def updateFromMoose(self):
"""Update the tick dt from the tick objects"""
ticks = moose.ematrix('/clock/tick')
# Items at position 0 are the column headers, hence ii+1
for ii in range(ticks[0].localNumField):
self.updateTextFromTick(ii)
self.updateCurrentTime()
def __getTickListWidget(self):
layout = QtGui.QGridLayout()
# Set up the column titles
layout.addWidget(QtGui.QLabel('Tick'), 0, 0)
layout.addWidget(QtGui.QLabel('dt'), 0, 1)
layout.addWidget(QtGui.QLabel('Targets (wildcard)'), 0, 2, 1, 2)
layout.setRowStretch(0, 1)
# Create one row for each tick. Somehow ticks.shape is
# (16,) while only 10 valid ticks exist. The following is a hack
ticks = moose.ematrix('/clock/tick')
for ii in range(ticks[0].localNumField):
tt = ticks[ii]
layout.addWidget(QtGui.QLabel(tt.path), ii+1, 0)
layout.addWidget(QtGui.QLineEdit(str(tt.dt)), ii+1, 1)
layout.addWidget(QtGui.QLineEdit(''), ii+1, 2, 1, 2)
layout.setRowStretch(ii+1, 1)
# We add spacer items to the last row so that expansion
# happens at bottom. All other rows have stretch = 1, and
# the last one has 0 (default) so that is the one that
# grows
rowcnt = layout.rowCount()
for ii in range(3):
layout.addItem(QtGui.QSpacerItem(1, 1), rowcnt, ii)
layout.setRowStretch(rowcnt, 10)
# layout.setColumnStretch(1, 1)
layout.setColumnStretch(2, 2)
widget = QtGui.QWidget()
widget.setLayout(layout)
return widget
def clearPreviousModel(self,modelpathTypeDict):
for path in modelpathTypeDict.keys():
if modelpathTypeDict[path] == 'NEUROML':
if moose.exists('/cells'):
moose.delete(moose.ematrix('/cells'))
if moose.exists('/elec'):
moose.delete(moose.ematrix('/elec'))
elif modelpathTypeDict[path] == 'KKIT':
if moose.exists('/KKIT'):
moose.delete(moose.ematrix('/KKIT'))
else:
print 'Did not delete previously loaded file. Restart moose instead'
'''Harsha Dict is also cleaned up '''
modelpathTypeDict = {}
for child in moose.element('/library').getField('children'):
moose.delete(child)
def create_tree(tree, parentpath=''):
if not tree:
return
node = tree[0]
parent = moose.ematrix(parentpath + '/' + node[0], 1, node[1])
if len(tree) < 2:
return
for sub in tree[1:]:
create_tree(sub, parent.path)
def create_population(container, size):
"""Create a population of `size` single compartmental neurons with
Na and K channels. Also create SpikeGen objects and SynChan
objects connected to these which can act as plug points for
setting up synapses later."""
path = container.path
comps = moose.ematrix(path+'/soma', size, 'Compartment')
Em = EREST_ACT+10.613e-3
comps.Em = np.random.normal(Em, np.abs(Em) * 0.1, size)
comps.initVm = np.random.normal(EREST_ACT, np.abs(EREST_ACT) * 0.1, size)
comps.Cm = [7.85e-9] * size
comps.Rm = [4.2e5] * size
comps.Ra = [190.98] * size
nachan = moose.copy(create_na_proto(), container, 'na', size)
nachan.Gbar = [0.942e-3] * size
nachan.Ek = [115e-3+EREST_ACT] * size
moose.connect(nachan, 'channel', comps, 'channel', 'OneToOne')
kchan = moose.copy(create_k_proto(), container, 'k', size)
kchan.Gbar = [0.2836e-4] * size
kchan.Ek = [-12e-3+EREST_ACT] * size
moose.connect(kchan, 'channel', comps, 'channel', 'OneToOne')
synchan = moose.ematrix(path + '/synchan', size, 'SynChan')
synchan.Gbar = [1e-8] * size
synchan.tau1 = [2e-3] * size
synchan.tau2 = [2e-3] * size
# Question: What is this going to do? Connect comps[ii] to comps[ii]/synchan?
# if we had synchan under each compartment created like: synchan = moose.SynChan(comps.path + '/synchan')
m = moose.connect(comps, 'channel', synchan, 'channel', 'OneToOne')
## Or would this have been the correct approach?
# for c in comps: moose.connect(c, 'channel', moose.SynChan(c.path+'/synchan'), 'channel', 'Single')
spikegen = moose.ematrix(path + '/spikegen', size, 'SpikeGen')
spikegen.threshold = [0.0] * size
m = moose.connect(comps, 'VmOut', spikegen, 'Vm', 'OneToOne')
return {'compartment': comps,
'spikegen': spikegen,
'synchan': synchan}
def restorestate(filename):
wfields = {}
for cinfo in moose__.element('/classes').children:
cname = cinfo[0].name
wfields[cname] = [f[len('set_'):] for f in moose__.getFieldNames(cname, 'destFinfo')
if f.startswith('set_') and f not in ['set_this', 'set_name', 'set_lastDimension', 'set_runTime'] and not f.startswith('set_num_')]
with h5.File(filename, 'r') as fd:
typeinfo = fd['/metadata/typeinfo'][:]
classdict = {}
dimsdict = dict(zip(typeinfo['path'], typeinfo['dims']))
classdict = dict(zip(typeinfo['path'], typeinfo['class']))
parentdict = dict(zip(typeinfo['path'], typeinfo['parent']))
sorted_paths = sorted(typeinfo['path'], key=lambda x: x.count('/'))
for path in sorted_paths:
name = path.rpartition('/')[-1].partition('[')[0]
moose__.ematrix(parentdict[path] + '/' + name, eval(dimsdict[path]), classdict[path])
for key in fd['/elements']:
dset = fd['/elements/'][key][:]
fieldnames = dset.dtype.names
for ii in range(len(dset)):
obj = moose__.element(dset['path'][ii])
for f in wfields[obj.class_]:
obj.setField(f, dset[f][ii])
def extract_ftype_doc(cinfo, finfotype, docio):
"""Extract field documentation for all fields of type `finfotype`
in class `cinfo` into `docio`.
Parameters
----------
cinfo: moose.Cinfo
class info object in MOOSE.
finfotype: str
finfo type (valueFinfo/srcFinfo/destFinfo/lookupFinfo/sharedFinfo
docio: StringIO
IO object to write the documentation into
"""
numfinfo = moose.getField(cinfo, 'num_'+finfotype, 'unsigned')
finfo = moose.ematrix('%s/%s' % (cinfo.path, finfotype))
data = []
inf = float( 'Inf' )
max_width_name = -inf
max_width_type = -inf
for ii in range(numfinfo):
fid = moose.melement(finfo, 0, ii, 0)
if finfotype == 'destFinfo' and (fid.name.startswith('get_') or
fid.name.startswith('set_')):
continue
dtype = type_mangling_regex.sub('', fid.type)
name = '**`{0}`**'.format( fid.name )
dtype = '`{0}`'.format( dtype )
doc = fid.docs
data.append( [ name, dtype, doc ] )
if len( name ) > max_width_name:
max_width_name = len( name )
if len( dtype ) > max_width_type:
max_width_type = len( dtype )
if len( data ) == 0:
return
padding = 2
format_string = '{{0: <{width}}}'
format_strings = (
format_string.format( width = max_width_name + padding ),
format_string.format( width = max_width_type + padding ),
'{0}'
)
col3_alignment = format_strings[0].format('') + format_strings[1].format('')
for row in data:
row[2] = row[2].replace( '\n', '\n' + col3_alignment )
column_headings = ( 'Field', 'Type', 'Description' )
docio.write( '\n' )
for ( column_heading, format_string ) in zip( column_headings, format_strings ):
docio.write( format_string.format( column_heading ) )
docio.write( '\n' )
for format_string in format_strings:
docio.write( format_string.format( '----' ) )
docio.write( '\n' )
for row in data:
for ( field, format_string ) in zip( row, format_strings ):
docio.write( format_string.format( field ) )
docio.write( '\n' )
def updateTextFromTick(self, tickNo):
tick = moose.ematrix('/clock/tick')[tickNo]
widget = self.tickListWidget.layout().itemAtPosition(tickNo + 1, 1).widget()
if widget is not None and isinstance(widget, QtGui.QLineEdit):
widget.setText(str(tick.dt))
