alignlog(1)                                                        alignlog(1)

       alignlog - extract data from tiltalign log file

       alignlog  options  [a | b | log_filename]

       This Python script extracts useful sections from the output of Tiltal-
       ign(1).  One or more options may be entered in any order; if multiple
       options are given, the different sections are printed out in the order
       given.  If no filename is entered, alignlog will attempt to extract
       sections from the file align.log.  If a or b is entered instead of a
       filename after the options, then sections will be printed from
       aligna.log or alignb.log, respectively.

       Alignlog uses the PIP package for input (see the manual page for
       pip).  Options can be specified either as command line arguments
       (with the -) or one per line in a command file (without the -).
       Options can be abbreviated to unique letters; the currently valid
       abbreviations for short names are shown in parentheses.

       -m     Mappings: print variable mappings

       -e     Errors: print errors and ratio of measured to unknowns

       -s     Solution: print the alignment solution for each view

       -l     Local: print the location and size of each local area, the num-
              ber of fiducials on each surface, and the mean residual.

       -c     Coordinates: print the 3-D coordinates of the fiducials

       -r     Residuals: print large residuals

       -a     Angles: print planar fits and recommended change in angles

       -b     Beam tilt: print F values (RMS errors) from beam tilt search

       -w     Robust weighting: print output from robust fitting and weighted
              mean residuals

       -help (-h) OR -usage
              Print help output

              Read parameter entries from standard input

       Print solutions and errors from align.log:
           alignlog -s -e

       Print 3-D coordinates and angle recommendations from alignb.log:
           alignlog -c -a b

       David Mastronarde,  mast at colorado dot edu


IMOD                                 4.9.3                         alignlog(1)