findcontrast(1) General Commands Manual findcontrast(1)
NAME
findcontrast - Finds contrast settings for converting to bytes
SYNOPSIS
findcontrastl [options input_file output_file
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 val-
ues 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 trunca-
tion of the specified number of pixels, and the black and white con-
trast settings that would give this amount of truncation.
OPTIONS
Findcontrast uses the PIP package for input (see the manual page for
pip) and can still take sequential input interactively. The follow-
ing options can be specified either as command line arguments (with the
-) or one per line in a command file or parameter file (without the -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-input (-i) OR -InputFile File name
Input image file to bin down in 3D
-slices (-s) OR -SlicesMinAndMax Two integers
Starting and ending slices to analyze in Z, numbered from 1.
The default is to do all slices.
-xminmax (-x) 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 dimen-
sion.
-yminmax (-y) 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 dimen-
sion.
-flipyz (-f) OR -FlipYandZ
Treat coordinates as coming from a volume that was read into
3dmod with Y and Z sizes flipped with the -Y option. 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. The program assumes that flipping occurred by rotating
around the X axis, unless the "-old" option is given.
-oldflip (-o) OR -OldFlipping
Flipped coordinates are based on flipping by swapping X and Y
axes, not by rotating around X. This flipping occurred prior to
IMOD 4.6.18.
-truncate (-t) 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 (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
INTERACTIVE INPUTS
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 sec-
tion #'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
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 findcontrast(1)