def sum_stack(fn,sw):
'''Measures relative illumination between frames. Sums the values of each frame, divides by the number of pixels, and removes the mean.'''
dat, fs = retrieveData(fn[0],sw)
nframes = dat.shape[3]
print('processing image stack: %ix%i, %i frames ...' % (dat.shape[0], dat.shape[1], nframes))
s = zeros(nframes)
for k in arange(nframes):
s[k]=sum(dat[:,:,0,k])
numpix = float32(dat.shape[0]*dat.shape[1])
s = s/numpix
s -= s.mean()
if len(s.shape)==2:
s=s.reshape(-1,)
h = nmpdat.newHeader(fs=fs)
nd = nmpdat.newData(s, h)
doc = nmp.blankDocument()
doc.newElement(nd)
if sw.has_key('dir'):
a = io.write(doc,sw['dir'] + '/' + sw['sum_file'])
else:
a = io.write(doc,sw['sum_file'])
if a:
print "%s successfully written." % sw['sum_file']
else:
print "%s failed to write." % sw['sum_file']
return s, fs
def splitstack(fn,sw):
if not sw.get('numframes'):
print('loading image stack ...')
dat,fs = retrieveData(fn[0],sw)
print('writing image stack ...')
f = newFile(dat,{'StackSpacing':1./fs,'SampleType': 'image','ParentFile':fn[0]})
if sw.has_key('AOS_dir'):
fname=sw['AOS_dir']+'/'+sw['AOS_file']
else:
fname=sw['AOS_file']
a1=io.write(f,fname)
if a1:
print "Wrote %s." % fname
else:
print "Failed to write %s." % fname
if fn[1]:
print "writing stimulus file..."
if sw.get('startframe'):
sf[0]=sw['startframe']
else:
sf[0]=0
if sw.get('nframes'):
sf[1] = sw['nframes']
dat, fs=cropbin(fn[1],sf,fs)
h=nmpdat.newHeader(fs=fs)
b=newFile(dat,h)
if sw.has_key('bin_dir'):
fname=sw['bin_dir']+'/'+sw['bin_file']
else:
fname=sw['bin_file']
a2=io.write(b,fname)
if a2:
print "Wrote %s." % fname
else:
print "Failed to write %s." % fname
else:
n=sw['numframes']
if sw.get('jumpframes'):
j=sw['jumpframes']
else:
j=0
if sw.get('nframes'):
nf=sw['nframes']
else:
nf = 23000 # > max AOS buffer at 1000 Hz
if sw.get('startframe'):
sf=sw['startframe']
else:
sf=0
if sw.has_key('AOS_dir'):
basedig=getMaxDigit(sw['AOS_dir'])
else:
basedig=getMaxDigit(os.getcwd())
k=1
while sf + k*n + (k-1)*j <= nf:
sp= sf + (k-1)*(n + j)
kk='%03d' % (k+basedig)
s={'startframe':sp, 'nframes':n}
try:
print('loading image stack ...')
dat,fs,h = retrieveData(fn[0],s,header=True)
if k == 1:
nf = h['OriginalNumberofFrames']
print('writing image stack %03d...' %(k-1))
f = newFile(dat,h)
if sw.has_key('AOS_dir'):
fname=sw['AOS_dir']+'/'+kk+'_'+sw['AOS_file']
else:
fname=kk+'_'+sw['AOS_file']
a1=io.write(f,fname)
if a1:
print "Wrote %s." % fname
else:
print "Failed to write %s." % fname
if fn[1]:
dat, fs, sp=cropbin(fn[1],(sp,n),fs)
h={'SamplesPerSecond':fs,'OriginalFile':fn[1],'SampleType':'timeseries','StartTime':sp[0]/fs}
print "writing stimulus file..."
b=newFile(dat,h)
if sw.has_key('bin_dir'):
fname=sw['bin_dir']+'/'+kk+'_'+sw['bin_file']
else:
fname=kk+'_'+sw['bin_file']
a2=io.write(b,fname)
if a2:
print "Wrote %s." % fname
else:
print "Failed to write %s." % fname
except:
print "error while processing %s or %s" % (fn[0],fn[1])
import traceback
e= sys.exc_info()
apply(traceback.print_exception, e)
k+=1
def comp_series(fn,sw):
'''Compares illumination of movie images to stimulus generator record running the LED.'''
if 'n' in sw.keys():
s, fs = retrieveData(fn[0],sw)
else:
s, fs = sum_stack(fn,sw)
if len(s.shape)==2 and s.shape[1] == 1:
s=s.reshape(-1,)
b, fsb = retrieveData(fn[1],sw)
if 'e' in sw.keys():
es, esind = near_event_finder(s,fs,stdnum=5,numback=6)
eb, ebind = near_event_finder(b[:,0],fsb,thresh=0.1)
elif 'f' in sw.keys():
es, esind = subfs_event_finder(s,fs)
eb, ebind = subfs_event_finder(b[:,0],fsb,5)
else:
es, esind = event_finder(s,fs)
eb, ebind = event_finder(b[:,0],fsb,thresh=1)
df = len(eb) - len(es)
if df:
z=zeros(df,s.dtype)
es=hstack([es,z])
tdiff = es-eb
#Start: code to ensure all events are detected
bb = b[:,0]
z = zeros_like(bb)
z[ebind] = 1
btot = vstack([bb,z]).T
hb = nmpdat.newHeader(fs=fsb, l=['RawStimulus','Events'])
ndb = nmpdat.newData(btot, hb)
docb = nmp.blankDocument()
docb.newElement(ndb)
if sw.has_key('dir'):
a = io.write(docb,sw['dir'] + '/' + sw['stim_file'])
else:
a = io.write(docb,sw['stim_file'])
if a:
print "%s successfully written." % sw['stim_file']
else:
print "%s failed to write." % sw['stim_file']
zs = zeros_like(s)
zs[esind] = 1
stot = vstack([s,zs]).T
hs = nmpdat.newHeader(fs=fs, l=['CameraSum','Events'])
nds = nmpdat.newData(stot, hs)
docs = nmp.blankDocument()
docs.newElement(nds)
if sw.has_key('dir'):
a = io.write(docs,sw['dir'] + '/' + sw['cam_file'])
else:
a = io.write(docs,sw['cam_file'])
if a:
print "%s successfully written." % sw['cam_file']
else:
print "%s failed to write." % sw['cam_file']
#End: code to ensure all events are detected
tot = vstack([es,eb,tdiff]).T
h = nmpdat.newHeader(fs=1.0, l=['VideoEvents','StimulusEvents','TimeDifference'])
nd = nmpdat.newData(tot, h)
doc = nmp.blankDocument()
doc.newElement(nd)
if sw.has_key('dir'):
a = io.write(doc,sw['dir'] + '/' + sw['comp_file'])
else:
a = io.write(doc,sw['comp_file'])
if a:
print "%s successfully written." % sw['comp_file']
else:
print "%s failed to write." % sw['comp_file']
