imodtrans(1)                General Commands Manual               imodtrans(1)

       imodtrans - Transform an IMOD model file.

       imodtrans  [options]  input_model  output_model

       Applies transformations to an IMOD model and copies the result to a new
       IMOD model.  The transformations can be specified in three different
       ways: 1) as translations, rotations, and scaling factors; 2) as a list
       of 2-D transformations in a file, one for each section, such as are
       produced by Midas and Xfalign; 3) as a single 3-D transformation
       in a file, such as is produced by Solvematch.  When the transforma-
       tion is specified by individual components, they are applied in the
       order that they are entered, and any option can be entered more than
       once.  If you want your rotations to match those applied by the Slicer
       in 3dmod or by Rotatevol, specify rotations around Z, then Y,
       then X.

       If you plan to display the transformed model on a different image file
       from the one that it was built on, the program will not be able to
       translate the model to the correct location unless it knows the dimen-
       sions of the other image file.  If these dimensions differ from those
       of the original image file, enter them with the -n option.  With the
       dimensions known, the program will translate from the middle of the
       original volume to the middle of the new one, and you can specify addi-
       tional transformations if that center-to-center mapping is not appro-

       The situation may be more complicated when the original and new volumes
       have different pixel sizes in their headers.  3dmod takes a change
       in pixel size into account when a model is loaded onto a volume, unless
       coordinate scaling is overridden with the -n option to 3dmod.  If
       you scale a volume in 2D with newstack by binning, expansion, or
       squeezing, or in 3D with binvol or squeezevol, a model will dis-
       play correctly on the scaled volume with no need to run imodtrans on
       it.  When it is saved from 3dmod, it will be written with coordinates
       that match the new volume.  If you need to transform a model into those
       coordinates without having to load it into 3dmod, use imodtrans with
       the -i option and the name of the scaled image file, instead of using
       the -sx, -sy, -sz, and -n options. The transformed model will have the
       scaled coordinates and will also load correctly in 3dmod.  If for some
       reason you do use the scaling and new size options instead, do not use
       the -i option.  The resulting model will have the new coordinates, but
       it will not load correctly into 3dmod without using the -m option in

       For 3-D transformations, however they are specified, all contour points
       are transformed, as well as all mesh points, surface normals, and clip-
       ping planes.  The mesh is transformed because formerly it was not pos-
       sible to remesh contours that have been rotated out of the X/Y plane,
       but this is now possible.  For 2-D transformations, only contour points
       are transformed, so clipping planes are not preserved and the model
       will have to be remeshed.  However, if a single 2D transformation is
       applied to the whole model it is converted to a 3D transformation and
       the entire model is properly transformed.

       The program can also manipulate the flipped state of the model in Y and
       Z either by actually flipping the Y and Z coordinates, or by simply
       toggling the flag that indicates whether the model was loaded on data
       that were flipped in 3dmod.  Either way may be used after flipping a
       volume with "clip flipyz" to change a model built on the unflipped vol-
       ume so that it will load onto the flipped volume.  In addition, the
       model can be transformed to match a particular image file, just the
       same as if it were loaded onto that file in 3dmod.  The order of opera-
       tions is: flipping, then transforming to match an image file, then
       transforming either via transformations in a file or via the entered

       If a volume is rotated with "clip rotx", a model built on the original
       volume will load correctly in 3dmod on the rotated volume, and a model
       built on the rotated volume will load correctly on the original volume.
       To transform the model in this case without loading on the other vol-
       ume, use the -i option with the destination volume.  If that volume is
       not available, then the same operation can be done with the -R option,
       entering 1 to transform to a rotated volume or 0 to transform to the
       original volume.

       -tx value
       -ty value
       -tz value
              The -tx, -ty and -tz options can be used to translate the model
              in the particular direction by the given floating point value,
              in pixels.

       -sx value
       -sy value
       -sz value
              The -sx, -sy and -sz options can be used to scale the model in
              the particular dimension by the given floating point value.

       -rx value
       -ry value
       -rz value
              The -rx, -ry and -rz options can be used to rotate the model
              about the particular axis by the given value in degrees.

       -2 transform file
              Transform the model in 2-D sections using the given transform
              file as input.  One line is expected per section, and slices at
              Z values greater than the number of lines will not be trans-
              formed, unless the -l option is given to apply one transform to
              the whole model.  This option is useful for transforming a model
              to match an image stack that has been aligned with Xfalign or
              Midas.  This option cannot be entered with the scaling or rota-
              tion options or with -3.  The translation options -tx and -ty
              can be used with this option, and -tz can be used when applying
              one transform to the whole model.  In each case, the option can
              be entered only once, and the shift is applied after the trans-

       -l line #
              Transform the whole model with the single 2D transformation at
              the given line number in the transform file entered with -2.
              Lines are numbered from 0.

       -3 transform file
              Transform the model with the single 3-D transformation in the
              given file.  The format of the file is to have 3 lines, each
              with 4 numbers, the coefficients for multiplying the old X, Y,
              and Z coordinates and a translation value.  The first, second,
              and third lines are for computing new X, Y, and Z coordinates,
              respectively.  This option cannot be entered with the scaling or
              rotation options, or with -2.  It can be used with the transla-
              tion options, but each option can be entered only once, and the
              shift is applied after the transformation.

       -S factor
              Scale the X, Y, and Z shifts in the transformations from trans-
              form files by the given factor.  This option is needed, e.g., if
              transformations have shifts based on unbinned coordinates and
              the model is now in binned coordinates.

       -n NX,NY,NZ
              Specify the dimensions of the image file on which the model is
              to be displayed, if these dimensions are not the same as for the
              image file on which the model was originally built.  This entry
              is needed to have the model translated to the correct location
              when image file sizes differ.

       -z     Apply Z-scaling to the model, using the Z-scale from the model
              header, before transforming the model.  The transformed model
              will then be descaled in Z so that it will display correctly
              with the same Z-scale.  This option would be needed to retain
              the shape of a Z-scaled model, but it would probably prevent it
              from matching a transformed image file.

       -f     If the model was last displayed on images loaded into 3dmod with
              Y and Z flipped, use this option to apply the transformation to
              the flipped coordinates.  The default is to apply the transfor-
              mation to native, unflipped coordinates, which will work with
              transformations obtained from Solvematch.

       -i image file
              Transform the model coordinates as if the model were being
              loaded into 3dmod together with the given image file.  The maxi-
              mum coordinates in the model (reported as "max # # #" in the
              output from Imodinfo) will be changed to match those in the
              image file.  This transformation occurs before any of the other
              operations except flipping with the -Y option.

       -I image file
              Adjust the image coordinate reference information in the model
              to match that in the given image file, without modifying model
              coordinates.  This option is useful if the pixel spacing or ori-
              gin is changed in the header of the image file, such as with
              Alterheader, after a model has been built on that file.  Such
              changes in header would cause an inappropriate scaling or shift
              when loading the model on the modified image or other images
              files derived from it.  The model resulting from this operation
              would again load correctly on such image files.  This operation
              occurs before any others, including flipping with the -Y option.

       -Y     Exchange Y and Z coordinates in the model file, without changing
              the flag indicating the model's flip state.

       -T     Toggle the flag indicating the model's flip state, without actu-
              ally flipping the data.

       -R direction
              Rotate the model by 90 degrees around the X axis; if direction
              is 1 then the rotation is by -90 degrees, the same as for "clip
              rotx", and image origin information in the model header will be
              adjusted the same as it is for a volume by "clip rotx".  If
              direction is 0 the rotation is by +90 degrees and the origin is
              adjusted in the inverse direction. This option cannot be entered
              with -Y or -T.  If the model was built on a file that was loaded
              into 3dmod with the -Y option, it will first be flipped into the
              native orientation of that file, then rotated, and its flipped
              flag will be cleared.

       Example 1: Suppose a model is drawn on a raw stack ( and needs
       to be transformed to fit on a binned by 2 stack (set.ali) that was
       aligned with transformations in set.xg.  The aligned file might be a
       different size in X and Y than the size of the raw stack divided by the
       binning.  If the origin was adjusted when the aligned stack was cre-
       ated, using the -origin option to Newstack or Blendmont, then the
       command would be:
          imodtrans -2 set.xg -i set.ali -S 0.5 input_model output_model
       First, the program reduces all X and Y coordinates by 2 to match the
       coordinate system in set.ali, and shifts points based on the change in
       origin values.  Then it multiples the shifts in set.xg by 0.5, since
       they are in unbinned coordinates, and applies the transformations.

       However, if the origin was not adjusted for any size change, then it is
       necessary to add a translation to account for it.  The needed transla-
       tion is:
          xtrans = (alignedXsize - rawXsize / binning) / 2.
          ytrans = (alignedYsize - rawYsize / binning) / 2.
       And the command is
          imodtrans -2 set.xg -i set.ali -S 0.5 -tx xtrans -ty ytrans input

       Example 2: Suppose a model is drawn on one stack (seta.ali) and needs
       to fit on another stack (setb.ali) that is rotated by approximately 90
       degrees.  The file set_AtoB.xf has a single line with the transforma-
       tion that would align the images.  The command is:
          imodtrans -2 set.xg -l 0 -n bXsize,bYsize,bZsize input_model out-
       This command works because the input model has the size of
       stored as its maximum coordinates, and because the output file size is
       given.  The prgram is thus able to shift the model by the difference
       between the center coordinates of the two stack.

       Example 3: Suppose a model is drawn on a volume and a new volume is
       made with "clip flipyz".  If the first volume was loaded into 3dmod
       with the "-Y" option for rotation around X, the model was saved in
       flipped coordinates.  To load it on the new volume, the flip flag needs
       to be turned off with:
          imodtrans -T input_model output_model

       However, if the first volume was loaded in its native orientation, then
       the model needs to be flipped with:
          imodtrans -Y input_model output_model

       Example 4: Suppose a volume is rotated wih "clip rotx".  To transform a
       model built on the original volume to the coordinates of the rotated
       volume, you can use:
          imodtrans -i rotated_volume input_model output_model
          imodtrans -R 1 input_model output_model

       To transform a model built on the rotated volume to the coordinates of
       the original volume, you can use:
          imodtrans -i original_volume input_model output_model
          imodtrans -R 0 input_model output_model

       Jim Kremer and David Mastronarde

       midas, xfalign, solvematch, matchvol, rotatevol,
       clip, 3dmod

       Email bug reports to mast at colorado dot edu.

IMOD                                4.11.0                        imodtrans(1)