[ome-devel] Release of OME Files C++ 0.3.0
Manuel Stritt
manuel.stritt at actelion.com
Tue Feb 14 13:05:17 GMT 2017
Dear Roger,
short question regarding JPEG-XR compression. Do you see any chance for the
next future that OME-TIFF (it's reference implementation) supports JPEG-XR
compression?
Even if it doesn't support it - do you think it's feasible - maybe with an
external contribution?
I'm thinking about it because we'd like to store 16bit WSI images in a
standardized format...
Regards,
Manuel
OME Files C++ 0.3.0
> ===================
>
> OME Files is a reference implementation of the OME Data Model and
> OME-TIFF file format for the storage and interchange of biological
> imaging data and metadata. It provides support for:
>
> • the OME Data Model (model objects, metadata store, XSL transforms
> and XML validation)
> • OME-TIFF reading
> • OME-TIFF writing
>
> Changes in this release include:
>
> • updating the minimum C++ language standard to C++11 (from C++98)
> • adding support for TIFF compression
> • performance improvements for metadata reading and TIFF reading and
> writing
> • addition of the ome-model component, replacing bioformats' ome-xml
> (this is the data model specification and ome-xml library following
> decoupling from the Bio-Formats repository)
>
> Downloads
> ---------
>
> The software release is available at the OME Files C++ 0.3.0 download
> page (http://downloads.openmicroscopy.org/ome-files-cpp/0.3.0/). This
> page includes links to the individual repositories and source
> releases, as well as the documentation and binary builds of the
> collection for several common platforms, including Windows, Linux and
> MacOS X.
>
> Upgrading from 0.2.3
> --------------------
>
> The main change is the switch to C++11. No immediate source changes
> are strictly required; the compatibility headers will continue to work
> for now, however upgrading to the standard C++11 headers is highly
> recommended to avoid future breakage. Client code is free to use any
> C++11 features of their choosing. To update your code:
>
> • enable C++11 or later support for your compiler
> · MSVC users do not need to do anything (it doesn't have any
> special option)
> · GCC and Clang users need to add the "-std=c++11" or "-std=c++14"
> option (the most recent versions default to C++14 and don't need
> this)
> · CMake users can set CMAKE_CXX_STANDARD_REQUIRED=11 and
> CMAKE_CXX_STANDARD=14 to try C++14 and fall back to C++11 if
> C++14 is unavailable
> • replace <ome/compat/array.h> with <array> and use of
> ome::compat::array with std::array
> • replace <ome/compat/cstdint.h> with <cstdint>
> • replace <ome/compat/memory.h> with <memory> and use of
> ome::compat::shared_ptr with std::shared_ptr (likewise for related
> types and functions such as std::weak_ptr, std::make_shared and
> std::dynamic_pointer_cast)
> • replace <ome/compat/tuple.h> with <tuple> and use of
> ome::compat::tuple with std::tuple (likewise for related functions
> such as std::get)
> • the above compatibility headers, and their declared types in the
> ome::compat namespace still exist but are deprecated; they simply
> wrap the standard headers and types.
> • the deprecated headers will be removed for 0.4.0.
>
> Changes since ome-files-cpp 0.2.3
> ---------------------------------
>
> All components:
>
> • C++11 is now the minimum required language version, with C++14
> being used when available
> • enabled the use of a restricted number of C++11 features, including
> enum class, nullptr, initializer lists, range-based for loops and
> type traits
> • enabled the use of C++11 syntax changes including "<::" not being
> interpreted as a trigraph and ">>" being used to close nested
> templates instead of "> >"
> • additional features will be enabled in subsequent releases
> • Google Test (gtest) is no longer built separately in each source
> component; the latest gtest release now allows use as a
> conventional library
> • source releases are now made directly from git with "git archive";
> additional version metadata is no longer embedded in the source
> releases
>
> OME Common:
>
> • Boost MPL size limits are now set with MSVC only; they are no
> longer required for other compilers with C++11
> • <ome/compat/array.h>, <ome/compat/cstdint.h>, <ome/compat/memory.h>
> and <ome/compat/tuple.h> are now deprecated in favor of the
> standard headers; they wrap the standard headers for backward
> compatibility but will be removed in the next breaking release
>
> OME Model:
>
> The first release of the ome-model components (specification, xsd-fu
> and ome-xml) since decoupling from Bio-Formats.
>
> • sources use a Java maven source layout; this component is a dual
> language component building both C++ and Java libraries
> • specification OME-XML samples: Added ROI transform and mask samples
> • specification transforms: Corrected upgrade to preserve ROI
> transforms
> • AffineTransform: Initialized with the identity matrix when default
> constructed
> • migrated formats documentation from the ome-documentation
> repository, updated and integrated with cmake and maven builds
> • renamed toplevel project from ome-xml to ome-model; the library
> continues to be named ome-xml
>
> OME Files:
>
> • added support for TIFF compression, exposing all compression
> algorithms supported by libtiff. Deflate and LZW will work for all
> pixel types; JPEG support will be available if libtiff was compiled
> with support for libjpeg
> • OMETIFFReader now sets the interleaved property according to the
> TIFF PlanarConfiguration tag; previously it was set to false
> unconditionally
> • TIFF wrapper: Cache IFD offsets on reading; this speeds up reading
> by changing the complexity of indexed IFD access from O(n) to O(1)
> • OMETIFFWriter: Sets the interleaved property unconditionally, even
> when the samples per pixel count is 1; this is to ensure easy
> round-tripping of data between readers and writers using the same
> logical dimension ordering in the pixel buffer
> • all TIFF writers: Set a default strip size of 2^16 pixels, which is
> for example 64KiB for 8-bit greyscale data, or 192KiB for 8-bit RGB
> data; the previous default was to copy the Java behavior of one row
> per strip, which was much less efficient
>
> OME QtWidgets:
>
> • no changes
>
> Super-Build 0.3.0:
>
> • gtest: Build and install (into tool directory) like a regular
> package
> • renamed superbuild-install to stage
> • docs: Dropped PDF documentation; documented C++11 changes
> • added git-dir option to simplify building multiple repositories
> from git
> • Package changes:
> · boost 1.63: Updated package
> · ome-common 5.4.0: Updated package
> · ome-files 0.3.0: Updated package
> · ome-files-py: New experimental package (initial Python bindings
> for OME Files C++)
> · ome-model 5.5.0: New package (previously part of the Bio-Formats
> sources)
> · ome-qtwidgets 5.4.0: Updated package
> · png 1.6.28: Updated package
> · tiff 4.0.7: Updated package
> · zlib 1.2.10: Updated package
>
> Future changes
> --------------
>
> Upcoming improvements include:
>
> All components:
>
> • enabling of additional C++11 features following testing of compiler
> support and compatibility
> • further performance profiling and scalability improvements
>
> OME XML:
>
> • support for the use of custom annotations with the OME-XML data
> model API
> • this generalized annotation support will also be used for existing
> annotations including Modulo and OriginalMetadata
> • improved and more comprehensive OME-XML and OME-TIFF samples
> • Improved documentation and code samples
>
> OME Files:
>
> • improvements to automated integration testing of OME-TIFF files
>
> Super-Build:
>
> • further improvements for building on Windows, including initial
> VS2017 support
> • updating of the set of platforms binary builds are provided for
>
> You can find further information on which features will be included in
> upcoming releases via the Trello board for version 0.3.1
> (https://trello.com/b/nNwJHdpp/ome-files-0-3-1) and 0.4.0
> (https://trello.com/b/WFYWCvoV/ome-files-0-4-0) (note that these are a
> work in progress and are subject to change).
>
> Errata
> ------
>
> See the errata for this release
> (https://www.openmicroscopy.org/site/support/ome-files-cpp/
> ome-cmake-superbuild/manual/html/errata.html).
>
> Support
> -------
>
> For any problems or comments, please use the OME forums or mailing
> lists (http://www.openmicroscopy.org/site/community).
>
>
> Kind regards,
> Roger Leigh
>
> on behalf of the OME team
>
> --
> Dr Roger Leigh -- Open Microscopy Environment
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK Tel: (01382) 386364
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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>
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