Leginon

Hi Jian, The linux problem looks like you have the gatan camera configured in the instruments.cfg. This should only be configured in the instruments.cfg on the Windows machine. The Windows problem seems like it is because of too old a version of numextension. I will try to compile a new version, but until then you should be able to run main from Linux if instruments.cfg issue is resolved. Let me know if that works, otherwise report any new errors and set "Assigned to" back to me.
Jim

Does this mean that Orius itself does not respond to our request to retract? Leginon's script is suppose to set all unused camera that are above the camera for imaging to retracted before it sends the request to insert the imaging camera.

If I understand your last update correctly, camera insertion/retraction works correctly on T12 where your have CCD and Orius on the same plane, but it does not on Krios. If Orius does not ever respond to our call to

orius.Retract()

T12CCD.Insert()

Do you know if it is intended for Orius retraction not controlled from anything but manual (I suppose it means a button in DM still).

Can you try a direct call on both scope in the following:
I don't know if your orius would be loaded as gatan.Gatan0 or not. In this script I assume it is. Do this in python command window on the camera computer

from pyscope import gatan
orius = gatan.Gatan0()
orius.getRetractable() # This should return True
orius.getInserted() # This should return the current state of orius.  Retracted is False, Inserted is True
orius.setInserted(True) # This should insert orius
orius.setInserted(False) # This should retract orius

I've not done enough scripting at this level but I don't think I would cause harm as long as you start with all camera on the same plane retracted.

tifffile error is for decode compressed file. Lacking that part of the library does not affect any function we currently use in Leginon and Appion.

1) I didn't install and test Leginon on our T12 due to other constrains. I just listed it as a possible scenario. However, on Krios, Falcon and Orius are indeed on the same plane and push each other out of view. That is what happens in EPU, so that user can assign different camera to different presets, per se Orius for Low mag atlas, and Falcon for high mag image in SA range.

2) Your Orius test command runs as expected in the terminal. But within Leginon Manual node, I notice that nothing really happens in DM when I select the other camera from the list in setting window. The insert event only is trigged by acquiring an image.

3) Our EFCCD is gatan0 and Orius is Gatan1. If I choose Gatan1(Orius) and start acquire, the Orius will be inserted until then and collect an image correctly. After this, if I choose Gatan0(EFCCD) and start acquire, EFCCD will be selected in DM but return a blank image due to blockage. If I run "Orius.getInserted()" in terminal window, the return value will be True at this moment. I have to go to DM and click search or acquire button manually, DM will pop a window to ask "Retract nonselected camera?" and retract Orius after click OK. Maybe Orius did not get retracted in Leginon because the EFCCD is not insert-able and retractable, I suspect.

4) I will more interested in testing using Falcon and Orius simultaneously. Falcon control is not in TecnaiCCD.dll, but in other library files. I found a few candidates but would appreciate your help to load them into python and pyscope for testing. Let me know if you are interested.

Thanks,
Jian

Could you tell us the zplanes you assigned to each camera in your instruments.cfg? I wonder if you had it backward.

In fact, I am not sure what to put in for the z-plane. Any arbitrary number? Or relative distance to film drawer? In what unit? I will check the number I input there tomorrow.

Leginon will attempt to retract camera at higher zplane when a camera of lower zplane is about to acquire an image, which will be inserted if insertable. If the two cameras are assigned to the same zplane, then there is no retraction of the unused camera.

The number is relative, with no unit. You should assign the Orius a larger number, and the EFCCD a smaller number.

Your suggestion works great. Now all Gatan CCDs switch smoothly and seamlessly. Now the outstanding question is to control Falcon camera. Do you guys have any suggestion?

In summary, the need for two gatan camera on one scope controlled by the same computer is resolved by r17324 in trunk.

1. Update the pyscope installlation on the camera-controlling computer to the said version.
2. The two cameras need to be configured as two classes in pyscope/instrument.cfg at the camera-controlling computer. The way to set z-planes are described in Installation_on_the_microscope_computer