def load_project(self, fname):
file = File(fname)
print 'Loading project file: ', file.getAbsolutePath()
pm = ProjectManager()
project = pm.loadProject(file)
print pm.status()
return project
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert(len(project.getProjectDescription())>0)
assert(len(project.cellManager.getAllCells())>=7)
assert(len(project.cellGroupsInfo.getAllCellGroupNames())>=4)
assert(project.simulationParameters.getDt()-0.0125<=1e-6)
assert(project.neuronSettings.isVarTimeStep())
assert(project.neuronSettings.getDataSaveFormat().equals(NeuronSettings.DataSaveFormat.TEXT_NC))
assert(project.simulationParameters.getTemperature()- 6.3<=1e-6)
defSimConfig = project.simConfigInfo.getSimConfig("Default Simulation Configuration")
assert(str(defSimConfig.getCellGroups())=='[CellGroup_1]')
assert(project.cellGroupsInfo.getCellType("CellGroup_1")=='L5PC')
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert(len(project.getProjectDescription())>0)
assert(len(project.cellManager.getAllCells())>=6)
#assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE)
assert(abs(project.simulationParameters.getDt()-0.005)<=1e-9)
assert(abs(project.simulationParameters.getTemperature() - 10) < 1e-6)
assert(not project.neuronSettings.isVarTimeStep())
assert(project.neuronSettings.getDataSaveFormat().equals(NeuronSettings.DataSaveFormat.TEXT_NC))
#assert(project.genesisSettings.isSymmetricCompartments())
assert(project.genesisSettings.isSIUnits())
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert (len(project.getProjectDescription()) > 0)
assert (len(project.cellManager.getAllCells()) >= 6)
#assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE)
assert (abs(project.simulationParameters.getDt() - 0.01) <= 1e-9)
assert (abs(project.simulationParameters.getTemperature() - 6.3) < 1e-6)
assert (not project.neuronSettings.isVarTimeStep())
assert (project.neuronSettings.getDataSaveFormat().equals(
NeuronSettings.DataSaveFormat.TEXT_NC))
assert (project.genesisSettings.isSymmetricCompartments())
assert (project.genesisSettings.isSIUnits())
defSimConfig = project.simConfigInfo.getSimConfig(
"Default Simulation Configuration")
assert (str(defSimConfig.getCellGroups()) == '[baskets, pyramidals]')
smallNetSimConfig = project.simConfigInfo.getSimConfig("SmallNetwork")
assert (smallNetSimConfig.getCellGroups().size() == 2)
assert (smallNetSimConfig.getNetConns().size() == 4)
assert (smallNetSimConfig.getInputs().size() == 1)
assert (project.cellGroupsInfo.getCellPackingAdapter(
"pyramidals_48").getMaxNumberCells() == 48)
assert (project.cellGroupsInfo.getCellPackingAdapter(
"baskets_12").getMaxNumberCells() == 12)
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert len(project.getProjectDescription()) > 0
assert len(project.cellManager.getAllCells()) >= 22
assert len(project.cellGroupsInfo.getAllCellGroupNames()) >= 6
assert project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE
assert project.simulationParameters.getDt() - 0.025 <= 1e-6
assert not project.neuronSettings.isVarTimeStep()
assert project.neuronSettings.getDataSaveFormat().equals(NeuronSettings.DataSaveFormat.TEXT_NC)
assert project.simulationParameters.getTemperature() == 34
sci = project.simConfigInfo
cgi = project.cellGroupsInfo
assert cgi.getCellType("Channeltestgroup") == "Channeltest_Cell"
assert cgi.getCellType("CMLtestGroup") == "CMLtest_Cell"
assert cgi.getCellType("pyr_group") == "LarkumPyr"
assert cgi.getCellType("pyrCML_group") == "LarkumPyr_NML"
arrayListsIdentical(
sci.getSimConfig("Default Simulation Configuration").getCellGroups(), ["Channeltestgroup", "CMLtestGroup"]
)
arrayListsIdentical(sci.getSimConfig("test_IClamp").getCellGroups(), ["pyr_group", "pyrCML_group"])
arrayListsIdentical(sci.getSimConfig("background activity").getCellGroups(), ["pyr_group"])
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def __init__(self, pconf):
configDict = pconf.parse_project_data()
self.pconf = pconf
self.logger = pconf.get_logger("neurosim")
self.proj_path = self.pconf.local_path(configDict["proj_path"])
self.pm = ProjectManager()
projFile = File(self.proj_path)
self.sim_timeout = self.pconf.get_float("sim_timeout", "Simulation")
self.myProject = self.pm.loadProject(projFile)
self.simConfig = self.myProject.simConfigInfo.getSimConfig(self.pconf.get("sim_config", "Simulation"))
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert(len(project.getProjectDescription())>0)
assert(len(project.cellManager.getAllCells())>=6)
#assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE)
assert(abs(project.simulationParameters.getDt()-0.01)<=1e-9)
assert(abs(project.simulationParameters.getTemperature() - 6.3) < 1e-6)
assert(not project.neuronSettings.isVarTimeStep())
assert(project.neuronSettings.getDataSaveFormat().equals(NeuronSettings.DataSaveFormat.TEXT_NC))
assert(project.genesisSettings.isSymmetricCompartments())
assert(project.genesisSettings.isSIUnits())
defSimConfig = project.simConfigInfo.getSimConfig("Default Simulation Configuration")
assert(str(defSimConfig.getCellGroups())=='[baskets, pyramidals]')
smallNetSimConfig = project.simConfigInfo.getSimConfig("SmallNetwork")
assert(smallNetSimConfig.getCellGroups().size()==2)
assert(smallNetSimConfig.getNetConns().size()==4)
assert(smallNetSimConfig.getInputs().size()==1)
assert(project.cellGroupsInfo.getCellPackingAdapter("pyramidals_48").getMaxNumberCells()==48)
assert(project.cellGroupsInfo.getCellPackingAdapter("baskets_12").getMaxNumberCells()==12)
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert (len(project.getProjectDescription()) > 0)
assert (len(project.cellManager.getAllCells()) >= 7)
assert (len(project.cellGroupsInfo.getAllCellGroupNames()) >= 4)
assert (project.simulationParameters.getDt() - 0.0125 <= 1e-6)
assert (project.neuronSettings.isVarTimeStep())
assert (project.neuronSettings.getDataSaveFormat().equals(
NeuronSettings.DataSaveFormat.TEXT_NC))
assert (project.simulationParameters.getTemperature() == 34)
'''
sci = project.simConfigInfo
cgi = project.cellGroupsInfo
assert(cgi.getCellType("Channeltestgroup") == "Channeltest_Cell")
assert(cgi.getCellType("CMLtestGroup") == "CMLtest_Cell")
assert(cgi.getCellType("pyr_group") == "LarkumPyr")
assert(cgi.getCellType("pyrCML_group") == "LarkumPyr_NML")
arrayListsIdentical(sci.getSimConfig("Default Simulation Configuration").getCellGroups(), ["Channeltestgroup", "CMLtestGroup"])
arrayListsIdentical(sci.getSimConfig("test_IClamp").getCellGroups(), ["pyr_group", "pyrCML_group"])
arrayListsIdentical(sci.getSimConfig("background activity").getCellGroups(), ["pyr_group"])
'''
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert(len(project.getProjectDescription())>0)
assert(len(project.cellManager.getAllCells())>=7)
assert(len(project.cellGroupsInfo.getAllCellGroupNames())>=4)
assert(project.simulationParameters.getDt()-0.0125<=1e-6)
assert(project.neuronSettings.isVarTimeStep())
assert(project.neuronSettings.getDataSaveFormat().equals(NeuronSettings.DataSaveFormat.TEXT_NC))
assert(project.simulationParameters.getTemperature() == 34)
'''
sci = project.simConfigInfo
cgi = project.cellGroupsInfo
assert(cgi.getCellType("Channeltestgroup") == "Channeltest_Cell")
assert(cgi.getCellType("CMLtestGroup") == "CMLtest_Cell")
assert(cgi.getCellType("pyr_group") == "LarkumPyr")
assert(cgi.getCellType("pyrCML_group") == "LarkumPyr_NML")
arrayListsIdentical(sci.getSimConfig("Default Simulation Configuration").getCellGroups(), ["Channeltestgroup", "CMLtestGroup"])
arrayListsIdentical(sci.getSimConfig("test_IClamp").getCellGroups(), ["pyr_group", "pyrCML_group"])
arrayListsIdentical(sci.getSimConfig("background activity").getCellGroups(), ["pyr_group"])
'''
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert (len(project.getProjectDescription()) > 0)
assert (len(project.cellManager.getAllCells()) >= 1)
#assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE)
assert (abs(project.simulationParameters.getDt() - 0.02) <= 1e-9)
assert (abs(project.simulationParameters.getTemperature() - 6.3) < 1e-6)
assert (not project.neuronSettings.isVarTimeStep())
assert (project.neuronSettings.getDataSaveFormat().equals(
NeuronSettings.DataSaveFormat.TEXT_NC))
assert (project.genesisSettings.isSIUnits())
defSimConfig = project.simConfigInfo.getSimConfig(
"Default Simulation Configuration")
assert (str(defSimConfig.getCellGroups()) == '[SampleCellGroup]')
assert (defSimConfig.getCellGroups().size() == 1)
assert (defSimConfig.getInputs().size() == 1)
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert(len(project.getProjectDescription())>0)
assert(len(project.cellManager.getAllCells())>=1)
#assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE)
assert(abs(project.simulationParameters.getDt()-0.02)<=1e-9)
assert(abs(project.simulationParameters.getTemperature() - 6.3) < 1e-6)
assert(not project.neuronSettings.isVarTimeStep())
assert(project.neuronSettings.getDataSaveFormat().equals(NeuronSettings.DataSaveFormat.TEXT_NC))
assert(project.genesisSettings.isSIUnits())
defSimConfig = project.simConfigInfo.getSimConfig("Default Simulation Configuration")
assert(str(defSimConfig.getCellGroups())=='[SampleCellGroup]')
assert(defSimConfig.getCellGroups().size()==1)
assert(defSimConfig.getInputs().size()==1)
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
from math import *
# Load an existing neuroConstruct project
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath() + ", exists: " + str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
# Add a number of cells to the generatedCellPositions, connections to generatedNetworkConnections
# and electrical inputs to generatedElecInputs
numCells = 12
for i in range(0, numCells):
x = 100 * sin(i * 2 * pi / numCells)
y = 100 * cos(i * 2 * pi / numCells)
myProject.generatedCellPositions.addPosition("SampleCellGroup", i, x, y, 0)
if i != numCells - 1:
myProject.generatedNetworkConnections.addSynapticConnection("NC1", i, i + 1)
def testAll(argv=None):
if argv is None:
argv = sys.argv
# Load an existing neuroConstruct project
projFile = File("../CElegans.ncx")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
project = pm.loadProject(projFile)
print "Loaded project: " + project.getProjectName()
defSimConfig = project.simConfigInfo.getDefaultSimConfig()
cellsOnlySimConfig = project.simConfigInfo.getSimConfig("CellsOnly")
pharyngealSimConfig = project.simConfigInfo.getSimConfig("PharyngealNeurons")
mdl08SimConfig = project.simConfigInfo.getSimConfig("MDL08Connections")
expectedNumberCells = 302
##########################
print "\n----- Test 1: Check number of cells in sim config "+defSimConfig.getName()+"..."
pm.doGenerate(defSimConfig.getName(), 1234)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(defSimConfig)
sleep(2)
numGenerated = project.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
assert numGenerated == expectedNumberCells
print "Correct number of cells generated!"
##########################
print "\n---- Test 2: number of cells in sim config "+cellsOnlySimConfig.getName()+"..."
pm.doGenerate(cellsOnlySimConfig.getName(), 1234)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(cellsOnlySimConfig)
sleep(2)
numGenerated = project.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
assert numGenerated == expectedNumberCells
print "Correct number of cells generated!"
##########################
filename = "../../CElegansNeuronTables.xls"
print "\n---- Test 3: confirm settings in project match those in "+filename+"..."
from xlrd import open_workbook
rb = open_workbook(filename)
print "Opened Excel file: "+ filename
confirmed = 0
prefix = "NCXLS_"
for row in range(1,rb.sheet_by_index(0).nrows):
pre = rb.sheet_by_index(0).cell(row,0).value
post = rb.sheet_by_index(0).cell(row,1).value
syntype = rb.sheet_by_index(0).cell(row,2).value
num = int(rb.sheet_by_index(0).cell(row,3).value)
synclass = rb.sheet_by_index(0).cell(row,4).value
#print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
netConnName = prefix+pre+"_"+post
if "GapJunction" in syntype:
netConnName = netConnName + "_GJ"
src = project.morphNetworkConnectionsInfo.getSourceCellGroup(netConnName)
tgt = project.morphNetworkConnectionsInfo.getTargetCellGroup(netConnName)
synlist = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
#print synlist
assert synclass == synlist[0].getSynapseType()
if '_GJ' in synclass and synclass != 'Generic_GJ':
print "Only allowed gap junction synapse is Generic_GJ, not "+synclass
assert synclass == 'Generic_GJ'
if not (src == pre and tgt == post):
print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
print "*** Couldn't find connection: %s, src: %s, tgt: %s"%(netConnName, src, tgt)
assert src == pre
assert tgt == post
if src == tgt:
print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
print "*** This connection is from: %s, src: %s, tgt: %s, synaptic connection on same cell!!"%(netConnName, src, tgt)
confirmed += 1
print "Confirmed %i connections in project match spreadsheet"%confirmed
havePrefix = 0
allNetConnNames = project.morphNetworkConnectionsInfo.getAllSimpleNetConnNames()
for name in allNetConnNames:
if name.startswith(prefix):
havePrefix +=1
print "Project contains %i Network connections starting with %s"%(havePrefix, prefix)
assert havePrefix == confirmed
##########################
print "\n---- Test 4: number of cells in sim config "+pharyngealSimConfig.getName()+"..."
pm.doGenerate(pharyngealSimConfig.getName(), 1234471)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(pharyngealSimConfig)
sleep(2)
numCells = project.generatedCellPositions.getNumberInAllCellGroups()
numConns = project.generatedNetworkConnections.getNumAllSynConns()
print "Number of cells: %i, number of connections: %i"%(numCells,numConns)
expectedCells = 20
expectedNetConns = 269
assert numCells == expectedCells
assert numConns == expectedNetConns
print "Correct number of cells & connections generated!"
##########################
print "\n---- Test 5: number of cells in sim config "+mdl08SimConfig.getName()+"..."
pm.doGenerate(mdl08SimConfig.getName(), 1234471)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(mdl08SimConfig)
sleep(2)
numCells = project.generatedCellPositions.getNumberInAllCellGroups()
numConns = project.generatedNetworkConnections.getNumAllSynConns()
print "Number of cells: %i, number of connections: %i"%(numCells,numConns)
expectedCells = 9
expectedNetConns = 21
assert numCells == expectedCells
assert numConns == expectedNetConns
print "Correct number of cells & connections generated!"
##########################
print "\n---- Test 6: General neuroConstruct project settings..."
assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_NEURITE_SOLID)
assert(abs(project.simulationParameters.getDt()-0.025)<=1e-9)
assert(not project.neuronSettings.isVarTimeStep())
assert(project.neuronSettings.getDataSaveFormat().equals(NeuronSettings.DataSaveFormat.TEXT_NC))
assert(abs(project.simulationParameters.getTemperature() - 20.0) < 1e-6)
##########################
print "\n------------------------------------------All tests completed!\n"
exit()
def testAll(argv=None):
if argv is None:
argv = sys.argv
# Load an existing neuroConstruct project
projFile = File("../CElegans.ncx")
print "Loading project from file: " + projFile.getAbsolutePath() + ", exists: " + str(projFile.exists())
pm = ProjectManager()
project = pm.loadProject(projFile)
print "Loaded project: " + project.getProjectName()
defSimConfig = project.simConfigInfo.getDefaultSimConfig()
cellsOnlySimConfig = project.simConfigInfo.getSimConfig("CellsOnly")
pharyngealSimConfig = project.simConfigInfo.getSimConfig("PharyngealNeurons")
expectedNumberCells = 302
##########################
print "\n----- Test 1: Check number of cells in sim config " + defSimConfig.getName() + "..."
pm.doGenerate(defSimConfig.getName(), 1234)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: " + str(defSimConfig)
sleep(2)
numGenerated = project.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
assert numGenerated == expectedNumberCells
print "Correct number of cells generated!"
##########################
print "\n---- Test 2: number of cells in sim config " + cellsOnlySimConfig.getName() + "..."
pm.doGenerate(cellsOnlySimConfig.getName(), 1234)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: " + str(cellsOnlySimConfig)
sleep(2)
numGenerated = project.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
assert numGenerated == expectedNumberCells
print "Correct number of cells generated!"
##########################
filename = "../../CElegansNeuronTables.xls"
print "\n---- Test 3: confirm settings in project match those in " + filename + "..."
from xlrd import open_workbook
rb = open_workbook(filename)
print "Opened Excel file: " + filename
confirmed = 0
prefix = "NCXLS_"
for row in range(1, rb.sheet_by_index(0).nrows):
pre = rb.sheet_by_index(0).cell(row, 0).value
post = rb.sheet_by_index(0).cell(row, 1).value
syntype = rb.sheet_by_index(0).cell(row, 2).value
num = int(rb.sheet_by_index(0).cell(row, 3).value)
synclass = rb.sheet_by_index(0).cell(row, 4).value
# print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
netConnName = prefix + pre + "_" + post
if "GapJunction" in syntype:
netConnName = netConnName + "_GJ"
src = project.morphNetworkConnectionsInfo.getSourceCellGroup(netConnName)
tgt = project.morphNetworkConnectionsInfo.getTargetCellGroup(netConnName)
if not (src == pre and tgt == post):
print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" % (
row,
num,
pre,
post,
syntype,
synclass,
)
print "*** Couldn't find connection: %s, src: %s, tgt: %s" % (netConnName, src, tgt)
assert src == pre
assert tgt == post
if src == tgt:
print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" % (
row,
num,
pre,
post,
syntype,
synclass,
)
print "*** This connection is from: %s, src: %s, tgt: %s, synaptic connection on same cell!!" % (
netConnName,
src,
tgt,
)
confirmed += 1
print "Confirmed %i connections in project match spreadsheet" % confirmed
havePrefix = 0
allNetConnNames = project.morphNetworkConnectionsInfo.getAllSimpleNetConnNames()
for name in allNetConnNames:
if name.startswith(prefix):
havePrefix += 1
print "Project contains %i Network connections starting with %s" % (havePrefix, prefix)
assert havePrefix == confirmed
##########################
print "\n---- Test 4: number of cells in sim config " + pharyngealSimConfig.getName() + "..."
pm.doGenerate(pharyngealSimConfig.getName(), 1234471)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: " + str(pharyngealSimConfig)
sleep(2)
numCells = project.generatedCellPositions.getNumberInAllCellGroups()
numConns = project.generatedNetworkConnections.getNumAllSynConns()
print "Number of cells: %i, number of connections: %i" % (numCells, numConns)
expectedCells = 20
expectedNetConns = 269
assert numCells == expectedCells
assert numConns == expectedNetConns
print "Correct number of cells & connections generated!"
print "\n------------------------------------------All tests completed!\n"
exit()
set_tonic_GABA(work_dir, total_GABA_conductance_in_nS)
# scale excitatory conductance by modifying the AMPA and NMDA
# synaptic models. In general, the amplitude of the excitatory
# conductances is inversely proportional to the number of
# dendrites divided by 4, with the exc_cond_scaling parameter as
# the proportionality constant. If this is set to zero, the
# conductances are not scaled.
if point.exc_cond_scaling:
exc_scaling_factor = point.exc_cond_scaling / (float(point.n_grc_dend)/4)
scale_excitatory_conductances(work_dir, exc_scaling_factor)
# load project and initialise
project_file = java.io.File(work_dir + "/" + project_filename)
print ('Loading project from file: ' + project_file.getAbsolutePath() + ", exists: " + str(project_file.exists()))
pm = ProjectManager(None, None)
project = pm.loadProject(project_file)
print 'Loaded project: ' + project.getProjectName()
# load existing simulation configurations and set sim duration and a
# couple of neuron options
sim_config = project.simConfigInfo.getSimConfig(sim_config_name)
sim_config.setSimDuration(point.sim_duration)
project.neuronSettings.setNoConsole()
project.neuronSettings.setCopySimFiles(1)
# generate network
generate_nC_network(point, pm, project, sim_config)
# generate saves
generate_nC_saves(point, project)
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
from math import *
# Load an existing neuroConstruct project
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath(
) + ", exists: " + str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
# Add a number of cells to the generatedCellPositions, connections to generatedNetworkConnections
# and electrical inputs to generatedElecInputs
numCells = 12
for i in range(0, numCells):
x = 100 * sin(i * 2 * pi / numCells)
y = 100 * cos(i * 2 * pi / numCells)
myProject.generatedCellPositions.addPosition("SampleCellGroup", i, x, y, 0)
if i != numCells - 1:
myProject.generatedNetworkConnections.addSynapticConnection(
"NC1", i, i + 1)
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
from ucl.physiol.neuroconstruct.project import SimConfig
from math import *
from random import *
# Load an existing neuroConstruct project
projFile = File("../../CElegans.ncx")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
project = pm.loadProject(projFile)
print "Loaded project: " + project.getProjectName()
##########################
newSimConfig = "MDL08Connections"
newSimConfigDesc = "Generates a subset of the CElegans neural system consisting of the MDL08 muscle and motor neurons which connect to it. See https://github.com/openworm/OpenWorm/issues/53"
cells = ["AS1", "AS2", "DA1", "DA2", "DB1", "DD1", "SMDDL", "SMDDR", "MDL08"]
##########################
simConfig = SimConfig(newSimConfig, newSimConfigDesc)
def generateV_ICurve(self,
projFile,
simulator,
simConfig,
stimAmpLow, stimAmpInc, stimAmpHigh,
stimDur,
simDuration,
maxNumSimultaneousSims = 4):
# Load neuroConstruct project
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
self.myProject = pm.loadProject(projFile)
self.simulator = simulator
simConfig = self.myProject.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
pm.doGenerate(simConfig.getName(), self.neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(simConfig)
time.sleep(2)
numGenerated = self.myProject.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
simReferences = {}
if numGenerated > 0:
print "Generating scripts for simulator: %s..."%simulator
if simulator == 'NEURON':
self.myProject.neuronFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.neuronSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.neuronSettings.setGraphicsMode(0) # 0 hides graphs during execution
if simulator == 'GENESIS':
self.myProject.genesisFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.genesisSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.genesisSettings.setGraphicsMode(0) # 0 hides graphs during execution
stimAmp = stimAmpLow
ADD_TO_BEFORE_INIT = self.myProject.neuronSettings.getNativeBlock(NativeCodeLocation.BEFORE_INITIAL)
ADD_TO_RECORD_I = self.myProject.neuronSettings.getNativeBlock(NativeCodeLocation.AFTER_SIMULATION)
ADD_TO_START_FINITIALIZE = self.myProject.neuronSettings.getNativeBlock(NativeCodeLocation.START_FINITIALIZE)
while stimAmp <= stimAmpHigh:
while (len(self.simsRunning)>=maxNumSimultaneousSims):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(3) # wait a while...
self.updateSimsRunning()
simRef = "PySim_"+str(float(stimAmp))
print "Going to run simulation: "+simRef
######## Adjusting the amplitude of the Voltage clamp ###############
TEXT_BEFORE_CREATION = "objref clampobj" + "\n" + "objref record_current" + "\n" + "objref data_save" + "\n"
# TEXT_BEFORE_INIT = "GranuleCell_mod_tonic[0].Soma {\n" + "clampobj = new SEClamp(0.5)\n" + "clampobj.dur1 = 150.0" + "\n" + "clampobj.amp1 = -100.0" + "\n" + "clampobj.dur2 = " + str(stimDur) + "\n" + "clampobj.amp2 = " + str(stimAmp) + "\n" + "clampobj.dur3 = 150.0" + "\n" + "clampobj.amp3 = -100.0" + "\n" + "clampobj.rs = 0.00001\n " + "}\n" # This should do the trick
# TEXT_BEFORE_INIT = TEXT_BEFORE_INIT + ADD_TO_BEFORE_INIT
TEXT_START_FINITIALIZE = "GranuleCell_mod_tonic[0].Soma {\n" + "clampobj = new SEClamp(0.5)\n" + "clampobj.dur1 = 150.0" + "\n" + "clampobj.amp1 = -100.0" + "\n" + "clampobj.dur2 = " + str(stimDur) + "\n" + "clampobj.amp2 = " + str(stimAmp) + "\n" + "clampobj.dur3 = 150.0" + "\n" + "clampobj.amp3 = -40.0" + "\n" + "clampobj.rs = 0.00001\n" + "record_current = new Vector()" + "\n" + "record_current.record(&clampobj.i)" + "\n" + "}\n" #This should do the trick
TEXT_START_FINITIALIZE = TEXT_START_FINITIALIZE + ADD_TO_START_FINITIALIZE
TEXT_TO_RECORD_I = """data_save = new File() \n""" + """strdef filename \n""" + """sprint(filename, """" + self.myProject.getProjectMainDirectory().getAbsolutePath() + """/simulations/current%.3f.txt", clampobj.amp2) \n""" + """data_save.wopen(filename) \n""" + """record_current.printf(data_save) \n""" + """data_save.close() \n"""
TEXT_TO_RECORD_I = TEXT_TO_RECORD_I + ADD_TO_RECORD_I
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.BEFORE_CELL_CREATION, TEXT_BEFORE_CREATION)
# self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.BEFORE_INITIAL, TEXT_BEFORE_INIT)
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.START_FINITIALIZE, TEXT_START_FINITIALIZE)
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.AFTER_SIMULATION, TEXT_TO_RECORD_I)
print "Next stim: "+ str(stimAmp)
self.myProject.simulationParameters.setReference(simRef)
if simulator == "NEURON":
self.myProject.neuronFileManager.generateTheNeuronFiles(simConfig,
None,
NeuronFileManager.RUN_HOC,
self.simulatorSeed)
print "Generated NEURON files for: "+simRef
compileProcess = ProcessManager(self.myProject.neuronFileManager.getMainHocFile())
compileSuccess = compileProcess.compileFileWithNeuron(0,0)
print "Compiled NEURON files for: "+simRef
if compileSuccess:
pm.doRunNeuron(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
if simulator == "GENESIS":
compartmentalisation = GenesisCompartmentalisation()
self.myProject.genesisFileManager.generateTheGenesisFiles(simConfig,
None,
compartmentalisation,
self.simulatorSeed)
print "Generated GENESIS files for: "+simRef
pm.doRunGenesis(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
time.sleep(1) # Wait for sim to be kicked off
simReferences[simRef] = stimAmp
stimAmp = stimAmp +stimAmpInc
print
print "Finished running "+str(len(simReferences))+" simulations for project "+ projFile.getAbsolutePath()
print "These can be loaded and replayed in the previous simulation browser in the GUI"
print
while (len(self.simsRunning)>0):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(4) # wait a while...
self.updateSimsRunning()
#simReferences = {'PySim_0.3':0.3,'PySim_0.4':0.4,'PySim_0.5':0.5}
plotFrameVI = PlotManager.getPlotterFrame("V-I curve from project: "+str(self.myProject.getProjectFile())+" on "+simulator , 1, 1)
plotFrameVI.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "V-I curve for Simulation Configuration: "+str(simConfig)
dataSet = DataSet(info, info, "mV", "nA", "Voltage", "Current")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
simList = simReferences.keys()
simList.sort()
for sim in simList:
simDir = File(projFile.getParentFile(), "/neuroConstruct/models/Dan_GranCell/simulations/"+sim)
print
print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
try:
simData = SimulationData(simDir)
simData.initialise()
print "Data loaded: "
print simData.getAllLoadedDataStores()
times = simData.getAllTimes()
cellSegmentRef = simConfig.getCellGroups().get(0)+"_0"
cfilename = "E:/neuroConstruct/models/Dan_GranCell/simulations/" + sim + "/current.txt"
trace = "E:/neuroConstruct/models/Dan_GranCell/simulations/" + sim + ".txt"
# cFILE = open(cfilename, "r")
strom = 0.0
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
traceInfo = "Voltage at: %s in simulation: %s"%(cellSegmentRef, sim)
stimAmp = simReferences[sim]
print "Current at %f mV in sim %s: %f"%(stimAmp, sim, float(strom))
dataSet.addPoint(stimAmp,float(strom))
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()[0]
plotFrameVI.addDataSet(dataSet)
from ucl.physiol.neuroconstruct.gui.plotter import PlotManager
from ucl.physiol.neuroconstruct.gui.plotter import PlotCanvas
from ucl.physiol.neuroconstruct.dataset import DataSet
from math import *
import time
import shutil
import random
import os
import subprocess
# Load the original project
projName = "LarkumEtAl2009"
projFile = File("/home/matteo/neuroConstruct/models/"+projName+"/"+projName+".ncx")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
simConfig = myProject.simConfigInfo.getSimConfig("Default Simulation Configuration")#
randomseed = random.randint(1000,5000)
pm.doGenerate(simConfig.getName(), randomseed)
while pm.isGenerating():
print "Waiting for the project to be generated..."
time.sleep(2)
numGenerated = myProject.generatedCellPositions.getNumberInAllCellGroups()
simsRunning = []
def updateSimsRunning():
simsFinished = []
for sim in simsRunning:
timeFile = File(myProject.getProjectMainDirectory(), "simulations/"+sim+"/time.dat")
#print "Checking file: "+timeFile.getAbsolutePath() +", exists: "+ str(timeFile.exists())
def runColumnSimulation(simConfig="TempSimConfig",
simDuration=100,
simDt=0.025,
neuroConstructSeed=1234,
simulatorSeed=1234,
simulators=["NEURON"],
simRefPrefix="Net_",
suggestedRemoteRunTime=120,
defaultSynapticDelay=0.05,
mpiConf=MpiSettings.LOCAL_SERIAL,
scaleCortex=0.1,
scaleThalamus=0,
gabaScaling=1,
l4ssAmpaScaling=1,
l5PyrGapScaling=1,
inNrtTcrNmdaScaling=1,
pyrSsNmdaScaling=1,
deepBiasCurrent=-1,
maxElecLenFRB=0.01,
maxElecLenRS=0.01,
maxElecLenIN=0.01,
maxElecLenSS=0.01,
somaNseg=-1,
varTimestepNeuron=False,
verbose=True,
runInBackground=False):
print "Running new column simulation..."
############################################
# Full column populations
numFRB = 50 # full model: 50
numRS = 1000 # full model: 1000
numSupBask = 90 # full model: 90
numSupAxAx = 90 # full model: 90
numSupLTS = 90 # full model: 90
numL4SpinStell = 240 # full model: 240
numL5TuftIB = 800 # full model: 800
numL5TuftRS = 200 # full model: 200
numDeepBask = 100 # full model: 100
numDeepAxAx = 100 # full model: 100
numDeepLTS = 100 # full model: 100
numL6NonTuftRS = 500 # full model: 500
numTCR = 100 # full model: 100
numnRT = 100 # full model: 100
#######################################
### Load neuroConstruct project
import datetime
start = datetime.datetime.now()
print "Loading project %s from at %s " % (projFile.getCanonicalPath(),
start.strftime("%Y-%m-%d %H:%M"))
pm = ProjectManager()
project = pm.loadProject(projFile)
### Set duration & timestep & simulation configuration
project.simulationParameters.setDt(simDt)
simConfig = project.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
### Set simulation reference
index = 0
simRef = "%s%i" % (simRefPrefix, index)
while File("%s/simulations/%s_N" %
(project.getProjectMainDirectory().getCanonicalPath(),
simRef)).exists():
simRef = "%s%i" % (simRefPrefix, index)
index = index + 1
project.simulationParameters.setReference(simRef)
### Change num in each cell group
numFRB = int(scaleCortex * numFRB)
numRS = int(scaleCortex * numRS)
numSupBask = int(scaleCortex * numSupBask)
numSupAxAx = int(scaleCortex * numSupAxAx)
numSupLTS = int(scaleCortex * numSupLTS)
numL4SpinStell = int(scaleCortex * numL4SpinStell)
numL5TuftIB = int(scaleCortex * numL5TuftIB)
numL5TuftRS = int(scaleCortex * numL5TuftRS)
numDeepBask = int(scaleCortex * numDeepBask)
numDeepAxAx = int(scaleCortex * numDeepAxAx)
numDeepLTS = int(scaleCortex * numDeepLTS)
numL6NonTuftRS = int(scaleCortex * numL6NonTuftRS)
numTCR = int(scaleThalamus * numTCR)
numnRT = int(scaleThalamus * numnRT)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_L23PyrFRB").setMaxNumberCells(
numFRB) # Note only works if RandomCellPackingAdapter
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_L23PyrRS").setMaxNumberCells(numRS)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_SupBask").setMaxNumberCells(numSupBask)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_SupAxAx").setMaxNumberCells(numSupAxAx)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_SupLTS").setMaxNumberCells(numSupLTS)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_L4SpinStell").setMaxNumberCells(numL4SpinStell)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_L5TuftIB").setMaxNumberCells(numL5TuftIB)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_L5TuftRS").setMaxNumberCells(numL5TuftRS)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_DeepBask").setMaxNumberCells(numDeepBask)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_DeepAxAx").setMaxNumberCells(numDeepAxAx)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_DeepLTS").setMaxNumberCells(numDeepLTS)
project.cellGroupsInfo.getCellPackingAdapter(
"CG3D_L6NonTuftRS").setMaxNumberCells(numL6NonTuftRS)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_TCR").setMaxNumberCells(
numTCR)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_nRT").setMaxNumberCells(
numnRT)
### Change weights in synapses/gap junctions
for netConnName in simConfig.getNetConns():
if gabaScaling != 1:
SimulationsInfo.addExtraSimProperty("gabaWeightScaling",
str(gabaScaling))
synList = project.morphNetworkConnectionsInfo.getSynapseList(
netConnName)
for index in range(0, len(synList)):
synName = project.morphNetworkConnectionsInfo.getSynapseList(
netConnName).get(index).getSynapseType()
if synName.count("GABAA") > 0:
print "Changing synaptic weight for syn %s in net conn %s by factor %f" % (
synName, netConnName, gabaScaling)
project.morphNetworkConnectionsInfo.getSynapseList(
netConnName).get(index).setWeightsGenerator(
NumberGenerator(gabaScaling))
if l4ssAmpaScaling != 1:
SimulationsInfo.addExtraSimProperty("l4ssAmpaScaling",
str(l4ssAmpaScaling))
synList = project.morphNetworkConnectionsInfo.getSynapseList(
netConnName)
for index in range(0, len(synList)):
synName = project.morphNetworkConnectionsInfo.getSynapseList(
netConnName).get(index).getSynapseType()
if synName.count("Syn_AMPA_L4SS_L4SS") > 0:
print "Changing synaptic weight for syn %s in net conn %s by factor %f" % (
synName, netConnName, l4ssAmpaScaling)
project.morphNetworkConnectionsInfo.getSynapseList(
netConnName).get(index).setWeightsGenerator(
NumberGenerator(l4ssAmpaScaling))
if l5PyrGapScaling != 1:
SimulationsInfo.addExtraSimProperty("l5PyrGapScaling",
str(l5PyrGapScaling))
synList = project.morphNetworkConnectionsInfo.getSynapseList(
netConnName)
for index in range(0, len(synList)):
synName = project.morphNetworkConnectionsInfo.getSynapseList(
netConnName).get(index).getSynapseType()
tgtCG = project.morphNetworkConnectionsInfo.getTargetCellGroup(
netConnName)
if synName.count("Syn_Elect_DeepPyr_DeepPyr"
) > 0 and tgtCG.count("CG3D_L5") > 0:
print "Changing synaptic weight for syn %s in net conn %s by factor %f" % (
synName, netConnName, l5PyrGapScaling)
project.morphNetworkConnectionsInfo.getSynapseList(
netConnName).get(index).setWeightsGenerator(
NumberGenerator(l5PyrGapScaling))
if inNrtTcrNmdaScaling != 1:
SimulationsInfo.addExtraSimProperty("inNrtTcrNmdaScaling",
str(inNrtTcrNmdaScaling))
synList = project.morphNetworkConnectionsInfo.getSynapseList(
netConnName)
for index in range(0, len(synList)):
synName = project.morphNetworkConnectionsInfo.getSynapseList(
netConnName).get(index).getSynapseType()
if synName.count("NMDA") > 0 and (
synName.endswith("_IN") > 0
or synName.endswith("_DeepIN") > 0
or synName.endswith("_SupIN") > 0
or synName.endswith("_SupFS") > 0
or synName.endswith("_DeepFS") > 0
or synName.endswith("_SupLTS") > 0
or synName.endswith("_DeepLTS") > 0
or synName.endswith("_nRT") > 0
or synName.endswith("_TCR") > 0):
print "Changing synaptic weight for syn %s in net conn %s by factor %f" % (
synName, netConnName, inNrtTcrNmdaScaling)
project.morphNetworkConnectionsInfo.getSynapseList(
netConnName).get(index).setWeightsGenerator(
NumberGenerator(inNrtTcrNmdaScaling))
if pyrSsNmdaScaling != 1:
SimulationsInfo.addExtraSimProperty("pyrSsNmdaScaling",
str(pyrSsNmdaScaling))
synList = project.morphNetworkConnectionsInfo.getSynapseList(
netConnName)
for index in range(0, len(synList)):
synName = project.morphNetworkConnectionsInfo.getSynapseList(
netConnName).get(index).getSynapseType()
if synName.count("NMDA") > 0 and (
synName.endswith("_SupPyr") > 0
or synName.endswith("_DeepPyr") > 0
or synName.endswith("_L4SS") > 0
or synName.endswith("_L5Pyr") > 0
or synName.endswith("_L5RS") > 0
or synName.endswith("_L5IB") > 0
or synName.endswith("_L6NT") > 0
or synName.endswith("_Pyr") > 0):
print "Changing synaptic weight for syn %s in net conn %s by factor %f" % (
synName, netConnName, pyrSsNmdaScaling)
project.morphNetworkConnectionsInfo.getSynapseList(
netConnName).get(index).setWeightsGenerator(
NumberGenerator(pyrSsNmdaScaling))
### Change bias currents
for inputName in simConfig.getInputs():
stim = project.elecInputInfo.getStim(inputName)
if deepBiasCurrent >= 0:
if stim.getElectricalInput().TYPE == "IClamp" and (
stim.getCellGroup() == "CG3D_L5TuftIB"
or stim.getCellGroup() == "CG3D_L5TuftRS"
or stim.getCellGroup() == "CG3D_L6NonTuftRS"):
print "Changing offset current in %s to %f" % (
stim.getCellGroup(), deepBiasCurrent)
stim.setAmp(NumberGenerator(deepBiasCurrent))
project.elecInputInfo.updateStim(stim)
### Change spatial discretisation of some cells. This will impact accuracy & simulation speed
if maxElecLenFRB > 0:
frbCell = project.cellManager.getCell("L23PyrFRB_varInit")
info = CellTopologyHelper.recompartmentaliseCell(
frbCell, maxElecLenFRB, project)
print "Recompartmentalised FRB cell: " + info
if somaNseg > 0:
frbCell.getSegmentWithId(
0).getSection().setNumberInternalDivisions(somaNseg)
if maxElecLenRS > 0:
rsCell = project.cellManager.getCell("L23PyrRS")
info = CellTopologyHelper.recompartmentaliseCell(
rsCell, maxElecLenRS, project)
print "Recompartmentalised RS cell: " + info
if somaNseg > 0:
rsCell.getSegmentWithId(0).getSection().setNumberInternalDivisions(
somaNseg)
if maxElecLenIN > 0:
inCells = [
"SupBasket", "SupAxAx", "SupLTSInter", "DeepBasket", "DeepAxAx",
"DeepLTSInter"
]
for inCellName in inCells:
inCell = project.cellManager.getCell(inCellName)
info = CellTopologyHelper.recompartmentaliseCell(
inCell, maxElecLenIN, project)
print "Recompartmentalised " + inCellName + " cell: " + info
if somaNseg > 0:
inCell.getSegmentWithId(
0).getSection().setNumberInternalDivisions(somaNseg)
### Change parallel configuration
mpiSettings = MpiSettings()
simConfig.setMpiConf(mpiSettings.getMpiConfiguration(mpiConf))
print "Parallel configuration: " + str(simConfig.getMpiConf())
if suggestedRemoteRunTime > 0:
project.neuronFileManager.setSuggestedRemoteRunTime(
suggestedRemoteRunTime)
project.genesisFileManager.setSuggestedRemoteRunTime(
suggestedRemoteRunTime)
### Change synaptic delay associated with each net conn
for netConnName in simConfig.getNetConns():
if netConnName.count("gap") == 0:
print "Changing synaptic delay in %s to %f" % (
netConnName, defaultSynapticDelay)
delayGen = NumberGenerator(defaultSynapticDelay)
for synProps in project.morphNetworkConnectionsInfo.getSynapseList(
netConnName):
synProps.setDelayGenerator(delayGen)
# defaultSynapticDelay will be recorded in simulation.props and listed in SimulationBrowser GUI
SimulationsInfo.addExtraSimProperty("defaultSynapticDelay",
str(defaultSynapticDelay))
### Generate network structure in neuroConstruct
pm.doGenerate(simConfig.getName(), neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: " + str(
simConfig)
sleep(2)
print "Generated %i cells in %i cell groups" % (
project.generatedCellPositions.getNumberInAllCellGroups(),
project.generatedCellPositions.getNumberNonEmptyCellGroups())
print "Generated %i instances in %i network connections" % (
project.generatedNetworkConnections.getNumAllSynConns(),
project.generatedNetworkConnections.getNumNonEmptyNetConns())
print "Generated %i instances in %i elect inputs" % (
project.generatedElecInputs.getNumberSingleInputs(),
project.generatedElecInputs.getNonEmptyInputRefs().size())
if simulators.count("NEURON") > 0:
simRefN = simRef + "_N"
project.simulationParameters.setReference(simRefN)
nc.generateAndRunNeuron(project,
pm,
simConfig,
simRefN,
simulatorSeed,
verbose=verbose,
runInBackground=runInBackground,
varTimestep=varTimestepNeuron)
sleep(2) # wait a while before running GENESIS...
if simulators.count("GENESIS") > 0:
simRefG = simRef + "_G"
project.simulationParameters.setReference(simRefG)
nc.generateAndRunGenesis(project,
pm,
simConfig,
simRefG,
simulatorSeed,
verbose=verbose,
runInBackground=runInBackground)
sleep(2) # wait a while before running MOOSE...
if simulators.count("MOOSE") > 0:
simRefM = simRef + "_M"
project.simulationParameters.setReference(simRefM)
nc.generateAndRunMoose(project,
pm,
simConfig,
simRefM,
simulatorSeed,
verbose=verbose,
runInBackground=runInBackground)
sleep(2) # wait a while before running GENESIS...
print "Finished running all sims, shutting down..."
stop = datetime.datetime.now()
print
print "Started: %s, finished: %s" % (start.strftime("%Y-%m-%d %H:%M"),
stop.strftime("%Y-%m-%d %H:%M"))
print
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert(len(project.getProjectDescription())>0)
assert(len(project.cellManager.getAllCells())>=22)
assert(len(project.cellGroupsInfo.getAllCellGroupNames())>=36)
synSetupFile = open("netbuild/makeSyns.sh", 'r')
for line in synSetupFile:
line = line.strip()
if len(line)>0 and not line.startswith("#"):
words = line.split()
if len(words)>=6 and words[2].startswith("Syn_"):
synName = words[2]
cm = project.cellMechanismInfo.getCellMechanism(synName)
print "Checked syn %s"%cm.getInstanceName()
netConnList = open("netbuild/netConnList", 'r')
for line in netConnList:
line = line.strip()
if len(line)>0 and not line.startswith("#"):
#print "\n\n---- Deciphering line: "+ line
words = line.split()
source = words[0]
target = words[1]
syns = words[2].strip("[]").split(",")
netConnName = "NC3D_"+source[5:]+"_"+target[5:]
assert(source == project.morphNetworkConnectionsInfo.getSourceCellGroup(netConnName))
assert(target == project.morphNetworkConnectionsInfo.getTargetCellGroup(netConnName))
print "Checked %s"%netConnName
assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE)
assert(abs(project.simulationParameters.getDt()-0.025)<=1e-9)
assert(not project.neuronSettings.isVarTimeStep())
assert(project.neuronSettings.isForceCorrectInit())
assert(project.neuronSettings.getDataSaveFormat().equals(NeuronSettings.DataSaveFormat.TEXT_NC))
assert(not project.genesisSettings.isSymmetricCompartments())
assert(project.genesisSettings.isPhysiologicalUnits())
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
def runColumnSimulation(simConfig= "TempSimConfig",
simDuration = 100,
simDt = 0.025,
neuroConstructSeed = 1234,
simulatorSeed = 1234,
simulators = ["NEURON"],
simRefPrefix = "Net_",
suggestedRemoteRunTime = 120,
defaultSynapticDelay = 0.05,
mpiConf = MpiSettings.LOCAL_SERIAL,
scaleCortex = 0.1,
scaleThalamus = 0,
gabaScaling = 1,
l4ssAmpaScaling = 1,
l5PyrGapScaling = 1,
inNrtTcrNmdaScaling = 1,
pyrSsNmdaScaling = 1,
deepBiasCurrent = -1,
maxElecLenFRB = 0.01,
maxElecLenRS = 0.01,
maxElecLenIN = 0.01,
maxElecLenSS = 0.01,
somaNseg = -1,
varTimestepNeuron = False,
verbose = True,
runInBackground = False):
print "Running new column simulation..."
############################################
# Full column populations
numFRB = 50 # full model: 50
numRS = 1000 # full model: 1000
numSupBask = 90 # full model: 90
numSupAxAx = 90 # full model: 90
numSupLTS = 90 # full model: 90
numL4SpinStell = 240 # full model: 240
numL5TuftIB = 800 # full model: 800
numL5TuftRS = 200 # full model: 200
numDeepBask = 100 # full model: 100
numDeepAxAx = 100 # full model: 100
numDeepLTS = 100 # full model: 100
numL6NonTuftRS = 500 # full model: 500
numTCR = 100 # full model: 100
numnRT = 100 # full model: 100
#######################################
### Load neuroConstruct project
import datetime
start = datetime.datetime.now()
print "Loading project %s from at %s " % (projFile.getCanonicalPath(),start.strftime("%Y-%m-%d %H:%M"))
pm = ProjectManager()
project = pm.loadProject(projFile)
### Set duration & timestep & simulation configuration
project.simulationParameters.setDt(simDt)
simConfig = project.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
### Set simulation reference
index = 0
simRef = "%s%i"%(simRefPrefix,index)
while File( "%s/simulations/%s_N"%(project.getProjectMainDirectory().getCanonicalPath(), simRef)).exists():
simRef = "%s%i"%(simRefPrefix,index)
index = index+1
project.simulationParameters.setReference(simRef)
### Change num in each cell group
numFRB = int(scaleCortex * numFRB)
numRS = int(scaleCortex * numRS)
numSupBask = int(scaleCortex * numSupBask)
numSupAxAx = int(scaleCortex * numSupAxAx)
numSupLTS = int(scaleCortex * numSupLTS)
numL4SpinStell = int(scaleCortex * numL4SpinStell)
numL5TuftIB = int(scaleCortex * numL5TuftIB)
numL5TuftRS = int(scaleCortex * numL5TuftRS)
numDeepBask = int(scaleCortex * numDeepBask)
numDeepAxAx = int(scaleCortex * numDeepAxAx)
numDeepLTS = int(scaleCortex * numDeepLTS)
numL6NonTuftRS = int(scaleCortex * numL6NonTuftRS)
numTCR = int(scaleThalamus * numTCR)
numnRT = int(scaleThalamus * numnRT)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_L23PyrFRB").setMaxNumberCells(numFRB) # Note only works if RandomCellPackingAdapter
project.cellGroupsInfo.getCellPackingAdapter("CG3D_L23PyrRS").setMaxNumberCells(numRS)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_SupBask").setMaxNumberCells(numSupBask)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_SupAxAx").setMaxNumberCells(numSupAxAx)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_SupLTS").setMaxNumberCells(numSupLTS)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_L4SpinStell").setMaxNumberCells(numL4SpinStell)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_L5TuftIB").setMaxNumberCells(numL5TuftIB)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_L5TuftRS").setMaxNumberCells(numL5TuftRS)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_DeepBask").setMaxNumberCells(numDeepBask)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_DeepAxAx").setMaxNumberCells(numDeepAxAx)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_DeepLTS").setMaxNumberCells(numDeepLTS)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_L6NonTuftRS").setMaxNumberCells(numL6NonTuftRS)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_TCR").setMaxNumberCells(numTCR)
project.cellGroupsInfo.getCellPackingAdapter("CG3D_nRT").setMaxNumberCells(numnRT)
### Change weights in synapses/gap junctions
for netConnName in simConfig.getNetConns():
if gabaScaling != 1:
SimulationsInfo.addExtraSimProperty("gabaWeightScaling", str(gabaScaling))
synList = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
for index in range(0, len(synList)):
synName = project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).getSynapseType()
if synName.count("GABAA")>0:
print "Changing synaptic weight for syn %s in net conn %s by factor %f"%(synName, netConnName, gabaScaling)
project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).setWeightsGenerator(NumberGenerator(gabaScaling))
if l4ssAmpaScaling !=1:
SimulationsInfo.addExtraSimProperty("l4ssAmpaScaling", str(l4ssAmpaScaling))
synList = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
for index in range(0, len(synList)):
synName = project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).getSynapseType()
if synName.count("Syn_AMPA_L4SS_L4SS")>0:
print "Changing synaptic weight for syn %s in net conn %s by factor %f"%(synName, netConnName, l4ssAmpaScaling)
project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).setWeightsGenerator(NumberGenerator(l4ssAmpaScaling))
if l5PyrGapScaling !=1:
SimulationsInfo.addExtraSimProperty("l5PyrGapScaling", str(l5PyrGapScaling))
synList = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
for index in range(0, len(synList)):
synName = project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).getSynapseType()
tgtCG = project.morphNetworkConnectionsInfo.getTargetCellGroup(netConnName)
if synName.count("Syn_Elect_DeepPyr_DeepPyr")>0 and tgtCG.count("CG3D_L5")>0:
print "Changing synaptic weight for syn %s in net conn %s by factor %f"%(synName, netConnName, l5PyrGapScaling)
project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).setWeightsGenerator(NumberGenerator(l5PyrGapScaling))
if inNrtTcrNmdaScaling !=1:
SimulationsInfo.addExtraSimProperty("inNrtTcrNmdaScaling", str(inNrtTcrNmdaScaling))
synList = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
for index in range(0, len(synList)):
synName = project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).getSynapseType()
if synName.count("NMDA")>0 and (synName.endswith("_IN")>0 or
synName.endswith("_DeepIN")>0 or
synName.endswith("_SupIN")>0 or
synName.endswith("_SupFS")>0 or
synName.endswith("_DeepFS")>0 or
synName.endswith("_SupLTS")>0 or
synName.endswith("_DeepLTS")>0 or
synName.endswith("_nRT")>0 or
synName.endswith("_TCR")>0):
print "Changing synaptic weight for syn %s in net conn %s by factor %f"%(synName, netConnName, inNrtTcrNmdaScaling)
project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).setWeightsGenerator(NumberGenerator(inNrtTcrNmdaScaling))
if pyrSsNmdaScaling !=1:
SimulationsInfo.addExtraSimProperty("pyrSsNmdaScaling", str(pyrSsNmdaScaling))
synList = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
for index in range(0, len(synList)):
synName = project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).getSynapseType()
if synName.count("NMDA")>0 and (synName.endswith("_SupPyr")>0 or
synName.endswith("_DeepPyr")>0 or
synName.endswith("_L4SS")>0 or
synName.endswith("_L5Pyr")>0 or
synName.endswith("_L5RS")>0 or
synName.endswith("_L5IB")>0 or
synName.endswith("_L6NT")>0 or
synName.endswith("_Pyr")>0):
print "Changing synaptic weight for syn %s in net conn %s by factor %f"%(synName, netConnName, pyrSsNmdaScaling)
project.morphNetworkConnectionsInfo.getSynapseList(netConnName).get(index).setWeightsGenerator(NumberGenerator(pyrSsNmdaScaling))
### Change bias currents
for inputName in simConfig.getInputs():
stim = project.elecInputInfo.getStim(inputName)
if deepBiasCurrent >= 0:
if stim.getElectricalInput().TYPE == "IClamp" and (stim.getCellGroup()=="CG3D_L5TuftIB" or stim.getCellGroup()=="CG3D_L5TuftRS" or stim.getCellGroup()=="CG3D_L6NonTuftRS"):
print "Changing offset current in %s to %f"%(stim.getCellGroup(), deepBiasCurrent)
stim.setAmp(NumberGenerator(deepBiasCurrent))
project.elecInputInfo.updateStim(stim)
### Change spatial discretisation of some cells. This will impact accuracy & simulation speed
if maxElecLenFRB > 0:
frbCell = project.cellManager.getCell("L23PyrFRB_varInit")
info = CellTopologyHelper.recompartmentaliseCell(frbCell, maxElecLenFRB, project)
print "Recompartmentalised FRB cell: "+info
if somaNseg > 0:
frbCell.getSegmentWithId(0).getSection().setNumberInternalDivisions(somaNseg)
if maxElecLenRS > 0:
rsCell = project.cellManager.getCell("L23PyrRS")
info = CellTopologyHelper.recompartmentaliseCell(rsCell, maxElecLenRS, project)
print "Recompartmentalised RS cell: "+info
if somaNseg > 0:
rsCell.getSegmentWithId(0).getSection().setNumberInternalDivisions(somaNseg)
if maxElecLenIN > 0:
inCells = ["SupBasket", "SupAxAx","SupLTSInter","DeepBasket", "DeepAxAx","DeepLTSInter"]
for inCellName in inCells:
inCell = project.cellManager.getCell(inCellName)
info = CellTopologyHelper.recompartmentaliseCell(inCell, maxElecLenIN, project)
print "Recompartmentalised "+inCellName+" cell: "+info
if somaNseg > 0:
inCell.getSegmentWithId(0).getSection().setNumberInternalDivisions(somaNseg)
### Change parallel configuration
mpiSettings = MpiSettings()
simConfig.setMpiConf(mpiSettings.getMpiConfiguration(mpiConf))
print "Parallel configuration: "+ str(simConfig.getMpiConf())
if suggestedRemoteRunTime > 0:
project.neuronFileManager.setSuggestedRemoteRunTime(suggestedRemoteRunTime)
project.genesisFileManager.setSuggestedRemoteRunTime(suggestedRemoteRunTime)
### Change synaptic delay associated with each net conn
for netConnName in simConfig.getNetConns():
if netConnName.count("gap")==0:
print "Changing synaptic delay in %s to %f"%(netConnName, defaultSynapticDelay)
delayGen = NumberGenerator(defaultSynapticDelay)
for synProps in project.morphNetworkConnectionsInfo.getSynapseList(netConnName):
synProps.setDelayGenerator(delayGen)
# defaultSynapticDelay will be recorded in simulation.props and listed in SimulationBrowser GUI
SimulationsInfo.addExtraSimProperty("defaultSynapticDelay", str(defaultSynapticDelay))
### Generate network structure in neuroConstruct
pm.doGenerate(simConfig.getName(), neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(simConfig)
sleep(2)
print "Generated %i cells in %i cell groups" % (project.generatedCellPositions.getNumberInAllCellGroups(), project.generatedCellPositions.getNumberNonEmptyCellGroups())
print "Generated %i instances in %i network connections" % (project.generatedNetworkConnections.getNumAllSynConns(), project.generatedNetworkConnections.getNumNonEmptyNetConns())
print "Generated %i instances in %i elect inputs" % (project.generatedElecInputs.getNumberSingleInputs(), project.generatedElecInputs.getNonEmptyInputRefs().size())
if simulators.count("NEURON")>0:
simRefN = simRef+"_N"
project.simulationParameters.setReference(simRefN)
nc.generateAndRunNeuron(project,
pm,
simConfig,
simRefN,
simulatorSeed,
verbose=verbose,
runInBackground=runInBackground,
varTimestep=varTimestepNeuron)
sleep(2) # wait a while before running GENESIS...
if simulators.count("GENESIS")>0:
simRefG = simRef+"_G"
project.simulationParameters.setReference(simRefG)
nc.generateAndRunGenesis(project,
pm,
simConfig,
simRefG,
simulatorSeed,
verbose=verbose,
runInBackground=runInBackground)
sleep(2) # wait a while before running MOOSE...
if simulators.count("MOOSE")>0:
simRefM = simRef+"_M"
project.simulationParameters.setReference(simRefM)
nc.generateAndRunMoose(project,
pm,
simConfig,
simRefM,
simulatorSeed,
verbose=verbose,
runInBackground=runInBackground)
sleep(2) # wait a while before running GENESIS...
print "Finished running all sims, shutting down..."
stop = datetime.datetime.now()
print
print "Started: %s, finished: %s" % (start.strftime("%Y-%m-%d %H:%M"),stop.strftime("%Y-%m-%d %H:%M"))
print
numnRT = 100 # full model: 100
#######################################
### Load neuroConstruct project
import datetime
start = datetime.datetime.now()
print "Loading project %s from at %s " % (projFile.getCanonicalPath(),start.strftime("%Y-%m-%d %H:%M"))
pm = ProjectManager()
project = pm.loadProject(projFile)
### Set duration & timestep & simulation configuration
project.simulationParameters.setDt(simDt)
simConfig = project.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
### Set simulation reference
index = 0
simRef = "%s%i"%(simRefPrefix,index)
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
import sys
from time import *
from ucl.physiol.neuroconstruct.project import ProjectManager
# Load an existing neuroConstruct project
projFile = File("../CElegans.ncx")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
project = pm.loadProject(projFile)
print "Loaded project: " + project.getProjectName()
simConfig = project.simConfigInfo.getSimConfig("CellsOnly")
expectedNumberCells = 302
##########################
pm.doGenerate(simConfig.getName(), 1234)
while pm.isGenerating():
def SingleCellNML2generator(projString=" ",ConfigDict={},ElecLenList=[],somaNseg=None,savingDir=None,shell=None):
projFile=File(os.getcwd(),projString)
pm=ProjectManager()
for config in ConfigDict.keys():
project=pm.loadProject(projFile)
nmlfm = NeuroMLFileManager(project)
compSummary={}
compSummary[config]={}
if " " in config:
configPath=config.replace(" ","_")
else:
configPath=config
if savingDir !=None:
full_path_to_config=r'../%s/%s'%(savingDir,configPath)
else:
full_path_to_config=r'../%s'%(configPath)
for maxElecLen in ElecLenList:
compSummary[config][str(maxElecLen)]={}
cell=project.cellManager.getCell(ConfigDict[config])
if maxElecLen > 0:
info = CellTopologyHelper.recompartmentaliseCell(cell, maxElecLen, project)
print "Recompartmentalising cell %s"%ConfigDict[config]
if somaNseg != None:
cell.getSegmentWithId(0).getSection().setNumberInternalDivisions(somaNseg)
if savingDir !=None:
cellpath = r'../%s/%s/%s_%f'%(savingDir,configPath,configPath,maxElecLen)
else:
cellpath = r'../%s/%s_%f'%(configPath,configPath,maxElecLen)
else:
if savingDir !=None:
cellpath = r'../%s/%s/%s_default'%(savingDir,configPath,configPath)
else:
cellpath = r'../%s/%s_default'%(configPath,configPath)
summary=str(cell.getMorphSummary())
summary_string=summary.split("_")
for feature in summary_string:
feature_split=feature.split(":")
compSummary[config][str(maxElecLen)][feature_split[0]]=feature_split[1]
# the format of summary : Segs:122_Secs:61_IntDivs:1458
print("Will be printing a cell morphology summary")
print compSummary[config][str(maxElecLen)]
######### it turns out that this does not save recompartmentalized cells - all saved cells have identical spatial discretization;
##### generateNeuroML2 receives the parent projFile but not the loaded project which is modified by the CellTopologyHelper.recompartmentaliseCell()
##################### neuroConstruct block #############################################################################
neuroConstructSeed=1234
verbose=True
pm.doGenerate(config, neuroConstructSeed)
while pm.isGenerating():
if verbose:
print("Waiting for the project to be generated with Simulation Configuration: "+config)
time.sleep(5)
simConfig = project.simConfigInfo.getSimConfig(config)
seed=1234
genDir = File(projFile.getParentFile(), "generatedNeuroML2")
nmlfm.generateNeuroMLFiles(simConfig,
NeuroMLConstants.NeuroMLVersion.getLatestVersion(),
LemsConstants.LemsOption.LEMS_WITHOUT_EXECUTE_MODEL,
OriginalCompartmentalisation(),
seed,
False,
True,
genDir,
"GENESIS Physiological Units",
False)
########################################################################################################################
if not os.path.exists(cellpath):
print("Creating a new directory %s"%cellpath)
os.makedirs(cellpath)
else:
print("A directory %s already exists"%cellpath)
src_files = os.listdir("../../neuroConstruct/generatedNeuroML2/")
for file_name in src_files:
full_file_name = os.path.join("../../neuroConstruct/generatedNeuroML2/", file_name)
if (os.path.isfile(full_file_name)):
print("Moving generated NeuroML2 to files to %s"%cellpath)
shutil.copy(full_file_name, cellpath)
with open(os.path.join(full_path_to_config,"compSummary.json"),'w') as fout:
json.dump(compSummary, fout)
if shell ==None:
extension='sh'
else:
extension=shell
os.chdir("../../neuroConstruct/pythonScripts")
subprocess.call("%s/nC.%s -python ../../neuroConstruct/pythonScripts/RegenerateNml2.py -f"%(os.environ["NC_HOME"],extension),shell=True)
os.chdir("../../NeuroML2/pythonScripts")
numnRT = 100 # full model: 100
#######################################
### Load neuroConstruct project
import datetime
start = datetime.datetime.now()
print "Loading project %s from at %s " % (projFile.getCanonicalPath(),start.strftime("%Y-%m-%d %H:%M"))
pm = ProjectManager()
project = pm.loadProject(projFile)
### Set duration & timestep & simulation configuration
project.simulationParameters.setDt(simDt)
simConfig = project.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
### Set simulation reference
index = 0
simRef = "%s%i"%(simRefPrefix,index)
peakThreshold = 3 # In synchrony, what constitutes a peak
maxRadius = 300
radiusRing = 40
cellGroupName = "CellGroup_1"
inputStimRef = "Input_0"
#################################################
from ucl.physiol.neuroconstruct.project import ProjectManager
print 'Loading project file: ', projFile.getAbsolutePath()
pm = ProjectManager()
project = pm.loadProject(projFile)
print 'Successfully loaded project: ', project.getProjectName()
innerRadius = 0
outerRadius = radiusRing*2.5 #most inner compartment
while innerRadius < maxRadius:
plotFrame = PlotManager.getPlotterFrame("Analysis of synchrony in ring %f -> %f"%(innerRadius,outerRadius), False)
plotFrame2 = PlotManager.getPlotterFrame("Peak times in ring %f -> %f"%(innerRadius,outerRadius), False)
def make_fF_Curve(self,
projFile,
simulator,
simConfig,
nTrains,
simDuration,
analyseStartTime, analyseStopTime,
analyseThreshold,
maxNumSimultaneousSims = 4):
# Load neuroConstruct project
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
self.myProject = pm.loadProject(projFile)
self.simulator = simulator
simConfig = self.myProject.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
pm.doGenerate(simConfig.getName(), self.neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(simConfig)
time.sleep(2)
numGenerated = self.myProject.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
simReferences = {}
if numGenerated > 0:
print "Generating scripts for simulator: %s..."%simulator
if simulator == 'NEURON':
self.myProject.neuronFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.neuronSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.neuronSettings.setGraphicsMode(0) # 0 hides graphs during execution
if simulator == 'GENESIS':
self.myProject.genesisFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.genesisSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.genesisSettings.setGraphicsMode(0) # 0 hides graphs during execution
currentTrain = 0
ADD_TO_START_FINITIALIZE = self.myProject.neuronSettings.getNativeBlock(NativeCodeLocation.START_FINITIALIZE)
ADD_TO_RECORD_I = self.myProject.neuronSettings.getNativeBlock(NativeCodeLocation.AFTER_SIMULATION)
while currentTrain <= nTrains:
while (len(self.simsRunning)>=maxNumSimultaneousSims):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(3) # wait a while...
self.updateSimsRunning()
simRef = "PySim_"+str(currentTrain)
print "Going to run simulation: "+simRef
######## Adjusting the amplitude of the Voltage clamp ###############
TEXT_BEFORE_CREATION = """objref vector, gTrainFile\n""" + "objectvar clamp\n"
### TEXT_BEFORE_INIT = "GranuleCell_mod_tonic[0].Soma {\n" + "clampobj = new VClamp(0.5)\n" + "clampobj.dur[0] = " + str(stimDur) + "\n" + "clampobj.amp[0] = " + str(stimAmp) + "\n" + "}\n" # This should do the trick
TEXT_START_FINITIALIZE = "\n" + "gTrainFile = new File() \n" + "vector = new Vector(100000) \n" + "access GranuleCell_mod_tonic[0].Soma \n" + "clamp = new SEClamp(0.5) \n" + "clamp.amp1 = 0 \n" + "clamp.dur1 = 1e9 \n" + """gTrainFile.ropen("E:/neuroConstruct/models/Dan_GranCell/gTrains_nS/gAMPA_""" + str(currentTrain) + """.txt") \n""" + "vector.scanf(gTrainFile) \n" + "gTrainFile.close \n" + "for i = 0, vector.size() -1 { \n" + " if (vector.x[i] <= 0) { \n" + " vector.x[i] = 1e-20 \n" + " } \n" + " } \n" + "for i = 0, vector.size() -1 { \n" + " vector.x[i] = ( 1 / vector.x[i] ) * 1000 \n" + " } \n" + "vector.play(&clamp.rs, 0.03) \n" # This
TEXT_START_FINITIALIZE = TEXT_START_FINITIALIZE + ADD_TO_START_FINITIALIZE
TEXT_TO_RECORD_I = """// currently not used \n"""
TEXT_TO_RECORD_I = TEXT_TO_RECORD_I + ADD_TO_RECORD_I
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.BEFORE_CELL_CREATION, TEXT_BEFORE_CREATION)
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.START_FINITIALIZE, TEXT_START_FINITIALIZE)
self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.AFTER_SIMULATION, TEXT_TO_RECORD_I)
print "Next Train: "+ str(currentTrain)
self.myProject.simulationParameters.setReference(simRef)
if simulator == "NEURON":
self.myProject.neuronFileManager.generateTheNeuronFiles(simConfig,
None,
NeuronFileManager.RUN_HOC,
self.simulatorSeed)
print "Generated NEURON files for: "+simRef
compileProcess = ProcessManager(self.myProject.neuronFileManager.getMainHocFile())
compileSuccess = compileProcess.compileFileWithNeuron(0,0)
print "Compiled NEURON files for: "+simRef
if compileSuccess:
pm.doRunNeuron(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
if simulator == "GENESIS":
compartmentalisation = GenesisCompartmentalisation()
self.myProject.genesisFileManager.generateTheGenesisFiles(simConfig,
None,
compartmentalisation,
self.simulatorSeed)
print "Generated GENESIS files for: "+simRef
pm.doRunGenesis(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
time.sleep(1) # Wait for sim to be kicked off
simReferences[simRef] = currentTrain
currentTrain = currentTrain + 1
print
print "Finished running "+str(len(simReferences))+" simulations for project "+ projFile.getAbsolutePath()
print "These can be loaded and replayed in the previous simulation browser in the GUI"
print
while (len(self.simsRunning)>0):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(4) # wait a while...
self.updateSimsRunning()
#simReferences = {'PySim_0.3':0.3,'PySim_0.4':0.4,'PySim_0.5':0.5}
plotFrameFf = PlotManager.getPlotterFrame("F-f curve from project: "+str(self.myProject.getProjectFile())+" on "+simulator , 1, 1)
plotFrameVolts = PlotManager.getPlotterFrame("VoltageTraces from project: "+str(self.myProject.getProjectFile())+" on "+simulator , 1, 1)
plotFrameFf.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "F-f curve for Simulation Configuration: "+str(simConfig)
dataSet = DataSet(info, info, "Hz", "Hz", "Input_Freq", "Output_Freq")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
simList = simReferences.keys()
simList.sort()
traininfos = open("E:/neuroConstruct/models/Dan_GranCell/gAMPA_traininfo.txt")
train_info_list = traininfos.readlines()
currentTrain = 0
for sim in simList:
simDir = File(projFile.getParentFile(), "E:/neuroConstruct/models/Dan_GranCell/simulations/"+sim)
print
print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
try:
simData = SimulationData(simDir)
simData.initialise()
print "Data loaded: "
print simData.getAllLoadedDataStores()
times = simData.getAllTimes()
cellSegmentRef = simConfig.getCellGroups().get(0)+"_0"
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
time.sleep(2)
traceInfo = "Voltage at: %s in simulation: %s"%(cellSegmentRef, sim)
dataSetV = DataSet(traceInfo, traceInfo, "ms", "mV", "Time", "Membrane Potential")
Spike_List = []
Spike_List.append(0.00)
for i in range(len(times)):
dataSetV.addPoint(times[i], volts[i])
for i in range(len(times)):
if (volts[i] > 0.0):
if (times[i] - Spike_List[len(Spike_List)-1] > 0.50):
Spike_List.append(times[i])
Spike_List.remove(0.00)
plotFrameVolts.addDataSet(dataSetV)
spikeTimes = SpikeAnalyser.getSpikeTimes(volts, times, analyseThreshold, analyseStartTime, analyseStopTime)
currentTrain_Freq = float(train_info_list[currentTrain-1])
print "Number of spikes in sim %s: %i"%(sim, len(spikeTimes))
avgFreq = 0
if len(Spike_List)>0:
avgFreq = 1000.0 / ((Spike_List[len(Spike_List)-1] - Spike_List[0]) / (len(Spike_List) -1))
dataSet.addPoint(currentTrain_Freq,avgFreq)
currentTrain = currentTrain + 1
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()[0]
plotFrameFf.addDataSet(dataSet)
def generateF_ICurve(self,
projFile,
simulator,
simConfig,
preStimAmp, preStimDel, preStimDur,
stimAmpLow, stimAmpInc, stimAmpHigh,
stimDel, stimDur,
simDuration,
analyseStartTime, analyseStopTime,
analyseThreshold,
maxNumSimultaneousSims = 4):
# Load neuroConstruct project
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
self.myProject = pm.loadProject(projFile)
self.simulator = simulator
simConfig = self.myProject.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
pm.doGenerate(simConfig.getName(), self.neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(simConfig)
time.sleep(2)
numGenerated = self.myProject.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
simReferences = {}
if numGenerated > 0:
print "Generating scripts for simulator: %s..."%simulator
if simulator == 'NEURON':
self.myProject.neuronFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.neuronSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.neuronSettings.setGraphicsMode(0) # 0 hides graphs during execution
if simulator == 'GENESIS':
self.myProject.genesisFileManager.setQuitAfterRun(1) # Remove this line to leave the NEURON sim windows open after finishing
self.myProject.genesisSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
self.myProject.genesisSettings.setGraphicsMode(0) # 0 hides graphs during execution
stimAmp = stimAmpLow
while stimAmp <= stimAmpHigh:
while (len(self.simsRunning)>=maxNumSimultaneousSims):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(3) # wait a while...
self.updateSimsRunning()
simRef = "PySim_"+str(float(stimAmp))
print "Going to run simulation: "+simRef
######## Adjusting the amplitude of the current clamp ###############
# preStim = self.myProject.elecInputInfo.getStim(simConfig.getInputs().get(0))
preStim = self.myProject.elecInputInfo.getStim("Input_3")
preStim.setAmp(NumberGenerator(preStimAmp))
preStim.setDel(NumberGenerator(preStimDel))
preStim.setDur(NumberGenerator(preStimDur))
self.myProject.elecInputInfo.updateStim(preStim)
# stim = self.myProject.elecInputInfo.getStim(simConfig.getInputs().get(1))
stim = self.myProject.elecInputInfo.getStim("Input_4")
stim.setAmp(NumberGenerator(stimAmp))
stim.setDel(NumberGenerator(stimDel))
stim.setDur(NumberGenerator(stimDur))
self.myProject.elecInputInfo.updateStim(stim)
print "Next stim: "+ str(stim)
self.myProject.simulationParameters.setReference(simRef)
if simulator == "NEURON":
self.myProject.neuronFileManager.generateTheNeuronFiles(simConfig,
None,
NeuronFileManager.RUN_HOC,
self.simulatorSeed)
print "Generated NEURON files for: "+simRef
compileProcess = ProcessManager(self.myProject.neuronFileManager.getMainHocFile())
compileSuccess = compileProcess.compileFileWithNeuron(0,0)
print "Compiled NEURON files for: "+simRef
if compileSuccess:
pm.doRunNeuron(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
if simulator == "GENESIS":
compartmentalisation = GenesisCompartmentalisation()
self.myProject.genesisFileManager.generateTheGenesisFiles(simConfig,
None,
compartmentalisation,
self.simulatorSeed)
print "Generated GENESIS files for: "+simRef
pm.doRunGenesis(simConfig)
print "Set running simulation: "+simRef
self.simsRunning.append(simRef)
time.sleep(1) # Wait for sim to be kicked off
simReferences[simRef] = stimAmp
stimAmp = stimAmp +stimAmpInc
print
print "Finished running "+str(len(simReferences))+" simulations for project "+ projFile.getAbsolutePath()
print "These can be loaded and replayed in the previous simulation browser in the GUI"
print
while (len(self.simsRunning)>0):
print "Sims currently running: "+str(self.simsRunning)
print "Waiting..."
time.sleep(4) # wait a while...
self.updateSimsRunning()
#simReferences = {'PySim_0.3':0.3,'PySim_0.4':0.4,'PySim_0.5':0.5}
plotFrameFI = PlotManager.getPlotterFrame("F-I curve from project: "+str(self.myProject.getProjectFile())+" on "+simulator , 1, 1)
plotFrameVolts = PlotManager.getPlotterFrame("VoltageTraces from project: "+str(self.myProject.getProjectFile())+" on "+simulator , 1, 1)
plotFrameFI.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "F-I curve for Simulation Configuration: "+str(simConfig)
dataSet = DataSet(info, info, "nA", "Hz", "Current injected", "Firing frequency")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
simList = simReferences.keys()
simList.sort()
for sim in simList:
simDir = File(projFile.getParentFile(), "/neuroConstruct/models/Dan_GranCell/simulations/"+sim)
print
print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
try:
simData = SimulationData(simDir)
simData.initialise()
print "Data loaded: "
print simData.getAllLoadedDataStores()
times = simData.getAllTimes()
cellSegmentRef = simConfig.getCellGroups().get(0)+"_0"
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
traceInfo = "Voltage at: %s in simulation: %s"%(cellSegmentRef, sim)
dataSetV = DataSet(traceInfo, traceInfo, "mV", "ms", "Membrane potential", "Time")
for i in range(len(times)):
dataSetV.addPoint(times[i], volts[i])
plotFrameVolts.addDataSet(dataSetV)
spikeTimes = SpikeAnalyser.getSpikeTimes(volts, times, analyseThreshold, analyseStartTime, analyseStopTime)
stimAmp = simReferences[sim]
print "Number of spikes at %f nA in sim %s: %i"%(stimAmp, sim, len(spikeTimes))
avgFreq = 0
if len(spikeTimes)>1:
avgFreq = len(spikeTimes)/ ((analyseStopTime - analyseStartTime)/1000.0)
dataSet.addPoint(stimAmp,avgFreq)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()[0]
plotFrameFI.addDataSet(dataSet)
simDt = 0.01 # ms
neuroConstructSeed = 1234
simulatorSeed = 1111
simRefPrefix = "SB_"
defaultSynapticDelay = 0.2 # ms
runInBackground = True
#######################################
# Load neuroConstruct project
print "Loading project from "+ projFile.getCanonicalPath()
pm = ProjectManager()
myProject = pm.loadProject(projFile)
myProject.simulationParameters.setDt(simDt)
index = 0
while File( "%s/simulations/%s%i"%(myProject.getProjectMainDirectory().getCanonicalPath(), simRefPrefix,index)).exists():
index = index+1
simRef = "%s%i"%(simRefPrefix,index)
myProject.simulationParameters.setReference(simRef)
# Use this so defaultSynapticDelay will be recorded in simulation.props and listed in SimulationBrowser GUI
SimulationsInfo.addExtraSimProperty("defaultSynapticDelay", str(defaultSynapticDelay))
simConfig = myProject.simConfigInfo.getSimConfig(simConfig)
simConfig = "Propagation delayed connection"
simDuration = 100 # ms
simDt = 0.01 # ms
neuroConstructSeed = 1234
simulatorSeed = 1111
simRefPrefix = "RandomWeights_"
runInBackground = True
#######################################
# Load neuroConstruct project
print "Loading project from " + projFile.getCanonicalPath()
pm = ProjectManager()
myProject = pm.loadProject(projFile)
myProject.simulationParameters.setDt(simDt)
index = 0
while File("%s/simulations/%s%i" %
(myProject.getProjectMainDirectory().getCanonicalPath(),
simRefPrefix, index)).exists():
index = index + 1
simRef = "%s%i" % (simRefPrefix, index)
myProject.simulationParameters.setReference(simRef)
simConfig = myProject.simConfigInfo.getSimConfig(simConfig)
varTimestepNeuron = False
verbose = True
runInBackground= False
suggestedRemoteRunTime = 120
#######################################
### Load neuroConstruct project
print "Loading project from "+ projFile.getCanonicalPath()
pm = ProjectManager()
project = pm.loadProject(projFile)
### Set duration & timestep & simulation configuration
project.simulationParameters.setDt(simDt)
simConfig = project.simConfigInfo.getSimConfig(simConfig)
simConfig.setSimDuration(simDuration)
if saveDataAsHdf5:
project.neuronSettings.setDataSaveFormat(NeuronSettings.DataSaveFormat.HDF5_NC)
### Set simulation reference
import sys
from time import *
from ucl.physiol.neuroconstruct.project import ProjectManager
from ucl.physiol.neuroconstruct.neuroml import NeuroMLFileManager
from ucl.physiol.neuroconstruct.neuroml import NeuroMLConstants
# Load an existing neuroConstruct project
projFile = File("../CElegans.ncx")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
project = pm.loadProject(projFile)
print "Loaded project: " + project.getProjectName()
simConfig = project.simConfigInfo.getSimConfig("CellsOnly")
expectedNumberCells = 302
##########################
pm.doGenerate(simConfig.getName(), 1234)
while pm.isGenerating():
#
# Author: Padraig Gleeson
#
# This file has been developed as part of the neuroConstruct project
# This work has been funded by the Medical Research Council and the
# Wellcome Trust
#
#
try:
from java.io import File
from java.lang import System
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
file = File("../osb/showcase/neuroConstructShowcase/Ex1_Simple/Ex1_Simple.ncx")
print 'Loading project file: ', file.getAbsolutePath()
pm = ProjectManager()
myProject = pm.loadProject(file)
print pm.status()
# Remove this line to remain in interactive mode
System.exit(0)
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
projectManager = ProjectManager()
project = projectManager.loadProject(projFile)
assert (len(project.getProjectDescription()) > 0)
assert (len(project.cellManager.getAllCells()) >= 22)
assert (len(project.cellGroupsInfo.getAllCellGroupNames()) >= 36)
synSetupFile = open("netbuild/makeSyns.sh", 'r')
for line in synSetupFile:
line = line.strip()
if len(line) > 0 and not line.startswith("#"):
words = line.split()
if len(words) >= 6 and words[2].startswith("Syn_"):
synName = words[2]
syn_dir = "../cellMechanisms/%s" % synName
if os.path.isdir(syn_dir):
cm = project.cellMechanismInfo.getCellMechanism(synName)
print "Checked syn %s" % cm.getInstanceName()
else:
print("Problem finding directory: %s!! This is probably due to the synapses not having been generated \n"%syn_dir+ \
"from netbuild/makeSyns.sh (they need to be generated loacally; too many to commit to repository)")
netConnList = open("netbuild/netConnList", 'r')
for line in netConnList:
line = line.strip()
if len(line) > 0 and not line.startswith("#"):
#print "\n\n---- Deciphering line: "+ line
words = line.split()
source = words[0]
target = words[1]
syns = words[2].strip("[]").split(",")
netConnName = "NC3D_" + source[5:] + "_" + target[5:]
assert (source == project.morphNetworkConnectionsInfo.
getSourceCellGroup(netConnName))
assert (target == project.morphNetworkConnectionsInfo.
getTargetCellGroup(netConnName))
print "Checked %s" % netConnName
assert (project.proj3Dproperties.getDisplayOption() ==
Display3DProperties.DISPLAY_SOMA_SOLID_NEURITE_LINE)
assert (abs(project.simulationParameters.getDt() - 0.025) <= 1e-9)
assert (not project.neuronSettings.isVarTimeStep())
assert (project.neuronSettings.isForceCorrectInit())
assert (project.neuronSettings.getDataSaveFormat().equals(
NeuronSettings.DataSaveFormat.TEXT_NC))
assert (not project.genesisSettings.isSymmetricCompartments())
assert (project.genesisSettings.isPhysiologicalUnits())
print "\n**************************************"
print " All tests passed!"
print "**************************************\n"
#
# Author: Padraig Gleeson
#
# This file has been developed as part of the neuroConstruct project
# This work has been funded by the Medical Research Council and the
# Wellcome Trust
#
#
try:
from java.io import File
from java.lang import System
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
file = File("../nCexamples/Ex1_Simple/Ex1_Simple.ncx")
print 'Loading project file: ', file.getAbsolutePath()
pm = ProjectManager()
myProject = pm.loadProject(file)
print pm.status()
# Remove this line to remain in interactive mode
System.exit(0)
def SingleCellNML2generator(projString=" ",
ConfigDict={},
ElecLenList=[],
somaNseg=None,
savingDir=None):
projFile = File(os.getcwd(), projString)
pm = ProjectManager()
compSummary = {}
for config in ConfigDict.keys():
project = pm.loadProject(projFile)
nmlfm = NeuroMLFileManager(project)
compSummary[config] = {}
if " " in config:
configPath = config.replace(" ", "_")
else:
configPath = config
for maxElecLen in ElecLenList:
compSummary[config][str(maxElecLen)] = {}
cell = project.cellManager.getCell(ConfigDict[config])
if maxElecLen > 0:
info = CellTopologyHelper.recompartmentaliseCell(
cell, maxElecLen, project)
print "Recompartmentalising cell %s" % ConfigDict[config]
if somaNseg != None:
cell.getSegmentWithId(
0).getSection().setNumberInternalDivisions(somaNseg)
if savingDir != None:
cellpath = r'../../NeuroML2/%s/%s/%s_%f' % (
savingDir, configPath, configPath, maxElecLen)
else:
cellpath = r'../../NeuroML2/%s/%s_%f' % (
configPath, configPath, maxElecLen)
else:
if savingDir != None:
cellpath = r'../../NeuroML2/%s/%s/%s_default' % (
savingDir, configPath, configPath)
else:
cellpath = r'../../NeuroML2/%s/%s_default' % (configPath,
configPath)
summary = str(cell.getMorphSummary())
summary_string = summary.split("_")
for feature in summary_string:
feature_split = feature.split(":")
compSummary[config][str(maxElecLen)][
feature_split[0]] = feature_split[1]
# the format of summary : Segs:122_Secs:61_IntDivs:1458
print("Will be printing a cell morphology summary")
print compSummary[config][str(maxElecLen)]
######### it turns out that this does not save recompartmentalized cells - all saved cells have identical spatial discretization;
##### generateNeuroML2 receives the parent projFile but not the loaded project which is modified by the CellTopologyHelper.recompartmentaliseCell()
##################### neuroConstruct block #############################################################################
neuroConstructSeed = 1234
verbose = True
pm.doGenerate(config, neuroConstructSeed)
while pm.isGenerating():
if verbose:
print(
"Waiting for the project to be generated with Simulation Configuration: "
+ config)
time.sleep(5)
simConfig = project.simConfigInfo.getSimConfig(config)
seed = 1234
genDir = File(projFile.getParentFile(), "generatedNeuroML2")
nmlfm.generateNeuroMLFiles(
simConfig, NeuroMLConstants.NeuroMLVersion.getLatestVersion(),
LemsConstants.LemsOption.LEMS_WITHOUT_EXECUTE_MODEL,
OriginalCompartmentalisation(), seed, False, True, genDir,
"GENESIS Physiological Units", False)
########################################################################################################################
if not os.path.exists(cellpath):
print("Creating a new directory %s" % cellpath)
os.makedirs(cellpath)
else:
print("A directory %s already exists" % cellpath)
src_files = os.listdir("../generatedNeuroML2/")
for file_name in src_files:
full_file_name = os.path.join("../generatedNeuroML2/",
file_name)
if (os.path.isfile(full_file_name)):
print("Moving generated NeuroML2 to files to %s" %
cellpath)
shutil.copy(full_file_name, cellpath)
#with open("compSummary.json",'w') as fout:
#json.dump(compSummary, fout)
subprocess.call(["~/neuroConstruct/nC.sh -python RegenerateNml2.py -f"],
shell=True)
#subprocess.call(["cp compSummary.json ~/Thalamocortical/NeuroML2/"],shell=True)
quit()
from java.io import File
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
from ucl.physiol.neuroconstruct.cell.converters import MorphMLConverter
# Load an existing neuroConstruct project
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath(
) + ", exists: " + str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
morphDir = File(
"../osb/showcase/neuroConstructShowcase/Ex3_Morphology/importedMorphologies/"
)
morphmlFile = File(morphDir, "SimplePurkinjeCell.morph.xml")
print "Going to load morphology from: " + morphmlFile.getCanonicalPath()
converter = MorphMLConverter()
cell = converter.loadFromMorphologyFile(morphmlFile, "NewCell")
print "Loaded cell: " + cell.getInstanceName() + " with " + str(
cell.getAllSegments().size()) + " segments"
class MultiSim(object):
pconf = None
logger = None
proj_path = None
pm = None
myProject = None
simConfig = None
stimulation = None
cellName = None
simulatorSeed = None
numGenerated = 0
maxNumSimultaneousSims = 1
simsRunning = []
# A value of 0 or lower deactivates timeout.
sim_timeout = 0
def __init__(self, pconf):
configDict = pconf.parse_project_data()
self.pconf = pconf
self.logger = pconf.get_logger("neurosim")
self.proj_path = self.pconf.local_path(configDict["proj_path"])
self.pm = ProjectManager()
projFile = File(self.proj_path)
self.sim_timeout = self.pconf.get_float("sim_timeout", "Simulation")
self.myProject = self.pm.loadProject(projFile)
self.simConfig = self.myProject.simConfigInfo.getSimConfig(self.pconf.get("sim_config", "Simulation"))
#-----------------------------------------------------------
def generate(self):
neuroConstructSeed = int(self.pconf.get("neuroConstructSeed", "NeuroConstruct"))
self.stimulation = self.pconf.get("stimulation", "Simulation")
self.cellName = self.pconf.get("cell", "Simulation")
self.simulatorSeed = int(self.pconf.get("simulatorSeed", "NeuroConstruct"))
self.pm.doGenerate(self.simConfig.getName(), neuroConstructSeed)
self.logger.debug("Waiting for the project to be generated...")
t = 0.0
startTime = time.time()
while self.pm.isGenerating():
self.logger.debug("Waiting...")
time.sleep(0.050)
t += 0.050
if t > 5.0:
self.logger.debug("Waiting...")
t = 0.0
if self.sim_timeout > 0 and (time.time() - startTime) > self.sim_timeout:
self.logger.error("Project data could not be created due to timeout.")
raise SimTimeoutError(self.sim_timeout, "Simulation timeout occured during project generation.")
self.numGenerated = self.myProject.generatedCellPositions.getNumberInAllCellGroups()
self.logger.debug("Number of cells generated: " + str(self.numGenerated))
if self.numGenerated > 0:
self.logger.info("Generating NEURON scripts...")
self.myProject.neuronSettings.setCopySimFiles(1) # 1 copies hoc/mod files to PySim_0 etc. and will allow multiple sims to run at once
# hier kann man entscheiden, ob Bilder angezeigt werden sollen oder nicht:
# ist ersteres auskommentiert, werden Bilder angezeigt und bei Einkommentierung des Zweiten auch automatisch wieder geschlossen
self.myProject.neuronSettings.setNoConsole()
max_sim_threads = self.pconf.get("maxSimThreads")
if max_sim_threads == "auto":
self.maxNumSimultaneousSims = available_cpu_count()
else:
self.maxNumSimultaneousSims = max(1, int(max_sim_threads))
#-----------------------------------------------------------
def run(self, prefix, dataList):
"""Runs all simulations defined by dataList for the loaded project.
Each sim will be named (prefix + i) and dataList contains a
dict with at least "densities", "channels" and "locations" keys.
"""
try:
for i in range(len(dataList)):
self.waitForSimsRunning(self.maxNumSimultaneousSims - 1)
if not self.runSim(i, prefix, dataList[i]):
sys.exit(0)
self.waitForSimsRunning(0)
self.logger.info("Finished running " + str(len(dataList)) + " simulations for project " + self.proj_path)
return
except (KeyboardInterrupt, SystemExit):
raise
except SimTimeoutError, e:
self.logger.warning("Timeout occured: " + e.msg)
sys.exit(10)
Vervaeke2012. """ import os import random import time from java.lang import System from java.io import File from java.util import ArrayList from ucl.physiol.neuroconstruct.project import ProjectManager from ucl.physiol.neuroconstruct.neuron import NeuronFileManager from ucl.physiol.neuroconstruct.nmodleditor.processes import ProcessManager from ucl.physiol.neuroconstruct.cell.utils import CellTopologyHelper timestamp = str(time.time()) pm = ProjectManager(None, None) project_path = '../GJGolgi_ReducedMorph.ncx' project_file = File(project_path) project = pm.loadProject(project_file) sim_config_name = 'dendritic_attenuation' sim_config = project.simConfigInfo.getSimConfig(sim_config_name) project.neuronSettings.setNoConsole() n_points = 18 detailed_distance_bounds = range(10.,190.,10.) rec_segs_reduced = [0,4,5,6] dendritic_group = 'apical_dend_2' # switch off Na channels (TTX)
set_tonic_GABA(work_dir, total_GABA_conductance_in_nS)
# scale excitatory conductance by modifying the AMPA and NMDA
# synaptic models. In general, the amplitude of the excitatory
# conductances is inversely proportional to the number of
# dendrites divided by 4, with the exc_cond_scaling parameter as
# the proportionality constant. If this is set to zero, the
# conductances are not scaled.
if point.exc_cond_scaling:
exc_scaling_factor = point.exc_cond_scaling / (float(point.n_grc_dend)/4)
scale_excitatory_conductances(work_dir, exc_scaling_factor)
# load project and initialise
project_file = java.io.File(work_dir + "/" + project_filename)
print ('Loading project from file: ' + project_file.getAbsolutePath() + ", exists: " + str(project_file.exists()))
pm = ProjectManager(None, None)
project = pm.loadProject(project_file)
print 'Loaded project: ' + project.getProjectName()
# load existing simulation configurations and set sim duration and a
# couple of neuron options
sim_config = project.simConfigInfo.getSimConfig(sim_config_name)
sim_config.setSimDuration(point.sim_duration)
project.neuronSettings.setNoConsole()
project.neuronSettings.setCopySimFiles(1)
# generate network
generate_nC_network(point, pm, project, sim_config)
# generate saves
generate_nC_saves(point, project)
