# miscfuncs.py -- miscellaneous Python functions to be callable from the
# running interpreter
# Various functions to be callable from the Python interpreter.
# This is kind of the dumping place for new function to be more properly
# place later or functions that don't fit elsewhere, but are helpful.
#
# Note: This code should not make calls to Python functions in the scope
# of the outer Python scope this Python / hoc code mixture uses.
#
# Also, this needs to run in the context of numpy namespace being loaded.
#
# Last update: 10/8/12 (georgec)
#
# Functions to ease interactive interface with hoc code
#
# Convert a hoc variable (passed as string) into a numpy array.
def hv2narr (hocvar='vec'):
exec('%s = h.%s.to_python()' % (hocvar, hocvar))
exec('%s = array(%s)' % (hocvar, hocvar))
exec('x = %s' % hocvar)
return x
# Convert a numpy array into a hoc variable (passed as string).
def narr2hv (hocvar,narr):
h('objref %s' % hocvar)
h('%s = new Vector()' % hocvar)
h('objref tmp')
h.tmp = narr
h('{%s.from_python(tmp)}' % hocvar)
# Do a gethdrs() for an NQS table.
def shownqshdr (nqsvar='col[0].cellsnq'):
print nqsvar
h('%s.gethdrs()' % nqsvar)
# Do a pr(numrows) for an NQS table.
def nqspr (nqsvar='col[0].cellsnq', numrows=10):
print nqsvar
h('%s.pr(%d)' % (nqsvar, numrows))
# Convert a hoc NQS column into a numpy array.
def nqscol2narr (nqsvar='col[0].cellsnq', colstr='col'):
h('objref tmpv')
h('tmpv = new Vector()')
h('tmpv = %s.getcol("%s")' % (nqsvar, colstr))
tmpv = h.tmpv.to_python()
tmpv = array(tmpv)
return tmpv
# Get the CTYP number from the string (e.g. 'E2').
def get_ctyp_num (ctyp_str):
ctyp_ind = -1
for ii in range(int(h.CTYPi)):
if (h.CTYP.o(ii).s == ctyp_str):
ctyp_ind = ii
return ctyp_ind
# Get the CTYP string from the CTYP number.
def get_ctyp_str (ctyp_num):
return h.CTYP.o(ctyp_num).s
# Get the STYP number from the string (e.g. 'AM2').
def get_styp_num (styp_str):
styp_ind = -1
for ii in range(int(h.STYPi)):
if (h.STYP.o(ii).s == styp_str):
styp_ind = ii
return styp_ind
# Get the STYP string from the STYP number.
def get_styp_str (styp_num):
return h.STYP.o(styp_num).s
# Get the average intracolumnar weight of a certain type between two
# cell types.
def get_ave_conn_wt (fromtype, totype, syntype, thecol=0):
print 'wmat entry: %f' % \
h.wmat[get_ctyp_num(fromtype)][get_ctyp_num(totype)][get_styp_num(syntype)][0]
if (h.wsetting_INTF6):
h.col[thecol].connsnq.verbose = 0
h.col[thecol].selectconns2(get_ctyp_num(fromtype),get_ctyp_num(totype))
if (syntype in ['AM','AM2','GA','GA2']):
h('vec = col[%d].connsnq.getcol("wt1")' % thecol)
else:
h('vec = col[%d].connsnq.getcol("wt2")' % thecol)
print 'actual weight average from connsnq: %f' % hv2narr('vec').mean()
h('col[%d].connsnq.tog("db")' % thecol)
h.col[thecol].connsnq.verbose = 1
#
# Parameter setting / reading functions (not in params.hoc)
#
#
# vq input reading / setting functions (not usable for NetStim method)
#
# Show each of the input weights for each used cell type / synapse type
def show_ctyp_input_wts (thecol=0):
ctyplist = ['E2','I2','I2L','E5R','E5B','I5','I5L','E6','I6','I6L']
# ctyplist = ['E2','I2','I2L','E4','I4','I4L','E5R','E5B','I5','I5L', \
# 'E6','I6','I6L']
styplist = ['AM2','NM2','GA','GA2']
# Set up a hoc vector.
h('objref tmpv')
h('tmpv = new Vector()')
# Turn off verbosity of table.
h('lcstim.o(%d).vq.verbose = 0' % thecol)
# Print the table header.
print 'ctyp\tstyp\twt'
# For each of the cell types...
for ctyp in ctyplist:
# Find the first cell ID of this type.
h('tmpv = col[%d].cellsnq.getrow("celltype",%s)' % (thecol, ctyp))
cell_id = int(h.tmpv[1])
# For all of the used synapse types...
for styp in styplist:
h('{lcstim.o(%d).vq.select("ind",%d,"sy",%d)}' % \
(thecol, cell_id, get_styp_num(styp)))
h('tmpv = lcstim.o(%d).vq.getrow(0)' % thecol)
print ctyp, '\t', styp, '\t',
print h.tmpv[2]
# Reset the vq table
h('lcstim.o(%d).vq.tog("DB")' % thecol)
h('lcstim.o(%d).vq.verbose = 1' % thecol)
# Set all weights of a certain cell type / synapse type to newwt.
def set_ctyp_input_wts (ctyp='E2', styp='AM2', newwt=3.75):
# Set up a hoc vector.
h('objref tmpv')
h('tmpv = new Vector()')
# Turn off verbosity of table.
thecol = 0
h('lcstim.o(%d).vq.verbose = 0' % thecol)
# Find the first cell ID of this type.
h('tmpv = col[%d].cellsnq.getrow("celltype",%s)' % (thecol, ctyp))
cell_id = int(h.tmpv[1])
# Get the old weight for the type.
h('{lcstim.o(%d).vq.select("ind",%d,"sy",%d)}' % \
(thecol, cell_id, get_styp_num(styp)))
h('tmpv = lcstim.o(%d).vq.getrow(0)' % thecol)
oldwt = h.tmpv[2]
# For all of the columns...
for ii in range(int(h.numcols)):
h('lcstim.o(%d).mulwts(%s, %s, %f)' % (ii, ctyp, styp, (newwt / oldwt)))
# Reset the vq table
h('lcstim.o(%d).vq.tog("DB")' % thecol)
h('lcstim.o(%d).vq.verbose = 1' % thecol)
# Reset all weights of a certain cell type / synapse type to a multiplied
# version of their original value.
def resetmult_ctyp_input_wts (ctyp='E2', styp='AM2', wtmult=1.0):
# Reset the CSTIMs to their original value.
h.setcstim()
# For all of the columns...
for ii in range(int(h.numcols)):
h('lcstim.o(%d).mulwts(%s, %s, %f)' % (ii, ctyp, styp, wtmult))
# Set all weights of a certain cell type / synapse type to a multiplied
# version of their original value.
def mult_ctyp_input_wts (ctyp='E2', styp='AM2', wtmult=1.0):
# For all of the columns...
for ii in range(int(h.numcols)):
h('lcstim.o(%d).mulwts(%s, %s, %f)' % (ii, ctyp, styp, wtmult))
#
# grvec functions
#
# Load saved grvec simulation info.
# NOTE: Both the file and its dot-prefixed equivalent need to be present for gvnew() to succeed.
def ldgrvec (grvec_fname):
h.gvnew(grvec_fname)
# Look at the grvec printlist for the current sim or a saved grvec file.
def lookgrveclist (gvcobjnum=0):
if (gvcobjnum == 0):
gvcstr = 'current simulation'
else:
gvcstr = h.panobjl.o(gvcobjnum).filename
print 'GRVEC List #%d (%s)' % (gvcobjnum, gvcstr)
print '--------------------------------------------'
if (gvcobjnum == 0):
for ii in range(int(h.printlist.count())):
prstr = '%d %s %d ' % (ii, h.printlist.o(ii).name, \
h.printlist.o(ii).vec.size())
print prstr,
if (h.printlist.o(ii).tvec == None):
print '(vec only)'
else:
print '\n',
else:
for ii in range(int(h.panobjl.o(gvcobjnum).printlist.count())):
print '%d %s %d' % (ii, h.panobjl.o(gvcobjnum).printlist.o(ii).name, \
h.panobjl.o(gvcobjnum).printlist.o(ii).size)
# Get tvec and vec (in numpy form) from grvec (gvcobjnum=0 means current
# sim; >0 means saved grvec file)
def getgrvecdat (gvcobjnum=0, vecname='C0_X0_Y0_SPKS'):
found_ind = -1
for ii in range(int(h.panobjl.o(gvcobjnum).printlist.count())):
if (h.panobjl.o(gvcobjnum).printlist.o(ii).name == vecname):
found_ind = ii
if (found_ind == -1):
print 'No such array is on the printlist.'
return None, None
elif (gvcobjnum == 0):
vec = h.printlist.o(found_ind).vec.to_python()
tvec = h.printlist.o(found_ind).tvec
if (tvec == None):
tvec = linspace(0,len(vec)-1,len(vec))
else:
tvec = array(tvec.to_python())
else:
h('goodread = panobjl.o(%d).rv_readvec(%d,tvec,vec)' % (gvcobjnum, found_ind))
if (not h.goodread):
h('panobjl.o(%d).rv_readvec(%d,vec)' % (gvcobjnum, found_ind))
vec = h.vec.to_python()
tvec = linspace(0,len(vec)-1,len(vec))
else:
tvec = array(h.tvec.to_python())
vec = h.vec.to_python()
vec = array(vec)
return tvec, vec
# Plot tvec and vec (in numpy form) from grvec (gvcobjnum=0 means current
# sim; >0 means saved grvec file)
def plotgrvecdat (gvcobjnum=0, vecname='C0_X0_Y0_SPKS'):
tvec,vec = getgrvecdat(gvcobjnum, vecname)
if (tvec != None):
plot(tvec,vec)
#
# Miscellaneous functions
#
