Leginon

Currently, we have used the same instrument class for Titan and tecnai since we have not yet used any Titan specific function.

Therefore, use Class: tecnai.Tecnai.

Beware if you were able to read the magTable but not other field. Please check to see that the instrument reference in the database whether it has indeed linked the magnifications to the right instrument (your Krios). A bug in pyscope allows you to go quite far without a proper instrument in your instruments.cfg. We have not
seen this in TEM but have seen that with Camera such as the very confusing mess in http://emg.nysbc.org/boards/6/topics/1320?r=1321#message-1321

from leginon import leginondata
mags = leginondata.MagnificationsData().query(results=1)
print mags['instrument']
print mags['instrument']['host'],mags['instrument']['name']

If the first printout gives "None", instruments.cfg is not set right. You will not see the instrument later.

Please also let us know which version of Leginon you are installing if you still have trouble.

Anchi

Hi Anchi,

a) I downloaded the trunk version and installed them. The output of 'start-leginon -v' is pre2.2

b)The output of your short testing scripts as following

print mags['instrument']

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: list indices must be integers, not str

Beside Falcon camera, our Krios have pre-GIF Gatan Orius(2k) and post-GIF Gatan CCDwhich I would like to use at current stage

c)I successfully start client on Krios computer and main on Linux computer and load Manual application successfully. The instrument and the microscope info show correctly on client. However, there is no camera in the instrument pulldown list, neither camera records in the intrumentData table. No matter how I play with instruments.cfg, no camera info was picked up. I unmask the 'Sim TEM' and 'Sim Cam' in instrument config, the 'Sim Tem' showed up right away, but not 'Sim Cam'.
I remember there was a place on webtool before(2010) where you can add instrument, however I could not find it anymore in this version.

Noted, I used 'centosautoinstall tool' to install Leginon...etc on Linux PC, and went through a few issues, which I reported separately.

d) I try to find Camera info in Python, but it gives errors as attached screen copy. I did run updatecom.py couple of times and the corresponding py file for the dll has been generated.

e) I manually enter a camera record in the instrumentData, it doesn't work either.

Change the second line of my test script to

results = leginondata.MagnificationsData().query(results=1)
mags = results[0]

then the script should run.

Don't you have Falcon camera? You configured your camera1 and camera2 as gatan.Gatan in both. If there is no Gatan camera nor DigitalMicrograph, your configuration will not able to load them. We do not yet have a Falcon module.

Your scrips work fine now and it print microscope record correctly.

I did config camera1 and camera2 in instument.cfg. Please see the update on my last post. Thanks

See issue #1886 for a workaround. Jim is assigned to fix it properly but I guess it is not, yet.

About the instrument adding web page in older Leginon, we have gotten rid of it in favor of instruments.cfg. People kept getting hostname and instrument class name wrong with the web page entry. Instruments.cfg is more logical.

Do you acquire Falcon image through TIA? Just curious.

Images acquired by Falcon camera go to TIA,indeed. In fact, any images acquired through latest TUI go into TIA, no matter the camera. Switching between Falcon and orius has to be done through TUI as well.

Thanks for the tip. After modify baseinstrument.py, I can see two Gatan cameras listed in instrument node, as I specificed in instrument.cfg. But I still have a couple of issues regarding to using camera.

1) After refresh camera in instrument node, both camera items are updated, but both updated to the camera currently selected in DM. That is, if the orius was selected in DM, all Gatan is updated to info of Orius, otherwise EFCCD.
In the setting of Manual node, there is only one Gatan item, also only one record in the 'instrumentData' table with NULL in 'type' field.
To take images with different camera, I have to manually select and insert the one to be used in DM.

2) If I refresh camera again after I change the camera in DM, I will get an error message in DM.

3) I can take images in Manual node whiie start leginon-main on Linux. But if I run Leginon-main on microscope PC, I got an error.

To be noted, Orius comes with Falcon camera and it means to be used for low-mag survey. And FEI-EPU use both camera in that way.