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}