Leginon

Just found the same problem in the the rctacquisition.py trackStage function:

                result = libCVwrapper.MatchImages(arrayold, arraynew, minsize, maxsize)
                #try:
                #    result = pyami.timedproc.call('leginon.libCVwrapper', 'MatchImages', args=(arrayold, arraynew, minsize, maxsize), timeout=timeout)
                #    self.logger.info("result matrix= "+str(numpy.asarray(result*100, dtype=numpy.int8).ravel()))
                #except:
                #    self.logger.error('libCV MatchImages failed')
                #    return None,None

                #difftilt = degrees(abs(tilts[int(i)])-abs(tilts[int(i-1)]))
                #result = self.apTiltShiftMethod(arrayold, arraynew, difftilt)

I haven't seen this error before. timeout = 300 seems to be ad hoc number. I've looked at pyami.timedproc.call and it seems that setting timeout = None, or removing timeout=timeout from pyami.timedproc.call would have similar effect.

Hi guys,

I am experiencing the same error in Leginon 3.0. I first noticed it when trying to setup the RCT node. Clicking on the test acquire camera icon reproduced the "FindRegions failed" error.

If I apply the workaround suggested by Scott, it works and points are detected.

I also had to edit the MatchImages function to allow RCT to progress through the standard target submission process. It was previously giving a "MatchImages failed" error.

However, this step is very slow. Each MatchImage calculation (after each consecutive tilt step) can take varying amounts of times (up to minutes) and often hogs the cpus of the processing computer.

I hope this info helps with the debug.

Regards,
Jason

Thanks for the test script. As I suspected, there seems to be problem with my libCV instance. When I meant slow, I didn't mean seconds, I meant minutes.

Perhaps this is why it's timing out in the error described above.

My results are as follows:

Image min and max are 0 589896
Image 1: keypoints: 765; descriptors: 1171
Image min and max are 0 597938
Image 2: keypoints: 652; descriptors: 909
Found 433 matches between images
Found matrix that fit 79 out of the 433 matches.
Freeing all mem
1.00 -0.01 0.00
-0.00 0.94 0.00
-53.89 3.54 1.00
process time = 1284.1 seconds

On a "Intel(R) Pentium(R) 4 CPU 3.00GHz" with 3 gigs of memory.

Is there a way to get a more verbose output from MatchImage to see where it is going wrong?

O.K. This is most strange.

With Craig's help, I recompiled libcv with some debug prints and then found that it got stuck just like you two do. We have been going back and forth with the change applied in r17816. Issue #1291 was resolved by using AffineTransformImage function in place of SeparableAffineTransform. Then Issue #1500 was resolved by changing it back. Now we have this problem. I replace the current SeparableAffineTransform call with AffineTransformImage, and then it runs and fast.

Craig said it means that it hits a bug that wasn't encountered before. I wonder if it has to do with compiling with different compilers. He promised to look into it, but I don't know how long it will be.

For now, revert the change in r17816. It might be just what you need.

I changed SeparableAffineTransform(source,patch,TR,IT) back to AffineTransformImage(source,patch,TR,IT) in csift.c before recompiling and it's much faster:

Image min and max are 0 589896
Image 1: keypoints: 765; descriptors: 1273
Image min and max are 0 597938
Image 2: keypoints: 652; descriptors: 1005
Found 457 matches between images
Found matrix that fit 65 out of the 457 matches.
Freeing all mem
1.00 -0.00 0.00
-0.01 0.94 0.00
-53.36 1.19 1.00
process time = 5.4 seconds

I will test it in practise when I have machine time next week.

Thanks!

Found another case in which this error happens at U Washington.

The source of the problem is related to permission of the file. They put all leginon files in a path that is included in PYTHONPATH environment variable. However, the files have permission

-rw-r--r-- 1 root root  23571 Apr  8 12:30 rctacquisition.py

pyami.timedproc.call uses subprocess which requires the file it calls to have executable permission. Changing all files *.py in that leginon and pyami directory owned by root to mode 755 solved the problem.