reducemont(1) General Commands Manual reducemont(1)
NAME
reducemont - recuts montaged images and reduces them by pixel binning
SYNOPSIS
reducemont [options] -plo output_piece_file input_image output_image
DESCRIPTION
Reducemont will reduce images in size by an integral factor (1, 2, 3,
etc.) using simple averaging of blocks of pixels. It will also
"recut" an image into different sized pieces. Specifically, it can
take either a whole or a montaged image as input and produce a whole or
a montaged image as output, with the montage pieces of a desired size,
and with a different total size if desired. Header scaling information
is modified so that the new images will have the same coordinate system
as the original images, provided that they are loaded into 3dmod
with the piece list file generated by the program. Thus, models will
display properly on reduced image stacks.
The main use for this program is to break a large image into tiles for
more efficient access within 3dmod. If an image is a single frame,
size reduction is better done in Newstack, either with binning or
shrinking. Floating of images is also better done in Newstack.
Reduction of a montage in size before blending is better done in
Edmont.
When you specify the maximum frame size and minimum overlap of the out-
put image, the program will pick the largest frame size less than that
maximum, with the smallest overlap greater than that minimum, so that
the resulting image will contain at least as many pixels as the desired
output image. It picks a frame size that is a multiple of 2 and has no
prime factor greater than 19 (so that Fourier transforms can be run on
the resulting pieces in IMOD packages not using FFTW), unless the
-nofft option is given.
OPTIONS
Reducemont uses the PIP package for input exclusively (see the manual
page for pip). 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 parentheses.
-imin (-imi) OR -ImageInputFile File name
Image input file, which may or may not be a montage. If this
option is not entered, the first non-option argument is taken as
the input file.
-plin (-pli) OR -PieceListInput File name
File with list of piece coordinates for image input file, if it
is a montage.
-imout (-imo) OR -ImageOutputFile File name
Output file for montaged images. If this option is not entered,
the second non-option argument is taken as the output file.
-plout (-plo) OR -PieceListOutput File name
File for list of coordinates of pieces in output image file.
(Successive entries accumulate)
-sections (-s) OR -SectionsToDo List of integer ranges
List of sections to use from input file, numbered from 0.
Ranges may be entered (e.g., 1-3,5,8). If no list is entered,
all sections will be used. Note that montages can have missing
sections, and a list that includes such missing sections will
generate an error. (Successive entries accumulate)
-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. Mode 12 is allowed
only if the output format is MRC.
-float (-fl) OR -FloatToRange
Rescale densities of sections separately to fill data range
-bin (-b) OR -BinByFactor Integer
Use binning to reduce images in size by the given factor
(default 1)
-xminmax (-x) OR -StartingAndEndingX Two integers
Minimum and maximum X index coordinates to output (numbered from
0). The default is to output the entire image.
-yminmax (-y) OR -StartingAndEndingY Two integers
Minimum and maximum Y index coordinates to output (numbered from
0).
-frame (-fr) OR -MaximumFrameSizeXandY Two integers
Maximum size of output pieces in X and Y; pieces will be made
smaller as needed to divide the output region into equal pieces.
Enter 0,0 to output data in a single frame (which is the
default)
-overlap (-o) OR -MinimumOverlapXandY Two integers
Minimum overlap between output pieces in X and Y. Pieces may
overlap more than this as needed to divide the output region
into equal pieces. The default is 0,0 for no overlap.
-nofft (-n) OR -NoResizeForFFT
Do not increase the size of the output to be suitable for taking
an FFT. By default, output sizes are increased to have no
higher prime factor than 19. This option suppresses that
increase, and the only constraint is that the output frame sizes
be even.
-line (-l) OR -LineLoadLimit Integer
When the input image is a single frame, it will be loaded in
strips when loading an entire section would take more than the
given number of meagabytes of memory. The default is 1000.
-param (-pa) OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
HISTORY
Written by David Mastronarde, February 1993
Converted to PIP and enhanced to handle large images, 2/6/13
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 reducemont(1)