Appion

read box size from file, rather than calculate it.

Does this fail gracefully if the file does not exist? I see it checks for the file right above and gives an error message, but what happens if you try to use it when it is not there?

That file is the main result of the program; without that file the program failed to work.

I've setup appion to have three print functions:

1. apDisplay.printMsg() -- prints a message to stderr uncolored and continue
2. apDisplay.printWarning() -- prints a warning to stderr colored yellow and continue
3. apDisplay.printError() -- prints a error to stderr colored red and then exit the program with status 1

Like you said it checks for the file and printError print the error message and dies. The imagicfile is generated by the createAlignedStacks() function. I noticed several inconsistencies in how I named the file, so I fixed those in r13266.

I ran the script trying to reproduce the initial bug, i.e. setting boxsize to 72, and it worked fine.

I have checked the script now, and it gets the boxsize from the actual boxsize associated with the file, rather than calculating it out, as Neil pointed out in the above thread.

I also added a check on the clipsize (if clipsize % 2 == 1: clipsize += 1) into line 375-6 of maxlikeAlignment.py to make sure that the stack is not being clipped to an odd value. This may have been the initial reason for the failure.

Dmitry, in addition to the error checking that you mentioned in r14391, you are also printing out the clipsize and commented out some clipsize error checking. Was this intentional?

my mistake, that's been in my local sandbox and was accidentally checked in.

r14397 (for some reason, revisions are not showing up in this issue correctly)

Not merging the % 2 fix to the branch. The Neils changes are in the branch since they we submitted before the branch was created.