edpiecepoint(1) General Commands Manual edpiecepoint(1) NAME edpiecepoint - edit a list of piece coordinates SYNOPSIS edpiecepoint [options] [input_file] output_file 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 val- ues 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 addi- tion, one can create a new piece list for single frame images or mon- taged images. The pieces can be ordered in rows, in columns, or even progressing in Z first for each montage position. The remapping of Z values is specified by a list of values (comma-sepa- rated 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 points 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. OPTIONS Edpiecepoint uses the PIP package for input (see the manual page for pip) and can still take sequential input interactively. The follow- ing 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. -input (-i) 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 (-ou) 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 (-cr) OR -CreateForSections Integer Number of sections to create a new piece list for -pieces (-pi) OR -PiecesInXandY Two integers Number of pieces in X and Y in the newly created piece list -spacing (-sp) 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 coordi- nates put out in inverse order, from high to low coordinates. For how to determine the desired spacing, see above. -columns (-co) 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). -stacks (-st) OR -StacksOfPieces Integer Order pieces in a newly created piece list so that successive pieces go through the entire set of Z values at each position in X and Y. Enter 1 to have pieces in order by Z, or -1 for pieces in inverse order. This option can be used together with the -columns option. -divide (-d) 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 coordi- nates 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 (-ov) 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 (-si) 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 (-b) OR -BinnedSizeInXandY Two integers New, binned size of pieces in X and Y (required to divide by binning) -new (-n) OR -NewZList List of integer ranges List of Z values to map old list to. There must be as many val- ues in this list as in the list of Z values to remap. See notes above on the contents of this list. -add (-a) OR -AddToAllCoordinates Three floats Amount to add to all coordinates in X, Y, and Z, after remapping -param (-pa) OR -ParameterFile Parameter file Read parameter entries as keyword-value pairs from a parameter file. -help (-h) OR -usage Print help output -StandardInput Read parameter entries from standard input. INTERACTIVE 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 BUGS Email bug reports to mast at colorado dot edu. IMOD 4.9.10 edpiecepoint(1)