def create(modelroot, element,field):
"""Create table to record `field` from element `element`
Tables are created under `dataRoot`, the names are generally
created by removing `/model` in the beginning of `elementPath`
and replacing `/` with `_`. If this conflicts with an existing
table, the id value of the target element (elementPath) is
appended to the name.
"""
dataroot = modelroot+"/" + "data"
if not _moose.exists(dataroot):
_moose.Neutral(dataroot)
'''
if len(field) == 0 or ((element, field) in self._recordDict):
return
'''
field = lst = [word[0].upper() + word[1:] for word in field.split()]
field = " ".join(lst)
if len(field) == 0 or len(element.neighbors['get%s'%(field)]) > 0:
return
# The table path is not foolproof - conflict is
# possible: e.g. /model/test_object and
# /model/test/object will map to same table. So we
# check for existing table without element field
# path in recording dict.
relativePath = element.path.partition(modelroot)[-1]
if relativePath.startswith('/'):
relativePath = relativePath[1:]
#Convert to camelcase
tablePath = relativePath.replace('/', '_') + '.' + field
tablePath = re.sub('.', lambda m: {'[':'_', ']':'_'}.get(m.group(), m.group()),tablePath)
if tablePath.startswith("_0__"):
tablePath = tablePath[4:]
#tablePath = dataroot + '/' +tablePath
tablePath = dataroot+'/'+element.name+'.'+field[:2]
if _moose.exists(tablePath):
tablePath = '%s_%d' % (tablePath, element.getId().value)
if not _moose.exists(tablePath):
table = _moose.Table(tablePath)
print 'Created', table.path, 'for plotting', '%s.%s' % (element.path, field)
target = element
_moose.connect(table, 'requestOut', target, 'get%s' % (field))
tableEmitter.emit(QtCore.SIGNAL('tableCreated()'))
#tableCreated.emit()
return True
#self.emit(QtCore.SIGNAL('tableCreated(PyQt_PyObject)'))
#self.created.emit()
return False
def setupTable(name, obj, qtyname, tables_path=None):
""" Sets up a table with 'name' which stores 'qtyname' field from 'obj'.
The table is created under tables_path if not None, else under obj.path . """
if tables_path is None:
tables_path = obj.path + "/data"
## in case tables_path does not exist, below wrapper will create it
_moose.Neutral(tables_path)
vmTable = _moose.Table(tables_path + "/" + name)
## stepMode no longer supported, connect to 'input'/'spike' message dest to record Vm/spiktimes
# vmTable.stepMode = TAB_BUF
_moose.connect(vmTable, "requestData", obj, "get_" + qtyname)
return vmTable
def create_table(tablePath, element, field, tableType):
"""Create table to record `field` from element `element`
Tables are created under `dataRoot`, the names are generally
created by removing `/model` in the beginning of `elementPath`
and replacing `/` with `_`. If this conflicts with an existing
table, the id value of the target element (elementPath) is
appended to the name.
"""
if _moose.exists(tablePath):
table = _moose.element(tablePath)
else:
if tableType == "Table2":
table = _moose.Table2(tablePath)
elif tableType == "Table":
table = _moose.Table(tablePath)
_moose.connect(table, 'requestOut', element, 'get%s' % (field))
return table
def create_table(tablePath, element, field,tableType):
"""Create table to record `field` from element `element`
Tables are created under `dataRoot`, the names are generally
created by removing `/model` in the beginning of `elementPath`
and replacing `/` with `_`. If this conflicts with an existing
table, the id value of the target element (elementPath) is
appended to the name.
"""
if _moose.exists(tablePath):
table = _moose.element(tablePath)
else:
if tableType == "Table2":
table = _moose.Table2(tablePath)
elif tableType == "Table":
table = _moose.Table(tablePath)
_moose.connect(table, 'requestOut', element, 'get%s' % (field))
return table
def test_autoposition(self):
"""Simple check for automatic generation of positions.
A spherical soma is created with 20 um diameter. A 100
compartment cable is created attached to it with each
compartment of length 100 um.
"""
testid = 'test%s' % (uuid.uuid4())
container = _moose.Neutral('/test')
model = _moose.Neuron('/test/%s' % (testid))
soma = _moose.Compartment('%s/soma' % (model.path))
soma.diameter = 20e-6
soma.length = 0.0
parent = soma
comps = []
for ii in range(100):
comp = _moose.Compartment('%s/comp_%d' % (model.path, ii))
comp.diameter = 10e-6
comp.length = 100e-6
_moose.connect(parent, 'raxial', comp, 'axial')
comps.append(comp)
parent = comp
soma = autoposition(model)
sigfig = 8
self.assertAlmostEqual(soma.x0, 0.0, sigfig)
self.assertAlmostEqual(soma.y0, 0.0, sigfig)
self.assertAlmostEqual(soma.z0, 0.0, sigfig)
self.assertAlmostEqual(soma.x, 0.0, sigfig)
self.assertAlmostEqual(soma.y, 0.0, sigfig)
self.assertAlmostEqual(soma.z, soma.diameter / 2.0, sigfig)
for ii, comp in enumerate(comps):
print comp.path, ii
self.assertAlmostEqual(comp.x0, 0, sigfig)
self.assertAlmostEqual(comp.y0, 0.0, sigfig)
self.assertAlmostEqual(comp.z0, soma.diameter / 2.0 + ii * 100e-6,
sigfig)
self.assertAlmostEqual(comp.x, 0.0, sigfig)
self.assertAlmostEqual(comp.y, 0.0, sigfig)
self.assertAlmostEqual(comp.z,
soma.diameter / 2.0 + (ii + 1) * 100e-6,
sigfig)
def setupTable(name, obj, qtyname, tables_path=None, threshold=None, spikegen=None):
""" Sets up a table with 'name' which stores 'qtyname' field from 'obj'.
The table is created under tables_path if not None, else under obj.path . """
if tables_path is None:
tables_path = obj.path+'/data'
## in case tables_path does not exist, below wrapper will create it
tables_path_obj = _moose.Neutral(tables_path)
qtyTable = _moose.Table(tables_path_obj.path+'/'+name)
## stepMode no longer supported, connect to 'input'/'spike' message dest to record Vm/spiktimes
# qtyTable.stepMode = TAB_BUF
if spikegen is None:
if threshold is None:
## below is wrong! reads qty twice every clock tick!
#_moose.connect( obj, qtyname+'Out', qtyTable, "input")
## this is the correct method
_moose.connect( qtyTable, "requestOut", obj, 'get'+qtyname)
else:
## create new spikegen
spikegen = _moose.SpikeGen(tables_path_obj.path+'/'+name+'_spikegen')
## connect the compartment Vm to the spikegen
_moose.connect(obj,"VmOut",spikegen,"Vm")
## spikegens for different synapse_types can have different thresholds
spikegen.threshold = threshold
spikegen.edgeTriggered = 1 # This ensures that spike is generated only on leading edge.
else:
_moose.connect(spikegen,'spikeOut',qtyTable,'input') ## spikeGen gives spiketimes
return qtyTable
def setupTable(name,
obj,
qtyname,
tables_path=None,
threshold=None,
spikegen=None):
""" Sets up a table with 'name' which stores 'qtyname' field from 'obj'.
The table is created under tables_path if not None, else under obj.path . """
if tables_path is None:
tables_path = obj.path + '/data'
## in case tables_path does not exist, below wrapper will create it
tables_path_obj = _moose.Neutral(tables_path)
qtyTable = _moose.Table(tables_path_obj.path + '/' + name)
## stepMode no longer supported, connect to 'input'/'spike' message dest to record Vm/spiktimes
# qtyTable.stepMode = TAB_BUF
if spikegen is None:
if threshold is None:
## below is wrong! reads qty twice every clock tick!
#_moose.connect( obj, qtyname+'Out', qtyTable, "input")
## this is the correct method
_moose.connect(qtyTable, "requestOut", obj, 'get' + qtyname)
else:
## create new spikegen
spikegen = _moose.SpikeGen(tables_path_obj.path + '/' + name +
'_spikegen')
## connect the compartment Vm to the spikegen
_moose.connect(obj, "VmOut", spikegen, "Vm")
## spikegens for different synapse_types can have different thresholds
spikegen.threshold = threshold
spikegen.edgeTriggered = 1 # This ensures that spike is generated only on leading edge.
else:
_moose.connect(spikegen, 'spikeOut', qtyTable,
'input') ## spikeGen gives spiketimes
return qtyTable
def test_autoposition(self):
"""Simple check for automatic generation of positions.
A spherical soma is created with 20 um diameter. A 100
compartment cable is created attached to it with each
compartment of length 100 um.
"""
testid = 'test%s' % (uuid.uuid4())
container = _moose.Neutral('/test')
model = _moose.Neuron('/test/%s' % (testid))
soma = _moose.Compartment('%s/soma' % (model.path))
soma.diameter = 20e-6
soma.length = 0.0
parent = soma
comps = []
for ii in range(100):
comp = _moose.Compartment('%s/comp_%d' % (model.path, ii))
comp.diameter = 10e-6
comp.length = 100e-6
_moose.connect(parent, 'raxial', comp, 'axial')
comps.append(comp)
parent = comp
soma = autoposition(model)
sigfig = 8
self.assertAlmostEqual(soma.x0, 0.0, sigfig)
self.assertAlmostEqual(soma.y0, 0.0, sigfig)
self.assertAlmostEqual(soma.z0, 0.0, sigfig)
self.assertAlmostEqual(soma.x, 0.0, sigfig)
self.assertAlmostEqual(soma.y, 0.0, sigfig)
self.assertAlmostEqual(soma.z, soma.diameter/2.0, sigfig)
for ii, comp in enumerate(comps):
print comp.path, ii
self.assertAlmostEqual(comp.x0, 0, sigfig)
self.assertAlmostEqual(comp.y0, 0.0, sigfig)
self.assertAlmostEqual(comp.z0, soma.diameter/2.0 + ii * 100e-6, sigfig)
self.assertAlmostEqual(comp.x, 0.0, sigfig)
self.assertAlmostEqual(comp.y, 0.0, sigfig)
self.assertAlmostEqual(comp.z, soma.diameter/2.0 + (ii + 1) * 100e-6, sigfig)
def connect_CaConc(compartment_list):
""" Connect the Ca pools and channels within each of the compartments in compartment_list
Ca channels should have a child Mstring named 'ion' with value set in MOOSE.
Ca dependent channels like KCa should have a child Mstring called 'ionDependency' with value set in MOOSE.
Call this only after instantiating cell so that all channels and pools have been created. """
for compartment in compartment_list:
caconc = None
for child in compartment.children:
neutralwrap = _moose.Neutral(child)
if neutralwrap.class_ == "CaConc":
caconc = _moose.CaConc(child)
break
if caconc is not None:
## B has to be set for caconc based on thickness of Ca shell and compartment l and dia.
## I am using a translation from Neuron, hence this method.
## In Genesis, gmax / (surfacearea*thick) is set as value of B!
caconc.B = 1 / (2 * FARADAY) / (math.pi * compartment.diameter * compartment.length * caconc.thick)
for child in compartment.children:
neutralwrap = _moose.Neutral(child)
if neutralwrap.class_ == "HHChannel":
channel = _moose.HHChannel(child)
## If child Mstring 'ion' is present and is Ca, connect channel current to caconc
for childid in channel.children:
child = _moose.Neutral(childid)
if child.class_ == "Mstring" and child.name == "ion":
child = _moose.Mstring(child)
if child.value in ["Ca", "ca"]:
_moose.connect(channel, "IkOut", caconc, "current")
print "Connected IkOut of", channel.path, "to current of", caconc.path
if neutralwrap.class_ == "HHChannel2D":
channel = _moose.HHChannel2D(child)
## If child Mstring 'ionDependency' is present, connect caconc Ca conc to channel
for childid in channel.children:
child = _moose.Neutral(childid)
if child.class_ == "Mstring" and child.name == "ionDependency":
child = _moose.Mstring(child)
if child.value in ["Ca", "ca"]:
_moose.connect(caconc, "concOut", channel, "concen")
print "Connected concOut of", caconc.path, "to concen of", channel.path
def connect_CaConc(compartment_list, temperature=None):
""" Connect the Ca pools and channels within each of the compartments in compartment_list
Ca channels should have a child Mstring named 'ion' with value set in MOOSE.
Ca dependent channels like KCa should have a child Mstring called 'ionDependency' with value set in MOOSE.
Call this only after instantiating cell so that all channels and pools have been created. """
for compartment in compartment_list:
caconc = None
for child in compartment.children:
neutralwrap = _moose.Neutral(child)
if neutralwrap.className == 'CaConc':
caconc = _moose.CaConc(child)
break
if caconc is not None:
child = get_child_Mstring(caconc,'phi')
if child is not None:
caconc.B = float(child.value) # B = phi by definition -- see neuroml 1.8.1 defn
else:
## B has to be set for caconc based on thickness of Ca shell and compartment l and dia,
## OR based on the Mstring phi under CaConc path.
## I am using a translation from Neuron for mitral cell, hence this method.
## In Genesis, gmax / (surfacearea*thick) is set as value of B!
caconc.B = 1 / (2*FARADAY) / \
(math.pi*compartment.diameter*compartment.length * caconc.thick)
for child in compartment.children:
neutralwrap = _moose.Neutral(child)
if neutralwrap.className == 'HHChannel':
channel = _moose.HHChannel(child)
## If child Mstring 'ion' is present and is Ca, connect channel current to caconc
for childid in channel.children:
# in async13, gates which have not been created still 'exist'
# i.e. show up as a child, but cannot be wrapped.
try:
child = _moose.element(childid)
if child.className=='Mstring':
child = _moose.Mstring(child)
if child.name=='ion':
if child.value in ['Ca','ca']:
_moose.connect(channel,'IkOut',caconc,'current')
print 'Connected IkOut of',channel.path,'to current of',caconc.path
## temperature is used only by Nernst part here...
if child.name=='nernst_str':
nernst = _moose.Nernst(channel.path+'/nernst')
nernst_params = string.split(child.value,',')
nernst.Cout = float(nernst_params[0])
nernst.valence = float(nernst_params[1])
nernst.Temperature = temperature
_moose.connect(nernst,'Eout',channel,'setEk')
_moose.connect(caconc,'concOut',nernst,'ci')
print 'Connected Nernst',nernst.path
except TypeError:
pass
if neutralwrap.className == 'HHChannel2D':
channel = _moose.HHChannel2D(child)
## If child Mstring 'ionDependency' is present, connect caconc Ca conc to channel
for childid in channel.children:
# in async13, gates which have not been created still 'exist'
# i.e. show up as a child, but cannot be wrapped.
try:
child = _moose.element(childid)
if child.className=='Mstring' and child.name=='ionDependency':
child = _moose.Mstring(child)
if child.value in ['Ca','ca']:
_moose.connect(caconc,'concOut',channel,'concen')
print 'Connected concOut of',caconc.path,'to concen of',channel.path
except TypeError:
pass
def connect_CaConc(compartment_list, temperature=None):
""" Connect the Ca pools and channels within each of the compartments in compartment_list
Ca channels should have a child Mstring named 'ion' with value set in MOOSE.
Ca dependent channels like KCa should have a child Mstring called 'ionDependency' with value set in MOOSE.
Call this only after instantiating cell so that all channels and pools have been created. """
for compartment in compartment_list:
caconc = None
for child in compartment.children:
neutralwrap = _moose.Neutral(child)
if neutralwrap.className == 'CaConc':
caconc = _moose.CaConc(child)
break
if caconc is not None:
child = get_child_Mstring(caconc, 'phi')
if child is not None:
caconc.B = float(
child.value
) # B = phi by definition -- see neuroml 1.8.1 defn
else:
## B has to be set for caconc based on thickness of Ca shell and compartment l and dia,
## OR based on the Mstring phi under CaConc path.
## I am using a translation from Neuron for mitral cell, hence this method.
## In Genesis, gmax / (surfacearea*thick) is set as value of B!
caconc.B = 1 / (2*FARADAY) / \
(math.pi*compartment.diameter*compartment.length * caconc.thick)
for child in compartment.children:
neutralwrap = _moose.Neutral(child)
if neutralwrap.className == 'HHChannel':
channel = _moose.HHChannel(child)
## If child Mstring 'ion' is present and is Ca, connect channel current to caconc
for childid in channel.children:
# in async13, gates which have not been created still 'exist'
# i.e. show up as a child, but cannot be wrapped.
try:
child = _moose.element(childid)
if child.className == 'Mstring':
child = _moose.Mstring(child)
if child.name == 'ion':
if child.value in ['Ca', 'ca']:
_moose.connect(channel, 'IkOut',
caconc, 'current')
#print 'Connected IkOut of',channel.path,'to current of',caconc.path
## temperature is used only by Nernst part here...
if child.name == 'nernst_str':
nernst = _moose.Nernst(channel.path +
'/nernst')
nernst_params = string.split(
child.value, ',')
nernst.Cout = float(nernst_params[0])
nernst.valence = float(nernst_params[1])
nernst.Temperature = temperature
_moose.connect(nernst, 'Eout', channel,
'setEk')
_moose.connect(caconc, 'concOut', nernst,
'ci')
#print 'Connected Nernst',nernst.path
except TypeError:
pass
if neutralwrap.className == 'HHChannel2D':
channel = _moose.HHChannel2D(child)
## If child Mstring 'ionDependency' is present, connect caconc Ca conc to channel
for childid in channel.children:
# in async13, gates which have not been created still 'exist'
# i.e. show up as a child, but cannot be wrapped.
try:
child = _moose.element(childid)
if child.className == 'Mstring' and child.name == 'ionDependency':
child = _moose.Mstring(child)
if child.value in ['Ca', 'ca']:
_moose.connect(caconc, 'concOut', channel,
'concen')
#print 'Connected concOut of',caconc.path,'to concen of',channel.path
except TypeError:
pass
