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