img2db usage

What is it for?

• Deposit multiple tld/mrc micrograph images into the database with a single run. tld format images will be converted to mrc format before deposit.

• Download multiple micrograph/CCDFrame images from the database with a single run.

• Transfer multiple tld/mrc images to other computers. tld format images will be converted to mrc format before transfer.

• Deposit calculated CTF parameters to the databases.

• Send an ISO image to the database server to burn a CD/DVD for data backup.

• Upload/download box data files for micrographs.

How to install it?

1. download it from here.
2. run: tar xvf img2db.tar
3. run: cd img2db
4. follow the instructions in file 'INSTALL'.

What's the latest release?

How to use it?

1. run img2db -h to get the options:

      Usage 1: check in micrographs to database:
   
           img2db [-a averagefactor] [-b brightness] [-c contrast] [-e exposuretime] [-g gain] [-m scanner] [-n] [-p] [-s scanstep]  image1 [image2 ...]
             -a: averagefactor; default = 1.0
             -b: brightness; default = 30.0
             -c: contrast; default = 68.0
             -e: exposuretime; default = 0.0
             -g: gain; default = 0.0
             -m: scanner; default = Zeiss
             -n: comments; default =
             -p: parameters; default = 1
             -s: scanstep; default = 7.0
   
      Usage 2: download micrographs:
           img2db [-f] -d n
             n: shrinkfactor: 1, 1.5, 2, 3, ...
   
            -f: fast download: download the latest object without ask
   
      Usage 3: download CCD Frames:
           img2db [-f] -F
            -f: fast download: download the latest object without ask
   
      Usage 4: download box data files:
           img2db [-f] -D
            -f: fast download: download the latest object without ask
   
      Usage 5: check in box data files:
           img2db -B LP0001.box [LP0002.txt ...]
   
      Usage 6: check in ctf parameters:
           img2db -C ctfparm1.txt [ctfparm2.txt ...]
   
      Usage 7: send an ISO image to burn a CD:
           img2db -I isoimage
   
      Usage 8: check version number:
             -v: version number
   		

2. Examples:
   1. deposit your micrograph images to the databases with your 'brightness' and 'contrast' values; use 'tld2mrc' to average 'tld' image to 'mrc' image.
      % img2db -a 1 -b 20 -c 70 lp0001.tld lp0002.tld

   2. deposit .tld images to database. add a comment to each image. set 'brightness' = 10, 'constrast' = 60.
      % img2db -b 10 -c 60 -n lp0001.tld lp0002.tld
      With -n, the program will ask for the comments for each image interactively at run-time.

   3. average 'tld' image to 'mrc' image by a factor of 1.5. use default values for other options.
      % img2db -a 1.5 lp0001.tld lp0002.tld

   4. download micrographs 'lp0001', 'lp0002'. shrink images by a factor of 1.5. run:
      % img2db -d 1.5
      Input "lp0001 lp0002" when the program asks for the micrograph film ids.

3. Parameters:
   
   1. There are 3 types of options:

      1) set value on command-line. e.g., brightness, contrast, averagefactor, etc. you use them like
      img2db -b 20.0 -c 70.0 -a 1.5 lp0001.tld

      2) don't set the value on command-line. the value is micrograph-specific, and will be asked interactively at run-time. e.g., comment, parameters, etc. use them like
      img2db -n -p lp0001.tld lp0002.tld

      3) set the type of usage. e.g., '-d' for download, '-f' for ftp-only, use them like
      img2db -f lp0001.tld lp0002.tld

   2. averagefactor: valid values are:
      • 1: use 'tld2mrc' to do the averaging.
      • 1.5: use 'tld2mrc3-1' to do the averaging.
      • 2: use 'tld2mrc2' to do the averaging.

How to interrupt the program?

Use Ctrl-C.

How to run the program in the background?

1. run dbpass first.
2. Use -U username -P in the command line. For example,

    img2db -U lpeng -P LP*.tld > mylog.txt & 

   All error messages and logs will go to file mylog.txt. You may want to check it later for any errors.

What are required to use img2db?

• Zope Database account: username, and password
• To deposit a micrograph image, the user must have already created a micrograph record in the database.

Where to report bugs?

Bug Report

Know Bugs