def loadFile(self, path):
try:
try:
with open(path, "r") as data_file:
data = json.load(data_file)
self.loadData(data, path)
except UnicodeDecodeError:
with open(path, "rb") as data_file:
byte_data = data_file.read()
data = msgpack.unpackb(byte_data)
self.loadData(data, path)
except FileNotFoundError:
LogObject().print("File {} not found".format(path))
return False
except json.JSONDecodeError:
LogObject().print("Invalid JSON file".format(path))
return False
#except:
# LogObject().print("Unexpected error:", sys.exc_info()[1])
# return False
self.previous_path = path
self.fast_save_enabled = True
self.file_loaded_event.emit()
return True
def saveDetectionsToFile(self, path):
"""
Writes current detections to a file at path. Values are separated by ';'.
"""
# Default formatting
f1 = "{:.5f}"
lineBase1 = "{};" + "{};{};{};".format(f1, f1, f1)
try:
with open(path, "w") as file:
file.write(
"frame;length;distance;angle;corner1 x;corner1 y;corner2 x;corner2 y;corner3 x;corner3 y;corner4 x;corner4 y\n"
)
for frame, dets in enumerate(self.detections):
if dets is not None:
for d in dets:
if d.corners is not None:
file.write(
lineBase1.format(frame, d.length,
d.distance, d.angle))
file.write(d.cornersToString(";"))
file.write("\n")
LogObject().print("Detections saved to path:", path)
except PermissionError as e:
LogObject().print(
"Cannot open file {}. Permission denied.".format(path))
def __init__(self, pol_shape, cart_height, radius_limits, beam_angle):
"""
Initializes the mapping function.
Parameters:
pol_shape -- Shape of the polar frame
cart_height -- Height of the cartesian (output) image.
radius_limits -- Min and max radius of the beam.
beam_angle -- Angle covered by the beam (radians).
"""
LogObject().print("Init mapping")
self.pol_shape = pol_shape
self.setCartShape(cart_height, beam_angle)
self.radius_limits = radius_limits
self.angle_limits = (np.pi / 2 - beam_angle / 2,
np.pi / 2 + beam_angle / 2)
self.center = (0, (self.cart_shape[1] - 1) / 2)
self.metric_cart_shape = (radius_limits[1], self.cart_shape[1] /
self.cart_shape[0] * radius_limits[1])
self.map_x = np.zeros(self.cart_shape, dtype=np.float32)
self.map_y = np.zeros(self.cart_shape, dtype=np.float32)
for j in range(self.cart_shape[0]):
if j % 100 == 0:
LogObject().print("Mapping:", j)
for i in range(self.cart_shape[1]):
_j = self.cart_shape[0] - j - 1
self.map_y[j, i], self.map_x[j, i] = self.cart2polImage(_j, i)
LogObject().print("End mapping")
def track(self):
"""
Handles the tracking process. Opens file and connects detection and tracking
calls to the appropriate signals, so that they can be started when the file
has been loaded.
"""
if self.testFile:
self.playback_manager.openTestFile()
else:
self.playback_manager.loadFile(self.file)
LogObject().print("Frame count:",
self.playback_manager.getFrameCount())
if self.display:
self.playback_manager.frame_available.connect(
self.forwardImageDisplay)
else:
self.playback_manager.frame_available.connect(self.forwardImage)
self.detector.mog_parameters.nof_bg_frames = 500
self.detector._show_detections = True
self.playback_manager.mapping_done.connect(self.startTrackingProcess)
self.tracker.all_computed_signal.connect(self.onAllComputed)
if self.display:
self.figure = TestFigure(self.playback_manager.togglePlay)
self.main_window.setCentralWidget(self.figure)
LogObject().print(self.detector.parameters)
LogObject().print(self.detector.parameters.mog_parameters)
LogObject().print(self.tracker.parameters)
if self.display:
self.main_window.show()
def loadDetectionsFromFile(self, path):
"""
Loads a file from path. Values are expected to be separated by ';'.
"""
try:
with open(path, 'r') as file:
self.clearDetections()
nof_frames = self.image_provider.getFrameCount()
ignored_dets = 0
header = file.readline()
for line in file:
split_line = line.split(';')
frame = int(split_line[0])
if frame >= nof_frames:
ignored_dets += 1
continue
length = float(split_line[1])
distance = float(split_line[2])
angle = float(split_line[3])
c1 = [float(split_line[5]), float(split_line[4])]
c2 = [float(split_line[7]), float(split_line[6])]
c3 = [float(split_line[9]), float(split_line[8])]
c4 = [float(split_line[11]), float(split_line[10])]
corners = np.array([c1, c2, c3, c4])
det = Detection(0)
det.init_from_file(corners, length, distance, angle)
if self.detections[frame] is None:
self.detections[frame] = [det]
else:
self.detections[frame].append(det)
self.updateVerticalDetections()
self.compute_on_event = False
if ignored_dets > 0:
LogObject().print(
"Encountered {} detections that were out of range {}.".
format(ignored_dets, nof_frames))
except PermissionError as e:
LogObject().print(
"Cannot open file {}. Permission denied.".format(path))
def data(self, index, role):
if role == Qt.DisplayRole:
row = index.row()
col = index.column()
if row >= len(self.fish_list):
LogObject().print("Bad index {}/{}".format(row, len(self.fish_list) - 1))
return QtCore.QVariant()
if col == 0:
return self.fish_list[row].id
elif col == 1:
return self.fish_list[row].length
elif col == 2:
return self.fish_list[row].direction.name
elif col == 3:
return self.fish_list[row].frame_in
elif col == 4:
return self.fish_list[row].frame_out
elif col == 5:
return self.fish_list[row].duration
elif col == 6:
return len(self.fish_list[row].tracks)
else:
return QtCore.QVariant()
else:
return QtCore.QVariant()
def __init__(self,
display,
files,
save_directory,
parallel=1,
create_directory=True):
super().__init__()
LogObject().print("Display: ", display)
self.files = files
self.display = display
if create_directory:
date_time_directory = "batch_{}".format(
datetime.now().strftime("%Y-%m-%d-%H%M%S"))
self.save_directory = os.path.join(save_directory,
date_time_directory)
if not os.path.exists(self.save_directory):
os.mkdir(self.save_directory)
else:
self.save_directory = save_directory
self.thread_pool = QtCore.QThreadPool()
self.thread_pool.setMaxThreadCount(parallel + 1)
self.processes = []
self.active_processes = []
self.state = ProcessState.INITIALIZING
self.exit_time = time.time()
self.n_processes = 0
self.total_processes = len(self.files)
def finishTerminated(self):
"""
Handles the shutdown process initiated by method terminate.
"""
for proc_info in self.processes:
try:
proc_info.connection.send((-1, "Terminate"))
except BrokenPipeError as e:
# Process not yet active
pass
while True:
try:
id, msg = proc_info.connection.recv()
if id == -1:
break
except EOFError:
break
except ValueError:
# Received message with no id
continue
LogObject().print("File [{}] terminated.".format(proc_info.id))
for proc_info in self.processes:
if proc_info.process is not None:
proc_info.process.terminate()
self.exit_signal.emit(False)
def updateVerticalDetections(self):
LogObject().print("Updated")
self.vertical_detections = [
[d.center[0] for d in dets
if d.center is not None] if dets is not None else []
for dets in self.detections
]
def applySaveDictionary(self, data, dets):
"""
Load fish entries from data provided by SaveManager.
"""
self.clear()
for id, f_data in data.items():
f = None
for frame, det_label, track in f_data:
if f is None:
f = FishEntry(id, frame, frame)
if det_label is not None:
# Goes through detections in the same frame and tries to assign the
# corresponding detection based on the label.
frame_dets = dets[frame]
match_found = False
for fd in frame_dets:
if fd.label == det_label:
# Adds track with a matching detection to the FishEntry
f.addTrack(track, fd, frame)
match_found = True
break
if not match_found:
LogObject().print("Warning: Match not found in frame {} for label {}".format(frame, det_label))
else:
f.addTrack(track, None, frame)
self.all_fish[id] = f
self.trimFishList()
def terminate(self):
"""
Clears the thread pool and sets system state to TERMINATING,
which leads to clean shutdown of the processes.
"""
self.thread_pool.clear()
LogObject().print("Terminating")
self.state = ProcessState.TERMINATING
def run(self):
self.showWindow()
self.detector.initMOG()
for i in range(self.getFrameCount()):
self.readParameters()
images = self.detector.compute(i, self.getFrame(i), True)
LogObject().print(images)
self.updateWindows(*images)
def clearDetections(self):
LogObject().print("Cleared")
nof_frames = self.image_provider.getFrameCount()
self.detections = [None] * nof_frames
self.vertical_detections = []
#self.detections_clearable = False
self.applied_parameters = None
self.compute_on_event = True
self.state_changed_event()
def setParameterDict(self, dict):
for key, value in dict.items():
if hasattr(self, key) and key in PARAMETER_TYPES:
try:
setattr(self, key, PARAMETER_TYPES[key](value))
except ValueError as e:
LogObject().print(
"Error: Invalid value in detector parameters file,", e)
elif hasattr(self.mog_parameters, key) and key in PARAMETER_TYPES:
try:
setattr(self.mog_parameters, key,
PARAMETER_TYPES[key](value))
except ValueError as e:
LogObject().print(
"Error: Invalid value in detector parameters file,", e)
else:
LogObject().print("Error: Invalid parameters: {}: {}".format(
key, value))
def trackAll(self, detection_frames):
"""
Tracks all detections in the given frames. Updates tracks_by_frame and
signals when the computation has finished.
"""
self.tracking = True
self.stop_tracking = False
self.state_changed_signal.emit()
self.init_signal.emit()
if self.detector.allCalculationAvailable():
self.detector.computeAll()
if self.detector.allCalculationAvailable():
LogObject().print("Stopped before tracking.")
self.abortComputing(True)
return
count = len(detection_frames)
self.tracks_by_frame = {}
self.mot_tracker = Sort(max_age=self.parameters.max_age,
min_hits=self.parameters.min_hits,
search_radius=self.parameters.search_radius)
KalmanBoxTracker.count = 0
ten_perc = 0.1 * count
print_limit = 0
for i, dets in enumerate(detection_frames):
if i > print_limit:
LogObject().print("Tracking:", int(float(i) / count * 100),
"%")
print_limit += ten_perc
if self.stop_tracking:
LogObject().print("Stopped tracking at", i)
self.abortComputing(False)
return
self.tracks_by_frame[i] = self.trackBase(dets, i)
LogObject().print("Tracking: 100 %")
self.tracking = False
self.applied_parameters = self.parameters.copy()
self.applied_detector_parameters = self.detector.parameters.copy()
self.state_changed_signal.emit()
self.all_computed_signal.emit()
def connectToLogObject(self, format=None):
"""
Connect text_edit field to LogObject signal. A formatting function, which takes a string as input
and returns the modified string, can be provided for custom formatting, e.g. for adding a time stamp.
"""
log = LogObject()
if format:
log.connect(lambda s: self.appendText(format(s)))
else:
log.connect(lambda s: self.appendText(s + "\n"))
log.disconnectDefault()
def update_use_times(author):
"""
「./user_log/ユーザー名.csv」を読み込み、「date」、「use_times」列で一意のkeyとして
利用回数をインクリメントして更新する
Parameters
------------------------------
author : str
ユーザー名
Returns
------------------------------
Nothing
"""
current_date = datetime.date.today().strftime(
'%Y-%m-%d') #date型のままだとqueryの条件で型が一致しないため、strに変換する
user_log_data = pd.read_csv(f'{USER_FILE_PATH}/{author}.csv',
encoding='utf-8',
engine='python')
current_user_data = user_log_data.query(
'user_id == @author and date == @current_date')
log_obj = LogObject()
log_obj.user_id = author
log_obj.date = current_date
if len(current_user_data) == 0:
# 今日初めての利用の場合は、行が存在しないので、利用回数1回の行を新規で作成し、DataFrameに追加してcsvを更新する
log_obj.use_times = 1
s = pd.Series([log_obj.user_id, log_obj.date, log_obj.use_times],
index=user_log_data.columns)
user_log_data = user_log_data.append(s, ignore_index=True)
elif current_user_data['use_times'].values[0] != DATE_USE_LIMIT:
# 今日の今までの利用回数が19回以下の場合は、該当ユーザーのDataFrameの利用回数を+1してcsvを更新する
use_times = current_user_data['use_times'].values[0] + 1
user_log_data.loc[(user_log_data['user_id'] == author) &
(user_log_data['date'] == current_date),
['use_times']] = use_times
user_log_data.to_csv(f'{USER_FILE_PATH}/{author}.csv',
encoding='utf-8',
index=False)
def saveToFile(self, path):
"""
Tries to save all fish information (from all_fish dictionary) to a file.
"""
if(self.playback_manager.playback_thread is None):
LogObject().print("No file open, cannot save.")
return
try:
with open(path, "w") as file:
file.write("id;frame;length;distance;angle;direction;corner1 x;corner1 y;corner2 x;corner2 y;corner3 x;corner3 y;corner4 x;corner4 y; detection\n")
lines = self.getSaveLines()
lines.sort(key = lambda l: (l[0].id, l[1]))
for _, _, line in lines:
file.write(line)
LogObject().print("Tracks saved to path:", path)
except PermissionError as e:
LogObject().print("Cannot open file {}. Permission denied.".format(path))
def init_from_file(self, corners, length, distance, angle):
"""
Initialize detection parameters from a csv file. Data is not stored when exporting a csv file,
which means it cannot be recovered here. This mainly affects the visualization of the detection.
"""
self.corners = np.array(corners)
self.center = np.average(self.corners, axis=0)
LogObject().print(self.center)
self.length = length
self.distance = distance
self.angle = angle
def onBatchExit(self, finished):
"""
Called when the system is ready to start a new batch.
"""
LogObject().print("--- On batch exit ---")
self.start_btn.setText("Start")
self.start_btn.setEnabled(True)
self.batch_track = None
self.setStatusLabel()
def beginTrack(self, test=False):
"""
For each file in files, creates a Worker that runs track and places it in thread_pool.
Main thread is occupied with a call to communicate method.
"""
self.state = ProcessState.RUNNING
id = 0
worker = Worker(self.communicate)
self.thread_pool.start(worker)
if test:
# If using test file (defined in conf.json)
parent_conn, child_conn = mp.Pipe()
file = fh.getTestFilePath()
proc_info = ProcessInfo(id, file, parent_conn)
self.processes.append(proc_info)
worker = Worker(self.track, proc_info, child_conn, True)
self.thread_pool.start(worker)
LogObject().print("Created Worker for file " + file)
self.n_processes = 1
self.total_processes = 1
else:
# Normal use
for file in self.files:
parent_conn, child_conn = mp.Pipe()
proc_info = ProcessInfo(id, file, parent_conn)
self.processes.append(proc_info)
worker = Worker(self.track, proc_info, child_conn, False)
self.thread_pool.start(worker)
LogObject().print("Created Worker for file " + file)
id += 1
self.n_processes += 1
LogObject().print("Total processes:", self.n_processes)
def playbackTest():
"""
Test code to assure tracker works with detector.
"""
def forwardImage(tuple):
ind, frame = tuple
detections = detector.getDetection(ind)
image = cv2.applyColorMap(frame, cv2.COLORMAP_OCEAN)
image = tracker.visualize(image, ind)
figure.displayImage((ind, image))
def startDetector():
detector.initMOG()
detector.computeAll()
tracker.trackAll(detector.detections)
playback_manager.play()
app = QtWidgets.QApplication(sys.argv)
main_window = QtWidgets.QMainWindow()
playback_manager = PlaybackManager(app, main_window)
detector = Detector(playback_manager)
tracker = Tracker(detector)
playback_manager.fps = 10
playback_manager.openTestFile()
playback_manager.frame_available.connect(forwardImage)
detector.mog_parameters.nof_bg_frames = 500
detector._show_detections = True
playback_manager.mapping_done.connect(startDetector)
figure = TestFigure(playback_manager.togglePlay)
main_window.setCentralWidget(figure)
LogObject().print(detector.parameters)
LogObject().print(detector.parameters.mog_parameters)
LogObject().print(tracker.parameters)
main_window.show()
sys.exit(app.exec_())
def loadData(self, data, path):
try:
file_path = os.path.abspath(data["path"])
secondary_path = os.path.abspath(
os.path.join(os.path.dirname(path),
os.path.basename(file_path)))
self.playback_manager.checkLoadedFile(file_path, secondary_path,
True)
self.fish_manager.setUpDownInversion(data["inverted upstream"])
self.detector.parameters.setParameterDict(data["detector"])
self.tracker.parameters.setParameterDict(data["tracker"])
self.detector.applySaveDictionary(data["detections"])
dets = self.detector.detections
self.fish_manager.applySaveDictionary(data["fish"], dets)
except ValueError as e:
LogObject().print("Error: Invalid value(s) in save file,", e)
self.playback_manager.closeFile()
except KeyError as e:
LogObject().print("Error: Invalid key(s) in save file,", e)
self.playback_manager.closeFile()
def computeAll(self):
self.computing = True
self.stop_computing = False
self.compute_on_event = False
self.state_changed_event()
if self.mogParametersDirty():
self.initMOG()
if self.mogParametersDirty():
LogObject().print("Stopped before detecting.")
self.abortComputing(True)
return
count = self.image_provider.getFrameCount()
ten_perc = 0.1 * count
print_limit = 0
for ind in range(count):
if ind > print_limit:
LogObject().print("Detecting:", int(float(ind) / count * 100),
"%")
print_limit += ten_perc
if self.stop_computing:
LogObject().print("Stopped detecting at", ind)
self.abortComputing(False)
return
img = self.image_provider.getFrame(ind)
self.computeBase(ind, img)
LogObject().print("Detecting: 100 %")
self.computing = False
#self.detections_clearable = True
self.applied_parameters = self.parameters.copy()
self.updateVerticalDetections()
self.state_changed_event()
self.all_computed_event()
def processFinished(self, proc_info):
"""
Reduces n_processes by one and if none are remaining, emits the exit_signal
"""
LogObject().print("File {} finished.".format(proc_info.file))
self.n_processes -= 1
if self.n_processes <= 0:
# Let main thread (running communicate) know the process is about to quit
# and emit exit signal.
if self.state is not ProcessState.TERMINATING:
self.state = ProcessState.FINISHED
self.exit_time = time.time()
self.exit_signal.emit(True)
def removeFish(self, rows, update=True):
if(len(rows) > 0):
for row in sorted(rows, reverse=True):
if row >= len(self.fish_list):
continue
fish_id = self.fish_list[row].id
try:
del_f = self.all_fish.pop(fish_id)
del del_f
except KeyError:
LogObject().print("KeyError occured when removing entry with id:", fish_id)
if update:
self.trimFishList()
def communicate(self):
"""
Polls through all running processes and forwards all messages to LogObject.
"""
while self.state is ProcessState.RUNNING or self.state is ProcessState.INITIALIZING or time.time(
) < self.exit_time + 1:
for proc_info in self.processes:
if (proc_info.process and proc_info.process.is_alive()
and proc_info.connection.poll()):
LogObject().print(proc_info.id,
proc_info.connection.recv(),
end="")
time.sleep(0.01)
if self.state is ProcessState.TERMINATING:
self.finishTerminated()
def __init__(self,
app,
display,
file,
save_directory,
connection=None,
testFile=False):
super().__init__()
self.app = app
self.display = display
self.figure = None
self.file = file
self.save_directory = os.path.abspath(save_directory)
self.connection = connection
self.testFile = testFile
self.alive = True
self.save_detections = True
self.save_tracks = True
if display:
self.main_window = QtWidgets.QMainWindow()
else:
self.main_window = None
self.playback_manager = PlaybackManager(self.app, self.main_window)
self.detector = Detector(self.playback_manager)
self.tracker = Tracker(self.detector)
self.fish_manager = FishManager(self.playback_manager, self.tracker)
self.playback_manager.fps = 100
self.playback_manager.runInThread(self.listenConnection)
log = LogObject()
log.disconnectDefault()
#log.connect(writeToFile)
log.connect(self.writeToConnection)
log.print("Process created for file: ", self.file)
def showFish(self, fishNumber, inputDict):
## TODO _
# ffigure = self.MyFigureWidget
# ffigure.clear()
# self.MyFigureWidget.clear()
counter = 0
LogObject().print("Fish = ", fishNumber)
for i in inputDict["frames"]:
# ffigure.setUpdatesEnabled(False)
self.UI_FRAME_INDEX = i
x = int( inputDict["locations"][counter][0])
y = int( inputDict["locations"][counter][1])
self.marker = str(x)+','+str(y)
self.FSlider.setValue(self.UI_FRAME_INDEX)
self.marker = None
self.repaint()
counter +=1
self.marker = None
return
def trackBase(self, frame, ind):
"""
Performs tracking step for a single frame.
Returns (track, detection) if the track was updated this frame, otherwise (track, None).
"""
if frame is None:
LogObject().print(
"Invalid detector results encountered at frame " + str(ind) +
". Consider rerunning the detector.")
return self.mot_tracker.update()
detections = [d for d in frame if d.corners is not None]
if len(detections) > 0:
dets = np.array([
np.min(d.corners, 0).flatten().tolist() +
np.max(d.corners, 0).flatten().tolist() for d in detections
])
tracks = self.mot_tracker.update(dets)
else:
tracks = self.mot_tracker.update()
return [(tr, detections[int(tr[7])]) if tr[7] >= 0 else (tr, None)
for tr in tracks]
