trimvol(1) trimvol(1) NAME trimvol - Trim a volume and optionally rotate or scale to bytes or integers SYNOPSIS trimvol [options] <input file> <output file> DESCRIPTION Trimvol provides a command-line interface to the programs Findcon- trast(1) and Newstack, for copying a selected portion of an MRC image volume into a new file, with automatic scaling to bytes. There are options for specifying the volume to be extracted, and for control- ling the scaling to bytes. There is also an option to scale floating point numbers to integers. By default, coordinates are numbered from 1. If you use the -sz option, then Findcontrast will be run on the specified sections. By default, regions within 10% of the lateral bor- ders of each section are omitted, but a different region can be set with -sx and -sy. A scaling is chosen which saturates the intensities of one pixel per slice, on average, at the dark and the light end. If you use -sz The coordinates specified with these options will be treated as coming from a flipped volume only if the -f option is entered. By default, the origin of the output file will be adjusted so that a model built on the input volume will display correctly on the output file. This will even work for a volume rotated with -rx but not for one flipped with -yz. This adjustment can be turned off with the -k option. Options You can enter only one of -c, -sz or -mm. Similarly, you cannot enter both -x and -nx, both -y and -ny, or both -z and -nz. You can also enter only one of -yz and -rx. Trimvol 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 -): -x OR -XStartAndEnd Two integers Starting and ending X coordinate of region to cut out -y OR -YStartAndEnd Two integers Starting and ending Y coordinate of region to cut out -z OR -ZStartAndEnd Two integers Starting and ending Z coordinate of region to cut out -nx OR -XSize Integer Number of pixels to cut out in X, centered on the middle in X -ny OR -YSize Integer Number of pixels to cut out in Y, centered on the middle in Y -nz OR -ZSize Integer Number of slices to cut out in Z, centered on the middle in Z -sz OR -ZFindStartAndEnd Two integers Scale to bytes, determining the optimal scaling to bytes by ana- lyzing intensities from sections between the two given numbers, inclusive. Coordinates are treated as coming from a flipped volume only if the "-f" option is given. Slices are numbered from 1 regardless of whether the "-i" option is used. -sx OR -XFindStartAndEnd Two integers Analyze the region between this starting and ending coordinate in X to determine the scaling to bytes. The default is to use 80% of the range in X. -sy OR -YFindStartAndEnd Two integers Analyze the region between this starting and ending coordinate in Y to determine the scaling to bytes. The default is to use 80% of the range in Y. -c OR -ContrastBlackWhite Two integers Scale to bytes, with relative intensities between the two entered numbers (representing black and white values on a scale of 0 to 255) stretched to occupy the full range of byte values. -mm OR -IntegerMinMax Two integers Scale to integers (mode 1), so that the current minimum and max- imum of the file would be scaled to the given values of minimum and maximum. Newstack is run with the -scale option and the entered values. This option would be used to scale from mode 2 (floating point) to mode 1. -yz OR -FlipYZ Flip Y and Z in the output volume by first creating a temporary trimmed volume with newstack then running "clip flipyz" on this volume to create the final output file. -rx OR -RotateX Rotate the output volume by -90 degrees around the X axis, by first creating a temporary trimmed volume with newstack then running "clip rotx" on this volume to create the final output file. The slices will look the same as with the "-eyz" option but rotating instead of flipping will preserve the handedness of structures. -i OR -IndexCoordinates Interpret "-x", "-y", "-z", "-sx", and "-sy" entries as index coordinates numbered from 0, rather than as 3dmod coordinates numbered from 1. -f OR -FlippedCoordinates Interpret "-y", "-z", "-ny", "-nz", "-sy", and "-sz" entries as referring to a flipped volume, with Y and Z transposed. In other words, if the volume is loaded into 3dmod with flipping (the -Y option), this option allows you to enter the coordinates as they appear in 3dmod. -k OR -KeepOrigin Keep the origin the same in the output from Newstack instead of passing it the -origin option to adjust the origin for the location of the subvolume being created. This option can be used to reproduce a volume created with earlier versions of IMOD. -StandardInput Read parameter entries from standard input FILES If the output file already exists a backup image of the original is created with the ~ extension. The temporary file needed when flipping or rotating is created in the current directory with ".tmp.nnn" added to the input filename, where "nnn" is the process ID. AUTHOR David Mastronarde <mast at colorado dot edu> SEE ALSO newstack, findcontrast BL3DEMC 4.3.7 trimvol(1)