ISIS Application Documentation
     Correct jitter in input cubes and output corrected undistorted cubes
  
 
          Description
        
  
     This application computes angular corrections from pixel offsets in the
     input jitter file and applies the corrections to the undistorted output 
     cube.  This application is procedural in that it runs other applications.
     It runs through a series of applications twice.  The first time it applies 
     the jitter corrections and calculates additional pitch rate and yaw angles 
     to center the remaining camera pointing errors around zero.  The output 
     cube files are deleted and the series of applications is run again, 
     including the additional pitch rate and yaw corrections.
     The first step it performs is to run spiceinit on all the FROMLIST cubes 
     with the parameter attach=no.  A version of the MASTER file is saved and 
     run through the application spicefit to remove noise in the camera 
     pointing.  This file will be used in the noproj runs as the match cube.  
     The next application run is appjit and it needs to load the Spice from the 
     files directly in order have access to Spice information not typically 
     stored on the Isis cube labels. This application applies the corrections 
     from the JITTER file to the camera pointing in the FROMLIST cubes.  Now the 
     FROMLIST cubes are run through noproj, removing the jitter from the pixel 
     positions and the camera distortion.  The results are measured on adjacent
     ccd's by the application hijitreg and used to compute the additional pitch 
     rate and yaw required to center the errors around zero.  
     Now the procedure is repeated with the calculated pitch and yaw passed into 
     appjit as input parameters.  The jitter-reduced and distortion-free output 
     cubes are created by the final set of noproj runs on adjacent ccd's. 
     If crop=true then the application crops the extended portion of the   
     image. The starting line and number of lines parameter for crop 
     application is calculated from the ephemeris time in the  jitter  
     correction file. LineRate is used to get the starting and ending line 
     information.
    
   
 
          Categories
        
 
              History
          
| Steven Lambright | 2008-12-17 | 
     Original Version
    | 
 
| Debbie A. Cook | 2009-01-14 | 
      Added documentation
     | 
 
| Jai Rideout | 2011-08-04 | 
      Made a small modification to the code in FindRed(...) that created a Pvl
      object for each file in the file list. FileList's overloaded
      '[]' operator that was used inside of the call to Filename's constructor
      confused the compiler on Ubuntu 10.04 systems.
     | 
 
| Debbie A. Cook | 2011-08-15 | 
      Added an option to run ckwriter to create a ck with jitter for correcting
      image geometry.
     | 
 
| Debbie A. Cook | 2011-12-21 | 
      Fixed the loop that calculated pitch to only loop the number of overlaps
      (count).
     | 
 
| Sharmila Prasad | 2011-12-27 | 
     Added an option to crop the extended portion of the image using the jitter 
     correction file 
     | 
 
| Sharmila Prasad | 2012-02-05 | 
     Crop option false by default 
     | 
 
| Debbie A. Cook | 2012-07-06 | 
     Updated Spice members to be more compliant with Isis standards. References #972.
     | 
 
| Jeannie Backer | 2012-11-21 | 
     Modified to work with IR and BG ccd images.  Fixed bug with computation of 
     yaw and pitch. Fixes #795.
     | 
 
 
 | 
 
 
                Parameter Groups
            
Input Files
| 
                    Name
                     | 
                    Description
                     | 
 
| FROMLIST | 
          Cubes to correct
         | 
 
| JITTER | 
          Ascii table of pixel offsets representing jitter for a given time
         | 
 
| REGDEF | 
          The Auto Registration template used in hijitreg
         | 
 
| TOLIST | 
          The list of the corrected undistorted cubes to be created
         | 
 
 
Options
| 
                    Name
                     | 
                    Description
                     | 
 
| MASTER | 
          The file to use as the MASTER
         | 
 
| DEGREE | 
          The degree of fit used in appjit
         | 
 
| JITTERCK | 
          Optional jittery ck file for using to correct spice"
         | 
 
| CROP | 
          Crop the top and bottom extending portion of the image
         | 
 
 
 | 
 
Options:
                        MASTER
                         Description
                       
            The application appjit applies the jitter corrections to the 
            camera pointing in the MASTER file first and then copies it to the 
            other files in the FROMLIST.  The MASTER file is also used as the 
            MATCH file in the application NOPROJ
        
| 
                             Type
                            | integer | 
| 
                               Default
                              | 5 | 
| 
                               Minimum
                              | 0
                                   (inclusive)
                                  | 
| 
                               Maximum
                              | 13
                                   (inclusive)
                                  | 
 
 
Options:
                        DEGREE
                         Description
                       
          Enter the degree of the polynomial to fit to the data
        
 
Options:
                        JITTERCK
                         Description
                       
          Optionally enter the name of an output Naif ck containing
          the jittery pointing data.  This ck can be used in spiceinit
          as the csmithed camera pointing to get correct pointing on
          mission cubes (not noproj'd).  The default is to not create
          the jittery ck.
        
| 
                             Type
                            | filename | 
| 
                               Internal Default
                              | None | 
 
 
Options:
                        CROP
                         Description
                       
          Crop the top and bottom extending portion of CCDs in the image using 
          the jitter file's first and last non zero corrections. This option 
          when enabled removes the lines at the beginning and end of the image 
          as determined by the jitter file
        
| 
                             Type
                            | boolean | 
| 
                               Default
                              | false |