Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells TAPEROUTVOL(1) TAPEROUTVOL(1) NAME taperoutvol - to excise a subset of a volume, taper and pad outside SYNOPSIS taperoutvol DESCRIPTION Taperoutvol will cut a subset out of an image volume, pad it into a larger volume, and taper the intensity down to the mean value of the volume over the extent of the padding region, i.e., from the edge of the actual excised pixels to the edge of the new volume. None of the original excised pixels are attenuated by this method. The resulting volume will have dimensions suitable for taking the FFT unless the -nofft option is entered. Taperoutvol uses the PIP package for input (see the manual page for pip) and can still take sequential input interactively, to maintain compatibility with old command files. The following options can be specified either as command line arguments (with the -) or one per line in a command file or parameter file (without the -): -input OR -InputFile File name Input image file -output OR -OutputFile File name Output image file -xminmax OR -XMinAndMax Two integers Starting and ending X index coordinates to extract, numbered from 0. The default is the whole width in X. -yminmax OR -YMinAndMax Two integers Starting and ending Y index coordinates to extract, numbered from 0. The default is the whole height in Y. -zminmax OR -ZMinAndMax Two integers Starting and ending Z index coordinates to extract, numbered from 0. The default is the whole depth in Z. -taper OR -TaperPadsInXYZ Three integers Number of pixels over which to taper and pad the patches in X, Y and Z. The default is 0. Unless the -nofft option is entered, the amount of tapering in any dimension may be increased to make that dimension suitable for taking an FFT. -nofft OR -NoFFTSizes Do not adjust the padding to give sizes suitable for an FFT. This option is particularly important if you want no tapering and padding. -param OR -ParameterFile Parameter file Read parameter entries as keyword-value pairs from a parameter file. -help OR -usage Print help output -StandardInput Read parameter entries from standard input. If there are no command-line arguments, Taperoutvol takes sequential input the old way, with the following entries: Inputs to the program: Name of input file Name of output file The starting and ending X index coordinates (number from 0), the starting and ending Y index coordinates, and the starting and ending Z index coordinates to extract. The default is the whole volume. The width of the borders, in X, Y, and Z, with which to pad the image block. Borders will be made larger as necessary to make the output image size suitable for taking a 3D FFT, with the exception that if a single Z slice is requested with no padding, only a single slice is produced without padding. The program will stop with an error message if memory cannot be allocated for the output image, or if the subset is not entirely within the input volume. HISTORY Written by David Mastronarde 3/1/01 Converted to PIP, 1/8/10