xfsimplex(1) General Commands Manual xfsimplex(1)NAMExfsimplex - Searches for best transformation between two imagesSYNOPSISxfsimplex [options] input_file_a input_file_b output_fileDESCRIPTIONThis program searches for the best general linear transform between a pair of images by varying either the six formal parameters of the transform, the six "semi-natural" parameters underlying such a trans- form, or restricted subsets of those semi-natural parameters. These semi-natural parameters are, in the order in which the program will consider them: Delta X Delta Y Global rotation (average rotation of X & Y axes) Global magnification (average stretch of X & Y axes) Difference between stretch along Y- & X-axis Difference between rotation of Y- & X-axis With the -variables option, one enters either zero to search for formal parameters, or a number specifying how many of the natural parameters are to be varied. If one selects 2, only Delta X and Delta Y will be varied; if one selects 4, global rotation and magnification will be varied also. At the end, the program outputs a six-parameter transformation (the 2x2 A matrix and DX and DY) in the standard format. Because the search method used by this program works iteratively from a given starting point, it is unlikely to find the proper alignment if it requires a large displacement. To overcome this problem, the program can be given an initial transformation to work from. This allows a large displacement to be found by cross-correlation and passed to this program. To find the best fit between images, the search can optimize either a simple point-by-point difference between the images, the cross-correla- tion coefficient, or a measure of the distance between points of simi- lar intensities in the images. The resulting transformation is applied to the second image to align it to the first. The search uses a so-called simplex minimization routine which starts searching with an initial step size and refines the step size near a minimum. It terminates the minimization when either 1) the most recent points under consideration gave difference measures all within a cer- tain fractional tolerance of the point with the minimum measure; or 2) the most recent points had transformation parameters all within a cer- tain tolerance of the point with the minimum measure. The latter toler- ances are expressed as fractions of the following basic step sizes: 1 for delta X and Y; 0.025 for the 4 parameters of the transformation matrix, if using formal parameters; or 2 degrees for global rotation and differences between X and Y rotations, and 0.025 for global magni- fication and difference between X and Y magnifications, if using semi- natural parameters. By default, the program will perform an initial minimization with a coarse tolerance for termination, then it will restart the minimization at the best point, and terminate with a finer tolerance. If the overall alignment method involves two stages, coarse and fine, then you should omit the initial minimization by specifying tolerances of zero for it. At the end of the search, the program outputs the number of iterations, the minimum difference/distance or maximum correlation value found, and the transformation parameters. If semi-natural parameters were searched for, first those parameters are output, then the formal param- eter matrix is output. The difference measure is normalized to be the mean difference per pixel as a multiple of the standard deviation of the first image. If correlation coefficients are used, then the mea- sure of difference being minimized is one minus the correlation coeffi- cient. The distance measure is expressed as the mean distance per com- parison point.OPTIONSXfsimplex uses the PIP package for input (see the manual page for pip) and can still take sequential input interactively, to maintain compatibility with old command scripts. 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.-aimage(-ai)OR-AImageFileFilenameInput image file with reference image to be aligned to. If this option is not entered, the first non-option argument will be used for this input file.-bimage(-bim)OR-BImageFileFilenameName of image file with image to align to reference. If this option is not entered, the second non-option argument will be used for this input file.-output(-o)OR-OutputFileFilenameOutput file for transformation. If this option is not entered, the third non-option argument will be used for this output file.-initial(-i)OR-InitialTransformFileFilenameInput file with transformation to start search with. The final reported transformation will include the initial one rather than being incremental to it.-useline(-use)OR-UseTransformLineIntegerLine number of initial transform in file, numbered from 0 (default 0)-sections(-se)OR-SectionsToUseTwointegersSections to use from the first and second file (default 0,0)-variables(-v)OR-VariablesToSearchIntegerNumber of semi-natural variables to search, or 0 to search for formal parameters. See above for the meaning and order of the variables selected by this option.-limits(-lim)OR-LimitsOnSearchMultiplefloatsLimits for each of the variables being searched. Each number entered specifies the maximum amount that the respective vari- able can change from its initial value. Enter a 0 to avoid lim- iting a parameter. If the search is being done on formal param- eters, then only the first two (shift in X and Y) can be lim- ited, so only 1 or 2 values can be entered. If the search is on semi-natural parameters, then you can enter more or fewer values than the number of variables being searched. Extra values are ignored, missing values are assumed to be zero.-edge(-e)OR-EdgeToIgnoreFloatingpointFraction or number of pixels to ignore on edges of image. Enter a value less than 0.5 for a fraction, or a value greater than 1 for a number of pixels. The default is 0.05.-xminmax(-x)OR-XMinAndMaxTwointegersStarting and ending coordinates to analyze in X (numbered from 1). This entry overrides the X coordinates implied by the -edge entry or default.-yminmax(-y)OR-YMinAndMaxTwointegersStarting and ending coordinates to analyze in Y (numbered from 1). This entry overrides the Y coordinates implied by the -edge entry or default.-binning(-bin)OR-BinningToApplyIntegerBinning to apply to the images. The default is 2.-antialias(-an)OR-AntialiasFilterIntegerType of antialiasing filter to use for image reduction instead of binning. Antialiasing becomes important when the images are highly reduced in size. Ordinary binning reduces aliasing, but not as much as these filters do. This option makes any filter- ing be applied after the image reduction (thus it implies the -after option). As in Newstack, the available types here are: 2: Blackman - fast but not as good at antialiasing as slower filters 3: Triangle - fast but smooths more than Blackman 4: Mitchell - good at antialiasing, smooths a bit 5: Lanczos 2 lobes - good at antialiasing, less smoothing than Mitchell 6: Lanczos 3 lobes - slower, even less smoothing but more risk of ringing -1: Use the default filter, currently Lanczos 2-sig1OR-FilterSigma1FloatingpointSigma value to filter low frequencies in both images with a curve that is an inverted Gaussian. This filter is 0 at 0 fre- quency and decays up to 1 with the given sigma value. However, if a negative value of radius1 is entered, this filter will be zero from 0 to |radius1| then decay up to 1.-rad1OR-FilterRadius1FloatingpointLow spatial frequencies in both images will be attenuated by a Gaussian curve that is 1 at this cutoff radius and falls off below this radius with a standard deviation specified by Filter- Sigma2. Spatial frequency units range from 0 to 0.5. Use Fil- terSigma1 instead of this entry for more predictable attenuation of low frequencies.-rad2OR-FilterRadius2FloatingpointHigh spatial frequencies in both images will be attenuated by a Gaussian curve that is 1 at this cutoff radius and falls off above this radius with a standard deviation specified by Filter- Sigma2.-sig2OR-FilterSigma2FloatingpointSigma value for the Gaussian rolloff below and above the cutoff frequencies specified by FilterRadius1 and FilterRadius2-after(-af)OR-FilterAfterBinningApply the Fourier filter after binning data. This will be much faster, but it may introduce aliased noise from the higher fre- quencies in the original data unless antialiased reduction is used. The radius and sigma values represent frequencies in the binned image, not the original image. If antialias reduction is not used, the default is to filter before binning, in which case the high frequencies can be removed before binning; if antialiasing is used, the filtering always happens after reduc- tion and this option is redundant.-sobel(-so)OR-SobelFilterApply edge-detecting Sobel filter to both images. This filter will be applied after binning and filtering if any.-float(-fl)OR-FloatOptionInteger0 to float images to have the same range, 1 to float them to have the same mean and standard deviation, or -1 to leave inten- sities alone. Only pixels within the range being analyzed will be considered when determining the scaling. The default is 1.-ccc(-cc)OR-CorrelationCoefficientCompute the standard cross-correlation coefficient instead of difference between images. The difference measure that is mini- mized will be 1 minus the CCC, but the CCC itself is printed in the trace and final output. It takes < 5% more time to compute the CCC.-local(-lo)OR-LocalPatchSizeIntegerSize of square subareas (patches) within which to compute a mea- sure of image difference, in pixels before binning, if any. The image will be divided into patches of this size and the measure will be computed separately within each patch; then a weighted average will be formed, weighted by the number of pixels actu- ally available for comparison within each patch. If image dif- ference is being computed, the measure will be the standard deviation of the difference; otherwise the correlation coeffi- cient is computed. Patches with less than half the full number of pixels will be pooled with the nearest patches containing enough pixels. This option should prevent the need for low fre- quency filtering, which would increase execution time by roughly 10%. Patch sizes on the order of 1/20 to 1/10 of the image size should be effective.-linear(-lin)OR-LinearInterpolationUse linear interpolation instead of nearest pixel interpolation when computing image differences or correlation coefficients.-distance(-di)OR-DistanceMeasureUse distance instead of difference or correlation measure-near(-n)OR-NearestDistanceIntegerDistance to search to eliminate redundant points, or 0 not to search, when using the distance measure. The default is 0 for # of pixels < 240*180, 1 if # of pixels is between 240*180 and 480*360, 2 if # of pixels > 480*360.-radius(-radi)OR-RadiusToSearchFloatingpointRadius to search for matching pixels when using the distance measure. The default is 4 if binning by 2, or 5 if not.-density(-de)OR-DensityDifferenceFloatingpointMaximum density difference that constitutes a match when using the distance measure, as a fraction of the density range. The default is 0.05.-percent(-pe)OR-PercentileRangesMultiplefloatsLower and upper limits of percentile ranges to match. The default is to have two ranges, i.e., 0,8,92,100, for images less than 320*240, scaling down to 5% ranges as image size increases from 320*240 to 640*480.-coarse(-co)OR-CoarseTolerancesTwofloatsFractional tolerances in difference and parameters for the ini- tial search. Enter 0,0 to skip the initial search. The default values are 0.005 and 0.2 of the basic step size.-final(-fi)OR-FinalTolerancesTwofloatsFractional tolerances in difference and parameters for the final or only search. The default values are 0.0005 and 0.02 of the basic step size, or 0.001 and 0.04 for images no bigger than 128 by 128.-step(-st)OR-StepSizeFactorFloatingpointFactor to multiply basic step size by to get initial step size. The default is 2.-trace(-t)OR-TraceOutputInteger1 for output at each step, 2 for output at new minima-param(-pa)OR-ParameterFileParameterfileRead parameter entries as keyword-value pairs from a parameter file.-help(-h)OR-usagePrint help output-StandardInputRead parameter entries from standard input.INTERACTIVEINPUTA subset of entries can still be made by running the program interac- tively. All of the parameters have defaults which may be selected with , or / (the values in [] below and contained in [] in the prompts) ***lines 1-4 first image file second image file data file into which to place the best fitting transformation name of file file with starting transformation, or Return if none *** line 5 (6 values): Fractional tolerances in the difference/distance measure and in the transformation parameter values, to allow termination of final or only minimization [.0005 and 0.02, or .001 and 0.04 for images no bigger than 128 by 128] Fractional tolerances in the difference/distance measure and in the transformation parameter values, to allow termination of initial minimization [.005 and 0.2]. Enter 0,0 to skip initial search. Factor to apply to basic step sizes to get initial step sizes [2] 1 for trial-by-trial output, 2 for output of trials that yield new minima only. ***line 6 0 for search on formal parameters, or # of natural parameters to vary [0] ***lines 7-10 Fraction of images to ignore at edges [0.05]; or number of pixels if the number entered is 1 or greater float images to have same range (0) or same mean and S.D. (1), or do not float images (-1) [1] binning factor for reducing images in x and y [2] use difference (0) or distance (1) measure [0] If difference measure is chosen, one more line of input: ***line 11 1 to use bilinear interpolation during the search [0] If distance measure is chosen, 5 more lines of input: *** lines 11-14 distance to search to eliminate redundant points with similar densities from comparison [default depends on image size after reduction, if any: 0 for # of pixels < 240*180, 1 if # of pixels between 240*180 and 480*360, 2 if # of pixels > 480*360 distance to search for matching densities [4 if reduce by 2, 5 if not] maximum density difference constituting a match [0.05] Number of ranges of densities to make comparisons with [2] *** line 15 lower and upper PERCENTILES for these ranges. The default is 0,8,92, 100 for small images. This means that the darkest 8% and brightest 8% of pixels will be used for comparison (minus ones eliminated because of redundancy). The default depends on image size after reduction, if any; the range is scaled from 8% down to 5% as image size increases from 320*240 to 640*480 The distance measure has been little used and the defaults for it are based on limited experimentation. These defaults are set in an attempt to limit the number of "points for comparison" to several thousand. If there are more than about "5000 points for comparison", you should depart from the defaults in order to reduce this number.HISTORYWritten by David Mastronarde, 4/5/91 (adapted from XFSEARCH) 7/1/08: Converted to PIP, added search limits, filtering, CCCBUGSEmail bug reports to mast at colorado dot edu. IMOD 4.11.0 xfsimplex(1)