def populate_treeview_model(self, index):
"""populate the tree view and the scroll_area when the tab is
activated"""
if not self.tab_model_already_populated and index == 3 :
self.models = Models()
# Populating the treeview with the dictionary
for model_name in self.models.get_model_names():
model = self.models.get_model(model_name)
model_item = QtGui.QTreeWidgetItem(self.ui.tree_models, 'Models')
model_item.setText(self.YEAR, model.get_year())
model_item.setText(self.AUTHORS, model.get_authors())
model_item.setText(self.TITLE, model.get_title())
model_item.setData(self.ID, 0, model.get_id())
# tooltip
cols = self.ui.tree_models.columnCount()
for i in range (cols):
tooltip = model.get_tooltip()
model_item.setToolTip(i, tooltip)
#Resizing the column.
#self.ui.tree_models.resizeColumnToContents(0)
self.ui.tree_models.resizeColumnToContents(self.YEAR)
self.ui.tree_models.resizeColumnToContents(self.TITLE)
self.ui.tree_models.resizeColumnToContents(self.ID)
self.ui.textBrowser_readme.clear()
self.ui.textBrowser_readme.insertPlainText("No model selected.")
self.tab_model_already_populated = True #we populated only once.
def __init__(self):
app = QtGui.QApplication.instance()
self.ui_dir = 'ui'
# Loading the UI
self.ui = uic.loadUi(os.path.join(os.path.dirname(__file__),
self.ui_dir,
"neuronvisio.ui"))
# Connecting
self.ui.Plot3D.connect(self.ui.Plot3D,
QtCore.SIGNAL('clicked()'), self.launch_visio)
self.ui.plot_vector_btn.connect(self.ui.plot_vector_btn,
QtCore.SIGNAL('clicked()'), self.plot_vector)
self.ui.init_btn.connect(self.ui.init_btn,
QtCore.SIGNAL('clicked()'), self.init)
self.ui.run_btn.connect(self.ui.run_btn,
QtCore.SIGNAL('clicked()'), self.run)
self.ui.dtSpinBox.connect(self.ui.dtSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.dt_changed)
self.ui.tstopSpinBox.connect(self.ui.tstopSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.tstop_changed)
self.ui.vSpinBox.connect(self.ui.vSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.v_changed)
self.ui.create_vector.connect(self.ui.create_vector,
QtCore.SIGNAL('clicked()'),
self.create_vector)
self.ui.actionAbout.connect(self.ui.actionAbout,
QtCore.SIGNAL('triggered()'),
self.about)
self.ui.timelineSlider.connect(self.ui.timelineSlider,
QtCore.SIGNAL("valueChanged(int)"),
self.on_timeline_value_changed)
self.ui.animationTime.connect(self.ui.animationTime,
QtCore.SIGNAL('returnPressed()'),
self.on_animation_time_return_pressed)
self.ui.actionLoad.connect(self.ui.actionLoad,
QtCore.SIGNAL("triggered()"),
self.load)
self.ui.actionSave.connect(self.ui.actionSave,
QtCore.SIGNAL("triggered()"),
self.save_hdf)
self.ui.tabWidget.connect(self.ui.tabWidget,
QtCore.SIGNAL('currentChanged(int)'),
self.populate_treeview_model)
self.ui.tree_models.connect(self.ui.tree_models,
QtCore.SIGNAL('itemSelectionChanged ()'),
self.select_model_treeview)
self.ui.load_model_btn.connect(self.ui.load_model_btn,
QtCore.SIGNAL('clicked()'),
self.load_selected_model)
self.ui.load_model_btn.connect(self.ui.filter_list_btn,
QtCore.SIGNAL('clicked()'),
self.filter_list)
self.ui.filter_input.connect(self.ui.filter_input,
QtCore.SIGNAL('returnPressed()'),
self.filter_list)
### Connection with the console
widgetDic = {'dt' : self.ui.dtSpinBox,
'tstop' : self.ui.tstopSpinBox,
'v_init' : self.ui.vSpinBox,
'time_label' : self.ui.time_label
}
self.timeLoop = Timeloop(widgetDic)
app.connect( self.timeLoop, QtCore.SIGNAL("updateDt(double)"), self.update_dt )
app.connect( self.timeLoop, QtCore.SIGNAL("updateTstop(double)"), self.update_tstop )
app.connect( self.timeLoop, QtCore.SIGNAL("updateVInit(double)"), self.update_v_init )
self.timeLoop.start()
### Manager class
self.manager = manager.Manager()
self.path_to_hdf = None
self.visio = None
self.tab_model_already_populated = False
self.ui.show()
# Start the main event loop.
#app.exec_()
self.AUTHORS = 1
self.YEAR = 0
self.TITLE = 2
self.ID = 3
# Dictionary to hold the models class for the ModelDb integration
self.models = Models()
class Controls(object):
"""Main class Neuronvisio"""
def __init__(self):
app = QtGui.QApplication.instance()
self.ui_dir = 'ui'
# Loading the UI
self.ui = uic.loadUi(os.path.join(os.path.dirname(__file__),
self.ui_dir,
"neuronvisio.ui"))
# Connecting
self.ui.Plot3D.connect(self.ui.Plot3D,
QtCore.SIGNAL('clicked()'), self.launch_visio)
self.ui.plot_vector_btn.connect(self.ui.plot_vector_btn,
QtCore.SIGNAL('clicked()'), self.plot_vector)
self.ui.init_btn.connect(self.ui.init_btn,
QtCore.SIGNAL('clicked()'), self.init)
self.ui.run_btn.connect(self.ui.run_btn,
QtCore.SIGNAL('clicked()'), self.run)
self.ui.dtSpinBox.connect(self.ui.dtSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.dt_changed)
self.ui.tstopSpinBox.connect(self.ui.tstopSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.tstop_changed)
self.ui.vSpinBox.connect(self.ui.vSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.v_changed)
self.ui.create_vector.connect(self.ui.create_vector,
QtCore.SIGNAL('clicked()'),
self.create_vector)
self.ui.actionAbout.connect(self.ui.actionAbout,
QtCore.SIGNAL('triggered()'),
self.about)
self.ui.timelineSlider.connect(self.ui.timelineSlider,
QtCore.SIGNAL("valueChanged(int)"),
self.on_timeline_value_changed)
self.ui.animationTime.connect(self.ui.animationTime,
QtCore.SIGNAL('returnPressed()'),
self.on_animation_time_return_pressed)
self.ui.actionLoad.connect(self.ui.actionLoad,
QtCore.SIGNAL("triggered()"),
self.load)
self.ui.actionSave.connect(self.ui.actionSave,
QtCore.SIGNAL("triggered()"),
self.save_hdf)
self.ui.tabWidget.connect(self.ui.tabWidget,
QtCore.SIGNAL('currentChanged(int)'),
self.populate_treeview_model)
self.ui.tree_models.connect(self.ui.tree_models,
QtCore.SIGNAL('itemSelectionChanged ()'),
self.select_model_treeview)
self.ui.load_model_btn.connect(self.ui.load_model_btn,
QtCore.SIGNAL('clicked()'),
self.load_selected_model)
self.ui.load_model_btn.connect(self.ui.filter_list_btn,
QtCore.SIGNAL('clicked()'),
self.filter_list)
self.ui.filter_input.connect(self.ui.filter_input,
QtCore.SIGNAL('returnPressed()'),
self.filter_list)
### Connection with the console
widgetDic = {'dt' : self.ui.dtSpinBox,
'tstop' : self.ui.tstopSpinBox,
'v_init' : self.ui.vSpinBox,
'time_label' : self.ui.time_label
}
self.timeLoop = Timeloop(widgetDic)
app.connect( self.timeLoop, QtCore.SIGNAL("updateDt(double)"), self.update_dt )
app.connect( self.timeLoop, QtCore.SIGNAL("updateTstop(double)"), self.update_tstop )
app.connect( self.timeLoop, QtCore.SIGNAL("updateVInit(double)"), self.update_v_init )
self.timeLoop.start()
### Manager class
self.manager = manager.Manager()
self.path_to_hdf = None
self.visio = None
self.tab_model_already_populated = False
self.ui.show()
# Start the main event loop.
#app.exec_()
self.AUTHORS = 1
self.YEAR = 0
self.TITLE = 2
self.ID = 3
# Dictionary to hold the models class for the ModelDb integration
self.models = Models()
def populate_treeview_model(self, index, filter=""):
"""populate the tree view and the scroll_area when the tab is
activated"""
if index == 3 and (filter or not self.tab_model_already_populated):
self.ui.tree_models.clear()
# Populating the treeview with the dictionary
for model_name in self.models.get_model_names(filter):
model = self.models.get_model(model_name)
model_item = QtGui.QTreeWidgetItem(self.ui.tree_models, 'Models')
model_item.setText(self.YEAR, model.get_year())
model_item.setText(self.AUTHORS, model.get_authors())
model_item.setText(self.TITLE, model.get_title())
model_item.setData(self.ID, 0, model.get_id())
self._set_tooltip(model, model_item)
#Resizing the column.
#self.ui.tree_models.resizeColumnToContents(0)
self.ui.tree_models.resizeColumnToContents(self.YEAR)
self.ui.tree_models.resizeColumnToContents(self.TITLE)
self.ui.tree_models.resizeColumnToContents(self.ID)
self.ui.textBrowser_readme.clear()
self.ui.textBrowser_readme.insertPlainText("No model selected.")
self.tab_model_already_populated = True #we populated only once.
def _set_tooltip(self, model, model_item):
# tooltip
cols = self.ui.tree_models.columnCount()
for i in range (cols):
tooltip = model.get_tooltip()
model_item.setToolTip(i, tooltip)
def _retrieve_selected_model(self):
"Return the model selected in the "
items = self.ui.tree_models.selectedItems()
if items:
selected_item = items[0] #first element
model_id = int(selected_item.text(self.ID))
models_name = self.models.get_model_names()
for name in models_name:
mod = self.models.get_model(name)
if model_id == mod.get_id():
return mod
else:
logging.info('No model selected!')
return None
def filter_list(self):
"Filter the models list using the given text."
filter = self.ui.filter_input.text()
logger.debug("Filtering list using keyword '%s'" %(filter))
self.populate_treeview_model(3, filter)
def about(self):
self.aboutUi = uic.loadUi(os.path.join(os.path.dirname(__file__),
self.ui_dir,
"qtAbout.ui"))
import neuronvisio
name = '<font size=24><b>Neuronvisio %s<b><font>' %neuronvisio.__version__
authors = '%s' %neuronvisio.__authors__
self.aboutUi.name.setText(name)
self.aboutUi.authors.setText(authors)
self.aboutUi.show()
def animation(self):
self.ui.timelineSlider.setRange(0, len (self.manager.groups['t']))
self.ui.timelineSlider.setEnabled(True)
self.ui.show()
def create_vector(self):
var = self.ui.var.text()
if not var:
msgBox = QtGui.QMessageBox()
msgBox.setText("No var specified.")
msgBox.setIcon(QtGui.QMessageBox.Warning)
msgBox.exec_()
else:
if self.ui.all_sections.isChecked():
allCreated = self.manager.add_all_vecRef(str(var))
elif self.ui.selected_section.isChecked():
if self.visio.selected_cyl is not None:
sec = self.visio.cyl2sec[self.visio.selected_cyl]
self.manager.add_vecRef(str(var), sec)
else:
msgBox = QtGui.QMessageBox()
msgBox.setText("<b>No vector has been created.</b>")
msg = "You need to select the section where you want to create the vector"
msgBox.setInformativeText(msg)
msgBox.setIcon(QtGui.QMessageBox.Warning)
msgBox.exec_()
self.update_tree_view()
def dt_changed(self):
h.dt = self.ui.dtSpinBox.value()
def init(self):
"""Set the vm_init from the spin button and prepare the simulator"""
if not self.manager.refs.has_key('VecRef') :
message = "No vector Created. Create at least one vector to run the simulation"
logger.info(message)
self.ui.statusbar.showMessage(message, 3500)
return False
else:
v_init = self.ui.vSpinBox.value()
# Set the v_init
h.v_init = v_init
h.finitialize(v_init)
h.fcurrent()
# Reset the time in the GUI
self.ui.time_label.setNum(h.t)
return True
def insert_item_treeview(self, groupName, section_name, vecs,
details = None):
"""Insert a new item in the treewidget.
Items are grouped by types. If a new type is provided a new group is added.
Items are then grouped by section.
In one section more than one variable is allowed.
Each variable can have a detail associated in a dictionary form """
group_root = self.get_unique_parent(groupName)
sec_root = self.get_unique_parent(section_name,
parentItem = group_root)
for var,vec in vecs.iteritems():
item = ItemRef(sec_root, vec)
item.setText(0, var)
item.setText(1, details)
sec_root.addChild(item)
def insert_refs_in_treeview(self):
for group, ref_list in self.manager.refs.iteritems():
for ref in ref_list:
self.insert_item_treeview(group,
ref.sec_name,
ref.vecs,
ref.detail)
def launch_visio(self):
msg = "Plotting..."
self.ui.statusbar.showMessage(msg, 3500)
if self.visio == None:
# Checking there are sections in the model.
i = 0
for sec in h.allsec():
i += 1
if i > 0:
self.visio = Visio(self.ui.sec_info_label, self.manager)
self.visio.draw_model()
self.ui.selected_section.setEnabled(True)
else:
msg = """No model found, no section created. You need
to have at least one."""
logger.warning(msg)
else:
#Raise the visio window
self.visio.container.show()
# Enabling the animation
try:
self.animation()
except KeyError:
# No simulation run an nothing loaded.
# just pass
pass
def load(self, path_to_file=None):
"""General loading method. It loads either an hoc file or
a hdf5 file. The file type is recognised on the extension"""
if path_to_file == None:
filename = QtGui.QFileDialog.getOpenFileName()
if filename:
path_to_file = str(filename)
base_name, file_extension = os.path.splitext(path_to_file)
if (file_extension == '.hoc'):
file_path, hoc_file = os.path.split(path_to_file)
self.load_hoc_model(file_path, hoc_file)
else:
self.load_hdf(path_to_file)
def load_hdf(self, path_to_hdf):
if path_to_hdf != None:
self.path_to_hdf=os.path.abspath(path_to_hdf)
self.manager.load_from_hdf(self.path_to_hdf)
self.update_tree_view()
msg = "Loaded db: %s" % self.path_to_hdf
self.ui.statusbar.showMessage(msg, 3500)
# Enablig the Animation button
self.animation()
# Disabling all the rest
self.ui.init_btn.setEnabled(False)
self.ui.run_btn.setEnabled(False)
self.ui.create_vector.setEnabled(False)
def load_hoc_model(self, model_dir, hoc_file):
"""Load an hoc files. It compiles the mod
before loading the hoc."""
try:
os.path.isfile(os.path.join (model_dir, hoc_file))
except IOError:
logger.error("Not existing file: %s" %e.value)
old_dir = os.path.abspath(os.getcwd())
logger.info("Path changed to %s" %(os.path.abspath(model_dir)))
if model_dir != '' :
os.chdir(model_dir)
try:
# Add all mod files into current directory
self.find_mod_files()
# If windows
if os.name == 'nt':
self.windows_compile_mod_files('.')
from neuron import h
h.nrn_load_dll('./nrnmech.dll')
else: # Anything else.
call(['nrnivmodl'])
import neuron
neuron.load_mechanisms('.') # Auto loading. Not needed anymore.
from neuron import gui # to not freeze neuron gui
from neuron import h
logger.info("Loading model in %s from %s"%(model_dir, hoc_file))
h.load_file(hoc_file)
except Exception as e:
logger.warning("Error running model: " + e.message)
logger.info("Path changed back to %s" %old_dir)
os.chdir(old_dir)
return True
def load_selected_model(self):
"Load the model selected in the treeview."
mod = self._retrieve_selected_model()
if mod:
model_path = mod.download_model()
# tooltip
cols = self.ui.tree_models.columnCount()
items = self.ui.tree_models.selectedItems()
model_item = items[0]
for i in range (cols):
tooltip = mod.get_tooltip()
model_item.setToolTip(i, tooltip)
if os.path.exists(os.path.join(mod.get_dir(), 'mosinit.hoc')):
self.load_hoc_model(mod.get_dir(), 'mosinit.hoc')
else:
path_info = "Could not locate a predefined mosinit.hoc. Can't automatically load the model. \
Check the README for hints on which hoc to use and copy it to %s/mosinit.hoc" %model_path
logging.warning(path_info)
self.ui.statusbar.showMessage(path_info, 10000)
mod.browse()
def on_animation_time_return_pressed(self):
"Getting the value from the text"
time = self.ui.animationTime.text()
try:
time = int (time)
time_list = self.manager.groups['t']
time_point_indx = 0
# If it's a vector on the just ran sim.
if hasattr(time_list, 'to_python'):
time_list = time_list.to_python()
time_list = np.around(time_list, 3)
time_point_indx = np.where(time_list==time)[0]
# If it's a numpy array saved on the disk
else:
rounded = time_list.read().round(3)
time_point_indx = np.where(rounded==time)[0]
self.sync_visio_3d(time_point_indx)
self.ui.timelineSlider.setValue(time_point_indx)
except:
logger.warning("Value not present in the array.")
def on_timeline_value_changed(self):
"""Draw the animation according to the value of the timeline"""
time_point_indx = self.ui.timelineSlider.value()
self.sync_visio_3d(time_point_indx)
def plot_vector(self):
items = self.ui.treeWidget.selectedItems()
x = None
# Plot legend if required
legend_status = self.ui.legend.isChecked() #return True if toggled.
points_status = self.ui.points.isChecked()
# Retrieve the fig num
fig_num = self.ui.fig_num_spinBox.value()
for item in items:
if item.childCount() == 0: # Leaf, so it is the variable to plot
sectionItem = item.parent()
sectionName = str(sectionItem.text(0)) #Column used
var = str(item.text(0))
detail = str(item.text(1))
groupName = str(sectionItem.parent().text(0))
x = self.manager.groups[groupName]
key = sectionName + "_" + var
vecs_to_plot = { key : item.vec}
self.manager.plot_vecs(vecs_to_plot, x=x, legend=legend_status,
figure_num=fig_num, points=points_status)
def get_unique_parent(self, name, parentItem = None):
"""Search the name in the treeview and return the qtElement.
Raise an exception if not unique"""
search = self.ui.treeWidget.findItems(name ,
Qt.MatchFixedString)
root_item = None
if len(search) == 0: # We create the group
root_item = None
if parentItem is None:
root_item = QtGui.QTreeWidgetItem(self.ui.treeWidget)
else:
root_item = QtGui.QTreeWidgetItem(parentItem)
root_item.setText(0, name)
elif len(search) == 1:
root_item = search[0]
else:
error = "ERROR - too many match: %d. Group Name not \
unique." %len(search)
raise NameError(error)
return root_item
def run(self):
"""Run the simulator till tstop"""
#Initializing
if self.init():
# Run
msg = "Running simulation. It will take a while maybe..."
self.ui.statusbar.showMessage(msg, 5000)
while h.t < h.tstop:
h.fadvance()
self.ui.time_label.setText("<b>" + str(h.t) + "</b>")
self.animation()
def save_hdf(self):
if not self.path_to_hdf:
filename = QtGui.QFileDialog.getSaveFileName()
self.path_to_hdf = str(filename) # It will go with python 3
if self.path_to_hdf != None:
self.manager.save_to_hdf(self.path_to_hdf)
msg = "Saved hdf file: %s" % self.path_to_hdf
self.ui.statusbar.showMessage(msg, 3500)
def select_model_treeview(self):
"""Synch the README and the modelOverview with the selected model."""
mod = self._retrieve_selected_model()
if mod:
readme = mod.get_readme_html()
overview = mod.get_overview()
self.ui.textBrowser_readme.clear()
self.ui.textBrowser_readme.insertHtml(readme)
self.ui.textBrowser_model_overview.clear()
self.ui.textBrowser_model_overview.insertHtml(overview)
def select_sections(self, list_of_sections):
"""Select an arbitrary number of sections from the
command line.
:param: list_of_section - the list of sections to select. Each section should
be given by the name (sec.name() from Neuron point
of view.
"""
if self.visio is not None:
selection_scalar = self.visio.get_selection_scalar(list_of_sections)
self.visio.redraw_color(selection_scalar, 'v')
self.visio.update_sections_info(list_of_sections)
else:
logger.warning("You have to launch the 3D Visio window first!")
def sync_visio_3d(self, time_point_indx):
var = self.ui.varToShow.text()
var = str(var) # This will go with Py3
#
# #Update the label on the scale
if len (self.manager.groups['t']) == time_point_indx:
time_point_indx = time_point_indx - 1 # Avoid to go out of scale
time = self.manager.groups['t'][time_point_indx]
self.ui.animationTime.setText(str(time))
start_value = float(self.ui.startValue.text())
end_value = float(self.ui.endValue.text())
self.visio.show_variable_timecourse(var, time_point_indx,
start_value, end_value)
def tstop_changed(self):
h.tstop = self.ui.tstopSpinBox.value()
def update_dt(self, new_dt):
self.ui.dtSpinBox.setValue(new_dt)
def update_tree_view(self):
# Fill the treeview wit all the vectors created
#Clear all the row
self.ui.treeWidget.clear()
self.insert_refs_in_treeview()
def update_tstop(self, new_tstop):
self.ui.tstopSpinBox.setValue(new_tstop)
def update_v_init(self, new_v_init):
self.ui.vSpinBox.setValue(new_v_init)
def v_changed(self):
h.v_init = self.ui.vSpinBox.value()
# create the command line to compile mod files into nrnmech.dll and launch it. command line is
# <cygwin-dir>\bin\bash.exe -c "cd <model-dir>; /usr/bin/sh -c '<nrnhome>/lib/mknrndll.sh <nrnhome>'"
def windows_compile_mod_files(self, model_dir):
# Get the required pathes
if os.environ.has_key('NEURONHOME'):
s1=os.environ['NEURONHOME']
s2=os.environ['NEURONHOME']
else:
import _winreg
k1=_winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "SOFTWARE\\Cygwin\\setup")
s1=_winreg.QueryValueEx(k1, 'rootdir')[0]
_winreg.CloseKey(k1)
k2=_winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "SOFTWARE\\NEURON\\nrn72")
s2=_winreg.QueryValueEx(k2, 'Install_Dir')[0]
_winreg.CloseKey(k2)
s1u=s1.replace('\\', '/')
s2u=s2.replace('\\', '/')
cmd=s1+"\\bin\\bash.exe"
arg="cd "+model_dir+";"+s1u+"/bin/sh -c '" + s2u + "/lib/mknrndll.sh " + s2u + "'"
import subprocess
subprocess.Popen([cmd, '-c', arg], stdin=subprocess.PIPE).communicate(input="\r\n")
# Copy all mod files under model directory into the root directory
def find_mod_files(self):
import shutil
mod_files = []
for root, dirnames, filenames in os.walk('.'):
if (root == '.'): continue
for filename in filenames:
base_name, file_extension = os.path.splitext(filename)
if file_extension == '.mod':
logger.info('Copy %s into model directory'%os.path.join(root, filename))
# Double checking we are not copying over the same file.
logger.debug("%s %s" %(root, filename))
filename_src = os.path.join(root, filename)
filename_dest = os.path.join('.', filename)
if not os.path.isfile(filename_dest):
shutil.copy(filename_src, filename_dest)
class Controls(object):
"""Main class Neuronvisio"""
def __init__(self):
dynamic_neuron_home()
app = QtGui.QApplication.instance()
self.ui_dir = "ui"
# Loading the UI
self.ui = uic.loadUi(os.path.join(os.path.dirname(__file__), self.ui_dir, "neuronvisio.ui"))
# Connecting
self.ui.Plot3D.connect(self.ui.Plot3D, QtCore.SIGNAL("clicked()"), self.launch_visio)
self.ui.plot_vector_btn.connect(self.ui.plot_vector_btn, QtCore.SIGNAL("clicked()"), self.plot_vector)
self.ui.init_btn.connect(self.ui.init_btn, QtCore.SIGNAL("clicked()"), self.init)
self.ui.run_btn.connect(self.ui.run_btn, QtCore.SIGNAL("clicked()"), self.run)
self.ui.dtSpinBox.connect(self.ui.dtSpinBox, QtCore.SIGNAL("valueChanged(double)"), self.dt_changed)
self.ui.tstopSpinBox.connect(self.ui.tstopSpinBox, QtCore.SIGNAL("valueChanged(double)"), self.tstop_changed)
self.ui.vSpinBox.connect(self.ui.vSpinBox, QtCore.SIGNAL("valueChanged(double)"), self.v_changed)
self.ui.create_vector.connect(self.ui.create_vector, QtCore.SIGNAL("clicked()"), self.create_vector)
self.ui.actionAbout.connect(self.ui.actionAbout, QtCore.SIGNAL("triggered()"), self.about)
self.ui.timelineSlider.connect(
self.ui.timelineSlider, QtCore.SIGNAL("valueChanged(int)"), self.on_timeline_value_changed
)
self.ui.animationTime.connect(
self.ui.animationTime, QtCore.SIGNAL("returnPressed()"), self.on_animation_time_return_pressed
)
self.ui.actionLoad.connect(self.ui.actionLoad, QtCore.SIGNAL("triggered()"), self.load)
self.ui.actionSave.connect(self.ui.actionSave, QtCore.SIGNAL("triggered()"), self.save_hdf)
self.ui.tabWidget.connect(self.ui.tabWidget, QtCore.SIGNAL("currentChanged(int)"), self.populate_treeview_model)
self.ui.tree_models.connect(
self.ui.tree_models, QtCore.SIGNAL("itemSelectionChanged ()"), self.select_model_treeview
)
self.ui.load_model_btn.connect(self.ui.load_model_btn, QtCore.SIGNAL("clicked()"), self.load_selected_model)
self.ui.load_model_btn.connect(self.ui.filter_list_btn, QtCore.SIGNAL("clicked()"), self.filter_list)
self.ui.filter_input.connect(self.ui.filter_input, QtCore.SIGNAL("returnPressed()"), self.filter_list)
### Connection with the console
widgetDic = {
"dt": self.ui.dtSpinBox,
"tstop": self.ui.tstopSpinBox,
"v_init": self.ui.vSpinBox,
"time_label": self.ui.time_label,
}
self.timeLoop = Timeloop(widgetDic)
app.connect(self.timeLoop, QtCore.SIGNAL("updateDt(double)"), self.update_dt)
app.connect(self.timeLoop, QtCore.SIGNAL("updateTstop(double)"), self.update_tstop)
app.connect(self.timeLoop, QtCore.SIGNAL("updateVInit(double)"), self.update_v_init)
self.timeLoop.start()
### Manager class
self.manager = manager.Manager()
self.path_to_hdf = None
self.visio = None
self.tab_model_already_populated = False
self.ui.show()
# Start the main event loop.
# app.exec_()
self.AUTHORS = 1
self.YEAR = 0
self.TITLE = 2
self.ID = 3
# Dictionary to hold the models class for the ModelDb integration
self.models = Models()
def populate_treeview_model(self, index, filter=""):
"""Populate the tree view on the gui and the scroll_area when the tab is
activated.
Args:
index (int): the index of the activated tab
filter (string): the string used to filter the search on the treeview
"""
if index == 3 and (filter or not self.tab_model_already_populated):
self.ui.tree_models.clear()
# Populating the treeview with the dictionary
for model_name in self.models.get_model_names(filter):
model = self.models.get_model(model_name)
model_item = QtGui.QTreeWidgetItem(self.ui.tree_models, "Models")
model_item.setText(self.YEAR, model.get_year())
model_item.setText(self.AUTHORS, model.get_authors())
model_item.setText(self.TITLE, model.get_title())
model_item.setData(self.ID, 0, model.get_id())
self._set_tooltip(model, model_item)
# Resizing the column.
# self.ui.tree_models.resizeColumnToContents(0)
self.ui.tree_models.resizeColumnToContents(self.YEAR)
self.ui.tree_models.resizeColumnToContents(self.TITLE)
self.ui.tree_models.resizeColumnToContents(self.ID)
self.ui.textBrowser_readme.clear()
self.ui.textBrowser_readme.insertPlainText("No model selected.")
self.tab_model_already_populated = True # we populated only once.
def _set_tooltip(self, model, model_item):
# tooltip
cols = self.ui.tree_models.columnCount()
for i in range(cols):
tooltip = model.get_tooltip()
model_item.setToolTip(i, tooltip)
def _retrieve_selected_model(self):
"Return the model selected in the treeview"
items = self.ui.tree_models.selectedItems()
if items:
selected_item = items[0] # first element
model_id = int(selected_item.text(self.ID))
models_name = self.models.get_model_names()
for name in models_name:
mod = self.models.get_model(name)
if model_id == mod.get_id():
return mod
else:
logger.info("No model selected!")
return None
def filter_list(self):
"Filter the models list using the given text in the filter box"
filter = self.ui.filter_input.text()
logger.debug("Filtering list using keyword '%s'" % (filter))
self.populate_treeview_model(3, filter)
def about(self):
self.aboutUi = uic.loadUi(os.path.join(os.path.dirname(__file__), self.ui_dir, "qtAbout.ui"))
import neuronvisio
name = "<font size=24><b>Neuronvisio %s<b><font>" % neuronvisio.__version__
authors = "%s" % neuronvisio.__authors__
self.aboutUi.name.setText(name)
self.aboutUi.authors.setText(authors)
self.aboutUi.show()
def animation(self):
self.ui.timelineSlider.setRange(0, len(self.manager.groups["t"]))
self.ui.timelineSlider.setEnabled(True)
self.ui.show()
def create_vector(self):
var = self.ui.var.text()
if not var:
msgBox = QtGui.QMessageBox()
msgBox.setText("No var specified.")
msgBox.setIcon(QtGui.QMessageBox.Warning)
msgBox.exec_()
else:
if self.ui.all_sections.isChecked():
allCreated = self.manager.add_all_vecRef(str(var))
elif self.ui.selected_section.isChecked():
if self.visio.selected_cyl is not None:
sec = self.visio.cyl2sec[self.visio.selected_cyl]
self.manager.add_vecRef(str(var), sec)
else:
msgBox = QtGui.QMessageBox()
msgBox.setText("<b>No vector has been created.</b>")
msg = "You need to select the section where you want to create the vector"
msgBox.setInformativeText(msg)
msgBox.setIcon(QtGui.QMessageBox.Warning)
msgBox.exec_()
self.update_tree_view()
def dt_changed(self):
h.dt = self.ui.dtSpinBox.value()
def init(self):
"""Set the vm_init from the spin button and prepare the simulator"""
if not self.manager.refs.has_key("VecRef"):
message = "No vector Created. Create at least one vector to run the simulation"
logger.info(message)
self.ui.statusbar.showMessage(message, 3500)
return False
else:
v_init = self.ui.vSpinBox.value()
# Set the v_init
h.v_init = v_init
h.finitialize(v_init)
h.fcurrent()
# Reset the time in the GUI
self.ui.time_label.setNum(h.t)
return True
def insert_item_treeview(self, groupName, section_name, vecs, details=None):
"""Insert a new item in the treewidget.
Items are grouped by types. If a new type is provided a new group is added.
Items are then grouped by section.
In one section more than one variable is allowed.
Each variable can have a detail associated in a dictionary form """
group_root = self.get_unique_parent(groupName)
sec_root = self.get_unique_parent(section_name, parentItem=group_root)
for var, vec in vecs.iteritems():
item = ItemRef(sec_root, vec)
item.setText(0, var)
item.setText(1, details)
sec_root.addChild(item)
def insert_refs_in_treeview(self):
for group, ref_list in self.manager.refs.iteritems():
for ref in ref_list:
self.insert_item_treeview(group, ref.sec_name, ref.vecs, ref.detail)
def launch_visio(self):
msg = "Plotting..."
self.ui.statusbar.showMessage(msg, 3500)
if self.visio == None:
# Checking there are sections in the model.
i = 0
for sec in h.allsec():
i += 1
if i > 0:
self.visio = Visio(self.ui.sec_info_label, self.manager)
self.visio.draw_model()
self.ui.selected_section.setEnabled(True)
else:
msg = """No model found, no section created. You need
to have at least one."""
logger.warning(msg)
else:
# Raise the visio window
self.visio.container.show()
# Enabling the animation
try:
self.animation()
except KeyError:
# No simulation run an nothing loaded.
# just pass
pass
def load(self, path_to_file=None):
"""
General loading method for any kind of format.
Extensions recognised:
.xml - NeuroML
.hoc - NEURON hoc file
.h5 - HDF file formatted according to Neuronvisio format.
The file type is recognised using the extension.
"""
if path_to_file == None:
filename = QtGui.QFileDialog.getOpenFileName()
if filename:
path_to_file = str(filename)
base_name, file_extension = os.path.splitext(path_to_file)
try:
if file_extension == ".hoc":
file_path, hoc_file = os.path.split(path_to_file)
self.load_hoc_model(file_path, hoc_file)
elif file_extension == ".xml":
self.manager.load_neuroml(path_to_file)
elif file_extension == ".h5":
self.load_hdf(path_to_file)
else:
raise ExtensionNotRecognised
except ExtensionNotRecognised:
msg = """
File extension not recognised!!
Neuronvisio was not able to recognise the file extension.
Extensions recognised:
.xml - NeuroML
.hoc - NEURON hoc file
.h5 - HDF file formatted according to Neuronvisio format.
"""
logger.error(msg)
def load_hdf(self, path_to_hdf):
if path_to_hdf != None:
self.path_to_hdf = os.path.abspath(path_to_hdf)
self.manager.load_from_hdf(self.path_to_hdf)
self.update_tree_view()
msg = "Loaded db: %s" % self.path_to_hdf
self.ui.statusbar.showMessage(msg, 3500)
# Enablig the Animation button
self.animation()
# Disabling all the rest
self.ui.init_btn.setEnabled(False)
self.ui.run_btn.setEnabled(False)
self.ui.create_vector.setEnabled(False)
def load_hoc_model(self, model_dir, hoc_file):
"""Load an hoc files. It compiles the mod
before loading the hoc."""
try:
os.path.isfile(os.path.join(model_dir, hoc_file))
except IOError:
logger.error("Not existing file: %s" % e.value)
old_dir = os.path.abspath(os.getcwd())
logger.info("Path changed to %s" % (os.path.abspath(model_dir)))
if model_dir != "":
os.chdir(model_dir)
try:
# Add all mod files into current directory
self.find_mod_files()
# If windows
if os.name == "nt":
self.windows_compile_mod_files(".")
from neuron import h
h.nrn_load_dll("./nrnmech.dll")
else: # Anything else.
call(["nrnivmodl"])
import neuron
neuron.load_mechanisms(".") # Auto loading. Not needed anymore.
from neuron import gui # to not freeze neuron gui
from neuron import h
logger.info("Loading model in %s from %s" % (model_dir, hoc_file))
h.load_file(hoc_file)
except Exception as e:
logger.warning("Error running model: " + e.message)
logger.info("Path changed back to %s" % old_dir)
os.chdir(old_dir)
return True
def load_selected_model(self):
"Load the model selected in the treeview."
mod = self._retrieve_selected_model()
if mod:
model_path = mod.download_model()
# tooltip
cols = self.ui.tree_models.columnCount()
items = self.ui.tree_models.selectedItems()
model_item = items[0]
for i in range(cols):
tooltip = mod.get_tooltip()
model_item.setToolTip(i, tooltip)
if os.path.exists(os.path.join(mod.get_dir(), "mosinit.hoc")):
self.load_hoc_model(mod.get_dir(), "mosinit.hoc")
else:
log_warning = """No mosinit.hoc present. I can't locate the `mosinit.hoc` therefore I can't load automatically the model."""
logger.warning(log_warning)
self.ui.statusbar.showMessage("WARNING: Can't load the model automatically.", 10000)
info_warning = """<h3>No <code>mosinit.hoc</code> present!</h3>
<p>I couldn't find any <code>mosinit.hoc</code>, therefore I have no idea how to
load this model.</p>
<p>What I can do is to open the folder where the model has been downloaded.
Then, you need to read the docs of the model to know which file you need to load
to get the model up.</p>
<p>How to load an arbitrary hoc file with Neuronvisio is written on the docs:
<a href='http://neuronvisio.org/gettingstarted.html#loading-a-file'>Loading a file</a></p>
"""
warning_box = QtGui.QMessageBox()
warning_box.setTextFormat(QtCore.Qt.RichText)
warning_box.setText(info_warning)
warning_box.exec_()
mod.browse()
def make_animation_screenshots(self, time_start, time_stop=None, saving_dir="anim"):
"""Creates a series of screenshots which can be put together using memcoder
to make a movie
Args:
time_start (float): time from where to start to take the screenshots
time_stop (float): time where to stop. If None will continue till the end
saving_dir (string): directory where to save the screenshots. Default is anim
"""
from mayavi import mlab
t = self.manager.get_time()
indx_start = t.indwhere("==", time_start)
indx_stop = None
if time_stop:
indx_stop = t.indwhere("==", time_stop)
else:
indx_stop = len(t)
if not os.path.exists(saving_dir):
os.mkdir(saving_dir)
png_format = "%09d.png"
for i in range(int(indx_start), int(indx_stop)):
figure_filename_animation = png_format % (i - indx_start)
logger.debug(figure_filename_animation)
self.sync_visio_3d(i)
mlab.savefig(os.path.join(saving_dir, figure_filename_animation))
logger.info("files created in %s" % saving_dir)
logger.info("To create a video run:")
logger.info("ffmpeg -f image2 -r 10 -i %s -sameq anim.mov -pass 2" % png_format)
def on_animation_time_return_pressed(self):
"Getting the value from the text"
time = self.ui.animationTime.text()
try:
time = int(time)
time_list = self.manager.groups["t"]
time_point_indx = 0
# If it's a vector on the just ran sim.
if hasattr(time_list, "to_python"):
time_list = time_list.to_python()
time_list = np.around(time_list, 3)
time_point_indx = np.where(time_list == time)[0]
# If it's a numpy array saved on the disk
else:
rounded = time_list.read().round(3)
time_point_indx = np.where(rounded == time)[0]
self.sync_visio_3d(time_point_indx)
self.ui.timelineSlider.setValue(time_point_indx)
except:
logger.warning("Value not present in the array.")
def on_timeline_value_changed(self):
"""Draw the animation according to the value of the timeline"""
time_point_indx = self.ui.timelineSlider.value()
self.sync_visio_3d(time_point_indx)
def plot_vector(self):
items = self.ui.treeWidget.selectedItems()
x = None
# Plot legend if required
legend_status = self.ui.legend.isChecked() # return True if toggled.
points_status = self.ui.points.isChecked()
# Retrieve the fig num
fig_num = self.ui.fig_num_spinBox.value()
for item in items:
if item.childCount() == 0: # Leaf, so it is the variable to plot
sectionItem = item.parent()
sectionName = str(sectionItem.text(0)) # Column used
var = str(item.text(0))
detail = str(item.text(1))
groupName = str(sectionItem.parent().text(0))
x = self.manager.groups[groupName]
key = sectionName + "_" + var
vecs_to_plot = {key: item.vec}
self.manager.plot_vecs(
vecs_to_plot, x=x, legend=legend_status, figure_num=fig_num, points=points_status
)
def get_unique_parent(self, name, parentItem=None):
"""Search the name in the treeview and return the qtElement.
Raise an exception if not unique"""
search = self.ui.treeWidget.findItems(name, Qt.MatchFixedString)
root_item = None
if len(search) == 0: # We create the group
root_item = None
if parentItem is None:
root_item = QtGui.QTreeWidgetItem(self.ui.treeWidget)
else:
root_item = QtGui.QTreeWidgetItem(parentItem)
root_item.setText(0, name)
elif len(search) == 1:
root_item = search[0]
else:
error = (
"ERROR - too many match: %d. Group Name not \
unique."
% len(search)
)
raise NameError(error)
return root_item
def run(self):
"""Run the simulator till tstop"""
# Initializing
if self.init():
# Run
msg = "Running simulation. It will take a while maybe..."
self.ui.statusbar.showMessage(msg, 5000)
while h.t < h.tstop:
h.fadvance()
self.ui.time_label.setText("<b>" + str(h.t) + "</b>")
self.animation()
def save_hdf(self):
if not self.path_to_hdf:
filename = QtGui.QFileDialog.getSaveFileName()
self.path_to_hdf = str(filename) # It will go with python 3
if self.path_to_hdf != None:
self.manager.save_to_hdf(self.path_to_hdf)
msg = "Saved hdf file: %s" % self.path_to_hdf
self.ui.statusbar.showMessage(msg, 3500)
def select_model_treeview(self):
"""Synch the README and the modelOverview with the selected model."""
mod = self._retrieve_selected_model()
if mod:
readme = mod.get_readme_html()
overview = mod.get_overview()
self.ui.textBrowser_readme.clear()
self.ui.textBrowser_readme.insertHtml(readme)
self.ui.textBrowser_model_overview.clear()
self.ui.textBrowser_model_overview.insertHtml(overview)
def sync_visio_3d(self, time_point_indx):
var = self.ui.varToShow.text()
var = str(var) # This will go with Py3
#
# #Update the label on the scale
if len(self.manager.groups["t"]) == time_point_indx:
time_point_indx = time_point_indx - 1 # Avoid to go out of scale
time = self.manager.groups["t"][time_point_indx]
time_point_string = "%.3f" % round(time, 3)
self.ui.animationTime.setText(time_point_string)
start_value = float(self.ui.startValue.text())
end_value = float(self.ui.endValue.text())
self.visio.show_variable_timecourse(var, time_point_indx, start_value, end_value)
def tstop_changed(self):
h.tstop = self.ui.tstopSpinBox.value()
def update_dt(self, new_dt):
self.ui.dtSpinBox.setValue(new_dt)
def update_tree_view(self):
# Fill the treeview wit all the vectors created
# Clear all the row
self.ui.treeWidget.clear()
self.insert_refs_in_treeview()
def update_tstop(self, new_tstop):
self.ui.tstopSpinBox.setValue(new_tstop)
def update_v_init(self, new_v_init):
self.ui.vSpinBox.setValue(new_v_init)
def v_changed(self):
h.v_init = self.ui.vSpinBox.value()
# create the command line to compile mod files into nrnmech.dll and launch it. command line is
# <cygwin-dir>\bin\bash.exe -c "cd <model-dir>; /usr/bin/sh -c '<nrnhome>/lib/mknrndll.sh <nrnhome>'"
def windows_compile_mod_files(self, model_dir):
# Get the required pathes
if os.environ.has_key("NEURONHOME"):
s1 = os.environ["NEURONHOME"]
s2 = os.environ["NEURONHOME"]
else:
import _winreg
k1 = _winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "SOFTWARE\\Cygwin\\setup")
s1 = _winreg.QueryValueEx(k1, "rootdir")[0]
_winreg.CloseKey(k1)
k2 = _winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "SOFTWARE\\NEURON\\nrn72")
s2 = _winreg.QueryValueEx(k2, "Install_Dir")[0]
_winreg.CloseKey(k2)
s1u = s1.replace("\\", "/")
s2u = s2.replace("\\", "/")
cmd = s1 + "\\bin\\bash.exe"
arg = "cd " + model_dir + ";" + s1u + "/bin/sh -c '" + s2u + "/lib/mknrndll.sh " + s2u + "'"
import subprocess
subprocess.Popen([cmd, "-c", arg], stdin=subprocess.PIPE).communicate(input="\r\n")
# Copy all mod files under model directory into the root directory
def find_mod_files(self):
import shutil
mod_files = []
for root, dirnames, filenames in os.walk("."):
if root == ".":
continue
for filename in filenames:
base_name, file_extension = os.path.splitext(filename)
if file_extension == ".mod":
logger.info("Copy %s into model directory" % os.path.join(root, filename))
# Double checking we are not copying over the same file.
logger.debug("%s %s" % (root, filename))
filename_src = os.path.join(root, filename)
filename_dest = os.path.join(".", filename)
if not os.path.isfile(filename_dest):
shutil.copy(filename_src, filename_dest)
class Controls():
"""Main class Neuronvisio"""
def __init__(self):
app = QtGui.QApplication.instance()
self.ui_dir = 'ui'
# Loading the UI
self.ui = uic.loadUi(os.path.join(os.path.dirname(__file__),
self.ui_dir,
"neuronvisio.ui"))
# Connecting
self.ui.Plot3D.connect(self.ui.Plot3D,
QtCore.SIGNAL('clicked()'), self.launch_visio)
self.ui.plot_vector_btn.connect(self.ui.plot_vector_btn,
QtCore.SIGNAL('clicked()'), self.plot_vector)
self.ui.init_btn.connect(self.ui.init_btn,
QtCore.SIGNAL('clicked()'), self.init)
self.ui.run_btn.connect(self.ui.run_btn,
QtCore.SIGNAL('clicked()'), self.run)
self.ui.dtSpinBox.connect(self.ui.dtSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.dt_changed)
self.ui.tstopSpinBox.connect(self.ui.tstopSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.tstop_changed)
self.ui.vSpinBox.connect(self.ui.vSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.v_changed)
self.ui.create_vector.connect(self.ui.create_vector,
QtCore.SIGNAL('clicked()'),
self.create_vector)
self.ui.actionAbout.connect(self.ui.actionAbout,
QtCore.SIGNAL('triggered()'),
self.about)
self.ui.timelineSlider.connect(self.ui.timelineSlider,
QtCore.SIGNAL("valueChanged(int)"),
self.on_timeline_value_changed)
self.ui.animationTime.connect(self.ui.animationTime,
QtCore.SIGNAL('returnPressed()'),
self.on_animation_time_return_pressed)
self.ui.actionLoad.connect(self.ui.actionLoad,
QtCore.SIGNAL("triggered()"),
self.load_hdf)
self.ui.actionSave.connect(self.ui.actionSave,
QtCore.SIGNAL("triggered()"),
self.save_hdf)
self.ui.tabWidget.connect(self.ui.tabWidget,
QtCore.SIGNAL('currentChanged(int)'),
self.populate_treeview_model)
self.ui.tree_models.connect(self.ui.tree_models,
QtCore.SIGNAL('itemSelectionChanged ()'),
self.select_model_treeview)
self.ui.load_model_btn.connect(self.ui.load_model_btn,
QtCore.SIGNAL('clicked()'),
self.load_selected_model)
### Connection with the console
widgetDic = {'dt' : self.ui.dtSpinBox,
'tstop' : self.ui.tstopSpinBox,
'v_init' : self.ui.vSpinBox,
'time_label' : self.ui.time_label
}
self.timeLoop = Timeloop(widgetDic)
self.timeLoop.start()
### Manager class
self.manager = manager.Manager()
self.path_to_hdf = None
self.visio = None
self.tab_model_already_populated = False
self.ui.show()
# Start the main event loop.
#app.exec_()
self.AUTHORS = 1
self.YEAR = 0
self.TITLE = 2
self.ID = 3
# Dictionary to old the models class for the ModelDb integration
self.models = None
def populate_treeview_model(self, index):
"""populate the tree view and the scroll_area when the tab is
activated"""
if not self.tab_model_already_populated and index == 3 :
self.models = Models()
# Populating the treeview with the dictionary
for model_name in self.models.get_model_names():
model = self.models.get_model(model_name)
model_item = QtGui.QTreeWidgetItem(self.ui.tree_models, 'Models')
model_item.setText(self.YEAR, model.get_year())
model_item.setText(self.AUTHORS, model.get_authors())
model_item.setText(self.TITLE, model.get_title())
model_item.setData(self.ID, 0, model.get_id())
# tooltip
cols = self.ui.tree_models.columnCount()
for i in range (cols):
tooltip = model.get_tooltip()
model_item.setToolTip(i, tooltip)
#Resizing the column.
#self.ui.tree_models.resizeColumnToContents(0)
self.ui.tree_models.resizeColumnToContents(self.YEAR)
self.ui.tree_models.resizeColumnToContents(self.TITLE)
self.ui.tree_models.resizeColumnToContents(self.ID)
self.ui.textBrowser_readme.clear()
self.ui.textBrowser_readme.insertPlainText("No model selected.")
self.tab_model_already_populated = True #we populated only once.
def select_model_treeview(self):
"""Synch the README and the modelOverview with the selected model."""
mod = self._retrieve_selected_model()
if mod:
readme = mod.get_readme_html()
overview = mod.get_overview()
self.ui.textBrowser_readme.clear()
self.ui.textBrowser_readme.insertHtml(readme)
self.ui.textBrowser_model_overview.clear()
self.ui.textBrowser_model_overview.insertHtml(overview)
def _retrieve_selected_model(self):
"Return the model selected in the "
items = self.ui.tree_models.selectedItems()
if items:
selected_item = items[0] #first element
model_id = int(selected_item.text(self.ID))
models_name = self.models.get_model_names()
for name in models_name:
mod = self.models.get_model(name)
if model_id == mod.get_id():
return mod
else:
logging.info('No model selected!')
return None
def load_selected_model(self):
"Load the model selected in the treeview."
mod = self._retrieve_selected_model()
if mod:
model_path = mod.download_model()
# tooltip
cols = self.ui.tree_models.columnCount()
items = self.ui.tree_models.selectedItems()
model_item = items[0]
for i in range (cols):
tooltip = mod.get_tooltip()
model_item.setToolTip(i, tooltip)
self.run_extracted_model(mod)
# create the command line to compile mod files into nrnmech.dll and launch it. command line is
# <cygwin-dir>\bin\bash.exe -c "cd <model-dir>; /usr/bin/sh -c '<nrnhome>/lib/mknrndll.sh <nrnhome>'"
def windows_compile_mod_files(self, model_dir):
import _winreg
k1=_winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "SOFTWARE\\Cygwin\\setup")
s1=_winreg.QueryValueEx(k1, 'rootdir')[0]
_winreg.CloseKey(k1)
k2=_winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "SOFTWARE\\NEURON\\nrn72")
s2=_winreg.QueryValueEx(k2, 'Install_Dir')[0]
s2=s2.replace('\\', '/')
_winreg.CloseKey(k2)
cmd=s1+"\\bin\\bash.exe"
arg="cd "+model_dir+";/usr/bin/sh -c '" + s2 + "/lib/mknrndll.sh " + s2 + "'"
import subprocess
subprocess.Popen([cmd, '-c', arg], stdin=subprocess.PIPE).communicate(input="\r\n")
def run_extracted_model(self, mod):
model_dir = mod.get_dir()
if os.path.exists(os.path.join (model_dir, 'mosinit.hoc')):
old_dir = os.path.abspath(os.getcwd())
logger.info("Path changed to %s" %(os.path.abspath(model_dir)))
os.chdir(model_dir)
try:
# If windows
if os.name == 'nt':
self.windows_compile_mod_files('.')
from neuron import h
h.nrn_load_dll('./nrnmech.dll')
else: # Anything else.
call(['nrnivmodl'])
import neuron
neuron.load_mechanisms('./')
from neuron import gui # to not freeze neuron gui
from neuron import h
logger.info("Loading model in %s" %model_dir)
h.load_file('mosinit.hoc')
except Exception as e:
logger.warning("Error running model: "+e.message)
logger.info("Path changed back to %s" %old_dir)
os.chdir(old_dir)
else:
response = """We didn't find any mosinit.hoc . Unfortunately we can't
automatically run the model. Check the README, maybe there is an
hint."""
logging.warning(response)
path_info = "You can find the extracted model in %s" %model_dir
mod.browse()
logging.info(path_info)
def load_hdf(self, path_to_hdf=None):
if path_to_hdf != None:
self.path_to_hdf=os.path.abspath(path_to_hdf)
else:
filename = QtGui.QFileDialog.getOpenFileName()
if filename:
self.path_to_hdf = str(filename)
if self.path_to_hdf != None:
self.manager.load_from_hdf(self.path_to_hdf)
self.update_tree_view()
msg = "Loaded db: %s" % self.path_to_hdf
self.ui.statusbar.showMessage(msg, 3500)
# Enablig the Animation button
self.animation()
# Disabling all the rest
self.ui.init_btn.setEnabled(False)
self.ui.run_btn.setEnabled(False)
self.ui.create_vector.setEnabled(False)
def save_hdf(self):
if not self.path_to_hdf:
filename = QtGui.QFileDialog.getSaveFileName()
self.path_to_hdf = str(filename) # It will go with python 3
if self.path_to_hdf != None:
self.manager.save_to_hdf(self.path_to_hdf)
msg = "Saved hdf file: %s" % self.path_to_hdf
self.ui.statusbar.showMessage(msg, 3500)
def launch_visio(self):
msg = "Plotting..."
self.ui.statusbar.showMessage(msg, 3500)
if self.visio == None:
# Checking there are sections in the model.
i = 0
for sec in h.allsec():
i += 1
if i > 0:
self.visio = Visio(self.ui.sec_info_label, self.manager)
self.visio.draw_model()
self.ui.selected_section.setEnabled(True)
else:
msg = """No model found, no section created. You need
to have at least one."""
logger.warning(msg)
else:
#Raise the visio window
self.visio.container.show()
# Enabling the animation
try:
self.animation()
except KeyError:
# No simulation run an nothing loaded.
# just pass
pass
def init(self):
"""Set the vm_init from the spin button and prepare the simulator"""
if not self.manager.refs.has_key('VecRef') :
logger.info("No vector Created. Create at least one vector to run the simulation")
return False
else:
v_init = self.ui.vSpinBox.value()
# Set the v_init
h.v_init = v_init
h.finitialize(v_init)
h.fcurrent()
# Reset the time in the GUI
self.ui.time_label.setNum(h.t)
return True
def run(self):
"""Run the simulator till tstop"""
#Initializing
if self.init():
# Run
msg = "Running simulation. It will take a while maybe..."
self.ui.statusbar.showMessage(msg, 5000)
while h.t < h.tstop:
h.fadvance()
self.ui.time_label.setText("<b>" + str(h.t) + "</b>")
def tstop_changed(self):
h.tstop = self.ui.tstopSpinBox.value()
def dt_changed(self):
h.dt = self.ui.dtSpinBox.value()
def v_changed(self):
h.v_init = self.ui.vSpinBox.value()
def plot_vector(self):
items = self.ui.treeWidget.selectedItems()
x = None
# Plot legend if required
legend_status = self.ui.legend.isChecked() #return True if toggled.
points_status = self.ui.points.isChecked()
# Retrieve the fig num
fig_num = self.ui.fig_num_spinBox.value()
for item in items:
if item.childCount() == 0: # Leaf, so it is the variable to plot
sectionItem = item.parent()
sectionName = str(sectionItem.text(0)) #Column used
var = str(item.text(0))
detail = str(item.text(1))
groupName = str(sectionItem.parent().text(0))
x = self.manager.groups[groupName]
key = sectionName + "_" + var
vecs_to_plot = { key : item.vec}
self.manager.plot_vecs(vecs_to_plot, x=x, legend=legend_status,
figure_num=fig_num, points=points_status)
def create_vector(self):
var = self.ui.var.text()
if var.isEmpty():
msgBox = QtGui.QMessageBox()
msgBox.setText("No var specified.")
msgBox.setIcon(QtGui.QMessageBox.Warning)
msgBox.exec_()
else:
if self.ui.all_sections.isChecked():
allCreated = self.manager.add_all_vecRef(str(var))
elif self.ui.selected_section.isChecked():
if self.visio.selected_cyl is not None:
sec = self.visio.cyl2sec[self.visio.selected_cyl]
self.manager.add_vecRef(str(var), sec)
else:
msgBox = QtGui.QMessageBox()
msgBox.setText("<b>No vector has been created.</b>")
msg = "You need to select the section where you want to create the vector"
msgBox.setInformativeText(msg)
msgBox.setIcon(QtGui.QMessageBox.Warning)
msgBox.exec_()
self.update_tree_view()
def get_unique_parent(self, name, parentItem = None):
"""Search the name in the treeview and return the qtElement.
Raise an exception if not unique"""
search = self.ui.treeWidget.findItems(name ,
Qt.MatchFixedString)
root_item = None
if len(search) == 0: # We create the group
root_item = None
if parentItem is None:
root_item = QtGui.QTreeWidgetItem(self.ui.treeWidget)
else:
root_item = QtGui.QTreeWidgetItem(parentItem)
root_item.setText(0, name)
elif len(search) == 1:
root_item = search[0]
else:
error = "ERROR - too many match: %d. Group Name not \
unique." %len(search)
raise NameError(error)
return root_item
def insert_item_treeview(self, groupName, section_name, vecs,
details = None):
"""Insert a new item in the treewidget.
Items are grouped by types. If a new type is provided a new group is added.
Items are then grouped by section.
In one section more than one variable is allowed.
Each variable can have a detail associated in a dictionary form """
group_root = self.get_unique_parent(groupName)
sec_root = self.get_unique_parent(section_name,
parentItem = group_root)
for var,vec in vecs.iteritems():
item = ItemRef(sec_root, vec)
item.setText(0, var)
item.setText(1, details)
sec_root.addChild(item)
def insert_refs_in_treeview(self):
for group, ref_list in self.manager.refs.iteritems():
for ref in ref_list:
self.insert_item_treeview(group,
ref.sec_name,
ref.vecs,
ref.detail)
def update_tree_view(self):
# Fill the treeview wit all the vectors created
#Clear all the row
self.ui.treeWidget.clear()
self.insert_refs_in_treeview()
def animation(self):
self.ui.timelineSlider.setRange(0,
len (self.manager.groups['t']))
self.ui.timelineSlider.setEnabled(True)
self.ui.show()
def select_sections(self, list_of_sections):
"""Select an arbitrary number of sections from the
command line.
:param: list_of_section - the list of sections to select. Each section should
be given by the name (sec.name() from Neuron point
of view.
"""
if self.visio is not None:
selection_scalar = self.visio.get_selection_scalar(list_of_sections)
self.visio.redraw_color(selection_scalar, 'v')
self.visio.update_sections_info(list_of_sections)
else:
logger.warning("You have to launch the 3D Visio window first!")
def on_animation_time_return_pressed(self):
"Getting the value from the text"
time = self.ui.animationTime.text()
try:
time = int (time)
time_list = self.manager.groups['t']
time_point_indx = 0
# If it's a vector on the just ran sim.
if hasattr(time_list, 'to_python'):
time_list = time_list.to_python()
time_list = np.around(time_list, 3)
time_point_indx = np.where(time_list==time)[0]
# If it's a numpy array saved on the disk
else:
rounded = time_list.read().round(3)
time_point_indx = np.where(rounded==time)[0]
self.sync_visio_3d(time_point_indx)
self.ui.timelineSlider.setValue(time_point_indx)
except:
logger.warning("Value not present in the array.")
def on_timeline_value_changed(self):
"""Draw the animation according to the value of the timeline"""
time_point_indx = self.ui.timelineSlider.value()
self.sync_visio_3d(time_point_indx)
def sync_visio_3d(self, time_point_indx):
var = self.ui.varToShow.text()
var = str(var) # This will go with Py3
#
# #Update the label on the scale
if len (self.manager.groups['t']) == time_point_indx:
time_point_indx = time_point_indx - 1 # Avoid to go out of scale
time = self.manager.groups['t'][time_point_indx]
self.ui.animationTime.setText(str(time))
start_value = float(self.ui.startValue.text())
end_value = float(self.ui.endValue.text())
self.visio.show_variable_timecourse(var, time_point_indx,
start_value, end_value)
def about(self):
self.aboutUi = uic.loadUi(os.path.join(os.path.dirname(__file__),
self.ui_dir,
"qtAbout.ui"))
import neuronvisio
name = '<font size=24><b>Neuronvisio %s<b><font>' %neuronvisio.__version__
authors = '%s' %neuronvisio.__authors__
self.aboutUi.name.setText(name)
self.aboutUi.authors.setText(authors)
self.aboutUi.show()
def __init__(self):
dynamic_neuron_home()
app = QtGui.QApplication.instance()
self.ui_dir = 'ui'
# Loading the UI
self.ui = uic.loadUi(
os.path.join(os.path.dirname(__file__), self.ui_dir,
"neuronvisio.ui"))
# Connecting
self.ui.Plot3D.connect(self.ui.Plot3D, QtCore.SIGNAL('clicked()'),
self.launch_visio)
self.ui.plot_vector_btn.connect(self.ui.plot_vector_btn,
QtCore.SIGNAL('clicked()'),
self.plot_vector)
self.ui.init_btn.connect(self.ui.init_btn, QtCore.SIGNAL('clicked()'),
self.init)
self.ui.run_btn.connect(self.ui.run_btn, QtCore.SIGNAL('clicked()'),
self.run)
self.ui.dtSpinBox.connect(self.ui.dtSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.dt_changed)
self.ui.tstopSpinBox.connect(self.ui.tstopSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.tstop_changed)
self.ui.vSpinBox.connect(self.ui.vSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.v_changed)
self.ui.create_vector.connect(self.ui.create_vector,
QtCore.SIGNAL('clicked()'),
self.create_vector)
self.ui.actionAbout.connect(self.ui.actionAbout,
QtCore.SIGNAL('triggered()'), self.about)
self.ui.timelineSlider.connect(self.ui.timelineSlider,
QtCore.SIGNAL("valueChanged(int)"),
self.on_timeline_value_changed)
self.ui.animationTime.connect(self.ui.animationTime,
QtCore.SIGNAL('returnPressed()'),
self.on_animation_time_return_pressed)
self.ui.actionLoad.connect(self.ui.actionLoad,
QtCore.SIGNAL("triggered()"), self.load)
self.ui.actionSave.connect(self.ui.actionSave,
QtCore.SIGNAL("triggered()"), self.save_hdf)
self.ui.tabWidget.connect(self.ui.tabWidget,
QtCore.SIGNAL('currentChanged(int)'),
self.populate_treeview_model)
self.ui.tree_models.connect(self.ui.tree_models,
QtCore.SIGNAL('itemSelectionChanged ()'),
self.select_model_treeview)
self.ui.load_model_btn.connect(self.ui.load_model_btn,
QtCore.SIGNAL('clicked()'),
self.load_selected_model)
self.ui.load_model_btn.connect(self.ui.filter_list_btn,
QtCore.SIGNAL('clicked()'),
self.filter_list)
self.ui.filter_input.connect(self.ui.filter_input,
QtCore.SIGNAL('returnPressed()'),
self.filter_list)
### Connection with the console
widgetDic = {
'dt': self.ui.dtSpinBox,
'tstop': self.ui.tstopSpinBox,
'v_init': self.ui.vSpinBox,
'time_label': self.ui.time_label
}
self.timeLoop = Timeloop(widgetDic)
app.connect(self.timeLoop, QtCore.SIGNAL("updateDt(double)"),
self.update_dt)
app.connect(self.timeLoop, QtCore.SIGNAL("updateTstop(double)"),
self.update_tstop)
app.connect(self.timeLoop, QtCore.SIGNAL("updateVInit(double)"),
self.update_v_init)
self.timeLoop.start()
### Manager class
self.manager = manager.Manager()
self.path_to_hdf = None
self.visio = None
self.tab_model_already_populated = False
self.ui.show()
# Start the main event loop.
#app.exec_()
self.AUTHORS = 1
self.YEAR = 0
self.TITLE = 2
self.ID = 3
# Dictionary to hold the models class for the ModelDb integration
self.models = Models()
class Controls(object):
"""Main class Neuronvisio"""
def __init__(self):
dynamic_neuron_home()
app = QtGui.QApplication.instance()
self.ui_dir = 'ui'
# Loading the UI
self.ui = uic.loadUi(
os.path.join(os.path.dirname(__file__), self.ui_dir,
"neuronvisio.ui"))
# Connecting
self.ui.Plot3D.connect(self.ui.Plot3D, QtCore.SIGNAL('clicked()'),
self.launch_visio)
self.ui.plot_vector_btn.connect(self.ui.plot_vector_btn,
QtCore.SIGNAL('clicked()'),
self.plot_vector)
self.ui.init_btn.connect(self.ui.init_btn, QtCore.SIGNAL('clicked()'),
self.init)
self.ui.run_btn.connect(self.ui.run_btn, QtCore.SIGNAL('clicked()'),
self.run)
self.ui.dtSpinBox.connect(self.ui.dtSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.dt_changed)
self.ui.tstopSpinBox.connect(self.ui.tstopSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.tstop_changed)
self.ui.vSpinBox.connect(self.ui.vSpinBox,
QtCore.SIGNAL('valueChanged(double)'),
self.v_changed)
self.ui.create_vector.connect(self.ui.create_vector,
QtCore.SIGNAL('clicked()'),
self.create_vector)
self.ui.actionAbout.connect(self.ui.actionAbout,
QtCore.SIGNAL('triggered()'), self.about)
self.ui.timelineSlider.connect(self.ui.timelineSlider,
QtCore.SIGNAL("valueChanged(int)"),
self.on_timeline_value_changed)
self.ui.animationTime.connect(self.ui.animationTime,
QtCore.SIGNAL('returnPressed()'),
self.on_animation_time_return_pressed)
self.ui.actionLoad.connect(self.ui.actionLoad,
QtCore.SIGNAL("triggered()"), self.load)
self.ui.actionSave.connect(self.ui.actionSave,
QtCore.SIGNAL("triggered()"), self.save_hdf)
self.ui.tabWidget.connect(self.ui.tabWidget,
QtCore.SIGNAL('currentChanged(int)'),
self.populate_treeview_model)
self.ui.tree_models.connect(self.ui.tree_models,
QtCore.SIGNAL('itemSelectionChanged ()'),
self.select_model_treeview)
self.ui.load_model_btn.connect(self.ui.load_model_btn,
QtCore.SIGNAL('clicked()'),
self.load_selected_model)
self.ui.load_model_btn.connect(self.ui.filter_list_btn,
QtCore.SIGNAL('clicked()'),
self.filter_list)
self.ui.filter_input.connect(self.ui.filter_input,
QtCore.SIGNAL('returnPressed()'),
self.filter_list)
### Connection with the console
widgetDic = {
'dt': self.ui.dtSpinBox,
'tstop': self.ui.tstopSpinBox,
'v_init': self.ui.vSpinBox,
'time_label': self.ui.time_label
}
self.timeLoop = Timeloop(widgetDic)
app.connect(self.timeLoop, QtCore.SIGNAL("updateDt(double)"),
self.update_dt)
app.connect(self.timeLoop, QtCore.SIGNAL("updateTstop(double)"),
self.update_tstop)
app.connect(self.timeLoop, QtCore.SIGNAL("updateVInit(double)"),
self.update_v_init)
self.timeLoop.start()
### Manager class
self.manager = manager.Manager()
self.path_to_hdf = None
self.visio = None
self.tab_model_already_populated = False
self.ui.show()
# Start the main event loop.
#app.exec_()
self.AUTHORS = 1
self.YEAR = 0
self.TITLE = 2
self.ID = 3
# Dictionary to hold the models class for the ModelDb integration
self.models = Models()
def populate_treeview_model(self, index, filter=""):
"""Populate the tree view on the gui and the scroll_area when the tab is
activated.
Args:
index (int): the index of the activated tab
filter (string): the string used to filter the search on the treeview
"""
if index == 3 and (filter or not self.tab_model_already_populated):
self.ui.tree_models.clear()
# Populating the treeview with the dictionary
for model_name in self.models.get_model_names(filter):
model = self.models.get_model(model_name)
model_item = QtGui.QTreeWidgetItem(self.ui.tree_models,
'Models')
model_item.setText(self.YEAR, model.get_year())
model_item.setText(self.AUTHORS, model.get_authors())
model_item.setText(self.TITLE, model.get_title())
model_item.setData(self.ID, 0, model.get_id())
self._set_tooltip(model, model_item)
#Resizing the column.
#self.ui.tree_models.resizeColumnToContents(0)
self.ui.tree_models.resizeColumnToContents(self.YEAR)
self.ui.tree_models.resizeColumnToContents(self.TITLE)
self.ui.tree_models.resizeColumnToContents(self.ID)
self.ui.textBrowser_readme.clear()
self.ui.textBrowser_readme.insertPlainText("No model selected.")
self.tab_model_already_populated = True #we populated only once.
def _set_tooltip(self, model, model_item):
# tooltip
cols = self.ui.tree_models.columnCount()
for i in range(cols):
tooltip = model.get_tooltip()
model_item.setToolTip(i, tooltip)
def _retrieve_selected_model(self):
"Return the model selected in the treeview"
items = self.ui.tree_models.selectedItems()
if items:
selected_item = items[0] #first element
model_id = int(selected_item.text(self.ID))
models_name = self.models.get_model_names()
for name in models_name:
mod = self.models.get_model(name)
if model_id == mod.get_id():
return mod
else:
logger.info('No model selected!')
return None
def filter_list(self):
"Filter the models list using the given text in the filter box"
filter = self.ui.filter_input.text()
logger.debug("Filtering list using keyword '%s'" % (filter))
self.populate_treeview_model(3, filter)
def about(self):
self.aboutUi = uic.loadUi(
os.path.join(os.path.dirname(__file__), self.ui_dir, "qtAbout.ui"))
import neuronvisio
name = '<font size=24><b>Neuronvisio %s<b><font>' % neuronvisio.__version__
authors = '%s' % neuronvisio.__authors__
self.aboutUi.name.setText(name)
self.aboutUi.authors.setText(authors)
self.aboutUi.show()
def animation(self):
self.ui.timelineSlider.setRange(0, len(self.manager.groups['t']))
self.ui.timelineSlider.setEnabled(True)
self.ui.show()
def create_vector(self):
var = self.ui.var.text()
if not var:
msgBox = QtGui.QMessageBox()
msgBox.setText("No var specified.")
msgBox.setIcon(QtGui.QMessageBox.Warning)
msgBox.exec_()
else:
if self.ui.all_sections.isChecked():
allCreated = self.manager.add_all_vecRef(str(var))
elif self.ui.selected_section.isChecked():
if self.visio.selected_cyl is not None:
sec = self.visio.cyl2sec[self.visio.selected_cyl]
self.manager.add_vecRef(str(var), sec)
else:
msgBox = QtGui.QMessageBox()
msgBox.setText("<b>No vector has been created.</b>")
msg = "You need to select the section where you want to create the vector"
msgBox.setInformativeText(msg)
msgBox.setIcon(QtGui.QMessageBox.Warning)
msgBox.exec_()
self.update_tree_view()
def dt_changed(self):
h.dt = self.ui.dtSpinBox.value()
def init(self):
"""Set the vm_init from the spin button and prepare the simulator"""
if not self.manager.refs.has_key('VecRef'):
message = "No vector Created. Create at least one vector to run the simulation"
logger.info(message)
self.ui.statusbar.showMessage(message, 3500)
return False
else:
v_init = self.ui.vSpinBox.value()
# Set the v_init
h.v_init = v_init
h.finitialize(v_init)
h.fcurrent()
# Reset the time in the GUI
self.ui.time_label.setNum(h.t)
return True
def insert_item_treeview(self,
groupName,
section_name,
vecs,
details=None):
"""Insert a new item in the treewidget.
Items are grouped by types. If a new type is provided a new group is added.
Items are then grouped by section.
In one section more than one variable is allowed.
Each variable can have a detail associated in a dictionary form """
group_root = self.get_unique_parent(groupName)
sec_root = self.get_unique_parent(section_name, parentItem=group_root)
for var, vec in vecs.iteritems():
item = ItemRef(sec_root, vec)
item.setText(0, var)
item.setText(1, details)
sec_root.addChild(item)
def insert_refs_in_treeview(self):
for group, ref_list in self.manager.refs.iteritems():
for ref in ref_list:
self.insert_item_treeview(group, ref.sec_name, ref.vecs,
ref.detail)
def launch_visio(self):
msg = "Plotting..."
self.ui.statusbar.showMessage(msg, 3500)
if self.visio == None:
# Checking there are sections in the model.
i = 0
for sec in h.allsec():
i += 1
if i > 0:
self.visio = Visio(self.ui.sec_info_label, self.manager)
self.visio.draw_model()
self.ui.selected_section.setEnabled(True)
else:
msg = """No model found, no section created. You need
to have at least one."""
logger.warning(msg)
else:
#Raise the visio window
self.visio.container.show()
# Enabling the animation
try:
self.animation()
except KeyError:
# No simulation run an nothing loaded.
# just pass
pass
def load(self, path_to_file=None):
"""
General loading method for any kind of format.
Extensions recognised:
.xml - NeuroML
.hoc - NEURON hoc file
.h5 - HDF file formatted according to Neuronvisio format.
The file type is recognised using the extension.
"""
if path_to_file == None:
filename = QtGui.QFileDialog.getOpenFileName()
if filename:
path_to_file = str(filename)
base_name, file_extension = os.path.splitext(path_to_file)
try:
if (file_extension == '.hoc'):
file_path, hoc_file = os.path.split(path_to_file)
self.load_hoc_model(file_path, hoc_file)
elif (file_extension == ".xml"):
self.manager.load_neuroml(path_to_file)
elif (file_extension == ".h5"):
self.load_hdf(path_to_file)
else:
raise ExtensionNotRecognised
except ExtensionNotRecognised:
msg = """
File extension not recognised!!
Neuronvisio was not able to recognise the file extension.
Extensions recognised:
.xml - NeuroML
.hoc - NEURON hoc file
.h5 - HDF file formatted according to Neuronvisio format.
"""
logger.error(msg)
def load_hdf(self, path_to_hdf):
if path_to_hdf != None:
self.path_to_hdf = os.path.abspath(path_to_hdf)
self.manager.load_from_hdf(self.path_to_hdf)
self.update_tree_view()
msg = "Loaded db: %s" % self.path_to_hdf
self.ui.statusbar.showMessage(msg, 3500)
# Enablig the Animation button
self.animation()
# Disabling all the rest
self.ui.init_btn.setEnabled(False)
self.ui.run_btn.setEnabled(False)
self.ui.create_vector.setEnabled(False)
def load_hoc_model(self, model_dir, hoc_file):
"""Load an hoc files. It compiles the mod
before loading the hoc."""
try:
os.path.isfile(os.path.join(model_dir, hoc_file))
except IOError:
logger.error("Not existing file: %s" % e.value)
old_dir = os.path.abspath(os.getcwd())
logger.info("Path changed to %s" % (os.path.abspath(model_dir)))
if model_dir != '':
os.chdir(model_dir)
try:
# Add all mod files into current directory
self.find_mod_files()
# If windows
if os.name == 'nt':
self.windows_compile_mod_files('.')
from neuron import h
h.nrn_load_dll('./nrnmech.dll')
else: # Anything else.
call(['nrnivmodl'])
import neuron
neuron.load_mechanisms(
'.') # Auto loading. Not needed anymore.
from neuron import gui # to not freeze neuron gui
from neuron import h
logger.info("Loading model in %s from %s" % (model_dir, hoc_file))
h.load_file(hoc_file)
except Exception as e:
logger.warning("Error running model: " + e.message)
logger.info("Path changed back to %s" % old_dir)
os.chdir(old_dir)
return True
def load_selected_model(self):
"Load the model selected in the treeview."
mod = self._retrieve_selected_model()
if mod:
model_path = mod.download_model()
# tooltip
cols = self.ui.tree_models.columnCount()
items = self.ui.tree_models.selectedItems()
model_item = items[0]
for i in range(cols):
tooltip = mod.get_tooltip()
model_item.setToolTip(i, tooltip)
if os.path.exists(os.path.join(mod.get_dir(), 'mosinit.hoc')):
self.load_hoc_model(mod.get_dir(), 'mosinit.hoc')
else:
log_warning = """No mosinit.hoc present. I can't locate the `mosinit.hoc` therefore I can't load automatically the model."""
logger.warning(log_warning)
self.ui.statusbar.showMessage(
"WARNING: Can't load the model automatically.", 10000)
info_warning = """<h3>No <code>mosinit.hoc</code> present!</h3>
<p>I couldn't find any <code>mosinit.hoc</code>, therefore I have no idea how to
load this model.</p>
<p>What I can do is to open the folder where the model has been downloaded.
Then, you need to read the docs of the model to know which file you need to load
to get the model up.</p>
<p>How to load an arbitrary hoc file with Neuronvisio is written on the docs:
<a href='http://neuronvisio.org/gettingstarted.html#loading-a-file'>Loading a file</a></p>
"""
warning_box = QtGui.QMessageBox()
warning_box.setTextFormat(QtCore.Qt.RichText)
warning_box.setText(info_warning)
warning_box.exec_()
mod.browse()
def make_animation_screenshots(self,
time_start,
time_stop=None,
saving_dir='anim'):
"""Creates a series of screenshots which can be put together using memcoder
to make a movie
Args:
time_start (float): time from where to start to take the screenshots
time_stop (float): time where to stop. If None will continue till the end
saving_dir (string): directory where to save the screenshots. Default is anim
"""
from mayavi import mlab
t = self.manager.get_time()
indx_start = t.indwhere("==", time_start)
indx_stop = None
if time_stop:
indx_stop = t.indwhere("==", time_stop)
else:
indx_stop = len(t)
if not os.path.exists(saving_dir):
os.mkdir(saving_dir)
png_format = "%09d.png"
for i in range(int(indx_start), int(indx_stop)):
figure_filename_animation = png_format % (i - indx_start)
logger.debug(figure_filename_animation)
self.sync_visio_3d(i)
mlab.savefig(os.path.join(saving_dir, figure_filename_animation))
logger.info("files created in %s" % saving_dir)
logger.info("To create a video run:")
logger.info("ffmpeg -f image2 -r 10 -i %s -sameq anim.mov -pass 2" %
png_format)
def on_animation_time_return_pressed(self):
"Getting the value from the text"
time = self.ui.animationTime.text()
try:
time = int(time)
time_list = self.manager.groups['t']
time_point_indx = 0
# If it's a vector on the just ran sim.
if hasattr(time_list, 'to_python'):
time_list = time_list.to_python()
time_list = np.around(time_list, 3)
time_point_indx = np.where(time_list == time)[0]
# If it's a numpy array saved on the disk
else:
rounded = time_list.read().round(3)
time_point_indx = np.where(rounded == time)[0]
self.sync_visio_3d(time_point_indx)
self.ui.timelineSlider.setValue(time_point_indx)
except:
logger.warning("Value not present in the array.")
def on_timeline_value_changed(self):
"""Draw the animation according to the value of the timeline"""
time_point_indx = self.ui.timelineSlider.value()
self.sync_visio_3d(time_point_indx)
def plot_vector(self):
items = self.ui.treeWidget.selectedItems()
x = None
# Plot legend if required
legend_status = self.ui.legend.isChecked() #return True if toggled.
points_status = self.ui.points.isChecked()
# Retrieve the fig num
fig_num = self.ui.fig_num_spinBox.value()
for item in items:
if item.childCount() == 0: # Leaf, so it is the variable to plot
sectionItem = item.parent()
sectionName = str(sectionItem.text(0)) #Column used
var = str(item.text(0))
detail = str(item.text(1))
groupName = str(sectionItem.parent().text(0))
x = self.manager.groups[groupName]
key = sectionName + "_" + var
vecs_to_plot = {key: item.vec}
self.manager.plot_vecs(vecs_to_plot,
x=x,
legend=legend_status,
figure_num=fig_num,
points=points_status)
def get_unique_parent(self, name, parentItem=None):
"""Search the name in the treeview and return the qtElement.
Raise an exception if not unique"""
search = self.ui.treeWidget.findItems(name, Qt.MatchFixedString)
root_item = None
if len(search) == 0: # We create the group
root_item = None
if parentItem is None:
root_item = QtGui.QTreeWidgetItem(self.ui.treeWidget)
else:
root_item = QtGui.QTreeWidgetItem(parentItem)
root_item.setText(0, name)
elif len(search) == 1:
root_item = search[0]
else:
error = "ERROR - too many match: %d. Group Name not \
unique." % len(search)
raise NameError(error)
return root_item
def run(self):
"""Run the simulator till tstop"""
#Initializing
if self.init():
# Run
msg = "Running simulation. It will take a while maybe..."
self.ui.statusbar.showMessage(msg, 5000)
while h.t < h.tstop:
h.fadvance()
self.ui.time_label.setText("<b>" + str(h.t) + "</b>")
self.animation()
def save_hdf(self):
if not self.path_to_hdf:
filename = QtGui.QFileDialog.getSaveFileName()
self.path_to_hdf = str(filename) # It will go with python 3
if self.path_to_hdf != None:
self.manager.save_to_hdf(self.path_to_hdf)
msg = "Saved hdf file: %s" % self.path_to_hdf
self.ui.statusbar.showMessage(msg, 3500)
def select_model_treeview(self):
"""Synch the README and the modelOverview with the selected model."""
mod = self._retrieve_selected_model()
if mod:
readme = mod.get_readme_html()
overview = mod.get_overview()
self.ui.textBrowser_readme.clear()
self.ui.textBrowser_readme.insertHtml(readme)
self.ui.textBrowser_model_overview.clear()
self.ui.textBrowser_model_overview.insertHtml(overview)
def sync_visio_3d(self, time_point_indx):
var = self.ui.varToShow.text()
var = str(var) # This will go with Py3
#
# #Update the label on the scale
if len(self.manager.groups['t']) == time_point_indx:
time_point_indx = time_point_indx - 1 # Avoid to go out of scale
time = self.manager.groups['t'][time_point_indx]
time_point_string = "%.3f" % round(time, 3)
self.ui.animationTime.setText(time_point_string)
start_value = float(self.ui.startValue.text())
end_value = float(self.ui.endValue.text())
self.visio.show_variable_timecourse(var, time_point_indx, start_value,
end_value)
def tstop_changed(self):
h.tstop = self.ui.tstopSpinBox.value()
def update_dt(self, new_dt):
self.ui.dtSpinBox.setValue(new_dt)
def update_tree_view(self):
# Fill the treeview wit all the vectors created
#Clear all the row
self.ui.treeWidget.clear()
self.insert_refs_in_treeview()
def update_tstop(self, new_tstop):
self.ui.tstopSpinBox.setValue(new_tstop)
def update_v_init(self, new_v_init):
self.ui.vSpinBox.setValue(new_v_init)
def v_changed(self):
h.v_init = self.ui.vSpinBox.value()
# create the command line to compile mod files into nrnmech.dll and launch it. command line is
# <cygwin-dir>\bin\bash.exe -c "cd <model-dir>; /usr/bin/sh -c '<nrnhome>/lib/mknrndll.sh <nrnhome>'"
def windows_compile_mod_files(self, model_dir):
# Get the required pathes
if os.environ.has_key('NEURONHOME'):
s1 = os.environ['NEURONHOME']
s2 = os.environ['NEURONHOME']
else:
import _winreg
k1 = _winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE,
"SOFTWARE\\Cygwin\\setup")
s1 = _winreg.QueryValueEx(k1, 'rootdir')[0]
_winreg.CloseKey(k1)
k2 = _winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE,
"SOFTWARE\\NEURON\\nrn72")
s2 = _winreg.QueryValueEx(k2, 'Install_Dir')[0]
_winreg.CloseKey(k2)
s1u = s1.replace('\\', '/')
s2u = s2.replace('\\', '/')
cmd = s1 + "\\bin\\bash.exe"
arg = "cd " + model_dir + ";" + s1u + "/bin/sh -c '" + s2u + "/lib/mknrndll.sh " + s2u + "'"
import subprocess
subprocess.Popen([cmd, '-c', arg],
stdin=subprocess.PIPE).communicate(input="\r\n")
# Copy all mod files under model directory into the root directory
def find_mod_files(self):
import shutil
mod_files = []
for root, dirnames, filenames in os.walk('.'):
if (root == '.'): continue
for filename in filenames:
base_name, file_extension = os.path.splitext(filename)
if file_extension == '.mod':
logger.info('Copy %s into model directory' %
os.path.join(root, filename))
# Double checking we are not copying over the same file.
logger.debug("%s %s" % (root, filename))
filename_src = os.path.join(root, filename)
filename_dest = os.path.join('.', filename)
if not os.path.isfile(filename_dest):
shutil.copy(filename_src, filename_dest)
