def create_tabs(self):
#Text Area
s = ("Welcome to the S.Pombe kinetochore motion "
"Simulator")
self.simLog = QtGui.QTextEdit(s)
self.simLog.setReadOnly(True)
#Plotting Areas
span = self.paramtree.relative_dic['span']
self.plotarea1 = MyMplCanvas(span)
mpl_toolbar = NavigationToolbar(self.plotarea1, self.centralwidget)
vbox1 = QtGui.QVBoxLayout()
vbox1.setSpacing(5)
vbox1.addWidget(self.plotarea1)
vbox1.addWidget(mpl_toolbar)
self.w1 = QtGui.QWidget()
self.w1.setLayout(vbox1)
self.plotarea2 = MyMplCanvas(span)
mpl_toolbar = NavigationToolbar(self.plotarea2, self.centralwidget)
vbox2 = QtGui.QVBoxLayout()
vbox2.setSpacing(5)
vbox2.addWidget(self.plotarea2)
vbox2.addWidget(mpl_toolbar)
self.w2 = QtGui.QWidget()
self.w2.setLayout(vbox2)
#All this goes in a tab widget
self.tabWidget = QtGui.QTabWidget()
self.tabWidget.setTabsClosable(True)
self.tabWidget.addTab(self.simLog, "Log")
#self.tabWidget.tabCloseRequested.connect(self.tabWidget.removeTab)
self.connect(self.tabWidget, QtCore.SIGNAL('tabCloseRequested(int)'),
self.closeTab)
class MainWindow(QtGui.QMainWindow):
def __init__(self, parent=None):
self.paramtree = ParamTree(PARAMFILE)
self.measuretree = ParamTree(MEASUREFILE, adimentionalized=False)
self.measures = self.measuretree.absolute_dic
self.mt = None
QtGui.QMainWindow.__init__(self, parent)
self.centralwidget = QtGui.QWidget()
self.setCentralWidget(self.centralwidget)
self.create_docks()
self.create_tabs()
self.create_buttons()
#self.prepare_simulation()
def create_docks(self):
#Parameter Setting in a Dock Widget
self.paramdock = QtGui.QDockWidget('Parameters Setting')
self.setParameters = SetParameters(self.paramtree)
scrollArea = QtGui.QScrollArea()
scrollArea.setWidget(self.setParameters)
self.paramdock.setWidget(scrollArea)
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self.paramdock)
#Measures Setting in another Dock Widget
self.measuredock = QtGui.QDockWidget('Measures Setting')
self.setMeasures = SetMeasures(self.measuretree)
scrollArea = QtGui.QScrollArea()
scrollArea.setWidget(self.setMeasures)
self.measuredock.setWidget(scrollArea)
self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self.measuredock)
def create_tabs(self):
#Text Area
s = ("Welcome to the S.Pombe kinetochore motion "
"Simulator")
self.simLog = QtGui.QTextEdit(s)
self.simLog.setReadOnly(True)
#Plotting Areas
span = self.paramtree.relative_dic['span']
self.plotarea1 = MyMplCanvas(span)
mpl_toolbar = NavigationToolbar(self.plotarea1, self.centralwidget)
vbox1 = QtGui.QVBoxLayout()
vbox1.setSpacing(5)
vbox1.addWidget(self.plotarea1)
vbox1.addWidget(mpl_toolbar)
self.w1 = QtGui.QWidget()
self.w1.setLayout(vbox1)
self.plotarea2 = MyMplCanvas(span)
mpl_toolbar = NavigationToolbar(self.plotarea2, self.centralwidget)
vbox2 = QtGui.QVBoxLayout()
vbox2.setSpacing(5)
vbox2.addWidget(self.plotarea2)
vbox2.addWidget(mpl_toolbar)
self.w2 = QtGui.QWidget()
self.w2.setLayout(vbox2)
#All this goes in a tab widget
self.tabWidget = QtGui.QTabWidget()
self.tabWidget.setTabsClosable(True)
self.tabWidget.addTab(self.simLog, "Log")
#self.tabWidget.tabCloseRequested.connect(self.tabWidget.removeTab)
self.connect(self.tabWidget, QtCore.SIGNAL('tabCloseRequested(int)'),
self.closeTab)
# self.closeTab)
#self.tabWidget.addTab(w1, "All trajectories")
#self.tabWidget.addTab(w2, "One trajectory")
def closeTab(self, idx):
self.tabWidget.removeTab(idx)
def create_buttons(self):
#Buttons
#self.buttonGroup = QtGui.QButtonGroup()
runButton = QtGui.QPushButton('Run the simulation')
exec_icon = os.path.join(os.path.dirname(__file__),
"images", "exec.svg")
runButton.setIcon(QtGui.QIcon(exec_icon))
self.connect(runButton, QtCore.SIGNAL('clicked()'), self.run_simulation)
showTrajButton = QtGui.QPushButton('Show trajectories')
self.connect(showTrajButton, QtCore.SIGNAL('clicked()'), self.show_trajs)
self.traj_num = 0
showOneButton = QtGui.QPushButton('Show one trajectory')
self.connect(showOneButton, QtCore.SIGNAL('clicked()'), self.show_one)
self.interactiveButton = QtGui.QRadioButton('Interactive Simulation')
self.interactiveButton.setChecked(True)
#self.buttonGroup.addButton(runButton)
#Progress Bar
self.progressBar = QtGui.QProgressBar()
hbox = QtGui.QHBoxLayout()
hbox.setSpacing(5)
hbox.addWidget(runButton)
hbox.addWidget(showTrajButton)
hbox.addWidget(showOneButton)
hbox.addWidget(self.progressBar)
hbox.addWidget(self.interactiveButton)
vbox = QtGui.QVBoxLayout()
vbox.setSpacing(5)
vbox.addLayout(hbox) #self.buttonGroup)
vbox.addWidget(self.tabWidget)
self.centralwidget.setLayout(vbox)
self.createActions()
self.createMenus()
self.createToolBars()
self.createStatusBar()
currentDirName = os.path.abspath(os.path.curdir)
currentFileName = '_'.join(time.asctime().split()[:-1])
currentFileName = 'simul_' + \
'_'.join(currentFileName.split(':')) + \
'.xml'
currentFileName = os.path.join(currentDirName, currentFileName)
self.setCurrentFile(currentFileName)
self.setWindowTitle(self.tr("Kinetochore Dynamics Simulation"))
self.setMinimumSize(160, 160)
self.resize(1000, 600)
def prepare_simulation(self):
plug_idx = self.attachCombo.currentIndex()
initial_plug = self.attachment_list[plug_idx]
self.mt = SigMetaphase(self.paramtree, self.measuretree,
initial_plug=initial_plug)
self.progressBar.setMaximum(int(self.paramtree.absolute_dic['span']))
self.progressBar.setMinimum(0)
self.connect(self.mt, QtCore.SIGNAL('plugCheckPoint'),
self.active_checkpoint)
self.connect(self.mt, QtCore.SIGNAL('stepDone'),
self.progressBar.setValue)
self.connect(self.mt, QtCore.SIGNAL('simulDone'),
self.print_report)
run_interactively = self.interactiveButton.isChecked()
if run_interactively:
self.iw = InteractiveCellWidget(self.mt)
idx = self.tabWidget.currentIndex() + 1
self.tabWidget.insertTab(idx, self.iw, "Interactive Simulation")
self.tabWidget.setCurrentIndex(idx)
self.connect(self.mt, QtCore.SIGNAL('simulDone'),
self.iw.startAnim)
def run_simulation(self):
self.prepare_simulation()
QtGui.QApplication.setOverrideCursor(QtCore.Qt.WaitCursor)
self.mt.sig_simul()
QtGui.QApplication.restoreOverrideCursor()
def show_trajs(self):
self.plotarea1.update_figure(self.mt)
self.tabWidget.insertTab(1, self.w1, "All trajectories")
self.tabWidget.setCurrentIndex(1)
def show_one(self):
#self.tabWidget.removeTab(2)
t_num = mod(self.traj_num, 3)
self.plotarea2.update_figure(self.mt, t_num)
self.traj_num += 1
self.tabWidget.insertTab(2, self.w2, "Trajectory of chromosome # %i" %(t_num + 1) )
self.tabWidget.setCurrentIndex(2)
def update_progressBar(self, val):
self.progressBar.setValue(val)
def print_report(self, report):
self.simLog.append("Simulation's done!")
for l in report:
ls = l
self.simLog.append(ls)
self.progressBar.setValue(0)
def active_checkpoint(self, cp):
if cp:
self.statusBar().showMessage(self.tr("Active Plug/unplug checkpoint"), 2000)
else:
self.statusBar().showMessage(self.tr(" "), 2000)
def closeEvent(self, event):
if self.maybeSave():
event.accept()
else:
event.ignore()
def newFile(self):
if self.maybeSave():
self.textEdit.clear()
self.setCurrentFile("")
def open(self):
if self.maybeSave():
fileName, selectedFilter = QtGui.QFileDialog.getOpenFileName(self, filter="XML files (*.xml);;All Files (*.*)")
self.loadFile(fileName)
self.setCurrentFile(fileName)
def save(self):
# if not os.path.isfile(self.curFile):
# self.curFile = default_filename
# #return self.saveAs()
# else:
return self.saveFile(self.curFile)
# TODO: The saveAs functions trigs a segfault
# def saveAs(self):
# #'test_save'#
# saveDiag = QtGui.QFileDialog()
# fileName = saveDiag.getSaveFileName(self,
# self.tr("Save Simulation"),
# self.tr("default.xml"),
# self.tr("Simulations (*.xml)"))
### SegFaults here, I don't know why ###
# print filename
# if fileName.isEmpty():
# fileName = "default.xml"
# self.saveFile(fileName)
# del saveDiag
def about(self):
QtGui.QMessageBox.about(self, self.tr("About Application"),
self.tr("This little stuff allows to simulate "
"kinetochore dynamics in S.Pombe "))
def documentWasModified(self):
self.setWindowModified(self.setParameters.isModified)
def createActions(self):
open_icon = os.path.join(os.path.dirname(__file__),
"images", "open.png")
self.openAct = QtGui.QAction(QtGui.QIcon(open_icon),
self.tr("&Open Simulation File"), self)
self.openAct.setShortcut(self.tr("Ctrl+O"))
self.openAct.setStatusTip(self.tr("Open an existing simulation file"))
self.connect(self.openAct, QtCore.SIGNAL("triggered()"), self.open)
save_icon = os.path.join(os.path.dirname(__file__),
"images", "save.png")
self.saveAct = QtGui.QAction(QtGui.QIcon(save_icon),
self.tr("&Save"), self)
self.saveAct.setShortcut(self.tr("Ctrl+S"))
self.saveAct.setStatusTip(self.tr("Save the simulation to disk"))
self.connect(self.saveAct, QtCore.SIGNAL("triggered()"), self.save)
# self.saveAsAct = QtGui.QAction(self.tr("Save &As..."), self)
# self.saveAsAct.setStatusTip(self.tr("Save the simulation under a new name"))
# self.connect(self.saveAsAct, QtCore.SIGNAL("triggered()"), self.saveAs)
self.exitAct = QtGui.QAction(self.tr("E&xit"), self)
self.exitAct.setShortcut(self.tr("Ctrl+Q"))
self.exitAct.setStatusTip(self.tr("Exit the application"))
self.connect(self.exitAct, QtCore.SIGNAL("triggered()"), self, QtCore.SLOT("close()"))
self.aboutAct = QtGui.QAction(self.tr("&About"), self)
self.aboutAct.setStatusTip(self.tr("Show the application's About box"))
self.connect(self.aboutAct, QtCore.SIGNAL("triggered()"), self.about)
self.aboutQtAct = QtGui.QAction(self.tr("About &Qt"), self)
self.aboutQtAct.setStatusTip(self.tr("Show the Qt library's About box"))
self.connect(self.aboutQtAct, QtCore.SIGNAL("triggered()"), QtGui.qApp, QtCore.SLOT("aboutQt()"))
def createMenus(self):
self.fileMenu = self.menuBar().addMenu(self.tr("&File"))
self.fileMenu.addAction(self.openAct)
self.fileMenu.addAction(self.saveAct)
# self.fileMenu.addAction(self.saveAsAct)
self.fileMenu.addSeparator()
self.fileMenu.addAction(self.exitAct)
self.menuBar().addSeparator()
self.helpMenu = self.menuBar().addMenu(self.tr("&Help"))
self.helpMenu.addAction(self.aboutAct)
self.helpMenu.addAction(self.aboutQtAct)
def createToolBars(self):
self.fileToolBar = self.addToolBar(self.tr("File"))
self.fileToolBar.addAction(self.openAct)
self.fileToolBar.addAction(self.saveAct)
self.attachCombo = QtGui.QComboBox()
self.attachCombo.addItem("No attachment") #0
self.attachCombo.addItem("Amphitelic attachment") #1
self.attachCombo.addItem("Merotelic attachment") #2
self.attachCombo.addItem("Syntelic attachment") #3
self.attachCombo.addItem("Monotelic attachment") #4
self.attachCombo.addItem("Random attachment") #5
self.configToolBar = self.addToolBar(self.tr("config"))
self.configToolBar.addWidget(self.attachCombo)
self.attachment_list = ['null',
'amphitelic',
'merotelic',
'syntelic',
'monotelic',
'random']
self.attachCombo.setCurrentIndex(5)
def createStatusBar(self):
self.statusBar().showMessage(self.tr("Ready"))
def maybeSave(self):
if self.setParameters.isModified:
ret = QtGui.QMessageBox.warning(self, self.tr("Application"),
self.tr("The document has been modified.\n"
"Do you want to save your changes?"),
QtGui.QMessageBox.Yes | QtGui.QMessageBox.Default,
QtGui.QMessageBox.No,
QtGui.QMessageBox.Cancel | QtGui.QMessageBox.Escape)
if ret == QtGui.QMessageBox.Yes:
return self.save()
elif ret == QtGui.QMessageBox.Cancel:
return False
return True
def loadFile(self, fileName):
QtGui.QApplication.setOverrideCursor(QtCore.Qt.WaitCursor)
self.prepare_simulation()
tmp_m = get_fromfile(str(fileName))
self.paramtree = tmp_m.paramtree
self.measuretree = tmp_m.measuretree
self.removeDockWidget(self.paramdock)
del self.paramdock
self.removeDockWidget(self.measuredock)
del self.measuredock
self.create_docks()
self.prepare_simulation()
self.mt = SigMetaphase(tmp_m.paramtree, tmp_m.measuretree)
self.mt.KD = tmp_m.KD
del tmp_m
self.mt.emit(QtCore.SIGNAL('simulDone'),self.mt.report)
QtGui.QApplication.restoreOverrideCursor()
self.setCurrentFile(fileName)
self.statusBar().showMessage(self.tr("Loaded"), 2000)
def saveFile(self, fileName):
if not fileName.endsWith('.xml'):
xmlfname = fileName+'.xml'
datafname = fileName+'_data.npy'
else:
xmlfname = fileName
datafname = fileName.split('.')[-2]+'_data.npy'
self.mt.write_results(str(xmlfname), str(datafname))
self.setCurrentFile(fileName);
self.statusBar().showMessage(self.tr("File saved"), 2000)
return True
def setCurrentFile(self, fileName):
self.curFile = fileName
self.setParameters.setModified(False)
self.setWindowModified(False)
def strippedName(self, fullFileName):
return QtCore.QFileInfo(fullFileName).fileName()