make FAML running

[xulabs]

entry function
aitom.average.ml.faml.faml.test_EM_real_data

The method is based on the following paper:

Zhao Y, Zeng X, Guo Q, Xu M. An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification. ISMB 2018. Bioinformatics. 2018 Jul 1; 34(13): i227–i236. doi:10.1093/bioinformatics/bty267. arXiv:1804.01203

Let's first fix the bugs to make the program run.

@ijinjay for technical questions, can consult with @xiangruz .

[ijinjay]

1. io.db.lsm_db not found
2. tomominer_mbc not found
3. statistics.vol not found
4. pls provide some image data for FAML

@xiangruz @xulabs

[xulabs]

added statistics.vol and lsm_db

[ijinjay]

@xiangruz Pls add image db data for FAML. 😃

[xiangruz]

@ijinjay I added database preparation commands into the faml tutorial.

[ijinjay]

Pls add fast_rotation_align function in align.fast.util. 😃

[xulabs]

added to align.fast.util.fast_rotation_align()
moved align.util to align.fast.util

[ijinjay]

test_EM_real_data(img_data, 20, 2, 5, "output")
got RuntimeError: v2.max() == v2.min() in tomominer.core.core.rot_search_cor()
Is there any error in the sample data or the code?

[xulabs]

@ijinjay this is normally because v2 has only a single value across the whole array. So it is invalid for alignment.
@xiangruz can you check the data?

[ijinjay]

aitom/aitom/average/ml/faml/faml.py

Line 834 in 956fa7e

m2 = np.ones((n, n, n))

aitom/aitom/average/ml/faml/faml.py

Line 850 in 956fa7e

m2 = np.ones((n, n, n))

Before align.fast_align(v1, m1, v2, m2), m2 is assigned ones in the above lines, which causes the bugs. Pls fix it. @xiangruz

[xiangruz]

Fixed the problem with fast_align