densmatch(1) General Commands Manual densmatch(1)
NAME
densmatch - Scale densities in one volume to match another volume or to
have a given mean/SD
SYNOPSIS
densmatch [options] Reference_file File_to_scale [Output_file]
DESCRIPTION
Densmatch scales the density values in one volume so that its mean and
standard deviation match that of another volume or match a given mean
and SD. To determine the mean and S.D. for each volume, by default it
samples up to 1000000 pixels in the central eighth of each volume (cen-
tral half in X, Y, and Z). There are options to control the region
sampled or to use all pixels instead of sampling. The program can
write the scaled values either to a new file or back into the file of
the volume being scaled. THE LATTER WILL DESTROY THE ORIGINAL VALUES
IN THAT FILE.
OPTIONS
Densmatch uses the PIP package for input (see the manual page for
pip) and can still take sequential input interactively, but with no
options. 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 -). Options can be abbreviated to unique letters;
the currently valid abbreviations for short names are shown in paren-
theses.
-reference (-ref) OR -ReferenceFile File name
Input file with reference volume (the one being matched to).
This file can be entered on the command line as the first non-
option argument.
-scaled (-s) OR -ScaledFile File name
Input file with volume to be scaled to match. This file can be
entered on the command line as the second non-option argument,
or as the first non-option argument if -target is entered
instead of a reference file.
-output (-ou) OR -OutputFile File name
Output file for the scaled volume. This file can be entered on
the command line as the third non-option argument, or the second
non-option argument if -target is entered instead of a reference
file. If this file is omitted, the program will write the
scaled values back to the input file.
-target (-t) OR -TargetMeanAndSD Two floats
Mean and standard deviation to scale the volume to (the one
entered with -scaled). The reference file is not entered in
this case. If you have a byte or integer image file and you
want to scale to a small target SD value (such as 1, as opposed
to 40), then you need to change the mode of the output file to
floating point.
-mode (-m) OR -ModeToOutput Integer
The storage mode of the output file; 0 for byte, 1 for 16-bit
signed integer, 6 for 16-bit unsigned integer, 2 for 32-bit
floating point, or 12 for 16-bit floating point. The default is
the mode of the input file, although the default mode of float-
ing point output for MRC files is governed by the value of envi-
ronment variable IMOD_WRITE_FLOATS_16BIT. This entry is allowed
only when writing to a new output file. Mode 12 is allowed only
if the output format is MRC.
-report (-rep) OR -ReportOnly
Report scaling factors without writing scaled data to file. The
program will report two numbers, a factor to multiply by then a
constant to add; these numbers can be supplied to the -multadd
option of Newstack.
-xminmax (-x) OR -XMinAndMax Two integers
Starting and ending X coordinates of region to analyze for mean
and SD in reference volume. An ending X of 0 will be converted
to NX - 1, so 0,0 can be entered to use the full extent in X.
The default is NX/4, 3*NX/4, where NX is the size of the scaled
volume in X. X, Y, and Z coordinates are numbered from 0.
-yminmax (-y) OR -YMinAndMax Two integers
Starting and ending Y coordinates of region to analyze in refer-
ence volume. An ending Y of 0 will be converted to NY - 1. The
default is NY/4, 3*NY/4, where NY is the size of the scaled vol-
ume in Y.
-zminmax (-z) OR -ZMinAndMax Two integers
Starting and ending Z values of region to analyze in reference
volume. An ending Z of 0 will be converted to NZ - 1. The
default is NZ/4, 3*NZ/4, where NZ is the number of slices in the
scaled volume.
-all (-a) OR -UseAllPixels
Compute mean and SD from all pixels in the files, not from a
sample of pixels. With this option, it is not necessary or
allowed to enter any minimum and maximum coordinates. Use this
option to get an exact match to target values for small volumes
(say, several megapixels). For larger volumes, use "-xm 0,0 -ym
0,0 -zm 0,0" instead to sample the entire volume, unless you
really need a precise match; with sampling, the SD will be accu-
rate to within about 0.2%.
-offset (-of) OR -OffsetRefToScaledXYZ Three integers
Displacement of the volume being scaled relative to the refer-
ence volume in X, Y, and Z; namely, the amount to add to a pixel
coordinate in the reference volume to obtain the coordinate of
the corresponding pixel in the file being scaled.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
INTERACTIVE INPUT
If there are no command-line arguments, Densmatch takes sequential
input the old way, with the following entries:
Name of the first volume, the one whose densities are being matched
Name of the second volume, the one being scaled
Name of an output file, or a blank line to have the scaled values writ-
ten back into the second file.
HISTORY
Written by David Mastronarde, November 1995
Converted to PIP input, added reporting option, 8/23/04
Added options for target, mode, and all pixels, increased sample size
by 10, 2/11/15
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 densmatch(1)