... | ... | @@ -8,7 +8,7 @@ This will generate a 500k image dataset of noise-free diffraction intensities. I |
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where the `-q` flag results in the diffraction intensities being quantized to simulate photon counts on the detector. The overall fluence is increased from the the default given in amo86615.beam by the `-s` flag, resulting in a total fluence of 1e13 photons per diffraction shot. Additional types of noise can be simulated as follows:
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`python sim_spinifel.py -b amo86615.beam -p 3iyf.pdb -d 128 0.08 0.2 -n 500000 -s 10 -q -bj 1 -fj 0.2 -o 3iyf_noisy.h5`
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`python sim_spinifel.py -b amo86615.beam -p 3iyf.pdb -d 128 0.08 0.2 -n 500000 -s 10 -q -bj 0.2 -fj 0.1 -o 3iyf_noisy.h5`
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where the `-bj` and `-fj` flags respectively add beam and fluence jitter. A custom sloped background, which results in systematic rather than uncorrelated errors between shots, can also be simulated by supplying the path to a numpy array of the desired background and using the `-sb` flag.
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