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Bug #1112

closed

makestack and all other appionloop functions use non-rejected images even though the right option is checked in myamiweb

Added by Anchi Cheng over 13 years ago. Updated almost 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Amber Herold
Category:
-
Target version:
-
Start date:
12/23/2010
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.2.0
Show in known bugs:
No
Workaround:

Description

appionloop includes in its command both --no-rejects and --best-images flags. python-side script in appionlib/appionLoop2.py ignored the second flag


Related issues 1 (1 open0 closed)

Related to Appion - Bug #1680: When --best-images flag is set in command, non-exemplars are still being processed New03/26/2012

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Actions #1

Updated by Anna-Clare Milazzo over 13 years ago

Hi Anchi,

I just found the same issue for running CTFfind where choosing "--best-images" flag seems to be ignored. Maybe this has to do with the wrapper /opt/myamisnap/bin/appion" as the same issue does not seem to occur with the release version? I would use the release version as a make stack workaround but I'm getting a different error for that which I will file a bug report on.

--Anna

Actions #2

Updated by Anchi Cheng over 13 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Anchi Cheng to Amber Herold

It looks like we have been doing so for 2 years. It is now broken because the change in r15182 on appionlib.appionLoop2.py.

The way before:

elif self.params['norejects'] is True and apDatabase.getImgCompleteStatus(imgdata) is False:

and then
elif self.params['bestimages'] is True and apDatabase.getImgCompleteStatus(imgdata) is not True:

now it is more like:

elif self.params['norejects'] is True:
  if apDatabase.getImgCompleteStatus(imgdata) is False:
  else:

and then
elif self.params['bestimages'] is True:
  if apDatabase.getImgCompleteStatus(imgdata) is False:
  else:

In the new code if norejects is True and bestimage is True, the elif for bestimages will not be reached.

I think it is better to fix myamiweb part any way, so I did so in r15210 and leave appionlib.appionLoop2.py alone for the new feature.

This a bug after 2.1 release

test:
1. Put one image in the exemplar list
1. Use any myamiweb pages that uses the loop, such as runDogPicker.py and choose to process Exemplar and keep images only.
2. Click Just show commands, the flag --no-rejects should not be there. You should see --best-images flag,
3. Run this command and make sure that only the image in the exemplar list is processed by following its progress,

Actions #3

Updated by Anchi Cheng over 13 years ago

  • Affected Version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0 (trunk)
Actions #4

Updated by Anchi Cheng over 13 years ago

On second thought, the php change is not enough. The way appionLoop2.py behaves, it will ignore all elif after noject or bestimages condition lines so that tiltangle flag will not be checked for skipping. committed r15211 to fix that.

Testing:
1. Use session with tilt data and choose tilt angle other than "all tilt angles" in runDogPicker.php to see if only the specified tilt range is used to restrict the image processed.

Actions #5

Updated by Anchi Cheng over 13 years ago

  • Subject changed from makestack use non-rejected images even though the right option is checked in myamiweb to makestack and all other appionloop functions use non-rejected images even though the right option is checked in myamiweb
Actions #6

Updated by Amber Herold about 12 years ago

  • Status changed from In Code Review to In Test
Actions #7

Updated by Amber Herold about 12 years ago

The web side of this fix tests OK.The python seems to still have an issue as noted in #1680

Actions #8

Updated by Amber Herold almost 10 years ago

  • Status changed from In Test to Closed
  • Affected Version changed from Appion/Leginon 2.2.0 (trunk) to Appion/Leginon 2.2.0
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