def plotextdat (self, recalcErr=True):
# plot 'external' data (e.g. from experiment/other simulation)
try:
#self.plotsimdat()
if recalcErr: calcerr(ddat) # recalculate/save the error?
lerr, errtot = ddat['lerr'], ddat['errtot']
hassimdata = self.hassimdata() # has the simulation been run yet?
if not hasattr(self,'axdipole'): self.setupaxdipole() # do we need an axis for drawing?
elif self.axdipole is None: self.setupaxdipole()
ax = self.axdipole
yl = ax.get_ylim()
cmap=plt.get_cmap('nipy_spectral')
csm = plt.cm.ScalarMappable(cmap=cmap);
csm.set_clim((0,100))
self.clearlextdatobj() # clear annotation objects
ddx = 0
for fn,dat in ddat['dextdata'].items():
shp = dat.shape
clr = csm.to_rgba(self.getnextcolor())
c = min(shp[1],1)
self.lextdatobj.append(ax.plot(dat[:,0],dat[:,c],color=clr,linewidth=self.gui.linewidth+1))
yl = ((min(yl[0],min(dat[:,c]))),(max(yl[1],max(dat[:,c]))))
fx = int(shp[0] * float(c) / shp[1])
if lerr:
tx,ty=dat[fx,0],dat[fx,c]
txt='RMSE:' + str(round(lerr[ddx],2))
self.lextdatobj.append(ax.annotate(txt,xy=(dat[0,0],dat[0,c]),xytext=(tx,ty),color=clr,fontweight='bold'))
self.lpatch.append(mpatches.Patch(color=clr, label=fn.split(os.path.sep)[-1].split('.txt')[0]))
ddx+=1
ax.set_ylim(yl)
if self.lextdatobj and self.lpatch:
self.lextdatobj.append(ax.legend(handles=self.lpatch))
if errtot:
tx,ty=0,0
txt='Avg. RMSE:' + str(round(errtot,2))
self.annot_avg = ax.annotate(txt,xy=(0,0),xytext=(0.005,0.005),textcoords='axes fraction',fontweight='bold')
if not hassimdata: # need axis labels
left = 0.08
w,h=getscreengeom()
if w < 2800: left = 0.1
ax.set_xlabel('Time (ms)',fontsize=dconf['fontsize'])
ax.set_ylabel('Dipole (nAm)',fontsize=dconf['fontsize'])
myxl = ax.get_xlim()
if myxl[0] < 0.0: ax.set_xlim((0.0,myxl[1]+myxl[0]))
self.figure.subplots_adjust(left=left,right=0.99,bottom=0.0,top=0.99,hspace=0.1,wspace=0.1) # reduce padding
except:
print('simdat ERR: could not plotextdat')
return False
return True
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 plotsimdat (self):
# plot the simulation data
if not updatedat(self.paramf): return # if no data from sim, or data load problem return
self.clearaxes()
plt.close(self.figure);
if len(ddat.keys()) == 0: return
dinty = self.getInputs() # get dict of input types used (influences which/how plots drawn)
# whether to draw the specgram - should draw if user saved it or have ongoing, poisson, or tonic inputs
DrawSpec = find_param(dfile['outparam'],'save_spec_data') or dinty['Ongoing'] or dinty['Poisson'] or dinty['Tonic']
try:
ds = None
xl = (0,find_param(dfile['outparam'],'tstop'))
dt = find_param(dfile['outparam'],'dt')
# get spectrogram if it exists, then adjust axis limits but only if drawing spectrogram
if DrawSpec and 'spec' in ddat:
if ddat['spec'] is not None:
ds = ddat['spec'] # spectrogram
xl = (ds['time'][0],ds['time'][-1]) # use specgram time limits
gRow = 0
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
if dinty['Ongoing'] or dinty['Evoked'] or dinty['Poisson']:
xo = self.plotinputhist(xl, dinty)
if xo: gRow = xo[1]
if DrawSpec: # dipole axis takes fewer rows if also drawing specgram
self.axdipole = ax = self.figure.add_subplot(self.G[gRow:5,0]); # dipole
self.lax.append(ax)
else:
self.axdipole = ax = self.figure.add_subplot(self.G[gRow:-1,0]); # dipole
self.lax.append(ax)
N_trials = self.getNTrials()
if debug: print('simdat: N_trials:',N_trials)
yl = [np.amin(ddat['dpl'][sidx:eidx,1]),np.amax(ddat['dpl'][sidx:eidx,1])]
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]))
ax.plot(olddpl[:,0],olddpl[:,1],'--',color='black',linewidth=self.gui.linewidth)
yl[0] = min(yl[0],olddpl[sidx:eidx,1].min())
yl[1] = max(yl[1],olddpl[sidx:eidx,1].max())
if N_trials>1 and dconf['drawindivdpl'] and len(ddat['dpltrials']) > 0: # plot dipoles from individual trials
for dpltrial in ddat['dpltrials']:
ax.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 dinty['Evoked']: self.drawEVInputTimes(ax,yl,0.1,(xl[1]-xl[0])*.02,(yl[1]-yl[0])*.02)#15.0)
#if dinty['Evoked']: self.drawEVInputTimes(ax,yl,0.1,15.0)
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
ax.plot(ddat['dpl'][:,0],ddat['dpl'][:,1],'k',linewidth=self.gui.linewidth+1)
scalefctr = getscalefctr(self.paramf)
NEstPyr = int(self.getNPyr() * scalefctr)
if NEstPyr > 0:
ax.set_ylabel(r'Dipole (nAm $\times$ '+str(scalefctr)+')\nFrom Estimated '+str(NEstPyr)+' Cells',fontsize=dconf['fontsize'])
else:
ax.set_ylabel(r'Dipole (nAm $\times$ '+str(scalefctr)+')\n',fontsize=dconf['fontsize'])
ax.set_xlim(xl); ax.set_ylim(yl)
bottom = 0.0
left = 0.08
w,h=getscreengeom()
if w < 2800: left = 0.1
if DrawSpec: #
if debug: print('ylim is : ', np.amin(ddat['dpl'][sidx:eidx,1]),np.amax(ddat['dpl'][sidx:eidx,1]))
gRow = 6
self.axspec = ax = self.figure.add_subplot(self.G[gRow:10,0]); # specgram
self.lax.append(ax)
cax = ax.imshow(ds['TFR'],extent=(ds['time'][0],ds['time'][-1],ds['freq'][-1],ds['freq'][0]),aspect='auto',origin='upper',cmap=plt.get_cmap('jet'))
ax.set_ylabel('Frequency (Hz)',fontsize=dconf['fontsize'])
ax.set_xlabel('Time (ms)',fontsize=dconf['fontsize'])
ax.set_xlim(xl)
ax.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
for ax in self.lax:
if ax: ax.set_xlim(xl)
bottom = 0.08
else:
ax.set_xlabel('Time (ms)',fontsize=dconf['fontsize'])
except:
print('ERR: in plotsimdat')
self.figure.subplots_adjust(left=left,right=0.99,bottom=bottom,top=0.99,hspace=0.1,wspace=0.1) # reduce padding
def plotextdat (self, recalcErr=True):
if not 'dextdata' in ddat or len(ddat['dextdata']) == 0:
return
# plot 'external' data (e.g. from experiment/other simulation)
hassimdata = self.hassimdata() # has the simulation been run yet?
if hassimdata:
if recalcErr:
calcerr(ddat, ddat['dpl'][-1,0]) # recalculate/save the error?
lerr, errtot = ddat['lerr'], ddat['errtot']
if self.optMode:
initial_err = initial_ddat['errtot']
else:
lerr = None
errtot = None
if self.axdipole is None:
self.axdipole = self.figure.add_subplot(self.G[0:-1,0]) # dipole
yl = (-0.001,0.001)
else:
yl = self.axdipole.get_ylim()
xl = (0.0,1.0)
cmap=plt.get_cmap('nipy_spectral')
csm = plt.cm.ScalarMappable(cmap=cmap);
csm.set_clim((0,100))
self.clearlextdatobj() # clear annotation objects
ddx = 0
for fn,dat in ddat['dextdata'].items():
shp = dat.shape
clr = csm.to_rgba(self.getnextcolor())
c = min(shp[1],1)
self.lextdatobj.append(self.axdipole.plot(dat[:,0],dat[:,c],color=clr,linewidth=self.gui.linewidth+1))
xl = ((min(xl[0],min(dat[:,0]))),(max(xl[1],max(dat[:,0]))))
yl = ((min(yl[0],min(dat[:,c]))),(max(yl[1],max(dat[:,c]))))
fx = int(shp[0] * float(c) / shp[1])
if lerr:
tx,ty=dat[fx,0],dat[fx,c]
txt='RMSE: %.2f' % round(lerr[ddx],2)
if not self.optMode:
self.lextdatobj.append(self.axdipole.annotate(txt,xy=(dat[0,0],dat[0,c]),xytext=(tx,ty),color=clr,fontweight='bold'))
self.lpatch.append(mpatches.Patch(color=clr, label=fn.split(os.path.sep)[-1].split('.txt')[0]))
ddx+=1
self.axdipole.set_xlim(xl)
self.axdipole.set_ylim(yl)
if self.lextdatobj and self.lpatch:
self.lextdatobj.append(self.axdipole.legend(handles=self.lpatch, loc=2))
if errtot:
tx,ty=0,0
if self.optMode:
clr = 'black'
txt='RMSE: %.2f' % round(initial_err,2)
self.annot_avg = self.axdipole.annotate(txt,xy=(0,0),xytext=(0.005,0.005),textcoords='axes fraction',color=clr,fontweight='bold')
clr = 'gray'
txt='RMSE: %.2f' % round(errtot,2)
self.annot_avg = self.axdipole.annotate(txt,xy=(0,0),xytext=(0.86,0.005),textcoords='axes fraction',color=clr,fontweight='bold')
else:
clr = 'black'
txt='Avg. RMSE: %.2f' % round(errtot,2)
self.annot_avg = self.axdipole.annotate(txt,xy=(0,0),xytext=(0.005,0.005),textcoords='axes fraction',color=clr,fontweight='bold')
if not hassimdata: # need axis labels
left = 0.08
w,h=getscreengeom()
if w < 2800: left = 0.1
self.axdipole.set_xlabel('Time (ms)',fontsize=dconf['fontsize'])
self.axdipole.set_ylabel('Dipole (nAm)',fontsize=dconf['fontsize'])
myxl = self.axdipole.get_xlim()
if myxl[0] < 0.0: self.axdipole.set_xlim((0.0,myxl[1]+myxl[0]))
self.figure.subplots_adjust(left=left,right=0.99,bottom=0.0,top=0.99,hspace=0.1,wspace=0.1) # reduce padding