contourmod(1)               General Commands Manual              contourmod(1)



NAME
       contourmod - to generate contour maps as a model file

SYNOPSIS
       contourmod

DESCRIPTION
       Contourmod will generate contour maps of selected sections in an image
       file and place them into an IMOD model that can then be displayed on
       the images.  You can produce contours at regularly spaced intervals or
       at individually specified levels.  Each contour level may have a dif-
       ferent color.

       The contours are lines connecting points spaced about 1 pixel apart or
       less; thus a complete set of contour lines for one image can have quite
       a large number of points, especially if the image is large or has a lot
       of fine detail.  The program will give an error message and stop adding
       points to the model if no further points can fit in the model storage
       arrays.  If this happens when contouring several sections, you need to
       make more than one model file.  If it happens when contouring a single
       image, the image is too large or too detailed and needs to be reduced
       in size or filtered.

       Entries to the program are:

       Name of file with images to contour

       Name of model file to place contours into

       List of sections to contour, or / for all sections in the image file.
       Ranges may be entered, e.g. 0-2,5,7

       X and Y scaling factors to apply to the model relative to the image
       pixels, or / for 1,1.  If you are going to display the contours on an
       image that has been expanded by a certain factor with a transformation,
       it is recommended that you generate the contours on the original rather
       than the expanded image, so as to avoid getting a contour model with a
       vast number of points.  In this case, you would enter that expansion
       factor as the X and Y scaling factors, and the contour model would fit
       the expanded images.

       Enter a positive number of contours for regularly spaced contours, or
       the negative of the number of contours if you want to specify each con-
       tour level individually.

       IF you entered a positive number greater than 1, next enter the lowest
       and highest contour levels desired.

       IF you entered 0 or 1, instead enter the single contour level desired.

       IF you entered a negative number, instead enter all of the desired con-
       tour levels.

       Finally, enter an intensity level or color (0 to 255) for each contour
       level.  If you might need to change the colors or turn any contours off
       inside IMOD, it is recommended that you give each level a unique color
       value.  For example, if you want several bright white or several black
       lines, make them 240, 239, 238, etc or 0, 1, 2, etc.

HISTORY
       Written by David Mastronarde 12/1/90, using CONTUR package from Tim Baker

BUGS
       Email bug reports to mast at colorado dot edu.



IMOD                                 5.0.2                       contourmod(1)