def __init__(self, parent=None, host=None, title="Plot"):
"""
Constructor
"""
#super class constructor
super(PlotWidgetController, self).__init__(parent)
self.setupUi(self)
self.setWindowTitle(title)
self._initialize()
self.timeUnit = "a.u." #default ?
self.speciesUnit = "a.u." #default ?
self.speciesLabel = "Concentration" #default ?
if host:
self.timeUnit = str(host.optionTimeUnit)
self.speciesUnit = str(host.optionSpeciesUnit)
self.speciesLabel = str(host.optionSpeciesLabel)
#options: time unit, logarithmic y-axis and 'show legend'
# 24.2.2015 td
#options: species label, species unit
self.options = {
OPTION_LABEL_X: "Time [%s]" % (self.timeUnit), #default
OPTION_LABEL_Y: "%s [%s]" % (self.speciesLabel,self.speciesUnit), #default
OPTION_LOG_Y_AXIS: self.checkBoxLogYAxis.isChecked(),
OPTION_SHOW_LEGEND: self.checkBoxShowLegend.isChecked()
}
self.host = host
self.title = title
self.data = None
self.labels = None
self.fig = None
self.canvas = None
self.axes = None
self.mpl_toolbar = None
self.dpi = None
self.useGrayColor = False
self.plotStyleManager = PlotStyleManager()
if self.title!='Plot': self.plotStyleManager.setDataType(self.title)
self.plotStyle = {
0: PLOT_LINE} #default plot style; if there are more elements, each numbered element corresponds to one data source
self.plotColors = {} # will be filled with colors on the first plot
class PlotWidgetController(AbstractViewController, Ui_PlotWidget):
"""
The controller part for a plotting widget. The UI part is declared
in plotwidget_v1.ui and then converted to ui_plotwidget.py.
This plot widget can be fed with data via set methods and has several
options to adjust the visualization of that data.
@since: 2010-11-08
"""
__author__ = "Moritz Wade"
__contact__ = "*****@*****.**"
__copyright__ = "Zuse Institute Berlin 2010"
def __init__(self, parent=None, host=None, title="Plot"):
"""
Constructor
"""
#super class constructor
super(PlotWidgetController, self).__init__(parent)
self.setupUi(self)
self.setWindowTitle(title)
self._initialize()
self.timeUnit = "a.u." #default ?
if host:
self.timeUnit = str(host.optionTimeUnit)
#options: time unit, logarithmic y-axis and 'show legend'
self.options = {
OPTION_LABEL_X: "Time [%s]" % (self.timeUnit), #default
OPTION_LOG_Y_AXIS: self.checkBoxLogYAxis.isChecked(),
OPTION_SHOW_LEGEND: self.checkBoxShowLegend.isChecked()
}
self.host = host
self.title = title
self.data = None
self.labels = None
self.fig = None
self.canvas = None
self.axes = None
self.mpl_toolbar = None
self.dpi = None
self.useGrayColor = False
self.plotStyleManager = PlotStyleManager()
if self.title!='Plot': self.plotStyleManager.setDataType(self.title)
self.plotStyle = {
0: PLOT_LINE} #default plot style; if there are more elements, each numbered element corresponds to one data source
self.plotColors = {} # will be filled with colors on the first plot
def _updateView(self, data=None):
'''
'''
#wrap it in a try-catch
try:
#if the data argument is not None
#assign it to the instance var data
if data:
self.data = data
if not self.fig: # on first plot
self.dpi = self.logicalDpiX()
logging.info("Plotting at %s dpi." % self.dpi)
self.fig = Figure(dpi=self.dpi)
self.canvas = FigureCanvas(self.fig)
self.axes = self.fig.add_subplot(111)
self.mpl_toolbar = NavigationToolbar(self.canvas, None)
left_vbox = QVBoxLayout(self.plotWrapper)
left_vbox.addWidget(self.canvas)
left_vbox.addWidget(self.mpl_toolbar)
self.setAxesAndData()
self.canvas.draw()
else:
self.axes.clear()
self.setAxesAndData()
self.canvas.draw()
except Exception as e:
logging.debug("PlotWidgetController._updateView: Error occurred: %s" % e)
def _clearView(self):
if self.axes:
self.axes.clear()
if self.canvas:
self.canvas.draw()
def setAxesAndData(self):
try:
#TODO: deprecated since a new plot style manager class!!!
#if not self.plotStyleManager.colorMap: self.plotStyleManager.setColorMap('spectral')
self.computeColors()
#if no color map specified yet - set default to spectral
from plotstylemanager import DATA_TYPES
if not self.plotStyleManager.dataType and self.title in DATA_TYPES:self.plotStyleManager.dataType = self.title
# some of this has to be done before the data is set
self.setAxes()
self.setData()
# has to be done after the data is set
if OPTION_SHOW_LEGEND in self.options and self.options[OPTION_SHOW_LEGEND]:
self.axes.legend()
except Exception as e:
logging.debug("PlotWidgetController.setAxesAndData: Error occurred: %s" % e)
def setAxes(self):
'''
Defines the plot's axes.
'''
try:
self.axes.clear()
self.axes.grid(True)
# set x label
for entityDataList in self.data.values():
for entityData in entityDataList:
yLabel = str(entityData.getAxisLabel())
break
self.axes.set_ylabel(yLabel)
# set y label
if OPTION_LABEL_X in self.options:
self.axes.set_xlabel(str(self.options[OPTION_LABEL_X]))
else:
self.axes.set_xlabel("N/A")
if OPTION_LOG_Y_AXIS in self.options and self.options[OPTION_LOG_Y_AXIS]:
self.axes.set_yscale('log')
except Exception as e:
logging.debug("PlotWidgetController.setAxes: Error occurred: %s" % e)
def setData(self):
try:#wrap it in a try-catch close
#BEGIN if-if there's some data
if self.data:
#get new cyclic iterators over the marker styles, line style and color
markerIt, lineIt= self.plotStyleManager.getMarkerIterator(), self.plotStyleManager.getLineIterator()
expPlot = True
markr = None
#BEGIN for-iterating over the data values
for j, entityDataList in enumerate(self.data.values()):
#BEGIN for-iterating over the data entities
for entityData in entityDataList:
timepoints = entityData.timepoints
datapoints = entityData.datapoints
label = entityData.getId()
#first, get the right plotting style info for
#the current data entity:
#
#1. getting the associated entity id
if entityData.getAssociatedDataSet():
originID = entityData.getAssociatedDataSet().getId()
#if no such id
else:
originID = None
#TODO: deprecated!!!
#2. check if there is some data source id associated
# with data entity id
#if originID in self.dataSourceIDs:
# dataIndex = self.dataSourceIDs.index(originID)
#
# #2a. if there is, get the corresponding plotting style
# if dataIndex in self.plotStyle:
# plotStyle = self.plotStyle[dataIndex]
#2b. if no such style is there, take the default plotting
# # style always associated with 0-key,
# else:
# plotStyle = self.plotStyle[0]
#2c. if no such source id found, use default plotting style
#else:
# plotStyle = self.plotStyle[0]
# handle colour (prepend the colour code to style string)
if self.checkBoxOneColorPerRow.isChecked():
if label in self.plotColors: # for string-based DataSet keys (e.g. loaded data file)
color = self.plotColors[label]
elif entityData.sbmlEntity and entityData.sbmlEntity in self.plotColors: # for sbmlEntity-based DataSet keys (e.g. simulation run)
color = self.plotColors[entityData.sbmlEntity]
else:
color = "black" # default... should never happen :)
logging.debug("PlotWidgetController.setData(): Reverting to default line color. This should not happen. ID: %s" % label)
else:
if (originID, label) in self.plotColors: # for string-based DataSet keys (e.g. loaded data file)
color = self.plotColors[(originID, label)]
elif entityData.sbmlEntity and (originID, entityData.sbmlEntity) in self.plotColors: # for sbmlEntity-based DataSet keys (e.g. simulation run)
color = self.plotColors[(originID, entityData.sbmlEntity)]
else:
color = "black" # default... should never happen :)
logging.debug("PlotWidgetController.setData(): Reverting to default line color. This should not happen. ID: %s" % label)
#print 'data type: '+str((originID,label,self.title))
# 31.07.12 td
# inserted an additional space in front of plotLabel
# (in case of IDs with underscore as first character)
# 26.07.12 td
# the following line yields no originID in plot label if only one column
# is selected in sens overview...
# if len(entityDataList) > 1:
if not self.useGrayColor:
if originID and ("Sensitivity (Plot)" in self.title): # awful hack
plotLabel = " %s (%s) " % (label, originID)
else:
plotLabel = " %s " % (label)
if expPlot: markr = markerIt.next()
if 'Simulation' in self.title:
if 'Simulation' in originID:
self.axes.plot(timepoints,datapoints,color=color,linestyle='-',label=plotLabel)#,marker=markr,markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = True
else:
self.axes.plot(timepoints,datapoints,color=color,linestyle='-',marker='o',markeredgecolor='black',markerfacecolor=color,label=plotLabel)#,marker=markr,markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = False
else:
#while markr=='o': markr = markerIt.next()
self.axes.plot(timepoints,datapoints,color=color,linestyle=lineIt.next(),marker='o',markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = True
#if plotStyle == PLOT_LINE:
# self.axes.plot(timepoints, datapoints, color=color, linestyle=lineIt.next(), label=plotLabel)
#elif plotStyle == PLOT_POINT or plotStyle == PLOT_CIRCLE:
# self.axes.plot(timepoints, datapoints, color=color, linestyle= "", marker=plotStyle, label=plotLabel)
else:
if originID and ("Sensitivity (Plot)" in self.title): # awful hack
plotLabel = " %s (%s) " % (label, originID)
else:
plotLabel = " %s " % (label)
if expPlot: markr = markerIt.next()
if 'Simulation' in self.title:
if 'Simulation' in originID:
self.axes.plot(timepoints,datapoints,color=color,linestyle=lineIt.next(),marker=markr,markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = True
else:
self.axes.plot(timepoints,datapoints,color=color,linestyle=lineIt.next(),marker='o',markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = False
else:
if markr in 'o': markr = markerIt.next()
self.axes.plot(timepoints,datapoints,color=color,linestyle=lineIt.next(),marker='o',markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = True
#END for
#END for
#END if
#catch exception and write to the debug logger
except Exception as e:
logging.debug("PlotWidgetController.setData: Error occurred: %s" % e)
def computeColors(self):
"""
Takes the number of data items (e.g. Species) and computes one color for each one.
"""
#check data object present
if not self.data:
#error - info: no data source to color
logging.error("PlotWidgetController: Can't compute colors without data.")
return
try:
#check, whether the color per row checkbox is activated
if self.checkBoxOneColorPerRow.isChecked():
entityIDs = self.getEntityIDs()
#no entries - nothing to color
if not entityIDs:
return
#number of entity ids determines the number of color object to construct
#numItems = len(entityIDs)
else:
selectedSourceEntityTuples = self.getSelectedCombinations()
#numItems = len(selectedSourceEntityTuples)
#TODO: fix color item issue - only 10 items in 'spectral' though should
#TODO: be 22 ?!
#
#get the color map - one color object per item (entity)
#colors = self.map_colors(range(numItems), DEFAULT_COLORMAP)
#if self.plotStyleManager.items<numItems:
if self.checkBoxOneColorPerRow.isChecked() and entityIDs: self.plotStyleManager.setItems(len(entityIDs))
elif selectedSourceEntityTuples:self.plotStyleManager.setItems(len(selectedSourceEntityTuples))
colorIt = self.plotStyleManager.getColorIterator()
self.plotColors = {}
if self.checkBoxOneColorPerRow.isChecked():
for j, entityID in enumerate(entityIDs):
self.plotColors[entityID] = colorIt.next()
else:
for j, sourceEntityCombination in enumerate(selectedSourceEntityTuples):
self.plotColors[sourceEntityCombination] = colorIt.next()
except Exception, e:
logging.debug("PlotWidgetController.computeColors(): Error while computing colors: %s" % e)
class PlotWidgetController(AbstractViewController, Ui_PlotWidget):
"""
The controller part for a plotting widget. The UI part is declared
in plotwidget_v1.ui and then converted to ui_plotwidget.py.
This plot widget can be fed with data via set methods and has several
options to adjust the visualization of that data.
@since: 2010-11-08
"""
__author__ = "Moritz Wade"
__contact__ = "*****@*****.**"
__copyright__ = "Zuse Institute Berlin 2010"
def __init__(self, parent=None, host=None, title="Plot"):
"""
Constructor
"""
#super class constructor
super(PlotWidgetController, self).__init__(parent)
self.setupUi(self)
self.setWindowTitle(title)
self._initialize()
self.timeUnit = "a.u." #default ?
self.speciesUnit = "a.u." #default ?
self.speciesLabel = "Concentration" #default ?
if host:
self.timeUnit = str(host.optionTimeUnit)
self.speciesUnit = str(host.optionSpeciesUnit)
self.speciesLabel = str(host.optionSpeciesLabel)
#options: time unit, logarithmic y-axis and 'show legend'
# 24.2.2015 td
#options: species label, species unit
self.options = {
OPTION_LABEL_X: "Time [%s]" % (self.timeUnit), #default
OPTION_LABEL_Y: "%s [%s]" % (self.speciesLabel,self.speciesUnit), #default
OPTION_LOG_Y_AXIS: self.checkBoxLogYAxis.isChecked(),
OPTION_SHOW_LEGEND: self.checkBoxShowLegend.isChecked()
}
self.host = host
self.title = title
self.data = None
self.labels = None
self.fig = None
self.canvas = None
self.axes = None
self.mpl_toolbar = None
self.dpi = None
self.useGrayColor = False
self.plotStyleManager = PlotStyleManager()
if self.title!='Plot': self.plotStyleManager.setDataType(self.title)
self.plotStyle = {
0: PLOT_LINE} #default plot style; if there are more elements, each numbered element corresponds to one data source
self.plotColors = {} # will be filled with colors on the first plot
def _updateView(self, data=None):
'''
'''
#wrap it in a try-catch
try:
#if the data argument is not None
#assign it to the instance var data
if data:
self.data = data
if not self.fig: # on first plot
self.dpi = self.logicalDpiX()
logging.info("Plotting at %s dpi." % self.dpi)
self.fig = Figure(dpi=self.dpi)
self.canvas = FigureCanvas(self.fig)
self.axes = self.fig.add_subplot(111)
self.mpl_toolbar = NavigationToolbar(self.canvas, None)
left_vbox = QVBoxLayout(self.plotWrapper)
left_vbox.addWidget(self.canvas)
left_vbox.addWidget(self.mpl_toolbar)
self.setAxesAndData()
self.canvas.draw()
else:
self.axes.clear()
self.setAxesAndData()
self.canvas.draw()
except Exception as e:
logging.debug("PlotWidgetController._updateView: Error occurred: %s" % e)
def _clearView(self):
if self.axes:
self.axes.clear()
if self.canvas:
self.canvas.draw()
def setAxesAndData(self):
try:
#TODO: deprecated since a new plot style manager class!!!
#if not self.plotStyleManager.colorMap: self.plotStyleManager.setColorMap('spectral')
self.computeColors()
#if no color map specified yet - set default to spectral
from plotstylemanager import DATA_TYPES
if not self.plotStyleManager.dataType and self.title in DATA_TYPES:self.plotStyleManager.dataType = self.title
# some of this has to be done before the data is set
self.setAxes()
self.setData()
# has to be done after the data is set
if OPTION_SHOW_LEGEND in self.options and self.options[OPTION_SHOW_LEGEND]:
self.axes.legend()
except Exception as e:
logging.debug("PlotWidgetController.setAxesAndData: Error occurred: %s" % e)
def setAxes(self):
'''
Defines the plot's axes.
'''
try:
self.axes.clear()
self.axes.grid(True)
# set x label
if OPTION_LABEL_Y in self.options:
yLabel = str(self.options[OPTION_LABEL_Y])
else:
for entityDataList in self.data.values():
for entityData in entityDataList:
yLabel = str(entityData.getAxisLabel())
break
self.axes.set_ylabel(yLabel,fontsize="x-large")
# set y label
if OPTION_LABEL_X in self.options:
self.axes.set_xlabel(str(self.options[OPTION_LABEL_X]),fontsize="x-large")
else:
self.axes.set_xlabel("N/A")
if OPTION_LOG_Y_AXIS in self.options and self.options[OPTION_LOG_Y_AXIS]:
self.axes.set_yscale('log')
except Exception as e:
logging.debug("PlotWidgetController.setAxes: Error occurred: %s" % e)
def setData(self):
try:#wrap it in a try-catch close
#BEGIN if-if there's some data
if self.data:
#get new cyclic iterators over the marker styles, line style and color
markerIt, lineIt= self.plotStyleManager.getMarkerIterator(), self.plotStyleManager.getLineIterator()
expPlot = True
markr = None
#BEGIN for-iterating over the data values
for j, entityDataList in enumerate(sorted(self.data.values())):
#BEGIN for-iterating over the data entities
for entityData in entityDataList:
timepoints = entityData.timepoints
datapoints = entityData.datapoints
label = entityData.getId()
#first, get the right plotting style info for
#the current data entity:
#
#1. getting the associated entity id
if entityData.getAssociatedDataSet():
originID = entityData.getAssociatedDataSet().getId()
#if no such id
else:
originID = None
#TODO: deprecated!!!
#2. check if there is some data source id associated
# with data entity id
#if originID in self.dataSourceIDs:
# dataIndex = self.dataSourceIDs.index(originID)
#
# #2a. if there is, get the corresponding plotting style
# if dataIndex in self.plotStyle:
# plotStyle = self.plotStyle[dataIndex]
#2b. if no such style is there, take the default plotting
# # style always associated with 0-key,
# else:
# plotStyle = self.plotStyle[0]
#2c. if no such source id found, use default plotting style
#else:
# plotStyle = self.plotStyle[0]
# handle colour (prepend the colour code to style string)
if self.checkBoxOneColorPerRow.isChecked():
if label in self.plotColors: # for string-based DataSet keys (e.g. loaded data file)
color = self.plotColors[label]
elif entityData.sbmlEntity and entityData.sbmlEntity in self.plotColors: # for sbmlEntity-based DataSet keys (e.g. simulation run)
color = self.plotColors[entityData.sbmlEntity]
else:
color = "black" # default... should never happen :)
logging.debug("PlotWidgetController.setData(): Reverting to default line color. This should not happen. ID: %s" % label)
else:
if (originID, label) in self.plotColors: # for string-based DataSet keys (e.g. loaded data file)
color = self.plotColors[(originID, label)]
elif entityData.sbmlEntity and (originID, entityData.sbmlEntity) in self.plotColors: # for sbmlEntity-based DataSet keys (e.g. simulation run)
color = self.plotColors[(originID, entityData.sbmlEntity)]
else:
color = "black" # default... should never happen :)
logging.debug("PlotWidgetController.setData(): Reverting to default line color. This should not happen. ID: %s" % label)
#print 'data type: '+str((originID,label,self.title))
# 31.07.12 td
# inserted an additional space in front of plotLabel
# (in case of IDs with underscore as first character)
# 26.07.12 td
# the following line yields no originID in plot label if only one column
# is selected in sens overview...
# if len(entityDataList) > 1:
if not self.useGrayColor:
if originID and ("Sensitivity (Plot)" in self.title): # awful hack
plotLabel = " %s (%s) " % (label, originID)
else:
plotLabel = " %s " % (label)
if expPlot: markr = markerIt.next()
if 'Simulation' in self.title:
if 'Simulation' in originID:
self.axes.plot(timepoints,datapoints,color=color,linestyle='-',label=plotLabel)#,marker=markr,markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = True
else:
self.axes.plot(timepoints,datapoints,color=color,linestyle='-',marker='o',markeredgecolor='black',markerfacecolor=color,label=plotLabel)#,marker=markr,markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = False
elif 'Sensitivity' in self.title:
self.axes.plot(timepoints,datapoints,color=color,linestyle='-',label=plotLabel)#,marker=markr,markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = False
else: #while markr=='o': markr = markerIt.next()
self.axes.plot(timepoints,datapoints,color=color,linestyle=lineIt.next(),marker='o',markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = True
#if plotStyle == PLOT_LINE:
# self.axes.plot(timepoints, datapoints, color=color, linestyle=lineIt.next(), label=plotLabel)
#elif plotStyle == PLOT_POINT or plotStyle == PLOT_CIRCLE:
# self.axes.plot(timepoints, datapoints, color=color, linestyle= "", marker=plotStyle, label=plotLabel)
else:
if originID and ("Sensitivity (Plot)" in self.title): # awful hack
plotLabel = " %s (%s) " % (label, originID)
else:
plotLabel = " %s " % (label)
if not expPlot: markr = markerIt.next()
if 'Simulation' in self.title:
if expPlot: markr = markerIt.next()
if 'Simulation' in originID:
if markr=='o': markr = markerIt.next()
self.axes.plot(timepoints,datapoints,color=color,linestyle=lineIt.next(),marker=markr,markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = True
else:
self.axes.plot(timepoints,datapoints,color=color,linestyle=lineIt.next(),marker='o',markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = False
elif 'Sensitivity' in self.title:
self.axes.plot(timepoints,datapoints,color=color,linestyle=lineIt.next(),marker=markr,markeredgecolor='black',markerfacecolor=color,label=plotLabel)#,marker=markr,markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = False
else:
if markr in 'o': markr = markerIt.next()
self.axes.plot(timepoints,datapoints,color=color,linestyle=lineIt.next(),marker='o',markeredgecolor='black',markerfacecolor=color,label=plotLabel)
expPlot = True
#END for
#END for
#END if
#catch exception and write to the debug logger
except Exception as e:
logging.debug("PlotWidgetController.setData: Error occurred: %s" % e)
def computeColors(self):
"""
Takes the number of data items (e.g. Species) and computes one color for each one.
"""
#check data object present
if not self.data:
#error - info: no data source to color
logging.error("PlotWidgetController: Can't compute colors without data.")
return
try:
#check, whether the color per row checkbox is activated
if self.checkBoxOneColorPerRow.isChecked():
entityIDs = self.getEntityIDs()
#no entries - nothing to color
if not entityIDs:
return
#number of entity ids determines the number of color object to construct
#numItems = len(entityIDs)
else:
selectedSourceEntityTuples = self.getSelectedCombinations()
#numItems = len(selectedSourceEntityTuples)
#TODO: fix color item issue - only 10 items in 'spectral' though should
#TODO: be 22 ?!
#
#get the color map - one color object per item (entity)
#colors = self.map_colors(range(numItems), DEFAULT_COLORMAP)
#if self.plotStyleManager.items<numItems:
if self.checkBoxOneColorPerRow.isChecked() and entityIDs: self.plotStyleManager.setItems(len(entityIDs))
elif selectedSourceEntityTuples:self.plotStyleManager.setItems(len(selectedSourceEntityTuples))
colorIt = self.plotStyleManager.getColorIterator()
self.plotColors = {}
if self.checkBoxOneColorPerRow.isChecked():
for j, entityID in enumerate(entityIDs):
self.plotColors[entityID] = colorIt.next()
else:
for j, sourceEntityCombination in enumerate(selectedSourceEntityTuples):
self.plotColors[sourceEntityCombination] = colorIt.next()
except Exception, e:
logging.debug("PlotWidgetController.computeColors(): Error while computing colors: %s" % e)