Leginon

Hi Anchi,

Is phase plate functioning. I saw some code in the respository but I can't find the tool in any node or application. I am using latest 19600 version. I would happy to test it for you on our Krios.

Regards,
Jian

I was working with Matthias Wolf when I committed these changes. There is no TEM scripting for advancing phase plate, so the node simply wait for the user. However, we locally on his scope used a cursor/mouse button manipulation program called AutoIt to "click" the "Next Phase Plate" button on TUI to achieve automation effect.

The node class is PhasePlateAligner. It needs PhasePlatePublishEvent binding from Exposure node. The usage and settings is similar to AlignZLP for energy filter. Therefore, you will need to define a reference target (empty) somewhere on the grid.

FEI promise a scripting access but it has not happened, yet.

Nearly in-focus phase plate usage also needs multi-point focus measurement averaging. Issue #3785

These will be release on 3.3. Matthias is fairly happy with it, but there are still details to clean up. You are welcome to try out. Maybe you will notice different problems.

committed pyscope/tecnai.py that calls AutoIt script executable to go with Matthias's instruction above as r19640

I got AUTOIT script and exe working, and installed latest GIT version includes the function all. But I am not quite sure how tecnai.py call the exe? Is there a node, or setting to control it?

Jian Shi wrote:

I got AUTOIT script and exe working, and installed latest GIT version includes the function call. But I am not quite sure how tecnai.py call the exe? Is there a node, or setting to control it?

Hi Jian,
there is a variable AUTOIT_EXE_PATH in tecnai.py on the microscopy PC, which points to the path and name of the executable. Compile the autoit script, store it in a readable place and modify this path.
Matthias

Hi Matthia,

I have done what you have pointed out, and it works well when I double click the exe on Krios PC. Tecnai.py was also modified to the path.

But I am wondering if there is a node/setting in Leginon to activate the function call to the exe. ie. How to control the intervals and incubating time etc.

There is some code in wx folder, suggesting there may be a node for phase plate, just like LN2 filler. But I didn't see it anywhere in latest applications.

Thanks a million, Matthias.

Regards, Jian

Matthias,

Thanks for helping Jian. To answer your questions, yes the applications live in the database.

See Applications regarding "Exporting to Leginon application XML file

It can then imported at the other end.

I will add PP control in 3.3 applications.

NM found it in fei.cfg

Saved nextphaseplate.au3.txt as NextPhasePlate.au3 in pyscope/autoit

Also changed the fei.cfg key to

AUTOIT_PHASE_PLATE_EXE_PATH