Bug #1166
closedenergy filter property not found with Gatan Camera
0%
Description
GIF 2000, Gatan Ultracam 4K CCD, GMS 1.6.2 DM 3.11.2 TUI 2.1.8 Windows 2000
Energy filter related attributes are not found with Gatan CCD camera object, error message show while trying to update energy filter status manually in preset editing, see attached screen copy. Other CCD functions works fine, no problem taking images besides AZLP.
It hasn't been a problem with Leginon 1.8.
Files
Updated by Anchi Cheng over 13 years ago
- Project changed from Appion to Leginon
- Category deleted (
unknown)
Updated by Jim Pulokas over 13 years ago
- File gatantest.py gatantest.py added
I have attached a test script that you can try. This is exactly cut out of the current gatan.py, so it will likely show you the functions that are missing. Copy the file to the microscope computer desktop and double click it to run. If it fails to launch, copy it to c:\python25\Lib\site-packages\pyscope\gatantest.py, then start python and run "import pyscope.gatantest" to show you the exception.
Right now I know of the functions that are named either "AF..." or "IFC...", so that is what the script is testing for. It should be able to find one or the other.
The problem is that I do not know the alternative function name that would replace these if they do not work, so maybe one of you has current documentation for the energy filter scripting functions.
Updated by Jian Shi over 13 years ago
- File gatanGIFfunTest.jpg gatanGIFfunTest.jpg added
Hi Jim,
This is the test result on our microscope from your script. Seems AF functions all are supported and only half of IFC functions are supported.
BTW, there is one more annoying message on DM result window when cycling the preset. Such message only occurs in Leginon2 but not 1.8 before. I am wondering if they are related with GIF problem.
Line 1: No match for if( void, void, void )
Potential matches are
void if( RealNumber, Expression )
void if( RealNumber, Expression, Expression )
Jian
Updated by Scott Stagg over 13 years ago
I think I have a similar situation to Jian. Below are the results of my test:
SUPPORTED: AFGetSlitState
SUPPORTED: AFSetSlitState
SUPPORTED: AFGetSlitWidth
SUPPORTED: AFSetSlitWidth
SUPPORTED: AFDoAlignZeroLoss
UNSUPPORTED: IFCGetSlitState
UNSUPPORTED: IFCSetSlitState
SUPPORTED: IFCGetSlitWidth
SUPPORTED: IFCSetSlitWidth
UNSUPPORTED: IFCDoAlignZeroLoss
enter to quit
Do you have a suggestion as to where I would look to find the Gatan scripting documentation? Also, if we make the changes locally, how will you support multiple versions of DM?
Updated by Jian Shi over 13 years ago
Hi Guys,
Here is my modification of gatan.py, which fixed the GIF communication problem. I believe it address the AZLP problem Scott reported as well.
The only small glitch I noticed so far is if you change the slit width only in filter control, you have to toggle the slit in/out so that the preset update from scope can pick up the new value. If you change slit width and slit in/out state both, you don't have to.
Hope it is useful to the community.
Jian
Updated by Jim Pulokas over 13 years ago
Jian and Scott,
I took Jian's gatan.py and tried to make it into a version that will work in all cases, both old and new. Mainly I have improved the automatic detection of which function is supported by the current version of DM. I have not tested this at all, so please try it out and let me know if it works for your case.
Jim
Updated by Jim Pulokas over 13 years ago
- Status changed from Assigned to In Test
- Assignee changed from Jim Pulokas to Jian Shi
Updated by Scott Stagg over 13 years ago
I tested the attached file on the Titan, and some things worked but others didn't. First, I had to copy the Gatan class to GatanGIF (which is how I had to set it up with our dual camera system). After I did that, it would connect to the camera and take pictures. It changes from imaging to filtered modes according to the preset, but when it tries to zero the energy loss peak, I get a message saying "Energy filter methods are not available on this instrument."
Updated by Jian Shi over 13 years ago
If it is a warning message in AZLP node, it doesn't matter, as long as the AZLP did run on instrument and show result in DM result window. The warning message is due to an obsolete tomography.py calls of a no-longer-exist GIF function in gatan.py.
I will try to find a some time to test Jim's version on our system.
Updated by Jian Shi over 13 years ago
Jim, I tested your version of gatan.py just now. IFCSetSlitWidth and GTCenterZeroLoss are not working, the rest are OK. You probably can't use these two in the if statement. My 2 cents.
Updated by Scott Stagg over 13 years ago
When I run gatantest.py, I now get the following:
SUPPORTED: AFGetSlitState
SUPPORTED: AFSetSlitState
SUPPORTED: AFGetSlitWidth
SUPPORTED: AFSetSlitWidth
SUPPORTED: AFDoAlignZeroLoss
UNSUPPORTED: IFCGetSlitState
UNSUPPORTED: IFCSetSlitState
SUPPORTED: IFCGetSlitWidth
SUPPORTED: IFCSetSlitWidth
UNSUPPORTED: IFCDoAlignZeroLoss
enter to quit
Jian, it's not just a warning. The zero loss peak is not being aligned.
Updated by Anchi Cheng over 6 years ago
- Status changed from In Test to Closed
GIF attribute name does change from version to version. We will just have to ask for the new ones each time when we get into this problem.