def findPeak(self, stack):
if os.path.exists(self.peakfile):
os.remove(self.peakfile)
out = open(self.peakfile, "w")
stackRead = mrc.read(stack)
number, ydim, xdim = stackRead.shape
for i in range(number):
image = stackRead[i, :, :]
output = peakfinder.findPixelPeak(image, guess=None, limit=None, lpf=None)
coord = output["pixel peak"]
out.write("%d %s %s\n" % (i, coord[0], coord[1]))
return out
def findPeak(self,stack):
if os.path.exists(self.peakfile):
os.remove(self.peakfile)
out = open(self.peakfile,'w')
stackRead = mrc.read(stack)
number, ydim, xdim = stackRead.shape
for i in range(number):
image = stackRead[i,:,:]
output = peakfinder.findPixelPeak(image, guess=None, limit=None, lpf=None)
coord = output['pixel peak']
out.write('%d %s %s\n' %(i,coord[0],coord[1]))
return out
def alignZeroShiftImages(imgtree,zerotilts):
"""Align 0 degree images for tilt series where data is collect in two halves"""
#index for imgtree images are one less than index in zerotilts b/c protomo images start at 1
im1=imgtree[zerotilts[0]-1]['image']
im2=imgtree[zerotilts[1]-1]['image']
print "correlating images",zerotilts[0], "and", zerotilts[1]
cc=correlator.cross_correlate(im1,im2)
peak=peakfinder.findPixelPeak(cc)
#print peak
newy,newx=shiftPeak(cc,peak)
print "new origin for image", zerotilts[0], "is", newx, newy
shifty=cc.shape[0]/2 - newy
shiftx=cc.shape[1]/2 - newx
return {'shiftx':shiftx, 'shifty':shifty}
def alignZeroShiftImages(imgtree, zerotilts):
"""Align 0 degree images for tilt series where data is collect in two halves"""
#index for imgtree images are one less than index in zerotilts b/c protomo images start at 1
im1 = imgtree[zerotilts[0] - 1]['image']
im2 = imgtree[zerotilts[1] - 1]['image']
print "correlating images", zerotilts[0], "and", zerotilts[1]
cc = correlator.cross_correlate(im1, im2)
peak = peakfinder.findPixelPeak(cc)
#print peak
newy, newx = shiftPeak(cc, peak)
print "new origin for image", zerotilts[0], "is", newx, newy
shifty = cc.shape[0] / 2 - newy
shiftx = cc.shape[1] / 2 - newx
return {'shiftx': shiftx, 'shifty': shifty}
