Loading/saving masks in pixel coordinates

[jo-moeller]

We would need the masks to be saved and loaded in the same shape as the detector data. As for example for AGIPD as (16,512,128) array. This would make the masks reusable, even if the geomertry of the quadrants changes. And in general, a bad pixel stays bad, even if the quadrant moves.

Also, it would make EXtra-foam masks compatible with other programs, as for example the the ADU_histogram device in Karabo.

[zhujun98]

Do you have a sample file for the mask?

I would like to make you realize that in the deployed new version 0.8.1, there is an option in the Geometry panel to select assembler. Unlike LPD and DSSC, now the default assembler for AGIPD is still EXtra-geom and I will switch it to EXtra-foam at some point. The assembler in EXtra-foam is implemented in C++ and is 5 - 10 times faster than EXtra-geom on the online cluster.

As the C++ assembler now support all the three modular detectors, it is time to implement the universal mask that you requested.

[jo-moeller]

You can find an example mask at /gpfs/exfel/exp/MID/201901/p002542/usr/Software/mask.npy

[zhujun98]

I just deployed a test version 0.8.3dev at EXtra-foam/alpha. Can you test it when you have time? Thank you!

[zhujun98]

We can reopen the issue or start another one if you find any bug or need some additional features.

[zhujun98]

Forgot to mention that I also updated the documentation

https://extra-foam.readthedocs.io/en/latest/image_tool.html#mask-panel

[jo-moeller]

Hi,
there might be still an issue. I have selected this geometry: /gpfs/exfel/exp/MID/202022/p002693/usr/Software/geom_20200912.geom with Assembler: extra-foam.
When I now create a mask in extra-foam, save it and reload it, I get the follwing error:
ERROR- Shape of the image mask (1259,1092) is different form the image (1357,1195)!

[zhujun98]

Yes, there is something not easy to fix in order to synchronize the mask in the processors and the GUI sides. If I still remember correctly, you will need to keep the image tool showing the geometry panel and wait for the new mask to get updated. Otherwise, there is a chance to get the error you mentioned if you switched to other pannels.