def calculate_FOM(self):
"""Process the acquired images"""
from numpy import zeros,sum
from numimage import numimage
from peak_integration import peak_integration_mask
images = self.images
FOM = zeros(self.scan_N)
for self.Nanalyzed in range(0,self.scan_N):
if self.Nanalyzed % 10 == 0:
info("analysis %.f%%" % (float(self.Nanalyzed)/self.scan_N*100))
image = images[self.Nanalyzed]
FOM[self.Nanalyzed] = sum(peak_integration_mask(image)*image)
logfile = self.logfile
logfile["FOM"] = FOM
logfile.save()
def calculate_FOM_Fast(self):
"""Process the acquired images"""
from numpy import zeros,sum,uint32
from peak_integration import peak_integration_mask
images = self.images
sum_image = sum(images.astype(uint32),axis=0)
info("Peak mask of summed image...")
mask = peak_integration_mask(sum_image)
info("FOM...")
FOM = zeros(self.scan_N)
for self.Nanalyzed in range(0,self.scan_N):
FOM[self.Nanalyzed] = sum(mask*images[self.Nanalyzed])
info("FOM done.")
logfile = self.logfile
logfile["FOM"] = FOM
logfile.save()
def show_image(image_file):
from time import time
from pylab import figure,imshow,title,show,cm
from numimage import numimage
from peak_integration import spot_mask,peak_integration_mask
from numpy import minimum
from scipy.ndimage.measurements import label
I0 = numimage(image_file)
ROIX,ROIY,WIDTH = sample_frozen.ROIX,sample_frozen.ROIY,sample_frozen.WIDTH
I = I0[ROIX:ROIX+WIDTH,ROIY:ROIY+WIDTH]
# Time the 'peak_integration_mask' function.
t0 = time()
mask = spot_mask(I+20)
info('spot_mask = %.3f [s]' %(time()-t0))
##N_spots = mask.sum()
labelled_mask,N_spots = label(mask)
# Display the image.
chart = figure(figsize=(8,8))
title("%s: %d spots" % (image_file,N_spots))
imshow(minimum(I,1000).T,cmap=cm.jet,origin='upper',interpolation='nearest')
if N_spots != 0:
# Spot integration
t0 = time()
SB_mask = peak_integration_mask(I)
t1 = time()
print "Time to find Spots and generate S_mask (s):",t1-t0
# Perform the spot integration.
print "Integrated intensity: ",sum(I*SB_mask)
# Display 'mask'
chart = figure(figsize=(8,8))
title('SB_mask')
imshow(SB_mask.T,cmap=cm.jet,origin='upper',interpolation='nearest')
show()