def spot_mask(self):
from numpy import zeros,sum,uint32
from peak_integration import spot_mask
from numimage import numimage
images = self.images
sum_image = sum(images.astype(uint32),axis=0)
info("Peak mask of summed image...")
mask = spot_mask(sum_image)
mask = numimage(mask)
mask.filename = self.spot_mask_filename
return mask
def diffraction_spots_of_image(self,image_file):
from peak_integration import spot_mask
from numimage import numimage
from scipy.ndimage.measurements import label
from os.path import basename
I = numimage(image_file)
ROIX,ROIY,WIDTH = self.ROIX,self.ROIY,self.WIDTH
I = I[ROIX:ROIX+WIDTH,ROIY:ROIY+WIDTH] # part of image
mask = spot_mask(I+20)
##total_spots = mask.sum()
labelled_mask,total_spots = label(mask)
if total_spots > 0: debug("%s: %s spots" % (basename(image_file),total_spots))
return total_spots
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()
def crystal_mask(self):
"""bitmap showing location of crystals. 1 = crystal, 0 = no crystal"""
from peak_integration import spot_mask
FOM = self.FOM_image
mask = spot_mask(FOM,self.peak_detection_threshold)
return mask