<newline> <tt>volview</tt>: A S-Lang Guilet For Volume Visualization <newline> Reference Manual, Version 0.1.3 <author> Michael S. Noble, <tt>mnoble@space.mit.edu</tt> <date> Mar 10, 2009 <toc> <chapt>Preface <tscreen><verb> Volview is an extension module which adds volume visulization capability to the S-Lang interpreter, using the Gtk widget set and volpack rendering library. Copyright (C) 2008 Massachusetts Institute of Technology Author: Michael S. Noble <mnoble@space.mit.edu> This software was developed with SLIRP at the MIT Kavli Institute for Astrophysics; it was funded in part by NASA and the Smithsonian Institution, through the AISRP grant NNG05GC23G and Smithsonian Astrophysical Observatory contract SV3-73016. Permission to use, copy, modify, distribute, and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in the supporting documentation, and that the name of the Massachusetts Institute of Technology not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. The Massachusetts Institute of Technology makes no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty. THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. </verb></tscreen> <chapt>Introduction <tt>volview</tt> is an extension module which adds volume visualization capability to the S-Lang interpreter, using the <tt>volpack</tt> rendering library and Gtk widget set (see <url url="http://graphics.stanford.edu/software/volpack/" > and <url url="http://www.gtk.org/" >). Like VWhere (<url url="http://arxiv.org/abs/astro-ph/0412003" >), <tt>volview</tt> is also an example of the notion of a guilet (pronounced "gooey-let"), by which we mean to connote visual interfaces of a small-ish, scriptable nature, that may be easily embedded within -- and launched from -- other programs, even applications with interactive command lines and no ostensible graphical interface. For example, <tt>volview</tt> is frequently used in ISIS (<url url="http://space.mit.edu/cxc/isis/" >), our platform for robust, high-performance astrophysical analysis and modeling, whose main interface is an interactive <tt>Matlab</tt>(tm)-style command line prompt. Guilets fill an important software niche, the middle ground between novice users -- who often argue that visual interfaces make software easier to use -- and power users -- who frequently complain that GUIs are more cumbersome and inflexible than command lines. Experience suggests that the code size and development cycle of the typical guilet is considerably smaller than that of traditional, monolithic GUIs (by which we mean to connote applications coded from scratch, typically in a compiled language such as C or C++, to have only a visual interface). Moreover, given their scripting heritage, guilets can be more amenable to changing requirements or ad-hoc experimentation and customization by the end-user. This is especially important in the scientific and engineering research arenas. <sect>Building <tt>volview</tt> ships with a configure script generated by autoconf, and in most cases can be built by issuing the following standard commands within a UNIX-like (e.g. Linux or Cygwin) environment: <tscreen><verb> ./configure [options] make make install </verb></tscreen> Beyond S-Lang itself, <tt>volview</tt> has three explicit dependencies: SLIRP, <tt>volpack</tt>, and SLgtk. The latter two of these, if not present on your system, may be automatically downloaded from our site and installed on your system by using the <tt>--enable-download</tt> configure option. Issue a <tt>./configure --help</tt> command for more information. <tt>volview</tt> can be loaded at runtime into any suitably configured application which embeds the S-Lang interpreter, using either <tscreen><verb> require("volview"); </verb></tscreen> or <tscreen><verb> () = evalfile("volview"); </verb></tscreen> <sect>Examples Volumes are visualized from arrays, of either 3 or 4 dimensions, none of which may be zero in length. When a 4D array is given the first element is selected as the 3D volume to be visualized (using a 4D array to perform a 3D slideshow will be supported in the near future). For example, this statement sequence <tscreen><verb> variable volume = tan([1:8000]); reshape(volume,[20,20,20]); volview(volume); </verb></tscreen> yields <tscreen><verb> </verb></tscreen> <img src="tan.png"> <tscreen><verb> </verb></tscreen> Since volumes are just arrays they may be read from virtually any source. For example, consider a classic brain MRI scan example, stored in HDF5 format and read using the <tt>slh5</tt> module: <tscreen><verb> require("h5"); volview( h5_read("brain.h5")); </verb></tscreen> <img src="brain.png"> <tscreen><verb> </verb></tscreen> Here the HDF5 file was converted from a "raw volume" format used by <tt>volpack</tt> (representing an MRI scan of a human head, derived from public domain data provided by SoftLab at UNC Chapel Hill). Our final example is drawn from astronomy, and utilizes a spectral cube in the FITS file format, generated by CUBISM (<url url="http://ssc.spitzer.caltech.edu/archanaly/contributed/cubism" >) from Spitzer observation 3310 of the Cassiopeia A supernova remnant and graciously provided by Dr. Tracey Delaney. The visual is useful because many popular astronomical visualization tools only support visualizing 2D slices of 3D images, which does not reveal interesting structure in the 3rd dimension (e.g. here wavelength). By visualizing the entire volume as a single array <tscreen><verb> require("fits"); volview( fits_read_image("casa_ll2_s12.fits") ); </verb></tscreen> we see instantly the clumpy areas which correspond to areas of strong emission: <img src="casa.png"> <chapt>Command Reference <tscreen><verb> volview SYNOPSIS Display a 3D volume array within a graphical user interface USAGE volview(3D_or_4D_volume_array [; x=<x0>, y=<y0>, z=<z0>]) DESCRIPTION This function will launch a GUI in which the given volume will be displayed, using the optional x,y,z qualifiers to set the initial viewing angle. From there the volume may be rotated along any axis, zoomed in or out, or saved to a variety of output file formats. Right-clicking on the image after rendering will launch a menu from which rendering parameters (e.g. colormap, opacity) may be modified. NOTES The input array may have either 3 or 4 dimensions, none of which may be zero in length. When a 4D array is given the first element is selected as the 3D volume to be visualized. SEE ALSO volpack, SLgtk -------------------------------------------------------------- </verb></tscreen> </book>