remapmodel(1)                                                    remapmodel(1)

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

       remapmodel  [options]  input_file  output_file

       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

       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, enter-
       ing 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 exist-
       ing Z values in the model.  The following options can be specified
       either as command line arguments (with the -) or one per line in a com-
       mand file or parameter file (without the -).  Options can be abbrevi-
       ated to unique letters; the currently valid abbreviations for short
       names are shown in parentheses.

       -input (-i) OR -InputFile      File name
              Input model file.  If this option is not entered, the first non-
              optional argument will be used.

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

       -old (-ol) 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

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

       -reorder (-r) 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 mono-
              tonically decreasing (for a value of -1)

       -fromchunks (-fr) 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 (-t) 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 (-h) OR -usage
              Print help output.

              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 modifica-

       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.

       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

       Email bug reports to mast at colorado dot edu.

BL3DEMC                              4.7.3                       remapmodel(1)