This folder contains the source code of the V3D project.

There are a few sub-folders:

* bin:                     the folder where the final executable and plugins will be copied to 
* v3d_main:                the main V3D program. 
* matlab_io_basicdatatype: matlab toolbox for file IO of some basic V3D data formats,
                           including image file, surface files, neuron, markers, etc.
* imagej_io:               imagej plugin toolboxes for file IO of some basic V3D data formats. 
* released_plugins:        the "standard" V3D plugins, including both examples and some 
                           real utilities.
* 2010_hackathon:          the source code of various projects developed in the 2010
                           V3D hackathons. The V3D ITK plugins are also included there.


*** Note that different sub-folders contain different software LICENSES. You MUST agree to
these license terms before you access any parts of these source code.



* How to build the V3D program

(step 1) You need to ensure that you have QT installed on your machine, and thus "qmake" is visible
in your system's path. 

(step 2) You should also have c++ compiler, such as gcc 4.0 and above.

(step 3) You will need to enter v3d_main/common_lib/src_packages folder, unzip the two packages:

	tiff-3.8.2.1.tar.gz: run "tar zxvf tiff-3.8.2.1.tar.gz"
	boost_1_38_0.tar.gz: run "tar zxvf boost_1_38_0.tar.gz" and 
                             then run "mv boost_1_38_0/boost ../include/."

	If you have a Windows system, you will need to unzip and put these packages into the respective
	folders as well.
 
(step 4) To build V3D is very simple, just find a command line terminal and type one of the following 
commands:

	Mac, gcc compiler, 32bit build:  "sh ./build.macx -n -B -j4"
	Mac, gcc compiler, 64bit build:  "sh ./build.macx -m -B -j4"
	Linux, gcc compiler (32- or 64-bit will depend on your OS automatically):  "sh ./build.linux -B -j4"
	Windows, MinGW compiler, 32bit build:  "build.bat -B -j4"
	Windows, MSVC compiler, 32bit build:  "build_msvc32.bat -B -j4"
	Windows, MSVC compiler, 64bit build:  "build_msvc64.bat -B -j4"

The successful, the V3D program will launch after the build. The actual program will be put
under the ./v3d folder. You can directly run it next time, without a rebuild.

Trouble-shooting: If after you have successfully built the V3D application, but cannot run it, it is
                  likely to be a dynamic library dependency issue. This means that your QT library
                  or something else has a dependency on a missing library. For example, on Ubuntu,
                  sometimes the system lacks a libtiff library, which QT often needs it. Although
                  V3D builds libtiff automatically and renames it as libv3dtiff, QT still needs 
                  the library called libtiff.so. Thus you can copy the libtiff.so to a folder where
                  searchable (e.g. by setting LD_LIBRARY_PATH environment variable).

If you write/use additional plugins for V3D, be sure to put these plugins into a subfolder
called "plugins", which should be in the same folder where the execitable of v3d program resides. 
You can then use V3D programs to rescan the plugins, without the need to restart V3D. Of course,
these plugins should be produced using the same version of QT (of compatable versions), the same 
operating system, the same compiler, and the same release type ("Release" or "Debug") of the 
build.

If you have a question, see the V3D website http://penglab.janelia.org/proj/v3d .

<Aug 10, 2011>