Dose symmetry does not work as expected

[MohamadHarastani]

Hello James, There seems to be a problem with dose symmetry. The dose damage seems to be always from the leftmost to the rightmost image in the tilt series. I am on the master branch. Cheers Mohamad

[MohamadHarastani]

A couple more related issues: 1- I noticed that the option phase_plate: true does not have have any effect on the output. I examined the Fourier space of the optics output and there is no sign of phase plates in it. 2- I need to simulate the dose damage on a semi-dose symmetric tilting scheme: [0, -4, -8, 4, 8, -12, -16, 12, 16, ...]. So I added this to the angles parameter in the config. However, I found that the angles did not override the start_angle, step_angle and num_images. So that was not simulated, nor sorted out the dose symmetry. Here is the config file to reproduce this issue (changed extension to txt to upload of Github). config.txt

Cheers Mohamad

[jmp1985]

Hi @MohamadHarastani

I've addressed this second issue so that now you can do the following:

• if you set the scan mode to "dose_symmetric" it will generate a list of angles and execute them in dose symmetric order.
• if you set the scan mode to "manual" the specified angles will be used.

Regarding the first issue, I've had a quick look and it's not obvious to me what is wrong, so I will have to take a deeper look to figure out what is happening.

Best wishes James

[MohamadHarastani]

All issues reported here are solved :-)