patch2imod(1) patch2imod(1)NAMEpatch2imod - makes model from patch displacement, warping, or residual fileSYNOPSISpatch2imod [options] patch_file IMOD_model_fileDESCRIPTIONpatch2imod creates an IMOD model from a file containing 3-D displace- ments at a series of positions, such as the patch file generated by corrsearch3d. Each displacement will be represented by a vector starting at the position of the patch, and whose magnitude and direc- tion are determined by the 3-D displacement multiplied by a scale fac- tor. These vectors are simply open contours consisting of two points. In addition, if the patch file contains correlation coefficients or residual values, these values will be stored in the model. The resulting model can be viewed to determine the location of patches with aberrant displacements and even edited to remove such patches. The easiest way to do this is to start 3dmod with just the model file and no image file, open the model view window, and use the right mouse button in the model view window to select vectors that differ greatly from their neighbors. The currently selected vector(s) will be high- lighted by being thicker. They may then be deleted with the D hot key. The edited model can be converted back to a patch file with imod2patch. The correlation or residual values can be visualized by opening the "Values" panel in the model view Object Edit window and selecting "Show stored values". The color display can be manipulated and subsets of vectors can be selected. If the patch file contains a column of numbers after the correlation coefficient or residual values, these will also be stored as secondary values in the model but cannot be visualized. They will be output to a new patch file by imod2patch. In fact, there can be up to six columns of numbers, and any two can be chosen to be stored in the model file with the-voption. One can also read the model in on top of a tomogram; by default it is marked as flipped so that it will display correctly on tomograms in their original orientations. The scaling is stored as the pixel size in the model header. Do not change this value, or imod2patch will not be able to convert the dis- placements back correctly. The program will also convert a list of 2-D residuals produced by Tiltalign. In this case, the model is not marked as flipped, so that it can be displayed on top of the original image file. A file of warping transformations can also be converted to vectors, and again the model is not marked as flipped.OPTIONS-svalueChange the vector length scaling to the given value; the default is 10.-fDo not flip Y and Z coordinates in the model. Use this option to display the model on a tomogram that has been flipped or rotated from its original orientation. The option is not needed with a Tiltalign residual file or with a warping transformation file.-csizeInclude four clipping planes in the model to enclose a square area of the given size in the center of the model. These planes will not be on by default, but can be turned on and manipulated together in the model view Object Edit window. These planes could be helpful for seeing a subset of vectors when the model is rotated.-nname>Give this name to the model object. The name is useful for indicating what kind of values are stored with the vectors.-dSet the flag to display stored values in false color in 3dmod. This option has the same effect as turning on the "Show stored values" button in the Values panel of the Edit-Objects dialog of the Model View window.-zIgnore zero values when computing the mean and SD of values. The program computes the actual maximum value and the mean and SD, and then stores a maximum value that is limited to 10 SDs above the mean. This stored value determines the maximum that is shown in the model view object edit window of 3dmod. This option is needed when there are a very large numbers of zero values.-vID/-colStore the value column with the given ID number, or with the negative of the given column number, as the primary values in the model. Value columns are numbered from 1 and there can be up to 6 of them. Programs that create patch vector output files (Corrsearch3d(1), Refinematch, Findwarp), now assign an ID number to each type of data; these ID numbers are listed in order in first line of the file. The default is to store the first value column as primary (corresponding to an entry of "-1").-lRead all lines in the file as lines with vectors. By default, the program reads the first line to determine the number of lines, then reads that number of lines as vectors.-wRead the input file as a warping transformation file like those produced by Midas and Tiltxcorr. Both control point and warping grid files can be converted. The negative of the warp- ing vector values will be displayed because those values are inverse transform values.-tAssign a time to each contour, equal to its Z value plus 1. This option may be useful when examining vector models from a warping transformation file or from the edge function output of Blendmont, because it would allow one to examine vectors for one section or edge function at a time in the Model View window instead of in the Zap window. One can step through times with the 1 and 2 hot keys, but there may be no good way to select a specific time out of many.FILESUnless the-loption or the-woption is given, the first line of the file must have the number of vectors in the file. If this line con- tains "residuals", then each succeeding line should have five values: X, Y, Z, delta X and delta Y. X and Y may be floating point values in this case, and Z must be an integer. Other than the residual case, each line may have 6 to 8 values, where the first 6 are X, Y, Z, delta X, delta Y, and delta Z. X, Y, and Z must all be integers in this case. A seventh value is stored at a general value displayable in 3dmod, and an eighth value is stored as the second type of general value. If the model file already exists, it becomes a backup file with ~ added to its name.AUTHORDavid MastronardeSEEALSOimod2patch, patchcrawl3d, patchcorr3d, 3dmod, 3dmodv, findwarp, refinematch, tiltalign, tiltxcorr, midasBUGSEmail bug reports to mast at colorado dot edu. IMOD 4.9.5 patch2imod(1)