combinefft(1)                                                    combinefft(1)



NAME
       combinefft - combine FFTs of tomograms from a double-axis tilt series

SYNOPSIS
       combinefft  options

DESCRIPTION
       Combinefft combines the FFTs from the two tomograms of a double-axis
       tilt series, taking into account the tilt range of each tilt series and
       the transformation used to match one tomogram to the other.  For a
       location in Fourier space where there is data from one tilt series but
       not the other, it takes the Fourier value from just the one appropriate
       FFT; everywhere else it averages the Fourier values from the two FFTs.

       The program can take input files that are either both FFTs or both
       matching tomograms.  The FFTs would generally be from a subvolume of
       the tomogram; and if the tomograms are used as input, a subvolume would
       generally be processed.  The program will consume 8 times as much mem-
       ory as the number of voxels being processed in either case.  It uses
       dynamic memory allocation but will refuse to process subvolumes bigger
       than 1 gigavoxel.  On 32-bit systems, the allocation will fail for size
       above 250-370 megavoxels, depending on the operating system.

       There is an option (-reduce) to reduce amplitudes in regions of the FFT
       derived from only one tomogram to match the reduction in amplitudes in
       regions where data were averaged.  Apparently, the averaged data have
       lower amplitudes when there is substantial noise in the reconstruction
       because some of the noise averages out, while the noise in regions
       derived from one tomogram is unattenuated.  This may result in direc-
       tionally patterned noise.  The reduction option will reduce the noise
       (and signal) in the regions derived from one tomogram in attempt to
       keep it from dominating over the rest of the data.

       There is an option (-weight) for more sophisticated weighting that
       gives worse results with test data.

OPTIONS
       Combinefft uses the PIP package for input (see the manual page for
       pip) and can take input interactively for options that existed when
       it was converted, to maintain compatibility with old command files.
       The following options can be specified either as command line arguments
       (with the -) or one per line in a command file or parameter file (with-
       out the -).  Options can be abbreviated to unique letters; the cur-
       rently valid abbreviations for short names are shown in parentheses.


       -ainput (-ai) OR -AInputFFT    File name
              Input file from the first tomogram (the one being matched to):
              either the FFT of a chunk from the tomogram, or the tomogram
              itself, from which a chunk can be extracted with the 'MinAndMax'
              options

       -binput (-bi) OR -BInputFFT    File name
              Input file from the second tomogram (the transformed one):
              either the FFT of a chunk from the tomogram, or the tomogram
              itself, from which a chunk can be extracted with the 'MinAndMax'
              options

       -output (-o) OR -OutputFFT     File name
              Output file for the combined FFTs or real-space volumes.  An
              output file must be entered with real-space input, but the file
              can be omitted for FFT input, in which case the program will
              write the combined FFT back to the second input file.

       -xminmax (-x) OR -XMinAndMax   Two integers
              Starting and ending X index coordinates to extract from the
              tomograms, numbered from 0.  The default is the whole width in
              X.

       -yminmax (-y) OR -YMinAndMax   Two integers
              Starting and ending Y index coordinates to extract from the
              tomograms, numbered from 0.  The default is the whole height in
              Y.

       -zminmax (-z) OR -ZMinAndMax   Two integers
              Starting and ending Z index coordinates to extract from the
              tomograms, numbered from 0.  The default is the whole depth in
              Z.

       -taper (-t) OR -TaperPadsInXYZ      Three integers
              Number of pixels over which to taper and pad the patches in X, Y
              and Z.  The default is 0.  The amount of tapering in any dimen-
              sion may be increased to make that dimension suitable for taking
              an FFT.

       -atiltfile (-at) OR -ATiltFile      File name
              File with tilt angles used to generate first tomogram.  The file
              should have one tilt angle per line.  The first and last line in
              the file are assumed to have the starting and ending tilt
              angles.

       -btiltfile (-bt) OR -BTiltFile      File name
              File with tilt angles used to generate second tomogram, in the
              same format as for ATiltFile.

       -ahighest (-ah) OR -AHighestTilts   Two floats
              Starting and ending tilt angles used to generate first tomogram.
              This entry and ATiltFile are mutually exclusive.

       -bhighest (-bh) OR -BHighestTilts   Two floats
              Starting and ending tilt angles used to generate second tomo-
              gram.  This entry and BTiltFile are mutually exclusive.

       -inverse (-i) OR -InverseTransformFile   File name
              Name of file with inverse of transformation used to match the
              two tomograms (output by Matchvol).  This entry is required.

       -reduce (-re) OR -ReductionFraction      Floating point
              This option can be used to reduce the amplitudes in regions
              where data is taken only from one tomogram (missing wedge
              regions).  Mean amplitudes are measured by dividing the volume
              into a number of slabs in the Y dimension, then dividing each
              slab into rings based on radius from the origin.  Within each
              ring, the mean is obtained for points in the region where data
              is averaged between the two tomograms (joint data region), and
              the regions where data are available only from A or only from B
              (A-only or B-only regions).  With a fraction of 1, the values in
              the A-only region will be reduced by the ratio of the combined
              mean to the mean in A-only region, and similarly for the B-only
              region.  If the ratio is greater than 1, no reduction occurs.  A
              smaller fraction will reduce values by a proportionally smaller
              amount.

       -separate (-s) OR -SeparateReduction
              With this option, values in regions where data are available
              only from A will be reduced by the ratio of the mean combined
              value in the joint data region to the mean value from A in the
              joint data region, and similarly for B.

       -joint (-j) OR -JointReduction
              With this option, for points in the region where data is aver-
              aged between the two tomograms (joint data region), the mean is
              obtained within each ring for values from A, values from B, and
              the combined values.  The values in missing wedge regions will
              be reduced by the ratio of the combined mean to the average of
              the means from A and B.

       -ring (-ri) OR -RingWidth      Floating point
              Width of rings or shells used to reduce amplitudes.  The default
              is 0.01.

       -nslabs (-n) OR -NumberOfSlabsInY   Integer
              Number of divisions in Y dimension when reducing amplitudes.
              The default is 1, which will use spherical shells not divided
              into slabs.  If this number is increased, the ring width should
              be increased as well to avoid dividing the volume into too many
              regions with too few pixels.

       -radius (-ra) OR -MinimumRadiusToReduce       Floating point
              Radius at which to start the first ring when reducing amplitudes
              (default 0.02)

       -points (-po) OR -MinimumPointsInRing    Integer
              Minimum number of points required in each region of a ring for
              reducing amplitudes (default 30)

       -both (-bo) OR -LowFromBothRadius   Floating point
              Radius below which data will always be averaged from both tomo-
              grams.  Sometimes a combined tomogram shows lines between the
              separate pieces that were run through Combinefft, particularly
              for pieces containing a boundary between dense material and
              resin.  This option will eliminate this effect by ensuring that
              the low-frequency components match between the combined pieces.
              A value of 0.01 to 0.015 should be effective.

       -verbose (-v) OR -VerboseOutput
              With this option, the program will print the amplitudes and
              reduction factors for every region being reduced.  The columns
              output are: the ring number; the slab number (slabs are numbered
              sequentially from negative to positive Y); the zone, which is 1
              for the region with data from the first tomogram only, and 3 for
              the region with data from the second tomogram only; the mean
              amplitude of the joint data region; the mean for data relevant
              to the zone in question; the target value for the reduction in
              mean; and the reduction factor.

       -weight (-w) OR -WeightingPower     Floating point
              This option allows a weighted combination of values instead of
              simple averaging when data are available from both FFTs.  A
              local sampling density is computed for the point in each of the
              FFTs, based upon its radius from the origin and the local den-
              sity of tilted views.  These densities are raised to the given
              power, normalized to add to one, and used as weights in combin-
              ing the two Fourier values.  Values between 0 and 1 should be
              tried; 0 gives no weighting.

       -param (-pa) OR -ParameterFile      Parameter file
              Read parameter entries from file

       -help (-h) OR -usage
              Print help output

       -StandardInput
              Read parameter entries from standard input.


INTERACTIVE INPUT
       If the program is started with no command line arguments, it reverts to
       interactive input with the following entries:

       File name of FFT of first tomogram (the one matched TO)

       File name of FFT of second tomogram (the one produced by MATCHVOL)

       Name of output file for resulting FFT, or Return to write into the
           file of the second FFT, overwriting that FFT.

       Name of file with inverse of transformation used to match the two
           tomograms (output by MATCHVOL)

       For the first tomogram file, either the starting and ending tilt
          angles, or the name of a file with tilt angles in it.  In the
          latter case, the first number on the first line will be taken as
          the starting tilt angle; the first number on the last line will
          be taken as the ending tilt angle.

       For the second tomogram file, either the starting and ending tilt
          angles, or the name of a file with tilt angles in it.

HISTORY
       Written by David Mastronarde, November 1995
       Converted to PIP and experimental options added, 7/12/04

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                       combinefft(1)