Normalization error during atlas publishing
Added by Jason Porta over 6 years ago
Hi Everyone,
I am getting a numpy broadcast error while trying to publish a grid atlas. I have located and determined what is causing the issue, but am unsure on how to correct it. I was wondering if anyone has had a similar error? The error is in the "grid targeting" node, and is:
"Normalize failed: operands could not be broadcast together with shapes (0,0) (924,924)"
I have also attached a screenshot of the error in Leginon.
I know that (924,924) is the camera area (4X binned) for the "gr" preset in Leginon and that numpy.broadcast requires the dimensions to either be equal, or that one dimension is equal to 1. However, I am unsure how to solve this issue. Any help/advice would be greatly appreciated.
Best regards,
Jason
| Normalize_Error.png (102 KB) Normalize_Error.png |
Replies (2)
RE: Normalization error during atlas publishing - Added by Anchi Cheng over 6 years ago
Hi, Jason,
The real error occurred during normalization step of an single image acquisition in "Grid" node as you posted.
The error you got indicates that the image acquisition failed and returned an array of dimension (0,0) instead of the expected (924,924). I recommend that you examine your preset parameters. In particular the assignment of the TEM and Digital Camera.
You should also take test image with the more basic Navigation Node. Send the preset and then acquire an image with the "camera" tool. I expect that you get the same error there.
Does other presets work from the same camera ? If they do and use use the same instrument combination, then we will have to debug this. I have not seen this before happening to only one camera configuration but not others.
If the other presets from the same camera does not work, either, and that it used to work, I recommend that you restart Digital Micrograph and Leginon Client on it. Check that you can get image within DM interface in case you need to reboot the camera system.
RE: Normalization error during atlas publishing - Added by Jason Porta over 6 years ago
Hi Anchi,
Thank you for your response. We did find that restarting Digital Micrograph and the Leginon client had resolved the issue.
Best regards,
Jason