imodtrans(1) General Commands Manual imodtrans(1)NAMEimodtrans - Transform an IMOD model file.SYNOPSISimodtrans [options] input_model output_modelDESCRIPTIONApplies 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-noption. 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-noption 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-ioption and the name of the scaled image file, instead of using the-sx,-sy,-sz,and-noptions. 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-ioption. The resulting model will have the new coordinates, but it will not load correctly into 3dmod without using the-moption in 3dmod. 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. 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-ioption with the destination volume. If that volume is not available, then the same operation can be done with the-Roption, entering 1 to transform to a rotated volume or 0 to transform to the original volume.OPTIONS-txvalue-tyvalue-tzvalueThe-tx,-tyand-tzoptions can be used to translate the model in the particular direction by the given floating point value, in pixels.-sxvalue-syvalue-szvalueThe-sx,-syand-szoptions can be used to scale the model in the particular dimension by the given floating point value.-rxvalue-ryvalue-rzvalueThe-rx,-ryand-rzoptions can be used to rotate the model about the particular axis by the given value in degrees.-2transformfileTransform 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-loption 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-txand-tycan be used with this option, and-tzcan 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- formation.-lline#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.-3transformfileTransform 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.-SfactorScale 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.-nNX,NY,NZSpecify 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.-zApply 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.-fIf 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.-iimagefileTransform 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-Yoption.-IimagefileAdjust 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-Yoption.-YExchange Y and Z coordinates in the model file, without changing the flag indicating the model's flip state.-TToggle the flag indicating the model's flip state, without actu- ally flipping the data.-RdirectionRotate the model by 90 degrees around the X axis; ifdirectionis 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". Ifdirectionis 0 the rotation is by +90 degrees and the origin is adjusted in the inverse direction. This option cannot be entered with-Yor-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.ExamplesExample 1: Suppose a model is drawn on a raw stack (set.st) 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-originoption 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 output 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- put_model This command works because the input model has the size of seta.st 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 or 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 or imodtrans -R 0 input_model output_modelAUTHORJim Kremer and David MastronardeSEEALSOmidas, xfalign, solvematch, matchvol, rotatevol, clip, 3dmodBUGSEmail bug reports to mast at colorado dot edu. IMOD 4.10.18 imodtrans(1)