def createPumpGroupBox(self):
self.pumpForm = QGroupBox("Pump settings")
self.pumpFormLayout = QFormLayout()
self.flowOff1_btn = QtGui.QPushButton('Increase')
self.flowOff0_btn = QtGui.QPushButton('Decrease')
self.flowOn1_btn = QtGui.QPushButton('Increase')
self.flowOn0_btn = QtGui.QPushButton('Decrease')
self.flowOn1_btn.clicked.connect(self.on_flowOn1)
self.flowOn0_btn.clicked.connect(self.on_flowOn0)
self.flowOff1_btn.clicked.connect(self.on_flowOff1)
self.flowOff0_btn.clicked.connect(self.on_flowOff0)
self.ardReset_btn = QtGui.QPushButton('reset flow')
self.ardReset_btn.clicked.connect(self.on_ARDreset)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.flowOn0_btn)
hbox.addWidget(self.flowOn1_btn)
hboxOff = QtGui.QHBoxLayout()
hboxOff.addWidget(self.flowOff0_btn)
hboxOff.addWidget(self.flowOff1_btn)
self.pumpFormLayout.addRow(QLabel("On time:"), hbox)
self.pumpFormLayout.addRow(QLabel("Off time:"), hboxOff)
self.pumpFormLayout.addRow(self.ardReset_btn)
self.pumpForm.setLayout(self.pumpFormLayout)
def createImageGroupBox(self):
self.imageForm = QGroupBox('Imaging')
self.imageLayout = QGridLayout()
##raw image
self.imv1 = RawImageWidget(scaled=True)
## tracking
self.imv2 = RawImageWidget(scaled=True)
## mask
self.imv3 = RawImageWidget(scaled=True)
## avergae
self.imv4 = RawImageWidget(scaled=True)
## set background image
self.imv1.setImage(self.bkImage)
self.imageLayout.addWidget(QLabel("Raw:"), 0, 0, 1, 1)
self.imageLayout.addWidget(QLabel("Detection:"), 0, 1, 1, 1)
self.imageLayout.addWidget(self.imv1, 1, 0, 1, 1)
self.imageLayout.addWidget(self.imv2, 1, 1, 1, 1)
self.imageLayout.addWidget(QLabel("Mask:"), 2, 0, 1, 1)
self.imageLayout.addWidget(QLabel("Moving average:"), 2, 1, 1, 1)
self.imageLayout.addWidget(self.imv3, 3, 0, 1, 1)
self.imageLayout.addWidget(self.imv4, 3, 1, 1, 1)
self.imageForm.setLayout(self.imageLayout)
def __init__(self, scheme, parent):
super(EditorSchemeDesigner, self).__init__(parent, Qt.Dialog)
self.original_style = copy.copy(resources.CUSTOM_SCHEME)
self._avoid_on_loading, self.saved, self._components = True, False, {}
self.setWindowTitle(translations.TR_PREFERENCES_EDITOR_SCHEME_DESIGNER)
self.setMinimumSize(450, 480)
self.setMaximumSize(500, 900)
self.resize(450, 600)
# all layouts and groupboxes
group0 = QGroupBox(translations.TR_PROJECT_NAME) # scheme filename
group1 = QGroupBox(translations.TR_PROJECT_PROPERTIES) # properties
group2 = QGroupBox(translations.TR_PREVIEW) # quick preview thingy
group0_hbox, group1_vbox = QHBoxLayout(group0), QVBoxLayout(group1)
this_dialog_vbox, group2_vbox = QVBoxLayout(self), QVBoxLayout(group2)
self._grid, scrollArea, frame = QGridLayout(), QScrollArea(), QFrame()
# widgets
self.line_name, btnSave = QLineEdit(), QPushButton(
translations.TR_SAVE)
self.line_name.setPlaceholderText(getuser().capitalize() + "s_scheme")
group0_hbox.addWidget(self.line_name)
group0_hbox.addWidget(btnSave)
self.connect(btnSave, SIGNAL("clicked()"), self.save_scheme)
_demo = "<center>" + ascii_letters # demo text for preview
self.preview_label1, self.preview_label2 = QLabel(_demo), QLabel(_demo)
group2_vbox.addWidget(self.preview_label1)
group2_vbox.addWidget(self.preview_label2)
# rows titles
self._grid.addWidget(QLabel("<b>" + translations.TR_PROJECT_NAME), 0,
0)
self._grid.addWidget(QLabel("<b>" + translations.TR_CODE), 0, 1)
self._grid.addWidget(
QLabel("<b>" + translations.TR_EDITOR_SCHEME_PICK_COLOR), 0, 2)
# fill rows
for key in sorted(tuple(resources.COLOR_SCHEME.keys())):
self.add_item(key, scheme)
self.preview_label1.setStyleSheet('background:transparent')
self.preview_label2.setStyleSheet('color: transparent')
# fill the scroll area
frame.setLayout(self._grid)
scrollArea.setWidget(frame)
group1_vbox.addWidget(scrollArea)
# put groups on the dialog
this_dialog_vbox.addWidget(group1)
this_dialog_vbox.addWidget(group2)
this_dialog_vbox.addWidget(group0)
self._avoid_on_loading = self._modified = False
def createCalibrationFormGroupBox(self):
self.calibrationForm = QGroupBox("Image Calibration")
self.calibrationLayout = QFormLayout()
self.slider = QSlider(Qt.Horizontal)
self.slider.setMinimum(0)
self.slider.setMaximum(255)
self.slider.setValue(self.pVal)
self.slider.setTickPosition(QSlider.TicksBelow)
self.slider.setTickInterval(10)
self.slider.valueChanged.connect(self.on_slidervaluechange)
self.textSlider = QtGui.QLineEdit(str(self.pVal))
hbox_mn = QtGui.QHBoxLayout()
hbox_mn.addWidget(self.slider)
hbox_mn.addWidget(self.textSlider)
self.slider2 = QSlider(Qt.Horizontal)
self.slider2.setMinimum(0)
self.slider2.setMaximum(255)
self.slider2.setValue(self.pVal_mx)
self.slider2.setTickPosition(QSlider.TicksBelow)
self.slider2.setTickInterval(10)
self.slider2.valueChanged.connect(self.on_slider2valuechange)
self.textSlider2 = QtGui.QLineEdit(str(self.pVal_mx),self.win)
hbox_mx = QtGui.QHBoxLayout()
hbox_mx.addWidget(self.slider2)
hbox_mx.addWidget(self.textSlider2)
self.ROIslider= QSlider(Qt.Horizontal)
self.ROIslider.setMinimum(0)
self.ROIslider.setMaximum(1000)
self.ROIslider.setValue(self.area_mn)
self.ROIslider.setTickPosition(QSlider.TicksBelow)
self.ROIslider.setTickInterval(100)
self.ROIslider.valueChanged.connect(self.on_ROIslidervaluechange)
self.ROItextSlider = QLineEdit(str(self.area_mn))
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.ROIslider)
hbox.addWidget(self.ROItextSlider)
self.calibrationLayout.addRow(QLabel("ROI max area:"),hbox)
self.calibrationLayout.addRow(QLabel("px min:"), hbox_mn)
self.calibrationLayout.addRow(QLabel("px max:"), hbox_mx)
self.calibrationForm.setLayout(self.calibrationLayout)
def createTextGroupBox(self):
self.textForm = QGroupBox('Imaging')
self.textLayout = QFormLayout()
## parameters
self.maxArea_box = QtGui.QLineEdit()
self.num_detected_box = QtGui.QLineEdit()
self.maxArea_box.setText('0')
self.num_detected_box.setText('0')
hbox = QtGui.QHBoxLayout()
hbox.addWidget(QLabel("max area:"))
hbox.addWidget(self.maxArea_box)
hboxD = QtGui.QHBoxLayout()
hboxD.addWidget(QLabel("fish #:"))
hboxD.addWidget(self.num_detected_box)
self.textLayout.addRow(hbox)
self.textLayout.addRow(hboxD)
self.textForm.setLayout(self.textLayout)
def createParamGroupBox(self):
self.paramForm = QGroupBox("Trial parameters")
self.paramFormLayout = QFormLayout()
self.Timer_tbox = QtGui.QLineEdit()
self.trialTime_tbox = QtGui.QLineEdit()
self.trialTime_tbox.textChanged.connect(self.on_trialTime_changed)
self.trialSleepTime_tbox = QtGui.QLineEdit()
self.trialSleepTime_tbox.textChanged.connect(self.on_trialSleepTime_changed)
self.trialTime_tbox.setText(str(self.trialTime))
self.trialSleepTime_tbox.setText(str(self.trialSleepTime))
self.Timer_tbox.setText(str(0))
self.paramFormLayout.addRow(QLabel("Trial time:"), self.trialTime_tbox)
self.paramFormLayout.addRow(QLabel("Stimulus time:"), self.trialSleepTime_tbox)
self.paramFormLayout.addRow(QLabel("Time left:"), self.Timer_tbox)
self.paramFormLayout.addRow(QLabel("Time:"), QSpinBox())
self.paramForm.setLayout(self.paramFormLayout)
def createSwitchFormGroupBox(self):
self.switchForm = QGroupBox("Controller")
self.switchLayout = QFormLayout()
######################
#### Trial/Lights
#####################
self.lightOn_btn = QtGui.QPushButton('Light On', self.win)
self.lightOn_btn.clicked.connect(self.on_lightOn)
self.lightOff_btn = QtGui.QPushButton('Light Off', self.win)
self.lightOff_btn.clicked.connect(self.on_lightOff)
self.trialOn_btn = QtGui.QPushButton('Start Trial', self.win)
self.trialOn_btn.clicked.connect(self.on_trialOn)
self.trialOff_btn = QtGui.QPushButton('Stop Trial', self.win)
self.trialOff_btn.clicked.connect(self.on_trialOff)
self.switchLayout.addRow(self.lightOn_btn, self.lightOff_btn)
self.switchLayout.addRow(self.trialOn_btn, self.trialOff_btn)
self.switchForm.setLayout(self.switchLayout)
def __init__(self, parent):
super(EditorCompletion, self).__init__()
self._preferences = parent
vbox = QVBoxLayout(self)
groupBoxClose = QGroupBox(translations.TR_PREF_EDITOR_COMPLETE)
formClose = QGridLayout(groupBoxClose)
formClose.setContentsMargins(5, 15, 5, 5)
self._checkParentheses = QCheckBox(
translations.TR_PREF_EDITOR_PARENTHESES + " ()")
self._checkParentheses.setChecked('(' in settings.BRACES)
self._checkKeys = QCheckBox(translations.TR_PREF_EDITOR_KEYS + " {}")
self._checkKeys.setChecked('{' in settings.BRACES)
self._checkBrackets = QCheckBox(translations.TR_PREF_EDITOR_BRACKETS +
" []")
self._checkBrackets.setChecked('[' in settings.BRACES)
self._checkSimpleQuotes = QCheckBox(
translations.TR_PREF_EDITOR_SIMPLE_QUOTES)
self._checkSimpleQuotes.setChecked("'" in settings.QUOTES)
self._checkDoubleQuotes = QCheckBox(
translations.TR_PREF_EDITOR_DOUBLE_QUOTES)
self._checkDoubleQuotes.setChecked('"' in settings.QUOTES)
self._checkCompleteDeclarations = QCheckBox(
translations.TR_PREF_EDITOR_COMPLETE_DECLARATIONS.format(
resources.get_shortcut("Complete-Declarations").toString(
QKeySequence.NativeText)))
self._checkCompleteDeclarations.setChecked(
settings.COMPLETE_DECLARATIONS)
formClose.addWidget(self._checkParentheses,
1,
1,
alignment=Qt.AlignTop)
formClose.addWidget(self._checkKeys, 1, 2, alignment=Qt.AlignTop)
formClose.addWidget(self._checkBrackets, 2, 1, alignment=Qt.AlignTop)
formClose.addWidget(self._checkSimpleQuotes,
2,
2,
alignment=Qt.AlignTop)
formClose.addWidget(self._checkDoubleQuotes,
3,
1,
alignment=Qt.AlignTop)
vbox.addWidget(groupBoxClose)
groupBoxCode = QGroupBox(translations.TR_PREF_EDITOR_CODE_COMPLETION)
formCode = QGridLayout(groupBoxCode)
formCode.setContentsMargins(5, 15, 5, 5)
self._checkCodeDot = QCheckBox(
translations.TR_PREF_EDITOR_ACTIVATE_COMPLETION)
self._checkCodeDot.setChecked(settings.CODE_COMPLETION)
formCode.addWidget(self._checkCompleteDeclarations,
5,
1,
alignment=Qt.AlignTop)
formCode.addWidget(self._checkCodeDot, 6, 1, alignment=Qt.AlignTop)
vbox.addWidget(groupBoxCode)
vbox.addItem(
QSpacerItem(0, 10, QSizePolicy.Expanding, QSizePolicy.Expanding))
self.connect(self._preferences, SIGNAL("savePreferences()"), self.save)
class MyLiveTracker(object):
def __init__(self, opt=1):
##########################
##### default saving directory
##########################
self.default_path = '/Users/virginiarutten/Documents/deep_fish/videos'
self.filename = 'test'
self.ext = '.avi'
self.dt = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")[2:]
self.foldername = self.default_path + '/' + self.dt[:6]
self.path = self.get_path()
self.check_dir()
self.save = False
self.cameraPort = 1
self.recording = False
self.trialOn = False
self.flowOn = False
self.ARD = False
self.trialTime = 10
self.trialSleepTime = 10
##########################
##### Arduino settings
##########################
self.flowOffDelay = 1
self.flowOnDelay = 1
self.imW = int(640 / 2)
self.imH = int(360 / 2)
self.imfps = 25
self.trialTimer = MyTimer()
self.trialTimer.restart()
self.ite = 0
self.args = self.initialise_tracking_variables()
self.win = self.initialise_window()
self.recorder = self.initialise_videorecorder()
self.Tracker = self.initialise_tracker()
##########################
##### Arduino
##########################
self.ARDPort = self.ArdPortComboBox.currentData()
self.Ard = self.initialise_Ard()
##########################
##### Threads
##########################
self.recordingThread = MyThread(self.start_recording)
self.recordingThread.start()
self.trialThread = MyThread(self.start_trial)
self.trialThread.start()
self.recording = True
def check_dir(self):
''' check that directory of the day exisits
and that filename is unique'''
if not os.path.isdir(self.foldername):
print('creating directory...')
os.mkdir(self.foldername)
file_num = 1
while os.path.exists(self.path):
print('file already exisits...\nrenaming')
print(self.path)
self.filename = self.filename + str(file_num)
file_num += 1
self.path = self.get_path()
def initialise_tracker(self):
self.Tracker = MyRealTimeTracker(self.args)
return self.Tracker
def initialise_tracking_variables(self):
''' default values '''
self.keypoints = {}
self.mvAvgFrame = None
self.fishNum = 4
self.area_mn = 35
## threshold mask value
self.pVal = 180
self.pVal_mx = 255
self.text = None
self.pre_frames = 5
self.args = {}
self.args['pVal'] = self.pVal
self.args['pVal_mx'] = self.pVal_mx
self.args['fishNum'] = self.fishNum
self.args['area_mn'] = self.area_mn
self.args['keypoints'] = self.keypoints
self.args['pre_frames'] = self.pre_frames
return self.args
def get_path(self):
return self.foldername + '/' + self.dt + self.filename + self.ext
def initialise_videorecorder(self):
''' initialises recorder'''
self.num_saved_frame = 0
self.cameraPort = self.cameraComboBox.currentIndex()
self.check_dir()
if self.path[-3:] != 'avi':
print('please check extension')
print('initialising recording...\noutput file:{0}'.\
format(self.path))
self.recorder = MyVideoRecorder(cameraport = self.cameraPort,\
path = self.path,\
imH = self.imH,\
imW = self.imW,\
fps = self.imfps)
wasrecording = False
if self.recording:
wasrecording = True
self.recording = False
self.recorder.initialise_camera() ### reinitialise camera
self.camera = self.recorder.camera ### test camera works
if self.camera.grab() == False:
if self.cameraPort == 1:
self.cameraPort = 0
self.cameraComboBox.setCurrentIndex(self.cameraPort)
print('no camera detected... camera changed')
if wasrecording:
self.recording = True
else:
self.recording = False
wasrecording = False
return self.recorder
def initialise_Ard(self):
try:
self.Ard = MyArduino()
self.ARDport = self.Ard.port
self.ARD = True
except:
print('no valid port found \nplease check')
self.ARD = False
return self.Ard
def load_picture(self):
file_path = '/Users/virginiarutten/Documents/deep_fish/assets/pavlov_dog.jpg'
self.bkImage = np.array(Image.open(file_path)).T
def initialise_window(self):
self.load_picture()
self.app = QApplication([])
self.win = MyQtWidget()
#####################################
## Layout
#####################################
self.layout = QGridLayout()
self.win.setLayout(self.layout)
self.createRecordGroupBox()
self.createDefaultGroupBox()
self.createImageGroupBox()
self.createSwitchFormGroupBox()
self.createCalibrationFormGroupBox()
self.createParamGroupBox()
self.createPumpGroupBox()
self.createTextGroupBox()
self.resetPath()
self.layout.addWidget(self.imageForm, 0, 0, 1, 3)
self.layout.addWidget(self.textForm, 0, 4, 1, 3)
self.layout.addWidget(self.paramForm, 2, 0, 1, 1)
self.layout.addWidget(self.calibrationForm, 2, 1, 1, 1)
self.layout.addWidget(self.pumpForm, 2, 2, 1, 1)
self.layout.addWidget(self.switchForm, 3, 1, 1, 1)
self.layout.addWidget(self.defaultForm, 3, 2, 1, 1)
self.layout.addWidget(self.recordForm, 3, 0, 1, 1)
self.win.show()
return self.win
def createImageGroupBox(self):
self.imageForm = QGroupBox('Imaging')
self.imageLayout = QGridLayout()
##raw image
self.imv1 = RawImageWidget(scaled=True)
## tracking
self.imv2 = RawImageWidget(scaled=True)
## mask
self.imv3 = RawImageWidget(scaled=True)
## avergae
self.imv4 = RawImageWidget(scaled=True)
## set background image
self.imv1.setImage(self.bkImage)
self.imageLayout.addWidget(QLabel("Raw:"), 0, 0, 1, 1)
self.imageLayout.addWidget(QLabel("Detection:"), 0, 1, 1, 1)
self.imageLayout.addWidget(self.imv1, 1, 0, 1, 1)
self.imageLayout.addWidget(self.imv2, 1, 1, 1, 1)
self.imageLayout.addWidget(QLabel("Mask:"), 2, 0, 1, 1)
self.imageLayout.addWidget(QLabel("Moving average:"), 2, 1, 1, 1)
self.imageLayout.addWidget(self.imv3, 3, 0, 1, 1)
self.imageLayout.addWidget(self.imv4, 3, 1, 1, 1)
self.imageForm.setLayout(self.imageLayout)
def createTextGroupBox(self):
self.textForm = QGroupBox('Imaging')
self.textLayout = QFormLayout()
## parameters
self.maxArea_box = QtGui.QLineEdit()
self.num_detected_box = QtGui.QLineEdit()
self.maxArea_box.setText('0')
self.num_detected_box.setText('0')
hbox = QtGui.QHBoxLayout()
hbox.addWidget(QLabel("max area:"))
hbox.addWidget(self.maxArea_box)
hboxD = QtGui.QHBoxLayout()
hboxD.addWidget(QLabel("fish #:"))
hboxD.addWidget(self.num_detected_box)
self.textLayout.addRow(hbox)
self.textLayout.addRow(hboxD)
self.textForm.setLayout(self.textLayout)
def createSwitchFormGroupBox(self):
self.switchForm = QGroupBox("Controller")
self.switchLayout = QFormLayout()
######################
#### Trial/Lights
#####################
self.lightOn_btn = QtGui.QPushButton('Light On', self.win)
self.lightOn_btn.clicked.connect(self.on_lightOn)
self.lightOff_btn = QtGui.QPushButton('Light Off', self.win)
self.lightOff_btn.clicked.connect(self.on_lightOff)
self.trialOn_btn = QtGui.QPushButton('Start Trial', self.win)
self.trialOn_btn.clicked.connect(self.on_trialOn)
self.trialOff_btn = QtGui.QPushButton('Stop Trial', self.win)
self.trialOff_btn.clicked.connect(self.on_trialOff)
self.switchLayout.addRow(self.lightOn_btn, self.lightOff_btn)
self.switchLayout.addRow(self.trialOn_btn, self.trialOff_btn)
self.switchForm.setLayout(self.switchLayout)
def createCalibrationFormGroupBox(self):
self.calibrationForm = QGroupBox("Image Calibration")
self.calibrationLayout = QFormLayout()
self.slider = QSlider(Qt.Horizontal)
self.slider.setMinimum(0)
self.slider.setMaximum(255)
self.slider.setValue(self.pVal)
self.slider.setTickPosition(QSlider.TicksBelow)
self.slider.setTickInterval(10)
self.slider.valueChanged.connect(self.on_slidervaluechange)
self.textSlider = QtGui.QLineEdit(str(self.pVal))
hbox_mn = QtGui.QHBoxLayout()
hbox_mn.addWidget(self.slider)
hbox_mn.addWidget(self.textSlider)
self.slider2 = QSlider(Qt.Horizontal)
self.slider2.setMinimum(0)
self.slider2.setMaximum(255)
self.slider2.setValue(self.pVal_mx)
self.slider2.setTickPosition(QSlider.TicksBelow)
self.slider2.setTickInterval(10)
self.slider2.valueChanged.connect(self.on_slider2valuechange)
self.textSlider2 = QtGui.QLineEdit(str(self.pVal_mx), self.win)
hbox_mx = QtGui.QHBoxLayout()
hbox_mx.addWidget(self.slider2)
hbox_mx.addWidget(self.textSlider2)
self.ROIslider = QSlider(Qt.Horizontal)
self.ROIslider.setMinimum(0)
self.ROIslider.setMaximum(1000)
self.ROIslider.setValue(self.area_mn)
self.ROIslider.setTickPosition(QSlider.TicksBelow)
self.ROIslider.setTickInterval(100)
self.ROIslider.valueChanged.connect(self.on_ROIslidervaluechange)
self.ROItextSlider = QLineEdit(str(self.area_mn))
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.ROIslider)
hbox.addWidget(self.ROItextSlider)
self.calibrationLayout.addRow(QLabel("ROI max area:"), hbox)
self.calibrationLayout.addRow(QLabel("px min:"), hbox_mn)
self.calibrationLayout.addRow(QLabel("px max:"), hbox_mx)
self.calibrationForm.setLayout(self.calibrationLayout)
def createPumpGroupBox(self):
self.pumpForm = QGroupBox("Pump settings")
self.pumpFormLayout = QFormLayout()
self.flowOff1_btn = QtGui.QPushButton('Increase')
self.flowOff0_btn = QtGui.QPushButton('Decrease')
self.flowOn1_btn = QtGui.QPushButton('Increase')
self.flowOn0_btn = QtGui.QPushButton('Decrease')
self.flowOn1_btn.clicked.connect(self.on_flowOn1)
self.flowOn0_btn.clicked.connect(self.on_flowOn0)
self.flowOff1_btn.clicked.connect(self.on_flowOff1)
self.flowOff0_btn.clicked.connect(self.on_flowOff0)
self.ardReset_btn = QtGui.QPushButton('reset flow')
self.ardReset_btn.clicked.connect(self.on_ARDreset)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.flowOn0_btn)
hbox.addWidget(self.flowOn1_btn)
hboxOff = QtGui.QHBoxLayout()
hboxOff.addWidget(self.flowOff0_btn)
hboxOff.addWidget(self.flowOff1_btn)
self.pumpFormLayout.addRow(QLabel("On time:"), hbox)
self.pumpFormLayout.addRow(QLabel("Off time:"), hboxOff)
self.pumpFormLayout.addRow(self.ardReset_btn)
self.pumpForm.setLayout(self.pumpFormLayout)
def createParamGroupBox(self):
self.paramForm = QGroupBox("Trial parameters")
self.paramFormLayout = QFormLayout()
self.Timer_tbox = QtGui.QLineEdit()
self.trialTime_tbox = QtGui.QLineEdit()
self.trialTime_tbox.textChanged.connect(self.on_trialTime_changed)
self.trialSleepTime_tbox = QtGui.QLineEdit()
self.trialSleepTime_tbox.textChanged.connect(
self.on_trialSleepTime_changed)
self.trialTime_tbox.setText(str(self.trialTime))
self.trialSleepTime_tbox.setText(str(self.trialSleepTime))
self.Timer_tbox.setText(str(0))
self.paramFormLayout.addRow(QLabel("Trial time:"), self.trialTime_tbox)
self.paramFormLayout.addRow(QLabel("Stimulus time:"),
self.trialSleepTime_tbox)
self.paramFormLayout.addRow(QLabel("Time left:"), self.Timer_tbox)
self.paramFormLayout.addRow(QLabel("Time:"), QSpinBox())
self.paramForm.setLayout(self.paramFormLayout)
def createDefaultGroupBox(self):
self.defaultForm = QtGui.QGroupBox("Video capture")
self.defaultFormLayout = QFormLayout()
self.ArdPortComboBox = QComboBox()
self.ArdPortComboBox.addItem("Port 14511", '/dev/cu.usbmodem14511')
self.ArdPortComboBox.addItem("Port 14311", '/dev/cu.usbmodem14311')
self.ArdPortComboBox.addItem("Port 1461", '/dev/cu.usbmodem1461')
self.ArdPortComboBox.currentIndexChanged.connect(self.on_setARDport)
self.cameraComboBox = QComboBox()
self.cameraComboBox.addItem("0", '0')
self.cameraComboBox.addItem("1", '1')
self.cameraComboBox.currentIndexChanged.connect(self.on_setcameraport)
self.start_btn = QtGui.QPushButton('start')
self.start_btn.clicked.connect(self.on_start)
## stop flow button
self.stop_btn = QtGui.QPushButton('stop')
self.stop_btn.clicked.connect(self.on_stop)
## quit app button
self.qbtn = QtGui.QPushButton('exit')
self.qbtn.clicked.connect(self.on_quit)
self.qbtn.clicked.connect(QtCore.QCoreApplication.instance().quit)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.start_btn)
hbox.addWidget(self.stop_btn)
hbox.addWidget(self.qbtn)
self.defaultFormLayout.addRow(hbox)
self.defaultFormLayout.addRow(QLabel("Arduino Port:"),\
self.ArdPortComboBox)
self.defaultFormLayout.addRow(QLabel("camera:"),\
self.cameraComboBox)
self.defaultForm.setLayout(self.defaultFormLayout)
def createRecordGroupBox(self):
self.recordForm = QtGui.QGroupBox("Video capture")
self.recordFormLayout = QFormLayout()
self.path_bx = QtGui.QLineEdit()
self.resetPath()
self.file_btn = QtGui.QPushButton("save to")
self.file_btn.clicked.connect(self.on_getfile)
self.file_bx = QtGui.QLineEdit()
self.file_bx.textChanged.connect(self.on_fileChange)
self.file_bx.setText(self.filename)
self.save_btn = QtGui.QCheckBox()
self.save_btn.setChecked(self.save)
self.save_btn.stateChanged.connect(self.on_saveClick)
hbox = QtGui.QHBoxLayout()
self.recordFormLayout.addRow(self.file_btn, self.file_bx)
self.recordFormLayout.addRow(QLabel("path:"), self.path_bx)
self.recordFormLayout.addRow(QLabel("save:"), self.save_btn)
self.recordForm.setLayout(self.recordFormLayout)
#################
### slots
################
@pyqtSlot()
def on_getfile(self):
self.foldername = QtGui.QFileDialog.getExistingDirectory()
self.resetPath()
@pyqtSlot()
def on_fileChange(self):
self.filename = self.file_bx.text()
self.resetPath()
@pyqtSlot()
def on_setcameraport(self):
self.initialise_videorecorder()
@pyqtSlot()
def on_trialTime_changed(self):
try:
self.trialTime = int(self.trialTime_tbox.text())
except:
self.trialTime_tbox.setText(str(1))
print('only integrs valid')
@pyqtSlot()
def on_trialSleepTime_changed(self):
try:
self.trialSleepTime = int(self.trialSleepTime_tbox.text())
except:
self.trialSleepTime_tbox.setText(str(1))
print('only integrs valid')
@pyqtSlot()
def on_setARDport(self):
pass
# if self.ARD:
# self.ARDPort = self.ArdPortComboBox.currentData()
# print('ARD port set to ={0}'.format(self.ARDPort))
# else:
# print('no ARD detected')
@pyqtSlot()
def on_trialOn(self):
print('trial starting')
self.flowOn = False
self.resetARD()
self.trialTimer.restart()
self.trialOn = True
@pyqtSlot()
def on_trialOff(self):
print('trial ended')
self.trialTimer.restart()
self.trialOn = False
self.flowOn = False
self.resetARD()
@pyqtSlot()
def on_ARDreset(self):
print('resetting ARD')
self.resetFlowRate()
@pyqtSlot()
def on_flowOn1(self):
print('changing flow rate')
try:
self.Ard.sendChar('u')
self.resetARD()
except:
pass
@pyqtSlot()
def on_flowOn0(self):
print('changing flow rate')
try:
self.Ard.sendChar('d')
self.resetARD()
except:
pass
@pyqtSlot()
def on_flowOff1(self):
print('changing flow rate')
try:
self.Ard.sendChar('k')
self.resetARD()
except:
pass
@pyqtSlot()
def on_flowOff0(self):
print('changing flow rate')
try:
self.Ard.sendChar('j')
self.resetARD()
except:
pass
@pyqtSlot()
def on_lightOn(self):
self.flowOn = True
self.resetARD()
@pyqtSlot()
def on_lightOff(self):
self.flowOn = False
self.resetARD()
@pyqtSlot()
def on_slidervaluechange(self):
self.pVal = int(self.slider.value())
self.Tracker.pVal = self.pVal
self.textSlider.setText(str(self.pVal))
@pyqtSlot()
def on_slider2valuechange(self):
self.pVal_mx = int(self.slider2.value())
self.Tracker.pVal_mx = self.pVal_mx
self.textSlider2.setText(str(self.pVal_mx))
@pyqtSlot()
def on_ROIslidervaluechange(self):
self.area_mn = int(self.ROIslider.value())
self.Tracker.area_mn = self.area_mn
self.ROItextSlider.setText(str(self.area_mn))
@pyqtSlot()
def on_start(self):
if self.recording:
print('current recording being stopping...')
print('number of previously saved frames:\n{0}'.\
format(self.num_saved_frame))
self.recording = False
sleep(0.02)
try:
self.recorder.release_writer()
except:
pass
sleep(0.02)
print('new recording starting...')
self.initialise_videorecorder()
self.recording = True
@pyqtSlot()
def on_saveClick(self):
self.on_start()
if self.save_btn.isChecked():
try:
self.recorder.initialise_writer()
print('writer initialised')
sleep(0.02)
self.save = self.save_btn.isChecked()
except:
print('couldn\'t initialise writer')
else:
try:
self.recorder.release_writer()
except:
print('couldn\'t release writer')
pass
@pyqtSlot()
def on_stop(self):
print('current recording being stopping...')
print('number of previously saved frames:\n{0}'.\
format(self.num_saved_frame))
self.recording = False
self.save = False
self.save_btn.setChecked(self.save)
try:
self.recorder.release_writer()
self.num_saved_frame = 0
except:
pass
@pyqtSlot()
def on_ROIinit(self):
print('initiliase ROI')
self.initialise_ROI()
@pyqtSlot()
def on_quit(self):
print('stopping threads...')
self.flowOn = False
self.resetARD()
self.recording = False
self.trialOn = False
sleep(0.5)
print('number saved frames:\n{0}'.\
format(self.num_saved_frame))
try:
self.recorder.release_writer()
except:
pass
try:
self.recorder.release_camera()
except:
pass
self.recordingThread.stop()
self.trialThread.stop()
def resetARD(self):
if self.flowOn == False:
if self.ARD:
print('0')
self.Ard.sendChar('0')
if self.flowOn == True:
if self.ARD:
self.Ard.sendChar('1')
def resetFlowRate(self):
if self.ARD:
self.Ard.sendChar('r')
self.resetARD()
def resetPath(self):
self.dt = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")[2:]
self.path = self.get_path()
self.path_bx.setText(self.path)
def kill_threads(self):
self.recording = False
self.trialOn = False
def start_recording(self):
while self.recording:
self.frame_loop()
def start_trial(self):
while self.trialOn:
self.trial_loop()
##########################
##### Thread functions
##########################
def trial_loop(self):
time_ = self.trialTimer.get_time()
self.time_left = self.trialTime - int(time_)
self.Timer_tbox.setText(str(self.time_left))
if time_ > self.trialTime:
print('new trial')
self.flowOn = True
self.resetARD()
sleep(int(self.trialSleepTime))
self.flowOn = False
self.resetARD()
self.trialTimer.restart()
def frame_loop(self):
self.gray = self.grab_frame()
self.blur = self.Tracker.blur_frame(self.gray)
self.mvAvgFrame = self.update_avg()
self.fD = self.Tracker.delta_frame(self.mvAvgFrame, self.blur)
self.mask, self.masked = self.Tracker.mask_frame(self.fD,
pVal=self.pVal,
pVal_mx=self.pVal_mx)
self.fD_, self.keypoints, self.num_fish_detected, self.max_a\
= self.Tracker.get_frame_contours(self.masked, self.fD)
self.maxArea_box.setText(str(self.max_a))
self.num_detected_box.setText(str(self.num_fish_detected))
if self.save:
self.num_saved_frame += 1
try:
self.recorder.save_frame(self.gray)
except:
print('couldn\'t save file')
self.show_frame()
##########################
##### detection functions
##########################
def grab_frame(self):
try:
(grabbed, frame) = self.camera.read()
self.frame = cv2.resize(frame, (self.imW, self.imH))
self.gray = cv2.cvtColor(self.frame, cv2.COLOR_BGR2GRAY)
#self.frame = cv2.cvtColor(self.frame , cv2.COLOR_BGR2HSV)[:,:,1] # saturation
except:
print('couldn\'t grab frame')
pass
return self.gray
def update_avg(self):
if self.mvAvgFrame is None:
self.mvAvgFrame = self.blur
else:
self.ite += 1
fr = self.ite
if fr > 10000:
print('reset')
self.ite = 1
self.mvAvgFrame = self.mvAvgFrame
else:
self.mvAvgFrame = self.mvAvgFrame * (
fr / (fr + 1)) + self.blur / (fr + 1)
return self.mvAvgFrame
def show_frame(self):
if self.ite % 4 == 0:
self.imv1.setImage(self.gray.T)
elif self.ite % 4 == 1:
self.imv4.setImage(self.mvAvgFrame.T.astype('uint8'))
elif self.ite % 4 == 2:
self.imv2.setImage(self.fD_.swapaxes(0, 1))
elif self.ite % 4 == 3:
self.imv3.setImage(self.mask.T)
def test(self):
window = QWidget()
layout = QVBoxLayout()
window.setLayout(layout)
stack = stackedwidget.AnimatedStackedWidget()
stack.transitionFinished.connect(self.app.exit)
layout.addStretch(2)
layout.addWidget(stack)
layout.addStretch(2)
window.show()
widget1 = QLabel("A label " * 10)
widget1.setWordWrap(True)
widget2 = QGroupBox("Group")
widget3 = QListView()
self.assertEqual(stack.count(), 0)
self.assertEqual(stack.currentIndex(), -1)
stack.addWidget(widget1)
self.assertEqual(stack.count(), 1)
self.assertEqual(stack.currentIndex(), 0)
stack.addWidget(widget2)
stack.addWidget(widget3)
self.assertEqual(stack.count(), 3)
self.assertEqual(stack.currentIndex(), 0)
def widgets():
return [stack.widget(i) for i in range(stack.count())]
self.assertSequenceEqual([widget1, widget2, widget3], widgets())
stack.show()
stack.removeWidget(widget2)
self.assertEqual(stack.count(), 2)
self.assertEqual(stack.currentIndex(), 0)
self.assertSequenceEqual([widget1, widget3], widgets())
stack.setCurrentIndex(1)
# wait until animation finished
self.app.exec_()
self.assertEqual(stack.currentIndex(), 1)
widget2 = QGroupBox("Group")
stack.insertWidget(1, widget2)
self.assertEqual(stack.count(), 3)
self.assertEqual(stack.currentIndex(), 2)
self.assertSequenceEqual([widget1, widget2, widget3], widgets())
stack.transitionFinished.disconnect(self.app.exit)
self.singleShot(2000, lambda: stack.setCurrentIndex(0))
self.singleShot(4000, lambda: stack.setCurrentIndex(1))
self.singleShot(6000, lambda: stack.setCurrentIndex(2))
self.app.exec_()