combinefft(1) General Commands Manual 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 (-xm) 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 (-ym) 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 (-zm) 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.
-chunk (-c) OR -ChunkSizeForHDF Three integers
Chunk sizes in X, Y, and Z, for an initial run to set up an HDF
file for direct writing of chunks by later runs.
-lock (-l) OR -LockFileForHDF File name
Name of lock file to use for parallel writing to chunked HDF
file. This option must be supplied both to the initial setup
run and to each later run. The file must already exist.
-xsave (-xs) OR -XSaveStartAndEnd Two integers
Starting & ending X coordinates in padded volume to save into
HDF chunk
-ysave (-ys) OR -YSaveStartAndEnd Two integers
Starting & ending Y coordinates in padded volume to save into
HDF chunk
-zsave (-zs) OR -ZSaveStartAndEnd Two integers
Starting & ending Z coordinates in padded volume to save into
HDF chunk
-place (-pl) OR -PlaceChunkAtXYZ Three integers
Starting X, Y, Z coordinates in HDF file at which to write chunk
-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.
IMOD 4.11.0 combinefft(1)