Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells EDPIECEPOINT(1) EDPIECEPOINT(1) NAME edpiecepoint - edit a list of piece coordinates SYNOPSIS edpiecepoint DESCRIPTION This program allows one to "edit" a list of piece coordinates, or a list of integer point coordinates, in three ways: 1) The set of Z values may be mapped, one-to-one, to any arbitrary new set of Z values; and 2) The X, Y or Z coordinates of all pieces or points may be shifted by a constant. 3) The overlap between pieces can be changed. In addition, one can create a new piece list for single frame images or montaged images. The pieces can be ordered in rows or in columns. The remapping of Z values is specified by a list of values (comma-separated ranges, e.g. 0-3,5-7). This list must have the same number of Z values as in the input list of Z values. The Z values in the input list will be mapped one-to-one onto the new list. Enter "/" to take the input list without modification Enter numbers between -999 and -990 to delete points with a particular Z value; e.g. if the input list has Z values from 0 to 9, entering 0-4,-999,5-8 will delete all points with Z between 4.5 and 5.5, and shift the Z of points with Z greater then 5.5 down by 1. If the input list has Z from 0-19, entering 0-9,-999--990 will remove all pooints with Z from 10 to 19. Enter -1 to replace each Z value with its negative. When you create a new piece list, you control the overlap between pieces by entering a spacing instead. This spacing is the frame size minus the overlap; e.g., for a size of 2048 and an overlap of 10%, one would enter 2048 - 204 = 1844. Spacing can be measured by taking the difference between the coordinates of corresponding points in adjacent pieces. For example, if a feature is at an X coordinate of 1800 in one piece and at 100 in the piece to the right, then the spacing in X is 1800 - 100 = 1700. Enter a negative number for X spacing if pieces are ordered from right to left, or a negative number for Y spacing if pieces are ordered from top to bottom. Enter / if you just have one piece. Edpiecepoint uses the PIP package for input (see the manual page for pip) and can still take sequential input interactively. 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 OR -InputFile File name Input piece list or point file. If this option is not entered and -create is not entered, the first non-optional argument will be used for an input file. -output OR -OutputFile File name Output piece list or point file. If this option is not entered, the second non-optional argument will be used if -create is not entered; otherwise the first non-option argument will be used for an output file. -create OR -CreateForSections Integer Number of sections to create a new piece list for -pieces OR -PiecesInXandY Two integers Number of pieces in X and Y in the newly created piece list -spacing OR -SpacingInXandY Two integers Spacing between the pieces in X and Y in the newly created piece list. Enter the negative of a spacing to have pieces coordinates put out in inverse order, from high to low coordinates. For how to determine the desired spacing, see above. -columns OR -ColumnsOfPieces Order pieces in a newly created piece list so that successive pieces occur in columns (in Y) rather than in rows (in X). -divide OR -DivideByBinning Integer This option can be used to make a new piece list that works with binned images. Rather than just dividing the existing coordinates by the binning, the program determines a new overlap value and makes sure that coordinates are regularly spaced apart. To do this, it needs the image sizes before and after binning, entered with -size and -binned. -overlap OR -NewOverlapInXandY Two integers This option can be used to change the overlap between pieces in a piece list. Enter the new overlaps in X and Y, and enter the size of the pieces with the -size option. -size OR -SizeInXandY Two integers Size of pieces in X and Y. This entry is required to adjust overlap or to divide by binning; in the latter case enter the full size of the unbinned images to which the input piece list corresponds. -binned OR -BinnedSizeInXandY Two integers New, binned size of pieces in X and Y (required to divide by binning) -new OR -NewZList List of integer ranges List of Z values to map old list to. There must be as many values in this list as in the list of Z values to remap. See notes above on the contents of this list. -add OR -AddToAllCoordinates Three floats Amount to add to all coordinates in X, Y, and Z, after remapping -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, Edpiecepoint takes sequential input the old way, with the following entries: Name of input piece or point list file, or Return if none IF you enter "Return", then the program will create a new piece list. Then make the following 4 entries: Number of sections (N) for which to make piece coordinates. The Z coordinates will initially run from 0 to N-1, and the lower left X and Y coordinates will be 0. Number of pieces in X and in Y (enter / for 1,1) Spacing between pieces in X and in Y. See above. 0 if pieces progress along rows in the image file, or 1 if they progress along columns. Name of output piece or point list file New list of Z values. See above. Amounts to add to all X, Y, and Z coordinates. These values will be added after the remapping of Z values, if any. HISTORY Written by David Mastronarde, 5/8/89