir, self._dbg_img_file),
"last_drawn_img": os.path.join(self._tmp_dir,
self._tmp_last_img_file),
"id": machine_id,
"name": name,
"version": version,
"db_name": self._db_credentials["name"],
"monitor_info": self._default_monitor_info,
"user_options": self._get_user_options(),
"experimental_info": {}
}
self._monit = None
self._parse_user_options(data)
DrawerClass = self._option_dict["drawer"]["class"]
drawer_kwargs = self._option_dict["drawer"]["kwargs"]
self._drawer = DrawerClass(**drawer_kwargs)
super(ControlThread, self).__init__()
@property
def info(self):
self._update_info()
return self._info
def _get_user_options(self):
out = {}
for key, value in self._option_dict.iteritems():
out[key] = []
for p in value["possible_classes"]:
try:
d = p.__dict__["_description"]
except KeyError:
continue
d["name"] = p.__name__
out[key].append(d)
out_currated = {}
for key, value in out.iteritems():
if len(value) > 0:
out_currated[key] = value
return out_currated
def _parse_one_user_option(self, field, data):
try:
subdata = data[field]
except KeyError:
logging.warning("No field %s, using default" % field)
return None, {}
Class = eval(subdata["name"])
kwargs = subdata["arguments"]
return Class, kwargs
def _parse_user_options(self, data):
if data is None:
return
#FIXME DEBUG
logging.warning("Starting control thread with data:")
logging.warning(str(data))
for key in self._option_dict.iterkeys():
Class, kwargs = self._parse_one_user_option(key, data)
# when no field is present in the JSON config, we get the default class
if Class is None:
self._option_dict[key]["class"] = self._option_dict[key][
"possible_classes"][0]
self._option_dict[key]["kwargs"] = {}
continue
self._option_dict[key]["class"] = Class
self._option_dict[key]["kwargs"] = kwargs
def _update_info(self):
if self._monit is None:
return
t = self._monit.last_time_stamp
frame_idx = self._monit.last_frame_idx
wall_time = time.time()
dt = wall_time - self._last_info_t_stamp
df = float(frame_idx - self._last_info_frame_idx)
if self._last_info_t_stamp == 0 or dt > 0:
f = round(df / dt, 2)
else:
f = "NaN"
#fixme, this is not available anymore since we have position list now
# possibly, we just don't need it altogether
# p = self._monit.last_positions
# pos = {}
# for k,v in p.items():
# if v is None:
# continue
# pos[k] = dict(v)
# pos[k]["roi_idx"] = k
if t is not None: # and p is not None:
self._info["monitor_info"] = {
# "last_positions":pos,
"last_time_stamp": t,
"fps": f
}
f = self._drawer.last_drawn_frame
if not f is None:
cv2.imwrite(self._info["last_drawn_img"], f)
self._last_info_t_stamp = wall_time
self._last_info_frame_idx = frame_idx
def run(self):
try:
self._info["status"] = "initialising"
logging.info("Starting Monitor thread")
self._info["error"] = None
self._last_info_t_stamp = 0
self._last_info_frame_idx = 0
try:
CameraClass = self._option_dict["camera"]["class"]
camera_kwargs = self._option_dict["camera"]["kwargs"]
ROIBuilderClass = self._option_dict["roi_builder"]["class"]
roi_builder_kwargs = self._option_dict["roi_builder"]["kwargs"]
InteractorClass = self._option_dict["interactor"]["class"]
interactor_kwargs = self._option_dict["interactor"]["kwargs"]
HardWareInterfaceClass = InteractorClass.__dict__[
"_hardwareInterfaceClass"]
TrackerClass = self._option_dict["tracker"]["class"]
tracker_kwargs = self._option_dict["tracker"]["kwargs"]
ResultWriterClass = self._option_dict["result_writer"]["class"]
result_writer_kwargs = self._option_dict["result_writer"][
"kwargs"]
cam = CameraClass(**camera_kwargs)
roi_builder = ROIBuilderClass(**roi_builder_kwargs)
rois = roi_builder.build(cam)
logging.info("Initialising monitor")
cam.restart()
#the camera start time is the reference 0
ExpInfoClass = self._option_dict["experimental_info"]["class"]
exp_info_kwargs = self._option_dict["experimental_info"][
"kwargs"]
self._info["experimental_info"] = ExpInfoClass(
**exp_info_kwargs).info_dic
self._info["time"] = cam.start_time
self._metadata = {
"machine_id": self._info["id"],
"machine_name": self._info["name"],
"date_time":
cam.start_time, #the camera start time is the reference 0
"frame_width": cam.width,
"frame_height": cam.height,
"version": self._info["version"]["id"],
"experimental_info": str(self._info["experimental_info"]),
"selected_options": str(self._option_dict)
}
hardware_interface = HardWareInterfaceClass()
interactors = [
InteractorClass(hardware_interface, **interactor_kwargs)
for _ in rois
]
kwargs = self._monit_kwargs.copy()
kwargs.update(tracker_kwargs)
self._monit = Monitor(cam,
TrackerClass,
rois,
interactors=interactors,
*self._monit_args,
**kwargs)
logging.info("Starting monitor")
#fixme
with ResultWriter(self._db_credentials,
rois,
self._metadata,
take_frame_shots=True) as rw:
self._info["status"] = "running"
logging.info("Setting monitor status as running: '%s'" %
self._info["status"])
self._monit.run(rw, self._drawer)
logging.info("Stopping Monitor thread")
self.stop()
finally:
try:
cam._close()
except:
logging.warning("Could not close camera properly")
pass
except EthoscopeException as e:
if e.img is not None:
cv2.imwrite(self._info["dbg_img"], e.img)
self.stop(traceback.format_exc(e))
except Exception as e:
self.stop(traceback.format_exc(e))
#for testing purposes
if self._evanescent:
import os
del self._drawer
self.stop()
os._exit(0)
def stop(self, error=None):
self._info["status"] = "stopping"
self._info["time"] = time.time()
self._info["experimental_info"] = {}
logging.info("Stopping monitor")
if not self._monit is None:
self._monit.stop()
self._monit = None
self._info["status"] = "stopped"
self._info["time"] = time.time()
self._info["error"] = error
self._info["monitor_info"] = self._default_monitor_info
if error is not None:
logging.error("Monitor closed with an error:")
logging.error(error)
else:
logging.info("Monitor closed all right")
def __del__(self):
self.stop()
shutil.rmtree(self._tmp_dir, ignore_errors=True)
def set_evanescent(self, value=True):
self._evanescent = value
# here, we generate ROIs automatically from the targets in the images
roi_builder = SleepMonitorWithTargetROIBuilderJanelia()
rois = roi_builder.build(cam)
# Build the stimulator
hc = HardwareConnection(JaneliaAdaptiveSleepDepriverInterface)
stimulators = [JaneliaAdaptiveSleepDepStimultor(hc) for _ in rois]
# Then, we go back to the first frame of the video
cam.restart()
# we use a drawer to show inferred position for each animal, display frames and save them as a video
drawer = DefaultDrawer(OUTPUT_VIDEO, draw_frames=False)
# We build our monitor
monitor = Monitor(cam, AdaptiveBGModel, rois, stimulators)
try:
# Now everything is ready, we run the monitor with a result writer and a drawer
with SQLiteResultWriter(OUTPUT_DB, rois) as rw:
monitor.run(rw, drawer)
finally:
hc.stop()
cam._close()
print('----Put the motor controller in low power mode----')
devs = ModularClients() # Might automatically find device if one available
if devs is not None:
dev0 = devs['ethoscope_stepper_controller']['5x3'][0]
dev1 = devs['ethoscope_stepper_controller']['5x3'][1]
dev0.sleep_all()
from ethoscope.utils.io import SQLiteResultWriter from ethoscope.hardware.input.cameras import MovieVirtualCamera from ethoscope.drawers.drawers import DefaultDrawer # You can also load other types of ROI builder. This one is for 20 tubes (two columns of ten rows) from ethoscope.roi_builders.roi_builders import DefaultROIBuilder from ethoscope.roi_builders.target_roi_builder import TargetGridROIBuilder # change these three variables according to how you name your input/output files INPUT_VIDEO = "/home/quentin/comput/ethoscope-git/src/ethoscope/tests/integration_server_tests/test_video.mp4" OUTPUT_VIDEO = "/tmp/my_output.avi" OUTPUT_DB = "/tmp/results.db" # We use a video input file as if it was a "camera" cam = MovieVirtualCamera(INPUT_VIDEO) # here, we generate ROIs automatically from the targets in the images roi_builder = TargetGridROIBuilder(n_rows=1, n_cols=2) rois = roi_builder.build(cam) # Then, we go back to the first frame of the video cam.restart() # we use a drawer to show inferred position for each animal, display frames and save them as a video drawer = DefaultDrawer(OUTPUT_VIDEO, draw_frames=True) # We build our monitor monitor = Monitor(cam, MultiFlyTracker, rois) # Now everything ius ready, we run the monitor with a result writer and a drawer # with SQLiteResultWriter(OUTPUT_DB, rois) as rw: monitor.run(None, drawer)
class MockSDInterface(MockLynxMotionInterface, SleepDepriverInterface):
pass
class MockSDStimulator(SleepDepStimulator):
_HardwareInterfaceClass = MockSDInterface
tmp = tempfile.mkstemp(suffix="_ethoscope_test.db")[1]
print("Making a tmp db: " + tmp)
cam = MovieVirtualCamera(VIDEO, drop_each=15)
rb = SleepMonitorWithTargetROIBuilder()
rois = rb.build(cam)
cam.restart()
connection = HardwareConnection(MockSDInterface)
stimulators = [
MockSDStimulator(connection, min_inactive_time=10) for _ in rois
]
mon = Monitor(cam, AdaptiveBGModel, rois, stimulators=stimulators)
drawer = DefaultDrawer(draw_frames=DRAW_FRAMES)
try:
with SQLiteResultWriter(tmp, rois) as rw:
mon.run(result_writer=rw, drawer=drawer)
finally:
print("Removing temp db (" + tmp + ")")
os.remove(tmp)
connection.stop()
self._crop_counter[0] += 1
except Exception as e:
print ("Error saving the positive file")
print("Saved %s positives and %s negatives so far" % (self._crop_counter[0], self._crop_counter[1]))
# the input video - we work on an mp4 acquired with the Record function
positive_video = "/home/gg/Downloads/test_video.mp4"
negative_video = "/home/gg/Downloads/whole_2020-08-25_13-10-07_2020f8bceb334c1c84518f62359ddc76_emptyarena_1280x960@25_00000.mp4"
camera = MovieVirtualCamera(negative_video)
# we use the default drawer and we show the video as we track - this is useful to understand how things are going
# disabling the video will speed things up
#drawer = DefaultDrawer(draw_frames = True, video_out = output_video, video_out_fps=25)
drawer = HaarCutter(filepath="/home/gg/haar_training", draw_frames = False, create_positives=False, create_negatives=True, interval=10, negatives_per_frame=30)
# One Big ROI using the Default ROIBuilder
roi_builder = DefaultROIBuilder()
rois = roi_builder.build(camera)
# Starts the tracking monitor
monit = Monitor(camera, MultiFlyTracker, rois, stimulators=None )
monit.run(drawer=drawer, result_writer = None)
