def reverbUniformity(self,cs):
"""
Analysis uniformity of reverb pattern
Workflow:
1. Define ROI of reverb (dependend on vertical profile)
2. Average ROI horizontally and calculate COV
3. Normalize profile as deviation wrt mean
4. Find dips in profile
"""
error = True
## 1. Define ROI of reverb (dependend on vertical profile)
yran = []
if self.fastmode:
print 'Uniformity: FASTMODE',cs.sens_basewavelength
if cs.sens_basewavelength >0:
ylim = int(cs.sens_basewavelength/self.pixels2mm(cs,1.)+.5)
yran = [self.offsetVER,ylim]
print yran
if len(yran) == 0:
yran = [self.offsetVER,cs.sens_ylim] if cs.sens_ylim>0 else [self.offsetVER]
crop = cropImage(cs.rect_image, [self.offsetHOR], yran)
uniformity = np.mean(crop,axis=1)
uniformitysmoothed = mymath.movingaverage(uniformity,self.smooth_uniformity)
## line uniformity
intemin = np.min(uniformity)
intemax = np.max(uniformity)
inteavg = np.mean(uniformity)
cs.unif_line = np.max([intemax-inteavg,inteavg-intemin])/inteavg
# Output of COV
meanvalue = np.mean(uniformity)
stdvalue = np.std(uniformity)
# normalized uniformity
if self.modeLocalNorm:
frac = .1
print "Uniformity, using Local Normalization",frac
normuniformity = mymath.localnormalization(uniformity, sigma=len(uniformity)*frac)
else:
normuniformity = ((uniformitysmoothed-meanvalue)/meanvalue)
if cs.testing:
try:
import QCUS_testing as mytest
mytest._exportProfile(normuniformity,fname='xprofile.tsv')
mytest._exportNDArray(cs.rect_image)
except:
pass
return self._uniformityAnalysis(cs, normuniformity)
def sensitivityAnalysis(self,cs):
"""
Workflow:
1. Calculate profile (vertically)
2. Determine noise level
3. Exponential fit to peaks in profile
4. total sensitivity = penetration depth (intercept fit and noise)
5. Repeat for subsets
"""
error = True
## 1. Calculate profile (vertically)
wid,hei = np.shape(cs.rect_image)
offsetHOR= wid/4 #10 ; adjusted to remove influence of annotations through reverb data (enhancement line)
if offsetHOR == 0:
offsetHOR = self.offsetHOR
crop = cropImage(cs.rect_image, [offsetHOR], [self.offsetVER])
wid,hei = np.shape(crop)
sensitivity = np.mean(crop,axis=0)
time0 = time.time()
self.fftAnalysis(cs,sensitivity,mode='sensitivity')
cs.report.append(('sens_fft',time.time()-time0))
nx = len(sensitivity)
sensitivitysmoothed = mymath.movingaverage(sensitivity,self.smooth_sensitivity)
if cs.testing:
try:
import QCUS_testing as mytest
mytest._exportProfile( [ (s,ss) for s,ss in zip(sensitivity,sensitivitysmoothed) ],fname='yprofile.tsv' )
except:
pass
##2. Determine noise level (mean of last n values of sensitivity)
cs.sens_noiseM = -1
noiseRange = 2
noise_av = np.mean(sensitivitysmoothed[-noiseRange:])
noise_sd = np.std(sensitivitysmoothed[-noiseRange:])
noise_snr = noise_av/noise_sd if noise_sd >0. else 0.
noise_inc = False # sometimes snr starts with a local max
for nr in range(noiseRange+2,nx/3):
av = np.mean(sensitivitysmoothed[-nr:])
sd = np.std(sensitivitysmoothed[-nr:])
snr = av/sd if sd >0. else 0.
if snr>noise_snr or not noise_inc:
if snr>noise_snr:
noise_inc = True
noise_av = av
noise_sd = sd
noise_snr = snr
else:
cs.sens_noiserange = nr
break
cs.sens_noiseM = noise_av
top_val = np.max(sensitivitysmoothed)
cut_val = cs.sens_noiseM+.1*(top_val-cs.sens_noiseM)
for kk in reversed(range(nx)):
if sensitivitysmoothed[kk]>cut_val:
cs.sens_ylim = kk
break
# peak detection
pmax = np.max(sensitivitysmoothed)
pmin = np.min(sensitivitysmoothed)
delta = (pmax-max(cs.sens_noiseM,pmin))*self.fdelta_sensitivity
xy_max,xy_min = wadwrapper_lib.peakdet(sensitivitysmoothed, delta=delta,x=range(nx))
# select only those peaks where max>noise; alternatively, select those peaks with min<noise
if self.sens_hicut:
xy_swap = []
for xy in xy_max:
if xy[1]>cs.sens_noiseM:
xy_swap.append(xy)
else:
break
xy_max = xy_swap
if len(xy_max)>0:
cs.sens_ylim = max(cs.sens_ylim,max(xy_max,key=operator.itemgetter(0))[0])
xy_swap = []
for xy in xy_min:
if xy[0]<cs.sens_ylim:
xy_swap.append(xy)
else:
xy_swap.append(xy) # last point
break
xy_min = xy_swap
else:
xy_swap = []
for xy in xy_min:
if xy[1]<cs.sens_noiseM or len(xy_swap)<3:
xy_swap.append(xy)
else:
break
xy_min = xy_swap
if len(xy_min)>1:
cs.sens_ylim = max(xy_min,key=operator.itemgetter(0))[0]
xy_swap = []
for xy in xy_max:
if xy[0]<cs.sens_ylim:
xy_swap.append(xy)
else:
xy_swap.append(xy) # last point
break
xy_max = xy_swap
cs.sens_numtops = len(xy_max)
cs.sens_numbots = len(xy_min)
if cs.testing:
try:
import QCUS_testing as mytest
mytest._exportProfile( xy_max, fname='xy_max.tsv' )
mytest._exportProfile( xy_min, fname='xy_min.tsv' )
except:
pass
if cs.verbose:
x_max = np.array([xy[0] for xy in xy_max])
y_max = np.array([xy[1] for xy in xy_max])
x_min = np.array([xy[0] for xy in xy_min])
y_min = np.array([xy[1] for xy in xy_min])
x = np.array(range(nx))
plt.figure()
plt.plot(x,sensitivitysmoothed,'k-')
plt.plot(x_min,y_min,'ro')
plt.plot(x_max,y_max,'bo')
cs.hasmadeplots = True
error = False
return error
def fftAnalysis(self,cs,profile,mode='sensitivity'):
"""
Fourier analysis: find main frequencies and power therein
"""
if cs.verbose:
try:
import QCUS_testing as mytest
if mode == 'sensitivity':
mytest._exportProfile( profile,fname='y2profile.tsv' )
else:
mytest._exportProfile( profile,fname='x2profile.tsv' )
except:
pass
fdelta = .1 # peak should differ by more than this fraction of max ps
if mode == 'sensitivity':
cs.sens_basewavelength = 0.
cs.sens_ylim2 = -1
# remove average component
ywork = profile-np.average(profile)
nx = len(ywork)
x = np.array(range(nx))
ffty = np.fft.rfft(ywork)
ps = np.abs(ffty)**2
integral = np.sum(ps[self.fft_skip:]) # calculate total content, but ignore zero component
freqs = rfftfreq(nx)
# find peaks
xy_max,xy_min = wadwrapper_lib.peakdet(ps, delta=fdelta*np.max(ps[self.fft_skip:])) # returns indices for freqs
# sort peaks from large to small
xy_max = sorted(xy_max,key=operator.itemgetter(1))
xy_max = xy_max[::-1]
# find max component which is not zero-component and represents larger than given fraction of power
base_ix = 0 # index of base-frequency
start_ix = 0 # index of zero-peak
for i,(xi,yi) in enumerate(xy_max):
if xi<=self.fft_skip: # zero-peak must be located in skip
start_ix = xi
if xi>self.fft_skip and base_ix<1:
base_ix = xi
if mode == 'sensitivity':
cs.sens_basewavelength = self.pixels2mm(cs, 1./freqs[xi])
break
# filter-out all non-background trend components to find extend of signal
for i in range(len(ffty)):
if i>(base_ix+start_ix)/2:
ffty[i] = 0.
# locate minimum (after zero-peak) of trend
fy = np.fft.irfft(ffty)
ix_max = np.argmax(fy)
ix_min = ix_max+np.argmin(fy[ix_max:])
if cs.verbose:
print 'max @',ix_max
print 'min @',ix_min
if mode == 'sensitivity':
cs.sens_ylim2 = ix_min
if cs.verbose:
plt.figure()
plt.plot(ywork)
plt.plot(fy)
if mode == 'sensitivity':
plt.title('sensitivity,filtered')
else:
plt.title('uniformity,filtered')
plt.figure()
plt.plot(ps)
if mode == 'sensitivity':
plt.title('sensitivity,powerspectrum')
else:
plt.title('uniformity,powerspectrum')
cs.hasmadeplots = True