Live visualization #35
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Before phasing on a new peak, it compares the shared-object projected diffraction to the actual measured diffraction (both with a 1-pixel gaussian blur). A difference map is defined as the absolute difference between the two blurred images divided by the blurred projection. A mask is generated from all the voxels where the difference map is greater than twice its own median. While the peak is being phased, the Fourier constraint is enforced using the measurement outside the mask and the projection inside.
…aint. The amount of feedback depends on that peak's confidence value.
Removed: - adaptive_weights (replaced by adapt_trigger) Added: - adapt_trigger: Puts the adaptive weighting in the operation/trigger format - adapt_power: Basically how harshly bad peaks are punished - adapt_alien_start: When to start removing aliens - adapt_alien_threshold: Voxels are masked where the error map exceeds this times its median Renamed: - weight_X << mp_weight_X - adapt_threshold_X << peak_threshold_X
# Conflicts: # cohere_core/controller/phasing.py
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Is the code in lines 174-275 necessary? Seems that the line 148 would do. |
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I think you're referring just to lines 274-275? In line 148, |
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Thanks, good explanation. |
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Potential solution to issue #10.
I added
live_operation()toRecandCoupledRec, which allows the reconstruction progress to be viewed in real time. For single-peak BCDI, it shows the amplitude, phase, and support, along with a plot of the error. For multipeak, the error/support panels are replaced by the diffraction pattern currently in rotation, before and after alien removal. The diffraction patterns are not central slices but are instead summed along one axis (this allows aliens to show up despite not being centered).The corresponding
live_triggergoes in config_rec and follows standard trigger notation. The documentation has been updated to include this. The trigger is activated immediately afterprogress_trigger.P.S. I don't know why this also included all of the commit history from my last PR (#32).