def __init__(self):
QtGui.QWidget.__init__(self)
self.resize(800, 1000)
self.layout = QtGui.QGridLayout()
self.layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.layout)
self.gw = pg.GraphicsLayoutWidget()
self.layout.addWidget(self.gw)
self.vb1 = self.gw.addViewBox()
self.img1 = pg.ImageItem()
self.vb1.addItem(self.img1)
self.vb2 = self.gw.addViewBox(row=1, col=0)
self.img2 = pg.ImageItem()
self.vb2.addItem(self.img2)
for vb in (self.vb1, self.vb2):
vb.invertY()
vb.setAspectLocked(True)
self.plt1 = self.gw.addPlot(row=2, col=0)
self.plt1.setLabels(bottom=('time', 's'))
self.plt1_items = []
self.rois = [
pg.RectROI([0, 0], [10, 10], pen=(i, 4)) for i in range(2)
]
for roi in self.rois:
self.vb1.addItem(roi)
roi.sigRegionChangeFinished.connect(self.roi_changed)
self.ignore_roi_change = False
self.plt2 = self.gw.addPlot(row=3, col=0)
self.plt2.setXLink(self.plt1)
self.plt2.setLabels(bottom=('time', 's'))
self.base_time_rgn = pg.LinearRegionItem([0.0, 0.1])
self.test_time_rgn = pg.LinearRegionItem([0.1, 0.11])
for time_rgn in (self.base_time_rgn, self.test_time_rgn):
self.plt1.addItem(time_rgn)
time_rgn.sigRegionChangeFinished.connect(self.time_rgn_changed)
time_rgn.sigRegionChangeFinished.connect(
self.update_sequence_analysis)
self.clamp_plots = []
self.plt3 = self.gw.addPlot(row=4, col=0)
self.plt3.setLabels(left="dF / F", bottom="trial")
self.show()
def __init__(self, plot, **opts):
opts['type'] = 'bool'
opts['value'] = True
if not 'name' in opts.keys():
opts['name'] = 'Region'
if 'color' in opts:
opts['color'] = pg.mkColor(opts['color']).setAlpha(50)
else:
opts['color'] = pg.mkColor((255,0,0,50))
parameterTypes.GroupParameter.__init__(self, **opts)
self.addChild({'name':'Start', 'type':'float', 'value':opts.get('startValue', 0), 'suffix':'s', 'siPrefix':True, 'step':0.1, 'dec':True})
self.addChild({'name':'End', 'type':'float', 'value': opts.get('endValue', 0.05), 'suffix':'s', 'siPrefix':True, 'step':0.1, 'dec':True})
self.addChild({'name':'Color', 'type':'color', 'value':opts['color']})
self.addChild({'name':'Display', 'type':'bool', 'value':True})
self.rgn = pg.LinearRegionItem(brush=self.child('Color').value())
self.rgn.setRegion([self.child('Start').value(), self.child('End').value()])
self.plot = plot
self.plot.addItem(self.rgn)
self.child('Start').sigValueChanged.connect(self.regionParamChanged)
self.child('End').sigValueChanged.connect(self.regionParamChanged)
self.rgn.sigRegionChangeFinished.connect(self.updateRegionParams)
self.child('Color').sigValueChanged.connect(self.colorChanged)
self.child('Display').sigValueChanged.connect(self.displayToggled)
def __init__(self):
QtGui.QWidget.__init__(self)
self.layout = QtGui.QVBoxLayout()
self.setLayout(self.layout)
self.imv1 = pg.ImageView()
self.layout.addWidget(self.imv1)
self.plt1 = pg.PlotWidget()
self.layout.addWidget(self.plt1)
self.base_time_rgn = pg.LinearRegionItem([0.07, 0.099])
self.test_time_rgn = pg.LinearRegionItem([0.104, 0.112])
for time_rgn in (self.base_time_rgn, self.test_time_rgn):
self.plt1.addItem(time_rgn)
time_rgn.sigRegionChangeFinished.connect(self.time_rgn_changed)
self.plot_data = []
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.background = None
#self.view = pg.GraphicsView()
self.ctrl = QtGui.QWidget()
l = QtGui.QGridLayout()
self.ctrl.setLayout(l)
self.ctrl.layout = l
#self.loadBgBtn = QtGui.QPushButton('load reference')
#l.addWidget(self.loadBgBtn, 0, 0)
self.addRoiBtn = QtGui.QPushButton('add ROI')
l.addWidget(self.addRoiBtn, 0, 0)
s = QtGui.QSpinBox()
s.setMaximum(10)
s.setMinimum(1)
self.nsegSpin = s
l.addWidget(s, 1, 0)
self.rois = []
self.data = []
## Setup basic GUI
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (200, 300), 'host': self, 'showFileTree': False}),
('Image', {'type': 'imageView', 'pos': ('right', 'File Loader'), 'size': (800, 300)}),
('Time Plot', {'type': 'plot', 'pos': ('bottom',), 'size': (800, 300)}),
('Trial Plot', {'type': 'plot', 'pos': ('bottom', 'Time Plot'), 'size': (800, 300)}),
('Line Scan', {'type': 'imageView', 'pos': ('right', 'Time Plot'), 'size': (800, 300)}),
#('Data Table', {'type': 'table', 'pos': ('below', 'Time Plot')}),
('Ctrl', {'type': 'ctrl', 'pos': ('bottom', 'File Loader'), 'size': (200,30), 'object': self.ctrl}),
])
self.initializeElements()
#self.traces = None
self.plot = self.getElement('Time Plot', create=True)
self.plot2 = self.getElement('Trial Plot', create=True)
self.lr = pg.LinearRegionItem([0, 1])
self.plot.addItem(self.lr)
self.view = self.getElement('Image', create=True)
## Add a color scale
## removed for now--seems to be causing crashes :(
#self.colorScale = pg.GradientLegend(self.plot1, (20, 150), (-10, -10))
#self.plot1.scene().addItem(self.colorScale)
## Plots are updated when the selected region changes
self.lr.sigRegionChanged.connect(self.updateAnalysis)
self.addRoiBtn.clicked.connect(self.addRoi)
self.view.sigProcessingChanged.connect(self.processData)
def __init__(self):
QtGui.QSplitter.__init__(self, QtCore.Qt.Horizontal)
self.resize(800, 1000)
self.params = pg.parametertree.Parameter(
name='params',
type='group',
children=[
dict(name='sequence',
type='group',
children=[
dict(name='analysis',
type='list',
values=['dF / F', 'SNR', 'noise']),
]),
])
self.ptree = pg.parametertree.ParameterTree()
self.ptree.setParameters(self.params)
self.params.child('sequence').sigTreeStateChanged.connect(
self.update_sequence_analysis)
self.leftPanel = QtGui.QWidget()
self.addWidget(self.leftPanel)
self.layout = QtGui.QGridLayout()
self.layout.setContentsMargins(0, 0, 0, 0)
self.leftPanel.setLayout(self.layout)
self.layout.addWidget(self.ptree, 0, 0)
self.gw = pg.GraphicsLayoutWidget()
self.addWidget(self.gw)
self.vb1 = self.gw.addViewBox()
self.img1 = pg.ImageItem()
self.vb1.addItem(self.img1)
self.vb2 = self.gw.addViewBox(row=1, col=0)
self.img2 = pg.ImageItem()
self.vb2.addItem(self.img2)
for vb in (self.vb1, self.vb2):
vb.invertY()
vb.setAspectLocked(True)
self.plt1 = self.gw.addPlot(row=2, col=0)
self.plt1.setLabels(bottom=('time', 's'))
self.plt1_items = []
self.rois = [
pg.EllipseROI([0, 0], [10, 10], pen=(i, 4)) for i in range(2)
]
for roi in self.rois:
self.vb1.addItem(roi)
roi.sigRegionChangeFinished.connect(self.roi_changed)
self.ignore_roi_change = False
self.plt2 = self.gw.addPlot(row=3, col=0)
self.plt2.setXLink(self.plt1)
self.plt2.setLabels(bottom=('time', 's'))
self.noise_time_rgn = pg.LinearRegionItem([0.01, 0.02],
brush=(255, 0, 0, 30))
self.base_time_rgn = pg.LinearRegionItem([0.025, 0.95],
brush=(0, 255, 0, 30))
self.test_time_rgn = pg.LinearRegionItem([0.1, 0.11],
brush=(0, 0, 255, 30))
for time_rgn in (self.base_time_rgn, self.test_time_rgn,
self.noise_time_rgn):
self.plt1.addItem(time_rgn)
time_rgn.sigRegionChangeFinished.connect(self.time_rgn_changed)
time_rgn.sigRegionChangeFinished.connect(
self.update_sequence_analysis)
self.clamp_plots = []
self.plt3 = self.gw.addPlot(row=4, col=0)
self.plt3.setLabels(left="dF / F", bottom="trial")
self.show()
def __init__(self, host):
AnalysisModule.__init__(self, host)
flowchartDir = os.path.join(
os.path.abspath(os.path.split(__file__)[0]), "flowcharts")
self.flowchart = Flowchart(filePath=flowchartDir)
self.flowchart.addInput('dataIn')
self.flowchart.addOutput('results')
self.flowchart.outputNode._allowAddInput = False ## make sure all data is coming out of output['results']
try:
## load default chart
self.flowchart.loadFile(os.path.join(flowchartDir, 'default.fc'))
except:
debug.printExc('Error loading default flowchart:')
tables = OrderedDict([(self.dbIdentity + '.traces',
'TimecourseAnalyzer_traces')])
self.dbGui = DatabaseGui(dm=host.dataManager(), tables=tables)
self.ctrl = Qt.QWidget()
self.ctrl.setLayout(Qt.QVBoxLayout())
self.analyzeBtn = Qt.QPushButton('Analyze')
self.storeToDBBtn = Qt.QPushButton('Store to DB')
self.ctrl.layout().addWidget(self.analyzeBtn)
self.ctrl.layout().addWidget(self.storeToDBBtn)
self._elements_ = OrderedDict([('Database', {
'type': 'ctrl',
'object': self.dbGui,
'size': (100, 100)
}),
('Analysis Options', {
'type': 'ctrl',
'object': self.flowchart.widget(),
'pos': ('above', 'Database'),
'size': (100, 400)
}),
('File Loader', {
'type': 'fileInput',
'size': (100, 100),
'pos':
('above', 'Analysis Options'),
'host': self
}),
('Experiment Plot', {
'type': 'plot',
'pos': ('right', 'File Loader'),
'size': (400, 100)
}),
('Traces Plot', {
'type': 'plot',
'pos':
('bottom', 'Experiment Plot'),
'size': (400, 200)
}),
('Results Plot', {
'type': 'plot',
'pos': ('bottom', 'Traces Plot'),
'size': (400, 200)
}),
('Results Table', {
'type': 'table',
'pos': ('bottom', 'Traces Plot'),
'size': (400, 200)
}),
('Store Ctrl', {
'type': 'ctrl',
'object': self.ctrl,
'size': (100, 100),
'pos': ('bottom', 'File Loader')
})])
self.initializeElements()
self.fileLoader = self.getElement('File Loader', create=True)
self.exptPlot = self.getElement('Experiment Plot', create=True)
self.tracesPlot = self.getElement('Traces Plot', create=True)
self.resultsTable = self.getElement('Results Table', create=True)
self.resultsTable.setSortingEnabled(False)
self.resultsPlot = self.getElement('Results Plot', create=True)
self.resultsPlot.getViewBox().setXLink(self.exptPlot.getViewBox(
)) ## link the x-axes of the exptPlot and the resultsPlot
### initialize variables
self.expStart = 0
self.traces = np.array([],
dtype=[('timestamp', float), ('data', object),
('fileHandle', object),
('results', object)])
self.files = []
self.traceSelectRgn = pg.LinearRegionItem()
self.traceSelectRgn.setRegion([0, 60])
self.exptPlot.addItem(self.traceSelectRgn)
self.traceSelectRgn.sigRegionChanged.connect(self.updateTracesPlot)
#self.traceSelectRgn.sigRegionChangeFinished.connect(self.updateAnalysis)
#self.flowchart.sigOutputChanged.connect(self.flowchartOutputChanged)
#self.addRegionParam = pg.parametertree.Parameter.create(name="Add Region", type='action')
#self.paramTree.addParameters(self.addRegionParam)
#self.addRegionParam.sigActivated.connect(self.newRegionRequested)
self.analyzeBtn.clicked.connect(self.analyzeBtnClicked)
self.storeToDBBtn.clicked.connect(self.storeToDBBtnClicked)
self.flowchart.sigChartLoaded.connect(self.connectPlots)
self.fileLoader.sigClearRequested.connect(self.clearFilesRequested)
def __init__(self, image=None, **opts):
"""
CanvasItem displaying an image.
The image may be 2 or 3-dimensional.
Options:
image: May be a fileHandle, ndarray, or GraphicsItem.
handle: May optionally be specified in place of image
"""
## If no image was specified, check for a file handle..
if image is None:
image = opts.get('handle', None)
item = None
self.data = None
self.currentT = None
if isinstance(image, QtGui.QGraphicsItem):
item = image
elif isinstance(image, np.ndarray):
self.data = image
elif isinstance(image, DataManager.FileHandle):
opts['handle'] = image
self.handle = image
self.data = self.handle.read()
if 'name' not in opts:
opts['name'] = self.handle.shortName()
try:
if 'transform' in self.handle.info():
tr = pg.SRTTransform3D(self.handle.info()['transform'])
tr = pg.SRTTransform(tr) ## convert to 2D
opts['pos'] = tr.getTranslation()
opts['scale'] = tr.getScale()
opts['angle'] = tr.getRotation()
else: ## check for older info formats
if 'imagePosition' in self.handle.info():
opts['scale'] = self.handle.info()['pixelSize']
opts['pos'] = self.handle.info()['imagePosition']
elif 'Downsample' in self.handle.info():
### Needed to support an older format stored by 2p imager
if 'pixelSize' in self.handle.info():
opts['scale'] = self.handle.info()['pixelSize']
if 'microscope' in self.handle.info():
m = self.handle.info()['microscope']
print 'm: ', m
print 'mpos: ', m['position']
opts['pos'] = m['position'][0:2]
else:
info = self.data._info[-1]
opts['pos'] = info.get('imagePosition', None)
elif hasattr(self.data, '_info'):
info = self.data._info[-1]
opts['scale'] = info.get('pixelSize', None)
opts['pos'] = info.get('imagePosition', None)
else:
opts['defaultUserTransform'] = {'scale': (1e-5, 1e-5)}
opts['scalable'] = True
except:
debug.printExc(
'Error reading transformation for image file %s:' %
image.name())
if item is None:
item = pg.ImageItem()
CanvasItem.__init__(self, item, **opts)
self.histogram = pg.PlotWidget()
self.blockHistogram = False
self.histogram.setMaximumHeight(100)
self.levelRgn = pg.LinearRegionItem()
self.histogram.addItem(self.levelRgn)
self.updateHistogram(autoLevels=True)
# addWidget arguments: row, column, rowspan, colspan
self.layout.addWidget(self.histogram, self.layout.rowCount(), 0, 1, 3)
self.timeSlider = QtGui.QSlider(QtCore.Qt.Horizontal)
#self.timeSlider.setMinimum(0)
#self.timeSlider.setMaximum(self.data.shape[0]-1)
self.layout.addWidget(self.timeSlider, self.layout.rowCount(), 0, 1, 3)
self.timeSlider.valueChanged.connect(self.timeChanged)
self.timeSlider.sliderPressed.connect(self.timeSliderPressed)
self.timeSlider.sliderReleased.connect(self.timeSliderReleased)
thisRow = self.layout.rowCount()
self.edgeBtn = QtGui.QPushButton('Edge')
self.edgeBtn.clicked.connect(self.edgeClicked)
self.layout.addWidget(self.edgeBtn, thisRow, 0, 1, 1)
self.meanBtn = QtGui.QPushButton('Mean')
self.meanBtn.clicked.connect(self.meanClicked)
self.layout.addWidget(self.meanBtn, thisRow + 1, 0, 1, 1)
self.tvBtn = QtGui.QPushButton('tv denoise')
self.tvBtn.clicked.connect(self.tvClicked)
self.layout.addWidget(self.tvBtn, thisRow + 2, 0, 1, 1)
self.maxBtn = QtGui.QPushButton('Max no Filter')
self.maxBtn.clicked.connect(self.maxClicked)
self.layout.addWidget(self.maxBtn, thisRow, 1, 1, 1)
self.maxBtn2 = QtGui.QPushButton('Max w/Gaussian')
self.maxBtn2.clicked.connect(self.max2Clicked)
self.layout.addWidget(self.maxBtn2, thisRow + 1, 1, 1, 1)
self.maxMedianBtn = QtGui.QPushButton('Max w/Median')
self.maxMedianBtn.clicked.connect(self.maxMedianClicked)
self.layout.addWidget(self.maxMedianBtn, thisRow + 2, 1, 1, 1)
self.filterOrder = QtGui.QComboBox()
self.filterLabel = QtGui.QLabel('Order')
for n in range(1, 11):
self.filterOrder.addItem("%d" % n)
self.layout.addWidget(self.filterLabel, thisRow + 3, 2, 1, 1)
self.layout.addWidget(self.filterOrder, thisRow + 3, 3, 1, 1)
self.zPlanes = QtGui.QComboBox()
self.zPlanesLabel = QtGui.QLabel('# planes')
for s in ['All', '1', '2', '3', '4', '5']:
self.zPlanes.addItem("%s" % s)
self.layout.addWidget(self.zPlanesLabel, thisRow + 3, 0, 1, 1)
self.layout.addWidget(self.zPlanes, thisRow + 3, 1, 1, 1)
## controls that only appear if there is a time axis
self.timeControls = [
self.timeSlider, self.edgeBtn, self.maxBtn, self.meanBtn,
self.maxBtn2, self.maxMedianBtn, self.filterOrder, self.zPlanes
]
if self.data is not None:
self.updateImage(self.data)
self.graphicsItem().sigImageChanged.connect(self.updateHistogram)
self.levelRgn.sigRegionChanged.connect(self.levelsChanged)
self.levelRgn.sigRegionChangeFinished.connect(
self.levelsChangeFinished)