pipeline:utilities:e2bdb

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pipeline:utilities:e2bdb [2018/02/21 13:13]
moriya
pipeline:utilities:e2bdb [2019/04/02 09:20]
lusnig
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 Usage in command line Usage in command line
  
-  e2bdb.py ​ --cleanup ​ --force ​ --delete ​ --all  --long ​ --short ​ --filt='​SUBSTRING' ​ --filtexclude='​SUBSTRING' ​ --match='​REGULAR_EXPRESSION' ​ --exclude='​BDB_NAME' ​ --dump ​ --smalldump ​ --extractplots ​ --check ​ --merge ​ --makevstack='​bdb:/​Home/​user/​project#​output' ​ --appendvstack='​bdb:​output' ​ --list='​abc.txt' ​ --exlist='​xyz.txt' ​ --restore='​bdb:​vstack' ​ --ppid=PPID ​ --checkctf ​ --step=STEP ​ --nocache ​ --verbose=LEVEL+  e2bdb.py ​ --cleanup ​ --force ​ --delete ​ --all  --long ​ --short ​ --filt='​SUBSTRING' ​ --filtexclude='​SUBSTRING' ​ --match='​REGULAR_EXPRESSION' ​ --exclude='​bdb_NAME' ​ --dump ​ --smalldump ​ --extractplots ​ --check ​ --merge ​ --makevstack='​bdb:/​Home/​user/​project#​output' ​ --appendvstack='​bdb:​output' ​ --list='​abc.txt' ​ --exlist='​xyz.txt' ​ --restore='​bdb:​vstack' ​ --ppid=PPID ​ --checkctf ​ --step=STEP ​ --nocache ​ --verbose=LEVEL
  
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   e2bdb.py --dump refine_01#​register ​   e2bdb.py --dump refine_01#​register ​
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- 6. Make a '​virtual' ​BDB image stack from one or more other stacks.+ 6. Make a '​virtual' ​bdb image stack from one or more other stacks.
  
   e2bdb.py bdb:db1 bdb:db2 --makevstack=bdb:​db3 ​   e2bdb.py bdb:db1 bdb:db2 --makevstack=bdb:​db3 ​
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   e2bdb.py . --makevstack=bdb:​data --filt=db ​   e2bdb.py . --makevstack=bdb:​data --filt=db ​
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- 7. Append to or create a '​virtual' ​BDB image stack with its own metadata.+ 7. Append to or create a '​virtual' ​bdb image stack with its own metadata.
  
   e2bdb.py bdb:db1 bdb:db2 --appendvstack=bdb:​db3 ​   e2bdb.py bdb:db1 bdb:db2 --appendvstack=bdb:​db3 ​
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- 8. Creates a new virtual ​BDB image stack by extracting images whose IDs are listed in the specified ASCII file from existed virtual stacks.+ 8. Creates a new virtual ​bdb image stack by extracting images whose IDs are listed in the specified ASCII file from existed virtual stacks.
  
   e2bdb.py bdb:#db1 bdb:#db2 --makevstack=bdb:​.#​db3 --list=abc.txt ​   e2bdb.py bdb:#db1 bdb:#db2 --makevstack=bdb:​.#​db3 --list=abc.txt ​
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   ; %%--%%extractplots : Extract plots as text files: If a database contains sets of plots, such as bdb:​refine_xx#​convergence.results,​ this will extract the plots as text files. (default False)   ; %%--%%extractplots : Extract plots as text files: If a database contains sets of plots, such as bdb:​refine_xx#​convergence.results,​ this will extract the plots as text files. (default False)
   ; %%--%%check : Check for self-consistency and errors: Check for self-consistency and errors in the structure of specified databases. (default False)   ; %%--%%check : Check for self-consistency and errors: Check for self-consistency and errors in the structure of specified databases. (default False)
-  ; %%--%%merge : Merge database contents: Merge the contents of BDB 2-N into BDB 1 (including ​BDB 1's contents). (default False) +  ; %%--%%merge : Merge database contents: Merge the contents of bdb 2-N into bdb 1 (including ​bdb 1's contents). (default False) 
-  ; %%--%%makevstack : Output virtual image stack: Make a '​virtual' ​BDB image stack with the specified name from one or more other stacks. (default none) +  ; %%--%%makevstack : Output virtual image stack: Make a '​virtual' ​bdb image stack with the specified name from one or more other stacks. (default none) 
-  ; %%--%%appendvstack : Append to or create virtual image stack: Append to or create a virtual ​BDB image stack with its own metadata. (default none) +  ; %%--%%appendvstack : Append to or create virtual image stack: Append to or create a virtual ​bdb image stack with its own metadata. (default none) 
-  ; %%--%%list : Image selection file: Input selection text file containing a list of selected image IDs (or indexes of the data subset) to create a new virtual ​BDB image stack from an existed stack or virtual stack. (default none) +  ; %%--%%list : Image selection file: Input selection text file containing a list of selected image IDs (or indexes of the data subset) to create a new virtual ​bdb image stack from an existed stack or virtual stack. (default none) : %%--%%exlist==none %%--%%step==0,​1 
-  ; %%--%%exlist : Image exclusion file: Input exclusion text file containing a list of excluded image IDs (or indexes of the data subset) to create a new virtual ​BDB image stacks from an existed stack or virtual stack. (default none)+  ; %%--%%exlist : Image exclusion file: Input exclusion text file containing a list of excluded image IDs (or indexes of the data subset) to create a new virtual ​bdb image stacks from an existed stack or virtual stack. (default none) : %%--%%list==none %%--%%step==0,​1
   ; %%--%%restore : Write changes in virtual stack back to original stack: Write changes in the derived virtual stack back to the original stack. (default none)   ; %%--%%restore : Write changes in virtual stack back to original stack: Write changes in the derived virtual stack back to the original stack. (default none)
   ; %%--%%ppid : Set PID of parent process: Set the PID of the parent process, used for cross platform PPID. (default -1)   ; %%--%%ppid : Set PID of parent process: Set the PID of the parent process, used for cross platform PPID. (default -1)
   ; %%--%%checkctf : Verifies CTF entry: Verify that all images in the file contain CTF information,​ and give some basic statistics. (default False)   ; %%--%%checkctf : Verifies CTF entry: Verify that all images in the file contain CTF information,​ and give some basic statistics. (default False)
-  ; %%--%%step : Processes only subset: Specify <​init>,<​step>​[,<​max>​]. Process only a subset of the input data. For example, 0,2 would process only the even numbered particles. (default ​'0,1')+  ; %%--%%step : Processes only subset: Specify <​init>,<​step>​[,<​max>​]. Process only a subset of the input data. For example, 0,2 would process only the even numbered particles. (default 0,1) : %%--list%%==none %%--%%exlist==none
  
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  • pipeline/utilities/e2bdb.txt
  • Last modified: 2019/04/02 09:20
  • by lusnig