Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

FINDCONTRAST(1)							FINDCONTRAST(1)

NAME
	findcontrast - Finds contrast settings for converting to bytes

SYNOPSIS
	findcontrast

DESCRIPTION
  FINDCONTRAST finds the black and white contrast settings that are
  used when converting an image file to bytes with newstack or mrcbyte.
  It computes a histogram of pixel values within a selected volume,
  which it uses to determine the contrast settings that would truncate
  the values of a specified, small number of pixels in the volume.
  
  The program reports the absolute minimum and maximum pixel values
  within the selected volume, the minimum and maximum values with
  truncation of the specified number of pixels, and the black and white
  contrast settings that would give this amount of truncation.

  Findcontrast uses the PIP package for input (see the manual page for pip)
  and can still take sequential input interactively.  The following options
  can be specified either as command line arguments (with the -) or one per
  line in a command file or parameter file (without the -):

 -input OR -InputFile   File name
    Input image file to bin down in 3D

 -slices OR -SlicesMinAndMax   Two integers
    Starting and ending slices to analyze in Z, numbered from 1.  The default
    is to do all slices.

 -xminmax OR -XMinAndMax   Two integers
    Starting and ending coordinates to analyze in X, numbered from 0.  The
    default is to omit borders equal to 10% of the X dimension.

 -yminmax OR -YMinAndMax   Two integers
    Starting and ending coordinates to analyze in Y, numbered from 0.  The
    default is to omit borders equal to 10% of the Y dimension.

 -flipyz OR -FlipYandZ
    Treat coordinates as coming from a volume that was read into 3dmod with Y
    and Z flipped.  Thus, for a newly created tomogram loaded into 3dmod
    flipped, you can use this option to enter X, Y, and Z coordinates read out
    from 3dmod.

 -truncate OR -TruncateBlackAndWhite   Two integers
    Number of pixels to truncate as black and white in the analyzed volume. 
    The default is one pixel per slice or one pixel per million, whichever is
    greater.

 -help OR -usage
    Print help output

  -StandardInput
     Read parameter entries from standard input.


  If there are no command-line arguments, Findcontrast takes sequential input
  the old way.  The program was originally designed to be used with
  newly-created tomograms, so coordinates in this case are always entered as
  they would be observed in a flipped volume, with Y and Z transposed.

  Inputs to the program are:
  
  Name of image file
  
  First and last slice to include in the volume to be analyzed.  The
  first slice is numbered 1, so the numbers entered can be the 
  3dmod section #'s in a flipped volume.
  
  Lower and upper X coordinates, and lower and upper Y coordinates,
  of the volume to analyze, as viewed in a flipped volume.  Enter /
  for the default, which omits a 10% border on each side.
  
  Maximum number of pixels to truncate (saturate) at black and at
  white within the analyzed volume.  Enter / for the default, which
  is one pixel per slice or one pixel per million, whichever is 
  greater.
  

HISTORY
  Written by David Mastronarde, January 2000