combinefft(1) General Commands Manual combinefft(1)NAMEcombinefft - combine FFTs of tomograms from a double-axis tilt seriesSYNOPSIScombinefft optionsDESCRIPTIONCombinefft 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.OPTIONSCombinefft 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-AInputFFTFilenameInput 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-BInputFFTFilenameInput 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-OutputFFTFilenameOutput 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-XMinAndMaxTwointegersStarting and ending X index coordinates to extract from the tomograms, numbered from 0. The default is the whole width in X.-yminmax(-y)OR-YMinAndMaxTwointegersStarting and ending Y index coordinates to extract from the tomograms, numbered from 0. The default is the whole height in Y.-zminmax(-z)OR-ZMinAndMaxTwointegersStarting and ending Z index coordinates to extract from the tomograms, numbered from 0. The default is the whole depth in Z.-taper(-t)OR-TaperPadsInXYZThreeintegersNumber 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-ATiltFileFilenameFile 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-BTiltFileFilenameFile with tilt angles used to generate second tomogram, in the same format as for ATiltFile.-ahighest(-ah)OR-AHighestTiltsTwofloatsStarting and ending tilt angles used to generate first tomogram. This entry and ATiltFile are mutually exclusive.-bhighest(-bh)OR-BHighestTiltsTwofloatsStarting and ending tilt angles used to generate second tomo- gram. This entry and BTiltFile are mutually exclusive.-inverse(-i)OR-InverseTransformFileFilenameName of file with inverse of transformation used to match the two tomograms (output by Matchvol). This entry is required.-reduce(-re)OR-ReductionFractionFloatingpointThis 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-SeparateReductionWith 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-JointReductionWith 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-RingWidthFloatingpointWidth of rings or shells used to reduce amplitudes. The default is 0.01.-nslabs(-n)OR-NumberOfSlabsInYIntegerNumber 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-MinimumRadiusToReduceFloatingpointRadius at which to start the first ring when reducing amplitudes (default 0.02)-points(-po)OR-MinimumPointsInRingIntegerMinimum number of points required in each region of a ring for reducing amplitudes (default 30)-both(-bo)OR-LowFromBothRadiusFloatingpointRadius 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-VerboseOutputWith 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-WeightingPowerFloatingpointThis 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-ParameterFileParameterfileRead parameter entries from file-help(-h)OR-usagePrint help output-StandardInputRead parameter entries from standard input.INTERACTIVEINPUTIf 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.HISTORYWritten by David Mastronarde, November 1995 Converted to PIP and experimental options added, 7/12/04BUGSEmail bug reports to mast at colorado dot edu. IMOD 4.9.10 combinefft(1)