def loaddat (fname):
try:
if fname.endswith('.txt'):
dat = np.loadtxt(fname)
print('Loaded data in ' + fname + '. Extracting Spectrograms.')
return dat
elif fname.endswith('.param'):
ntrial = paramrw.quickgetprm(paramf,'N_trials',int)
basedir = os.path.join(dconf['datdir'],paramf.split(os.path.sep)[-1].split('.param')[0])
#simdat.updatedat(paramf)
#return paramf,simdat.ddat
if ntrial > 1:
ddat = readdpltrials(basedir,quickgetprm(paramf,'N_trials',int))
#print('read dpl trials',ddat[0].shape)
dout = np.zeros((ddat[0].shape[0],1+ntrial))
#print('set dout shape',dout.shape)
dout[:,0] = ddat[0][:,0]
for i in range(ntrial):
dout[:,i+1] = ddat[i][:,1]
return dout
else:
ddat = np.loadtxt(os.path.join(basedir,'dpl.txt'))
#print('ddat.shape:',ddat.shape)
dout = np.zeros((ddat.shape[0],2))
#print('dout.shape:',dout.shape)
dout[:,0] = ddat[:,0]
dout[:,1] = ddat[:,1]
return dout
except:
print('Could not load data in ' + fname)
return None
return None
def getNPyr(self):
try:
x = quickgetprm(self.paramf, 'N_pyr_x', int)
y = quickgetprm(self.paramf, 'N_pyr_y', int)
if type(x) == int and type(y) == int:
return int(x * y * 2)
except:
return 0
def getNPyr (self):
# get the number of pyramidal neurons used in the simulation
try:
x = quickgetprm(self.paramf,'N_pyr_x',int)
y = quickgetprm(self.paramf,'N_pyr_y',int)
if type(x)==int and type(y)==int:
return int(x * y * 2)
except:
return 0
def getEVInputTimes (self):
nprox, ndist = countEvokedInputs(self.paramf)
ltprox, ltdist = [], []
try:
for i in range(nprox): ltprox.append(quickgetprm(self.paramf,'t_evprox_' + str(i+1), float))
for i in range(ndist): ltdist.append(quickgetprm(self.paramf,'t_evdist_' + str(i+1), float))
except:
print('except in getEVInputTimes')
return ltprox, ltdist
def getEVInputTimes (self):
# get the evoked input times
nprox, ndist = countEvokedInputs(self.paramf)
ltprox, ltdist = [], []
for i in range(nprox):
input_mu = quickgetprm(self.paramf,'t_evprox_' + str(i+1), float)
input_sigma = quickgetprm(self.paramf,'sigma_t_evprox_' + str(i+1), float)
ltprox.append((input_mu, input_sigma))
for i in range(ndist):
input_mu = quickgetprm(self.paramf,'t_evdist_' + str(i+1), float)
input_sigma = quickgetprm(self.paramf,'sigma_t_evdist_' + str(i+1), float)
ltdist.append((input_mu, input_sigma))
return ltprox, ltdist
def getNTrials(self):
N_trials = 1
try:
xx = quickgetprm(self.paramf, 'N_trials', int)
if type(xx) == int: N_trials = xx
except:
pass
return N_trials
def getscalefctr(paramf):
try:
xx = quickgetprm(paramf, 'dipole_scalefctr', float)
if type(xx) == float: return xx
except:
pass
if 'dipole_scalefctr' in dconf:
return dconf['dipole_scalefctr']
return 30e3
def getscalefctr (paramf):
# get dipole scaling factor parameter value from paramf file
try:
xx = quickgetprm(paramf,'dipole_scalefctr',float)
if type(xx) == float: return xx
except:
pass
if 'dipole_scalefctr' in dconf:
return dconf['dipole_scalefctr']
return 30e3
def getInputDistrib (self):
import scipy.stats as stats
dinput = {'evprox': [], 'evdist': [], 'prox': [], 'dist': [], 'pois': []}
try:
sim_tstop = quickgetprm(self.paramf,'tstop',float)
sim_dt = quickgetprm(self.paramf,'dt',float)
except FileNotFoundError:
return dinput
num_step = ceil(sim_tstop / sim_dt) + 1
times = np.linspace(0, sim_tstop, num_step)
ltprox, ltdist = self.getEVInputTimes()
for prox in ltprox:
pdf = stats.norm.pdf(times, prox[0], prox[1])
dinput['evprox'].append((times,pdf))
for dist in ltdist:
pdf = stats.norm.pdf(times, dist[0], dist[1])
dinput['evdist'].append((times,pdf))
return dinput
def updatedat (paramf):
# update data dictionary (ddat) from the param file
if debug: print('paramf:',paramf)
try:
getinputfiles(paramf)
for k in ['dpl','spk']:
if not os.path.isfile(dfile[k]): return False
ddat['dpl'] = np.loadtxt(dfile['dpl'])
if os.path.isfile(dfile['spec']): ddat['spec'] = np.load(dfile['spec'])
else: ddat['spec'] = None
ddat['spk'] = np.loadtxt(dfile['spk'])
ddat['dpltrials'] = readdpltrials(basedir,quickgetprm(paramf,'N_trials',int))
return True
except:
return False
def loadDisplayData(self, fname=None):
if fname is None or fname is False:
fname = QFileDialog.getOpenFileName(self,
'Open .param or .txt file',
'data')
fname = os.path.abspath(fname[0])
if not fname: return
dat = loaddat(fname)
self.dat = dat
try:
try:
fmax = quickgetprm(paramf, 'f_max_spec', float)
except:
fmax = 40.
f, lspec, avgdipole, avgspec = extractspec(dat, fmax=fmax)
self.ntrial = len(lspec)
self.updateCB()
self.printStat('Extracted ' + str(len(lspec)) +
' spectrograms from ' + fname)
self.lextspec = lspec
self.lextfiles.append(fname)
self.avgdipole = avgdipole
self.avgspec = avgspec
self.lF.append(f)
except:
self.printStat('Could not extract Spectrograms from ' + fname)
try:
if len(self.lextspec) > 0:
self.printStat('Plotting Spectrograms.')
self.m.lextspec = self.lextspec
self.m.dat = self.dat
self.m.avgspec = self.avgspec
self.m.avgdipole = self.avgdipole
self.m.plot()
self.m.draw() # make sure new lines show up in plot
self.printStat('')
except:
self.printStat('Could not plot data from ' + fname)
def updatedat (paramf):
# update data dictionary (ddat) from the param file
global basedir
if debug: print('paramf:',paramf)
getinputfiles(paramf)
for k in ['dpl','spk']:
if k in ddat:
del ddat[k]
silent = not os.path.exists(basedir)
ddat[k] = readtxt(dfile[k], silent)
if len(ddat[k]) == 0:
del ddat[k]
if not 'dpl' in ddat or not 'spk' in ddat:
raise ValueError
ddat['dpltrials'] = readdpltrials(basedir,quickgetprm(paramf,'N_trials',int))
if os.path.isfile(dfile['spec']):
ddat['spec'] = np.load(dfile['spec'])
else:
ddat['spec'] = None
else: plt.rcParams['font.size'] = dconf['fontsize'] = 10
# colors for the different cell types
dclr = {'L2_pyramidal' : 'g',
'L5_pyramidal' : 'r',
'L2_basket' : 'w',
'L5_basket' : 'b'}
ntrial = 1; tstop = -1; outparamf = spkpath = paramf = ''; EvokedInputs = OngoingInputs = PoissonInputs = False;
for i in range(len(sys.argv)):
if sys.argv[i].endswith('.txt'):
spkpath = sys.argv[i]
elif sys.argv[i].endswith('.param'):
paramf = sys.argv[i]
tstop = paramrw.quickgetprm(paramf,'tstop',float)
ntrial = paramrw.quickgetprm(paramf,'N_trials',int)
EvokedInputs = paramrw.usingEvokedInputs(paramf)
OngoingInputs = paramrw.usingOngoingInputs(paramf)
PoissonInputs = paramrw.usingPoissonInputs(paramf)
outparamf = os.path.join(dconf['datdir'],paramf.split('.param')[0].split(os.path.sep)[-1],'param.txt')
try:
extinputs = spikefn.ExtInputs(spkpath, outparamf)
except ValueError:
print("Error: could not load spike timings from %s" % spkpath)
extinputs.add_delay_times()
alldat = {}
tstop = -1
ntrial = 1
scalefctr = 30e3
dplpath = ''
paramf = ''
for i in range(len(sys.argv)):
if sys.argv[i].endswith('.txt'):
dplpath = sys.argv[i]
elif sys.argv[i].endswith('.param'):
paramf = sys.argv[i]
scalefctr = paramrw.find_param(paramf, 'dipole_scalefctr')
if type(scalefctr) != float and type(scalefctr) != int:
scalefctr = 30e3
tstop = paramrw.find_param(paramf, 'tstop')
ntrial = paramrw.quickgetprm(paramf, 'N_trials', int)
basedir = os.path.join(dconf['datdir'],
paramf.split(os.path.sep)[-1].split('.param')[0])
ddat = {}
ddat['dpltrials'] = readdpltrials(basedir, ntrial)
try:
ddat['dpl'] = np.loadtxt(os.path.join(basedir, 'dpl.txt'))
except:
print('Could not load', dplpath)
quit()
class DipoleCanvas(FigureCanvas):
def __init__(self,
def plotsimdat (self):
# plot the simulation data
self.gRow = 0
bottom = 0.0
only_create_axes = False
if not os.path.isfile(self.paramf):
only_create_axes = True
DrawSpec = False
xl = (0.0, 1.0)
else:
# setup the figure axis for drawing the dipole signal
dinty = self.getInputs()
# try loading data. ignore failures
try:
updatedat(self.paramf)
loaded_dat = True
except ValueError:
loaded_dat = False
pass
xl = (0.0, quickgetprm(self.paramf,'tstop',float))
if dinty['Ongoing'] or dinty['Evoked'] or dinty['Poisson']:
xo = self.plotinputhist(xl, dinty)
if xo:
self.gRow = xo[1]
# whether to draw the specgram - should draw if user saved it or have ongoing, poisson, or tonic inputs
DrawSpec = loaded_dat and \
'spec' in ddat and \
(find_param(dfile['outparam'],'save_spec_data') or dinty['Ongoing'] or dinty['Poisson'] or dinty['Tonic'])
if DrawSpec: # dipole axis takes fewer rows if also drawing specgram
self.axdipole = self.figure.add_subplot(self.G[self.gRow:5,0]) # dipole
bottom = 0.08
else:
self.axdipole = self.figure.add_subplot(self.G[self.gRow:-1,0]) # dipole
yl = (-0.001,0.001)
self.axdipole.set_ylim(yl)
self.axdipole.set_xlim(xl)
left = 0.08
w,h=getscreengeom()
if w < 2800: left = 0.1
self.figure.subplots_adjust(left=left,right=0.99,bottom=bottom,top=0.99,hspace=0.1,wspace=0.1) # reduce padding
if only_create_axes:
return
try:
updatedat(self.paramf)
except ValueError:
if 'dpl' not in ddat:
# failed to load dipole data, nothing more to plot
return
ds = None
xl = (0,ddat['dpl'][-1,0])
dt = ddat['dpl'][1,0] - ddat['dpl'][0,0]
# get spectrogram if it exists, then adjust axis limits but only if drawing spectrogram
if DrawSpec:
if ddat['spec'] is not None:
ds = ddat['spec'] # spectrogram
xl = (ds['time'][0],ds['time'][-1]) # use specgram time limits
else:
DrawSpec = False
sampr = 1e3/dt # dipole sampling rate
sidx, eidx = int(sampr*xl[0]/1e3), int(sampr*xl[1]/1e3) # use these indices to find dipole min,max
N_trials = self.getNTrials()
if debug: print('simdat: N_trials:',N_trials)
yl = [0,0]
yl[0] = min(yl[0],np.amin(ddat['dpl'][sidx:eidx,1]))
yl[1] = max(yl[1],np.amax(ddat['dpl'][sidx:eidx,1]))
if not self.optMode:
# skip for optimization
for lsim in lsimdat: # plot average dipoles from prior simulations
olddpl = lsim[1]
if debug: print('olddpl has shape ',olddpl.shape,len(olddpl[:,0]),len(olddpl[:,1]))
self.axdipole.plot(olddpl[:,0],olddpl[:,1],'--',color='black',linewidth=self.gui.linewidth)
if N_trials>1 and dconf['drawindivdpl'] and len(ddat['dpltrials']) > 0: # plot dipoles from individual trials
for dpltrial in ddat['dpltrials']:
self.axdipole.plot(dpltrial[:,0],dpltrial[:,1],color='gray',linewidth=self.gui.linewidth)
yl[0] = min(yl[0],dpltrial[sidx:eidx,1].min())
yl[1] = max(yl[1],dpltrial[sidx:eidx,1].max())
if conf.dconf['drawavgdpl'] or N_trials <= 1:
# this is the average dipole (across trials)
# it's also the ONLY dipole when running a single trial
self.axdipole.plot(ddat['dpl'][:,0],ddat['dpl'][:,1],'k',linewidth=self.gui.linewidth+1)
yl[0] = min(yl[0],ddat['dpl'][sidx:eidx,1].min())
yl[1] = max(yl[1],ddat['dpl'][sidx:eidx,1].max())
else:
for idx, opt in enumerate(optdat):
optdpl = opt[1]
if idx == len(optdat) - 1:
# only show the last optimization
self.axdipole.plot(optdpl[:,0],optdpl[:,1],'k',color='gray',linewidth=self.gui.linewidth+1)
yl[0] = min(yl[0],optdpl[sidx:eidx,1].min())
yl[1] = max(yl[1],optdpl[sidx:eidx,1].max())
if self.hasinitoptdata():
# show initial dipole in dotted black line
self.axdipole.plot(initial_ddat['dpl'][:,0],initial_ddat['dpl'][:,1],'--',color='black',linewidth=self.gui.linewidth)
yl[0] = min(yl[0],initial_ddat['dpl'][sidx:eidx,1].min())
yl[1] = max(yl[1],initial_ddat['dpl'][sidx:eidx,1].max())
scalefctr = getscalefctr(self.paramf)
NEstPyr = int(self.getNPyr() * scalefctr)
if NEstPyr > 0:
self.axdipole.set_ylabel(r'Dipole (nAm $\times$ '+str(scalefctr)+')\nFrom Estimated '+str(NEstPyr)+' Cells',fontsize=dconf['fontsize'])
else:
self.axdipole.set_ylabel(r'Dipole (nAm $\times$ '+str(scalefctr)+')\n',fontsize=dconf['fontsize'])
self.axdipole.set_xlim(xl); self.axdipole.set_ylim(yl)
if DrawSpec: #
if debug: print('ylim is : ', np.amin(ddat['dpl'][sidx:eidx,1]),np.amax(ddat['dpl'][sidx:eidx,1]))
p_exp = ExpParams(self.paramf, debug=debug)
if len(p_exp.expmt_groups) > 0:
expmt_group = p_exp.expmt_groups[0]
else:
expmt_group = None
p = p_exp.return_pdict(expmt_group, 0)
gRow = 6
self.axspec = self.figure.add_subplot(self.G[gRow:10,0]); # specgram
cax = self.axspec.imshow(ds['TFR'],extent=(ds['time'][0],ds['time'][-1],ds['freq'][-1],ds['freq'][0]),aspect='auto',origin='upper',cmap=plt.get_cmap(p['spec_cmap']))
self.axspec.set_ylabel('Frequency (Hz)',fontsize=dconf['fontsize'])
self.axspec.set_xlabel('Time (ms)',fontsize=dconf['fontsize'])
self.axspec.set_xlim(xl)
self.axspec.set_ylim(ds['freq'][-1],ds['freq'][0])
cbaxes = self.figure.add_axes([0.6, 0.49, 0.3, 0.005])
cb = plt.colorbar(cax, cax = cbaxes, orientation='horizontal') # horizontal to save space
else:
self.axdipole.set_xlabel('Time (ms)',fontsize=dconf['fontsize'])
def plotinputhist (self, xl, dinty):
""" plot input histograms
xl = x axis limits
dinty = dict of input types used, determines how many/which axes created/displayed
"""
extinputs = None
plot_distribs = False
sim_tstop = quickgetprm(self.paramf,'tstop',float)
sim_dt = quickgetprm(self.paramf,'dt',float)
num_step = ceil(sim_tstop / sim_dt) + 1
times = np.linspace(0, sim_tstop, num_step)
try:
extinputs = spikefn.ExtInputs(dfile['spk'], dfile['outparam'])
extinputs.add_delay_times()
dinput = extinputs.inputs
except ValueError:
dinput = self.getInputDistrib()
plot_distribs = True
if len(dinput['dist']) <= 0 and len(dinput['prox']) <= 0 and \
len(dinput['evdist']) <= 0 and len(dinput['evprox']) <= 0 and \
len(dinput['pois']) <= 0:
if debug: print('all hists 0!')
return False
self.hist=hist={x:None for x in ['feed_dist','feed_prox','feed_evdist','feed_evprox','feed_pois']}
hasPois = len(dinput['pois']) > 0 and dinty['Poisson'] # this ensures synaptic weight > 0
gRow = 0
self.axdist = self.axprox = self.axpois = None # axis objects
# check poisson inputs, create subplot
if hasPois:
self.axpois = self.figure.add_subplot(self.G[gRow,0])
gRow += 1
# check distal inputs, create subplot
if (len(dinput['dist']) > 0 and dinty['OngoingDist']) or \
(len(dinput['evdist']) > 0 and dinty['EvokedDist']):
self.axdist = self.figure.add_subplot(self.G[gRow,0])
gRow+=1
# check proximal inputs, create subplot
if (len(dinput['prox']) > 0 and dinty['OngoingProx']) or \
(len(dinput['evprox']) > 0 and dinty['EvokedProx']):
self.axprox = self.figure.add_subplot(self.G[gRow,0])
gRow+=1
# check input types provided in simulation
if extinputs is not None and self.hassimdata(): # only valid param.txt file after sim was run
if debug:
print(len(dinput['dist']),len(dinput['prox']),len(dinput['evdist']),len(dinput['evprox']),len(dinput['pois']))
if hasPois: # any Poisson inputs?
extinputs.plot_hist(self.axpois,'pois',times,'auto',xl,color='k',hty='step',lw=self.gui.linewidth+1)
if len(dinput['dist']) > 0 and dinty['OngoingDist']: # dinty condition ensures synaptic weight > 0
extinputs.plot_hist(self.axdist,'dist',times,'auto',xl,color='g',lw=self.gui.linewidth+1)
if len(dinput['prox']) > 0 and dinty['OngoingProx']: # dinty condition ensures synaptic weight > 0
extinputs.plot_hist(self.axprox,'prox',times,'auto',xl,color='r',lw=self.gui.linewidth+1)
if len(dinput['evdist']) > 0 and dinty['EvokedDist']: # dinty condition ensures synaptic weight > 0
extinputs.plot_hist(self.axdist,'evdist',times,'auto',xl,color='g',hty='step',lw=self.gui.linewidth+1)
if len(dinput['evprox']) > 0 and dinty['EvokedProx']: # dinty condition ensures synaptic weight > 0
extinputs.plot_hist(self.axprox,'evprox',times,'auto',xl,color='r',hty='step',lw=self.gui.linewidth+1)
elif plot_distribs:
if len(dinput['evprox']) > 0 and dinty['EvokedProx']: # dinty condition ensures synaptic weight > 0
prox_tot = np.zeros(len(dinput['evprox'][0][0]))
for prox in dinput['evprox']:
prox_tot += prox[1]
plot = self.axprox.plot(dinput['evprox'][0][0],prox_tot,color='r',lw=self.gui.linewidth,label='evprox distribution')
self.axprox.set_xlim(dinput['evprox'][0][0][0],dinput['evprox'][0][0][-1])
if len(dinput['evdist']) > 0 and dinty['EvokedDist']: # dinty condition ensures synaptic weight > 0
dist_tot = np.zeros(len(dinput['evdist'][0][0]))
for dist in dinput['evdist']:
dist_tot += dist[1]
plot = self.axdist.plot(dinput['evdist'][0][0],dist_tot,color='g',lw=self.gui.linewidth,label='evdist distribution')
self.axprox.set_xlim(dinput['evdist'][0][0][0],dinput['evdist'][0][0][-1])
ymax = 0
for ax in [self.axpois, self.axdist, self.axprox]:
if not ax is None:
if ax.get_ylim()[1] > ymax:
ymax = ax.get_ylim()[1]
if ymax == 0:
if debug: print('all hists None!')
return False
else:
for ax in [self.axpois, self.axdist, self.axprox]:
if not ax is None:
ax.set_ylim(0,ymax)
if self.axdist:
self.axdist.invert_yaxis()
for ax in [self.axpois,self.axdist,self.axprox]:
if ax:
ax.set_xlim(xl)
ax.legend(loc=1) # legend in upper right
return True,gRow