Bug #4505
closed
apCtf crashes on bad display rather than moving on
Added by Anchi Cheng about 8 years ago.
Updated almost 7 years ago.
Affected Version:
Appion/Leginon 3.2
Description
This happens from time to time that one of the printError statement is hit. While this is useful in debug, there need to be a general mechanism for appion script to move on in production mode.
These images would be thrown out at the end, but a run done during automated data collection should move on since the it needs to keep up with data collection.
Related issues
1 (1 open — 0 closed)
One possibility is to put them in
if self.debug:
An example of this is in normalizeCTF:
if self.res80 < 6 and self.conf3010 < 0.3:
print(numpy.around(confdata[:15],3))
apDisplay.printError("confendence below 0.3 and resolution better than 6A")
- Subject changed from apCtf crashes on bad display even though rather than moving on to apCtf crashes on bad display rather than moving on
This is to avoid false positive fits. What it needs to do is return None or something, so it is does upload the values to the database.
I initially put the crash in, because it usually meant something was wrong with the program.
- Assignee changed from Neil Voss to Anchi Cheng
There are many places that does this in the same module. Do you suggestt me to go through them one by one ? You should be better in judging which should be fatal. In addition, I start this issue to bounce ideas on how to make it possible to have both needs meet.
Okay, I see what you mean.
I am okay with adding self.debug flag, my test suite runs apCtf on 1000's of images looking for these fails and I do not reach them, so I like to know when they occur. Of course, I do not have time to work on any fix at the moment.
- Assignee changed from Anchi Cheng to Neil Voss
pushed two cases of this using self.debug is True
282249e0
- Related to Bug #4506: ctfinsert.py rejects angle of stigmation happens to be near 90 degrees. added
1d14cf39 add to self.debug failure when conf 30/10 failed to give back a number from scipy. The actually except happens when it is inserted to database.
Most problems come from images with defocus close to zero and from phase plate data. WIth -0.5 um defocus that I use with phase plate, ctfdisplay fails to create graph about 90% of the time.
- Status changed from Assigned to Closed
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