Appion

Hi Anchi,

RELION aborts if there is a piximit >= 4.5, so I selected 4.4 to avoid any rounding errors, but keep the majority of the data. I know it seems like a weird value.

Not sure if this error is related to these new image functions, but it dies when trying to high pass filter a rectangular K2 image:

['/gpfs/home/glander/myami/appion/appionlib', '/gpfs/home/glander/myami/appion']
Querying database for 1 specific images ...
Traceback (most recent call last):
File "/gpfs/home/glander/myami/appion/bin/templateCorrelator.py", line 8, in <module>
imgLoop.run()
File "/gpfs/home/glander/myami/appion/appionlib/appionLoop2.py", line 88, in run
results = self.loopProcessImage(imgdata)
File "/gpfs/home/glander/myami/appion/appionlib/particleLoop2.py", line 101, in loopProcessImage
self.peaktree = filterLoop.FilterLoop.loopProcessImage(self, imgdata)
File "/gpfs/home/glander/myami/appion/appionlib/filterLoop.py", line 81, in loopProcessImage
self.filtarray = self.imgFilter.processImage(imgdata['image'])
File "/gpfs/home/glander/myami/appion/appionlib/apImage/imageprocess.py", line 97, in processImage
simgarray = imagefilter.tanhHighPassFilter(simgarray, self.highPass, apix=self.apix, bin=self.bin)
File "/gpfs/home/glander/myami/appion/appionlib/apImage/imagefilter.py", line 445, in tanhHighPassFilter
fftdata *= filter

One note for consideration. K2 camera counting mode dimension is 3838 x 3710, not dividable by even 4. A flooring will be needed for any binning function.

Not sure if I tested this on rectangular images. Will take a look.

Hi Neil,

I see that in this diff you changed mpirun = self.checkMPI() to mpirun = None - http://emg.nysbc.org/projects/appion/repository/revisions/29e28f8c215cacb4a3756061f8a7e42dc5ea4e20/diff/appion/bin/maxlikeAlignment.py

Can we change it back since it's no longer able to run mpi jobs?

From what I can tell I changed it for debugging and never changed it back. So go ahead and change it back.

Thanks Neil. Changed back mpirun = self.checkMPI().