SVN: 34809

SVN: 34804

SVN: 34797

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: 34338

SSDM-2054: "Finalizer stops counting time during maintenance": Introducing IPause and FileBasedPause. WaitingHelper extended to be pausable.

SVN: 34337

SVN: 34330

SVN: 34182

SVN: 34127

SVN: 34031

SSDM-1930: Introducing MonitoredIOStreamCopier with unit tests and use it in multi data set archiving.

SVN: 34030

SSDM-1794: Refactoring package structure of jython and jython27 in common. Removing some duplicated classes.

SVN: 33994

SSDM-1768: monitoring based on rsync progress output if --progress option added to property extra-rsync-params

SVN: 33966

SSDM-1768 ProcessExecutor, IPathCopier and RsyncCopier extended to allow to monitor stdout and stderr during processing.

SVN: 33962

SVN: 33835

SVN: 33824

SVN: 33353

SVN: 33190

SVN: 33107

SVN: 33074

SVN: 33072

SVN: 33068

SVN: 33065

SSDM-1290 - CKAN - publication webapp bugfixing - added caching of mesh terms in an http session - fix tests

SVN: 32987

SVN: 32600

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

SSDM-773: Handle 12-bit microscopy images correctly in order to allow useful user defined transformation.

SVN: 32471

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: MixColors: Log time needed for mixing. IntensityRescaling refactored in order to remove code duplications. New tests added to IntensityRecsalingTest.

SVN: 32443

Fixed a failing uniprot test (data returned by http://www.uniprot.org/uniprot/?query=accession:p12345&format=tab&columns=id,entry%20name,existence,genes,last-modified,length,sequence,reviewed,version has changed on 03.09.2014)

SVN: 32420

SVN: 32394

SVN: 32393

SVN: 32391

SSDM-802: Extending AbstractScreeningSystemTestCase with helper classes for checking reference images with images loaded from image download servlet.

SVN: 32390

SSDM-85: FastaUtilities with a method to determine whether a string is a sequence of nucleic acid codes or amino acid codes.

SVN: 31436

SVN: 29963

SVN: 29893

SVN: 29791

SVN: 29790

SVN: 29788