def map_singlecell_inputs(cellName, cellTypeName):
if not (cellTypeName in exTypes) and not (cellTypeName in inhTypes):
errstr = 'Unknown cell type %s!'
raise TypeError(errstr)
startTime = time.time()
print 'Loading cell morphology...'
parser = sim.CellParser(cellName)
parser.spatialgraph_to_cell()
singleCell = parser.get_cell()
print 'Loading spreadsheets and bouton/PST densities...'
print ' Loading numberOfCells spreadsheet %s' % numberOfCellsSpreadsheetName
numberOfCellsSpreadsheet = sim.read_celltype_numbers_spreadsheet(
numberOfCellsSpreadsheetName)
print ' Loading connections spreadsheet %s' % connectionsSpreadsheetName
connectionsSpreadsheet = sim.read_connections_spreadsheet(
connectionsSpreadsheetName)
print ' Loading PST density %s' % ExPSTDensityName
ExPSTDensity = sim.read_scalar_field(ExPSTDensityName)
ExPSTDensity.resize_mesh()
print ' Loading PST density %s' % InhPSTDensityName
InhPSTDensity = sim.read_scalar_field(InhPSTDensityName)
InhPSTDensity.resize_mesh()
boutonDensities = {}
columns = numberOfCellsSpreadsheet.keys()
preCellTypes = numberOfCellsSpreadsheet[columns[0]]
for col in columns:
boutonDensities[col] = {}
for preCellType in preCellTypes:
boutonDensities[col][preCellType] = []
boutonDensityFolder = os.path.join(prefix, boutonDensityFolderName,
col, preCellType)
boutonDensityNames = glob.glob(
os.path.join(boutonDensityFolder, '*'))
print ' Loading %d bouton densities from %s' % (
len(boutonDensityNames), boutonDensityFolder)
for densityName in boutonDensityNames:
boutonDensity = sim.read_scalar_field(densityName)
boutonDensity.resize_mesh()
boutonDensities[col][preCellType].append(boutonDensity)
inputMapper = sim.NetworkMapper(singleCell, cellTypeName,
numberOfCellsSpreadsheet,
connectionsSpreadsheet, ExPSTDensity,
InhPSTDensity)
inputMapper.exCellTypes = exTypes
inputMapper.inhCellTypes = inhTypes
inputMapper.create_network_embedding(cellName, boutonDensities)
endTime = time.time()
duration = (endTime - startTime) / 60.0
print 'Runtime: %.1f minutes' % duration
def main(whisker, boutonFolder, outName):
fnames = []
scan_directory(boutonFolder, fnames, 'Boutons.am')
#4. go through all cell types
for cellType in cellTypes:
cellTypeDensities = []
cellTypeBounds = [1e6,-1e6,1e6,-1e6,1e6,-1e6] # min, max
cellTypeSpacing = None
activeColumns = []
#5. go through all surrounding columns
SuCs = surroundColumns[whisker].keys()
for column in SuCs:
spikeProb = cellTypePSTHs[cellType][surroundPSTHLookup[surroundColumns[whisker][column]]]
if not spikeProb:
continue
activeColumns.append(column)
#6. load bouton density
fileName = None
for fname in fnames:
if cellType in fname and column in fname:
fileName = fname
break
if fileName is None:
errstr = 'Bouton density of cell type %s in column %s not found' % (cellType, column)
raise IOError(errstr)
tmpDensity = sm.read_scalar_field(fileName)
#7. scale bouton density by PSTH
tmpDensity.mesh *= spikeProb # without pGlut for now; does not really change anything
cellTypeDensities.append(tmpDensity)
#8. add to cell type bouton density
for i in range(len(cellTypeDensities)):
if not i:
cellTypeSpacing = cellTypeDensities[i].spacing
tmpBounds = cellTypeDensities[i].boundingBox
for j in range(3):
if tmpBounds[2*j] < cellTypeBounds[2*j]:
cellTypeBounds[2*j] = tmpBounds[2*j]
if tmpBounds[2*j+1] > cellTypeBounds[2*j+1]:
cellTypeBounds[2*j+1] = tmpBounds[2*j+1]
dims, extent, origin = [], [], []
for i in range(3):
dims.append(int((cellTypeBounds[2*i+1]-cellTypeBounds[2*i])/cellTypeSpacing[i]+1.001))
extent.append(0)
extent.append(dims[i]-1)
origin.append(cellTypeBounds[2*i])
cellTypeMesh = np.zeros(shape=dims)
for i in range(len(cellTypeDensities)):
tmpBounds = cellTypeDensities[i].boundingBox
offset = []
for j in range(3):
minOffset = int((tmpBounds[2*j]-cellTypeBounds[2*j])/cellTypeSpacing[j]+0.001)
#maxOffset = extent[2*j+1] - int((cellTypeBounds[2*j+1]-tmpBounds[2*j+1])/cellTypeSpacing[j]+0.001)
maxOffset = minOffset + cellTypeDensities[i].extent[2*j+1]
diff = (maxOffset - minOffset) - (cellTypeDensities[i].extent[2*j+1])
if diff:
errstr = 'Offset difference does not match size of cell type density: maxOffset = %d - minOffset = %d - dim = %d' % (maxOffset, minOffset, cellTypeDensities[i].extent[2*j+1])
raise RuntimeError(errstr)
offset.append(minOffset)
offset.append(maxOffset)
cellTypeMesh[offset[0]:offset[1]+1,offset[2]:offset[3]+1,offset[4]:offset[5]+1] += cellTypeDensities[i].mesh
#9. write cell type-specific bouton density
cellTypeScalarField = sm.ScalarField(cellTypeMesh, origin, extent, cellTypeSpacing, cellTypeBounds)
cellTypeOutName = outName
cellTypeOutName += '_'
cellTypeOutName += whisker
cellTypeOutName += '_'
cellTypeOutName += cellType
cellTypeOutName += '_active_synapses'
sm.write_scalar_field(cellTypeOutName, cellTypeScalarField)
def computeInnervation(dendriteListPath, dendriteFolderName, cellTypeName,
boutonListPath, boutonFolderName, outputCSVName):
if not (cellTypeName in exTypes) and not (cellTypeName in inhTypes):
errstr = 'Unknown cell type %s!' % cellTypeName
print 'ERROR! %s' % errstr
raise TypeError(errstr)
startTime = time.time()
# Main Path
if sys.platform == 'win32':
prefix = '//nas1/nas1/Data_daniel/Network/L5/L5_InVitro/'
else:
prefix = '/nas1/Data_daniel/Network/L5/L5_InVitro/'
# Required data for calculation synapse density
connectionsSpreadsheetName = os.path.join(
prefix, 'data/CellTypeConnectionSpreadsheet.csv')
ExPSTDensityName = os.path.join(prefix, 'data/EXNormalizationPSTs.am')
connectionsSpreadsheet = sim.read_connections_spreadsheet(
connectionsSpreadsheetName)
ExPSTDensity = sim.read_scalar_field(ExPSTDensityName)
ExPSTDensity.resize_mesh()
InhPSTDensity = []
boutonDensityList = []
boutonDensityListName = []
# Load each bouton density and store it
with open(boutonListPath, 'r') as spreadsheet:
for line in spreadsheet:
# Load Bouton Density
tmpLine = line.strip('\n\r')
densityName = os.path.join(boutonFolderName, tmpLine)
boutonDensity = sim.read_scalar_field(densityName)
boutonDensity.resize_mesh()
boutonDensityList.append(boutonDensity)
boutonDensityListName.append(tmpLine)
if len(boutonDensityList) == 0:
errstr = 'No Bouton Densities were found'
print 'ERROR! %s' % errstr
raise TypeError(errstr)
outputstr = 'Presynapse,Postsynapse,synapsesBasal,synapsesApical\n'
# Go through all dendrites
with open(dendriteListPath, 'r') as spreadsheet:
for line in spreadsheet:
# Read in Dendrite
tmpLine = line.strip('\n\r')
cellNameDend = os.path.join(dendriteFolderName, tmpLine)
if cellNameDend[-4:] != '.hoc':
errstr = 'Can only read in hoc morphologies: %s!' % cellNameDend
print 'ERROR! %s' % errstr
raise TypeError(errstr)
# Load Postsynaptic hoc Morphology
print 'Loading cell morphology... %s' % tmpLine
parser = sim.CellParser(cellNameDend)
parser.spatialgraph_to_cell()
singleCell = parser.get_cell()
synapseDensityComputation = sim.SynapseDensity(singleCell, cellTypeName, connectionsSpreadsheet,\
exTypes, inhTypes, ExPSTDensity, InhPSTDensity)
# Compute Innervation
for b in range(len(boutonDensityList)):
syn = synapseDensityComputation.compute_synapse_density(
boutonDensityList[b], cellTypeName)
# Extract Innervation, if tmp == None, no innervation
synApical = 0
synBasal = 0
if syn is not None:
if 'Dendrite' in syn.keys():
synBasal = np.sum(syn['Dendrite'].mesh)
if 'ApicalDendrite' in syn.keys():
synApical = np.sum(syn['ApicalDendrite'].mesh)
# Name of Pre- and Postsynapse
dendName = cellNameDend.split('/')[-1]
dendName = dendName.replace(".am", "")
dendName = dendName.replace(".hoc", "")
boutonName = boutonDensityListName[b].replace(".am", "")
tmpStr = '%s,%s,%f,%f\n' % (boutonName, dendName, synBasal,
synApical)
outputstr += tmpStr
# Display runtime
endTime = time.time()
duration = (endTime - startTime) / 60.0
print 'Runtime: %.1f minutes' % duration
# Store Innervation as .csv file
with open(outputCSVName, 'w') as csvOutput:
csvOutput.write(outputstr)
print 'Saved data as csv in %s' % outputCSVName
def map_singlecell_inputs_invitro(cellName, cellTypeName):
if not (cellTypeName in exTypes) and not (cellTypeName in inhTypes):
errstr = 'Unknown cell type %s!' % cellTypeName
print 'ERROR! %s' % errstr
raise TypeError(errstr)
if cellName[-4:] != '.hoc':
errstr = 'Can only read in hoc morphologies: %s!' % cellName
print 'ERROR! %s' % errstr
raise TypeError(errstr)
startTime = time.time()
# Main Path
if sys.platform == 'win32':
prefix = '//nas1/nas1/Data_daniel/Network/L5/L5_InVitro/'
else:
prefix = '/nas1/Data_daniel/Network/L5/L5_InVitro/'
# Load Postsynaptic hoc Morphology
print 'Loading cell morphology...'
parser = sim.CellParser(cellName)
parser.spatialgraph_to_cell()
singleCell = parser.get_cell()
# Position of Postsynaptic Morphology and get path to correct bouton densities
strtmp = cellName.replace('_invivo', '')
s = strtmp.split('_')
postsynapse_y = s[-3]
postsynapse_x = s[-4]
if postsynapse_y == '0':
postsynapse_y = s[-1][:-4].strip('.am')
boutonDensityFolderName = os.path.join(prefix, 'BoutonDensity_y0')
elif postsynapse_x == '0':
postsynapse_x = s[-1][:-4].strip('.am')
boutonDensityFolderName = os.path.join(prefix, 'BoutonDensity_x0')
else:
errstr = 'Postsynaptic morphology lacks information about sliced dimension ( %s _ %s )!' % (
postsynapse_x, postsynapse_y)
print 'ERROR! %s' % errstr
raise TypeError(errstr)
# Required data for calculation synapse density
connectionsSpreadsheetName = os.path.join(
prefix, 'data/CellTypeConnectionSpreadsheet.csv')
ExPSTDensityName = os.path.join(prefix, 'data/EXNormalizationPSTs.am')
connectionsSpreadsheet = sim.read_connections_spreadsheet(
connectionsSpreadsheetName)
ExPSTDensity = sim.read_scalar_field(ExPSTDensityName)
ExPSTDensity.resize_mesh()
InhPSTDensity = []
outputfname = cellName.replace('.hoc', '.csv')
synapseDensityComputation = sim.SynapseDensity(singleCell, cellTypeName, connectionsSpreadsheet,\
exTypes, inhTypes, ExPSTDensity, InhPSTDensity)
boutonDensityList = os.path.join(boutonDensityFolderName, 'list.txt')
outputstr = 'Presynapse,Postsynapse,Presynapse_x,Presynapse_y,Postsynapse_x,Postsynapse_y,synapsesBasal,synapsesApical\n'
# Load each bouton density and compute Innervation
with open(boutonDensityList, 'r') as spreadsheet:
for line in spreadsheet:
# Load Bouton Density
tmpLine = line.strip('\n\r')
densityName = os.path.join(boutonDensityFolderName, tmpLine)
boutonDensity = sim.read_scalar_field(densityName)
boutonDensity.resize_mesh()
# Compute Innervation
syn = synapseDensityComputation.compute_synapse_density(
boutonDensity, cellTypeName)
# Extract Innervation, if tmp == None, no innervation
synApical = 0
synBasal = 0
if syn is not None:
if 'Dendrite' in syn.keys():
synBasal = np.sum(syn['Dendrite'].mesh)
if 'ApicalDendrite' in syn.keys():
synApical = np.sum(syn['ApicalDendrite'].mesh)
# Position of Presynapse/BoutonDensity
tmpLine = tmpLine.replace('_invivo', '')
s = tmpLine.split('_')
presynapse_y = s[-2]
presynapse_x = s[-3]
tmpStr = '%s,%s,%s,%s,%s,%s,%f,%f\n' % (
tmpLine, cellName.split('/')[-1], presynapse_x, presynapse_y,
postsynapse_x, postsynapse_y, synBasal, synApical)
outputstr += tmpStr
endTime = time.time()
duration = (endTime - startTime) / 60.0
print 'Runtime: %.1f minutes' % duration
with open(outputfname, 'w') as csvOutput:
csvOutput.write(outputstr)
print 'Saved data as csv in %s' % outputfname