reducemont

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 5.2.0 reducemont(1)