Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells BLENDMONT(1) BLENDMONT(1) NAME blendmont - aligns and blends overlapping edges of montaged images SYNOPSIS blendmont [options] DESCRIPTION BLENDMONT will take montaged images, blend their overlapping edges together, and output the blended images. Linear or warping transformations can be applied to align serial sections, and densities can be floated over whole sections so that density occupies the maximum range for each section. The program can also correct for minor or substantial displacements between pieces, using cross-correlation to find substantial shifts. The program performs these feats by examining each edge, or region of overlap, between adjacent pieces, and deriving a function that maps pixels in one piece to corresponding pixels in the adjacent piece. These "edge functions" are stored in two separate files (for pieces that are adjacent in X or Y, respectively). Thus, even if one needs to run the program more than once on the same input images, the edge functions need to be calculated only once, since they can be read from the files on later runs. However, if the input image file is changed in any way, the edge functions must be recalculated. To blend images at an overlap zone, the program considers each pixel in the output image in turn. It finds the two corresponding positions (in the two adjacent input pieces) whose weighted average equals the position of the desired output pixel, where the weights are proportional to the distance across the overlap zone. Near one edge of the overlap zone, the output pixel has very nearly the same position as the corresponding pixel in the nearby piece; in the middle of the overlap zone, the output pixel has a position midway between the positions of the corresponding pixels in the two pieces. If pieces are shifted by more than a few pixels from the positions specified by their piece coordinates, then the program will not be able to find the edge functions without doing an initial cross-correlation between the regions that overlap in adjacent pieces. Thus, if your montage is "sloppy" enough, you should select the option for initial cross-correlations. If the pieces are shifted at all from the positions specified by their piece coordinates, the program can correct for this. It can take the information about the shift between each pair of overlapping pieces and use it to find the amounts to shift each piece so as to fit the pieces together best. If the shifts are more than a few pixels, then an initial cross-correlation should be selected; otherwise this step is not needed. There are three ways to implement this correction step. One is based solely on the information in the edge functions. Another is a hybrid method based on both cross-correlation and edge functions; the program will solve for shifts twice, using the displacements implied by the edge functions then those implied by correlations, and select the solution that gives the smallest mean error. The third method is based on cross-correlations alone and is not as reliable as the hybrid method. This method should be used (with the -xcorr option) with older data if it is important to have an image stack that exactly matches that produce by Blendmont prior to June 1, 2001, when the hybrid option was implemented. It might also be useful in cases where the edge functions are not reliable, such as when there are large blank areas in the edge regions. It is also used by default (as of IMOD 4.2.3) when there is only one piece in one of the two directions, because in this case the mean error is zero regardless of whether correlations or edge functions are used. In such cases, you would have to use the -edge option to have it use the displacements from edge functions instead. In any case where cross-correlations are being computed, the program will write the displacements between pieces into a file with the extension ".ecd". On another run of the program, you can choose to have these displacements read in from the file, just as edge functions can be read in instead of recomputed. This allows you to edit bad displacements with Midas, then use Blendmont to get a stack with pieces properly shifted into register. If your montage frames have large displacements from their nominal positions, then a number of parameter changes can be needed to get reliable correlations. Select the VerySloppyMontage option to get these parameter settings (see below for full listing). If there are still numerous bad displacements in edges where there appears to be usable image information, then two of these parameters can be varied further. Experiment with larger values of AspectRatio, the ratio of length to width of the overlap areas being correlated (up to 10), and with a larger value of ExtraXcorrWidth, which makes the areas being correlated wider than the nominal overlap zone (up to 0.5 has been tried with good results). Sometimes there is simply not enough information in an overlap zone to allow the displacement between pieces to be determined. You can exclude such overlap zones from being considered in two different ways: 1) by marking edges to exclude in Midas; 2) by making a model marking each edge to be excluded. The simplest way to handle bad edges is just with Midas and not with a model file. Do an initial run of Blendmont then run Midas with the .ecd file. Find each bad edge and select the checkbox to exclude it. Save the .ecd file and rerun Blendmont with that .ecd file read in. To make a model instead, run 3dmod on the unblended montage, and edit the object type to make the type be scattered points with symbols displayed at each point, but with no sphere radius. Mark an edge to be excluded by placing a point near the middle of the line (discontinuity) that appears between the two adjacent pieces. This position is actually on one side of the overlap zone between the pieces, but Blendmont will be able to assign your points to edges based upon where it thinks each such line appears in 3dmod. Blendmont will correctly scale a model that was built on a montage at a different binning than the one being blended. Information about excluded edges is maintained in the edge displacement (.ecd) file written and read by both Blendmont and Midas. When Blendmont writes the file, it will mark all edges excluded by a model file. These edges will then show up as excluded when the .ecd file is read into Midas. You can fix a displacement and include an edge that was previously excluded, but if you do that, you should either remove the model file from the options to Blendmont or set the -nonzero option to 1 or 2, depending on whether you want to have an edge function computed for such edges. Otherwise, edges will be excluded if they either marked as excluded in the .ecd file or marked in the model file. Warping transformations can consist of either displacements at a set of control points, as output directly by Midas, or displacements on a regular grid, as produced by Xftoxg. Such warping files contain information about the size of the images that were aligned and their pixel size. The transforms will be adjusted for a difference between that pixel size and the pixel size of the image file being transformed. They will also be extrapolated as necessary to cover an image area larger than that specified in the warping file. If there is a size mismatch, the program assumes that the input images are centered on the images with which the warping file was prepared, unless the starting coordinates of the file that was used for alignment are entered with -unaligned option. Suitable values for this option were output when Blendmont was run to create the unaligned file with a line "Starting coordinates of output in X and Y =". By default, the program puts the output into a single frame. However, when you specify the maximum frame size and minimum overlap of the output 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 original input image. The program 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). This behavior is silly for very large images and can be overridden with the -nofft option. The program was originally written to handle montages digitized from multiple film negatives, with each negative transformed so as to produce the best fit between the negatives. This is unlikely to work, but here is the documentation for it. If sections come from more than one negative, this may be specified in either of two ways. If every section has the same division of pieces into negatives, then one can specify this universal division into negatives as an interactive input to the program. Alternatively, one may add negative numbers after the z coordinates in the file of piece coordinates. The only restriction on these numbers is that they should be non-zero, and every piece from the same negative should have the same number. Thus, one could number negatives 1, 2, 3 ... in each section that has multiple negatives, or one could use the identifying number on each negative. When pieces of a section come from more than one negative, the program uses the edge functions between the negatives to determine how each negative should be rotated and translated to align it with adjacent negatives. This collection of rotations and translations between adjacent negatives is then resolved into a single rotation and translation for each negative, so as to bring all of the negatives into best alignment. Blending of edges is performed after such rotations and translations have been applied. Blendmont 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 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 (without the -): INPUT AND OUTPUT FILE OPTIONS These options give information about input and output files. -imin OR -ImageInputFile File name Montaged image input file to be blended. -plin OR -PieceListInput File name File with list of piece coordinates for image input file. -imout OR -ImageOutputFile File name Output file for blended images. -plout OR -PieceListOutput File name File for list of coordinates of pieces in output image file. This entry may be omitted if the output images are not being cut into pieces. -rootname OR -RootNameForEdges Text string Root name for edge function and .ecd files. Two files will be created or sought for, with the extensions .xef and .yef attached to this root name. -oldedge OR -OldEdgeFunctions Use existing edge functions, if they exist, rather than computing new ones. -perneg OR -FramesPerNegativeXandY Two integers Number of frames in X and Y per negative for a multi-negative montage. This option could be used instead of having negative numbers in the piece list file. -missing OR -MissingFromFirstNegativeXandY Two integers Number of pieces missing from the first negative in X and Y. For example, if there are 3 negatives across, with 2, 4, and 1 pieces in X from each, then the number missing is 2. OUTPUT CONTROL OPTIONS These options control various aspects of the output. -mode OR -ModeToOutput Integer Mode for output file: 0 for bytes, 1 for integers, 2 for reals. The default is the same mode as the input file. -float OR -FloatToRange Stretch intensities of each output section to fill range of data mode. -xform OR -TransformFile File name File with g transformations to apply to align the images. -center OR -TransformCenterXandY Two floats X and Y coordinates of center of transformations. The default is the center of the input image. -unaligned OR -UnalignedStartingXandY Two integers Starting X and Y coordinates of file used to align images with warping. If warping transforms are being applied and the image region being output does not match the region used to align the images, these coordinates should be entered. If they are not entered, the program will assume that the unaligned file was centered on the input montage. -order OR -InterpolationOrder Integer Order of interpolation to use: 1 for linear, 2 for quadratic (the only one available before IMOD 3.6), 3 for cubic; the default is cubic when the program is run with PIP input and quadratic when run with sequential input. -sections OR -SectionsToDo List of integer ranges List of sections to blend into output file; comma-separated ranges are allowed. -xminmax OR -StartingAndEndingX Two integers Minimum and maximum X index coordinates to output (numbered from 0). The default is to output the entire image. -yminmax OR -StartingAndEndingY Two integers Minimum and maximum Y index coordinates to output. -nofft 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, but only when output is to a single frame. -origin OR -AdjustOrigin Adjust the origin values in the image file header based on the starting X, Y, and Y that are output. With this adjustment, a model built on the input stack should be correctly located when loaded onto the output stack in 3dmod. Model points will be correctly located in Z provided that a contiguous set of sections is output. This origin adjustment is inappropriate if an output piece list is used to read the data into 3dmod. -bin OR -BinByFactor Integer Use binning to reduce images in size by the given factor. Binning is applied to the data just before output, so the starting and ending X and Y coordinates to output should be specified in unbinned pixels. With binning, the output must be a single piece. -maxsize OR -MaximumNewSizeXandY Two integers Maximum size in X and Y of pieces in output file. The default is to make output be a single piece, unless it exceeds the limits of the program. -minoverlap OR -MinimumOverlapXandY Two integers Minimum overlap between pieces in X and Y in output file. The default is an overlap of 2. DISTORTION CORRECTION OPTIONS These options are related to corrections for an image distortion field and for distortion due to magnification gradients in tilted images. -distort OR -DistortionField File name Image distortion field file to use for undistorting images. The undistortion is applied when computing edge functions. -imagebinned OR -ImagesAreBinned Integer The current binning of the images, so that the image distortion field can be applied correctly. This entry is required when doing image distortion corrections unless the program can determine the binning unambiguously from the image size. -gradient OR -GradientFile File name File with magnification gradients to be applied for each section. This should be a file listing the tilt angle, the percent magnification change per micron of Z height, and the degrees of rotation per micron of Z height for each section, such as is produced by Extractmaggrad. The mag gradient correction is applied before a distortion field correction and is used when computing edge functions. -adjusted OR -AdjustedFocus Focus was adjusted for changing Z height when montage was acquired -addgrad OR -AddToGradient Two floats The magnification gradient correction is specified by two parameters: % of mag change per micron of Z height, and degrees of rotation per micron of Z height. If -gradient has been entered, this option can be used to increment the values in the gradient file for each section. If -gradient has not been entered, the values entered here will be used for all sections; but in this case the -geometry option must be entered to provide additional information, and also -tiltfile if the data are at different tilt angles. -tiltfile OR -TiltFile File name Name of file with tilt angles, one per line. These angles will be used in computing mag gradients, only if there is no mag gradient file to supply the tilt angles. -offset OR -OffsetTilts Floating point Add the given value to the tilt angles from the gradient file or the tilt file. Sometimes the gradient that gives the lowest error in registering the pieces will differ between the positive and negative side of the tilt series. This entry can be used to give a better overall error reduction. -geometry OR -TiltGeometry Three floats When magnification gradients are being corrected for, this entry can be used in place of a gradient file to specify the pixel size in nanometers, tilt axis rotation angle, and tilt angle to be used for the gradient computation. The entry has no effect if a gradient file is provided. -justUndistort OR -JustUndistort With this entry, the program can be used just to correct for magnification gradients and distortion fields, without computing edge functions or blending images. The resulting images are the same as those used to compute edge functions, and will be suitable for fixing edge functions in Midas. Either -distort or -gradient must be entered with this option. The sections to do may be specified, but all entries with regard to frame and total sizes in X and Y and edge functions will be ignored. -test OR -TestMode This entry runs the program in a special mode in which it will compute edge functions and find the best shifts of the pieces for a given magnification gradient correction. Output images will not be computed, although an empty output file will be produced. PIECE SHIFT OPTIONS These options are related to the determination of displacements between pieces in overlap zones and the shifting of pieces into best alignment. -sloppy OR -SloppyMontage Do initial cross-correlations for finding edge functions and shift pieces to minimize displacements in the overlap zones -very OR -VerySloppyMontage This option acts like SloppyMontage and also sets several parameters for dealing with very sloppy montages with displacements potentially bigger than half the width of the overlap zones. The aspect ratio of the area used for correlating the overlap zones is increased from 2 to 5 and the filter parameter radius1 is set to -0.01 to eliminate more low frequencies from the correlation. The area being correlated is made wider by setting the extra width fraction to 0.25. Up to 16 peaks in the correlation are evaluated by cross-correlation coefficient. If distortion corrections are being done, the default is changed to taper instead of trimming out fill areas for correlation. -shift OR -ShiftPieces Shift pieces to minimize displacements in the overlap zones. The default is to use information from edge functions and from cross-correlations for each section and pick the one that gives lowest error. -edge OR -ShiftFromEdges Use only edge functions for shifting pieces. -xcorr OR -ShiftFromXcorrs Use only cross-correlations of overlap zones for shifting pieces (legacy behavior). -readxcorr OR -ReadInXcorrs Read displacements in the overlap zones from an existing .ecd file instead of computing correlations. -ecdbin OR -BinningForEdgeShifts Floating point The binning of the images used to determine the edge displacements being read in, relative to the current binning of the images, if any. You can used binned images to determine edge displacements and fix them in Midas, then use those displacements directly with unbinned images by specifying the original binning with this option. -overlap OR -OverlapForEdgeShifts Two integers This option allows you to change the overlap between pieces and use edge displacements determined with the original overlaps. Bad artifacts can occur when the difference between the actual average overlap between pieces and the overlap in the piece list is big enough to change the actual coordinates of pieces by more than twice the piece size. The program will detect this situation and issue a warning advising that you change the overlap. You can use Edpiecepoint to get a new piece list with a different overlap in one or both dimensions. Set the new overlap to the old overlap minus the average edge displacement reported in the warning. If you want to use existing edge displacements rather than starting from scratch, use this option to specify the overlaps in the run originally used to compute edge displacements. If that run was done with binned images, enter the binned overlap value. -skip OR -SkipEdgeModelFile File name Model file with points near edges to exclude when computing edge functions and displacements. You can exclude edges where the overlap cannot be determined correctly in order to prevent bad displacements from affecting the placement of surrounding pieces. On an initial run of Blendmont, marked edges will be given zero correlation displacements and zero edge functions. On subsequent runs, the treatment of such edges may be affected by the -nonzero option described next. If an edge is marked in a model file, it will be excluded even if it is not marked as excluded in the edge displacement file that was read in. -nonzero OR -NonzeroSkippedEdgeUse Integer An indicator of how to treat excluded edges that have non-zero shifts read in from the edge displacement file. Possible values are: 0, to exclude the edge from computation of piece shifts and to give it a zero edge function; 1, to include the displacement in the computation of piece shifts but still give the edge a zero edge function; 2, to include the displacement in the computation of piece shifts and compute an edge function for it. The default is 0. -robust OR -RobustFitCriterion Floating point When solving for the piece shifts from the displacements between pieces, the program can give less weight to, or completely ignore, displacements that appear to be outliers. This option activates this robust fitting and specifies the criterion for determining an outlier. A value of 1 will generally find nearly all outliers but may downweight some edge displacements inappropriately and give a poor blend across those edges. Higher values, up to about 1.5, will avoid the latter problem but will tend not to catch actual outliers. This option is ideal for getting a higher quality blend quickly for a low-magnification map where grid bars ruin some of the displacements. For data to be analyzed, it is preferable to fix the bad displacements or mark edges to be excluded in Midas. Robust fitting is available only with more than 10 pieces. EDGE FUNCTION OPTIONS These options control the computation and use of the edge functions. -width OR -BlendingWidthXandY Two integers Width in X and Y across which to blend overlaps. The default is: 80% of the overlap zone width for overlap width less than 63, 50 pixels for overlap width between 63 and 100, or 50% of the overlap width for overlap width greater than 100. -boxsize OR -BoxSizeShortAndLong Two integers Size of box for finding edge functions in short and long directions. The short direction is across an overlap zone, the long direction is along it. The default size is 10 pixels in the short direction for frame sizes up to 512 pixels, increasing proportional to the maximum dimension of the frame above 512 and up to a value of 80. (For this and the next two options, there is no increase in the default above a frame size of 4096.) The default in the long direction is 1.5 times the size in the short direction. -grid OR -GridSpacingShortAndLong Two integers Spacing of edge function grid in short and long directions. The default is 6 pixels in each direction for frame sizes up to 512 pixels, increasing proportional to the maximum dimension of the frame above 512, up to a value of 48. -indents OR -IndentShortAndLong Two integers Borders at the edge of the overlap zone in the short and long directions which will be excluded when finding edge functions. The default size is 3 pixels in each direction for frame sizes up to 512 pixels, increasing proportional to the maximum dimension of the frame above 512 up to a value of 24 pixels. -goodedge OR -GoodEdgeLowAndHighZ Two integers Default lower and upper Z limits for where edge functions are good (numbered from 0). Beyond these limits, the edge functions will be taken from the last good Z value. If this option is entered, these limits will applied to all edges except ones specified with onegood. -onegood OR -OneGoodEdgeLimits Multiple integers This options specifies lower and upper Z limits for a specific edge; beyond these limits the edge functions will be taken from the last good Z value. Five values are expected: number of frame below the edge in X and Y (numbered from 1), 1 for an edge in X or 2 for an edge in Y, lower and upper Z limits (numbered from 0). (Successive entries accumulate) -exclude OR -ExcludeFillFromEdges With this option on, the program will detect image areas near an overlap zone that consist of uniform values and exclude these areas when computing the edge function. In addition, in areas along an edge where one piece consists of uniform values and the other has actual image data, it will use the actual data across the whole edge instead of transitioning to the uniform data. -unsmooth OR -UnsmoothedPatchFile File name Text file for edge functions before smoothing to be output as displacement vectors. This file can be converted to an IMOD model with "patch2imod -l -f"; use the -s option to control how much the vector lengths are scaled. Each edge is output at a different Z value, so the model can be viewed in the Zap window. You can use this model to assess whether the box size is large enough to give accurate edge functions. -smooth OR -SmoothedPatchFile File name Text file for edge functions after smoothing to be output as displacement vectors. This file can be converted to an IMOD model with "patch2imod -l -f". This model shows the functions actually applied when blending the overlap zones. PARALLEL BLENDING OPTIONS These options allow for running a blending operation in parallel using Splitblend. -parallel OR -ParallelMode Two integers Mode for setting up or running a parallel blend. The second value should be 0 for chunks in Z, or 1 for chunks in Y. The possibilities for the first value are: > 0: The program will check for the legality of blending in parallel and output subset section or line lists for running with the given number of target chunks. -1: The program will create and write the header for a common output file to be written directly by multiple blends. -2: The program will write the given subset of sections directly to a common output file. -3: The program will take the SubsetToDo as the SectionsToDo and write these sections to a new file; multiple files will need to be stacked afterwards. It should not be necessary to write multiple files; increase the boundary pixels if artifacts occur when writing to a single file. -subset OR -SubsetToDo List of integer ranges List of subset of sections to blend when running multiple blends in parallel. This option is ignored unless ParallelMode is negative. -lines OR -LineSubsetToDo Two integers Starting and ending Y values of lines to blend when running multiple blends in parallel. This option is ignored unless ParallelMode is negative. -boundary OR -BoundaryInfoFile File name File with information about boundary locations and files when directly writing in parallel to a single output file. -functions OR -EdgeFunctionsOnly Integer Compute edge functions (and correlations, if appropriate) then exit. Enter 1 or 2 for X or Y edges alone, or 3 to compute both. If 1 or 2 is entered and edge correlation displacements are being written to a file, then the first or second half of the file is produced in a file with extension ".xecd" or ".yecd", and the two halves may simply be concatenated to obtain the full file. Blendmont will produce a concatenated file when it is told to read in the edge displacements and it finds only these two partial files. CROSS-CORRELATION CONTROL OPTIONS These options control the cross-correlations used to find the initial alignment in the overlap zones when montages are sloppy. -aspect OR -AspectRatioForXcorr Floating point Maximum aspect ratio of areas cross-correlated in overlap zones. The default is 2, which is generally adequate. Larger values are required if the displacements can be very large, but the value should not be made much larger than necessary because the correlations will take longer to compute and may be poorer quality if there is substantial distortion between the two images in an overlap zone. The value determines the length of the area relative to the width of the overlap zone, before any expansion of the correlated width with the -extra option. -pad OR -PadFraction Floating point Areas from the overlap zones will be padded by this fraction on each side for correlation. The default value is 0.45, which allows large shifts to be measured unambiguously. Padding for the short dimension will be this fraction times the size in that dimension; padding in the long dimension will be either this fraction times the long dimension size, or 0.9 times the size in the short dimension, whichever is smaller. -extra OR -ExtraXcorrWidth Floating point This entry will increase the width of the areas correlated in overlap zones by including image area in the interior of each frame, i.e., outside the overlap zone. The width of the extra area is this fraction times the width of the area within the overlap zone. This option is appropriate if montages are very sloppy, particularly if they tend to overlap by much more than the nominal amount. -numpeaks OR -NumberOfXcorrPeaks Integer If this entry is greater than one, the program will keep track of this number of the strongest peaks in the cross-correlation, and for each peak, it will compute a correlation coefficient in real space from the pixels that overlap in the areas extracted from the overlap zone. The areas will each be filtered with the same filter applied in the cross-correlation. This option is appropriate if montages are very sloppy, because the raw peak strength of a correlation is less the lower the overlap between the areas correlated, and it is easy for a spurious peak to become stronger than the true peak when there is much displacement between the areas. The true peak will generally still give a stronger correlation coefficient in such a case. This value is set to 1 by default unless VerySloppyMontage is entered, in which case the default is 16. -radius1 OR -FilterRadius1 Floating point When this entry is positive, low spatial frequencies in the overlap zone cross-correlations 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 FilterSigma2. Spatial frequency units range from 0 to 0.5. A negative entry is used to set the starting point of the filter specified by FilterSigma1, which gives a more predictable attenuation of low frequencies. -radius2 OR -FilterRadius2 Floating point High spatial frequencies in the cross-correlation 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 FilterSigma2. The default is 0.35. -sigma1 OR -FilterSigma1 Floating point Sigma value to filter low frequencies in the correlations with a curve that is an inverted Gaussian. This filter is 0 at 0 frequency 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. The default is 0.05. -sigma2 OR -FilterSigma2 Floating point Sigma value for the Gaussian rolloff below and above the cutoff frequencies specified by FilterRadius1 and FilterRadius2. The default is 0.05. -treat OR -TreatFillForXcorr Integer Sets the treatment of fill areas created by distortion corrections for the cross-correlations. Enter 0 to do nothing, 1 to trim the correlation width to exclude possible fill areas, or 2 to taper image into fill areas. The default is 1, appropriate for image-shift based montages with reliable overlap widths. If trimming overlap areas produces too little overlap, the trimming can be avoided either with entry 0 or 2: 0 will leave edges that may produce spurious correlation, while 2 will taper the image down at the edges. When VerySloppyMontage is used, there are distortion corrections, and this option is not entered, the value is set to 2. -xcdbg OR -XcorrDebug Output image files with the padded images being correlated in the overlap zones and with the cross-correlations. Separate files are generated for X and Y edges, with extensions .xdbg and .ydbg. -taper OR -TaperFraction Floating point Discontinued option -param OR -ParameterFile Parameter file Read parameter entries as keyword-value pairs from a parameter file. -help OR -usage Print help output. -StandardInput Read parameter entries from standard input. If there are no command-line arguments, Blendmont takes sequential input the old way, with the following entries: Input image file Output image file Data mode for output file (the default is same as mode of input) 1 to float each section to maximum range for the data mode, 0 not to Name of file of g transforms to apply to align the sections, or a blank line for no transforms Name of input file with list of piece coordinates IF this file has entries specifying that pieces are on different negatives, enter 1 to do an initial cross-correlation in the overlap zones to find the average displacement between pieces IF this file does NOT have any entries specifying that pieces belong to different negatives, there are several possibilities for either specifying negatives or correcting for displacements between frames. Use the negative of an option to do initial cross-correlations to correct for sloppy montages: Enter 1 or -1 to specify how the sections should be divided into negatives OR 2 or -2 to use edge functions to find a shift for each frame that aligns the frames as well as possible OR 3 or -3 to use cross-correlations exclusively, rather than edge functions to find the best shift for each frame (obsolete, use 5/-5 except to replicate old data) OR 4 or -4 to use only cross-correlations read from an edge correlation displacement file to find the best shifts (obsolete, use 6/-6 except to replicate old data) OR 5 or -5 to use both cross-correlations and edge functions (whichever is better) to find the best shifts OR 6 or -6 to use both cross-correlations read from a file and edge functions to find the best shifts OR 0 for none of these options IF you enter 1 or 2 to specify division into negatives, enter 2 lines: # of frames (pieces) per negative in the X direction, and the # of frames missing from the left-most negative. E.g., if there are 2 frames from the left-most negative, 4 from the middle one, and 1 from the right-most one, there are 4 frames per negative, with 2 missing from the left-most one # of frames (pieces) per negative in the Y direction, and the # of frames missing from the bottom-most negative. Name of new file for list of coordinates of pieces in the output file, or Return to skip making this file, which is not needed when the output image is a single piece. IF you have g transforms, enter on the next line: X and Y center coordinates of the transforms, or / to accept the default, which is the center of the input image. List of sections to be included in output file, or / to include all sections from the input file in the output file. Ranges may be entered (e.g. 0-5,8-14,17-23) Minimum and maximum X, and minimum and maximum Y coordinates that should be included in the output image. Enter "/" to obtain the entire input image. Maximum limit on the X and Y frame size for output pieces, and minimum limit on overlap between output pieces. The program will then choose new frame sizes and overlaps based on these limits 0 to accept the program's choices of frame size and overlap. When running interactively, entering 1 will allow you to loop back and enter new minimum and maximum X and Y coordinates and a new maximum frame and minimum overlap. Note that on the first two entries, the program will enforce a minimum overlap of 2; if for some reason you want an overlap of 0, you need to loop back so that you enter the frame size and overlap 3 times. 0 to build new files of edge functions, 1 to use old files that were generated on a previous run of the program Root filename for edge function files. Widths over which to blend positions at an edge, in the X and Y directions. HISTORY Written by David Mastronarde, February 1989 12/21/98: added ability to do initial cross-correlation and to find best shifts to correct for sloppy montages 6/1/01: implemented ability to write and read in edge correlation displacements; added a search step to improve on cross-correlations 8/9/03: converted to PIP input.