How to add sample tilt in phaser?

[xielin1984]

Hi @hexane360 ,
Thanks for this great software. I have run into problems in adding sample tilt in the reconstruction because I cannot find any example or tutorial. I tried to add "tilt_hook" in json file, but I got "WARNING:phaser.engines.common.output:Tilt map (state.tilt) is missing, skipping plot_tilt". Any help is appreciated. Thanks

Best wishes,

[hexane360]

To initialize a uniform tilt map, you can use this:

init:
  tilt:
    type: global
    tilt: [0.0, 0.0]  # [y, x] in mrad (+ is down/right)

Then, in your reconstruction solvers you can add a solver for the tilt variable, and a tilt regularization:

engines:
  - type: 'gradient'
    ...
    solvers:
      ...
      tilt:
        type: sgd
        learning_rate: 50.0  # will have to tune this to give reasonable update magnitudes
        momentum: 0.5
        nesterov: True

      iter_constraints:
        ...
        - type: tilt_gaussian
          sigma: 1.5   # angstrom
          weight: 0.1 

The tilt_gaussian regularization blurs together tilts from nearby probe positions, to prevent atomic structure from ending up in the reconstructed tilts.

Also, I'd recommend using the develop branch for now, it's more up to date. I'm currently working on pushing a new stable release.

Let's keep this issue open until we include a better example file for tilt correction.

[xielin1984]

Hi @hexane360 ,
Great! Looking forward to a new stable release and the example. For my question, I am using the LSQML algorithm and comparing to fold_slice right now. Is there a way to update tilt as well?

Best regards,

[hexane360]

Currently the sample tilt update is not supported for the conventional solvers (ePIE and LSQML). However, existing tilts from other engines are respected. You may be able to use a LSQML engine followed by a gradient descent engine that mainly updates tilts, or LSQML -> gradient -> LSQML.

[xielin1984]

Hi @hexane360 ,
OK. I am now testing the hyperparameters systematically. One more question, can I get a print of tilt on screen after the reconstruction?

Best regards

[hexane360]

You can add 'tilt' to the list in save_options.images to save a tilt map. Also, plot_ext and plot_dpi in save_options can be used to control the plot output