Appion

Dmitry,
This may be a bit picky, but the message "old stack header is not numbered according to EMAN, and exists in a READ-only directory" does not seem accurate. This is printed after only checking that the directory is writable. It seems to me that you don't know yet if the numbering is incorrect, unless the stack numbering is always incorrect prior to this function. Perhaps the message could be changed to "old stack header exists in a READ-only directory and may not be numbered according to EMAN".

Or it might be better to put the directory check right before the call to numberParticlesInStack() inside the checkStackNumbering() function. This way the message would be more accurate and if the function is called from anywhere else, the error checking will already be in place.

I updated the message to read:

"old stack header exists in a READ-only directory and cannot be numbered according to EMAN," only if the check fails. I also removed the check from centerParticleStack.py and put it into the checkStackNumbering() function in apEMAN.py.