Appion

Actually the error you are getting is that is does not know the pixel size...

When I updated the database for your new pixelsize of 1.45, changed all the dates of the pixelsize calibration to the current time, so when python went to get the pixelsize for your images all the calibrations came after the image collection, so it failed.

You're stack making should work on the branch now since it was a database error, but I found another bug in r14427 that will break later on in the script.

I can't seem to test this because if I use http://cronus3.scripps.edu/~amiguest2/myamiweb/index.php? from my amiguest2 account, I cannot seem to log into goby as amilazzo to test the stack creation and amiguest2 does not have an account on goby.

Hi Amber,

Seems to be partially working now testing this off-site and logged into goby with the same preset. Trying to create a stack with a different preset failed though-- do I need to test this over at AMI logged in as amiguest2?

We decided to wait for Goby to be updated with 2.1 to test this. It is low risk for other users.
This should not prevent release of 2.1.

During these changes, I think something else was broken unless my database schema is not up to date. I am getting the following error:

Traceback (most recent call last):
  File "/home/sstagg/myami_dev/appion/bin/makestack2.py", line 1260, in <module>
    makeStack.run()
  File "/home/sstagg/myami_dev/appion/appionlib/appionLoop2.py", line 70, in run
    results = self.loopProcessImage(imgdata)
  File "/home/sstagg/myami_dev/appion/appionlib/appionLoop2.py", line 116, in loopProcessImage
    return self.processImage(imgdata)
  File "/home/sstagg/myami_dev/appion/bin/makestack2.py", line 1099, in processImage
    self.boxedpartdatas, self.imgstackfile, self.partmeantree = self.boxParticlesFromImage(imgdata)
  File "/home/sstagg/myami_dev/appion/bin/makestack2.py", line 192, in boxParticlesFromImage
    shiftdata = {'shiftx':shiftpeak['shift'][0], 'shifty':shiftpeak['shift'][1], 'scale':shiftpeak['scalefactor']}
  File "/home/sstagg/myami_dev/sinedon/data.py", line 492, in __getitem__
    return self.special_getitem(key, dereference=True)
  File "/home/sstagg/myami_dev/sinedon/data.py", line 471, in special_getitem
    value = super(Data, self).__getitem__(key)

        if self.params['defocpair'] is True and self.params['selectionid'] is not None:
            # using defocal pairs and particle picks
            partdatas, shiftpeak = apParticle.getDefocPairParticles(imgdata, self.params['selectionid'], self.params['particlelabel'])
            shiftdata = {'shiftx':shiftpeak['shift'][0], 'shifty':shiftpeak['shift'][1], 'scale':shiftpeak['scalefactor']}

I cannot see in the code where you are talking about this...

I created this for the fake defocal pairs (actually exposure pairs) from the DDD for Anna-Clare. So you create a stack from one defocal pair and want the second. We were having a problem that the cross-correlation between the exposure pairs. The cross-correlation should be (0,0) since it is the exact same image with different subimages included and we were getting values like (10,15) pixels or more screwing everything up, so that is why I wrote the output file.