class MplCanvas(FigureCanvas):
def __init__(self, parent=None, width=5, height=4, dpi=100):
matplotlib.rcParams['font.size'] = 8
self.figure = Figure(figsize=(width, height), dpi=dpi)
self.axes = self.figure.add_subplot(111)
FigureCanvas.__init__(self, self.figure)
self.setParent(parent)
self.toolbar = NavigationToolbar(self, parent)
self.toolbar.setIconSize(QSize(16, 16))
FigureCanvas.setSizePolicy(self,
QSizePolicy.Expanding,
QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
def getToolbar(self):
return self.toolbar
def clear(self):
self.figure.clear()
self.axes = self.figure.add_subplot(111)
def test(self):
self.axes.plot([1,2,3,4])
def saveAs(self, fname):
self.figure.savefig(fname)
class MplWidgetT(QtGui.QWidget):
def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
self.canvas = MplCanvas()
self.ntb = NavigationToolbar(self.canvas, self)
self.ntb.setIconSize(QtCore.QSize(16, 16))
self.vbl = QtGui.QVBoxLayout()
self.vbl.addWidget(self.canvas)
self.vbl.addWidget(self.ntb)
self.setLayout(self.vbl)
class MplWidgetT(QtGui.QWidget):
def __init__(self, parent = None):
QtGui.QWidget.__init__(self, parent)
self.canvas = MplCanvas()
self.ntb = NavigationToolbar(self.canvas, self)
self.ntb.setIconSize(QtCore.QSize(16, 16))
self.vbl = QtGui.QVBoxLayout()
self.vbl.addWidget(self.canvas)
self.vbl.addWidget(self.ntb)
self.setLayout(self.vbl)
def NewFigure_proc(self):
widget = QtGui.QWidget(self.MainFigTabWidget)
vlay = QtGui.QVBoxLayout(widget)
self.Figures.append(MplWidget(widget))
ntb = NavToolbar(self.Figures[-1], parent = widget)
ntb.setIconSize(QtCore.QSize(15,15))
vlay.setSpacing(0)
vlay.setMargin(0)
vlay.addWidget(self.Figures[-1])
vlay.addWidget(ntb)
widget.setLayout(vlay)
self.MainFigTabWidget.addTab(widget, 'Figure '+str(len(self.Figures)))
widget.setObjectName(str(self.MainFigTabWidget.count()))
self.Figures[-1].setObjectName(str(self.MainFigTabWidget.count()))
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.setWindowTitle("NeuroExplorer GUI")
self.MainWidget = QtGui.QWidget()
self.MainLayout = QtGui.QHBoxLayout(self.MainWidget)
self.WorkingDir = pth
# create a file dialog
self.fileDialog = QtGui.QFileDialog()
# create an open file action that gets triggered when called from menu
openAction = QtGui.QAction('&Open File', self)
openAction.setShortcut('Ctrl+O')
openAction.triggered.connect(self.OpenFile_proc)
# trigger settings from menu
settingsAction = QtGui.QAction('&Settings', self)
settingsAction.setShortcut('Ctrl+S')
settingsAction.triggered.connect(self.Settings_proc)
# trigger the closing of the application
closeAction = QtGui.QAction('&Close H5File', self)
closeAction.setShortcut('Ctrl+X')
closeAction.triggered.connect(self.CloseFile_proc)
# create the menubar
menubar = self.menuBar()
fileMenu = menubar.addMenu('&File')
fileMenu.addAction(openAction)
fileMenu.addAction(settingsAction)
fileMenu.addAction(closeAction)
showDock0Action = QtGui.QAction('&Show Figure Control', self)
showDock1Action = QtGui.QAction('&Show Analisys Centered', self)
showDock2Action = QtGui.QAction('&Show Unit Centered', self)
windowsMenu = menubar.addMenu('&Windows')
windowsMenu.addAction(showDock0Action)
windowsMenu.addAction(showDock1Action)
windowsMenu.addAction(showDock2Action)
############ add a dockable figure control widget
dock0 = QtGui.QDockWidget('Figure Control', self)
dock0.setAllowedAreas(QtCore.Qt.LeftDockWidgetArea | QtCore.Qt.RightDockWidgetArea)
dock0.setMinimumWidth(QtGui.QApplication.desktop().availableGeometry().width()/6)
showDock0Action.triggered.connect(dock0.show)
w = QtGui.QWidget(dock0)
w.setMaximumHeight(60)
vlay = QtGui.QVBoxLayout(w)
vlay.setSpacing(0)
vlay.setMargin(0)
hlay = QtGui.QHBoxLayout()
self.NewFigBtn = QtGui.QPushButton('New Figure')
self.NewFigBtn.setFont(QtGui.QFont('',8))
#self.NewFigBtn.setMaximumHeight(25)
self.NewFigBtn.clicked.connect(self.NewFigure_proc)
hlay.addWidget(self.NewFigBtn)
self.NewFigBtn = QtGui.QPushButton('Save Figure')
self.NewFigBtn.setFont(QtGui.QFont('',8))
#self.NewFigBtn.setMaximumHeight(25)
self.NewFigBtn.clicked.connect(self.SaveFig_proc)
hlay.addWidget(self.NewFigBtn)
vlay.addLayout(hlay)
hlay = QtGui.QHBoxLayout(w)
self.FigNameText = QtGui.QLineEdit()
self.FigNameText.setFont(QtGui.QFont('',8))
self.FigNameText.setMaximumHeight(25)
self.ChangeTabLabelBtn = QtGui.QPushButton('Set Current Fig Label')
self.ChangeTabLabelBtn.setFont(QtGui.QFont('',8))
self.ChangeTabLabelBtn.clicked.connect(self.ChangeCurTabLabel_proc)
hlay.addWidget(self.FigNameText)
hlay.addWidget(self.ChangeTabLabelBtn)
vlay.addLayout(hlay)
dock0.setWidget(w)
############ add a dockable toolbox widget
dock1 = QtGui.QDockWidget('Analisys Centered', self)
dock1.setAllowedAreas(QtCore.Qt.LeftDockWidgetArea | QtCore.Qt.RightDockWidgetArea)
w = QtGui.QWidget(dock1)
#mainlay = QtGui.QVBoxLayout(w)
showDock1Action.triggered.connect(dock1.show)
### h5 file operations group
vlay = QtGui.QVBoxLayout(w)
vlay.setMargin(2)
vlay.setSpacing(2)
hlay = QtGui.QHBoxLayout()
self.AnalisysTypeCombo = QtGui.QComboBox()
self.AnalisysTypeCombo.addItems(['PSTH','Autocorrelation','Crosscorrelation','Spectrum'])
self.AnalisysTypeCombo.setFont(QtGui.QFont('',8))
lbl = QtGui.QLabel('Analisys Type')
lbl.setFont(QtGui.QFont('',8))
hlay.addWidget(lbl)
hlay.addWidget(self.AnalisysTypeCombo)
vlay.addLayout(hlay)
# add a spin box to select the number of columns
hlay = QtGui.QHBoxLayout()
self.nColumnsAxesSpin = QtGui.QSpinBox()
self.nColumnsAxesSpin.setRange(0,10)
self.nColumnsAxesSpin.setValue(6)
lbl = QtGui.QLabel('Number of Columns')
lbl.setFont(QtGui.QFont('',8))
hlay.addWidget(lbl)
hlay.addWidget(self.nColumnsAxesSpin)
vlay.addLayout(hlay)
# time limits
hlay = QtGui.QHBoxLayout()
self.tWin1Spin = QtGui.QDoubleSpinBox()
#self.tWin1Spin.setMaximumHeight(20)
self.tWin1Spin.setRange(0,5)
self.tWin1Spin.setValue(1)
self.tWin1Spin.setSingleStep(0.1)
self.tWin1Spin.setFont(QtGui.QFont('',8))
self.tWin2Spin = QtGui.QDoubleSpinBox()
#self.tWin2Spin.setMaximumHeight(20)
self.tWin2Spin.setRange(0,5)
self.tWin2Spin.setValue(2)
self.tWin2Spin.setSingleStep(0.1)
self.tWin2Spin.setFont(QtGui.QFont('',8))
self.timePerBinSpin = QtGui.QSpinBox()
self.timePerBinSpin.setRange(5,500)
self.timePerBinSpin.setValue(20)
lbl = QtGui.QLabel('Twin1')
lbl.setFont(QtGui.QFont('',8))
hlay.addWidget(lbl)
hlay.addWidget(self.tWin1Spin)
hlay.addStretch(1)
lbl = QtGui.QLabel('Twin2')
lbl.setFont(QtGui.QFont('',8))
hlay.addWidget(lbl)
hlay.addWidget(self.tWin2Spin)
lbl = QtGui.QLabel('Resolution (milisec/bin)')
lbl.setFont(QtGui.QFont('',8))
hlay.addWidget(lbl)
hlay.addWidget(self.timePerBinSpin)
vlay.addLayout(hlay)
#ylim spin
hlay = QtGui.QHBoxLayout()
self.ylimSpin = QtGui.QSpinBox()
self.ylimSpin.setFont(QtGui.QFont('',8))
self.ylimSpin.setValue(50)
hlay.addWidget(QtGui.QLabel('PSTH Ylim'))
hlay.addWidget(self.ylimSpin)
vlay.addLayout(hlay)
# Plot Btn
self.PlotRasterBtn = QtGui.QPushButton('Plot Raster')
self.PlotRasterBtn.setFont(QtGui.QFont('', 8, weight=0))
self.PlotRasterBtn.clicked.connect(self.PlotRaster_proc)
vlay.addWidget(self.PlotRasterBtn)
# units table widget
self.UnitsTable = QtGui.QTableWidget(0,2, self)
vlay.addWidget(self.UnitsTable)
for k in range(self.UnitsTable.columnCount()):
self.UnitsTable.setColumnWidth(k, 60)
self.UnitsTable.setHorizontalHeaderLabels(['Unit','Plot?'])
# select all select none buttons
hlay = QtGui.QHBoxLayout()
self.SelectAllBtn = QtGui.QPushButton('Select All')
self.SelectAllBtn.setFont(QtGui.QFont('',8))
self.SelectAllBtn.setMaximumHeight(20)
self.SelectAllBtn.clicked.connect(self.SelectAll_proc)
self.SelectNoneBtn = QtGui.QPushButton('Select None')
self.SelectNoneBtn.setFont(QtGui.QFont('',8))
self.SelectNoneBtn.setMaximumHeight(20)
self.SelectNoneBtn.clicked.connect(self.SelectNone_proc)
hlay.addWidget(self.SelectAllBtn)
hlay.addWidget(self.SelectNoneBtn)
vlay.addLayout(hlay)
# create en event selecting combobox
hlay = QtGui.QHBoxLayout()
self.EventSelectCombo = QtGui.QComboBox()
self.EventSelectCombo.setFont(QtGui.QFont('',8))
self.EventSelectCombo.setMaximumHeight(20)
hlay.addWidget(QtGui.QLabel('Event'))
hlay.addWidget(self.EventSelectCombo)
vlay.addLayout(hlay)
# add the toolbox widget to the docking area
dock1.setWidget(w)
############ add a dockable unit centered toolbox widget
dock2 = QtGui.QDockWidget('Unit Centered Analisys', self)
dock2.setAllowedAreas(QtCore.Qt.LeftDockWidgetArea | QtCore.Qt.RightDockWidgetArea)
showDock2Action.triggered.connect(dock2.show)
w = QtGui.QWidget(dock2)
vlay = QtGui.QVBoxLayout(w)
vlay.setMargin(2)
vlay.setSpacing(2)
# add a unit selector combo box
hlay = QtGui.QHBoxLayout()
self.ChannelSelectCombo = QtGui.QComboBox(w)
self.ChannelSelectCombo.setFont(QtGui.QFont('',8))
self.ChannelSelectCombo.currentIndexChanged.connect(self.UpdateUnitSelectCombo_proc)
self.UnitSelectCombo = QtGui.QComboBox(w)
self.UnitSelectCombo.setFont(QtGui.QFont('',8))
hlay.addWidget(self.ChannelSelectCombo)
hlay.addWidget(self.UnitSelectCombo)
vlay.addLayout(hlay)
# add a spin box to select the number of columns
hlay = QtGui.QHBoxLayout()
self.nColumnsUnitAnalisys = QtGui.QSpinBox()
self.nColumnsUnitAnalisys.setRange(0,10)
self.nColumnsUnitAnalisys.setValue(3)
self.nColumnsUnitAnalisys.setFont(QtGui.QFont('',8))
lbl = QtGui.QLabel('Number of Columns')
lbl.setFont(QtGui.QFont('',8))
hlay.addWidget(lbl)
hlay.addWidget(self.nColumnsUnitAnalisys)
vlay.addLayout(hlay)
# add an analisys table
self.AnalisysTable = QtGui.QTableWidget(0,5,w)
for k in range(self.AnalisysTable.columnCount()):
self.AnalisysTable.setColumnWidth(k,80)
self.AnalisysTable.setColumnWidth(2,50)
self.AnalisysTable.setColumnWidth(3,50)
self.AnalisysTable.verticalHeader().setVisible(False)
self.AnalisysTable.setHorizontalHeaderLabels(['Analisys',
'Event',
'TWin1',
'TWin2',
'Unit 2'])
self.AnalisysTable.horizontalHeader().setFont(QtGui.QFont('',8))
vlay.addWidget(self.AnalisysTable)
dock2.setWidget(w)
### each created analisys creates an axes
hlay = QtGui.QHBoxLayout()
# add analisys btn
self.AddAnalisysBtn = QtGui.QPushButton('Add Analisys', w)
self.AddAnalisysBtn.setFont(QtGui.QFont('',8))
self.AddAnalisysBtn.setMaximumHeight(20)
self.AddAnalisysBtn.clicked.connect(self.AddAnalisys_proc)
hlay.addWidget(self.AddAnalisysBtn)
#remove analisys btn
self.RemoveAnalisysBtn = QtGui.QPushButton('Remove Analisys', w)
self.RemoveAnalisysBtn.setFont(QtGui.QFont('',8))
self.RemoveAnalisysBtn.setMaximumHeight(20)
self.RemoveAnalisysBtn.clicked.connect(self.RemoveAnalisys_proc)
hlay.addWidget(self.RemoveAnalisysBtn)
vlay.addLayout(hlay)
# Plot Btn
self.PlotAnalisysBtn = QtGui.QPushButton('Plot Analisys')
self.PlotAnalisysBtn.setFont(QtGui.QFont('', 8, weight=0))
self.PlotAnalisysBtn.clicked.connect(self.PlotAnalisys_proc)
vlay.addWidget(self.PlotAnalisysBtn)
############# add a figure tab widget
self.MainFigTabWidget = QtGui.QTabWidget()
self.MainFigTabWidget.setTabsClosable(True)
self.MainFigTabWidget.setMovable(True)
self.MainFigTabWidget.tabCloseRequested.connect(self.closeTab_proc)
widget = QtGui.QWidget()
vlay = QtGui.QVBoxLayout(widget)
self.Figures = []
self.Figures.append(MplWidget(widget))
ntb = NavToolbar(self.Figures[-1], parent = widget)
ntb.setIconSize(QtCore.QSize(15,15))
vlay.setSpacing(0)
vlay.setMargin(0)
vlay.addWidget(self.Figures[-1])
vlay.addWidget(ntb)
widget.setLayout(vlay)
self.MainFigTabWidget.addTab(widget, 'Figure 1')
widget.setObjectName(str(self.MainFigTabWidget.count()))
self.Figures[-1].setObjectName(str(self.MainFigTabWidget.count()))
#self.MainLayout.addWidget(self.MainFigTabWidget)
# add the dock to the left docking area
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, dock0)
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, dock1)
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, dock2)
# set central widget
self.setCentralWidget(self.MainFigTabWidget)
# if running in linux set a certain style for the buttons and widgets
if sys.platform == 'linux2':
QtGui.QApplication.setStyle(QtGui.QStyleFactory.create('Plastique'))
class SimulationGui(QMainWindow):
def __init__(self, net=None, parent=None, fname=None):
QMainWindow.__init__(self)
self.ui = Ui_SimulationWindow()
self.ui.setupUi(self)
if fname:
self.set_title(fname)
# context menu
self.ui.nodeInspector.addAction(self.ui.actionCopyInspectorData)
self.ui.nodeInspector.addAction(self.ui.actionShowLocalizedSubclusters)
# callbacks
self.ui.actionCopyInspectorData.activated\
.connect(self.on_actionCopyInspectorData_triggered)
self.ui.actionShowLocalizedSubclusters.activated\
.connect(self.on_actionShowLocalizedSubclusters_triggered)
self.dpi = 72
# take size of networDisplayWidget
self.fig = Figure((700 / self.dpi, 731 / self.dpi), self.dpi,
facecolor='0.9')
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self.ui.networkDisplayWidget)
self.nav = NavigationToolbar(self.canvas, self.ui.networkDisplayWidget,
coordinates=True)
self.nav.setGeometry(QRect(0, 0, 651, 36))
self.nav.setIconSize(QSize(24, 24))
self.axes = self.fig.add_subplot(111)
# matplotlib.org/api/figure_api.html#matplotlib.figure.SubplotParams
self.fig.subplots_adjust(left=0.03, right=0.99, top=0.92)
if net:
self.init_sim(net)
self.connect(self.ui.showNodes, SIGNAL('stateChanged(int)'),
self.refresh_visibility)
self.connect(self.ui.showEdges, SIGNAL('stateChanged(int)'),
self.refresh_visibility)
self.connect(self.ui.showMessages, SIGNAL('stateChanged(int)'),
self.refresh_visibility)
self.connect(self.ui.showLabels, SIGNAL('stateChanged(int)'),
self.refresh_visibility)
self.connect(self.ui.redrawNetworkButton, SIGNAL('clicked(bool)'),
self.redraw)
self.connect(self.ui.treeGroupBox, SIGNAL('toggled(bool)'),
self.refresh_visibility)
self.connect(self.ui.treeKey, SIGNAL('textEdited(QString)'),
self.redraw)
self.connect(self.ui.propagationError, SIGNAL('toggled(bool)'),
self.refresh_visibility)
self.connect(self.ui.locKey, SIGNAL('textEdited(QString)'),
self.redraw)
# callbacks
self.ui.actionOpenNetwork.activated\
.connect(self.on_actionOpenNetwork_triggered)
self.ui.actionSaveNetwork.activated\
.connect(self.on_actionSaveNetwork_triggered)
self.ui.actionRun.activated.connect(self.on_actionRun_triggered)
self.ui.actionStep.activated.connect(self.on_actionStep_triggered)
self.ui.actionReset.activated.connect(self.on_actionReset_triggered)
self.canvas.mpl_connect('pick_event', self.on_pick)
def handleInspectorMenu(self, pos):
menu = QMenu()
menu.addAction('Add')
menu.addAction('Delete')
menu.exec_(QCursor.pos())
def init_sim(self, net):
self.net = net
self.sim = Simulation(net)
self.connect(self.sim, SIGNAL("redraw()"), self.redraw)
self.connect(self.sim, SIGNAL("updateLog(QString)"), self.update_log)
self.redraw()
def update_log(self, text):
""" Add item to list widget """
print "Add: " + text
self.ui.logListWidget.insertItem(0, text)
# self.ui.logListWidget.sortItems()
def redraw(self):
self.refresh_network_inspector()
self.draw_network()
self.reset_zoom()
self.refresh_visibility()
def draw_network(self, net=None, clear=True, subclusters=None,
drawMessages=True):
if not net:
net = self.net
currentAlgorithm = self.net.get_current_algorithm()
if clear:
self.axes.clear()
self.axes.imshow(net.environment.im, vmin=0, cmap='binary_r',
origin='lower')
self.draw_tree(str(self.ui.treeKey.text()), net)
self.draw_edges(net)
self.draw_propagation_errors(str(self.ui.locKey.text()), net)
if subclusters:
node_colors = self.get_node_colors(net, subclusters=subclusters)
else:
node_colors = self.get_node_colors(net, algorithm=currentAlgorithm)
self.node_collection = self.draw_nodes(net, node_colors)
if drawMessages:
self.draw_messages(net)
self.draw_labels(net)
self.drawnNet = net
step_text = ' (step %d)' % self.net.algorithmState['step'] \
if isinstance(currentAlgorithm, NodeAlgorithm) else ''
self.axes.set_title((currentAlgorithm.name
if currentAlgorithm else '') + step_text)
self.refresh_visibility()
# To save multiple figs of the simulation uncomment next two lines:
#self.fig.savefig('network-alg-%d-step-%d.png' %
# (self.net.algorithmState['index'], self.net.algorithmState['step']))
def draw_nodes(self, net=None, node_colors={}, node_radius={}):
if not net:
net = self.net
if type(node_colors) == str:
node_colors = {node: node_colors for node in net.nodes()}
nodeCircles = []
for n in net.nodes():
c = NodeCircle(tuple(net.pos[n]), node_radius.get(n, 8.0),
color=node_colors.get(n, 'r'),
ec='k', lw=1.0, ls='solid', picker=3)
nodeCircles.append(c)
node_collection = PatchCollection(nodeCircles, match_original=True)
node_collection.set_picker(3)
self.axes.add_collection(node_collection)
return node_collection
def get_node_colors(self, net, algorithm=None, subclusters=None,
drawLegend=True):
COLORS = 'rgbcmyw' * 100
node_colors = {}
if algorithm:
color_map = {}
if isinstance(algorithm, NodeAlgorithm):
for ind, status in enumerate(algorithm.STATUS.keys()):
if status == 'IDLE':
color_map.update({status: 'k'})
else:
color_map.update({status: COLORS[ind]})
if drawLegend:
proxy = []
labels = []
for status, color in color_map.items():
proxy.append(Circle((0, 0), radius=8.0,
color=color, ec='k',
lw=1.0, ls='solid'))
labels.append(status)
self.fig.legends = []
self.fig.legend(proxy, labels, loc=8,
prop={'size': '10.0'}, ncol=len(proxy),
title='Statuses for %s:'
% algorithm.name)
for n in net.nodes():
if n.status == '' or not n.status in color_map.keys():
node_colors[n] = 'r'
else:
node_colors[n] = color_map[n.status]
elif subclusters:
for i, sc in enumerate(subclusters):
for n in sc:
if n in node_colors:
node_colors[n] = 'k'
else:
node_colors[n] = COLORS[i]
return node_colors
def draw_edges(self, net=None):
if not net:
net = self.net
self.edge_collection = nx.draw_networkx_edges(net, net.pos, alpha=0.6,
edgelist=None,
ax=self.axes)
def draw_messages(self, net=None):
if not net:
net = self.net
self.messages = []
msgCircles = []
for node in net.nodes():
for msg in node.outbox:
# broadcast
if msg.destination is None:
for neighbor in net.adj[node].keys():
nbr_msg = msg.copy()
nbr_msg.destination = neighbor
c = MessageCircle(nbr_msg, net, 'out', 3.0, lw=0,
picker=3, zorder=3, color='b')
self.messages.append(nbr_msg)
msgCircles.append(c)
else:
c = MessageCircle(msg, net, 'out', 3.0, lw=0, picker=3,
zorder=3, color='b')
self.messages.append(msg)
msgCircles.append(c)
for msg in node.inbox:
c = MessageCircle(msg, net, 'in', 3.0, lw=0, picker=3,
zorder=3, color='g')
self.messages.append(msg)
msgCircles.append(c)
if self.messages:
self.message_collection = PatchCollection(msgCircles,
match_original=True)
self.message_collection.set_picker(3)
self.axes.add_collection(self.message_collection)
def draw_labels(self, net=None):
if not net:
net = self.net
label_pos = {}
for n in net.nodes():
label_pos[n] = net.pos[n].copy() + 10
self.label_collection = nx.draw_networkx_labels(net, label_pos,
labels=net.labels,
ax=self.axes)
def refresh_visibility(self):
try:
self.node_collection.set_visible(self.ui.showNodes.isChecked())
self.edge_collection.set_visible(self.ui.showEdges.isChecked())
for label in self.label_collection.values():
label.set_visible(self.ui.showLabels.isChecked())
self.tree_collection.set_visible(self.ui.treeGroupBox.isChecked())
self.ini_error_collection.set_visible(self.ui.propagationError\
.isChecked())
self.propagation_error_collection.set_visible(self.ui\
.propagationError\
.isChecked())
# sould be last, sometimes there are no messages
self.message_collection.set_visible(self.ui.showMessages\
.isChecked())
except AttributeError:
print 'Refresh visibility warning'
self.canvas.draw()
def draw_tree(self, treeKey, net=None):
"""
Show tree representation of network.
Attributes:
treeKey (str):
key in nodes memory (dictionary) where tree data is stored
storage format can be a list off tree neighbors or a dict:
{'parent': parent_node,
'children': [child_node1, child_node2 ...]}
"""
if not net:
net = self.net
treeNet = net.get_tree_net(treeKey)
if treeNet:
self.tree_collection = draw_networkx_edges(treeNet, treeNet.pos,
treeNet.edges(),
width=1.8, alpha=0.6,
ax=self.axes)
def draw_propagation_errors(self, locKey, net):
SCALE_FACTOR = 0.6
if not net:
net = self.net
if any([not locKey in node.memory for node in net.nodes()]):
self.propagation_error_collection = []
self.ini_error_collection = []
return
rms = {'iniRms': {}, 'stitchRms': {}}
for node in net.nodes():
rms['iniRms'][node] = get_rms(self.net.pos,
(node.memory['iniLocs']), True) * \
SCALE_FACTOR
rms['stitchRms'][node] = get_rms(self.net.pos, node.memory[locKey],
True) * SCALE_FACTOR
self.propagation_error_collection = \
self.draw_nodes(net=net, node_colors='g',
node_radius=rms['stitchRms'])
self.ini_error_collection = self.draw_nodes(net=net, node_colors='b',
node_radius=rms['iniRms'])
def reset_zoom(self):
self.axes.set_xlim((0, self.net.environment.im.shape[1]))
self.axes.set_ylim((0, self.net.environment.im.shape[0]))
def set_title(self, fname):
new = ' - '.join([str(self.windowTitle()).split(' - ')[0], str(fname)])
self.setWindowTitle(new)
def refresh_network_inspector(self):
niModel = DictionaryTreeModel(dic=self.net.get_dic())
self.ui.networkInspector.setModel(niModel)
self.ui.networkInspector.expandToDepth(0)
"""
Callbacks
"""
def on_actionRun_triggered(self):
self.ui.logListWidget.clear()
print 'running ...',
self.sim.stepping = True
self.sim.run_all()
def on_actionStep_triggered(self):
print 'next step ...',
self.sim.run(self.ui.stepSize.value())
def on_actionReset_triggered(self):
print 'reset ...',
self.sim.reset()
self.redraw()
def on_actionCopyInspectorData_triggered(self):
string = 'Node inspector data\n-------------------'
# raise()
for qModelIndex in self.ui.nodeInspector.selectedIndexes():
string += '\n' + qModelIndex.internalPointer().toString(' ')
clipboard = app.clipboard()
clipboard.setText(string)
event = QEvent(QEvent.Clipboard)
app.sendEvent(clipboard, event)
def on_actionShowLocalizedSubclusters_triggered(self):
if len(self.ui.nodeInspector.selectedIndexes()) == 1:
qModelIndex = self.ui.nodeInspector.selectedIndexes()[0]
treeItem = qModelIndex.internalPointer()
assert(isinstance(treeItem.itemDataValue, Positions))
estimated = deepcopy(treeItem.itemDataValue)
estimatedsub = estimated.subclusters[0]
# rotate, translate and optionally scale
# w.r.t. original positions (pos)
align_clusters(Positions.create(self.net.pos), estimated, True)
net = self.net.subnetwork(estimatedsub.keys(), pos=estimatedsub)
self.draw_network(net=net, drawMessages=False)
edge_pos = numpy.asarray([(self.net.pos[node], estimatedsub[node][:2])
for node in net])
error_collection = LineCollection(edge_pos, colors='r')
self.axes.add_collection(error_collection)
rms = get_rms(self.net.pos, estimated, scale=False)
self.update_log('rms = %.3f' % rms)
self.update_log('localized = %.2f%% (%d/%d)' %
(len(estimatedsub) * 1. / len(self.net.pos) * 100,
len(estimatedsub), len(self.net.pos)))
def on_actionSaveNetwork_triggered(self, *args):
default_filetype = 'gz'
start = datetime.now().strftime('%Y%m%d') + default_filetype
filters = ['Network pickle (*.gz)', 'All files (*)']
selectedFilter = 'Network pickle (gz)'
filters = ';;'.join(filters)
fname = QFileDialog.getSaveFileName(self, "Choose a filename",
start, filters, selectedFilter)[0]
if fname:
try:
write_pickle(self.net, fname)
except Exception, e:
QMessageBox.critical(
self, "Error saving file", str(e),
QMessageBox.Ok, QMessageBox.NoButton)
else:
self.set_title(fname)
class SimulationGui(QMainWindow):
def __init__(self, net=None, parent=None, fname=None):
QMainWindow.__init__(self)
self.ui = Ui_SimulationWindow()
self.ui.setupUi(self)
if fname:
self.set_title(fname)
# context menu
self.ui.nodeInspector.addAction(self.ui.actionCopyInspectorData)
self.ui.nodeInspector.addAction(self.ui.actionShowLocalizedSubclusters)
# callbacks
self.ui.actionCopyInspectorData.activated\
.connect(self.on_actionCopyInspectorData_triggered)
self.ui.actionShowLocalizedSubclusters.activated\
.connect(self.on_actionShowLocalizedSubclusters_triggered)
self.dpi = 72
# take size of networDisplayWidget
self.fig = Figure((700 / self.dpi, 731 / self.dpi),
self.dpi,
facecolor='0.9')
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self.ui.networkDisplayWidget)
self.nav = NavigationToolbar(self.canvas,
self.ui.networkDisplayWidget,
coordinates=True)
self.nav.setGeometry(QRect(0, 0, 651, 36))
self.nav.setIconSize(QSize(24, 24))
self.axes = self.fig.add_subplot(111)
# matplotlib.org/api/figure_api.html#matplotlib.figure.SubplotParams
self.fig.subplots_adjust(left=0.03, right=0.99, top=0.92)
if net:
self.init_sim(net)
self.connect(self.ui.showNodes, SIGNAL('stateChanged(int)'),
self.refresh_visibility)
self.connect(self.ui.showEdges, SIGNAL('stateChanged(int)'),
self.refresh_visibility)
self.connect(self.ui.showMessages, SIGNAL('stateChanged(int)'),
self.refresh_visibility)
self.connect(self.ui.showLabels, SIGNAL('stateChanged(int)'),
self.refresh_visibility)
self.connect(self.ui.redrawNetworkButton, SIGNAL('clicked(bool)'),
self.redraw)
self.connect(self.ui.treeGroupBox, SIGNAL('toggled(bool)'),
self.refresh_visibility)
self.connect(self.ui.treeKey, SIGNAL('textEdited(QString)'),
self.redraw)
self.connect(self.ui.propagationError, SIGNAL('toggled(bool)'),
self.refresh_visibility)
self.connect(self.ui.locKey, SIGNAL('textEdited(QString)'),
self.redraw)
# callbacks
self.ui.actionOpenNetwork.activated\
.connect(self.on_actionOpenNetwork_triggered)
self.ui.actionSaveNetwork.activated\
.connect(self.on_actionSaveNetwork_triggered)
self.ui.actionRun.activated.connect(self.on_actionRun_triggered)
self.ui.actionStep.activated.connect(self.on_actionStep_triggered)
self.ui.actionReset.activated.connect(self.on_actionReset_triggered)
self.canvas.mpl_connect('pick_event', self.on_pick)
def handleInspectorMenu(self, pos):
menu = QMenu()
menu.addAction('Add')
menu.addAction('Delete')
menu.exec_(QCursor.pos())
def init_sim(self, net):
self.net = net
self.sim = Simulation(net)
self.connect(self.sim, SIGNAL("redraw()"), self.redraw)
self.connect(self.sim, SIGNAL("updateLog(QString)"), self.update_log)
self.redraw()
def update_log(self, text):
""" Add item to list widget """
print "Add: " + text
self.ui.logListWidget.insertItem(0, text)
# self.ui.logListWidget.sortItems()
def redraw(self):
self.refresh_network_inspector()
self.draw_network()
self.reset_zoom()
self.refresh_visibility()
def draw_network(self,
net=None,
clear=True,
subclusters=None,
drawMessages=True):
if not net:
net = self.net
currentAlgorithm = self.net.get_current_algorithm()
if clear:
self.axes.clear()
self.axes.imshow(net.environment.im,
vmin=0,
cmap='binary_r',
origin='lower')
self.draw_tree(str(self.ui.treeKey.text()), net)
self.draw_edges(net)
self.draw_propagation_errors(str(self.ui.locKey.text()), net)
if subclusters:
node_colors = self.get_node_colors(net, subclusters=subclusters)
else:
node_colors = self.get_node_colors(net, algorithm=currentAlgorithm)
self.node_collection = self.draw_nodes(net, node_colors)
if drawMessages:
self.draw_messages(net)
self.draw_labels(net)
self.drawnNet = net
step_text = ' (step %d)' % self.net.algorithmState['step'] \
if isinstance(currentAlgorithm, NodeAlgorithm) else ''
self.axes.set_title(
(currentAlgorithm.name if currentAlgorithm else '') + step_text)
self.refresh_visibility()
# To save multiple figs of the simulation uncomment next two lines:
#self.fig.savefig('network-alg-%d-step-%d.png' %
# (self.net.algorithmState['index'], self.net.algorithmState['step']))
def draw_nodes(self, net=None, node_colors={}, node_radius={}):
if not net:
net = self.net
if type(node_colors) == str:
node_colors = {node: node_colors for node in net.nodes()}
nodeCircles = []
for n in net.nodes():
c = NodeCircle(tuple(net.pos[n]),
node_radius.get(n, 8.0),
color=node_colors.get(n, 'r'),
ec='k',
lw=1.0,
ls='solid',
picker=3)
nodeCircles.append(c)
node_collection = PatchCollection(nodeCircles, match_original=True)
node_collection.set_picker(3)
self.axes.add_collection(node_collection)
return node_collection
def get_node_colors(self,
net,
algorithm=None,
subclusters=None,
drawLegend=True):
COLORS = 'rgbcmyw' * 100
node_colors = {}
if algorithm:
color_map = {}
if isinstance(algorithm, NodeAlgorithm):
for ind, status in enumerate(algorithm.STATUS.keys()):
if status == 'IDLE':
color_map.update({status: 'k'})
else:
color_map.update({status: COLORS[ind]})
if drawLegend:
proxy = []
labels = []
for status, color in color_map.items():
proxy.append(
Circle((0, 0),
radius=8.0,
color=color,
ec='k',
lw=1.0,
ls='solid'))
labels.append(status)
self.fig.legends = []
self.fig.legend(proxy,
labels,
loc=8,
prop={'size': '10.0'},
ncol=len(proxy),
title='Statuses for %s:' % algorithm.name)
for n in net.nodes():
if n.status == '' or not n.status in color_map.keys():
node_colors[n] = 'r'
else:
node_colors[n] = color_map[n.status]
elif subclusters:
for i, sc in enumerate(subclusters):
for n in sc:
if n in node_colors:
node_colors[n] = 'k'
else:
node_colors[n] = COLORS[i]
return node_colors
def draw_edges(self, net=None):
if not net:
net = self.net
self.edge_collection = nx.draw_networkx_edges(net,
net.pos,
alpha=0.6,
edgelist=None,
ax=self.axes)
def draw_messages(self, net=None):
if not net:
net = self.net
self.messages = []
msgCircles = []
for node in net.nodes():
for msg in node.outbox:
# broadcast
if msg.destination is None:
for neighbor in net.adj[node].keys():
nbr_msg = msg.copy()
nbr_msg.destination = neighbor
c = MessageCircle(nbr_msg,
net,
'out',
3.0,
lw=0,
picker=3,
zorder=3,
color='b')
self.messages.append(nbr_msg)
msgCircles.append(c)
else:
c = MessageCircle(msg,
net,
'out',
3.0,
lw=0,
picker=3,
zorder=3,
color='b')
self.messages.append(msg)
msgCircles.append(c)
for msg in node.inbox:
c = MessageCircle(msg,
net,
'in',
3.0,
lw=0,
picker=3,
zorder=3,
color='g')
self.messages.append(msg)
msgCircles.append(c)
if self.messages:
self.message_collection = PatchCollection(msgCircles,
match_original=True)
self.message_collection.set_picker(3)
self.axes.add_collection(self.message_collection)
def draw_labels(self, net=None):
if not net:
net = self.net
label_pos = {}
for n in net.nodes():
label_pos[n] = net.pos[n].copy() + 10
self.label_collection = nx.draw_networkx_labels(net,
label_pos,
labels=net.labels,
ax=self.axes)
def refresh_visibility(self):
try:
self.node_collection.set_visible(self.ui.showNodes.isChecked())
self.edge_collection.set_visible(self.ui.showEdges.isChecked())
for label in self.label_collection.values():
label.set_visible(self.ui.showLabels.isChecked())
self.tree_collection.set_visible(self.ui.treeGroupBox.isChecked())
self.ini_error_collection.set_visible(self.ui.propagationError\
.isChecked())
self.propagation_error_collection.set_visible(self.ui\
.propagationError\
.isChecked())
# sould be last, sometimes there are no messages
self.message_collection.set_visible(self.ui.showMessages\
.isChecked())
except AttributeError:
print 'Refresh visibility warning'
self.canvas.draw()
def draw_tree(self, treeKey, net=None):
"""
Show tree representation of network.
Attributes:
treeKey (str):
key in nodes memory (dictionary) where tree data is stored
storage format can be a list off tree neighbors or a dict:
{'parent': parent_node,
'children': [child_node1, child_node2 ...]}
"""
if not net:
net = self.net
treeNet = net.get_tree_net(treeKey)
if treeNet:
self.tree_collection = draw_networkx_edges(treeNet,
treeNet.pos,
treeNet.edges(),
width=1.8,
alpha=0.6,
ax=self.axes)
def draw_propagation_errors(self, locKey, net):
SCALE_FACTOR = 0.6
if not net:
net = self.net
if any([not locKey in node.memory for node in net.nodes()]):
self.propagation_error_collection = []
self.ini_error_collection = []
return
rms = {'iniRms': {}, 'stitchRms': {}}
for node in net.nodes():
rms['iniRms'][node] = get_rms(self.net.pos,
(node.memory['iniLocs']), True) * \
SCALE_FACTOR
rms['stitchRms'][node] = get_rms(self.net.pos, node.memory[locKey],
True) * SCALE_FACTOR
self.propagation_error_collection = \
self.draw_nodes(net=net, node_colors='g',
node_radius=rms['stitchRms'])
self.ini_error_collection = self.draw_nodes(net=net,
node_colors='b',
node_radius=rms['iniRms'])
def reset_zoom(self):
self.axes.set_xlim((0, self.net.environment.im.shape[1]))
self.axes.set_ylim((0, self.net.environment.im.shape[0]))
def set_title(self, fname):
new = ' - '.join([str(self.windowTitle()).split(' - ')[0], str(fname)])
self.setWindowTitle(new)
def refresh_network_inspector(self):
niModel = DictionaryTreeModel(dic=self.net.get_dic())
self.ui.networkInspector.setModel(niModel)
self.ui.networkInspector.expandToDepth(0)
"""
Callbacks
"""
def on_actionRun_triggered(self):
self.ui.logListWidget.clear()
print 'running ...',
self.sim.stepping = True
self.sim.run_all()
def on_actionStep_triggered(self):
print 'next step ...',
self.sim.run(self.ui.stepSize.value())
def on_actionReset_triggered(self):
print 'reset ...',
self.sim.reset()
self.redraw()
def on_actionCopyInspectorData_triggered(self):
string = 'Node inspector data\n-------------------'
# raise()
for qModelIndex in self.ui.nodeInspector.selectedIndexes():
string += '\n' + qModelIndex.internalPointer().toString(' ')
clipboard = app.clipboard()
clipboard.setText(string)
event = QEvent(QEvent.Clipboard)
app.sendEvent(clipboard, event)
def on_actionShowLocalizedSubclusters_triggered(self):
if len(self.ui.nodeInspector.selectedIndexes()) == 1:
qModelIndex = self.ui.nodeInspector.selectedIndexes()[0]
treeItem = qModelIndex.internalPointer()
assert (isinstance(treeItem.itemDataValue, Positions))
estimated = deepcopy(treeItem.itemDataValue)
estimatedsub = estimated.subclusters[0]
# rotate, translate and optionally scale
# w.r.t. original positions (pos)
align_clusters(Positions.create(self.net.pos), estimated, True)
net = self.net.subnetwork(estimatedsub.keys(), pos=estimatedsub)
self.draw_network(net=net, drawMessages=False)
edge_pos = numpy.asarray([
(self.net.pos[node], estimatedsub[node][:2]) for node in net
])
error_collection = LineCollection(edge_pos, colors='r')
self.axes.add_collection(error_collection)
rms = get_rms(self.net.pos, estimated, scale=False)
self.update_log('rms = %.3f' % rms)
self.update_log('localized = %.2f%% (%d/%d)' %
(len(estimatedsub) * 1. / len(self.net.pos) * 100,
len(estimatedsub), len(self.net.pos)))
def on_actionSaveNetwork_triggered(self, *args):
default_filetype = 'gz'
start = datetime.now().strftime('%Y%m%d') + default_filetype
filters = ['Network pickle (*.gz)', 'All files (*)']
selectedFilter = 'Network pickle (gz)'
filters = ';;'.join(filters)
fname = QFileDialog.getSaveFileName(self, "Choose a filename", start,
filters, selectedFilter)[0]
if fname:
try:
write_pickle(self.net, fname)
except Exception, e:
QMessageBox.critical(self, "Error saving file", str(e),
QMessageBox.Ok, QMessageBox.NoButton)
else:
self.set_title(fname)
class MplWidget(QtGui.QWidget):
"""Widget defined in Qt Designer"""
def __init__(self, tools, toolbar=True, menu=True, parent=None):
# initialization of Qt MainWindow widget
QtGui.QWidget.__init__(self, parent)
# set the canvas to the Matplotlib widget
self.canvas = MplCanvas()
# create a vertical box layout
self.layout = QtGui.QVBoxLayout()
# add mpl widget to layout
self.layout.addWidget(self.canvas)
# reference to toolsFrame
self.tool = tools
if toolbar:
# add navigation toolbar to layout
self.toolbar = NavigationToolbar(self.canvas, self)
self.layout.addWidget(self.toolbar)
# enable hover event handling
self.setAttribute(Qt.WA_Hover)
# create and install event filter
self.filter = Filter(self)
self.installEventFilter(self.filter)
# hide toolbar
self.initComponents()
else:
self.toolbar = None
# set the layout to th vertical box
self.setLayout(self.layout)
# active lines list
self.lines = []
# legend
self.legend = None
# autoscale
self.canvas.ax.autoscale_view(True, True, True)
if menu:
# setup context menu
self.setContextMenuPolicy(Qt.ActionsContextMenu)
self.initActions()
self.alwaysAutoScale.setChecked(True)
#-------------- initialization ---------------#
def initComponents(self):
if self.toolbar is not None:
self.toolbar.hide()
self.newIcons()
def initActions(self):
# toolbar
self.toggleLegendAction = QtGui.QAction(QtGui.QIcon(RES + ICONS + LEGEND), 'Toggle legend',
self, triggered=self.toggleLegend)
self.toggleLegendAction.setCheckable(True)
if self.toolbar is not None:
self.toolbar.addAction(self.toggleLegendAction)
# context menu
self.addAction(self.toggleLegendAction)
self.addAction(QtGui.QAction(QtGui.QIcon(RES + ICONS + COPY),'Copy data to table',
self, triggered=self.toTable))
self.addAction(QtGui.QAction(QtGui.QIcon(RES + ICONS + GRAPH),'Plot data in tools',
self, triggered=self.toGraphTool))
self.addAction(QtGui.QAction(QtGui.QIcon(RES + ICONS + SCALE), 'Autoscale',
self, triggered=self.updateScale))
self.alwaysAutoScale = QtGui.QAction('Scale on update', self)
self.alwaysAutoScale.setCheckable(True)
self.selectLinesMenu = QtGui.QMenu()
self.selectLines = (QtGui.QAction('Plots', self))
self.selectLines.setMenu(self.selectLinesMenu)
aSep = QtGui.QAction('', self)
aSep.setSeparator(True)
self.addAction(aSep)
self.addAction(self.selectLines)
self.addAction(self.alwaysAutoScale)
def newIcons(self):
for position in range(0, self.toolbar.layout().count()):
widget = self.toolbar.layout().itemAt(position).widget()
if isinstance(widget, QtGui.QToolButton):
icon = QtGui.QIcon(RES + ICONS + TOOLBAR_ICONS[position])
self.toolbar.layout().itemAt(position).widget().setIcon(icon)
self.toolbar.setIconSize(QSize(ICO_GRAPH, ICO_GRAPH))
def resetGraphicEffect(self):
if self.graphicsEffect() is not None:
self.graphicsEffect().setEnabled(False)
#------------- plotting methods ---------------#
## Hides axes in widget.
# @param axes Widget axes form canvas.
@staticmethod
def hideAxes(axes):
axes.get_xaxis().set_visible(False)
axes.get_yaxis().set_visible(False)
## Clears widget canvas, removing all data and clearing figure.
# @param repaint_axes Add standard plot after clearing figure.
def clearCanvas(self, repaint_axes=True):
self.canvas.ax.clear()
self.canvas.fig.clear()
if repaint_axes:
self.canvas.ax = self.canvas.fig.add_subplot(111)
## Update existing data or plot anew.
# @param data List or array to plot/update.
# @param line Which line (by index) to update (if any).
# @param label Data label (new or existing).
# @param style Line style (solid, dashed, dotted).
# @param color Line color.
def updatePlot(self, data, line=0, label=None, style='solid', color=None):
if not self.canvas.ax.has_data():
if label is not None:
if color is not None:
self.lines = self.canvas.ax.plot(data, label=label, linestyle=style, color=color)
else:
self.lines = self.canvas.ax.plot(data, label=label, linestyle=style)
else:
if color is not None:
self.lines = self.canvas.ax.plot(data, linestyle=style, color=color)
else:
self.lines = self.canvas.ax.plot(data, linestyle=style)
else:
if not self.lines:
self.lines = self.canvas.ax.get_lines()
if label is not None:
if label not in [l._label for l in self.lines]:
if color is not None:
self.lines.extend(self.canvas.ax.plot(data, label=label, linestyle=style, color=color))
else:
self.lines.extend(self.canvas.ax.plot(data, label=label, linestyle=style))
line = len(self.lines) - 1
else:
line = [l._label for l in self.lines].index(label)
line_to_update = self.lines[line]
if len(data) != len(line_to_update._x):
# x, y ~ data in y
line_to_update.set_data(np.arange(len(data)), data)
else:
# in case data length stays the same
line_to_update.set_data(line_to_update._x, data)
self.canvas.draw()
self.updateLegend()
self.updateLinesSubmenu()
if self.alwaysAutoScale.isChecked():
self.updateScale()
## Plots scalogram for wavelet decomposition.
# @param data Wavelet coefficients in matrix.
# @param top Axis position.
# @param colorbar Shows colorbar for data levels.
# @param power Scales resulting graph by power of 2.
def scalogram(self, data, top=True, colorbar=True, power=False):
# self.resetGraphicEffect()
self.clearCanvas()
x = np.arange(len(data[0]))
y = np.arange(len(data))
if power:
contour = self.canvas.ax.contourf(x, y, np.abs(data) ** 2)
else:
contour = self.canvas.ax.contourf(x, y, np.abs(data))
if colorbar:
self.canvas.fig.colorbar(contour, ax=self.canvas.ax, orientation='vertical', format='%2.1f')
if top:
self.canvas.ax.set_ylim((y[-1], y[0]))
else:
self.canvas.ax.set_ylim((y[0], y[-1]))
self.canvas.ax.set_xlim((x[0], x[-1]))
# self.canvas.ax.set_ylabel('scales')
self.canvas.draw()
## Plots list of arrays with shared x/y axes.
# @param data Arrays to plot (list or matrix).
def multiline(self, data):
# self.resetGraphicEffect()
# abscissa
axprops = dict(yticks=[])
# ordinate
yprops = dict(rotation=0,
horizontalalignment='right',
verticalalignment='center',
x=-0.01)
# level/figure ratio
ratio = 1. / len(data)
# positioning (fractions of total figure)
left = 0.1
bottom = 1.0
width = 0.85
space = 0.035
height = ratio - space
# legend
label = 'Lvl %d'
i = 0
bottom -= height
ax = self.canvas.fig.add_axes([left, bottom - space, width, height], **axprops)
ax.plot(data[i])
setp(ax.get_xticklabels(), visible=False)
ax.set_ylabel(label % i, **yprops)
i += 1
axprops['sharex'] = ax
axprops['sharey'] = ax
while i < len(data):
bottom -= height
ax = self.canvas.fig.add_axes([left, bottom, width, height], **axprops)
ax.plot(data[i], label='Lvl' + str(i))
ax.set_ylabel(label % i, **yprops)
i += 1
if i != len(data):
setp(ax.get_xticklabels(), visible=False)
#----------------- actions -----------------#
def getTopParent(self):
widget = self.parentWidget()
while True:
if widget.parentWidget() is None:
return widget
else:
widget = widget.parentWidget()
def toggleLegend(self):
self.updateLegend()
def updateLegend(self):
#NB: sometimes induces random exceptions from legend.py -> offsetbox.py
try:
prop = font_manager.FontProperties(size=11)
self.legend = DraggableLegend(self.canvas.ax.legend(fancybox=True, shadow=True, prop=prop))
if self.toggleLegendAction.isChecked():
self.legend.legend.set_visible(True)
else:
self.legend.legend.set_visible(False)
self.canvas.draw()
except Exception, e:
pass
class Sorting_Quality_Widget(QtGui.QWidget):
def __init__(self, h5file=None):
QtGui.QWidget.__init__(self)
# define a right side control panel
gLay = QtGui.QGridLayout()
row = 0
if isinstance(h5file, tables.file.File):
self.h5file = h5file
elif isinstance(h5file, str):
self.h5file = str(
QtGui.QFileDialog.getOpenFileName(caption='select an h5 file',
filter='*.h5'))
if self.h5file:
self.h5file = tables.openFile(self.h5file, 'r')
elif not h5file:
self.loadH5FileBtn = QtGui.QPushButton('Load H5File')
self.loadH5FileBtn.clicked.connect(self.loadH5FileProc)
gLay.addWidget(self.loadH5FileBtn, row, 0, 1, 2)
row += 1
self.setWindowTitle('Spike Sorting Quality Explorer')
self.FirstUnitCombo = QtGui.QComboBox()
gLay.addWidget(self.FirstUnitCombo, row, 0, 1, 2)
row += 1
self.selectBtn = QtGui.QPushButton('Select None')
self.selectBtn.clicked.connect(self.selectProc)
self.selectBtn.setCheckable(True)
gLay.addWidget(self.selectBtn, row, 0)
self.plotXCorrBtn = QtGui.QPushButton('Plot xCorr')
self.plotXCorrBtn.clicked.connect(self.plotXCorr)
gLay.addWidget(self.plotXCorrBtn, row, 1)
row += 1
self.UnitsSelector = QtGui.QTableWidget(0, 1)
self.UnitsSelector.verticalHeader().setVisible(False)
self.UnitsSelector.horizontalHeader().setVisible(False)
self.UnitsSelector.setColumnWidth(0, 200)
gLay.addWidget(self.UnitsSelector, row, 0, 1, 2)
row += 1
mainLay = QtGui.QHBoxLayout(self)
mainLay.addLayout(gLay)
# define a left side figure
vLay = QtGui.QVBoxLayout()
self.mainFig = MplWidget(self)
self.mainFig.figure.set_facecolor('k')
self.ntb = NavToolbar(self.mainFig, self)
self.ntb.setIconSize(QtCore.QSize(15, 15))
vLay.addWidget(self.mainFig)
vLay.addWidget(self.ntb)
mainLay.addLayout(vLay)
self.show()
self.UnitChecks = []
def loadH5FileProc(self):
if hasattr(self, 'h5file') and\
isinstance(self.h5file, tables.file.File) and\
self.h5file.isopen:
self.h5file.close()
self.h5file = str(
QtGui.QFileDialog.getOpenFileName(
caption='select an h5 file',
filter='*.h5',
directory='/home/hachi/Desktop/Data/Recording'))
if self.h5file:
self.h5file = tables.openFile(self.h5file, 'r')
self.updateUnitsList()
def selectProc(self):
if not self.selectBtn.isChecked():
self.selectBtn.setText('Select None')
for k in self.UnitChecks:
k.setChecked(True)
else:
self.selectBtn.setText('Select All')
for k in self.UnitChecks:
k.setChecked(False)
'''def getUnitsProc(self):
if not hasattr(self, 'h5file'): return
if h5file,close(): return
try:
nodes = self.h5file.listNodes('/Spikes')
except:
print 'There is a problem with the H5File'
count = 0
units = []
for group in nodes:
for member in group:
if member._v_name.find('Unit') != -1:
units.append(member)
self.UnitsSelector.insertRow(count)
count += 1'''
def updateUnitsList(self):
if not hasattr(self, 'h5file'): return
# clear the FirstUnit Selector
self.FirstUnitCombo.clear()
# clean the table, kill the checkboxes
self.UnitsSelector.setRowCount(0)
for k in self.UnitChecks:
k.deleteLater()
try:
nodes = self.h5file.listNodes('/Spikes')
except:
print 'There is a problem with the H5File'
count = 0
self.UnitChecks = []
self.unitIDs = []
for group in nodes:
for member in group:
if member._v_name.find('Unit') != -1:
self.UnitsSelector.insertRow(count)
unitID = group._v_name + ' ' + member._v_name
self.UnitChecks.append(QtGui.QCheckBox(unitID))
self.UnitsSelector.setCellWidget(count, 0,
self.UnitChecks[-1])
self.UnitsSelector.setRowHeight(count, 20)
self.FirstUnitCombo.addItem(unitID)
self.unitIDs.append(unitID)
count += 1
def plotXCorr(self):
self.mainFig.figure.clf()
baseUnit = str(self.FirstUnitCombo.currentText())
chan = baseUnit[0:8]
unit = baseUnit[9:]
#get the timestamps for that unit
baseNode = self.h5file.getNode('/Spikes/' + chan)
TS = baseNode.TimeStamp.read()
baseUnitTS = baseNode.__getattr__(unit).Indx.read()
baseUnitTS = TS[baseUnitTS]
# check wich units to plot
units2Plot = []
for k in range(self.UnitsSelector.rowCount()):
if self.UnitChecks[k].isChecked():
units2Plot.append(str(self.UnitChecks[k].text()))
# create a grid of subplots of 8 columns by n rows
nRows = np.ceil(len(units2Plot) / 8.0)
ylim = 0
axes_list = []
# iterate over the list of units and plot the crosscorrelation
for j, k in enumerate(units2Plot):
axes_list.append(self.mainFig.figure.add_subplot(nRows, 8, j + 1))
chan = k[0:8]
unit = k[9:]
axes_list[-1].set_title(chan + ' ' + unit, color='w')
#get the timestamps for that unit
node = self.h5file.getNode('/Spikes/' + chan)
TS = node.TimeStamp.read()
UnitTS = node.__getattr__(unit).Indx.read()
UnitTS = TS[UnitTS]
r = []
bin_size = 1
#r, t = cross_correlation(baseUnitTS, UnitTS, bins = 20, win_lag = [-10, 10])
for ts in baseUnitTS:
t = UnitTS - ts
r.extend(t[(t > -20) & (t < 20)])
r, t = np.histogram(r, bins=int(40 / bin_size))
#indx = np.flatnonzero((t>=-200) & (t<=200))
axes_list[-1].bar(t[:-1], r, edgecolor='none', color='w')
#ax.plot(t[indx], r[indx], 'w')
axes_list[-1].set_xlim(-20, 20)
ylim = max([ylim, max(r)])
# change the color of the axes to white
axes_list[-1].tick_params(axis='x', colors='w')
axes_list[-1].tick_params(axis='y', colors='w')
axes_list[-1].set_axis_bgcolor('none')
for key, spine in axes_list[-1].spines.iteritems():
spine.set_color('w')
#for ax in axes_list:
# ax.set_ylim(0, ylim)
self.mainFig.figure.tight_layout()
self.mainFig.figure.canvas.draw()
class Sorting_Quality_Widget(QtGui.QWidget):
def __init__(self, h5file = None):
QtGui.QWidget.__init__(self)
# define a right side control panel
gLay = QtGui.QGridLayout()
row = 0
if isinstance(h5file, tables.file.File):
self.h5file = h5file
elif isinstance(h5file, str):
self.h5file = str(QtGui.QFileDialog.getOpenFileName(caption='select an h5 file',
filter='*.h5'))
if self.h5file:
self.h5file = tables.openFile(self.h5file, 'r')
elif not h5file:
self.loadH5FileBtn = QtGui.QPushButton('Load H5File')
self.loadH5FileBtn.clicked.connect(self.loadH5FileProc)
gLay.addWidget(self.loadH5FileBtn, row, 0, 1, 2)
row += 1
self.setWindowTitle('Spike Sorting Quality Explorer')
self.FirstUnitCombo = QtGui.QComboBox()
gLay.addWidget(self.FirstUnitCombo, row, 0, 1, 2)
row += 1
self.selectBtn = QtGui.QPushButton('Select None')
self.selectBtn.clicked.connect(self.selectProc)
self.selectBtn.setCheckable(True)
gLay.addWidget(self.selectBtn, row, 0)
self.plotXCorrBtn = QtGui.QPushButton('Plot xCorr')
self.plotXCorrBtn.clicked.connect(self.plotXCorr)
gLay.addWidget(self.plotXCorrBtn, row, 1)
row += 1
self.UnitsSelector = QtGui.QTableWidget(0, 1)
self.UnitsSelector.verticalHeader().setVisible(False)
self.UnitsSelector.horizontalHeader().setVisible(False)
self.UnitsSelector.setColumnWidth(0, 200)
gLay.addWidget(self.UnitsSelector, row, 0, 1, 2)
row += 1
mainLay = QtGui.QHBoxLayout(self)
mainLay.addLayout(gLay)
# define a left side figure
vLay = QtGui.QVBoxLayout()
self.mainFig = MplWidget(self)
self.mainFig.figure.set_facecolor('k')
self.ntb = NavToolbar(self.mainFig, self)
self.ntb.setIconSize(QtCore.QSize(15, 15))
vLay.addWidget(self.mainFig)
vLay.addWidget(self.ntb)
mainLay.addLayout(vLay)
self.show()
self.UnitChecks = []
def loadH5FileProc(self):
if hasattr(self, 'h5file') and\
isinstance(self.h5file, tables.file.File) and\
self.h5file.isopen:
self.h5file.close()
self.h5file = str(QtGui.QFileDialog.getOpenFileName(caption='select an h5 file',
filter='*.h5',
directory = '/home/hachi/Desktop/Data/Recording'))
if self.h5file:
self.h5file = tables.openFile(self.h5file, 'r')
self.updateUnitsList()
def selectProc(self):
if not self.selectBtn.isChecked():
self.selectBtn.setText('Select None')
for k in self.UnitChecks:
k.setChecked(True)
else:
self.selectBtn.setText('Select All')
for k in self.UnitChecks:
k.setChecked(False)
'''def getUnitsProc(self):
if not hasattr(self, 'h5file'): return
if h5file,close(): return
try:
nodes = self.h5file.listNodes('/Spikes')
except:
print 'There is a problem with the H5File'
count = 0
units = []
for group in nodes:
for member in group:
if member._v_name.find('Unit') != -1:
units.append(member)
self.UnitsSelector.insertRow(count)
count += 1'''
def updateUnitsList(self):
if not hasattr(self, 'h5file'): return
# clear the FirstUnit Selector
self.FirstUnitCombo.clear()
# clean the table, kill the checkboxes
self.UnitsSelector.setRowCount(0)
for k in self.UnitChecks: k.deleteLater()
try:
nodes = self.h5file.listNodes('/Spikes')
except:
print 'There is a problem with the H5File'
count = 0
self.UnitChecks = []
self.unitIDs = []
for group in nodes:
for member in group:
if member._v_name.find('Unit') != -1:
self.UnitsSelector.insertRow(count)
unitID = group._v_name + ' ' + member._v_name
self.UnitChecks.append(QtGui.QCheckBox(unitID))
self.UnitsSelector.setCellWidget(count, 0, self.UnitChecks[-1])
self.UnitsSelector.setRowHeight(count, 20)
self.FirstUnitCombo.addItem(unitID)
self.unitIDs.append(unitID)
count += 1
def plotXCorr(self):
self.mainFig.figure.clf()
baseUnit = str(self.FirstUnitCombo.currentText())
chan = baseUnit[0:8]
unit = baseUnit[9:]
#get the timestamps for that unit
baseNode = self.h5file.getNode('/Spikes/'+chan)
TS = baseNode.TimeStamp.read()
baseUnitTS = baseNode.__getattr__(unit).Indx.read()
baseUnitTS = TS[baseUnitTS]
# check wich units to plot
units2Plot = []
for k in range(self.UnitsSelector.rowCount()):
if self.UnitChecks[k].isChecked():
units2Plot.append( str(self.UnitChecks[k].text()) )
# create a grid of subplots of 8 columns by n rows
nRows = np.ceil(len(units2Plot)/8.0)
ylim = 0
axes_list = []
# iterate over the list of units and plot the crosscorrelation
for j, k in enumerate(units2Plot):
axes_list.append(self.mainFig.figure.add_subplot(nRows, 8, j+1))
chan = k[0:8]
unit = k[9:]
axes_list[-1].set_title(chan+' '+unit, color = 'w')
#get the timestamps for that unit
node = self.h5file.getNode('/Spikes/'+chan)
TS = node.TimeStamp.read()
UnitTS = node.__getattr__(unit).Indx.read()
UnitTS = TS[UnitTS]
r = []
bin_size = 1
#r, t = cross_correlation(baseUnitTS, UnitTS, bins = 20, win_lag = [-10, 10])
for ts in baseUnitTS:
t = UnitTS - ts
r.extend(t[(t > -20) & (t < 20)])
r, t = np.histogram(r, bins = int(40/bin_size) )
#indx = np.flatnonzero((t>=-200) & (t<=200))
axes_list[-1].bar(t[:-1], r, edgecolor = 'none', color = 'w')
#ax.plot(t[indx], r[indx], 'w')
axes_list[-1].set_xlim(-20, 20)
ylim = max([ylim, max(r)])
# change the color of the axes to white
axes_list[-1].tick_params(axis = 'x', colors = 'w')
axes_list[-1].tick_params(axis = 'y', colors = 'w')
axes_list[-1].set_axis_bgcolor('none')
for key, spine in axes_list[-1].spines.iteritems():
spine.set_color('w')
#for ax in axes_list:
# ax.set_ylim(0, ylim)
self.mainFig.figure.tight_layout()
self.mainFig.figure.canvas.draw()
