def _import_from_directory(self, fname):
try:
try:
self.data = DirectoryData(unicode(fname))
except IOError as e:
em = QtGui.QErrorMessage(self)
em.setModal(True)
em.showMessage(
("Failed to open directory (%s).\n" % str(e))
+ "I will try now to import files in deprecated format.")
# If we do not call exec_ here, two dialogs may appear at
# the same time, confusing the user.
em.exec_()
self.data = OldDirectoryData(unicode(fname))
self.set_location(fname)
self.update_lists()
self.clear()
except IOError as e:
em = QtGui.QErrorMessage(self)
em.setModal(True)
em.exec_()
em.showMessage(
"Failed to open directory (%s).\n" % str(e))
class DesignerMainWindow(QtGui.QMainWindow, Ui_MainWindow):
"""Customization for Qt Designer created window"""
def __init__(self, parent = None):
# initialization of the superclass
super(DesignerMainWindow, self).__init__(parent)
# setup the GUI --> function generated by pyuic4
self.setupUi(self)
# In some lists we can select more than one item
self.speciesList.setSelectionMode(
QtGui.QAbstractItemView.ExtendedSelection)
self.reactList.setSelectionMode(
QtGui.QAbstractItemView.ExtendedSelection)
for w in [self.reactList, self.speciesList, self.speciesSourceList,
self.condList]:
w.horizontalHeader().setVisible(True)
self.plot_widgets = [self.condWidget,
self.densWidget,
self.reactWidget,
self.sourceWidget]
self.update_timer = QtCore.QTimer()
self.latest_dir = "."
# connect the signals with the slots
QtCore.QObject.connect(self.condButton,
QtCore.SIGNAL("clicked()"),
self.update_cond_graph)
QtCore.QObject.connect(self.plotButton,
QtCore.SIGNAL("clicked()"),
self.update_spec_graph)
QtCore.QObject.connect(self.sourceButton,
QtCore.SIGNAL("clicked()"),
self.update_source_graph)
QtCore.QObject.connect(self.reactButton,
QtCore.SIGNAL("clicked()"),
self.update_react_graph)
QtCore.QObject.connect(self.actionOpen,
QtCore.SIGNAL('triggered()'),
self.select_file)
QtCore.QObject.connect(self.actionStart_a_simulation,
QtCore.SIGNAL('triggered()'),
self.start_a_simulation)
QtCore.QObject.connect(self.actionImport_from_directory,
QtCore.SIGNAL('triggered()'),
self.import_from_directory)
QtCore.QObject.connect(self.actionUpdate,
QtCore.SIGNAL('triggered()'),
self.data_update)
QtCore.QObject.connect(self.actionExport_data,
QtCore.SIGNAL('triggered()'),
self.export_data)
QtCore.QObject.connect(self.actionSave,
QtCore.SIGNAL('triggered()'),
self.save_to_file)
QtCore.QObject.connect(self.actionLog_scale_in_time,
QtCore.SIGNAL('triggered()'),
self.action_set_logtime)
QtCore.QObject.connect(self.actionQuit,
QtCore.SIGNAL('triggered()'),
QtGui.qApp, QtCore.SLOT("quit()"))
QtCore.QObject.connect(self.update_timer,
QtCore.SIGNAL("timeout()"),
self.data_update)
# Drag'n'Drop. Implemented by Marc Foletto.
def dragEnterEvent(self, event):
if event.mimeData().hasUrls():
event.acceptProposedAction()
# Drag'n'Drop.
def dropEvent(self, event):
if event.mimeData().hasUrls():
for url in event.mimeData().urls():
fname = url.toLocalFile()
self.import_file_or_dir(fname)
event.acceptProposedAction()
#Chose if drop is a file or a directory
def import_file_or_dir(self, path):
if os.path.exists(path):
if os.path.isdir(path):
self._import_from_directory(path)
else:
# Let us allow the user to import files with any extension:
# if they are not in hdf5 format and exception will be raised
# anyhow.
self.load_h5file(path)
def set_location(self, location):
""" Sets the opened location. """
self.setWindowTitle("%s - QtPlaskin" % location)
self.location = location
@property
def xscale(self):
if self.actionLog_scale_in_time.isChecked():
return 'log'
else:
return 'linear'
def update_cond_graph(self):
"""Updates the graph with densities"""
try:
condition = list(iter_2_selected(self.condList))[0][0]
except AttributeError:
return
# clear the Axes
if not self.condWidget.axes:
self.condWidget.init_axes()
else:
self.condWidget.clear()
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.WaitCursor))
y = array(self.data.condition(condition))
condition_name = self.data.conditions[condition - 1]
flt = y > 0
label = CONDITIONS_PRETTY_NAMES.get(condition_name, condition_name)
self.condWidget.axes[0].plot(self.data.t[flt], y[flt], lw=LINE_WIDTH,
label=label,
zorder=10)
self.condWidget.set_scales(yscale='linear', xscale=self.xscale)
self.condWidget.axes[0].set_xlabel("t [s]")
self.condWidget.axes[0].set_ylabel(label)
# force an image redraw
self.condWidget.draw()
self.condWidget.add_data(self.data.t, y, label)
QtGui.QApplication.restoreOverrideCursor()
def update_spec_graph(self):
"""Updates the graph with densities"""
# clear the Axes
if not self.speciesList.selectedItems():
return
if not self.densWidget.axes:
self.densWidget.init_axes()
else:
self.densWidget.clear()
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.WaitCursor))
self.data.flush()
citer = cycle(COLOR_SERIES)
for item in iter_2_selected(self.speciesList):
name = item[1]
dens = self.data.density(item[0])
flt = dens > DENS_THRESHOLD
self.densWidget.axes[0].plot(self.data.t[flt], dens[flt],
lw=LINE_WIDTH,
c=citer.next(), label=name,
zorder=10)
self.densWidget.add_data(self.data.t, dens, name)
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))
# force an image redraw
self.densWidget.draw()
QtGui.QApplication.restoreOverrideCursor()
def update_source_graph(self):
"""Updates the graph with sources rates"""
try:
species = list(iter_2_selected(self.speciesSourceList))[0]
except AttributeError:
return
# clear the Axes
if not self.sourceWidget.axes:
self.sourceWidget.init_axes()
else:
self.sourceWidget.clear()
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.WaitCursor))
dreactions = self.data.sources(species[0])
reactions = dreactions.keys()
r = zeros((len(reactions), len(self.data.t)))
for i, react in enumerate(reactions):
r[i, :] = dreactions[react]
# Find the reactions that are at some point at least a delta of the total
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()]
spos = nanmax(where(r > 0, r, 0), axis=0)
fpos = r / spos
# This is b.c. numpy does not provide a nanargsort
fpos = where(isfinite(fpos), fpos, 0)
sneg = nanmin(where(r < 0, r, 0), axis=0)
fneg = r / sneg
# This is b.c. numpy does not provide a nanargsort
fneg = where(isfinite(fneg), fneg, 0)
icreation = select_rates(fpos, delta, max_rates=max_rates)
idestruct = select_rates(fneg, delta, max_rates=max_rates)
citer = cycle(COLOR_SERIES)
for i in icreation:
name = self.data.reactions[reactions[i]]
flt = abs(r[i, :]) > RATE_THRESHOLD
label = "[%d] %s" % (reactions[i] + 1, name)
self.sourceWidget.creationAx.plot(self.data.t[flt],
abs(r[i, flt]),
c=citer.next(),
lw=LINE_WIDTH,
label=label,
zorder=10)
self.sourceWidget.add_data(self.data.t, r[i, :], label)
citer = cycle(COLOR_SERIES)
for i in idestruct:
name = self.data.reactions[reactions[i]]
flt = abs(r[i, :]) > RATE_THRESHOLD
label = "[%d] %s" % (reactions[i] + 1, name)
self.sourceWidget.removalAx.plot(self.data.t[flt],
abs(r[i, flt]),
c=citer.next(),
lw=LINE_WIDTH,
label=label,
zorder=10)
self.sourceWidget.add_data(self.data.t, r[i, :], "- " + label)
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)
# force an image redraw
self.sourceWidget.draw()
QtGui.QApplication.restoreOverrideCursor()
def update_react_graph(self):
"""Updates the graph with reaction rates"""
if not self.reactList.selectedItems():
return
# clear the Axes
if not self.reactWidget.axes:
self.reactWidget.init_axes()
else:
self.reactWidget.clear()
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.WaitCursor))
citer = cycle(COLOR_SERIES)
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)
self.reactWidget.axes[0].plot(self.data.t[flt], rate[flt],
c=citer.next(),
lw=LINE_WIDTH,
label=label,
zorder=10)
self.reactWidget.add_data(self.data.t, rate, label)
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))
# force an image redraw
self.reactWidget.draw()
QtGui.QApplication.restoreOverrideCursor()
def select_file(self):
"""opens a file select dialog"""
# open the dialog and get the selected file
file = QtGui.QFileDialog.getOpenFileName(self, "Open data file",
".",
"HDF5 files (*.h5 *.hdf5);;"
"All files (*)")
# if a file is selected
if file:
try:
self.load_h5file(unicode(file))
self.set_location(file)
self.update_lists()
self.clear()
except IOError as e:
QtGui.QErrorMessage(self).showMessage(
"Failed to open file. Incorrect format? <%s>" % e)
def start_a_simulation(self):
self.data = RealtimeData('fpr_1', 'init_species.dat',
'field_constant.tsv',
max_dt=10e-3)
self.update_lists()
def import_from_directory(self):
fname = QtGui.QFileDialog.getExistingDirectory(
self, "Import data from directory",
self.latest_dir, QtGui.QFileDialog.ShowDirsOnly)
self._import_from_directory(fname)
self.latest_dir = fname
def _import_from_directory(self, fname):
try:
try:
self.data = DirectoryData(unicode(fname))
except IOError as e:
em = QtGui.QErrorMessage(self)
em.setModal(True)
em.showMessage(
("Failed to open directory (%s).\n" % str(e))
+ "I will try now to import files in deprecated format.")
# If we do not call exec_ here, two dialogs may appear at
# the same time, confusing the user.
em.exec_()
self.data = OldDirectoryData(unicode(fname))
self.set_location(fname)
self.update_lists()
self.clear()
except IOError as e:
em = QtGui.QErrorMessage(self)
em.setModal(True)
em.exec_()
em.showMessage(
"Failed to open directory (%s).\n" % str(e))
def data_update(self):
self.data.update()
self.update_cond_graph()
self.update_spec_graph()
self.update_source_graph()
self.update_react_graph()
def save_to_file(self):
"""opens a file select dialog"""
# open the dialog and get the selected file
fname = QtGui.QFileDialog.getSaveFileName(self, "Save to file",
".",
"HDF5 files (*.h5 *.hdf5);;"
"All files (*)")
# if a file is selected
if fname:
self.data.save(unicode(fname))
def export_data(self):
"""opens a file select dialog"""
# open the dialog and get the selected file
fname = QtGui.QFileDialog.getSaveFileName(self, "Export data to file",
".",
"TSV files (*.tsv);;"
"TXT files (*.txt);;"
"DAT files (*.dat);;"
"All files (*)")
# if a file is selected
if fname:
fname = unicode(fname)
self.plot_widgets[self.tabWidget.currentIndex()]\
.savedata(fname, self.location)
def action_set_logtime(self):
for w in self.plot_widgets:
w.set_scales(xscale=self.xscale, redraw=True)
def load_h5file(self, file):
self.data = HDF5Data(file)
self.update_lists()
self.clear()
def update_lists(self):
#self.species = sorted(self.data.species)
#self.reactions = sorted(self.data.reactions)
#self.conditions = sorted(self.data.conditions)
def _populate(qtable, list, pretty_names={}):
for i in xrange(qtable.rowCount()):
qtable.removeRow(0)
for n, item in enumerate(list):
row = qtable.rowCount()
qtable.insertRow(row)
# The + 1 is to move to the FORTRAN/ZdPlaskin convention
nitem = QtGui.QTableWidgetItem(u'%4d' % (n + 1))
nitem.setTextAlignment(Qt.AlignRight | Qt.AlignVCenter)
nitem.setTextColor(QtGui.QColor(160, 160, 160))
qtable.setItem(row, 0, nitem)
showed_item = pretty_names.get(item, item)
sitem = QtGui.QTableWidgetItem(showed_item)
sitem.setTextAlignment(Qt.AlignLeft | Qt.AlignVCenter)
qtable.setItem(row, 1, sitem)
_populate(self.speciesList, self.data.species)
_populate(self.speciesSourceList, self.data.species)
_populate(self.reactList, self.data.reactions)
_populate(self.condList, self.data.conditions,
pretty_names=CONDITIONS_PRETTY_NAMES)
def clear(self):
for w in self.plot_widgets:
w.clear()
def parse_file(self, filename):
pass
def start_a_simulation(self):
self.data = RealtimeData('fpr_1', 'init_species.dat',
'field_constant.tsv',
max_dt=10e-3)
self.update_lists()