usage: prog [options] <path or db> ... Various utilities related to BDB databases. examples : e2bdb.py -c Is perhaps the most critical function, as it cleans up the database cache. See the Wiki for more. e2bdb.py <path> -s will list the contents of the database in a directory in bdb: notation e2bdb.py <path> -l Will give useful summary info about stacks in a directory e2bdb.py <database> --dump Gives a mechanism to dump all of the metadata in a database, even if the database contains no images
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --cleanup, -c | None | This option will clean up the database cache so files can safely be moved or accessed on another computer via NFS. |
| --force, -F | None | This will force an action that would normally fail due to failed checks. |
| --delete | None | This will delete (or at least empty) the named database(s) |
| --all, -a | None | List per-particle info |
| --long, -l | None | Long listing |
| --short, -s | None | Dense listing of names only |
| --filt | str | Only include dictionary names containing the specified string |
| --filtexclude | str | Exclude dictionary names containing the specified string |
| --match | str | Only include dictionaries matching the provided Python regular expression |
| --exclude | str | The name of a database containing a list of exclusion keys |
| --dump, -D | None | List contents of an entire database, eg 'e2bdb.py -D refine_01#register |
| --smalldump | None | Lists contents of an entire database, but only list 2 items per dictionary to better see headers |
| --extractplots | None | If a database contains sets of plots, such as bdb:refine_xx#convergence.results, this will extract the plots as text files. |
| --check | None | Check for self-consistency and errors in the structure of specified databases |
| --nocache | None | Don't use the database cache for this operation |
| --merge | None | This will merge the contents of BDB 2-N into BDB 1 (including BDB 1's contents) |
| --makevstack | str | Creates a 'virtual' BDB stack with its own metadata, but the binary data taken from the (filtered) list of stacks |
| --appendvstack | str | Appends to/creates a 'virtual' BDB stack with its own metadata, but the binary data taken from the (filtered) list of stacks |
| --verbose, -v | int | verbose level [0-9], higher number means higher level of verboseness |
| --list | str | Specify the name of a file with a list of images to use in creation of virtual stacks. Please see source for details. |
| --exlist | str | Specify the name of a file with a list of images to exclude in creation of virtual stacks. Please see source for details. |
| --restore | str | Write changes in the derived virtual stack back to the original stack |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
| --checkctf | None | Verifies that all images in the file contain CTF information, and gives some basic statistics |
| --step | str | Specify <init>,<step>[,<max>]. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles |
For more information go to emanwiki/EMAN2/Programs/e2bdb.