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 __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 )
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 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()
def __init__(
self,
parent=None,
metadata=None,
Session=None,
session=None,
globalApplicationDict=None,
id_respirationsignal=None,
):
QDialog.__init__(self, parent)
self.metadata = metadata
self.session = Session()
self.globalApplicationDict = globalApplicationDict
self.id_respirationsignal = id_respirationsignal
self.respiration = self.session.query(RespirationSignal).filter_by(
id=id_respirationsignal).one()
#FIXME: do not work:
self.setModal(False)
self.setWindowModality(Qt.NonModal)
self.setWindowTitle(
self.tr('OpenElectrophy respiration for %d' %
(self.respiration.id)))
self.setWindowIcon(QIcon(':/respiration.png'))
self.mainLayout = QVBoxLayout()
self.setLayout(self.mainLayout)
h = QHBoxLayout()
self.mainLayout.addLayout(h)
c = SimpleCanvasAndTool()
h.addWidget(c, 3)
self.canvas = c.canvas
self.ax = self.canvas.fig.add_subplot(1, 1, 1)
v = QVBoxLayout()
h.addLayout(v, 2)
but = QPushButton(QIcon(':/TODO.txt'), 'Auto detect')
v.addWidget(but)
self.connect(but, SIGNAL('clicked()'), self.newDetection)
v.addSpacing(20)
v.addWidget(QLabel('<b>Repiratory cycles</b>'))
self.table = QTreeWidget()
#~ self.table.setMinimumWidth(100)
#~ self.table.setColumnWidth(0,80)
v.addWidget(self.table)
self.table.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.connect(self.table, SIGNAL('itemSelectionChanged()'),
self.newSelectionInTable)
self.table.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(self.table,
SIGNAL('customContextMenuRequested( const QPoint &)'),
self.contextMenuTable)
self.mainLayout.addSpacing(20)
buttonBox = QDialogButtonBox()
but = QPushButton(QIcon(':/document-save.png'), 'Save to DB')
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL('clicked()'), self.save_to_db)
but = QPushButton(QIcon(':/reload.png'), 'Reload from DB')
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL('clicked()'), self.reload_from_db)
but = QPushButton(QIcon(':/window-close.png'), 'Quit')
buttonBox.addButton(but, QDialogButtonBox.RejectRole)
self.connect(but, SIGNAL('clicked()'), self.close)
self.mainLayout.addWidget(buttonBox)
if self.respiration.cycle_times is None:
self.cycle_times = None
else:
self.cycle_times = self.respiration.cycle_times
self.vlines = {}
self.baseline = 0.
self.refreshPlot()
self.refreshTable()
self.canvas.mpl_connect('pick_event', self.onPick)
self.canvas.mpl_connect('button_release_event', self.releaseEvent)
self.canvas.mpl_connect('motion_notify_event', self.motionEvent)
#~ self.picked = None
#~ self.lineSelection = None
self.session.expunge_all()
def __init__(
self,
parent=None,
metadata=None,
Session=None,
globalApplicationDict=None,
id_analogsignal=None,
tablename=None,
mode="all signal",
):
QDialog.__init__(self, parent)
self.metadata = metadata
self.session = Session()
self.globalApplicationDict = globalApplicationDict
self.anaSig = self.session.query(AnalogSignal).filter_by(id=id_analogsignal).one()
self.mode = mode
# FIXME: do not work:
self.setModal(False)
self.setWindowModality(Qt.NonModal)
self.setWindowTitle(self.tr("OpenElectrophy Edit oscillation for %d" % (self.anaSig.id)))
self.setWindowIcon(QIcon(":/oscillation.png"))
self.mainLayout = QVBoxLayout()
self.setLayout(self.mainLayout)
self.tab = QTabWidget()
self.mainLayout.addWidget(self.tab)
if self.mode == "around epoch":
fr = QFrame()
self.tab.addTab(fr, "Epoch list")
v1 = QVBoxLayout()
fr.setLayout(v1)
# ~ default_query = "SELECT id_epoch FROM epoch WHERE epoch.id_trial = %d " % (self.elec.id_trial)
# ~ self.queryBoxEpoch = QueryResultBox(table = 'epoch', field_list = Epoch.list_field, default_query = default_query )
# ~ v1.addWidget(self.queryBoxEpoch)
# ~ self.queryBoxEpoch.treeview_result.setSelectionMode(QAbstractItemView.SingleSelection)
# ~ self.connect(self.queryBoxEpoch.treeview_result , SIGNAL('itemSelectionChanged()') , self.changeEpoch)
query = "SELECT event.id \nFROM event \nWHERE event.id_segment = %s\n" % (self.anaSig.id_segment)
self.queryEvent = QueryResultBox(
metadata=self.metadata,
session=self.session,
globalApplicationDict=self.globalApplicationDict,
table="event",
orientation=Qt.Horizontal,
query=query,
)
v1.addWidget(self.queryEvent, 2)
self.queryEvent.tree.treeview.setSelectionMode(QAbstractItemView.SingleSelection)
self.connect(self.queryEvent.tree.treeview, SIGNAL("clicked( QModelIndex )"), self.changeSelectedEvent)
# ~ params = [
# ~ ('t_start', {'value' : -1., }),
# ~ ('t_stop', {'value' : 3., }),
# ~ ]
# ~ self.paramEvent = ParamWidget(params ,
# ~ applicationdict = self.globalApplicationDict,
# ~ keyformemory = 'linedetector/event_window' ,
# ~ title = 'Choose the window',
# ~ )
# ~ v1.addWidget(self.paramEvent,0)
v1.addSpacing(0)
self.activeEvent = None
fr = QFrame()
self.tab.addTab(fr, "Oscillations")
h = QHBoxLayout()
fr.setLayout(h)
# Scalogram
v = QVBoxLayout()
h.addLayout(v)
self.paramMorlet = ParamWidget(
morletParams,
applicationdict=globalApplicationDict,
keyformemory="linedetector/morlet",
title="Parameters for scalogram",
)
v.addWidget(self.paramMorlet)
hb = QHBoxLayout()
v.addLayout(hb)
hb.addStretch(0)
but = QPushButton(QIcon(":/"), "Compute scalogram")
self.connect(but, SIGNAL("clicked()"), self.computeScalogram)
hb.addWidget(but)
# detection zone
v.addSpacing(20)
self.paramDetectionZone = ParamWidget(
detectionZoneParams,
applicationdict=globalApplicationDict,
keyformemory="linedetector/detection_zone",
title="Detection zone",
)
v.addWidget(self.paramDetectionZone)
self.connect(self.paramDetectionZone, SIGNAL("paramChanged( QString )"), self.plotDetectionZone)
hb = QHBoxLayout()
v.addLayout(hb)
hb.addStretch(0)
but = QPushButton(QIcon(":/"), "Redraw signal")
self.connect(but, SIGNAL("clicked()"), self.redrawSignal)
hb.addWidget(but)
v.addStretch(0)
# threshold
v = QVBoxLayout()
h.addLayout(v)
self.paramThreshold = ParamWidget(
thresholdParams,
applicationdict=globalApplicationDict,
keyformemory="linedetector/threshold",
title="Threshold",
)
v.addWidget(self.paramThreshold)
self.connect(self.paramThreshold, SIGNAL("paramChanged( QString )"), self.refreshThreshold)
hb = QHBoxLayout()
v.addLayout(hb)
hb.addStretch(0)
but = QPushButton(QIcon(":/"), "Detect maximas")
self.connect(but, SIGNAL("clicked()"), self.detectMaximas)
hb.addWidget(but)
but = QPushButton(QIcon(":/"), "Compute lines")
self.connect(but, SIGNAL("clicked()"), self.computeLines)
hb.addWidget(but)
# clean
v.addSpacing(20)
self.paramClean = ParamWidget(
cleanParams, applicationdict=globalApplicationDict, keyformemory="linedetector/clean", title="Clean"
)
v.addWidget(self.paramClean)
hb = QHBoxLayout()
v.addLayout(hb)
hb.addStretch(0)
but = QPushButton(QIcon(":/"), "Clean list")
hb.addWidget(but)
self.connect(but, SIGNAL("clicked()"), self.cleanList)
v.addSpacing(27)
but = QPushButton(QIcon(":/"), "Compute all")
v.addWidget(but)
self.connect(but, SIGNAL("clicked()"), self.computeAll)
v.addStretch(0)
# center
# ~ v = QVBoxLayout()
# ~ h.addLayout(v)
spv = QSplitter(Qt.Vertical)
# ~ spv.setOpaqueResize(False)
h.addWidget(spv, 10)
self.treeviewOscillations = QTreeWidget()
self.treeviewOscillations.setColumnCount(3)
self.treeviewOscillations.setHeaderLabels(["oscillation", "time_max", "freq_max", "amplitude_max"])
self.treeviewOscillations.setSelectionMode(QAbstractItemView.ExtendedSelection)
spv.addWidget(self.treeviewOscillations)
self.treeviewOscillations.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(
self.treeviewOscillations,
SIGNAL("customContextMenuRequested( const QPoint &)"),
self.contextMenuTreeviewOscillation,
)
self.connect(
self.treeviewOscillations,
SIGNAL("itemDoubleClicked(QTreeWidgetItem *, int)"),
self.zoomOscillationOnDoubleClick,
)
self.connect(self.treeviewOscillations, SIGNAL("itemSelectionChanged()"), self.selectionOscillationChanged)
# right side
# ~ v = QHBoxLayout()
# ~ h.addLayout(v)
self.canvas = SimpleCanvasAndTool(orientation=Qt.Vertical)
self.fig = self.canvas.fig
spv.addWidget(self.canvas)
# button
buttonBox = QDialogButtonBox()
but = QPushButton(QIcon(":/document-save.png"), "Save to DB (no delete)")
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL("clicked()"), self.save_to_db_no_delete)
but = QPushButton(QIcon(":/document-save.png"), "Save to DB (delete old in interest zone)")
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL("clicked()"), self.save_to_db_and_delete)
but = QPushButton(QIcon(":/reload.png"), "Reload from DB")
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL("clicked()"), self.reload_from_db_all)
but = QPushButton(QIcon(":/reload.png"), "Reload from DB (only interest zone)")
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL("clicked()"), self.reload_from_db_only_zone)
but = QPushButton(QIcon(":/window-close.png"), "Quit")
buttonBox.addButton(but, QDialogButtonBox.RejectRole)
self.connect(but, SIGNAL("clicked()"), self.close)
self.mainLayout.addWidget(buttonBox)
# context menu
self.menu = QMenu()
act = self.menu.addAction(self.tr("Delete"))
self.connect(act, SIGNAL("triggered()"), self.deleteSelection)
act = self.menu.addAction(self.tr("Recompute"))
self.connect(act, SIGNAL("triggered()"), self.recomputeSelection)
act = self.menu.addAction(self.tr("Clean"))
self.connect(act, SIGNAL("triggered()"), self.cleanSelection)
#
self.lineDetector = LineDetector(self.anaSig)
self.plotLineDetector = PlotLineDetector(figure=self.fig, lineDetector=self.lineDetector)
self.checkParam()
class OscillationDetection(QDialog):
"""
Scroll area resazible for stacking matplotlib canvas
"""
def __init__(
self,
parent=None,
metadata=None,
Session=None,
globalApplicationDict=None,
id_analogsignal=None,
tablename=None,
mode="all signal",
):
QDialog.__init__(self, parent)
self.metadata = metadata
self.session = Session()
self.globalApplicationDict = globalApplicationDict
self.anaSig = self.session.query(AnalogSignal).filter_by(id=id_analogsignal).one()
self.mode = mode
# FIXME: do not work:
self.setModal(False)
self.setWindowModality(Qt.NonModal)
self.setWindowTitle(self.tr("OpenElectrophy Edit oscillation for %d" % (self.anaSig.id)))
self.setWindowIcon(QIcon(":/oscillation.png"))
self.mainLayout = QVBoxLayout()
self.setLayout(self.mainLayout)
self.tab = QTabWidget()
self.mainLayout.addWidget(self.tab)
if self.mode == "around epoch":
fr = QFrame()
self.tab.addTab(fr, "Epoch list")
v1 = QVBoxLayout()
fr.setLayout(v1)
# ~ default_query = "SELECT id_epoch FROM epoch WHERE epoch.id_trial = %d " % (self.elec.id_trial)
# ~ self.queryBoxEpoch = QueryResultBox(table = 'epoch', field_list = Epoch.list_field, default_query = default_query )
# ~ v1.addWidget(self.queryBoxEpoch)
# ~ self.queryBoxEpoch.treeview_result.setSelectionMode(QAbstractItemView.SingleSelection)
# ~ self.connect(self.queryBoxEpoch.treeview_result , SIGNAL('itemSelectionChanged()') , self.changeEpoch)
query = "SELECT event.id \nFROM event \nWHERE event.id_segment = %s\n" % (self.anaSig.id_segment)
self.queryEvent = QueryResultBox(
metadata=self.metadata,
session=self.session,
globalApplicationDict=self.globalApplicationDict,
table="event",
orientation=Qt.Horizontal,
query=query,
)
v1.addWidget(self.queryEvent, 2)
self.queryEvent.tree.treeview.setSelectionMode(QAbstractItemView.SingleSelection)
self.connect(self.queryEvent.tree.treeview, SIGNAL("clicked( QModelIndex )"), self.changeSelectedEvent)
# ~ params = [
# ~ ('t_start', {'value' : -1., }),
# ~ ('t_stop', {'value' : 3., }),
# ~ ]
# ~ self.paramEvent = ParamWidget(params ,
# ~ applicationdict = self.globalApplicationDict,
# ~ keyformemory = 'linedetector/event_window' ,
# ~ title = 'Choose the window',
# ~ )
# ~ v1.addWidget(self.paramEvent,0)
v1.addSpacing(0)
self.activeEvent = None
fr = QFrame()
self.tab.addTab(fr, "Oscillations")
h = QHBoxLayout()
fr.setLayout(h)
# Scalogram
v = QVBoxLayout()
h.addLayout(v)
self.paramMorlet = ParamWidget(
morletParams,
applicationdict=globalApplicationDict,
keyformemory="linedetector/morlet",
title="Parameters for scalogram",
)
v.addWidget(self.paramMorlet)
hb = QHBoxLayout()
v.addLayout(hb)
hb.addStretch(0)
but = QPushButton(QIcon(":/"), "Compute scalogram")
self.connect(but, SIGNAL("clicked()"), self.computeScalogram)
hb.addWidget(but)
# detection zone
v.addSpacing(20)
self.paramDetectionZone = ParamWidget(
detectionZoneParams,
applicationdict=globalApplicationDict,
keyformemory="linedetector/detection_zone",
title="Detection zone",
)
v.addWidget(self.paramDetectionZone)
self.connect(self.paramDetectionZone, SIGNAL("paramChanged( QString )"), self.plotDetectionZone)
hb = QHBoxLayout()
v.addLayout(hb)
hb.addStretch(0)
but = QPushButton(QIcon(":/"), "Redraw signal")
self.connect(but, SIGNAL("clicked()"), self.redrawSignal)
hb.addWidget(but)
v.addStretch(0)
# threshold
v = QVBoxLayout()
h.addLayout(v)
self.paramThreshold = ParamWidget(
thresholdParams,
applicationdict=globalApplicationDict,
keyformemory="linedetector/threshold",
title="Threshold",
)
v.addWidget(self.paramThreshold)
self.connect(self.paramThreshold, SIGNAL("paramChanged( QString )"), self.refreshThreshold)
hb = QHBoxLayout()
v.addLayout(hb)
hb.addStretch(0)
but = QPushButton(QIcon(":/"), "Detect maximas")
self.connect(but, SIGNAL("clicked()"), self.detectMaximas)
hb.addWidget(but)
but = QPushButton(QIcon(":/"), "Compute lines")
self.connect(but, SIGNAL("clicked()"), self.computeLines)
hb.addWidget(but)
# clean
v.addSpacing(20)
self.paramClean = ParamWidget(
cleanParams, applicationdict=globalApplicationDict, keyformemory="linedetector/clean", title="Clean"
)
v.addWidget(self.paramClean)
hb = QHBoxLayout()
v.addLayout(hb)
hb.addStretch(0)
but = QPushButton(QIcon(":/"), "Clean list")
hb.addWidget(but)
self.connect(but, SIGNAL("clicked()"), self.cleanList)
v.addSpacing(27)
but = QPushButton(QIcon(":/"), "Compute all")
v.addWidget(but)
self.connect(but, SIGNAL("clicked()"), self.computeAll)
v.addStretch(0)
# center
# ~ v = QVBoxLayout()
# ~ h.addLayout(v)
spv = QSplitter(Qt.Vertical)
# ~ spv.setOpaqueResize(False)
h.addWidget(spv, 10)
self.treeviewOscillations = QTreeWidget()
self.treeviewOscillations.setColumnCount(3)
self.treeviewOscillations.setHeaderLabels(["oscillation", "time_max", "freq_max", "amplitude_max"])
self.treeviewOscillations.setSelectionMode(QAbstractItemView.ExtendedSelection)
spv.addWidget(self.treeviewOscillations)
self.treeviewOscillations.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(
self.treeviewOscillations,
SIGNAL("customContextMenuRequested( const QPoint &)"),
self.contextMenuTreeviewOscillation,
)
self.connect(
self.treeviewOscillations,
SIGNAL("itemDoubleClicked(QTreeWidgetItem *, int)"),
self.zoomOscillationOnDoubleClick,
)
self.connect(self.treeviewOscillations, SIGNAL("itemSelectionChanged()"), self.selectionOscillationChanged)
# right side
# ~ v = QHBoxLayout()
# ~ h.addLayout(v)
self.canvas = SimpleCanvasAndTool(orientation=Qt.Vertical)
self.fig = self.canvas.fig
spv.addWidget(self.canvas)
# button
buttonBox = QDialogButtonBox()
but = QPushButton(QIcon(":/document-save.png"), "Save to DB (no delete)")
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL("clicked()"), self.save_to_db_no_delete)
but = QPushButton(QIcon(":/document-save.png"), "Save to DB (delete old in interest zone)")
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL("clicked()"), self.save_to_db_and_delete)
but = QPushButton(QIcon(":/reload.png"), "Reload from DB")
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL("clicked()"), self.reload_from_db_all)
but = QPushButton(QIcon(":/reload.png"), "Reload from DB (only interest zone)")
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL("clicked()"), self.reload_from_db_only_zone)
but = QPushButton(QIcon(":/window-close.png"), "Quit")
buttonBox.addButton(but, QDialogButtonBox.RejectRole)
self.connect(but, SIGNAL("clicked()"), self.close)
self.mainLayout.addWidget(buttonBox)
# context menu
self.menu = QMenu()
act = self.menu.addAction(self.tr("Delete"))
self.connect(act, SIGNAL("triggered()"), self.deleteSelection)
act = self.menu.addAction(self.tr("Recompute"))
self.connect(act, SIGNAL("triggered()"), self.recomputeSelection)
act = self.menu.addAction(self.tr("Clean"))
self.connect(act, SIGNAL("triggered()"), self.cleanSelection)
#
self.lineDetector = LineDetector(self.anaSig)
self.plotLineDetector = PlotLineDetector(figure=self.fig, lineDetector=self.lineDetector)
self.checkParam()
def save_to_db(self, delete_old=False):
t1, t2, f1, f2 = self.lineDetector.detection_zone
if self.mode == "all signal" or self.mode == "around epoch":
# delete old oscillations in database
if delete_old:
query = self.session.query(Oscillation)
query = query.filter(Oscillation.id_analogsignal == self.anaSig.id)
query = query.filter(Oscillation.freq_max >= f1).filter(Oscillation.freq_max <= f2)
query = query.filter(Oscillation.time_max >= t1).filter(Oscillation.time_max <= t2)
for osci in query.all():
self.session.delete(osci)
self.session.commit()
# create new ones
for o, osci in enumerate(self.lineDetector.list_oscillation):
# ~ if osci in self.session:
# ~ self.session.expunge( osci )
# ~ self.session.commit()
# ~ osci.id = None
# ~ osci.id_analogsignal = self.anaSig.id
# ~ self.session.merge(osci)
# ~ osci2 = osci.copy()
# ~ osci2.id_analogsignal = self.anaSig.id
# ~ self.session.add(osci2)
self.anaSig._oscillations.append(osci.copy())
self.session.commit()
def save_to_db_no_delete(self):
self.save_to_db(delete_old=False)
def save_to_db_and_delete(self):
self.save_to_db(delete_old=True)
def reload_from_db(self, only_by_zone=True):
t1, t2, f1, f2 = self.lineDetector.detection_zone
if self.mode == "all signal" or self.mode == "around epoch":
self.lineDetector.list_oscillation = []
query = self.session.query(Oscillation)
query = query.filter(Oscillation.id_analogsignal == self.anaSig.id)
if only_by_zone:
query = query.filter(Oscillation.freq_max >= f1).filter(Oscillation.freq_max <= f2)
query = query.filter(Oscillation.time_max >= t1).filter(Oscillation.time_max <= t2)
self.lineDetector.list_oscillation = [osci for osci in query.all()]
self.refreshTreeview()
self.plotLineDetector.plotOscillations()
self.canvas.draw()
def reload_from_db_all(self):
self.reload_from_db(only_by_zone=False)
def reload_from_db_only_zone(self):
self.reload_from_db(only_by_zone=True)
def changeSelectedEvent(self, index):
# ~ print 'change', index.row()
ev = index.internalPointer()
if self.activeEvent is None:
shift = ev.time
else:
shift = ev.time - self.activeEvent.time
self.paramMorlet.update(
{"t_start": self.paramMorlet["t_start"] + shift, "t_stop": self.paramMorlet["t_stop"] + shift}
)
self.paramDetectionZone.update(
{"t1": self.paramDetectionZone["t1"] + shift, "t2": self.paramDetectionZone["t2"] + shift}
)
self.paramThreshold.update({"t1": self.paramThreshold["t1"] + shift, "t2": self.paramThreshold["t2"] + shift})
self.plotLineDetector.clear()
self.canvas.draw()
self.checkParam()
self.activeEvent = ev
self.plotLineDetector.axMap.axvline(ev.time, color="c", linewidth=2)
self.plotLineDetector.axSig.axvline(ev.time, color="c", linewidth=2)
self.redrawSignal()
self.computeScalogram()
def checkParam(self):
# get from UI
self.lineDetector.update(**self.paramMorlet.get_dict())
self.lineDetector.detection_zone = []
for i, k in enumerate(["t1", "t2", "f1", "f2"]):
self.lineDetector.detection_zone += [self.paramDetectionZone[k]]
for k in ["manual_threshold", "abs_threshold", "std_relative_threshold"]:
setattr(self.lineDetector, k, self.paramThreshold[k])
self.lineDetector.reference_zone = []
for i, k in enumerate(["t1", "t2", "f1", "f2"]):
self.lineDetector.reference_zone += [self.paramThreshold[k]]
self.lineDetector.update(**self.paramClean.get_dict())
# check
self.lineDetector.checkParam()
# refresh UI
for k in self.paramMorlet.get_dict():
self.paramMorlet[k] = self.lineDetector.__dict__[k]
for i, k in enumerate(["t1", "t2", "f1", "f2"]):
self.paramDetectionZone[k] = self.lineDetector.detection_zone[i]
for i, k in enumerate(["t1", "t2", "f1", "f2"]):
self.paramThreshold[k] = self.lineDetector.reference_zone[i]
enabled = not (self.paramThreshold["manual_threshold"])
for i, k in enumerate(["t1", "t2", "f1", "f2"]):
self.paramThreshold.params[k]["widget"].setEnabled(enabled)
self.paramThreshold.params["abs_threshold"]["widget"].setEnabled(not (enabled))
self.paramThreshold.params["std_relative_threshold"]["widget"].setEnabled(enabled)
def computeScalogram(self):
self.checkParam()
self.lineDetector.computeTimeFreq()
self.plotLineDetector.plotMap()
self.canvas.draw()
if self.mode == "around epoch" and self.activeEvent is not None:
self.plotLineDetector.axMap.axvline(self.activeEvent.time, color="c", linewidth=2)
# ~ self.plotLineDetector.axSig.axvline( self.activeEvent.time, color = 'c' , linewidth = 2)
def plotDetectionZone(self, *name):
self.checkParam()
# ~ self.plotLineDetector.plotFilteredSig()
self.plotLineDetector.plotDetectionZone()
self.canvas.draw()
def redrawSignal(self):
self.checkParam()
self.plotLineDetector.plotFilteredSig()
self.plotLineDetector.plotDetectionZone()
self.canvas.draw()
if self.mode == "around epoch" and self.activeEvent is not None:
# ~ self.plotLineDetector.axMap.axvline( self.activeEvent.time, color = 'c' , linewidth = 2)
self.plotLineDetector.axSig.axvline(self.activeEvent.time, color="c", linewidth=2)
def refreshThreshold(self, *name):
self.checkParam()
self.paramThreshold["abs_threshold"] = self.lineDetector.computeThreshold()
self.plotLineDetector.plotReferenceZone()
self.plotLineDetector.plotThreshold()
self.canvas.draw()
def detectMaximas(self):
self.refreshThreshold()
# ~ self.lineDetector.computeThreshold()
self.lineDetector.detectMax()
self.plotLineDetector.plotMax()
self.canvas.draw()
def computeLines(self):
self.lineDetector.computeThreshold()
self.lineDetector.detectLine()
self.plotLineDetector.plotOscillations()
self.canvas.draw()
self.refreshTreeview()
def cleanList(self):
self.lineDetector.update(**self.paramClean.get_dict())
self.lineDetector.cleanLine()
self.plotLineDetector.plotOscillations()
self.canvas.draw()
self.refreshTreeview()
def computeAll(self):
self.computeScalogram()
self.plotDetectionZone()
self.redrawSignal()
self.detectMaximas()
self.computeLines()
self.cleanList()
self.refreshTreeview()
# ~ print self.lineDetector.sampling_rate
# ~ print self.plotLineDetector.lineDetector.sampling_rate
def refreshTreeview(self):
self.treeviewOscillations.clear()
for o, osci in enumerate(self.lineDetector.list_oscillation):
item = QTreeWidgetItem(
["oscillation %s" % o, str(osci.time_max), str(osci.freq_max), str(osci.amplitude_max)]
)
self.treeviewOscillations.addTopLevelItem(item)
def contextMenuTreeviewOscillation(self, point):
# ~ for item in self.treeviewOscillations.selectedItems() :
# ~ pos = self.treeviewOscillations.indexFromItem(item).row()
self.menu.exec_(self.cursor().pos())
def zoomOscillationOnDoubleClick(self, item):
# push the current view to define home if stack is empty
if self.canvas.toolbar._views.empty():
self.canvas.toolbar.push_current()
pos = self.treeviewOscillations.indexFromItem(item).row()
osc = self.lineDetector.list_oscillation[pos]
fmin = osc.freq_line.min()
fmax = osc.freq_line.max()
delta_f = max(10.0, (fmax - fmin) / 3.0)
delta_t = (osc.time_stop - osc.time_start) / 2.0
self.plotLineDetector.axMap.set_ylim(max(0.0, fmin - delta_f), fmax + delta_f)
self.plotLineDetector.axMap.set_xlim(osc.time_start - delta_t, osc.time_stop + delta_t, emit=True)
self.canvas.draw()
# push the current view to add new view in the toolbar history
self.canvas.toolbar.push_current()
def selectionOscillationChanged(self):
for l in self.plotLineDetector.lineOscillations1:
l.set_linewidth(3)
l.set_color("m")
for l in self.plotLineDetector.lineOscillations2:
l.set_linewidth(1)
l.set_color("m")
for item in self.treeviewOscillations.selectedItems():
pos = self.treeviewOscillations.indexFromItem(item).row()
self.plotLineDetector.lineOscillations1[pos].set_linewidth(4)
self.plotLineDetector.lineOscillations1[pos].set_color("c")
self.plotLineDetector.lineOscillations2[pos].set_linewidth(5)
self.plotLineDetector.lineOscillations2[pos].set_color("c")
self.canvas.draw()
def deleteSelection(self):
toremove = []
for index in self.treeviewOscillations.selectedIndexes():
if index.column() == 0:
toremove.append(self.lineDetector.list_oscillation[index.row()])
for r in toremove:
self.lineDetector.list_oscillation.remove(r)
self.plotLineDetector.plotOscillations()
self.canvas.draw()
self.refreshTreeview()
def recomputeSelection(self):
l = []
for index in self.treeviewOscillations.selectedIndexes():
l.append(index.row())
self.lineDetector.recomputeSelection(l)
self.plotLineDetector.plotOscillations()
self.canvas.draw()
self.refreshTreeview()
def cleanSelection(self):
self.lineDetector.update(**self.paramClean.get_dict())
l = []
for index in self.treeviewOscillations.selectedIndexes():
l.append(index.row())
self.lineDetector.cleanSelection(l)
self.plotLineDetector.plotOscillations()
self.canvas.draw()
self.refreshTreeview()
