xfproduct(1)                General Commands Manual               xfproduct(1)

       xfproduct - forms product of two lists of transformations

       xfproduct [options] input_file1 input_file2 output_file

       Xfproduct  is used to concatenate two lists of transforms, or to multi-
       ply all of the transforms in one file by another transform.

       In the first case, for each line in the input files, it multiplies the
       transform in the first input file by the transform in the second file,
       and writes the product in the output file.  This can thus be used to
       implement two stage alignment: If the first set of transforms were
       obtained by a first stage of aligning raw images, and the second set
       are obtained by a second stage of alignment applied to images that have
       been aligned by the first set, then the products produced by this pro-
       gram can be applied to the raw images, in one step, to produce an
       alignment that incorporates both stages.

       To multiply all of the transforms in one file by a single transform,
       make the latter transform be the only one in a file.  The file with the
       single transform can be either the first or the second file.

       If transforms in the two files apply to images at different scales,
       then it is necessary to scale the X/Y translations of one of them to
       make the two sets of transforms correspond.  For example, if the first
       set of transforms align unbinned images, but the second set refines the
       alignment for images binned by 2, then the option "-scale 1,2" would be
       needed to make transforms to align the original unbinned images.

       Either or both input files can contain warping transformations instead
       of simple linear transforms.  The transforms can be either displace-
       ments at a set of control points or displacements on a regular grid of
       positions.  If two warping files are multiplied, the output will con-
       sist of grids of displacements regardless of the type of input.  If one
       file is a warping file and the other has linear transforms, then the
       output will have the same type of displacements as the warping input

       Warping transform files contain information about the pixel size and
       number of pixels of the images for which they were obtained.  When both
       input files have warping transforms, they must be for images of the
       same total size (the product of pixel size and pixel number must
       match).  If the pixel sizes differ, the transforms from the first file
       will be scaled to match that of the second one.  If you enter the
       -scale option, it overrides this default scaling but is not allowed to
       change the relative scaling between the two files.  Since an entry is
       not needed, since Newstack and Blendmont will compensate for a
       difference between the pixel size in the warping file and the pixel
       size of the images being transformed.  However, a -scale entry might be
       needed if one file has linear transforms and the other has warping

       The easiest way to run the program is on the command line, as shown in
       the synopsis.  Xfproduct uses the PIP package for input (see the manual
       page for pip). Thus, the following options can be specified either
       as command line arguments (with the -) or one per line in a command
       file (without the -).  Options can be abbreviated to unique letters;
       the currently valid abbreviations for short names are shown in paren-

       -in1 OR -InputFile1       File name
              File with transforms applied first.  If this option is not
              entered, the first non-option argument will be used for this
              input file.

       -in2 OR -InputFile2       File name
              File with transforms applied second.  If this option is not
              entered, the second non-option argument will be used for this
              input file.

       -output (-ou) OR -OutputFile   File name
              Output file C for product transforms.  If this option is not
              entered, the third non-option argument will be used for the out-
              put file.

       -scale (-s) OR -ScaleShifts    Two floats
              Factors by which to scale X/Y translations of the first and sec-
              ond transforms before multiplying them.  Use this option if a
              set of transforms is derived from data that were scaled down
              (e.g., from a model on binned images), so that the product
              transforms will apply to unscaled data.

       -one (-on) OR -OneXformToMultiply   Integer
              When one file has multiple transforms and the other has a single
              transform, use this entry to have only one transform in the file
              of multiple transforms be multiplied by the single transform.
              Transforms are numbered from zero.  This entry has no effect if
              both files have multiple transforms.

       -help (-h) OR -usage
              Print help output

              Read parameter entries from standard input.

       If the program is started with no command line arguments, it reverts to
       interactive input with the first input file, second input file, and
       output file entered on successive lines.

       Written by David Mastronarde, 1989
       Converted to PIP input and added scaling option, 1/25/04
       Added support for warping transforms, June 2011

       Email bug reports to mast at colorado dot edu.

IMOD                                4.12.32                       xfproduct(1)