SVN: 35381

SVN: 35066

SVN: 34516

SSDM-2328: The two problems described in the comment of the issue are solved. Many reference images of the system tests had to be changed. Most image changes are to small to be visible except merged images in MicroscopyImageDropboxTest.
IntensityRescaling.rescaleIntensityLevelTo8Bits: Improved algorithm which preserves color hue and satuarion.
ImageUtil: Version of rescale() with a representative color channel.
Hdf5ThumbnailGenerator.generateThumbnailInternally(): Using new ImageUtil.rescale function providing representative channel obtained from already available meta-data.
ImageChannelsUtils.rescaleIfNot8Bit: Parameter channelColorOrNull added. This is used to calculated correct levels (based on a threshold) and to re-scale intensities correctly.

SVN: 34515

SVN: 34407

SVN: 34296

SVN: 34003

SSDM-946: Simple16BitImageDropboxTest extended. High-quality thumbnail generation in SimpleImageDataConfig becomes the default.

SVN: 32563

SVN: 32558

SSDM-774: IImageGenerationAlgorithm simplified. MaximumIntensityProjectionGenerationAlgorithm uses ImageChannelUtils to get the original images with correct intensity scaling and colors. Unit tests for MaximumIntensityProjectionGenerationAlgorithm. System test MicroscopyImageDropboxTest extended.

SVN: 32554

SVN: 32553

SSDM-946: - Introducing IntensityRescaling.IImageToPixelsConverter in order to handle BioFormat Index16ColorModel in ImageUtil.rescale() if highQuality8Bit is set. This improves conversion of 12/16-bit images to 8-bit images for Nikon ND2 files considerable. It is also used when thumbnails are created.
- ImageChannelUtils: User defined image re-scaling is always done on 8-bit images.
- ImageChannelUtils: Many refactorings to make code better readable.
- System tests adapted and modified.

SVN: 32547

SVN: 32473

SVN: 32448

SSDM-864: Further refactoring of IntensityRescaling and included classes. MixColors.mixImages: White point calculation removed because IntensityRescaling.computeLevels() will be used in ImageChannelsUtils.mergeChannels(). ImageChannelsUtils refactored and improved (bugs fixed). New system tests: Simple16BitImageDropboxTest and PlatonicPlateImageDropboxTest.

SVN: 32447

SSDM-864: ImageChannelsUtils and related classes refactored. Bugs fixed. Change in behavior: Single channel images are shown in their colors. MicroscopyImageDropboxTest and SimpleImageDropboxTest adapted and slightly extended.

SVN: 32444

SVN: 32412

SVN: 32411

SVN: 32409

SVN: 32400

SVN: 32395

- modify wstx-asl jar not to be found by SAXParserFactory.newInstance() method call (see http://docs.oracle.com/javase/7/docs/api/javax/xml/parsers/SAXParserFactory.html#newInstance())
- generate missing sha1 checksums for the new jars
- remove javax.xml.parsers.SAXParserFactory property from launch configs - it is no longer needed when wstx-asl is not found

SVN: 32299

SVN: 32261

SVN: 32129

SVN: 32088

SVN: 32086

SVN: 32035

SVN: 32034

SVN: 31504

SWE-22 / SSDM-16: Launch configurations for generic/screening/proteomics openBIS prepared/compiled with gradle

SVN: 31269

SWE-22 / SSDM-16: Gradle based GWT prepare & GWT compile for generic, screening and proteomics openBIS

SVN: 31245

SP-1090, SWE-22: GWT prepare/compile: remove cifex.jar from 'prepareGWT', add gwt-image-loader to compile dependencies of openbis, add prepare/compileGWT to rtd_phosphonetx, add gradle launch configs

SVN: 30317

SVN: 30316

BIS-371 SP-569 allow feature vectors to have longer names. done use NAME as custom domain name in psql

SVN: 28634

SVN: 28521

SVN: 27302

SVN: 27065

SVN: 26592

SP-239, SWE-6: Add system property org.mortbay.util.FileResource.checkAliases=false to launch configurations. bug: delete symbolic links but do not follow symbolic links on deletion

SVN: 26472

MINOR : Dependency checking workaround for Improve performance of ScreeningPlateListReadOnlyPredicate.

SVN: 26171