joinwarp2model(1)                                            joinwarp2model(1)

       joinwarp2model - Make starting model for refining tomogram join from
       initial warping

       joinwarp2model  options  warping_xf_file  model_file

       Joinwarp2model produces a model file that can be used as a starting
       point for a refining model when joining serial tomograms where warping
       has been applied in the first alignment stage of joining.  Each warping
       control point introduced in Midas is converted to a contour with a
       pair of points.  These two points will display just below and just
       above the junction in the joined file that a refining model is being
       built on, as required by Xfjointomo.  The premise here is that you
       have already identified each such pair of points as corresponding
       between the two sections when you imposed the warping.  It is thus
       appropriate and important to keep all of these correspondences in the
       refining model.  In the ideal case, if the modeled trajectories are all
       perfectly consistent with these correspondences, then the correspon-
       dences will be retained and the transform fitting will produce a unit
       transformation at the correct gap between sections.  More realisti-
       cally, the correspondences implied by the trajectories will not agree
       perfectly with the correspondences created by warping, and the fitting
       will average over all of the data, producing a non-unit linear trans-
       formation and shifting the warping points out of correspondence to some

       Joinwarp2model uses the PIP package for input (see the manual page for
       pip).  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 parentheses.

       -input (-i) OR -InputWarpFile       File name
              Name of input transform file with warping control points.  When
              Etomo runs Finishjoin, this is the file "joinroot.xf".  If
              this option is not entered, the first nonoption argument is used
              for this filename.  One or the other entry is required.

       -output (-ou) OR -OutputModelFile   File name
              Name of output file for model of warp points.  If this option is
              not entered, the second nonoption argument is used for this
              filename.  One or the other entry is required.

       -joined (-j) OR -JoinedFile    File name
              Name of join file being modeled.  After "Refine Join" is pressed
              in Etomo, this is the file "joinroot_modeled.join".  If this
              filename is not entered, then the "-size" and "-pixel" options
              must be entered.

       -xform (-x) OR -AppliedTransformFile     File name
              Name of file of G transforms applied to make the join file.
              When Finishjoin is run without the "-xform" option, this is
              the file "joinroot.tomoxg", which is copied to "joinroot.warpxg"
              if there is warping.  However, when Finishjoin is run with
              the "-xform" option to make the refined join, "joinroot.tomoxg"
              is the final transform file, not the file needed here.  Thus,
              use "joinroot.warpxg".  This entry is required.

       -size (-s) OR -SizeOfJoinInXandY    Two integers
              Actual size in X and Y of the join file being modeled, in binned
              pixels if binning was used.  This entry is needed if "-joined"
              is not entered.

       -pixel (-p) OR -PixelSpacing   Floating point
              Actual pixel spacing in Angstroms of join file being modeled,
              which includes any binning applied to make the file.  This entry
              is needed if "-joined" is not entered.

       -offset (-of) OR -OffsetInXandY     Two integers
              Offset applied when building the join file, in unbinned pixels
              if binning was applied.  This entry should be the same as the
              "-offset" entry to Finishjoin, which is the negative of the
              "Shift" values in the text boxes in Etomo.

       -binning (-b) OR -BinningOfJoin     Integer
              Binning applied when building the join file; this entry is
              required if binning was applied.

       -chunks (-c) OR -ChunkSizes    Multiple integers
              Number of slices in each section of the join file.  This entry
              is required so that the program can put the model points at the
              right locations just before and after each junction between sec-

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

              Read parameter entries from standard input

       David Mastronarde

       xfjointomo, midas, finishjoin

       Email bug reports to mast at colorado dot edu.

IMOD                                 4.9.5                   joinwarp2model(1)