
These directories contain various programs developed at Lawrence Berkeley
Laboratory for use with HIPS2.

Brian Tierney, LBL
bltierney@lbl.gov

The following is the README from the HIPS-1 version of the directory, which
briefly describes only a fraction of the programs available in this directory:

-------------------------------OLD README-------------------------------------

The contents of this directory come courtesy of the Lawrence Berkeley
Laboratory.

Description of some of the contents of this directory:

  README:  this file

  doc/dna_segmentation.me  : copy of a paper which describes the use of
                     some of these programs

subdirectories:

lib/    : directory containing routines for allocating, reading, writing,
          and freeing dynamically allocated 2D and 3D arrays. Used by
          bclean.c, bthin.c, fill_holes.c, flip_quad.c, getobj.c, and hstat.c

doc/    : the above-mentioned paper

hips/	: standard HIPS filters, subroutines and man pages

include/: include files required for these filters (these are not installed
	but simply used in place)

xhips2/	: the routine xhips2 which is a raw X11 viewer (an improvement on
		drivers/xhips)

xwindows/: several XView-based image analysis programs

Some of the new HIPS filters:

	addmask - combines a HIPS image with a binary mask to create a new
		image.

	applylut - apply a text gray-level look-up table to a byte or short 
		formatted HIPS image.

	autocollage - collages a sequence of hips images into a single 
		frame with 50 pixels between each image.

	autoextract - generate a csh script file to automatically extract
		smaller images from a larger HIPS image.

	bdwindow - window on pixels in depth

	bin_mask - apply a bitmask to each pixel of an image

	clip - limit the upper and lower grey values of an images to a
		specified value

	fill_holes - fill small holes in binary HIPS images.

	flip_quad - flips the 4 quadrants of a HIPS image.

	getobj - Selects objects out of an image, and sets the
		rest of the image to a given background value. 

	gray_wedge - generate a gray value ramp image

	hfant - perform simple spatial transforms on a hips sequence of images

	hfant_sh - perform simple spatial transforms on a hips sequence of
		images

	hstat - computes statistics on objects in a HIPS image defined 
		by a binary mask.

	make_mask - create an edge detector mask

	maxseq - overlays two sequences.

	printxyz - makes list of x,y,z locations of objects in a binary image
		mask.

	scale_gray - do window based mapping and quadratic scaling of the
		pixel values of a sequence of images

Similar to previous HIPS filters

   bthin.c  : similar to thin, but uses a different algorithm, is MUCH
              faster, and has some possibly annoying artifacts ( see the
	      man page )

New versions of previous HIPS filters

   bclean2.c   : about 500 times faster than old version, but uses 3-4 times
                more memory
   checkers2 : generate a checker board pattern of gray values
   disphist_short : display histogram files as a bar graph (smaller output
		images)
   ftocc : converts floating images to complex (i and r equal to float
		image)
   histoeq2.c  : now handles short and int images, plus fixes a bug in the
                old version when using the -z option on a sequence
   mls_short : suppress random noise in an image
   suntohips2.c : now looks and sun raster colormap and converts colors
                 to grayscale.

getobj3d/	source code for getobj3d program
	getobj3d - is a 3D version of getobj, 
		which selects objects out of an image, and sets the
		rest of the image to a given background value.

mahe/		source code for mahe program
	mahe - "clipped" adaptive histogram equalization

scale_geom/	source code for scale_geom
	scale_geom - filtered image scale and translate

segal/		source code for segal 
	segal - An X-windows based image/mask viewer, editor, and analyser.

tiff/		source code for tifftoh and htotiff
	htotiff - reads a HIPS file and convert it to TIFF format
	tifftoh - convert a tiff image file to a hips image file

/***********************************************************************/
/*  COPYRIGHT NOTICE         *******************************************/
/***********************************************************************/

/*   These programs are copyright (C) 1990/1991, Regents  of  the
University  of  California.   Anyone may reproduce this software,
in whole or in part, provided that:
(1)  Any copy  or  redistribution  must  show  the
     Regents  of  the  University of California, through its
     Lawrence Berkeley Laboratory, as the source,  and  must
     include this notice;
(2)  Any use of this software must reference this  distribu-
     tion,  state that the software copyright is held by the
     Regents of the University of California, and  that  the
     software is used by their permission.

     It is acknowledged that the U.S. Government has  rights
to this software under  Contract DE-AC03-765F00098 between the U.S.
Department of Energy and the University of California.

     This software is provided as a professional  academic  
contribution for  joint exchange.  Thus it is experimental, is
provided ``as is'', with no warranties of any kind  whatsoever,
no  support,  promise  of updates, or printed documentation.
Bug reports or fixes may be sent to the author, who may or may
not act on them as he desires. 
*/

/*   Author:  Brian L. Tierney
 *            Lawrence Berkeley Laboratory
 *            Imaging and Distributed Computing Group
 *            email: bltierney@lbl.gov
*/

