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| ==== project.js ===== This file contains overall project parameters, such as A/pix, voltage, mass, etc. |
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| ==== ctf_parm.js ==== This file stores the CTF parameters for all images in the project as EMAN2CTF objects, keyed by '''basename'''. CTF objects are stored in ''.js'' files in a human-readable form as a dictionary, so individual values can be easily read and, if necessary, edited. |
==== notebook.js ==== This is where the projectmanager stores the text entered in the 'lab notebook'. |
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| ==== quality.js ==== This file stores user-assigned quality values per-micrograph. The key is the ''basename'' of the image file. Quality values run from 0-9 and may be used in any way the user prefers. They have no absolute meaning to any of the processing software, though there are places where higher will be assumed to indicate ''better'' images by whatever standard. |
==== <basename>_info.js ==== 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: [EMAN2CTF instance,signal 1D,background 1D,signal 2D, background 2D]|| ||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|| |
Metadata Stored 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.
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.js ===== This file contains overall project parameters, such as A/pix, voltage, mass, etc.
notebook.js
This is where the projectmanager stores the text entered in the 'lab notebook'.
<basename>_info.js
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: [EMAN2CTF instance,signal 1D,background 1D,signal 2D, background 2D] |
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 |