def exportToElphy(data_store_location,elphy_export_location,sheets=None,threshold=None):
import os.path
if not os.path.isdir(elphy_export_location):
if os.path.exists(elphy_export_location):
raise ValueError("The elphy export path is not a directory")
else:
os.makedirs(elphy_export_location)
setup_logging()
data_store = PickledDataStore(load=True,parameters=ParameterSet({'root_directory':data_store_location, 'store_stimuli' : False}))
ps = MP.parameter_value_list([MP.MozaikParametrized.idd(s) for s in data_store.get_stimuli()],'name')
for i,sn in enumerate(ps):
if sheets == None: sheets = data_store.sheets()
for shn in sheets:
dsv = param_filter_query(data_store,st_name = sn,sheet_name = shn)
if dsv.get_stimuli() == []: continue
varying_parameters = MP.varying_parameters([MP.MozaikParametrized.idd(s) for s in dsv.get_stimuli()])
segments,stimuli = MP.colapse(dsv.get_segments(),[MP.MozaikParametrized.idd(s) for s in dsv.get_stimuli()],parameter_list=['trial'],allow_non_identical_objects=True)
j = 0
for segs,st in zip(segments,stimuli):
# just make sure all segments are fully loaded, in future this should probably soreted out such that this line can be deleted
for s in segs: s.load_full()
# create file name:
filename = "name=" + sn + "#" + "sheet_name=" + shn
for pn in varying_parameters:
if pn != "trial":
filename += "#" + str(pn) + "=" + str(getattr(MP.MozaikParametrized.idd(st),pn))
path = os.path.join(elphy_export_location,filename+".dat")
# if the threshold is defined add spikes into Vms
if threshold != None:
for seg in segs : addSpikes(seg,threshold)
createFileFromSegmentList( segs, path)
print "Finished saving file %d/%d for sheet %s and %d-th stimulus" % (j+1,len(segments),shn,i)
# release segments from memory
for s in segs: s.release()
j = j + 1
print "Finished saving %d/%d stimulus" % (i+1,len(ps))
print sys.argv
import matplotlib
matplotlib.use('Agg')
import os
from mozaik.controller import setup_logging
import mozaik
from mozaik.storage.datastore import Hdf5DataStore,PickledDataStore
from mozaik.tools.mozaik_parametrized import colapse, colapse_to_dictionary, MozaikParametrized
from mozaik.analysis.technical import NeuronAnnotationsToPerNeuronValues
from parameters import ParameterSet
import numpy
from mozaik.storage import queries
from mozaik.controller import Global
Global.root_directory = sys.argv[1]+'/'
setup_logging()
data_store = PickledDataStore(load=True,parameters=ParameterSet({'root_directory':sys.argv[1],'store_stimuli' : False}),replace=True)
NeuronAnnotationsToPerNeuronValues(data_store,ParameterSet({})).analyse()
analog_ids = queries.param_filter_query(data_store,sheet_name="V1_Exc_L4").get_segments()[0].get_stored_esyn_ids()
dsv = queries.param_filter_query(data_store,st_name='FlashedBar')
for ads in dsv.get_analysis_result():
sid = MozaikParametrized.idd(ads.stimulus_id)
sid.x=0
ads.stimulus_id = str(sid)
for seg in dsv.get_segments():
sid = MozaikParametrized.idd(seg.annotations['stimulus'])
sid.x=0
from experiments import create_experiments
from model import VogelsAbbott
from mozaik.storage.datastore import Hdf5DataStore,PickledDataStore
from analysis_and_visualization import perform_analysis_and_visualization
from parameters import ParameterSet
#mpi_comm = MPI.COMM_WORLD
logger = mozaik.getMozaikLogger()
simulation_name = "VogelsAbbott2005"
simulation_run_name, _, _, _, modified_parameters = parse_workflow_args()
if True:
data_store,model = run_workflow(simulation_name,VogelsAbbott,create_experiments)
model.connectors['ExcExcConnection'].store_connections(data_store)
else:
setup_logging()
data_store = PickledDataStore(
load=True,
parameters=ParameterSet(
{
"root_directory": result_directory_name(
simulation_run_name, simulation_name, modified_parameters
),
"store_stimuli": False,
}
),
replace=True,
)
logger.info('Loaded data store')
#if mpi_comm.rank == 0:
def exportToElphy(data_store_location,
elphy_export_location,
sheets=None,
threshold=None):
import os.path
if not os.path.isdir(elphy_export_location):
if os.path.exists(elphy_export_location):
raise ValueError("The elphy export path is not a directory")
else:
os.makedirs(elphy_export_location)
setup_logging()
data_store = PickledDataStore(load=True,
parameters=ParameterSet({
'root_directory':
data_store_location,
'store_stimuli':
False
}))
ps = MP.parameter_value_list(
[MP.MozaikParametrized.idd(s) for s in data_store.get_stimuli()],
'name')
for i, sn in enumerate(ps):
if sheets == None: sheets = data_store.sheets()
for shn in sheets:
dsv = param_filter_query(data_store, st_name=sn, sheet_name=shn)
if dsv.get_stimuli() == []: continue
varying_parameters = MP.varying_parameters(
[MP.MozaikParametrized.idd(s) for s in dsv.get_stimuli()])
segments, stimuli = MP.colapse(
dsv.get_segments(),
[MP.MozaikParametrized.idd(s) for s in dsv.get_stimuli()],
parameter_list=['trial'],
allow_non_identical_objects=True)
j = 0
for segs, st in zip(segments, stimuli):
# just make sure all segments are fully loaded, in future this should probably soreted out such that this line can be deleted
for s in segs:
s.load_full()
# create file name:
filename = "name=" + sn + "#" + "sheet_name=" + shn
for pn in varying_parameters:
if pn != "trial":
filename += "#" + str(pn) + "=" + str(
getattr(MP.MozaikParametrized.idd(st), pn))
path = os.path.join(elphy_export_location, filename + ".dat")
# if the threshold is defined add spikes into Vms
if threshold != None:
for seg in segs:
addSpikes(seg, threshold)
createFileFromSegmentList(segs, path)
print "Finished saving file %d/%d for sheet %s and %d-th stimulus" % (
j + 1, len(segments), shn, i)
# release segments from memory
for s in segs:
s.release()
j = j + 1
print "Finished saving %d/%d stimulus" % (i + 1, len(ps))
