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Other Miscellaneous Files

While EMAN2 prefers HDF and JSON files for most tasks, there are a few other formats which are supported and used in specific contexts.

.lst files

LST files and LSTX files originated in EMAN1. They are text files containing a list of image filenames and numbers, which EMAN2 will treat as if they contained actual images. These files follow the following format:

# warning message
#<line length>
<img #>    <img path>    <comment><' ' padding>
<img #>    <img path>    <comment><' ' padding>
<img #>    <img path>    <comment><' ' padding>

Here is an example:

# This file is in fast LST format. All lines after the next line have exactly the number of characters shown on the nex
t line. This MUST be preserved if editing.
# 29
0       particles/1075.big.hdf    
1       particles/1075.big.hdf    
0       particles/1076.big.hdf    
1       particles/1076.big.hdf    
2       particles/1076.big.hdf    

Say, for example, that you have 3 image stack files: A.hdf, B.hdf and C.hdf, each containing 500 particles. You wish to combine them into a single stack for running a refinement. An LST file allows you to combine them virtually without actually having to duplicate the images.

The LST format is used for the files in the sets directory, and the command can be used to produce them.

While these files can, technically, be edited by hand, every line in the file after the <line length> must have exactly the same number of characters. For programmers, there is a class called LSXFile which allows easy reading & writing of these files.

.box files

These files also originated in EMAN1, and are not really used directly by EMAN2, but can be imported/exported. This is a simple text file with a list of particle locations within a micrograph. Here is an example:

5341    8216    256     256     -3
3269    1876    256     256     -3
3386    2801    256     256     -3
2669    1080    256     256     -3

There are 5 columns. The first 2 are the x/y coordinates of the lower left corner of the box. The next 2 are the box size in X and Y (normally the same). The fifth number is a 'mode', and isn't always present. This value is normally used to identify filament boxes (with a starting and ending coordinate on paired lines). Just use -3 for normal single particle box files.

Note that since the coordinate is the lower left corner of the box, if you want to change the box size, you also need to adjust the box coordinates, or the center of the box will shift.

Eman2OtherFiles (last edited 2013-08-12 00:50:14 by SteveLudtke)