Appion

Hi Lauren, I would probably do this as post stack feature like center particles. You sort the stack particles by image (they already are) figure out all the angles and then go back to the original image using the apBoxer command. ApBoxer takes an image and a list of x,y,angle coordinates and creates a new box.

WAIT, I guess this is complicated by CTF correction. We probably need to modularize the CTF stuff.

Okay, modified idea. Do this as post stack feature like center particles, but instead of creating a new stack, create a new particle picking run with angles posted in the database. Then you could run makestack separately without integrating yet another feature into makestack. I am worried that makestack is becoming incredibly hard to maintain.

How is your alignment in Fourier space working, because I've implemented Radon transforms into the pipeline (see apRadon.py), which I know Gabe was using offline to align his filaments -- I've been pretty happy with it -- at least it is quick. If you have python 2.5 or larger it has parallel processing built in.

Hi Neil,
I agree with you that makestack is becoming pretty bulky and hard to maintain. I can work on making the fine alignment a post stack feature or add it under the Particle Alignments page. I am only working at AMI 1 day a week now, so I apologize if my updates are few and far between and this process is drawn out. In the meantime, here is the code I wrote in makestack2.py to do the single interpolation (I did svn diff so you can see exactly what I added). It's not the most efficient process and I know the code is getting clunky, but it works. So do you think I should scrap it or check it in until I get a separate alignment protocol integrated?

t0 = time.time()
if self.params['rotate'] is True:
apBoxer.boxerRotate(imgpath, parttree, imgstackfile, self.params['boxsize'])
+ apXmipp.breakupStackIntoSingleFiles(imgstackfile, filetype="mrc")
+ rotcmd = "s_finealign %s %i" %(self.params['rundir'], self.params['boxsize'])
+ apParam.runCmd(rotcmd, "HIP", verbose=True)
+ # read in text file containing refined angles
+ anglepath = os.path.join(self.params['rundir'], 'partfiles/angles.out')
+ f = open(anglepath, 'r')
+ angles = f.readlines()
+ # loop through parttree and add refined angle to rough angle
+ for i in range(len(parttree)):
+ partdict = parttree[i]
+ fineangle = float(angles[i])
+ newangle = float(partdict['angle'])-fineangle
+ partdict['angle'] = newangle
+ # rerun apBoxer.boxerRotate with the new parttree containing final angles
+ apBoxer.boxerRotate(imgpath, parttree, imgstackfile, self.params['boxsize'])
else:
apBoxer.boxer(imgpath, parttree, imgstackfile, self.params['boxsize'])
self.batchboxertimes.append(time.time()-t0)

Right now the way I do the Fourier space alignment (s_finealign) is diffract the short helical repeat, background subtract and collapse the power spectrum, then calculate the height of the peak at the equator. Each filament is run through a range of angles using the Suprim program rota4 until the equatorial peak is maximized and the corresponding angle is applied to the filament. This procedure is time consuming, but it works really well. However, I am definitely up to new suggestions if you have something that works well and is more efficient.

Hi Lauren,

If it works, there is no reason to redo it, but for any future considerations I would try to avoid adding more to makestack. And I cannot think of anyway to really break make stack apart, but it definitely needs some reorganization for readability sake.