e2compress

usage: Usage: e2compress.py [options] <file1> <file2> <file3> 
converts a list of image files to compressed hdf files. If the input file is also HDF, it will overwrite the file, otherwise it will change
the file extension. When read by EMAN2, compressed HDF files will be rescaled to their original (rounded) values, not the integer
values stored in the file. If read using other software it is likely that the integer values will be seen.

The --nooutliers option will truncate extreme image values. This is an ALTERNATIVE to specifying --range or --sigrange. This will eliminate 
a small fraction of the most extreme values in the images.

Default behavior is to perform 10 bit integer compression, which is sufficient for pretty much any CryoEM image file
or reconstruction. Raw movie frames may need only 2-4 bits and aligned averaged micrographs are likely to be fine with 4-6 bits, so it
is wise to specify the number of bits to use. Specifying 0 bits is a special case which will cause compression of the native floating point
format. In most cases this will result in only 10-30% compression, whereas most files can be compressed by a factor of 5-10 with no impairment
of results.

Additionally, if the input file contains integer values, it will try to mak a mapping which will produce integer values in the file when read 
back in. If there are a significant number of values which are exactly 0.0, this value will also be preserved. 

The smaller the number of bits, the faster the compression, and the better the compression ratio. Noise compresses poorly, so eliminating bits
containing pure noise is benificial in multiple ways.

--compresslevel will not impact the quality of the stored images, but will impact compression size and time required. For example, when storing
a typical movie stack of 50 K2 frames using a single thread:
uncompressed   2848 MB   7.1 s
level 0         738      9.3     3.8x compression
level 1         193     15.7    14.7
level 2         184     16.9    15.5
level 3         175     24.7    16.3
level 4         165     21.2    17.3
level 5         158     32.8    18.0  (typical int-compressed tiff)
level 6         152     62.5    18.7
level 7         149     95.4    19.1

Typical usage:
e2compress.py --nooutliers --outpath ../micrographs_5bit --threads 32 -v 2 --bits 5 *.mrc