Image Alignment using PubSub

Carries out image alignment with the SPIDER operation: 'AP SH'. This operation compares a series of sample images to a series of reference images and selects the most similar reference image. It then determines the in-plane rotation and shift that aligns the sample image with that reference image. These alignment paramaters are placed in a SPIDER document file. (This procedure is for images referenced by micrograph.)

1. Login to master node of cluster, where PubSub is installed and running, e.g.:
   ssh   patroon
2. Access your working_dir, e.g.:
   cd   /usr1/user/align
3. Create input and output sub-directories, e.g.:
   mkdir   input   output
4. Copy the necessary input data files, i.e.:
   Micrograph selection doc. file,
   Sample images,
   Sample image selection doc. file,
   Reference images, and
   Reference image selection doc. file
   
   

   to your input directory e.g.:
   scp    'user@sylt.wadsworth.org:/usr1/user/ap/selmcg.dat'    input
   scp    'user@sylt.wadsworth.org:/usr1/user/ap/selimg.dat'    input
   scp    'user@sylt.wadsworth.org:/usr1/user/ap/img_*.dat'    input
   scp    'user@sylt.wadsworth.org:/usr1/user/ap/ref_*.dat'    input
   scp    'user@sylt.wadsworth.org:/usr1/user/ap/selref.dat'    input
   

   (If you do not have an Micrograph selection doc. file file, you can create it using: 'DOC CREATE' and entering the number of micrographs.

5. Copy apsh_pub.spi SPIDER procedure file to your working directory, e.g.:
   scp -v    '/net/bali/usr1/spider/docs/techs/recon/newprogs/apsh_pub.spi'    .
   (Note: /net/bali/usr1 is mounted on patroon)
6. Edit apsh_pub.spi to set necessary values for input parameters and input file names, e.g.
   xedit   apsh_pub.spi
   Number of images/partition depends on number of nodes available and their speed. Try 100 if unsure.
7. Create link in your working directory for a specific SPIDER (ensures that same SPIDER executable is used throughout whole run), e.g.:
   ln -s /usr/local/spider/bin/spider_linux_mpfftw.40    spider
8. Start Master SPIDER refinement process apsh_pub.spi, e.g.
   spider bat/dat    @apsh_pub 0 &
9. The master SPIDER refinement process will create and publish new SPIDER jobs as necessary. When all jobs are finished the master process consolidates the angles document files for each of the micrographs.