imodtrans(1) imodtrans(1) NAME imodtrans - Transform an IMOD model file. SYNOPSIS imodtrans [options] <input model> <output model> DESCRIPTION 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 are 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- priate. 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 the -m option. 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 options. Options -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 translation, scaling, or rotation options, or with -3. -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 transla- tion, scaling, or rotation options, or with -2. -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. -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. AUTHOR Jim Kremer and David Mastronarde SEE ALSO midas, xfalign, solvematch, matchvol, rotatevol, clip, 3dmod BUGS Email bug reports to mast at colorado dot edu. BL3DEMC 4.3.7 imodtrans(1)