makeDDRawFrameStack.py error
Added by Christopher Lilienthal almost 8 years ago
Hello,
we are receiving an odd error while running the makeDDRawFrameStack.py script. I was hoping someone would be able to point us in the right direction to fix whatever the problem is.
When we run this:
/usr/local/appion/bin/makeDDRawFrameStack.py \
--defergpu --bin=1 --ddstartframe=0 --alignoffset=7 --alignbfactor=1000 \
--alignccbox=96 --alignlabel=a --description=prx-apo_a8-35 \
--runname=ddstack2-113016 \
--rundir=[path omitted for brevity]/ddstack2-113016 \
--preset=ed --projectid=9 --session=16nov30a_prx-apo_a3 --no-rejects \
--no-wait --no-commit --no-continue --parallel --expid=127 \
--jobtype=makeddrawframestack
We receive this:
!!! WARNING: No norm reference for the image, use default
... Reference comes from current image
Traceback (most recent call last):
File "/usr/local/appion/bin/makeDDRawFrameStack.py", line 203, in <module>
makeStack.run()
File "/usr/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 86, in run
results = self.loopProcessImage(imgdata)
File "/usr/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 136, in loopProcessImage
return self.processImage(imgdata)
File "/usr/local/appion/bin/makeDDRawFrameStack.py", line 152, in processImage
self.dd.makeCorrectedFrameStack(self.params['rawarea'])
File "/usr/lib/python2.6/site-packages/appionlib/apDDprocess.py", line 975, in makeCorrectedFrameStack
return self.makeCorrectedFrameStack_cpu(use_full_raw_area)
File "/usr/lib/python2.6/site-packages/appionlib/apDDprocess.py", line 1034, in makeCorrectedFrameStack_cpu
array = self.__correctFrameImage([start_frame,],use_full_raw_area)
File "/usr/lib/python2.6/site-packages/appionlib/apDDprocess.py", line 726, in _correctFrameImage
self.setCameraInfo(nframe,use_full_raw_area)
File "/usr/lib/python2.6/site-packages/appionlib/apDDprocess.py", line 483, in setCameraInfo
self.camerainfo = self._getCameraInfoFromImage(nframe,use_full_raw_area)
File "/usr/lib/python2.6/site-packages/appionlib/apDDprocess.py", line 515, in __getCameraInfoFromImage
camerainfo['norm'] = self.getRefImageData('norm')
File "/usr/lib/python2.6/site-packages/appionlib/apDDprocess.py", line 432, in getRefImageData
oldrefname = refdata['filename']
TypeError: 'NoneType' object is unsubscriptable
Any suggestions or insights would be much appreciated.
Replies (2)
RE: makeDDRawFrameStack.py error - Added by Anchi Cheng almost 8 years ago
Is there a possibility that this image has no gain/dark reference ?
The error indicates that it could not find reference data. You can confirm that by going through image information data tree in image report of the web viewer (The "i" button). I include a picture of it in the link below.
You can also get this query result from leginon/getReferences.py
If for some reason this is indeed missing but you have an image that you know have the reference that you can apply to this image, you can add manually the option --refimgid=xxxxx at the end of the script. xxxxx is a numerical number that is unique to the image, found also in image report under image information heading/imageId.
RE: makeDDRawFrameStack.py error - Added by Christopher Lilienthal almost 8 years ago
Yes that is what the problem was there were approximately 10 that didn't have the reference and once those 10 were removed the script is working again. They must have been acquired before taking the gain/dark reference. Thank you for the help Anchi.
Now that you point it out it seems so obvious the issue was no reference, but I thought the error was happening after this check.
Thanks again