snaphu
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SNAPHU Statistical-Cost, Netowrk-Flow Algorithm for Phase Unwrapping Author: Curtis W. Chen Version 2.0.4, August 2020 Contents -------- 1. Bugs and Bug Reporting 2. Notes on Compiling 3. Run-Time Configuration Files 4. Copyright Bugs And Bug Reporting ---------------------- Not all parts of snaphu have been well tested, so your bug reports and feedback are appreciated. Please email them to [email protected] The man page included with the distribution lists known issues as well. Thanks, and good luck with the unwrapping. Notes on Compiling ------------------ To compile, edit the Makefile in the src directory to specify your compiler, the optimization flags, and the desired directory for the executable. After that, run make and see what happens. Most of the code should be pretty standard, but a few of the library functions that are used may be unavailable on some systems. In some cases, the problem code may only perform error checking, so you might be able to comment out the unavailable functions without ill effects. For example, the IsFinite() function in snaphu_util.c is a wrapper for calling the library function finite(), which is unavailable on some systems. You can modify IsFinite() to use an alternate implementation that you do have, or you can have it always return TRUE. The code was developed mainly with gcc, but has been tested with a number of vendor C compilers. The latter tend to produce faster executables. I have not tried running snaphu under Cygwin. I have not experimented with parallelizing compilers. The code is written to use multiple processors in tile mode by forking copies of itself to unwrap each tile. The structure of the solver does not lend itself to easy parallelization for a single tile, however. The CS2 MCF solver module is governed by the terms of the original authors (see the README.copyright file). In order to compile snaphu without this module, specify -D NO_CS2 as a compiler option in the Makefile. Run-Time Configuration Files ---------------------------- Two template run-time configuration files are provided in the config directory. The file snaphu.conf.brief contains the configuration parameters that a beginning user might need to specify. The file snaphu.conf.full contains all the options that the program will accept. Copyright --------- Copyright 2002-2020 Board of Trustees, Leland Stanford Jr. University Except as noted below, permission to use, copy, modify, and distribute, 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 supporting documentation, and that the name of the copyright holders be used in advertising or publicity pertaining to distribution of the software with specific, written prior permission, and that no fee is charged for further distribution of this software, or any modifications thereof. The copyright holder makes no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty. THE COPYRIGHT HOLDER DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA, PROFITS, QPA OR GPA, 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. The parts of this software derived from the CS2 minimum cost flow solver written by A. V. Goldberg and B. Cherkassky are governed by the terms of the copyright holder of that software. Permission has been granted to use and distrubute that software for strictly noncommercial purposes as part of this package, provided that the following copyright notice from the original distribution and URL accompany the software: COPYRIGHT C 1995 IG Systems, Inc. Permission to use for evaluation purposes is granted provided that proper acknowledgments are given. For a commercial licence, contact [email protected]. This software comes with NO WARRANTY, expressed or implied. By way of example, but not limitation, we make no representations of warranties of merchantability or fitness for any particular purpose or that the use of the software components or documentation will not infringe any patents, copyrights, trademarks, or other rights. https://www.igsystems.com/cs2