def __init__(self,
app,
args=None,
parent=None,
raw_data_visualization=False,
fullscreen=False):
self.app = app
self.settings = settings
self.raw_data_visualization = raw_data_visualization
self.no_subsampling = False
super(MainWindow, self).__init__(i=0, title='Data Visualization')
# play button
self.updateTimer = QtCore.QTimer()
self.updateTimer.timeout.connect(self.next_frame)
guiparts.load_config1(self)
self.fbox.addItems(FOLDERS.keys())
self.windowTA, self.windowBM = None, None # sub-windows
if args is not None:
self.root_datafolder = args.root_datafolder
else:
self.root_datafolder = os.path.join(os.path.expanduser('~'),
'DATA')
self.time, self.io, self.roiIndices, self.tzoom = 0, None, [], [0, 50]
self.CaImaging_bg_key = 'meanImg'
self.CaImaging_key = 'Fluorescence'
self.FILES_PER_DAY, self.FILES_PER_SUBJECT, self.SUBJECTS = {}, {}, {}
self.minView = False
self.showwindow()
def __init__(self, app,
args=None,
parent=None,
spatial_subsampling=1,
time_subsampling=1):
"""
sampling in Hz
"""
self.app = app
super(MainWindow, self).__init__(i=1,
title='Face-motion/Whisking tracking')
# self.refEx = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+E'), self)
# self.refEx.activated.connect(self.exclude_outlier)
# self.refPr = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+P'), self)
# self.refPr.activated.connect(self.process_outliers)
# self.refc1 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+1'), self)
# self.refc1.activated.connect(self.set_cursor_1)
# self.refc2 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+2'), self)
# self.refc2.activated.connect(self.set_cursor_2)
# self.refc3 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+3'), self)
# self.refc3.activated.connect(self.process_outliers)
self.process_script = os.path.join(str(pathlib.Path(__file__).resolve().parents[0]),
'process.py')
self.minView = False
self.showwindow()
pg.setConfigOptions(imageAxisOrder='row-major')
self.spatial_subsampling = spatial_subsampling
self.time_subsampling = time_subsampling
self.cwidget = QtGui.QWidget(self)
self.setCentralWidget(self.cwidget)
self.l0 = QtGui.QGridLayout()
self.cwidget.setLayout(self.l0)
self.win = pg.GraphicsLayoutWidget()
self.win.move(600,0)
self.win.resize(600,400)
self.l0.addWidget(self.win,1,3,37,15)
layout = self.win.ci.layout
# A plot area (ViewBox + axes) for displaying the image
self.p0 = self.win.addViewBox(lockAspect=False,row=0,col=0,invertY=True,
border=[100,100,100])
self.p0.setMouseEnabled(x=False,y=False)
self.p0.setMenuEnabled(False)
self.pimg = pg.ImageItem()
self.p0.setAspectLocked()
self.p0.addItem(self.pimg)
# image ROI
self.pFace = self.win.addViewBox(lockAspect=False,row=0,col=1,invertY=True,
border=[100,100,100])
self.pFace.setAspectLocked()
#self.p0.setMouseEnabled(x=False,y=False)
self.pFace.setMenuEnabled(False)
self.pFaceimg = pg.ImageItem(None)
self.pFace.addItem(self.pFaceimg)
# roi initializations
self.iROI = 0
self.nROIs = 0
self.saturation = 255
self.ROI = None
self.pupil = None
self.iframes, self.times, self.Pr1, self.Pr2 = [], [], [], []
self.times, self.imgfolder, self.nframes, self.FILES = None, None, None, None
# saturation sliders
self.sl = guiparts.Slider(0, self)
self.l0.addWidget(self.sl,1,6,1,7)
qlabel= QtGui.QLabel('saturation')
qlabel.setStyleSheet('color: white;')
self.l0.addWidget(qlabel, 0,8,1,3)
# # # adding blanks ("corneal reflections, ...")
# self.roiBtn = QtGui.QPushButton('set ROI')
# self.l0.addWidget(self.roiBtn, 1, 8+6, 1, 1)
# self.roiBtn.setEnabled(True)
# self.roiBtn.clicked.connect(self.add_ROI)
# # fit pupil
# self.fit_pupil = QtGui.QPushButton('fit Pupil [Ctrl+F]')
# self.l0.addWidget(self.fit_pupil, 1, 9+6, 1, 1)
# # self.fit_pupil.setEnabled(True)
# self.fit_pupil.clicked.connect(self.fit_pupil_size)
# # choose pupil shape
# self.pupil_shape = QtGui.QComboBox(self)
# self.pupil_shape.addItem("Ellipse fit")
# self.pupil_shape.addItem("Circle fit")
# self.l0.addWidget(self.pupil_shape, 1, 10+6, 1, 1)
# reset
self.reset_btn = QtGui.QPushButton('reset')
self.l0.addWidget(self.reset_btn, 1, 11+6, 1, 1)
self.reset_btn.clicked.connect(self.reset)
self.reset_btn.setEnabled(True)
self.debugBtn = QtGui.QPushButton('- Debug -')
self.l0.addWidget(self.debugBtn, 2, 11+6, 1, 1)
self.debugBtn.setEnabled(True)
self.debugBtn.clicked.connect(self.debug)
self.data = None
self.scatter, self.fit= None, None # the pupil size contour
self.p1 = self.win.addPlot(name='plot1',row=1,col=0, colspan=2, rowspan=4,
title='*face motion*')
self.p1.setMouseEnabled(x=True,y=False)
self.p1.setMenuEnabled(False)
self.p1.hideAxis('left')
self.scatter = pg.ScatterPlotItem()
self.p1.addItem(self.scatter)
self.p1.setLabel('bottom', 'time (frame #)')
self.xaxis = self.p1.getAxis('bottom')
self.p1.autoRange(padding=0.01)
self.win.ci.layout.setRowStretchFactor(0,5)
self.movieLabel = QtGui.QLabel("No datafile chosen")
self.movieLabel.setStyleSheet("color: white;")
self.l0.addWidget(self.movieLabel,0,1,1,5)
# create frame slider
self.timeLabel = QtGui.QLabel("time : ")
self.timeLabel.setStyleSheet("color: white;")
# self.timeLabel.setFixedWidth(300)
self.currentTime = QtGui.QLineEdit()
self.currentTime.setText('0 s')
self.currentTime.setFixedWidth(70)
# self.currentTime.returnPressed.connect(self.set_precise_time)
self.frameSlider = QtGui.QSlider(QtCore.Qt.Horizontal)
self.frameSlider.setMinimum(0)
self.frameSlider.setMaximum(200)
self.frameSlider.setTickInterval(1)
self.frameSlider.setTracking(False)
self.frameSlider.valueChanged.connect(self.go_to_frame)
istretch = 23
iplay = istretch+15
iconSize = QtCore.QSize(20, 20)
self.folderB = QtWidgets.QComboBox(self)
self.folderB.setMinimumWidth(150)
self.folderB.addItems(FOLDERS.keys())
self.processBtn = QtGui.QPushButton('process data')
self.processBtn.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.processBtn.clicked.connect(self.process)
# self.interpolate = QtGui.QPushButton('interpolate')
# self.interpolate.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
# self.interpolate.clicked.connect(self.interpolate_data)
self.motionCheckBox = QtGui.QCheckBox("display motion frames")
self.motionCheckBox.setStyleSheet("color: gray;")
self.runAsSubprocess = QtGui.QPushButton('run as subprocess')
self.runAsSubprocess.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.runAsSubprocess.clicked.connect(self.run_as_subprocess)
# self.runAsSubprocess.setEnabled(True)
self.load = QtGui.QPushButton(' load data [Ctrl+O] \u2b07')
self.load.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.load.clicked.connect(self.open_file)
sampLabel1 = QtGui.QLabel("spatial subsampling")
sampLabel1.setStyleSheet("color: gray;")
sampLabel1.setFixedWidth(220)
self.SsamplingBox = QtGui.QLineEdit()
self.SsamplingBox.setText(str(self.spatial_subsampling))
self.SsamplingBox.setFixedWidth(30)
sampLabel2 = QtGui.QLabel("temporal subsampling")
sampLabel2.setStyleSheet("color: gray;")
sampLabel2.setFixedWidth(220)
self.TsamplingBox = QtGui.QLineEdit()
self.TsamplingBox.setText(str(self.time_subsampling))
self.TsamplingBox.setFixedWidth(30)
self.addROI = QtGui.QPushButton("set ROI")
self.addROI.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.addROI.clicked.connect(self.add_ROI)
self.saveData = QtGui.QPushButton('save data')
self.saveData.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.saveData.clicked.connect(self.save_data)
iconSize = QtCore.QSize(30, 30)
self.playButton = QtGui.QToolButton()
self.playButton.setIcon(self.style().standardIcon(QtGui.QStyle.SP_MediaPlay))
self.playButton.setIconSize(iconSize)
self.playButton.setToolTip("Play")
self.playButton.setCheckable(True)
self.pauseButton = QtGui.QToolButton()
self.pauseButton.setCheckable(True)
self.pauseButton.setIcon(self.style().standardIcon(QtGui.QStyle.SP_MediaPause))
self.pauseButton.setIconSize(iconSize)
self.pauseButton.setToolTip("Pause")
btns = QtGui.QButtonGroup(self)
btns.addButton(self.playButton,0)
btns.addButton(self.pauseButton,1)
self.l0.addWidget(self.folderB,1,0,1,3)
self.l0.addWidget(self.load,2,0,1,3)
self.l0.addWidget(self.addROI,14,0,1,3)
self.l0.addWidget(self.saveData, 16, 0, 1, 3)
self.l0.addWidget(self.processBtn, 20, 0, 1, 3)
self.l0.addWidget(self.runAsSubprocess, 21, 0, 1, 3)
self.l0.addWidget(self.motionCheckBox, 18, 0, 1, 3)
self.l0.addWidget(sampLabel1, 8, 0, 1, 3)
self.l0.addWidget(self.SsamplingBox, 8, 2, 1, 3)
self.l0.addWidget(sampLabel2, 9, 0, 1, 3)
self.l0.addWidget(self.TsamplingBox, 9, 2, 1, 3)
self.l0.addWidget(QtGui.QLabel(''),istretch,0,1,3)
self.l0.setRowStretch(istretch,1)
self.l0.addWidget(self.timeLabel, istretch+10,0,1,3)
self.l0.addWidget(self.currentTime, istretch+10,1,1,3)
self.l0.addWidget(self.frameSlider, istretch+15,3,1,15)
self.l0.addWidget(QtGui.QLabel(''),17,2,1,1)
self.l0.setRowStretch(16,2)
# self.l0.addWidget(ll, istretch+3+k+1,0,1,4)
self.timeLabel.setEnabled(True)
self.frameSlider.setEnabled(True)
self.nframes = 0
self.cframe = 0
self.show()
def __init__(self, app, args=None, parent=None):
"""
sampling in Hz
"""
self.app = app
super(MainWindow, self).__init__()
self.setWindowTitle('Assembling')
self.setGeometry(50, 700, 300, 370)
# adding a "quit" keyboard shortcut
self.quitSc = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+Q'), self)
self.quitSc.activated.connect(self.quit)
self.process_script = os.path.join(
str(pathlib.Path(__file__).resolve().parents[0]), 'build_NWB.py')
self.script = os.path.join(
str(pathlib.Path(__file__).resolve().parents[1]),
'script.sh') # for batch processing
self.add2Bash = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+B'), self)
self.add2Bash.activated.connect(self.add_to_bash_script)
HEIGHT = 0
HEIGHT += 10
QtWidgets.QLabel("Root-folder:", self).move(10, HEIGHT)
self.folderB = QtWidgets.QComboBox(self)
self.folderB.setMinimumWidth(150)
self.folderB.move(100, HEIGHT)
self.folderB.addItems(FOLDERS.keys())
HEIGHT += 40
self.load = QtWidgets.QPushButton('[L]oad datafolder \u2b07', self)
self.load.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.load.clicked.connect(self.load_folder)
self.load.setMinimumWidth(200)
self.load.move(50, HEIGHT)
self.loadSc = QtWidgets.QShortcut(QtGui.QKeySequence('L'), self)
self.loadSc.activated.connect(self.load_folder)
HEIGHT += 50
QtWidgets.QLabel("=> Setting :", self).move(10, HEIGHT)
self.cbc = QtWidgets.QComboBox(self)
self.cbc.setMinimumWidth(150)
self.cbc.move(100, HEIGHT)
self.cbc.activated.connect(self.update_setting)
self.cbc.addItems(['custom', 'nidaq_only', 'lightweight', 'full'])
HEIGHT += 40
s = QtWidgets.QLabel("Photodiode-Sampling (Hz) ", self)
s.move(10, HEIGHT)
s.setMinimumWidth(200)
self.PHsamplingBox = QtWidgets.QLineEdit('', self)
self.PHsamplingBox.setText('500')
self.PHsamplingBox.setFixedWidth(40)
self.PHsamplingBox.move(200, HEIGHT)
HEIGHT += 30
s = QtWidgets.QLabel("Running-Speed-Sampling (Hz) ", self)
s.move(10, HEIGHT)
s.setMinimumWidth(200)
self.RsamplingBox = QtWidgets.QLineEdit('', self)
self.RsamplingBox.setText('50')
self.RsamplingBox.setFixedWidth(40)
self.RsamplingBox.move(200, HEIGHT)
HEIGHT += 30
s = QtWidgets.QLabel("Whisking-Sampling (Hz) ", self)
s.move(10, HEIGHT)
s.setMinimumWidth(200)
self.WsamplingBox = QtWidgets.QLineEdit('', self)
self.WsamplingBox.setText('0.05')
self.WsamplingBox.setFixedWidth(40)
self.WsamplingBox.move(200, HEIGHT)
HEIGHT += 30
s = QtWidgets.QLabel("Pupil-Sampling (Hz) ", self)
s.move(10, HEIGHT)
s.setMinimumWidth(200)
self.PsamplingBox = QtWidgets.QLineEdit('', self)
self.PsamplingBox.setText('0.5')
self.PsamplingBox.setFixedWidth(40)
self.PsamplingBox.move(200, HEIGHT)
HEIGHT += 30
s = QtWidgets.QLabel("FaceCamera-Sampling (Hz) ", self)
s.move(10, HEIGHT)
s.setMinimumWidth(200)
self.FsamplingBox = QtWidgets.QLineEdit('', self)
self.FsamplingBox.setText('0.001')
self.FsamplingBox.setFixedWidth(40)
self.FsamplingBox.move(200, HEIGHT)
HEIGHT += 50
self.gen = QtWidgets.QPushButton(' -= RUN =- ', self)
self.gen.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.gen.clicked.connect(self.run)
self.gen.setMinimumWidth(200)
self.gen.move(50, HEIGHT)
self.folder = ''
self.show()
def __init__(self,
app,
args=None,
parent=None,
raw_data_visualization=False,
df_width=600,
selector_height=30,
win1_Wmax=1200,
win1_Wmin=300,
win1_Hmax=300,
win2_Wmax=500,
fullscreen=False):
self.app = app
self.settings = settings
self.raw_data_visualization = raw_data_visualization
self.no_subsampling = False
super(MainWindow, self).__init__(i=0, title='Data Visualization')
# play button
self.updateTimer = QtCore.QTimer()
self.updateTimer.timeout.connect(self.next_frame)
self.cwidget = QtWidgets.QWidget(self)
self.setCentralWidget(self.cwidget)
self.statusBar.showMessage(
'open file [O], refresh plot [R], play/pause [Space], initial-view [I], max-window [M] '
)
mainLayout = QtWidgets.QVBoxLayout()
Layout1 = QtWidgets.QHBoxLayout()
mainLayout.addLayout(Layout1)
Layout11 = QtWidgets.QVBoxLayout()
Layout1.addLayout(Layout11)
guiparts.create_calendar(self, Layout11)
self.cal.setMaximumHeight(150)
# folder box
self.fbox = QtWidgets.QComboBox(self)
self.fbox.setFont(guiparts.smallfont)
self.fbox.activated.connect(self.scan_folder)
self.fbox.setMaximumHeight(selector_height)
self.folder_default_key = ' [root datafolder]'
self.fbox.addItem(self.folder_default_key)
self.fbox.setCurrentIndex(0)
Layout11.addWidget(self.fbox)
# subject box
self.sbox = QtWidgets.QComboBox(self)
self.sbox.setFont(guiparts.smallfont)
self.sbox.activated.connect(self.pick_subject) # To be written !!
self.sbox.setMaximumHeight(selector_height)
self.subject_default_key = ' [subject] '
self.sbox.addItem(self.subject_default_key)
self.sbox.setCurrentIndex(0)
Layout11.addWidget(self.sbox)
# notes
self.notes = QtWidgets.QLabel('\n[exp info]' + 5 * '\n', self)
self.notes.setFont(guiparts.smallfont)
self.notes.setMaximumHeight(60)
Layout11.addWidget(self.notes)
self.pbox = QtWidgets.QComboBox(self)
self.pbox.setFont(guiparts.smallfont)
self.pbox.activated.connect(self.display_quantities)
self.pbox.setMaximumHeight(selector_height)
self.pbox.addItem('[visualization/analysis]')
self.pbox.addItem('-> Show Raw Data')
self.pbox.addItem('-> Trial-average')
self.pbox.addItem('-> draw figures')
self.pbox.addItem('-> build PDF summary')
self.pbox.addItem('-> open PDF summary')
self.pbox.setCurrentIndex(0)
Layout11.addWidget(self.pbox)
Layout113 = QtWidgets.QHBoxLayout()
Layout11.addLayout(Layout113)
add_buttons(self, Layout113)
Layout12 = QtWidgets.QVBoxLayout()
Layout1.addLayout(Layout12)
self.dbox = QtWidgets.QComboBox(self)
self.dbox.setMinimumWidth(df_width)
self.dbox.setMaximumWidth(win1_Wmax)
self.dbox.setMinimumHeight(selector_height)
self.dbox.setMaximumHeight(selector_height)
self.dbox.activated.connect(self.pick_datafile)
Layout12.addWidget(self.dbox)
self.win1 = pg.GraphicsLayoutWidget()
self.win1.setMaximumHeight(int(win1_Hmax - 1.5 * selector_height))
Layout12.addWidget(self.win1)
self.winTrace = pg.GraphicsLayoutWidget()
mainLayout.addWidget(self.winTrace)
guiparts.build_slider(self, mainLayout)
self.init_panels()
self.plot = self.winTrace.addPlot()
self.plot.hideAxis('left')
self.plot.setMouseEnabled(x=True, y=False)
# self.plot.setMenuEnabled(False)
self.plot.setLabel('bottom', 'time (s)')
self.xaxis = self.plot.getAxis('bottom')
self.scatter = pg.ScatterPlotItem()
self.plot.addItem(self.scatter)
Layout122 = QtWidgets.QHBoxLayout()
Layout12.addLayout(Layout122)
self.stimSelect = QtWidgets.QCheckBox("vis. stim")
self.stimSelect.clicked.connect(self.select_stim)
self.stimSelect.setStyleSheet('color: grey;')
self.pupilSelect = QtWidgets.QCheckBox("pupil")
self.pupilSelect.setStyleSheet('color: red;')
self.gazeSelect = QtWidgets.QCheckBox("gaze")
self.gazeSelect.setStyleSheet('color: orange;')
self.faceMtnSelect = QtWidgets.QCheckBox("whisk.")
self.faceMtnSelect.setStyleSheet('color: magenta;')
self.runSelect = QtWidgets.QCheckBox("run")
self.photodiodeSelect = QtWidgets.QCheckBox("photodiode")
self.photodiodeSelect.setStyleSheet('color: grey;')
self.ephysSelect = QtWidgets.QCheckBox("ephys")
self.ephysSelect.setStyleSheet('color: blue;')
self.ophysSelect = QtWidgets.QCheckBox("ophys")
self.ophysSelect.setStyleSheet('color: green;')
for x in [
self.stimSelect, self.pupilSelect, self.gazeSelect,
self.faceMtnSelect, self.runSelect, self.photodiodeSelect,
self.ephysSelect, self.ophysSelect
]:
x.setFont(guiparts.smallfont)
Layout122.addWidget(x)
self.roiPick = QtWidgets.QLineEdit()
self.roiPick.setText(' [...] ')
self.roiPick.setMinimumWidth(50)
self.roiPick.setMaximumWidth(250)
self.roiPick.returnPressed.connect(self.select_ROI)
self.roiPick.setFont(guiparts.smallfont)
self.ephysPick = QtWidgets.QLineEdit()
self.ephysPick.setText(' ')
# self.ephysPick.returnPressed.connect(self.select_ROI)
self.ephysPick.setFont(guiparts.smallfont)
self.guiKeywords = QtWidgets.QLineEdit()
self.guiKeywords.setText(' [GUI keywords] ')
# self.guiKeywords.setFixedWidth(200)
self.guiKeywords.returnPressed.connect(self.keyword_update)
self.guiKeywords.setFont(guiparts.smallfont)
Layout122.addWidget(self.guiKeywords)
# Layout122.addWidget(self.ephysPick)
Layout122.addWidget(self.roiPick)
self.subsamplingSelect = QtWidgets.QCheckBox("subsampl.")
self.subsamplingSelect.setStyleSheet('color: grey;')
self.subsamplingSelect.setFont(guiparts.smallfont)
Layout122.addWidget(self.subsamplingSelect)
self.annotSelect = QtWidgets.QCheckBox("annot.")
self.annotSelect.setStyleSheet('color: grey;')
self.annotSelect.setFont(guiparts.smallfont)
Layout122.addWidget(self.annotSelect)
self.imgSelect = QtWidgets.QCheckBox("img")
self.imgSelect.setStyleSheet('color: grey;')
self.imgSelect.setFont(guiparts.smallfont)
self.imgSelect.setChecked(True)
self.imgSelect.clicked.connect(self.remove_img)
Layout122.addWidget(self.imgSelect)
self.cwidget.setLayout(mainLayout)
self.show()
self.fbox.addItems(FOLDERS.keys())
self.windowTA, self.windowBM = None, None # sub-windows
if args is not None:
self.root_datafolder = args.root_datafolder
else:
self.root_datafolder = os.path.join(os.path.expanduser('~'),
'DATA')
self.time, self.data, self.roiIndices, self.tzoom = 0, None, [], [
0, 50
]
self.CaImaging_bg_key, self.planeID = 'meanImg', 0
self.CaImaging_key = 'Fluorescence'
self.FILES_PER_DAY, self.FILES_PER_SUBJECT, self.SUBJECTS = {}, {}, {}
self.minView = False
self.showwindow()
if (args is not None) and hasattr(args, 'datafile') and os.path.isfile(
args.datafile):
self.datafile = args.datafile
self.load_file(self.datafile)
plots.raw_data_plot(self, self.tzoom)
def __init__(self, app,
args=None,
parent=None):
"""
sampling in Hz
"""
super(MainWindow, self).__init__()
self.setGeometry(350, 680, 300, 350)
# adding a "quit" keyboard shortcut
self.quitSc = QtWidgets.QShortcut(QtGui.QKeySequence('Q'), self) # or 'Ctrl+Q'
self.quitSc.activated.connect(self.quit)
self.setWindowTitle('Adding Ca-Imaging')
self.process_script = os.path.join(str(pathlib.Path(__file__).resolve().parents[1]),
'assembling', 'add_ophys.py')
HEIGHT = 0
HEIGHT += 10
QtWidgets.QLabel("Root Data:", self).move(10, HEIGHT)
self.folderD = QtWidgets.QComboBox(self)
self.folderD.setMinimumWidth(150)
self.folderD.move(100, HEIGHT)
self.folderD.activated.connect(self.update_setting)
self.folderD.addItems(FOLDERS.keys())
HEIGHT += 30
QtWidgets.QLabel("Root Imaging:", self).move(10, HEIGHT)
self.folderI = QtWidgets.QComboBox(self)
self.folderI.setMinimumWidth(150)
self.folderI.move(100, HEIGHT)
self.folderI.activated.connect(self.update_setting)
self.folderI.addItems(FOLDERS.keys())
HEIGHT += 40
self.load = QtWidgets.QPushButton('Load data \u2b07', self)
self.load.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.load.clicked.connect(self.load_data)
self.load.setMinimumWidth(200)
self.load.move(50, HEIGHT)
self.loadSc = QtWidgets.QShortcut(QtGui.QKeySequence('L'), self)
self.loadSc.activated.connect(self.load_data)
HEIGHT += 40
self.load = QtWidgets.QPushButton('Load imaging \u2b07', self)
self.load.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.load.clicked.connect(self.load_data)
self.load.setMinimumWidth(200)
self.load.move(50, HEIGHT)
self.loadSc = QtWidgets.QShortcut(QtGui.QKeySequence('L'), self)
self.loadSc.activated.connect(self.load_imaging)
HEIGHT += 40
self.find = QtWidgets.QPushButton('-* Find imaging *-', self)
self.find.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.find.clicked.connect(self.find_imaging)
self.find.setMinimumWidth(200)
self.find.move(50, HEIGHT)
HEIGHT += 30
self.imagingF = QtWidgets.QLabel("...", self)
self.imagingF.move(10, HEIGHT)
self.imagingF.setMinimumWidth(400)
HEIGHT += 40
QtWidgets.QLabel("=> Setting :", self).move(10, HEIGHT)
self.cbc = QtWidgets.QComboBox(self)
self.cbc.setMinimumWidth(150)
self.cbc.move(100, HEIGHT)
self.cbc.activated.connect(self.update_setting)
self.cbc.addItems(['standard', 'lightweight', 'full', 'NIdaq-only', 'custom'])
HEIGHT +=30
s = QtWidgets.QLabel("CaImaging-Sampling (Hz) ", self)
s.move(10, HEIGHT)
s.setMinimumWidth(200)
self.PsamplingBox = QtWidgets.QLineEdit('', self)
self.PsamplingBox.setText('0.0')
self.PsamplingBox.setFixedWidth(40)
self.PsamplingBox.move(200, HEIGHT)
HEIGHT +=40
self.gen = QtWidgets.QPushButton('-=- Run -=-', self)
self.gen.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.gen.clicked.connect(self.run)
self.gen.setMinimumWidth(200)
self.gen.move(50, HEIGHT)
self.filename, self.Ifolder = '', ''
self.show()
def __init__(self, app,
args=None,
parent=None,
spatial_subsampling=1,
time_subsampling=1):
"""
FaceMotion GUI
"""
self.app = app
super(MainWindow, self).__init__(i=2,
title='Face-motion/Whisking tracking')
##############################
##### keyboard shortcuts #####
##############################
self.refc1 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+1'), self)
self.refc1.activated.connect(self.set_cursor_1)
self.refc2 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+2'), self)
self.refc2.activated.connect(self.set_cursor_2)
self.refc3 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+3'), self)
self.refc3.activated.connect(self.interpolate_data)
#############################
##### module quantities #####
#############################
# initializing to defaults/None:
self.saturation = 255
self.ROI, self.pupil = None, None
self.times, self.imgfolder, self.nframes, self.FILES = None, None, None, None
self.data, self.scatter, self.fit= None, None, None # the pupil size contour
self.spatial_subsampling = spatial_subsampling
self.time_subsampling = time_subsampling
self.process_script = os.path.join(str(pathlib.Path(__file__).resolve().parents[0]),
'process.py') # for batch processing -> execute this script
########################
##### building GUI #####
########################
self.minView = False
self.showwindow()
# central widget
self.cwidget = QtWidgets.QWidget(self)
self.setCentralWidget(self.cwidget)
# layout
self.l0 = QtWidgets.QGridLayout()
self.cwidget.setLayout(self.l0)
self.win = pg.GraphicsLayoutWidget()
self.win.move(600,0)
self.win.resize(600,400)
self.l0.addWidget(self.win,1,3,37,15)
layout = self.win.ci.layout
# A plot area (ViewBox + axes) for displaying the image
self.p0 = self.win.addViewBox(lockAspect=False,row=0,col=0,invertY=True,
border=[100,100,100])
self.p0.setMouseEnabled(x=False,y=False)
self.p0.setMenuEnabled(False)
self.pimg = pg.ImageItem()
self.p0.setAspectLocked()
self.p0.addItem(self.pimg)
# image ROI
self.pFace = self.win.addViewBox(lockAspect=False,row=0,col=1,invertY=True,
border=[100,100,100])
self.pFace.setAspectLocked()
self.pFace.setMenuEnabled(False)
self.pFaceimg = pg.ImageItem(None)
self.pFace.addItem(self.pFaceimg)
# saturation sliders
self.sl = Slider(0, self)
self.l0.addWidget(self.sl,1,6,1,7)
qlabel= QtWidgets.QLabel('saturation')
qlabel.setStyleSheet('color: white;')
self.l0.addWidget(qlabel, 0,8,1,3)
# reset
self.reset_btn = QtWidgets.QPushButton('reset')
self.l0.addWidget(self.reset_btn, 1, 11+6, 1, 1)
self.reset_btn.clicked.connect(self.reset)
self.reset_btn.setEnabled(True)
# debug
self.debugBtn = QtWidgets.QPushButton('- Debug -')
self.l0.addWidget(self.debugBtn, 2, 11+6, 1, 1)
self.debugBtn.setEnabled(True)
self.debugBtn.clicked.connect(self.debug)
self.p1 = self.win.addPlot(name='plot1',row=1,col=0, colspan=2, rowspan=4,
title='*face motion*')
self.p1.setMouseEnabled(x=True,y=False)
self.p1.setMenuEnabled(False)
self.p1.hideAxis('left')
self.scatter = pg.ScatterPlotItem()
self.p1.addItem(self.scatter)
self.p1.setLabel('bottom', 'time (frame #)')
self.xaxis = self.p1.getAxis('bottom')
self.p1.autoRange(padding=0.01)
self.win.ci.layout.setRowStretchFactor(0,5)
self.movieLabel = QtWidgets.QLabel("No datafile chosen")
self.movieLabel.setStyleSheet("color: white;")
self.l0.addWidget(self.movieLabel,0,1,1,5)
# create frame slider
self.timeLabel = QtWidgets.QLabel("time : ")
self.timeLabel.setStyleSheet("color: white;")
# self.timeLabel.setFixedWidth(300)
self.currentTime = QtWidgets.QLineEdit()
self.currentTime.setText('0 s')
self.currentTime.setFixedWidth(70)
# self.currentTime.returnPressed.connect(self.set_precise_time)
self.frameSlider = QtWidgets.QSlider(QtCore.Qt.Horizontal)
self.frameSlider.setMinimum(0)
self.frameSlider.setMaximum(200)
self.frameSlider.setTickInterval(1)
self.frameSlider.setTracking(False)
self.frameSlider.valueChanged.connect(self.go_to_frame)
istretch = 23
iplay = istretch+15
iconSize = QtCore.QSize(20, 20)
self.folderB = QtWidgets.QComboBox(self)
self.folderB.setMinimumWidth(150)
self.folderB.addItems(FOLDERS.keys())
self.processBtn = QtWidgets.QPushButton('process data [Ctrl+P]')
self.processBtn.clicked.connect(self.process)
self.interpolate = QtGui.QPushButton('interpolate')
self.interpolate.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.interpolate.clicked.connect(self.interpolate_data)
self.motionCheckBox = QtWidgets.QCheckBox("display motion frames")
self.motionCheckBox.setStyleSheet("color: gray;")
self.runAsSubprocess = QtWidgets.QPushButton('run as subprocess')
self.runAsSubprocess.clicked.connect(self.run_as_subprocess)
self.load = QtWidgets.QPushButton(' load data [Ctrl+O] \u2b07')
self.load.clicked.connect(self.open_file)
sampLabel1 = QtWidgets.QLabel("spatial subsampling")
sampLabel1.setStyleSheet("color: gray;")
sampLabel1.setFixedWidth(220)
self.SsamplingBox = QtWidgets.QLineEdit()
self.SsamplingBox.setText(str(self.spatial_subsampling))
self.SsamplingBox.setFixedWidth(30)
sampLabel2 = QtWidgets.QLabel("temporal subsampling")
sampLabel2.setStyleSheet("color: gray;")
sampLabel2.setFixedWidth(220)
self.TsamplingBox = QtWidgets.QLineEdit()
self.TsamplingBox.setText(str(self.time_subsampling))
self.TsamplingBox.setFixedWidth(30)
self.loadLastGUIsettings = QtWidgets.QPushButton("last GUI settings")
self.loadLastGUIsettings.clicked.connect(self.load_last_gui_settings)
self.addROI = QtWidgets.QPushButton("set ROI")
self.addROI.clicked.connect(self.add_ROI)
self.saveData = QtWidgets.QPushButton('save data [Ctrl+S]')
self.saveData.clicked.connect(self.save_data)
sampLabel3 = QtWidgets.QLabel("grooming threshold")
sampLabel3.setStyleSheet("color: gray;")
sampLabel3.setFixedWidth(220)
self.groomingBox = QtWidgets.QLineEdit()
self.groomingBox.setText('-1')
self.groomingBox.setFixedWidth(40)
self.groomingBox.returnPressed.connect(self.update_grooming_threshold)
self.processGrooming = QtWidgets.QPushButton("process grooming")
self.processGrooming.clicked.connect(self.process_grooming)
for x in [self.processBtn, self.motionCheckBox, self.runAsSubprocess,
self.load, self.addROI, self.saveData, self.TsamplingBox,
self.SsamplingBox, self.groomingBox, self.processGrooming]:
x.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
iconSize = QtCore.QSize(30, 30)
self.playButton = QtWidgets.QToolButton()
self.playButton.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MediaPlay))
self.playButton.setIconSize(iconSize)
self.playButton.setToolTip("Play")
self.playButton.setCheckable(True)
self.pauseButton = QtWidgets.QToolButton()
self.pauseButton.setCheckable(True)
self.pauseButton.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MediaPause))
self.pauseButton.setIconSize(iconSize)
self.pauseButton.setToolTip("Pause")
btns = QtWidgets.QButtonGroup(self)
btns.addButton(self.playButton,0)
btns.addButton(self.pauseButton,1)
for wdg, loc in zip([self.load,self.folderB,
sampLabel1, sampLabel2,
self.loadLastGUIsettings, self.addROI, self.saveData,
sampLabel3, self.processGrooming,
self.motionCheckBox, self.processBtn, self.runAsSubprocess,
self.timeLabel],
[1,2,
8,9,
11, 12,14,
25,26,
19,20,21,
istretch+13]):
self.l0.addWidget(wdg,loc,0,1,3)
self.l0.addWidget(self.SsamplingBox, 8, 2, 1, 3)
self.l0.addWidget(self.TsamplingBox, 9, 2, 1, 3)
self.l0.addWidget(self.groomingBox, 19, 2, 1, 3)
self.l0.addWidget(QtWidgets.QLabel(''),istretch,0,1,3)
self.l0.setRowStretch(istretch,1)
self.l0.addWidget(self.currentTime, istretch+13,1,1,3)
self.l0.addWidget(self.frameSlider, istretch+17,3,1,15)
# self.l0.addWidget(QtWidgets.QLabel(''),17,2,1,1)
# self.l0.setRowStretch(16,2)
# # self.l0.addWidget(ll, istretch+3+k+1,0,1,4)
self.timeLabel.setEnabled(True)
self.frameSlider.setEnabled(True)
self.nframes = 0
self.cframe = 0
self.grooming_threshold = -1
self.show()
def __init__(self, app,
args=None,
parent=None,
gaussian_smoothing=0,
cm_scale_px=570,
subsampling=1000):
"""
sampling in Hz
"""
self.app = app
super(MainWindow, self).__init__()
self.setGeometry(500,150,400,400)
self.process_script = os.path.join(str(pathlib.Path(__file__).resolve().parents[0]),'process.py')
self.script = os.path.join(str(pathlib.Path(__file__).resolve().parents[1]), 'script.sh') # for batch processing
# adding a "quit" keyboard shortcut
self.quitSc = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+Q'), self)
self.quitSc.activated.connect(self.quit)
self.maxSc = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+M'), self)
self.maxSc.activated.connect(self.showwindow)
self.fitSc = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+F'), self)
self.fitSc.activated.connect(self.fit_pupil_size)
self.loadSc = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+O'), self)
self.loadSc.activated.connect(self.load_data)
self.refSc = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+R'), self)
self.refSc.activated.connect(self.jump_to_frame)
# self.refEx = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+E'), self)
# self.refEx.activated.connect(self.exclude_outlier)
self.refPr = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+P'), self)
self.refPr.activated.connect(self.process_ROIs)
self.refS = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+S'), self)
self.refS.activated.connect(self.save_pupil_data)
self.refc1 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+1'), self)
self.refc1.activated.connect(self.set_cursor_1)
self.refc2 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+2'), self)
self.refc2.activated.connect(self.set_cursor_2)
self.refc3 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+3'), self)
self.refc3.activated.connect(self.process_outliers)
self.add2Bash = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+B'), self)
self.add2Bash.activated.connect(self.add_to_bash_script)
self.minView = False
self.showwindow()
pg.setConfigOptions(imageAxisOrder='row-major')
self.gaussian_smoothing = gaussian_smoothing
self.subsampling = subsampling
self.cm_scale_px = cm_scale_px
self.cwidget = QtGui.QWidget(self)
self.setCentralWidget(self.cwidget)
self.l0 = QtGui.QGridLayout()
self.cwidget.setLayout(self.l0)
self.win = pg.GraphicsLayoutWidget()
self.win.move(600,0)
self.win.resize(600,400)
self.l0.addWidget(self.win,1,3,37,15)
layout = self.win.ci.layout
# A plot area (ViewBox + axes) for displaying the image
self.p0 = self.win.addViewBox(lockAspect=False,
row=0,col=0,#border=[100,100,100],
invertY=True)
self.p0.setMouseEnabled(x=False,y=False)
self.p0.setMenuEnabled(False)
self.pimg = pg.ImageItem()
self.p0.setAspectLocked()
self.p0.addItem(self.pimg)
# image ROI
self.pPupil = self.win.addViewBox(lockAspect=True,#row=0,col=1,
# border=[100,100,100],
invertY=True)
#self.p0.setMouseEnabled(x=False,y=False)
self.pPupil.setMenuEnabled(False)
self.pPupilimg = pg.ImageItem(None)
self.pPupil.addItem(self.pPupilimg)
self.pupilContour = pg.ScatterPlotItem()
self.pPupil.addItem(self.pupilContour)
self.pupilCenter = pg.ScatterPlotItem()
self.pPupil.addItem(self.pupilCenter)
# roi initializations
self.iROI = 0
self.nROIs = 0
self.saturation = 255
self.ROI = None
self.pupil = None
self.iframes, self.times, self.Pr1, self.Pr2 = [], [], [], []
# saturation sliders
self.sl = guiparts.Slider(0, self)
self.l0.addWidget(self.sl,1,6,1,7)
qlabel= QtGui.QLabel('saturation')
qlabel.setStyleSheet('color: white;')
self.l0.addWidget(qlabel, 0,8,1,3)
# adding blanks ("corneal reflections, ...")
self.reflector = QtGui.QPushButton('add blank')
self.l0.addWidget(self.reflector, 1, 8+6, 1, 1)
# self.reflector.setEnabled(True)
self.reflector.clicked.connect(self.add_reflectROI)
# fit pupil
self.fit_pupil = QtGui.QPushButton('fit Pupil [Ctrl+F]')
self.l0.addWidget(self.fit_pupil, 1, 9+6, 1, 1)
# self.fit_pupil.setEnabled(True)
self.fit_pupil.clicked.connect(self.fit_pupil_size)
# choose pupil shape
self.pupil_shape = QtGui.QComboBox(self)
self.pupil_shape.addItem("Ellipse fit")
self.pupil_shape.addItem("Circle fit")
self.l0.addWidget(self.pupil_shape, 1, 10+6, 1, 1)
# reset
self.reset_btn = QtGui.QPushButton('reset')
self.l0.addWidget(self.reset_btn, 1, 11+6, 1, 1)
self.reset_btn.clicked.connect(self.reset)
# self.reset_btn.setEnabled(True)
# draw pupil
self.refresh_pupil = QtGui.QPushButton('Refresh [Ctrl+R]')
self.l0.addWidget(self.refresh_pupil, 2, 11+6, 1, 1)
self.refresh_pupil.setEnabled(True)
self.refresh_pupil.clicked.connect(self.jump_to_frame)
self.data = None
self.rROI= []
self.reflectors=[]
self.scatter, self.fit= None, None # the pupil size contour
self.p1 = self.win.addPlot(name='plot1',row=1,col=0, colspan=2, rowspan=4,
title='Pupil diameter')
self.p1.setMouseEnabled(x=True,y=False)
self.p1.setMenuEnabled(False)
self.p1.hideAxis('left')
self.scatter = pg.ScatterPlotItem()
self.p1.addItem(self.scatter)
self.p1.setLabel('bottom', 'time (frame #)')
self.xaxis = self.p1.getAxis('bottom')
self.p1.autoRange(padding=0.01)
self.win.ci.layout.setRowStretchFactor(0,5)
self.movieLabel = QtGui.QLabel("No datafile chosen")
self.movieLabel.setStyleSheet("color: white;")
self.l0.addWidget(self.movieLabel,0,1,1,5)
# create frame slider
self.timeLabel = QtGui.QLabel("Current time (seconds):")
self.timeLabel.setStyleSheet("color: white;")
self.currentTime = QtGui.QLineEdit()
self.currentTime.setText('0')
self.currentTime.setValidator(QtGui.QDoubleValidator(0, 100000, 2))
self.currentTime.setFixedWidth(50)
self.currentTime.returnPressed.connect(self.set_precise_time)
self.frameSlider = QtGui.QSlider(QtCore.Qt.Horizontal)
self.frameSlider.setMinimum(0)
self.frameSlider.setMaximum(200)
self.frameSlider.setTickInterval(1)
self.frameSlider.setTracking(False)
self.frameSlider.valueChanged.connect(self.go_to_frame)
istretch = 23
iplay = istretch+15
iconSize = QtCore.QSize(20, 20)
self.folderB = QtWidgets.QComboBox(self)
self.folderB.setMinimumWidth(150)
self.folderB.addItems(FOLDERS.keys())
self.process = QtGui.QPushButton('process data [Ctrl+P]')
self.process.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.process.clicked.connect(self.process_ROIs)
self.cursor1 = QtGui.QPushButton('Set Cursor 1 [Ctrl+1]')
self.cursor1.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.cursor1.clicked.connect(self.set_cursor_1)
self.cursor2 = QtGui.QPushButton('Set Cursor 2 [Ctrl+2]')
self.cursor2.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.cursor2.clicked.connect(self.set_cursor_2)
self.runAsSubprocess = QtGui.QPushButton('run as subprocess')
self.runAsSubprocess.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.runAsSubprocess.clicked.connect(self.run_as_subprocess)
self.load = QtGui.QPushButton(' load data [Ctrl+O] \u2b07')
self.load.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.load.clicked.connect(self.load_data)
sampLabel = QtGui.QLabel("Subsampling (frame)")
sampLabel.setStyleSheet("color: gray;")
self.samplingBox = QtGui.QLineEdit()
self.samplingBox.setText(str(self.subsampling))
self.samplingBox.setFixedWidth(50)
smoothLabel = QtGui.QLabel("Smoothing (px)")
smoothLabel.setStyleSheet("color: gray;")
self.smoothBox = QtGui.QLineEdit()
self.smoothBox.setText(str(self.gaussian_smoothing))
self.smoothBox.setFixedWidth(30)
scaleLabel = QtGui.QLabel("1cm = (px)")
scaleLabel.setStyleSheet("color: gray;")
self.scaleBox = QtGui.QLineEdit()
self.scaleBox.setText(str(self.cm_scale_px))
self.scaleBox.setFixedWidth(30)
self.addROI = QtGui.QPushButton("add Pupil-ROI")
self.addROI.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.addROI.clicked.connect(self.add_ROI)
self.saverois = QtGui.QPushButton('save data [Ctrl+S]')
self.saverois.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.saverois.clicked.connect(self.save_ROIs)
# self.addOutlier = QtGui.QPushButton('exclude outlier [Ctrl+E]')
# self.addOutlier.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
# self.addOutlier.clicked.connect(self.exclude_outlier)
self.processOutliers = QtGui.QPushButton('Set blinking interval')
self.processOutliers.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.processOutliers.clicked.connect(self.process_outliers)
self.printSize = QtGui.QPushButton('print ROI size')
self.printSize.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.printSize.clicked.connect(self.print_size)
iconSize = QtCore.QSize(30, 30)
self.playButton = QtGui.QToolButton()
self.playButton.setIcon(self.style().standardIcon(QtGui.QStyle.SP_MediaPlay))
self.playButton.setIconSize(iconSize)
self.playButton.setToolTip("Play")
self.playButton.setCheckable(True)
self.pauseButton = QtGui.QToolButton()
self.pauseButton.setCheckable(True)
self.pauseButton.setIcon(self.style().standardIcon(QtGui.QStyle.SP_MediaPause))
self.pauseButton.setIconSize(iconSize)
self.pauseButton.setToolTip("Pause")
btns = QtGui.QButtonGroup(self)
btns.addButton(self.playButton,0)
btns.addButton(self.pauseButton,1)
self.l0.addWidget(self.folderB,1,0,1,3)
self.l0.addWidget(self.load,2,0,1,3)
self.l0.addWidget(sampLabel, 8, 0, 1, 3)
self.l0.addWidget(self.samplingBox, 8, 2, 1, 3)
self.l0.addWidget(smoothLabel, 9, 0, 1, 3)
self.l0.addWidget(self.smoothBox, 9, 2, 1, 3)
self.l0.addWidget(scaleLabel, 10, 0, 1, 3)
self.l0.addWidget(self.scaleBox, 10, 2, 1, 3)
self.l0.addWidget(self.addROI,14,0,1,3)
self.l0.addWidget(self.process, 16, 0, 1, 3)
self.l0.addWidget(self.runAsSubprocess, 17, 0, 1, 3)
self.l0.addWidget(self.saverois, 19, 0, 1, 3)
self.l0.addWidget(self.cursor1, 23, 0, 1, 3)
self.l0.addWidget(self.cursor2, 24, 0, 1, 3)
self.l0.addWidget(self.processOutliers, 25, 0, 1, 3)
self.l0.addWidget(self.printSize, 26, 0, 1, 3)
self.l0.addWidget(QtGui.QLabel(''),istretch,0,1,3)
self.l0.setRowStretch(istretch,1)
self.l0.addWidget(self.timeLabel, istretch+13,0,1,3)
self.l0.addWidget(self.currentTime, istretch+14,0,1,3)
self.l0.addWidget(self.frameSlider, istretch+15,3,1,15)
self.l0.addWidget(QtGui.QLabel(''),17,2,1,1)
self.l0.setRowStretch(16,2)
# self.l0.addWidget(ll, istretch+3+k+1,0,1,4)
self.updateFrameSlider()
self.nframes = 0
self.cframe, self.cframe1, self.cframe2, = 0, 0, 0
self.updateTimer = QtCore.QTimer()
self.win.show()
self.show()
self.processed = False
# self.datafile = args.datafile
self.show()
def __init__(self, app,
args=None,
parent=None):
"""
sampling in Hz
"""
super(MainWindow, self).__init__()
self.setGeometry(350, 470, 300, 260)
# adding a "quit" and "load" keyboard shortcuts
self.quitSc = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+Q'), self)
self.quitSc.activated.connect(self.quit)
self.loadSc = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+O'), self)
self.loadSc.activated.connect(self.load_imaging)
self.setWindowTitle('Ca-Preprocessing')
self.process_script = os.path.join(str(pathlib.Path(__file__).resolve().parents[1]),
'Ca_imaging', 'preprocessing.py')
HEIGHT = 0
HEIGHT += 10
QtWidgets.QLabel("Root Folder:", self).move(10, HEIGHT)
self.folderI = QtWidgets.QComboBox(self)
self.folderI.setMinimumWidth(150)
self.folderI.move(100, HEIGHT)
self.folderI.activated.connect(self.update_setting)
self.folderI.addItems(FOLDERS.keys())
HEIGHT += 40
self.load = QtWidgets.QPushButton('Upload (set of) TSeries \u2b07', self)
self.load.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.load.clicked.connect(self.load_imaging)
self.load.setMinimumWidth(200)
self.load.move(50, HEIGHT)
HEIGHT += 40
QtWidgets.QLabel("=> Setting :", self).move(10, HEIGHT)
self.cbc = QtWidgets.QComboBox(self)
self.cbc.setMinimumWidth(150)
self.cbc.move(100, HEIGHT)
self.cbc.activated.connect(self.update_setting)
self.cbc.addItems(list(PREPROCESSING_SETTINGS.keys()))
HEIGHT += 40
QtWidgets.QLabel(" delay ?", self).move(10, HEIGHT)
self.delayBox = QtWidgets.QComboBox(self)
self.delayBox.setMinimumWidth(150)
self.delayBox.move(100, HEIGHT)
self.delayBox.addItems(['None', '10min', '1h', '2h', '10h', '20h'])
HEIGHT +=40
self.gen = QtWidgets.QPushButton('-=- Run -=-', self)
self.gen.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.gen.clicked.connect(self.run)
self.gen.setMinimumWidth(200)
self.gen.move(50, HEIGHT)
HEIGHT +=40
self.gen = QtWidgets.QPushButton(' open Suite2p ', self)
self.gen.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.gen.clicked.connect(self.open_suite2p)
self.gen.setMinimumWidth(200)
self.gen.move(50, HEIGHT)
self.CMDS = []
self.show()
def __init__(self,
app,
args=None,
parent=None,
gaussian_smoothing=1,
cm_scale_px=570,
subsampling=1000):
"""
Cell Identification GUI for Z-stacks Imaging
"""
self.app = app
super(MainWindow, self).__init__(
i=-2,
size=(1000, 800),
title='Cell Identification GUI for Z-stacks Imaging')
##############################
##### keyboard shortcuts #####
##############################
self.refc1 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+N'), self)
self.refc1.activated.connect(self.next_frames)
self.refc2 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+B'), self)
self.refc2.activated.connect(self.previous_frames)
self.refc3 = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+C'), self)
self.refc3.activated.connect(self.new_ROI)
#############################
##### module quantities #####
#############################
self.ROIS = []
########################
##### building GUI #####
########################
self.cwidget = QtGui.QWidget(self)
self.setCentralWidget(self.cwidget)
self.grid = QtGui.QGridLayout()
self.folderB = QtWidgets.QComboBox(self)
self.folderB.setMinimumWidth(150)
self.folderB.addItems(FOLDERS.keys())
self.grid.addWidget(self.folderB, 1, 1, 1, 1)
self.load = QtGui.QPushButton(' load data [Ctrl+O] \u2b07')
self.load.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.load.clicked.connect(self.open_file)
self.grid.addWidget(self.load, 1, 2, 1, 1)
self.channelB = QtWidgets.QComboBox(self)
self.channelB.addItems(['Ch2', 'Ch1'])
self.grid.addWidget(self.channelB, 1, 3, 1, 1)
self.grid.addWidget(QtGui.QLabel("sampling (frame):"), 1, 4, 1, 1)
self.samplingB = QtWidgets.QComboBox(self)
self.samplingB.addItems(['1', '2', '3', '5', '7', '10'])
self.grid.addWidget(self.samplingB, 1, 5, 1, 1)
self.depth = QtGui.QLineEdit()
self.depth.setText("depth= %.1f um" % 0)
self.grid.addWidget(self.depth, 1, 6, 1, 2)
self.grid.addWidget(QtGui.QLabel("cell-range (um):"), 1, 8, 1, 1)
self.cellRange = QtWidgets.QComboBox(self)
self.cellRange.addItems(['1', '10', '20', '50', '100', '1000'])
self.cellRange.setCurrentIndex(2)
self.grid.addWidget(self.cellRange, 1, 9, 1, 1)
self.newRoiBtn = QtGui.QPushButton('new Cell [Ctrl+C]')
self.newRoiBtn.clicked.connect(self.new_ROI)
self.grid.addWidget(self.newRoiBtn, 2, 1, 1, 1)
self.showCells = QtGui.QCheckBox("show cells")
self.showCells.clicked.connect(self.display_frames)
self.grid.addWidget(self.showCells, 2, 2, 1, 2)
self.prevBtn = QtGui.QPushButton('next frames [Ctrl+N]')
self.prevBtn.clicked.connect(self.next_frames)
self.grid.addWidget(self.prevBtn, 2, 4, 1, 1)
self.nextBtn = QtGui.QPushButton('prev. frames [Ctrl+P]')
self.nextBtn.clicked.connect(self.previous_frames)
self.grid.addWidget(self.nextBtn, 2, 5, 1, 1)
self.saveCellsBtn = QtGui.QPushButton('save cells')
self.saveCellsBtn.clicked.connect(self.save_cells)
self.grid.addWidget(self.saveCellsBtn, 2, 7, 1, 1)
self.threeDBtn = QtGui.QPushButton('show 3D view')
self.threeDBtn.clicked.connect(self.show_3d_view)
self.grid.addWidget(self.threeDBtn, 2, 8, 1, 1)
self.resetBtn = QtGui.QPushButton('reset')
self.resetBtn.clicked.connect(self.reset)
self.grid.addWidget(self.resetBtn, 2, 10, 1, 1)
self.cwidget.setLayout(self.grid)
self.win = pg.GraphicsLayoutWidget()
self.grid.addWidget(self.win, 3, 1, 10, 10)
layout = self.win.ci.layout
# for i, key in enumerate(['pPrev', 'Prev', 'Center', 'Next', 'nNext']):
for i, key in enumerate(['Center']):
# A plot area (ViewBox + axes) for displaying the image
setattr(
self, 'view_%s' % key,
self.win.addViewBox(lockAspect=True,
row=0,
col=i,
border=[10, 10, 10],
invertY=True))
setattr(self, 'img_%s' % key, pg.ImageItem())
getattr(self,
'view_%s' % key).addItem(getattr(self, 'img_%s' % key))
if hasattr(args, 'folder'):
self.load_data(args.folder)
self.win.show()
self.show()
def __init__(self, app, args=None, parent=None):
"""
Intrinsic Imaging Analysis GUI
"""
self.app = app
super(AnalysisWindow,
self).__init__(i=2, title='intrinsic imaging analysis')
self.datafolder, self.img, self.vasculature_img = '', None, None
if args is not None:
self.datafolder = args.datafile
else:
self.datafolder = ''
########################
##### building GUI #####
########################
self.minView = False
self.showwindow()
# layout (from NewWindow class)
self.init_basic_widget_grid(wdgt_length=3, Ncol_wdgt=23, Nrow_wdgt=20)
# --- ROW (Nx_wdgt), COLUMN (Ny_wdgt)
self.add_widget(QtWidgets.QLabel('data folder:'), spec='small-left')
self.folderB = QtWidgets.QComboBox(self)
self.folderB.addItems(FOLDERS.keys())
self.add_widget(self.folderB, spec='large-right')
self.raw_trace = self.graphics_layout.addPlot(row=0,
col=0,
rowspan=1,
colspan=23)
self.spectrum_power = self.graphics_layout.addPlot(row=1,
col=0,
rowspan=2,
colspan=9)
self.spDot = pg.ScatterPlotItem()
self.spectrum_power.addItem(self.spDot)
self.spectrum_phase = self.graphics_layout.addPlot(row=1,
col=9,
rowspan=2,
colspan=9)
self.sphDot = pg.ScatterPlotItem()
self.spectrum_phase.addItem(self.sphDot)
# images
self.img1B = self.graphics_layout.addViewBox(row=3,
col=0,
rowspan=10,
colspan=10,
lockAspect=True,
invertY=True)
self.img1 = pg.ImageItem()
self.img1B.addItem(self.img1)
self.img2B = self.graphics_layout.addViewBox(row=3,
col=10,
rowspan=10,
colspan=9,
lockAspect=True,
invertY=True)
self.img2 = pg.ImageItem()
self.img2B.addItem(self.img2)
self.img = np.random.randn(30, 30)
self.img1.setImage(self.img)
self.img2.setImage(self.img)
for i in range(3):
self.graphics_layout.ci.layout.setColumnStretchFactor(i, 1)
self.graphics_layout.ci.layout.setColumnStretchFactor(3, 2)
self.graphics_layout.ci.layout.setColumnStretchFactor(12, 2)
self.graphics_layout.ci.layout.setRowStretchFactor(0, 3)
self.graphics_layout.ci.layout.setRowStretchFactor(1, 4)
self.graphics_layout.ci.layout.setRowStretchFactor(3, 5)
self.folderButton = QtWidgets.QPushButton("load data [Ctrl+O]", self)
self.folderButton.clicked.connect(self.open_file)
self.add_widget(self.folderButton, spec='large-left')
self.lastBox = QtWidgets.QCheckBox("last ")
self.lastBox.setStyleSheet("color: gray;")
self.add_widget(self.lastBox, spec='small-right')
self.lastBox.setChecked((self.datafolder == ''))
self.add_widget(QtWidgets.QLabel(' '))
self.vdButton = QtWidgets.QPushButton("vasc. img", self)
self.vdButton.clicked.connect(self.show_vasc_pic)
self.add_widget(self.vdButton, 'small-left')
self.rdButton = QtWidgets.QPushButton(" === show raw data === ", self)
self.rdButton.clicked.connect(self.show_raw_data)
self.add_widget(self.rdButton, 'large-right')
self.add_widget(QtWidgets.QLabel(' - high pass filtering:'),
spec='large-left')
self.hpBox = QtWidgets.QLineEdit()
self.hpBox.setText('0')
self.add_widget(self.hpBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' - protocol:'), spec='small-left')
self.protocolBox = QtWidgets.QComboBox(self)
self.protocolBox.addItems(['up', 'down', 'left', 'right'])
self.add_widget(self.protocolBox, spec='small-middle')
self.numBox = QtWidgets.QComboBox(self)
self.numBox.addItems(['sum'] + [str(i) for i in range(1, 10)])
self.add_widget(self.numBox, spec='small-right')
self.pmButton = QtWidgets.QPushButton(" ==== compute phase maps ==== ",
self)
self.pmButton.clicked.connect(self.compute_phase_maps)
self.add_widget(self.pmButton)
self.add_widget(QtWidgets.QLabel(' - direction:'), spec='small-left')
self.mapBox = QtWidgets.QComboBox(self)
self.mapBox.addItems(['azimuth', 'altitude'])
self.add_widget(self.mapBox, spec='small-middle')
self.twoPiBox = QtWidgets.QCheckBox("[0,2pi]")
self.twoPiBox.setStyleSheet("color: gray;")
self.add_widget(self.twoPiBox, spec='small-right')
self.rmButton = QtWidgets.QPushButton(
" === compute retinotopic maps === ", self)
self.rmButton.clicked.connect(self.compute_retinotopic_maps)
self.add_widget(self.rmButton)
# self.add_widget(QtWidgets.QLabel(' - spatial smoothing (px):'),
# spec='large-left')
# self.spatialSmoothingBox = QtWidgets.QLineEdit()
# self.spatialSmoothingBox.setText('5')
# self.add_widget(self.spatialSmoothingBox, spec='small-right')
# self.add_widget(QtWidgets.QLabel(' - temporal smoothing (ms):'),
# spec='large-left')
# self.temporalSmoothingBox = QtWidgets.QLineEdit()
# self.temporalSmoothingBox.setText('100')
# self.add_widget(self.temporalSmoothingBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' '))
self.pasButton = QtWidgets.QPushButton(
" == perform area segmentation == ", self)
self.pasButton.clicked.connect(self.perform_area_segmentation)
self.add_widget(self.pasButton)
self.add_widget(QtWidgets.QLabel(' - display:'), spec='small-left')
self.displayBox = QtWidgets.QComboBox(self)
self.displayBox.addItems(['sign map', 'areas (+vasc.)'])
self.add_widget(self.displayBox, spec='large-right')
# === -- parameters for area segmentation -- ===
# phaseMapFilterSigma
self.add_widget(QtWidgets.QLabel(' - phaseMapFilterSigma:'),
spec='large-left')
self.phaseMapFilterSigmaBox = QtWidgets.QLineEdit()
self.phaseMapFilterSigmaBox.setText('1.0')
self.phaseMapFilterSigmaBox.setToolTip(
'The sigma value (in pixels) of Gaussian filter for altitude and azimuth maps.\n FLOAT, default = 1.0, recommended range: [0.0, 2.0].\n Large "phaseMapFilterSigma" gives you more patches.\n Small "phaseMapFilterSigma" gives you less patches.'
)
self.add_widget(self.phaseMapFilterSigmaBox, spec='small-right')
# signMapFilterSigma
self.add_widget(QtWidgets.QLabel(' - signMapFilterSigma:'),
spec='large-left')
self.signMapFilterSigmaBox = QtWidgets.QLineEdit()
self.signMapFilterSigmaBox.setText('9.0')
self.signMapFilterSigmaBox.setToolTip(
'The sigma value (in pixels) of Gaussian filter for visual sign maps.\n FLOAT, default = 9.0, recommended range: [0.6, 10.0].\n Large "signMapFilterSigma" gives you less patches.\n Small "signMapFilterSigma" gives you more patches.'
)
self.add_widget(self.signMapFilterSigmaBox, spec='small-right')
# signMapThr
self.add_widget(QtWidgets.QLabel(' - signMapThr:'), spec='large-left')
self.signMapThrBox = QtWidgets.QLineEdit()
self.signMapThrBox.setText('0.35')
self.signMapThrBox.setToolTip(
'Threshold to binarize visual signmap.\n FLOAT, default = 0.35, recommended range: [0.2, 0.5], allowed range: [0, 1).\n Large signMapThr gives you fewer patches.\n Smaller signMapThr gives you more patches.'
)
self.add_widget(self.signMapThrBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' - splitLocalMinCutStep:'),
spec='large-left')
self.splitLocalMinCutStepBox = QtWidgets.QLineEdit()
self.splitLocalMinCutStepBox.setText('5.0')
self.splitLocalMinCutStepBox.setToolTip(
'The step width for detecting number of local minimums during spliting. The local minimums detected will be used as marker in the following open cv watershed segmentation.\n FLOAT, default = 5.0, recommend range: [0.5, 15.0].\n Small "splitLocalMinCutStep" will make it more likely to split but into less sub patches.\n Large "splitLocalMinCutStep" will make it less likely to split but into more sub patches.'
)
self.add_widget(self.splitLocalMinCutStepBox, spec='small-right')
# splitOverlapThr:
self.add_widget(QtWidgets.QLabel(' - splitOverlapThr:'),
spec='large-left')
self.splitOverlapThrBox = QtWidgets.QLineEdit()
self.splitOverlapThrBox.setText('1.1')
self.splitOverlapThrBox.setToolTip(
'Patches with overlap ration larger than this value will go through the split procedure.\n FLOAT, default = 1.1, recommend range: [1.0, 1.2], should be larger than 1.0.\n Small "splitOverlapThr" will split more patches.\n Large "splitOverlapThr" will split less patches.'
)
self.add_widget(self.splitOverlapThrBox, spec='small-right')
# mergeOverlapThr:
self.add_widget(QtWidgets.QLabel(' - mergeOverlapThr:'),
spec='large-left')
self.mergeOverlapThrBox = QtWidgets.QLineEdit()
self.mergeOverlapThrBox.setText('0.1')
self.mergeOverlapThrBox.setToolTip(
'Considering a patch pair (A and B) with same sign, A has visual coverage a deg2 and B has visual coverage b deg2 and the overlaping visual coverage between this pair is c deg2.\n Then if (c/a < "mergeOverlapThr") and (c/b < "mergeOverlapThr"), these two patches will be merged.\n FLOAT, default = 0.1, recommend range: [0.0, 0.2], should be smaller than 1.0.\n Small "mergeOverlapThr" will merge less patches.\n Large "mergeOverlapThr" will merge more patches.'
)
self.add_widget(self.mergeOverlapThrBox, spec='small-right')
self.pixROI = pg.ROI((10, 10),
size=(10, 10),
pen=pg.mkPen((255, 0, 0, 255)),
rotatable=False,
resizable=False)
self.img1B.addItem(self.pixROI)
self.show()
def __init__(self,
app,
args=None,
parent=None,
spatial_subsampling=4,
time_subsampling=1):
"""
Intrinsic Imaging GUI
"""
self.app = app
super(MainWindow, self).__init__(i=1, title='intrinsic imaging')
# some initialisation
self.running, self.stim, self.STIM = False, None, None
self.datafolder, self.img, self.vasculature_img = '', None, None
self.t0, self.period = 0, 1
### trying the camera
try:
# we initialize the camera
self.bridge = Bridge()
self.core = self.bridge.get_core()
self.exposure = self.core.get_exposure()
self.demo = False
auto_shutter = self.core.get_property('Core', 'AutoShutter')
self.core.set_property('Core', 'AutoShutter', 0)
except BaseException as be:
print(be)
print('')
print(' /!\ Problem with the Camera /!\ ')
print(' --> no camera found ')
print('')
self.exposure = -1 # flag for no camera
self.demo = True
########################
##### building GUI #####
########################
self.minView = False
self.showwindow()
# layout (from NewWindow class)
self.init_basic_widget_grid(wdgt_length=3, Ncol_wdgt=20, Nrow_wdgt=20)
# -- A plot area (ViewBox + axes) for displaying the image ---
self.view = self.graphics_layout.addViewBox(lockAspect=True,
invertY=True)
self.view.setMenuEnabled(False)
self.view.setAspectLocked()
self.pimg = pg.ImageItem()
# --- setting subject information ---
self.add_widget(QtWidgets.QLabel('subjects file:'))
self.subjectFileBox = QtWidgets.QComboBox(self)
self.subjectFileBox.addItems([
f for f in os.listdir(subjects_path)[::-1] if f.endswith('.json')
])
self.subjectFileBox.activated.connect(self.get_subject_list)
self.add_widget(self.subjectFileBox)
self.add_widget(QtWidgets.QLabel('subject:'))
self.subjectBox = QtWidgets.QComboBox(self)
self.get_subject_list()
self.add_widget(self.subjectBox)
self.add_widget(QtWidgets.QLabel(20 * ' - '))
self.vascButton = QtWidgets.QPushButton(
" - = save Vasculature Picture = - ", self)
self.vascButton.clicked.connect(self.take_vasculature_picture)
self.add_widget(self.vascButton)
self.add_widget(QtWidgets.QLabel(20 * ' - '))
# --- data acquisition properties ---
self.add_widget(QtWidgets.QLabel('data folder:'), spec='small-left')
self.folderB = QtWidgets.QComboBox(self)
self.folderB.addItems(FOLDERS.keys())
self.add_widget(self.folderB, spec='large-right')
self.add_widget(QtWidgets.QLabel(' - protocol:'), spec='small-left')
self.protocolBox = QtWidgets.QComboBox(self)
self.protocolBox.addItems(['ALL', 'up', 'down', 'left', 'right'])
self.add_widget(self.protocolBox, spec='large-right')
self.add_widget(
QtWidgets.QLabel(' - exposure: %.0f ms (from Micro-Manager)' %
self.exposure))
self.add_widget(QtWidgets.QLabel(' - Nrepeat :'), spec='large-left')
self.repeatBox = QtWidgets.QLineEdit()
self.repeatBox.setText('10')
self.add_widget(self.repeatBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' - stim. period (s):'),
spec='large-left')
self.periodBox = QtWidgets.QLineEdit()
self.periodBox.setText('10')
self.add_widget(self.periodBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' - bar size (degree):'),
spec='large-left')
self.barBox = QtWidgets.QLineEdit()
self.barBox.setText('6')
self.add_widget(self.barBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' - spatial sub-sampling (px):'),
spec='large-left')
self.spatialBox = QtWidgets.QLineEdit()
self.spatialBox.setText(str(spatial_subsampling))
self.add_widget(self.spatialBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' - acq. freq. (Hz):'),
spec='large-left')
self.freqBox = QtWidgets.QLineEdit()
self.freqBox.setText('10')
self.add_widget(self.freqBox, spec='small-right')
# self.add_widget(QtWidgets.QLabel(' - flick. freq. (Hz) /!\ > acq:'),
# spec='large-left')
# self.flickBox = QtWidgets.QLineEdit()
# self.flickBox.setText('10')
# self.add_widget(self.flickBox, spec='small-right')
self.demoBox = QtWidgets.QCheckBox("demo mode")
self.demoBox.setStyleSheet("color: gray;")
self.add_widget(self.demoBox, spec='large-left')
self.demoBox.setChecked(self.demo)
self.camBox = QtWidgets.QCheckBox("cam.")
self.camBox.setStyleSheet("color: gray;")
self.add_widget(self.camBox, spec='small-right')
self.camBox.setChecked(True)
# --- launching acquisition ---
self.liveButton = QtWidgets.QPushButton("-- live view -- ", self)
self.liveButton.clicked.connect(self.live_view)
self.add_widget(self.liveButton)
# --- launching acquisition ---
self.acqButton = QtWidgets.QPushButton("-- RUN PROTOCOL -- ", self)
self.acqButton.clicked.connect(self.launch_protocol)
self.add_widget(self.acqButton, spec='large-left')
self.stopButton = QtWidgets.QPushButton(" STOP ", self)
self.stopButton.clicked.connect(self.stop_protocol)
self.add_widget(self.stopButton, spec='small-right')
# --- launching analysis ---
self.add_widget(QtWidgets.QLabel(20 * ' - '))
self.analysisButton = QtWidgets.QPushButton(" - = Analysis GUI = - ",
self)
self.analysisButton.clicked.connect(self.open_analysis)
self.add_widget(self.analysisButton, spec='large-left')
self.pimg.setImage(0 * self.get_frame())
self.view.addItem(self.pimg)
self.view.autoRange(padding=0.001)
self.analysisWindow = None
def __init__(self, app,
args=None,
parent=None,
gaussian_smoothing=1,
subsampling=1000):
"""
Pupil Tracking GUI
"""
self.app = app
super(MainWindow, self).__init__(i=1,
title='Pupil tracking')
##############################
##### keyboard shortcuts #####
##############################
self.refc1 = QtWidgets.QShortcut(QtGui.QKeySequence('1'), self)
self.refc1.activated.connect(self.set_cursor_1)
self.refc2 = QtWidgets.QShortcut(QtGui.QKeySequence('2'), self)
self.refc2.activated.connect(self.set_cursor_2)
self.refc3 = QtWidgets.QShortcut(QtGui.QKeySequence('3'), self)
self.refc3.activated.connect(self.process_outliers)
self.refc4 = QtWidgets.QShortcut(QtGui.QKeySequence('4'), self)
self.refc4.activated.connect(self.interpolate)
self.refc5 = QtWidgets.QShortcut(QtGui.QKeySequence('E'), self)
self.refc5.activated.connect(self.find_outliers)
#############################
##### module quantities #####
#############################
self.gaussian_smoothing = gaussian_smoothing
self.subsampling = subsampling
self.process_script = os.path.join(str(pathlib.Path(__file__).resolve().parents[0]),
'process.py')
self.ROI, self.pupil, self.times = None, None, None
self.data = None
self.bROI, self.reflectors = [], []
self.scatter, self.fit= None, None # the pupil size contour
########################
##### building GUI #####
########################
self.cwidget = QtWidgets.QWidget(self)
self.setCentralWidget(self.cwidget)
self.l0 = QtWidgets.QGridLayout()
self.cwidget.setLayout(self.l0)
self.win = pg.GraphicsLayoutWidget()
self.win.move(600,0)
self.win.resize(600,400)
self.l0.addWidget(self.win,1,3,37,15)
layout = self.win.ci.layout
# A plot area (ViewBox + axes) for displaying the image
self.p0 = self.win.addViewBox(lockAspect=False,
row=0,col=0,#border=[100,100,100],
invertY=True)
self.p0.setMouseEnabled(x=False,y=False)
self.p0.setMenuEnabled(False)
self.pimg = pg.ImageItem()
self.p0.setAspectLocked()
self.p0.addItem(self.pimg)
# image ROI
self.pPupil = self.win.addViewBox(lockAspect=True,#row=0,col=1,
# border=[100,100,100],
invertY=True)
#self.p0.setMouseEnabled(x=False,y=False)
self.pPupil.setMenuEnabled(False)
self.pPupilimg = pg.ImageItem(None)
self.pPupil.addItem(self.pPupilimg)
self.pupilContour = pg.ScatterPlotItem()
self.pPupil.addItem(self.pupilContour)
self.pupilCenter = pg.ScatterPlotItem()
self.pPupil.addItem(self.pupilCenter)
# saturation sliders
self.sl = Slider(0, self)
self.sl.setValue(100)
self.l0.addWidget(self.sl,1,6,1,7)
qlabel= QtWidgets.QLabel('saturation')
qlabel.setStyleSheet('color: white;')
self.l0.addWidget(qlabel, 0,8,1,3)
# adding blanks (eye borders, ...)
self.blankBtn = QtWidgets.QPushButton('add blanks')
self.l0.addWidget(self.blankBtn, 1, 8+6, 1, 1)
self.blankBtn.setEnabled(True)
self.blankBtn.clicked.connect(self.add_blankROI)
# adding reflections ("corneal reflections, ...")
self.reflectorBtn = QtWidgets.QPushButton('add reflect.')
self.l0.addWidget(self.reflectorBtn, 2, 8+6, 1, 1)
self.reflectorBtn.setEnabled(True)
self.reflectorBtn.clicked.connect(self.add_reflectROI)
self.keepCheckBox = QtWidgets.QCheckBox("keep ROIs")
self.keepCheckBox.setStyleSheet("color: gray;")
self.keepCheckBox.setChecked(True)
self.l0.addWidget(self.keepCheckBox, 2, 8+7, 1, 1)
# fit pupil
self.fit_pupil = QtWidgets.QPushButton('fit Pupil [Ctrl+F]')
self.l0.addWidget(self.fit_pupil, 1, 9+6, 1, 1)
# self.fit_pupil.setEnabled(True)
self.fit_pupil.clicked.connect(self.fit_pupil_size)
# choose pupil shape
self.pupil_shape = QtWidgets.QComboBox(self)
self.pupil_shape.addItem("Ellipse fit")
self.pupil_shape.addItem("Circle fit")
self.l0.addWidget(self.pupil_shape, 1, 10+6, 1, 1)
# reset
self.reset_btn = QtWidgets.QPushButton('reset')
self.l0.addWidget(self.reset_btn, 1, 11+6, 1, 1)
self.reset_btn.clicked.connect(self.reset)
# self.reset_btn.setEnabled(True)
# draw pupil
self.refresh_pupil = QtWidgets.QPushButton('Refresh [Ctrl+R]')
self.l0.addWidget(self.refresh_pupil, 2, 11+6, 1, 1)
self.refresh_pupil.setEnabled(True)
self.refresh_pupil.clicked.connect(self.jump_to_frame)
self.p1 = self.win.addPlot(name='plot1',row=1,col=0, colspan=2, rowspan=4,
title='Pupil diameter')
self.p1.setMouseEnabled(x=True,y=False)
self.p1.setMenuEnabled(False)
self.p1.hideAxis('left')
self.scatter = pg.ScatterPlotItem()
self.p1.addItem(self.scatter)
self.p1.setLabel('bottom', 'time (frame #)')
self.xaxis = self.p1.getAxis('bottom')
self.p1.autoRange(padding=0.01)
self.win.ci.layout.setRowStretchFactor(0,5)
self.movieLabel = QtWidgets.QLabel("No datafile chosen")
self.movieLabel.setStyleSheet("color: white;")
self.l0.addWidget(self.movieLabel,0,1,1,5)
# create frame slider
self.timeLabel = QtWidgets.QLabel("Current time (seconds):")
self.timeLabel.setStyleSheet("color: white;")
self.currentTime = QtWidgets.QLineEdit()
self.currentTime.setText('0')
self.currentTime.setValidator(QtGui.QDoubleValidator(0, 100000, 2))
self.currentTime.setFixedWidth(50)
self.currentTime.returnPressed.connect(self.set_precise_time)
self.frameSlider = QtWidgets.QSlider(QtCore.Qt.Horizontal)
self.frameSlider.setMinimum(0)
self.frameSlider.setMaximum(200)
self.frameSlider.setTickInterval(1)
self.frameSlider.setTracking(False)
self.frameSlider.valueChanged.connect(self.go_to_frame)
istretch = 23
iplay = istretch+15
iconSize = QtCore.QSize(20, 20)
self.folderB = QtWidgets.QComboBox(self)
self.folderB.setMinimumWidth(150)
self.folderB.addItems(FOLDERS.keys())
self.process = QtWidgets.QPushButton('process data [Ctrl+P]')
self.process.clicked.connect(self.process_ROIs)
self.cursor1 = QtWidgets.QPushButton('Set Cursor 1 [Ctrl+1]')
self.cursor1.clicked.connect(self.set_cursor_1)
self.cursor2 = QtWidgets.QPushButton('Set Cursor 2 [Ctrl+2]')
self.cursor2.clicked.connect(self.set_cursor_2)
self.runAsSubprocess = QtWidgets.QPushButton('run as subprocess')
self.runAsSubprocess.clicked.connect(self.run_as_subprocess)
self.load = QtWidgets.QPushButton(' load data [Ctrl+O] \u2b07')
self.load.clicked.connect(self.load_data)
self.loadLastGUIsettings = QtWidgets.QPushButton("last GUI settings")
self.loadLastGUIsettings.clicked.connect(self.load_last_gui_settings)
sampLabel = QtWidgets.QLabel("Subsampling (frame)")
sampLabel.setStyleSheet("color: gray;")
self.samplingBox = QtWidgets.QLineEdit()
self.samplingBox.setText(str(self.subsampling))
self.samplingBox.setFixedWidth(50)
smoothLabel = QtWidgets.QLabel("Smoothing (px)")
smoothLabel.setStyleSheet("color: gray;")
self.smoothBox = QtWidgets.QLineEdit()
self.smoothBox.setText(str(self.gaussian_smoothing))
self.smoothBox.setFixedWidth(30)
self.addROI = QtWidgets.QPushButton("add Pupil-ROI")
self.addROI.clicked.connect(self.add_ROI)
self.saverois = QtWidgets.QPushButton('save data [Ctrl+S]')
self.saverois.clicked.connect(self.save)
stdLabel = QtWidgets.QLabel("std excl. factor: ")
stdLabel.setStyleSheet("color: gray;")
self.stdBox = QtWidgets.QLineEdit()
self.stdBox.setText('3.0')
self.stdBox.setFixedWidth(50)
wdthLabel = QtWidgets.QLabel("excl. width (s): ")
wdthLabel.setStyleSheet("color: gray;")
self.wdthBox = QtWidgets.QLineEdit()
self.wdthBox.setText('0.1')
self.wdthBox.setFixedWidth(50)
self.excludeOutliers = QtWidgets.QPushButton('exclude outlier [Ctrl+E]')
self.excludeOutliers.clicked.connect(self.find_outliers)
cursorLabel = QtWidgets.QLabel("set cursor 1 [Ctrl+1], cursor 2 [Ctrl+2]")
cursorLabel.setStyleSheet("color: gray;")
self.interpBtn = QtWidgets.QPushButton('interpolate only [Ctrl+4]')
self.interpBtn.clicked.connect(self.interpolate)
self.processOutliers = QtWidgets.QPushButton('Set blinking interval [Ctrl+3]')
self.processOutliers.clicked.connect(self.process_outliers)
self.printSize = QtWidgets.QPushButton('print ROI size')
self.printSize.clicked.connect(self.print_size)
for x in [self.process, self.cursor1, self.cursor2, self.runAsSubprocess, self.load,
self.saverois, self.addROI, self.interpBtn, self.processOutliers,
self.stdBox, self.wdthBox, self.excludeOutliers, self.printSize, cursorLabel,
self.loadLastGUIsettings,
sampLabel, smoothLabel, stdLabel, wdthLabel, self.smoothBox, self.samplingBox]:
x.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
iconSize = QtCore.QSize(30, 30)
self.playButton = QtWidgets.QToolButton()
self.playButton.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MediaPlay))
self.playButton.setIconSize(iconSize)
self.playButton.setToolTip("Play")
self.playButton.setCheckable(True)
self.pauseButton = QtWidgets.QToolButton()
self.pauseButton.setCheckable(True)
self.pauseButton.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MediaPause))
self.pauseButton.setIconSize(iconSize)
self.pauseButton.setToolTip("Pause")
btns = QtWidgets.QButtonGroup(self)
btns.addButton(self.playButton,0)
btns.addButton(self.pauseButton,1)
self.l0.addWidget(self.folderB,1,0,1,3)
self.l0.addWidget(self.load,2,0,1,3)
self.l0.addWidget(self.loadLastGUIsettings, 7, 0, 1, 3)
self.l0.addWidget(sampLabel, 8, 0, 1, 3)
self.l0.addWidget(self.samplingBox, 8, 2, 1, 3)
self.l0.addWidget(smoothLabel, 9, 0, 1, 3)
self.l0.addWidget(self.smoothBox, 9, 2, 1, 3)
self.l0.addWidget(self.addROI,14,0,1,3)
self.l0.addWidget(self.process, 16, 0, 1, 3)
self.l0.addWidget(self.runAsSubprocess, 17, 0, 1, 3)
self.l0.addWidget(self.saverois, 19, 0, 1, 3)
self.l0.addWidget(stdLabel, 21, 0, 1, 3)
self.l0.addWidget(self.stdBox, 21, 2, 1, 3)
self.l0.addWidget(wdthLabel, 22, 0, 1, 3)
self.l0.addWidget(self.wdthBox, 22, 2, 1, 3)
self.l0.addWidget(self.excludeOutliers, 23, 0, 1, 3)
self.l0.addWidget(cursorLabel, 25, 0, 1, 3)
self.l0.addWidget(self.processOutliers, 26, 0, 1, 3)
self.l0.addWidget(self.interpBtn, 27, 0, 1, 3)
self.l0.addWidget(self.printSize, 29, 0, 1, 3)
self.l0.addWidget(QtWidgets.QLabel(''),istretch,0,1,3)
self.l0.setRowStretch(istretch,1)
self.l0.addWidget(self.timeLabel, istretch+13,0,1,3)
self.l0.addWidget(self.currentTime, istretch+14,0,1,3)
self.l0.addWidget(self.frameSlider, istretch+15,3,1,15)
self.l0.addWidget(QtWidgets.QLabel(''),17,2,1,1)
self.l0.setRowStretch(16,2)
# self.l0.addWidget(ll, istretch+3+k+1,0,1,4)
self.updateFrameSlider()
self.nframes = 0
self.cframe, self.cframe1, self.cframe2, = 0, 0, 0
self.updateTimer = QtCore.QTimer()
self.win.show()
self.show()
def __init__(self, app, args=None, parent=None, debug=False):
"""
Red-Cell selection GUI
"""
self.app = app
self.debug = debug
super(RCGwindow, self).__init__(i=3, title='red-cell gui')
self.nextSc = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+N'), self)
self.nextSc.activated.connect(self.next_roi)
self.saveSc = QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+S'), self)
self.saveSc.activated.connect(self.save)
self.Sc1 = QtWidgets.QShortcut(QtGui.QKeySequence('1'), self)
self.Sc1.activated.connect(self.switch_to_1)
self.Sc2 = QtWidgets.QShortcut(QtGui.QKeySequence('2'), self)
self.Sc2.activated.connect(self.switch_to_2)
self.Sc3 = QtWidgets.QShortcut(QtGui.QKeySequence('3'), self)
self.Sc3.activated.connect(self.switch_to_3)
self.Sc4 = QtWidgets.QShortcut(QtGui.QKeySequence('4'), self)
self.Sc4.activated.connect(self.switch_to_4)
self.Sc5 = QtWidgets.QShortcut(QtGui.QKeySequence('5'), self)
self.Sc5.activated.connect(self.switch_to_5)
self.Sc6 = QtWidgets.QShortcut(QtGui.QKeySequence('6'), self)
self.Sc6.activated.connect(self.switch_to_6)
self.roiSc = QtWidgets.QShortcut(QtGui.QKeySequence('Space'), self)
self.roiSc.activated.connect(self.switch_roi_display)
self.roi_index = 0
########################
##### building GUI #####
########################
self.minView = False
self.showwindow()
# central widget
self.cwidget = QtGui.QWidget(self)
self.setCentralWidget(self.cwidget)
# layout
self.l0 = QtGui.QGridLayout()
self.cwidget.setLayout(self.l0)
self.win = pg.GraphicsLayoutWidget()
self.win.move(600, 0)
self.win.resize(600, 400)
self.l0.addWidget(self.win, 1, 3, 37, 15)
layout = self.win.ci.layout
# A plot area (ViewBox + axes) for displaying the image
self.p0 = self.win.addViewBox(lockAspect=False,
row=0,
col=0,
invertY=True,
border=[100, 100, 100])
self.p0.setMouseEnabled(x=False, y=False)
self.p0.setMenuEnabled(False)
self.pimg = pg.ImageItem()
self.p0.setAspectLocked()
self.p0.addItem(self.pimg)
# buttons and widgets
self.folderB = QtWidgets.QComboBox(self)
self.folderB.setMinimumWidth(150)
self.folderB.addItems(FOLDERS.keys())
self.imgB = QtWidgets.QComboBox(self)
self.imgB.setMinimumWidth(150)
self.imgB.addItems(KEYS)
self.imgB.activated.connect(self.draw_image)
self.load = QtGui.QPushButton(' load data [Ctrl+O] \u2b07')
self.load.clicked.connect(self.open_file)
self.nextB = QtGui.QPushButton('next roi [Ctrl+N]')
self.nextB.clicked.connect(self.next_roi)
self.prevB = QtGui.QPushButton('prev. roi [Ctrl+P]')
self.prevB.clicked.connect(self.process)
self.switchB = QtGui.QPushButton('SWITCH [Ctrl+Space]')
self.switchB.clicked.connect(self.hitting_space)
self.saveB = QtGui.QPushButton('save data [Ctrl+S]')
self.saveB.clicked.connect(self.save)
self.rstRoiB = QtGui.QPushButton('reset ALL rois to green')
self.rstRoiB.clicked.connect(self.reset_all_to_green)
self.roiShapeCheckBox = QtWidgets.QCheckBox("ROIs as circle")
self.roiShapeCheckBox.setChecked(True)
for wdgt, index in zip([
self.folderB, self.load, self.imgB, self.nextB, self.prevB,
self.switchB, self.saveB, self.rstRoiB, self.roiShapeCheckBox
], [1, 2, 6, 10, 11, 12, 16, 21, 23]):
wdgt.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
self.l0.addWidget(wdgt, index, 0, 1, 3)
self.rois_green = pg.ScatterPlotItem()
self.rois_red = pg.ScatterPlotItem()
self.rois_hl = pg.ScatterPlotItem()
self.folder, self.rois_on = '', True
self.show()