clean_maps

PURPOSE

clean_maps is an interactive program that allows one to remove portions of the maps output by register.  The overall aim is to clean off any suspect portions so that there won't be inconsistencies among the maps that are given to the align program to do 3-d stack alignment.  It is usually necessary to do this when the relaxation process of align results in a folded spring network (a bad situation that is difficult to recover from).  With the default thresholds for distortion and correlation, the clean_maps program does a reasonable job of guessing which map portions should be discarded.  However, in a few cases it is necessary to adjust the thresholds when valid map portions are shown in orange/yellow.  To comfirm that the map is valid one might run inspector in a separate window to recheck maps that are particularly suspicious.

TYPICAL USAGE

clean_maps -pairs pairs.lst -input images/ -maps maps/ -output corrected_maps/ -corr corr/

COMMAND LINE OPTIONS

-corr corr_directory

specifies where the files holding the corrections arre located.  The programs reads and writes to these files, and normally the user does not have to look at them.  In the event that clean_maps is run again, the previous map edits are automatically applied.

-input image_directory/

specifies where the input images are located.

-map maps_directory/

specifies where the maps relating the images are located.  These are only used as input files.

-output corrected_maps_directory/

specifies where the corrected maps will be written to.

-pairs pairs.lst

specifies the list of image pairs that will be displayed.  This list should be in the same format as the pairs list for find_rst and register, and often will be the same file as used with those programs.

COLOR CODES

The color codes for the map elements are:
    red - marked explicitly for exclusion
    orange - excluded due to excessive distortion
    yellow - excluded due to being part of an isolated region
    green - included because it has low distortion and is not in an isolated region
    blue - marked explicitly for inclusion

KEY AND BUTTON MAPPINGS

The available commands are:

     left mouse - mark the map element for exclusion
     CTRL left mouse - unmark the map element for exclusion
     SHIFT left mouse - mark the map element for inclusion
     CTRL SHIFT left mouse - unmark the map element for inclusion
 
     middle mouse - include an isolated region
     SHIFT middle mouse - exclude an isolated region
 
     right mouse - save the current pair and go to the next pair
                   (when the current pair is the last pair, just save it)
    SHIFT right mouse - save the current pair and go to the previous pair
                   (when the current pair is the first pair, just save it)
     CTRL right mouse - save the current pair and skip ahead 10 pairs
     CTRL SHIFT right mouse - save the current pair and skip backwards 10 pairs
 
     ESC - exit without saving the currently displayed pair