Metadata Stored in JSON files
JSON files in the info folder
The info folder is a replacement for the BDB-based EMAN2DB folder in the project directory. All information is stored in human-readable and editable JSON files with a .js extension.
If you have a micrograph called, for example, micrographs/DC19873.hdf, and have processed it with EMAN2, you will end up with other derived image files, such as particles/DC19873_ptcls.hdf and particles/DC19873ctf_flip.hdf, etc. Any information which needs to be stored about the micrograph as a whole, will be stored in info/DC19873_info.json. If you wish to copy micrographs from one file to another, all you need to do is copy the image file(s) and this JSON file to the info/ folder in the new project.
For each micrograph in the project a basename is assigned, to avoid confusion as the data goes from raw micrograph to particles, etc. That is, a file named micrographs/jj1234.mrc would use the basename jj1234. particles/jj1234.hdf would use the same basename.
project.json
This file contains overall project parameters, such as A/pix, voltage, mass, etc.
Parameter |
Description |
global.apix |
A/pixel value for this project. Generally speaking, if you want to downsample/rescale your data, you should do this in a separate project. |
global.microscope_voltage |
Default microscope voltage in kV when running CTF fitting and micrograph evaluation programs. While it is technically possible to combine data from multiple micrographs in a single project, it is not usually a good idea. If you are thinking about doing this you may wish to ask us about it first. |
global.microscope_cs |
Default Cs value in mm when running CTF fitting and micrograph evaluation programs. |
global.particle_mass |
The default mass of the particle being reconstructed in kDa. Clearly in some cases (assemblies in various stages of assembly, etc.) there will not be a single value for this. This value is primarily used as a default, and is really only used for setting reasonable isosurfaces in any case, so such situations should not really be a problem |
project_icon |
Used by the GUI |
project_name |
For recordkeeping purposes |
notebook.json
This is where the projectmanager stores the text entered in the 'lab notebook'.
<micrograph>_info.json
Per micorgraph information is stored in one file for each micrograph. This allows easy copying of micrographs with their metadata between projects. While there is, of course, metadata in the image headers, THIS metadata is not stored in the header because the information, such as CTF information, is associated with multiple image files, including the micrograph itself, as well as particle stacks, etc.
Parameter |
Description |
boxes |
The list of particle locations in the micrograph from e2boxer.py |
boxes_tilted |
The list of particle locations in the micrograph from e2boxer.py |
boxes_untilted |
The list of particle locations in the micrograph from e2boxer.py |
ctf |
A list of CTF related objects: [EMAN2CTF instance,signal 1D,background 1D,signal 2D, background 2D] computed from particles, not the overall frame |
ctf_frame |
A list of CTF related objects associated with the whole frame: [box size,EMAN2CTF instance,box coord,set of excluded boxnums] |
quality |
A single integer from 0-9. No predefined meaning, though 5 is the default value, and larger should be interpreted as better. This is to permit qualitative assessement by the user at various stages of analysis. |
sets |
A dicitionary containing lists of integers keyed by set name |
|
bad_particles - Particle numbers which have been determined to be 'bad'. The 'bad' particles may optionally be excluded when building sets |