Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

REMAPMODEL(1)							 REMAPMODEL(1)

NAME
	remapmodel - to remap Z values and shift coordinates of a model

SYNOPSIS
	remapmodel

DESCRIPTION
  This program allows one to remap coordinates in a model, in two 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 may be shifted by a constant.

  Also, a mapping can be set up easily for the case where serial section 
  tomograms are being rejoined with different spacings.
  
  The program works by mapping from an old list of Z values to a new list of
  Z values.  The old list is, by default, the list of actual Z values in the
  file, although you can enter a different list to map from.  The mapping of Z
  values is done by first converting each Z value to the nearest integer,
  looking up the new integral Z value that you wish to map that integer to,
  then shifting the actual Z value by the difference between the new and the
  original integral value.
  
  The new list of Z values should have the following form.  Use ranges 
  (e.g. 0-3,5-7,10-8) to specify a list of integers with the same number of Z
  values as in the list of values being mapped.  The latter Z values will be
  mapped one-to-one onto the new list.  Enter numbers between -999 and -990 to
  delete points with a particular Z value; e.g. if the input model 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 model has Z from 0-19, entering 0-9,-999--990 will
  remove all points with Z from 10 to 19.  Enter the single value -1 to
  replace each Z value by its negative.


  Remapmodel uses the PIP package for input (see the manual page for pip)
  and can take input interactively for a basic mapping of existing Z values in
  the model.  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 model file.  If this option is not entered, the first non-optional
    argument will be used.

 -output OR -OutputFile   File name
    Output model file.  If this option is not entered, the second non-optional
    argument will be used.

 -old OR -OldZList   List of integer ranges
    List of Z values in the input model that are to be remapped.  The default
    is the actual list of Z values, which could have gaps that make it
    difficult to compose the list of values to map to.

 -full OR -FullRangeInZ
    For the list of values to remap, use the complete range from 0 to NZ-1,
    where NZ is the Z size of the image file that the model was last loaded
    on, determined from the model header.

 -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 -AddToAllPoints   Three floats
    Amount to add to all coordinates in X, Y, and Z, after remapping

 -reorder OR -ReorderPointsInZ   Integer
    Go through each contour and reorder the points so that they are
    monotonically increasing in Z (for an input value of 1) or monotonically
    decreasing (for a value of -1)

 -fromchunks OR -FromChunkLimits   Multiple integers
    To remap Z values after changing the spacing between sections in a joined
    set of serial section tomograms, enter the original starting and ending
    slice for each tomogram in the join (start1, end1, start2, end2, etc).  If
    a tomogram was inverted in the join, be sure that the high Z number is
    listed as the start and the low Z number is listed as the end.

 -tochunks OR -ToChunkLimits   Multiple integers
    The new starting and ending slices for each tomogram in a serial section
    join, in the same format as for -fromchunks.  When these two options are
    entered, none of the other mapping options (-old, -new, -full) can be
    used.

 -help OR -usage
    Print help output.

  -StandardInput
     Read parameter entries from standard input.


  The program will accept input interactively if started with no command line
  arguments; the interactive entries to the program are:
  
  Name of input model file
  
  Name of output model file
  
  New list of Z values.  See notes above on the format of this list.  In
  addition, you can enter "/" to take the input list without modification.

  Amounts to add to all X, Y, and Z coordinates.  These values will be
     added after the remapping of Z values, if any.  Values should be
     in units of pixels (image index coordinates).
  
  IF your new list of Z values is not in monotonic order, enter 1 to
     have the program reorder the points within each object so that
     they occur with monotonically changing Z.  This option would be
     used if you wanted to switch two sections within a stack.

HISTORY
  Written by David Mastronarde, 5/8/89
  DNM 7/20/89  changes for new model format
  DNM 2/20/90  changes to negate Z and reorder by Z
  DNM 10/27/06: Convert to PIP and provide new options for tomogram joins