class PlotCrossCorrelogram(QWidget, PlotBase):
"""
widget to plot PlotCrossCorrelogram
"""
plotParamDefault = [
['plot_type', {
'value': 'line',
'possible': ['bar', 'line']
}],
['bin_width', {
'value': 2.,
'label': 'bin width (ms)'
}],
['limit', {
'value': 500.,
'label': 'max limit (ms)'
}],
['exact', {
'value': False,
'label': 'Compute exact crosscorrelogram'
}],
['max_spike', {
'value': 300,
'label': 'Otherwise bootstrap with'
}],
]
def __init__(
self,
parent=None,
spike_times=None,
sorted=None,
colors=None,
show_button=True,
plotParams=None,
):
QWidget.__init__(self, parent)
PlotBase.__init__(self, plotParams=plotParams)
self.colors = colors
self.spikeSortingWin = self.parent()
mainLayout = QVBoxLayout()
self.setLayout(mainLayout)
h = QHBoxLayout()
mainLayout.addLayout(h)
self.combo1 = QComboBox()
h.addWidget(self.combo1)
self.connect(self.combo1, SIGNAL('currentIndexChanged( int )'),
self.comboChanged)
self.combo2 = QComboBox()
h.addWidget(self.combo2)
self.connect(self.combo2, SIGNAL('currentIndexChanged( int )'),
self.comboChanged)
self.canvas = SimpleCanvasAndTool(orientation=Qt.Horizontal)
self.fig = self.canvas.fig
self.ax = self.fig.add_subplot(1, 1, 1)
mainLayout.addWidget(self.canvas)
if show_button:
but = QPushButton('', self.canvas.canvas)
#~ but = QPushButton('',parent = self.canvas)
but.setIcon(QIcon(':/configure.png'))
but.setGeometry(10, 10, 30, 30)
self.canvas.stackUnder(but)
self.connect(but, SIGNAL('clicked()'), self.changePlotOptions)
self.changeData(spike_times, sorted=sorted)
def refresh(self):
self.changeData(self.spike_times)
def changeData(self, spike_times, sorted=None, colors=None):
if spike_times is None: return
self.spike_times = spike_times
# sorted
if sorted is not None:
self.sorted = sorted
if self.sorted is None:
self.sorted = ones(waveforms.shape[0], dtype='i')
# colors
if colors is not None:
self.colors = colors
if self.colors is None:
self.colors = {}
cmap = get_cmap('jet', unique(self.sorted).size + 3)
for i, c in enumerate(unique(self.sorted)):
self.colors[c] = cmap(i + 2)
# combobox
self.allNeurons = unique(self.sorted)
self.combo1.clear()
self.combo1.addItems(['Neuron %d' % c for c in self.allNeurons])
self.combo2.clear()
self.combo2.addItems(['Neuron %d' % c for c in self.allNeurons])
def comboChanged(self, ind):
c1 = self.allNeurons[self.combo1.currentIndex()]
c2 = self.allNeurons[self.combo2.currentIndex()]
self.ax.clear()
width = self.plotParams['bin_width'] / 1000.
limit = self.plotParams['limit'] / 1000.
# corss correlogram
t1 = self.spike_times[c1 == self.sorted]
t2 = self.spike_times[c2 == self.sorted]
if not (self.plotParams['exact']):
max_spike = self.plotParams['max_spike']
t1 = t1[unique(random.randint(0, high=t1.size, size=max_spike))]
t2 = t2[unique(random.randint(0, high=t2.size, size=max_spike))]
m1 = numpy.tile(t1[:, numpy.newaxis], (1, t2.size))
m2 = numpy.tile(t2[numpy.newaxis, :], (t1.size, 1))
m = m2 - m1
m = m.flatten()
#~ m = m.reshape(m.size)
y, x = numpy.histogram(m, bins=numpy.arange(-limit, limit, width))
if self.plotParams['plot_type'] == 'bar':
self.ax.bar(x[:-1] * 1000, y, width=width * 1000)
elif self.plotParams['plot_type'] == 'line':
self.ax.plot(x[:-1] * 1000, y)
self.ax.set_xlim(-limit * 1000., limit * 1000.)
self.canvas.draw()
class PlotCrossCorrelogram(QWidget , PlotBase):
"""
widget to plot PlotCrossCorrelogram
"""
plotParamDefault = [
[ 'plot_type' , {'value' : 'line' , 'possible' : [ 'bar' , 'line'] }],
[ 'bin_width' , {'value' : 2. , 'label' : 'bin width (ms)'}],
[ 'limit' , {'value' : 500. , 'label' : 'max limit (ms)'}],
[ 'exact' , {'value' :False , 'label' : 'Compute exact crosscorrelogram'}],
[ 'max_spike' , {'value' :300 , 'label' : 'Otherwise bootstrap with'}],
]
def __init__(self , parent=None ,
spike_times = None,
sorted = None,
colors = None,
show_button = True,
plotParams = None,
):
QWidget.__init__(self,parent )
PlotBase.__init__(self,plotParams = plotParams)
self.colors = colors
self.spikeSortingWin = self.parent()
mainLayout = QVBoxLayout()
self.setLayout(mainLayout)
h = QHBoxLayout()
mainLayout.addLayout(h)
self.combo1 = QComboBox()
h.addWidget( self.combo1 )
self.connect( self.combo1, SIGNAL('currentIndexChanged( int )') , self.comboChanged )
self.combo2 = QComboBox()
h.addWidget( self.combo2 )
self.connect( self.combo2, SIGNAL('currentIndexChanged( int )') , self.comboChanged )
self.canvas = SimpleCanvasAndTool(orientation = Qt.Horizontal )
self.fig = self.canvas.fig
self.ax = self.fig.add_subplot(1,1,1)
mainLayout.addWidget(self.canvas)
if show_button:
but = QPushButton('',self.canvas.canvas)
#~ but = QPushButton('',parent = self.canvas)
but.setIcon(QIcon(':/configure.png'))
but.setGeometry(10,10,30,30)
self.canvas.stackUnder(but)
self.connect(but, SIGNAL('clicked()') , self.changePlotOptions)
self.changeData(spike_times , sorted = sorted )
def refresh(self):
self.changeData(self.spike_times)
def changeData(self, spike_times , sorted = None , colors = None):
if spike_times is None : return
self.spike_times = spike_times
# sorted
if sorted is not None:
self.sorted = sorted
if self.sorted is None:
self.sorted = ones( waveforms.shape[0] , dtype = 'i')
# colors
if colors is not None:
self.colors = colors
if self.colors is None:
self.colors = { }
cmap = get_cmap('jet', unique(self.sorted).size+3)
for i,c in enumerate(unique(self.sorted)):
self.colors[c] = cmap(i+2)
# combobox
self.allNeurons = unique(self.sorted)
self.combo1.clear()
self.combo1.addItems( ['Neuron %d' %c for c in self.allNeurons ])
self.combo2.clear()
self.combo2.addItems( ['Neuron %d' %c for c in self.allNeurons ])
def comboChanged(self, ind):
c1 = self.allNeurons[self.combo1.currentIndex()]
c2 = self.allNeurons[self.combo2.currentIndex()]
self.ax.clear()
width = self.plotParams['bin_width']/1000.
limit = self.plotParams['limit']/1000.
# corss correlogram
t1 = self.spike_times[c1==self.sorted]
t2 = self.spike_times[c2==self.sorted]
if not(self.plotParams['exact']):
max_spike = self.plotParams['max_spike']
t1 = t1[unique(random.randint(0,high = t1.size, size = max_spike))]
t2 = t2[unique(random.randint(0,high = t2.size, size = max_spike))]
m1 = numpy.tile(t1[:,numpy.newaxis] , (1,t2.size) )
m2 = numpy.tile(t2[numpy.newaxis,:] , (t1.size,1) )
m = m2-m1
m = m.flatten()
#~ m = m.reshape(m.size)
y,x = numpy.histogram(m, bins = numpy.arange(-limit,limit, width))
if self.plotParams['plot_type'] == 'bar':
self.ax.bar(x[:-1]*1000, y, width =width*1000)
elif self.plotParams['plot_type'] == 'line':
self.ax.plot(x[:-1]*1000, y )
self.ax.set_xlim(-limit*1000., limit*1000.)
self.canvas.draw()
class PlotISI(QWidget, PlotBase):
"""
widget to plot ISI (inter spike interval)
"""
plotParamDefault = [
['plot_type', {
'value': 'bar',
'possible': ['bar', 'line']
}],
['bin_width', {
'value': 2.,
'label': 'bin width (ms)'
}],
['limit', {
'value': 500.,
'label': 'max limit (ms)'
}],
]
def __init__(
self,
parent=None,
spike_times=None,
sorted=None,
colors=None,
show_button=True,
plotParams=None,
):
QWidget.__init__(self, parent)
PlotBase.__init__(self, plotParams=plotParams)
self.colors = colors
self.spikeSortingWin = self.parent()
mainLayout = QVBoxLayout()
self.setLayout(mainLayout)
self.combo = QComboBox()
mainLayout.addWidget(self.combo)
self.connect(self.combo, SIGNAL('currentIndexChanged( int )'),
self.comboChanged)
self.canvas = SimpleCanvasAndTool(orientation=Qt.Horizontal)
self.fig = self.canvas.fig
self.ax = self.fig.add_subplot(1, 1, 1)
mainLayout.addWidget(self.canvas)
if show_button:
but = QPushButton('', parent=self.canvas.canvas)
#~ but = QPushButton('',parent = self.canvas)
but.setIcon(QIcon(':/configure.png'))
but.setGeometry(10, 10, 30, 30)
self.canvas.stackUnder(but)
self.connect(but, SIGNAL('clicked()'), self.changePlotOptions)
self.changeData(spike_times, sorted=sorted)
def refresh(self):
self.changeData(self.spike_times)
def changeData(self, spike_times, sorted=None, colors=None):
if spike_times is None: return
self.spike_times = spike_times
# sorted
if sorted is not None:
self.sorted = sorted
if self.sorted is None:
self.sorted = ones(waveforms.shape[0], dtype='i')
# colors
if colors is not None:
self.colors = colors
if self.colors is None:
self.colors = {}
cmap = get_cmap('jet', unique(self.sorted).size + 3)
for i, c in enumerate(unique(self.sorted)):
self.colors[c] = cmap(i + 2)
# combobox
self.combo.clear()
self.allNeurons = unique(self.sorted)
self.combo.addItems(['Neuron %d' % c for c in self.allNeurons])
def comboChanged(self, ind):
c = self.allNeurons[ind]
self.ax.clear()
width = self.plotParams['bin_width'] / 1000.
limit = self.plotParams['limit'] / 1000.
st = self.spike_times[c == self.sorted]
#~ st.sort()
y, x = numpy.histogram(numpy.diff(st),
bins=numpy.arange(0, limit, width))
if self.plotParams['plot_type'] == 'bar':
self.ax.bar(x[:-1] * 1000,
y,
width=width * 1000,
color=self.colors[c])
elif self.plotParams['plot_type'] == 'line':
self.ax.plot(x[:-1] * 1000, y, color=self.colors[c])
self.ax.set_xlim(0, limit * 1000.)
self.canvas.draw()
class PlotISI(QWidget , PlotBase):
"""
widget to plot ISI (inter spike interval)
"""
plotParamDefault = [
[ 'plot_type' , {'value' : 'bar' , 'possible' : [ 'bar' , 'line'] }],
[ 'bin_width' , {'value' : 2. , 'label' : 'bin width (ms)'}],
[ 'limit' , {'value' : 500. , 'label' : 'max limit (ms)'}],
]
def __init__(self , parent=None ,
spike_times = None,
sorted = None,
colors = None,
show_button = True,
plotParams = None,
):
QWidget.__init__(self,parent )
PlotBase.__init__(self,plotParams = plotParams)
self.colors = colors
self.spikeSortingWin = self.parent()
mainLayout = QVBoxLayout()
self.setLayout(mainLayout)
self.combo = QComboBox()
mainLayout.addWidget( self.combo )
self.connect( self.combo, SIGNAL('currentIndexChanged( int )') , self.comboChanged )
self.canvas = SimpleCanvasAndTool(orientation = Qt.Horizontal )
self.fig = self.canvas.fig
self.ax = self.fig.add_subplot(1,1,1)
mainLayout.addWidget(self.canvas)
if show_button:
but = QPushButton('',parent = self.canvas.canvas)
#~ but = QPushButton('',parent = self.canvas)
but.setIcon(QIcon(':/configure.png'))
but.setGeometry(10,10,30,30)
self.canvas.stackUnder(but)
self.connect(but, SIGNAL('clicked()') , self.changePlotOptions)
self.changeData(spike_times , sorted = sorted )
def refresh(self):
self.changeData(self.spike_times)
def changeData(self, spike_times , sorted = None , colors = None):
if spike_times is None : return
self.spike_times = spike_times
# sorted
if sorted is not None:
self.sorted = sorted
if self.sorted is None:
self.sorted = ones( waveforms.shape[0] , dtype = 'i')
# colors
if colors is not None:
self.colors = colors
if self.colors is None:
self.colors = { }
cmap = get_cmap('jet', unique(self.sorted).size+3)
for i,c in enumerate(unique(self.sorted)):
self.colors[c] = cmap(i+2)
# combobox
self.combo.clear()
self.allNeurons = unique(self.sorted)
self.combo.addItems( ['Neuron %d' %c for c in self.allNeurons ])
def comboChanged(self, ind):
c = self.allNeurons[ind]
self.ax.clear()
width = self.plotParams['bin_width']/1000.
limit = self.plotParams['limit']/1000.
st = self.spike_times[c==self.sorted]
#~ st.sort()
y,x = numpy.histogram(numpy.diff(st), bins = numpy.arange(0,limit, width))
if self.plotParams['plot_type'] == 'bar':
self.ax.bar(x[:-1]*1000, y, width =width*1000, color = self.colors[c])
elif self.plotParams['plot_type'] == 'line':
self.ax.plot(x[:-1]*1000, y, color = self.colors[c])
self.ax.set_xlim(0, limit*1000.)
self.canvas.draw()
