def on_button_FromData_clicked(self):
try:
dataService = DataService()
expData = dataService.get_experimental_data()
timepointSet = set()
if expData:
for dataSet in expData.values():
if not dataSet.isSelected():
continue
if dataSet.dataDescriptors:
for dataDescriptor in dataSet.dataDescriptors:
timepointSet.add(float(dataDescriptor))
for entityData in dataSet.getData().values():
if not entityData.isSelected():
continue
if entityData.dataDescriptors:
for dataDescriptor in entityData.dataDescriptors:
timepointSet.add(float(dataDescriptor))
self.timepoints = list(timepointSet)
self.timepoints.sort()
timepointsStr = str(self.timepoints).replace(
",", " ").strip("[").strip("]")
if not timepointsStr:
timepointsStr = "No timepoint data."
self.plainTextEdit_Timepoints.clear()
self.plainTextEdit_Timepoints.insertPlainText(timepointsStr)
except Exception, e:
logging.error("Could not get timepoints from data. Error: %s" % e)
def on_button_FromData_clicked(self):
try:
dataService = DataService()
expData = dataService.get_experimental_data()
timepointSet = set()
if expData:
for dataSet in expData.values():
if not dataSet.isSelected():
continue
if dataSet.dataDescriptors:
for dataDescriptor in dataSet.dataDescriptors:
timepointSet.add(float(dataDescriptor))
for entityData in dataSet.getData().values():
if not entityData.isSelected():
continue
if entityData.dataDescriptors:
for dataDescriptor in entityData.dataDescriptors:
timepointSet.add(float(dataDescriptor))
self.timepoints = list(timepointSet)
self.timepoints.sort()
timepointsStr = str(self.timepoints).replace(",", " ").strip("[").strip("]")
if not timepointsStr:
timepointsStr = "No timepoint data."
self.plainTextEdit_Timepoints.clear()
self.plainTextEdit_Timepoints.insertPlainText(timepointsStr)
except Exception, e:
logging.error("Could not get timepoints from data. Error: %s" % e)
class DataImportWidget(QWidget, Ui_DataImportWidget):
"""
This is a very simple widget that provides some buttons
to load experimental data.
@since: 2011-08-24
"""
__author__ = "Moritz Wade"
__contact__ = "*****@*****.**"
__copyright__ = "Zuse Institute Berlin 2011"
updatedDataEvent = Signal(OrderedDict)
def __init__(self, parent, parkinController):
super(DataImportWidget, self).__init__(parent)
self.setupUi(self)
self.currentExpDataFilename = None
self.dataService = DataService()
self.parkinController = parkinController
def browseExpData(self):
"""
Shows a file open dialog.
"""
homeDir = filehelpers.getHomeDir()
openDir = self.currentExpDataFilename if self.currentExpDataFilename else homeDir
filenameTuple = QFileDialog.getOpenFileName(parent=self,
caption="Browse for data file...",
directory=openDir,
filter="BioPARKIN CSV data file (*.csv *.txt);;Legacy PARKIN data file (*.dat);;All filetypes (*.*")
self.setCurrentExpDataDirectory(filenameTuple[0])
def setCurrentExpDataDirectory(self, filename):
self.currentExpDataFilename = filename
self.lineEdit.setText(self.currentExpDataFilename)
def updateExpData(self, readFile=False):
if self.dataService.has_data(self.currentExpDataFilename): # don't load the same data twice (remove the data first, if you want to reload)
logging.info("This data file is already loaded: %s" % self.currentExpDataFilename)
return
if readFile:
self.currentExpDataFilename = self.lineEdit.text()
format = self.getExpDataFileFormat()
self.dataService.load_data([self.currentExpDataFilename], type=services.dataservice.EXPERIMENTAL,
parkinController=self.parkinController, format=format)
expData = self.dataService.get_experimental_data()
if expData:
self.updatedDataEvent.emit(expData)
def getExpDataFileFormat(self):
filename = self.currentExpDataFilename
if filename.endswith("csv") or filename.endswith("txt"):
format = datamanagement.dataset.FORMAT_EXP_SIMPLE_CSV
elif filename.endswith("dat"):
format = datamanagement.dataset.FORMAT_EXP_PARKIN
else:
format = None
return format
###### SLOTS #######
@Slot("")
def on_buttonBrowse_clicked(self):
#logging.debug("SimulationWorkbenchController: in on_buttonBrowseExpData_clicked()")
self.browseExpData()
if not self.currentExpDataFilename:
logging.info("No file selected. Can't import data.")
return
self.updateExpData(readFile=True)
self.lineEdit.clear()
@Slot("")
def on_buttonImport_clicked(self):
if not self.currentExpDataFilename:
logging.info("No filename given. Can't import data.")
return
#logging.debug("SimulationWorkbenchController: in on_buttonBrowseExpData_clicked()")
self.updateExpData(readFile=True)
self.lineEdit.clear()
class DataImportWidget(QWidget, Ui_DataImportWidget):
"""
This is a very simple widget that provides some buttons
to load experimental data.
@since: 2011-08-24
"""
__author__ = "Moritz Wade"
__contact__ = "*****@*****.**"
__copyright__ = "Zuse Institute Berlin 2011"
updatedDataEvent = Signal(OrderedDict)
def __init__(self, parent, parkinController):
super(DataImportWidget, self).__init__(parent)
self.setupUi(self)
self.currentExpDataFilename = None
self.dataService = DataService()
self.parkinController = parkinController
def browseExpData(self):
"""
Shows a file open dialog.
"""
homeDir = filehelpers.getHomeDir()
openDir = self.currentExpDataFilename if self.currentExpDataFilename else homeDir
filenameTuple = QFileDialog.getOpenFileName(
parent=self,
caption="Browse for data file...",
directory=openDir,
filter=
"BioPARKIN CSV data file (*.csv *.txt);;Legacy PARKIN data file (*.dat);;All filetypes (*.*"
)
self.setCurrentExpDataDirectory(filenameTuple[0])
def setCurrentExpDataDirectory(self, filename):
self.currentExpDataFilename = filename
self.lineEdit.setText(self.currentExpDataFilename)
def updateExpData(self, readFile=False):
if self.dataService.has_data(
self.currentExpDataFilename
): # don't load the same data twice (remove the data first, if you want to reload)
logging.info("This data file is already loaded: %s" %
self.currentExpDataFilename)
return
if readFile:
self.currentExpDataFilename = self.lineEdit.text()
format = self.getExpDataFileFormat()
self.dataService.load_data([self.currentExpDataFilename],
type=services.dataservice.EXPERIMENTAL,
parkinController=self.parkinController,
format=format)
expData = self.dataService.get_experimental_data()
if expData:
self.updatedDataEvent.emit(expData)
def getExpDataFileFormat(self):
filename = self.currentExpDataFilename
if filename.endswith("csv") or filename.endswith("txt"):
format = datamanagement.dataset.FORMAT_EXP_SIMPLE_CSV
elif filename.endswith("dat"):
format = datamanagement.dataset.FORMAT_EXP_PARKIN
else:
format = None
return format
###### SLOTS #######
@Slot("")
def on_buttonBrowse_clicked(self):
#logging.debug("SimulationWorkbenchController: in on_buttonBrowseExpData_clicked()")
self.browseExpData()
if not self.currentExpDataFilename:
logging.info("No file selected. Can't import data.")
return
self.updateExpData(readFile=True)
self.lineEdit.clear()
@Slot("")
def on_buttonImport_clicked(self):
if not self.currentExpDataFilename:
logging.info("No filename given. Can't import data.")
return
#logging.debug("SimulationWorkbenchController: in on_buttonBrowseExpData_clicked()")
self.updateExpData(readFile=True)
self.lineEdit.clear()
class DataViewingController(QDialog, Ui_DataViewWidget):
'''
A experimentalData view window (implemented as DockWidget, so it
can be docked inside the main application potentially)
to display plots, etc. (Maybe more than just plots in a future release?)
In MVC-naming this is the Controller. The View is in Ui_dataViewWidget.
@param parent: Standard Qt UI parent
@type parent: QWidget
@since: 2010-03-10
'''
__author__ = "Moritz Wade"
__contact__ = "*****@*****.**"
__copyright__ = "Zuse Institute Berlin 2010"
def __init__(self, parent=None):
'''
Creates a data model from the data (so that changes in the data
are reflected in the View).
'''
super(DataViewingController, self).__init__(parent)
self.setupUi(self)
self.dataService = DataService()
experimentalData = self.dataService.get_experimental_data()
simulationData = self.dataService.get_simulation_data()
#data = ordereddict()
self.data = OrderedDict()
if simulationData is not None and len(simulationData) > 0:
self.simulationData = simulationData
for (sbmlEntity, entityData) in self.simulationData.items():
#sbmlRef = entityData.sbmlEntity
dataTuple = (entityData, None)
self.data[sbmlEntity] = dataTuple
else:
self.simulationData = None
if experimentalData is not None:
self.experimentalData = experimentalData
for (sbmlEntity, entityData) in experimentalData.items():
#sbmlRef = entityData.sbmlEntity
if sbmlEntity in self.data:
dataTuple = self.data[sbmlEntity]
dataTuple = (dataTuple[0], entityData)
self.data[sbmlEntity] = dataTuple
else:
dataTuple = (entityData, None)
self.data[sbmlEntity] = dataTuple
else:
self.experimentalData = None
if self.experimentalData or self.simulationData:
self.dataModel = SourcesTableModel(
combinedData=self.data
#experimentalData = self.experimentalData,
#simulationData = self.simulationData
)
self.connect(self.dataModel,
SIGNAL("dataChanged(QModelIndex, QModelIndex)"),
self.update_plots)
#self.data = [] # create single list with all data entities
# for item in self.experimentalData:
# self.data.append(item)
# for item in self.simulationData:
# if item in self.data:
# continue
# self.data.append(item)
self.populate_sources_table()
# self.plotWindows = {}
# self.flatListOfPlotWidgets = []
self.existingPlotWindows = {}
self.update_plots() # testing
#QTimer.singleShot(0, self.update_plots)
def populate_sources_table(self):
'''
Sets the "sources" data model to the source table view.
'''
if self.dataModel is None:
logging.error(
"There is no model to populate with experimental Data.")
return
table = self.tableSources
table.setModel(self.dataModel)
def update_plots(self):
'''
Create all the plots based on the selection in the list widget
self.tableSources
This is rather complicated and should be refactored + broken
down.
'''
# gather information about what to show
windowTitlesToShow = {}
#for (dataID, dataItem) in self.experimentalData.items():
for (entity, dataTuple) in self.data.items():
dataID = entity.id
if self.dataModel.does_show_experimental_data_of(
dataID) and self.dataModel.does_show_simulation_data_of(
dataID):
windowTitle = "Experimental and simulation values of %s" % dataID
elif self.dataModel.does_show_experimental_data_of(dataID):
windowTitle = "Experimental values of %s" % dataID
elif self.dataModel.does_show_simulation_data_of(dataID):
windowTitle = "Simulation values of %s" % dataID
else:
windowTitle = None
if windowTitle is not None:
windowTitlesToShow[windowTitle] = (entity, dataTuple)
# close previous windows that show information we don't want now
for existingWindowTitle in self.existingPlotWindows.keys():
if not windowTitlesToShow.has_key(existingWindowTitle):
self.existingPlotWindows.pop(existingWindowTitle).close()
# create missing windows
#for (dataID, dataItem) in self.experimentalData.items():
for (windowTitle, (entity, dataTuple)) in windowTitlesToShow.items():
dataID = entity.id
if self.existingPlotWindows.has_key(
windowTitle
): # dont' create windows that are already there
continue
labelExperimental = "Experimental values of %s" % dataID
labelSimulation = "Simulation values of %s" % dataID
subWindow = QMdiSubWindow(parent=self.plotWindowsArea)
subWindow.setAttribute(Qt.WA_DeleteOnClose)
subWindow.setOption(QMdiSubWindow.RubberBandResize, True)
self.existingPlotWindows[windowTitle] = subWindow
# if self.dataModel.does_show_experimental_data_of(dataID):
# if self.simulationData.has_key(dataID):
# experimentalData = {dataID:dataItem}
# else:
# experimentalData = None
# else:
# experimentalData = None
#
# if self.dataModel.does_show_simulation_data_of(dataID):
# if self.simulationData.has_key(dataID):
# simulationData = {dataID + "_sim" : self.simulationData[dataID]}
# else:
# simulationData = None
# else:
# simulationData = None
if self.dataModel.does_show_experimental_data_of(dataID):
experimentalData = dataTuple[1]
else:
experimentalData = None
if self.dataModel.does_show_simulation_data_of(dataID):
simulationData = dataTuple[0]
else:
simulationData = None
plotWidget = PlotWidget(
parent=subWindow,
experimentalData=experimentalData,
simulationData=simulationData,
labelExperimental=labelExperimental,
labelSimulation=labelSimulation,
showLegend=self.checkBoxShowLegend.isChecked(),
logYAxis=self.checkBoxLogYAxis.isChecked())
subWindow.setWindowTitle(windowTitle)
subWindow.setWidget(plotWidget)
subWindow.show() # important!
@Slot("bool")
def on_checkBoxPlotGroupsAsTabs_toggled(self, isChecked):
'''
This is a slot for toggling a tab UI for the plots,
'''
logging.info("Plot Groups are shown as Tabs: %s" % isChecked)
if isChecked:
self.plotGroupsArea.setViewMode(QMdiArea.TabbedView)
else:
self.plotGroupsArea.setViewMode(QMdiArea.SubWindowView)
@Slot("QTableWidgetItem")
def on_tableSources_itemChanged(self, item):
'''
This is a slot. Whenever some item changes in the list view
(e.g. some data gets checked/unchecked), the plots are updated.
'''
self.update_plots()
@Slot("")
def on_pushButtonReplot_clicked(self):
'''
This is a slot. It causes the plots to be replotted.
'''
for existingWindowTitle in self.existingPlotWindows.keys():
self.existingPlotWindows.pop(existingWindowTitle).close()
self.update_plots()
