Used 'stable' flag for intersect (findDifferentRowIntoMatrix) and unique (gtCrystFindFamilies)

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

gtSegmentationLaunchOAR : OAR needs one big job, if not where will be some duplicates in the difspot table (it will be fixed soon)

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

gtGeoLabDefaultParameters : added correction for detrefpos(3) - the Z coordinate of the detector - if the sample bounding box position on the detector is not centered.

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

build_list_v2 : removed fable crystallographic fields (sg and symm), added symm structure and usedfam parameter for matching.

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

right order. Instead of renaming the images, it creates a directory which
holds links in the right order to the original images.

Signed-off-by: Stefan Schmiederer <sschmied@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

gtGetSummedDifSpot : commented header and indenting... Difspots images are supposed to be in 2_difspot/*0000 folders.

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

batch-dev-conf.xml : added new segmentation function "gtSegmentationDoubleThreshold" to the list of functions to be compiled

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

gtStatus : added check if the new segmentation has been run (method is 'doublethr_new' in this case)

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

gtCheckParameters/gtModifyStructure : fixed bug with structures with structure as field, handling correctly the filling of those parameters by default
build_structure  : only comments
make_parameters : Added debug flag

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

GtGuiAssembleVol3D : saved assembler params into the GrainsManager gui, in order to keep the choice of parameters for the assemble, if already done
GtGrainsManager    : added property 'assembler_params' to keep record of assembler parameters and pass them to the Assemble gui when launched.

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

  gtSegmentationInitialise : Set segmentation method to 'doublethr_new' to be distinguished from 'doublethr' (standard segmentation routine)
  NewSegmentationPreGUI    : Check existence of difspot images before running segmentation and asking for their deletion.
  gtSegmentationLaunchOAR  : implemented the OAR submission using more cores on a single machine (default are 6 cores on one machine with 8000 Mb/core)
                             Difspot images should be saved in 2_difspot/00000, 2_difspot/10000, etc...

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Yoann Guilhem <yoann.guilhem@esrf.fr>

gtCrystGetSigmas : calculates sigma values for cubic and hcp materials (extracted from GtAssembleVol3D). For hcp materials, 'X' and 'Y' conventions are taken into account.

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

                  Added parameter 'autoload' to defaults to be used in the GtGuiAssembleVol3D.
                  Added parameters 'convention' and 'merge_angle' to defaults to calculate the sigma equivalent values and performs the twin test.
                  Removed parameter 'symm' from defaults.

GtGuiAssembleVol3D : set 'merge_angle' assemble parameter not editable from GUI.

GtGrainsManager : enabled selection of 'phase volume' even if the field "phaseid" is 0 and disabled it if the volume to load is not the phase volume.
                  Added argument to GtGuiAssembleVol3D to automatic load the volume when clicking a button in the GUI.
GtGuiAssembleVol3D : added argument 'GMgui' to obj.conf in order to load automatically the volume in the connected GtGrainsManager GUI.

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

Signed-off-by: Yoann Guilhem <yoann.guilhem@esrf.fr>

Signed-off-by: Yoann Guilhem <yoann.guilhem@esrf.fr>

Signed-off-by: Yoann Guilhem <yoann.guilhem@esrf.fr>

gtSetup : added check of sample rotation motor to set properly the value for rotdir. 'pmo', 'diffrz' are taken into account.

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>