def update_react_graph(self, autoscale=None):
"""Updates the graph with reaction rates
Attributes
----------
autoscale
will keep timescale from last ax unless it's the first plot. Default None.
"""
if not self.reactList.selectedItems():
return
# Get current range
former_xrange = None
if self.firstAx is not None:
former_xrange = self.firstAx.get_xlim()
# clear the Axes
if not self.reactWidget.axes:
self.reactWidget.init_axes()
else:
self.reactWidget.clear()
QtWidgets.QApplication.setOverrideCursor(QtGui.QCursor(Qt.WaitCursor))
citer = cycle(COLOR_SERIES)
lines = []
for item in iter_2_selected(self.reactList):
name = item[1]
rate = array(self.data.rate(item[0]))
flt = rate > RATE_THRESHOLD
label = "[%d] %s" % (item[0], name)
lines.append(self.reactWidget.axes[0].plot(self.data.t[flt],
rate[flt],
c=next(citer),
lw=LINE_WIDTH,
label=label,
zorder=10)[0])
self.reactWidget.add_data(self.data.t, rate, label)
self.reactWidget.rateAx.cursorlines = lines
self.datacursor(self.reactWidget, unit='cm-3/s', labname='Reaction')
self.reactWidget.set_scales(yscale='log', xscale=self.xscale)
self.reactWidget.axes[0].set_xlabel("t [s]")
self.reactWidget.axes[0].set_ylabel(
"Rate [cm$^\mathdefault{-3}$s$^\mathdefault{-1}$]")
self.reactWidget.axes[0].legend(loc=(1.025, 0.0), prop=dict(size=8))
# Reset former xrange
if former_xrange is not None:
self.reactWidget.axes[0].set_xlim(former_xrange)
self.reactWidget.axes[0].xaxis.set_major_formatter(TimeFormatter())
# force an image redraw
self.reactWidget.draw()
QtWidgets.QApplication.restoreOverrideCursor()
def update_spec_graph(self, autoscale=None):
"""Updates the graph with densities
Attributes
----------
autoscale
will keep timescale from last ax unless it's the first plot. Default None.
"""
# Get current range
former_xrange = None
if self.firstAx is not None:
former_xrange = self.firstAx.get_xlim()
# clear the Axes
if not self.speciesList.selectedItems():
return
if not self.densWidget.axes:
self.densWidget.init_axes()
else:
self.densWidget.clear()
QtWidgets.QApplication.setOverrideCursor(QtGui.QCursor(Qt.WaitCursor))
self.data.flush()
citer = cycle(COLOR_SERIES)
lines = []
# Loop over all selected species
for item in iter_2_selected(self.speciesList):
name = item[1]
dens = self.data.density(item[0])
flt = dens > DENS_THRESHOLD
lines.append(self.densWidget.axes[0].plot(self.data.t[flt],
dens[flt],
lw=LINE_WIDTH,
scalex=False,
c=next(citer),
label=name,
zorder=10)[0])
self.densWidget.add_data(self.data.t, dens, name)
self.densWidget.densAx.cursorlines = lines
self.datacursor(self.densWidget, unit='cm-3', labname='Spec.')
self.densWidget.set_scales(yscale='log', xscale=self.xscale)
self.densWidget.axes[0].set_xlabel("t [s]")
self.densWidget.axes[0].set_ylabel("Density [cm$^\mathdefault{-3}$]")
self.densWidget.axes[0].legend(loc=(1.05, 0.0), prop=dict(size=11))
# Reset former xrange
if former_xrange is not None:
self.densWidget.axes[0].set_xlim(former_xrange)
else: # autoscale to full range
self.densWidget.axes[0].autoscale(True, axis='x')
self.densWidget.axes[0].xaxis.set_major_formatter(TimeFormatter())
# force an image redraw
self.densWidget.draw()
QtWidgets.QApplication.restoreOverrideCursor()
def update_source_graph(self, autoscale=None):
"""Updates the graph with sources rates
Attributes
----------
autoscale
will keep timescale from last ax unless it's the first plot. Default None.
"""
try:
species = list(iter_2_selected(self.speciesSourceList))[0]
except AttributeError:
return
# Get current range
former_xrange = None
if self.firstAx is not None:
former_xrange = self.firstAx.get_xlim()
# clear the Axes
if not self.sourceWidget.axes:
self.sourceWidget.init_axes()
else:
self.sourceWidget.clear()
QtWidgets.QApplication.setOverrideCursor(QtGui.QCursor(Qt.WaitCursor))
filters = {
0: (0.1, -1),
1: (0.01, -1),
2: (0.001, -1),
3: (1e-4, -1),
4: (0.0, -1)
}
delta, max_rates = filters[self.Combo_filter.currentIndex()]
icreation, idestruct = select_rates(self.data,
species[0],
delta,
max_rates=max_rates)
citer = cycle(COLOR_SERIES)
lines = []
for i in icreation:
name = self.data.reactions[i - 1]
rate = array(self.data.rate(i))
flt = rate > RATE_THRESHOLD
label = "[%d] %s" % (i, name)
lines.append(
self.sourceWidget.creationAx.plot(self.data.t[flt],
rate[flt],
c=next(citer),
lw=LINE_WIDTH,
label=label,
scalex=False,
zorder=10)[0])
self.sourceWidget.add_data(self.data.t, rate, label)
self.sourceWidget.creationAx.cursorlines = lines
citer = cycle(COLOR_SERIES)
lines = []
for i in idestruct:
name = self.data.reactions[i - 1]
rate = array(self.data.rate(i))
flt = rate > RATE_THRESHOLD
label = "[%d] %s" % (i, name)
lines.append(
self.sourceWidget.removalAx.plot(self.data.t[flt],
rate[flt],
c=next(citer),
lw=LINE_WIDTH,
label=label,
scalex=False,
zorder=10)[0])
self.sourceWidget.add_data(self.data.t, rate, "- " + label)
self.sourceWidget.removalAx.cursorlines = lines
self.datacursor(self.sourceWidget, unit='cm-3/s', labname='Reac.')
self.sourceWidget.creationAx.set_ylabel(
"Production [cm$^\mathdefault{-3}$s$^\mathdefault{-1}$]")
self.sourceWidget.creationAx.legend(loc=(1.05, 0.0), prop=dict(size=9))
self.sourceWidget.removalAx.set_ylabel(
"Losses [cm$^\mathdefault{-3}$s$^\mathdefault{-1}$]")
self.sourceWidget.removalAx.set_xlabel("t [s]")
self.sourceWidget.removalAx.legend(loc=(1.05, 0.0), prop=dict(size=9))
self.sourceWidget.set_scales(yscale='log', xscale=self.xscale)
# Reset former xrange
if former_xrange is not None:
self.sourceWidget.creationAx.set_xlim(former_xrange)
# self.sourceWidget.removalAx.set_xlim(former_xrange) # synchronized already
else: # autoscale to full range
self.sourceWidget.creationAx.autoscale(True, axis='x')
self.sourceWidget.creationAx.xaxis.set_major_formatter(TimeFormatter())
self.sourceWidget.removalAx.xaxis.set_major_formatter(TimeFormatter())
# force an image redraw
self.sourceWidget.draw()
QtWidgets.QApplication.restoreOverrideCursor()
def update_cond_graph(self):
"""Updates the graph with conditions
Attributes
----------
autoscale
will keep timescale from last ax unless it's the first plot. Default None.
"""
#
# try:
# condition = list(iter_2_selected(self.condList))[0][0]
# except AttributeError:
# return
# Get current range
former_xrange = None
if self.firstAx is not None:
former_xrange = self.firstAx.get_xlim()
# clear the Axes
if not self.condWidget.axes:
self.condWidget.init_axes()
else:
self.condWidget.clear()
QtWidgets.QApplication.setOverrideCursor(QtGui.QCursor(Qt.WaitCursor))
citer = cycle(COLOR_SERIES)
lines = []
label = ''
# Loop over all selected conditions
for item in iter_2_selected(self.condList):
name = item[1]
y = array(self.data.condition(item[0]))
condition_name = self.data.conditions[item[0] - 1]
flt = logical_and(isreal(y), isfinite(y))
label = CONDITIONS_PRETTY_NAMES.get(condition_name, condition_name)
lines.append(self.condWidget.axes[0].plot(
self.data.t[flt],
y[flt],
lw=LINE_WIDTH,
label=name, #scalex=False,
zorder=10,
c=next(citer))[0])
self.condWidget.condAx.cursorlines = lines
self.datacursor(self.condWidget)
self.condWidget.set_scales(yscale='linear', xscale=self.xscale)
self.condWidget.axes[0].set_xlabel("t [s]")
self.condWidget.axes[0].set_ylabel(label)
# Reset former xrange
if former_xrange is not None:
self.condWidget.axes[0].set_xlim(former_xrange)
else: # autoscale to full range
self.condWidget.axes[0].autoscale(True, axis='x')
self.condWidget.axes[0].xaxis.set_major_formatter(TimeFormatter())
# force an image redraw
self.condWidget.draw()
self.condWidget.add_data(self.data.t, y, label)
QtWidgets.QApplication.restoreOverrideCursor()