Squashed commit of the following:

commit 0970bb93a0cd1f5dbe2d7afa0127b1fd456c425f
Author: Nicola Vigano <nicola.vigano@esrf.fr>
Date:   Wed Mar 14 20:27:36 2012 +0100

    GtAssembleVol3D: added the possibility to produce maps containing the conflicting regions

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

commit a2c5e52349639c6ecea2cb5565af20b24bf4645c
Author: Nicola Vigano <nicola.vigano@esrf.fr>
Date:   Tue Mar 13 19:35:22 2012 +0100

    Fixed mistake in volume assembly

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

commit e347a02430a493ed8922729b8f1aa0c24d8f7bcd
Author: Nicola Vigano <nicola.vigano@esrf.fr>
Date:   Tue Mar 13 17:53:14 2012 +0100

    GtAssembleVol3D: completed volume.mat generation

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

commit f22b83eb3867856842623f737e4887aeffb6cc0d
Author: Nicola Vigano <nicola.vigano@esrf.fr>
Date:   Tue Mar 13 17:49:30 2012 +0100

    C functions to loop through ROIs in big volumes are now CPP functions, to deal with matlab types

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

commit 892b5657636a29bfb4d8b99b381e34cbf8594158
Author: Nicola Vigano <nicola.vigano@esrf.fr>
Date:   Mon Mar 12 21:40:03 2012 +0100

    GtAssembleVol3D: initial proper support for files/dirs new structure

    It should be able to write to the complete volume, but it fails right now to assemble the phases.

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

commit 99f73ade75d9e1c3f67f09ab60256524235241c3
Author: Nicola Vigano <nicola.vigano@esrf.fr>
Date:   Mon Mar 12 16:02:27 2012 +0100

    GtAssembleVol3D: imported some twins stuff from function gtnew_assemble_vol4_3D

    The idea is to enhance in the future the assembling logic, in order to be able to merge automatically those grains which overlap by the majority of the volume and have the same orientation.
    The imported code is a nice idea, but needs to be refined, because can deal both with twins and overlapping similar grains.

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

commit 164fd07e92f0962d5b6669477a5f4e385c63d33a
Author: Nicola Vigano <nicola.vigano@esrf.fr>
Date:   Mon Mar 12 12:22:07 2012 +0100

    Added missing statement for setting assembled volumes to zero, when interfering

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

commit d6ad590d0b7969f5b5ebd74cfccd849a10df56f2
Author: Nicola Vigano <nicola.vigano@esrf.fr>
Date:   Fri Mar 9 20:11:41 2012 +0100

    Fixed Phase volumes assembly, and enhanced gtPlaceSubVolume (it's now even faster)

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

commit 9c525d6be62bed674159b0d56691f77c4a6f0624
Author: Nicola Vigano <nicola.vigano@esrf.fr>
Date:   Fri Mar 9 18:44:08 2012 +0100

    Added initial Assembling Class.

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@270 4c865b51-4357-4376-afb4-474e03ccb993