http://www.xuvtools.org/ 2012-05-20T05:35:12+02:00 http://www.xuvtools.org/ http://www.xuvtools.org/lib/images/favicon.ico text/html 2010-06-18T21:36:49+02:00 http://www.xuvtools.org/devel:changelog?rev=1276889809&do=diff Entries are in the order newest first, date format is DD.MM.YYYY: Not yet released * 11.04.2010: (Mario) Collected many new test data sets on the server, see server_datasets * 11.04.2010: (Mario) Closed as invalid: HDF5 test testWriteReadStringDataSet fails on Linux * 29.01.2010, r3336: (Mario) Many updates and improvements to libBlitzBioFormats and its compile system text/html 2009-05-31T22:52:06+02:00 http://www.xuvtools.org/devel:coding_guidelines?rev=1243803126&do=diff Here is some example C++ code that should help you getting started. Coding style is not strict, but please try to stick to these guidelines in order to avoid obliteration. // Return type, class quantifier and function name all go on separate lines. // Function arguments are CamelCase, but start with a small letter 'a'. bool MyClass:: ParseTimePointAndChannel(size_t& aTimePoint, size_t& aChannel) { // Indent with two spaces. No tabs, and no more than two spaces. aTimePoint =… text/html 2010-10-09T13:24:22+02:00 http://www.xuvtools.org/devel:collection_development_problems?rev=1286623462&do=diff Several issues can arise when developing XuvTools. Here we collect common mistakes, unfixed thirdparty software errors, and other problems that are likely to arise. Visual Studio Intel Compiler: "qmake project is in a zombie state" When an application project contains a version number, the Intel project converter will generate an incorrect vsproj file. Visual Studio will show an error message saying “project is in a zombie state”. This error can be avoided by removing the version number from t… text/html 2009-06-09T15:29:42+02:00 http://www.xuvtools.org/devel:compile-debian-ubuntu?rev=1244554182&do=diff currently this is just a loose collection of stuff you need to build a toolchain on a fresh debian/ubuntu system to compile XuvTools packages required: build-essential libqt4-dev colorgcc bison set env-vars: export LMBSOFTSRC=/PATH/TO/SRC export LMBSOFTDEST=/PATH/TO/DST export LMBSOFTTEMP=/PATH/TO/TMP text/html 2010-10-14T20:36:04+02:00 http://www.xuvtools.org/devel:compile-unix-xuvbuild?rev=1287081364&do=diff Prerequisites * GNU Compiler Collection * Any recent version of gcc should do. We have tested gcc-4.3.4 and some newer versions. To compile XuvTools on Linux, you have to fulfill several build-dependencies. It is recommended that you use a change-root environment, because the compile-process might be disturbed by other/older/newer libraries that you have installed on your Linux. We provide pages that help you setup the compile environment: text/html 2010-06-18T22:01:16+02:00 http://www.xuvtools.org/devel:compile-unix?rev=1276891276&do=diff To compile XuvTools on Linux, you have to fulfill several build-dependencies. It is recommended that you use a change-root environment, because the compile-process might be disturbed by other/older/newer libraries that you have installed on your Linux. We provide pages that help you setup the compile environment: text/html 2010-10-14T20:38:25+02:00 http://www.xuvtools.org/devel:compile-win-xuvbuild?rev=1287081505&do=diff Prerequisites * Visual Studio: * It is required to have a copy of Visual Studio. Visual Studio 2008 Professional is preferred. For all other compiles, see our Windows Build Systems and Compilers overview. * Cygwin: * An installation of Cygwin is required in order to run the build scripts. There are also certain package requirements for Cygwin: * required Cygwin packages: coreutils bash grep sed tar bzip2 gzip unzip make findutils wget * recommended Cygwin packages: subversion p… text/html 2010-03-12T11:35:39+02:00 http://www.xuvtools.org/devel:compile-win?rev=1268390139&do=diff Compiling on Windows Prerequisites: currently this is Visual Studio 2008 and Qt (see below for Qt build-instructions). In addition, it is heavily recommended to use Intel's C++ Compiler for Windows to build XuvTools, and for a more comfortable way a cygwin-installation is heavily recommended. text/html 2010-10-26T20:13:40+02:00 http://www.xuvtools.org/devel:development?rev=1288116820&do=diff Common build notes XuvTools includes all nonstandard thirdparty libraries that it relies on. It uses qmake for configuration, so you need a recent Qt library. Compiling Qt is described alongside the compilation notes for your platform. XuvTools compiles on many platforms and architectures, so you should expect it to “just work”. We have tested at least the following build systems: Linux Ubuntu 8.04 (Hardy), MacOS 10.6 (Snow Leopard) with XCode 3.2, and Windows XP Professional x64 with Visual S… text/html 2010-04-22T20:45:58+02:00 http://www.xuvtools.org/devel:development_ide?rev=1271961958&do=diff I know it's hard, but please don't start an editor war here! Emacs Eclipse Setting up Eclipse for development of XuvTools: Setting up Eclipse SlickEdit Setting up SlickEdit for development of XuvTools: Setting up SlickEdit based on version 14.0.2.2 for Linux text/html 2010-04-22T20:44:36+02:00 http://www.xuvtools.org/devel:development_ide_slickedit?rev=1271961876&do=diff Setting up SlickEdit for development of XuvTools: Creating a new Workspace [Start new Workspace] [Setup 01] [Setup 02] [Setup 03] [Setup 04] Adding and Tagging Source Files [Adding Source Files] Setting Environment Variables [Setting Environment Variables] text/html 2010-10-26T20:23:50+02:00 http://www.xuvtools.org/devel:fileio?rev=1288117430&do=diff This is a collection of the File reader/writer libraries available in the XuvTools framework. * libBlitzBioFormats: an Java-based biological file reader library using OME-LOCI Bio-Formats, see <http://www.loci.wisc.edu/software/bio-formats> for details * libBlitzBioImage: a C-based based biological file reader library using the Bio-Image library from Dmitry Fedorov, see <http://biodev.ece.ucsb.edu/projects/imgcnv/wiki/libioimg> for details * libBlitzLSM: a libtiff-based biological file r… text/html 2010-04-10T10:36:34+02:00 http://www.xuvtools.org/devel:improving_data_structures?rev=1270888594&do=diff The Stitcher does not currently employ the concept of data bundeling. Every date is in an individual variable (possibly n-dimensional, though). It would be appropriate to bundle several dates that are commonly used together in algorithms. Highly related data The data type 'tileXXXX' is used tightly with: text/html 2012-05-04T17:28:07+02:00 http://www.xuvtools.org/devel:install_ubuntu_chroot?rev=1336145287&do=diff This short introduction is based on a more detailed guide at <https://wiki.ubuntu.com/DebootstrapChroot>. Installing Ubuntu into a Chroot prerequisites: sudo aptitude install debootstrap schroot first, create a new chroot-environment (Ubuntu hardy, 64-bit): text/html 2009-07-23T22:31:35+02:00 http://www.xuvtools.org/devel:install_windows_buildsystem?rev=1248381095&do=diff Installing Visual Studio 2008 is straightforward, but remember to explicitly enable x64 compilers - they are not enabled by default. If you want to install only required components, follow these instructions: [Select Visual Studio custom install] [Select only required components to save space] text/html 2010-10-26T20:42:16+02:00 http://www.xuvtools.org/devel:libblitzbioformats?rev=1288118536&do=diff [SystemsX Logo] SystemsX Collaboration This library project has been funded by and developed in cooperation with SystemsX, the The Swiss Initiative in Systems Biology (<http://www.systemsx.ch/>). About LOCI OME Bio-Formats Library C++ Bindings The Bio-Formats C++ bindings provide language bindings for calling into the Bio-Formats Java library from C++ in a cross-platform manner. They provide a set of Bio-Formats C++ bindings using Jace. Jace generates C++ proxy classes, one per Java class,… text/html 2010-10-26T20:46:41+02:00 http://www.xuvtools.org/devel:libblitzbioimage?rev=1288118801&do=diff About Bio-Image Library C++ Bindings Documentation Pointers * Bio-Image library: <http://biodev.ece.ucsb.edu/projects/imgcnv/wiki/libioimg> Download Sources Please refer to the general file reader/writer page at XuvTools File Readers / Writers for detailed instructions on getting the sources. text/html 2010-12-05T11:34:38+02:00 http://www.xuvtools.org/devel:navigate?rev=1291545278&do=diff Navigation: * Home * Screenshots * Download * Documentation * Support * MailingList * FAQ * Development * Windows * Linux/Mac * Changelog * Links * About text/html 2010-12-22T20:06:00+02:00 http://www.xuvtools.org/devel:project_files?rev=1293044760&do=diff XuvTools 1.8.1 Plain Text Format The plain text project file format is simple and straightforward. It contains an arbitrary number of key-value-pairs, one per line. Key and value are separated by the assignment operator '='. The following shows a simple example: text/html 2009-12-17T21:04:32+02:00 http://www.xuvtools.org/devel:qt_designer?rev=1261080272&do=diff When designing a user interface element with Qt designer, several ways to include this new element into the GUI are possible. In order to have a defined coding style for XuvTools, please stick to the following instructions when using the designer. The detailed explanation of this approach can be found in Qt's Designer manual, in the section “Multiple Inheritance” (for Qt-4.6.0 here: <http://doc.qt.nokia.com/4.6/uitools-multipleinheritance.html>). text/html 2010-03-31T11:03:44+02:00 http://www.xuvtools.org/devel:simplify_interest_points?rev=1270026224&do=diff Current Concept Currently, for each pair of tiles, the overlapping are is computed, and inside an interest point detection takes place. Algorithmic description: * While running xuvstitch, for every tested pair of stacks (stackX, stackY), do: * Compute start and end points of overlapping area: range R * Let stackX be the stack with higher average brightness in range R * Compute voxel gradient magnitude in range R of stackX: gradmagX_R * downscale gradmagX_R by the size of the mo… text/html 2009-04-10T17:08:01+02:00 http://www.xuvtools.org/devel:sizeof?rev=1239376081&do=diff Sizes of frequently used Data Types These numbers where generated with the xuvsizeof executable. It resides in xuvtools/src/helper directory of LMBSOFT. To compile and run xuvsizeof, use on Unix cd $LMBSOFTSRC/xuvtools/project/helper/ qmake -r xuvsizeof.pro make $LMBSOFTDEST/release_*/bin/xuvsizeof text/html 2010-01-14T14:20:02+02:00 http://www.xuvtools.org/devel:subversion_examples?rev=1263475202&do=diff For tags, the tag name pattern “xuvtools-<Major>.<Minor>.<Patch>” should be used. For branches, the branch name pattern “xuvtools-<Major>.<Minor>.x” should be used. For branches, the patch level is undefined because from this branch, higher patch levels may originate. text/html 2011-05-01T14:39:26+02:00 http://www.xuvtools.org/devel:windows_build_systems_compilers?rev=1304253566&do=diff Visual Studio Professional IDE * Fully supported, works well. * Use something like “devenv.com /Useenv <slnfile>” to compile Use the qmake option ”-tp vc” to generate project files for Visual Studio qmake -tp vc Afterwards you need to use perl, if you want to build for x64, because qmake doesn't support the x64 target.