Appion

The shape of imgstackmemmap at line 746 of makestack2.py is (boxsize, boxsize) when there is only one particle per image.
It creates the following error message in makestack2.py

This is reported by Vijay Reddy. I was able to repeat it with a manual picking run that picks only one particle and then make a stack with default parameters.

... boxing 1 particles into temp file: /emg/data00/appion/acheng/15aug27anchitestJ2/stacks/stack1/15aug27anchitestJ2_01hl_01en.hed
 ... writing stack to disk from memory: /emg/data00/appion/acheng/15aug27anchitestJ2/stacks/stack1/15aug27anchitestJ2_01hl_01en.hed
 ... wrote 1 particles to header file
 ... finished in 56.16 msec
 ... reading stack from disk into memory: 15aug27anchitestJ2_01hl_01en.hed
 ... read 1 particles equaling 324.0 kB in size
 ... finished in 1.84 msec
 ... gathering mean and stdev data
 ... not phase flipping particles
 ... 1 particles were boxed out from 15aug27anchitestJ2_01hl_01en
 ... do not break function now otherwise it will corrupt stack
 ... filtering particles and adding to stack
Traceback (most recent call last):
  File "/home/acheng/myami/appion/bin/makestack2.py", line 1210, in <module>
    makeStack.run()
  File "/home/acheng/myami/appion/appionlib/appionLoop2.py", line 86, in run
    results = self.loopProcessImage(imgdata)
  File "/home/acheng/myami/appion/appionlib/appionLoop2.py", line 136, in loopProcessImage
    return self.processImage(imgdata)
  File "/home/acheng/myami/appion/appionlib/apParticleExtractor.py", line 510, in processImage
    total_processed_particles = self.processParticles(imgdata,partdatas,shiftdata)
  File "/home/acheng/myami/appion/bin/makestack2.py", line 89, in processParticles
    totalpart = self.mergeImageStackIntoBigStack(self.imgstackfile, imgdata)
  File "/home/acheng/myami/appion/bin/makestack2.py", line 767, in mergeImageStackIntoBigStack
    if self.boxsize <= particle.shape[0] and self.boxsize <= particle.shape[1]:
IndexError: tuple index out of range

The particle was boxed at 288 pixel.
imgstackmemmap.shape = (288,288)
My print statement says that particle.shape = (288,)