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Mlf_align2d_v3
Parameters
$: Metadata or stack with input images $`--nref <int`1> $`--ref <reference_file`> $`--oroot <rootname`mlf2d> $: Also check mirror image of each reference $``: Use pre-centered images to pre-calculate significant orientations. If this flag is set part of the integration over all references, rotations and translations is skipped. The program will store all (N_imgs*N_refs) origin offsets that yield the maximum probability of observing each experimental image, given each of the references. In the first iterations a complete integration over all references, rotations and translations is performed for all images. In all subsequent iterations, for all combinations of experimental images, references and rotations, the probability of observing the image given the optimal origin offsets from the previous iteration is calculated. Then, if this probability is not considered "significant", we assume that none of the other translations will be significant, and we skip the integration over the translations. A combination of experimental image, reference and rotation is considered as "significant" if the probability at the corresponding optimal origin offsets is larger than C times the maximum of all these probabilities for that experimental image and reference (by default C=1e-12) This version may run up to ten times faster than the original, complete-search approach, while practically identical results may be obtained.
Additional options $--eps <float5e-5> $--iter <int100> $--psi_step <float5.> $--noise <float1> $--offset <float3.> $--frac <docfile> $-C <double1e-12> $: Kick-start the fast algorithm from all-zero offsets $`--restart <iter`1> $: Do not re-estimate the standard deviation in the pixel noise $: Do not re-estimate the standard deviation in the origin offsets $: Do not re-estimate the model fractions $--student <df6> =: Use t-distributed instead of Gaussian model for the noise df Degrees of freedom for the t-distribution: Refined normalization parameters for each particle $: Save memory A(deprecated) $: Save memory B(deprecated) $--search_shift <int3> $--reduce_snr <factor1> $: Use this if the experimental images have not been phase flipped $: Use this if the references (-ref) are not CTF-deconvoluted $--limit_resolution <first_high0> <high=0> <low=999> $--fix_high <float-1> $``: