OMERO C++ language bindings

Using the Ice C++ language mapping from ZeroC, OMERO provides native access to your data from C++ code. CMake is used for building the C++ bindings.

Binaries are not provided, therefore it will be necessary for you to compile your own.

Prerequisites

The OMERO source code
A C++ compiler
- GCC is recommended for Linux and MacOS X
- Visual Studio or the Platform SDK for Windows
The ZeroC Ice libraries, headers and slice definitions
cmake
Google Test (optional; needed to build the unit and integration tests)

Note

Users of Visual Studio with Ice 3.6 will encounter this error while building OmeroCpp: LINK : fatal error LNK1189: library limit of 65535 objects exceeded and will be unable to build OMERO C++ language bindings for Windows as a result of a 16-bit limitation in the Windows PE-COFF executable format used for DLLs, even on 64-bit systems. It is hoped that Ice 3.7 will resolve the problem since it generates far fewer symbols than 3.6.

Restrictions

If you are restricted to a specific version of GCC or Ice, you may need to obtain or build a compatible version of Ice or GCC, respectively.

Preparing to build

Begin by following the instructions under Installing OMERO from source to acquire the source code. Be sure that the git branch you are using matches the version of your server!

The location of your Ice installation should be automatically detected if installed into a standard location. If this is not the case, set the location of your Ice installation using the ICE_HOME environment variable or the cmake -DIce_HOME or cmake -DIce_SLICE_DIR cmake options for your Ice installation (see below). Some possible locations for the 3.6.5 version of Ice follow. Note these are just examples; you need to adjust them for the Ice installation path and version in use on your system.

Ice built from source and installed into /opt:
```
export ICE_HOME=/opt/Ice-3.6.5
```
Ice installed on Linux using RPM packages:
```
export ICE_HOME=/usr/share/Ice-3.6.5
```

MacOS X with homebrew:

export ICE_HOME=/usr/local/Cellar/ice/3.6.5

Windows using Visual Studio:

set ICE_HOME=C:\Program Files (x86)\ZeroC\Ice-3.6.5

Note

If the Ice headers and libraries are not automatically discovered, these will need to be specified using appropriate cmake options (see below).

Building the library

The shared library and examples are always built by default. The unit and integration tests are built if Google test (gtest) is detected.

On Linux, Unix or MacOS X with make:

export GTEST_ROOT=/path/to/gtest
mkdir omero-build
cd omero-build
cmake [-Dtest=(TRUE|FALSE)] [cmake options] /path/to/openmicroscopy
make

For example:

cmake "-DCMAKE_CXX_FLAGS=$CMAKE_CXX_FLAGS" \
"-DCMAKE_EXE_LINKER_FLAGS=$CMAKE_LD_FLAGS" \
"-DCMAKE_MODULE_LINKER_FLAGS=$CMAKE_LD_FLAGS" \
"-DCMAKE_SHARED_LINKER_FLAGS=$CMAKE_LD_FLAGS" \
-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON /path/to/openmicroscopy
make -j8

If you would like to build the C++ tests, run the above with the GTEST_ROOT environment variable set.

Note

When cmake is run, it will run ./build.py build-default in the openmicroscopy source tree to generate some of the C++ and Ice sources. If you have previously done a build by running ./build.py, this step will be skipped. However, if you have recently switched branches without cleaning the source tree, please run ./build.py clean in the source tree to clean up all the generated files prior to running cmake.

If the build fails with errors such as

/usr/include/Ice/ProxyHandle.h:176:13: error: ‘upCast’ was not declared in this scope,
and no declarations were found by argument-dependent lookup at the point of
instantiation

this is caused by the Ice headers being buggy, and newer versions of GCC rejecting the invalid code. To compile in this situation, add -fpermissive to CXXFLAGS to allow the invalid code to be accepted, but do note that this may also mask other problems so should not be used unless strictly needed.

cmake build configuration

cmake supports configuration of the build using many different environment variables and options; for a full list, see the cmake reference documentation. The following environment variables are commonly needed:

CMAKE_INCLUDE_PATH

Directories to be searched for include files, for example

/opt/Ice-3.6.5/include

A : or ; separator character is used to separate directories, depending on the platform. Note these are used only for feature tests, not for passing to the compiler when building, for which CMAKE_CXX_FLAGS is needed.

CMAKE_LIBRARY_PATH

Directories to be searched for libraries, for example

/opt/Ice-3.6.5/lib

Directories are separated by : or ; as with CMAKE_INCLUDE_PATH. Note these are used only for feature tests and finding libraries, not for passing to the linker when building, for which CMAKE_*_LINKER_FLAGS is needed.

CXX

C++ compiler executable. Useful with ccache.

CXXFLAGS

C++ compiler flags. Use of CMAKE_CXX_FLAGS is preferred.

ICE_HOME

The location of the Ice installation. If this is not sufficient to discover the correct binary and library directories, they may otherwise be manually specified with the options below. Likewise for the include and slice directories. This may also be set as a cmake cache variable (see below).

VERBOSE

If set to 1, show the actual build commands rather than the pretty “Compiling XYZ…” statements.

In addition, cmake options may be defined directly when running cmake. Commonly needed options include:

-DCMAKE_PREFIX_PATH: Search this location when searching for programs, headers and libraries. Use to search /usr/local or /opt/Ice, for example. More specific search locations may be specified using cmake -DCMAKE_INCLUDE_PATH, cmake -DCMAKE_LIBRARY_PATH and cmake -DCMAKE_PROGRAM_PATH separately, if required.

-DCMAKE_INCLUDE_PATH: Search this location when searching for headers. Use to include /usr/local/include or /opt/Ice/include, for example.

-DCMAKE_LIBRARY_PATH: Search this location when searching for libraries. Use to include /usr/local/lib or /opt/Ice/lib, for example.

-DCMAKE_PROGRAM_PATH: Search this location when searching for programs. Use to include /usr/local/bin or /opt/Ice/bin, for example.

-DCMAKE_CXX_FLAGS: C++ compiler flags. Use to set any additional linker flags desired.

-DCMAKE_EXE_LINKER_FLAGS: Executable linker flags. Use to set any additional linker flags desired.

-DCMAKE_MODULE_LINKER_FLAGS: Loadable module linker flags. Use to set any additional linker flags desired.

-DCMAKE_SHARED_LINKER_FLAGS: Shared library linker flags. Use to set any additional linker flags desired.

-DCMAKE_VERBOSE_MAKEFILE: Default to printing all commands executed by make. This may be overridden with the make VERBOSE variable.

-DIce_HOME: The location of the Ice installation. If this is not sufficient to discover the correct binary and library directories, they may otherwise be manually specified with the options below. Likewise for the include and slice directories.

-DIce_SLICE2XXX_EXECUTABLE: Specific location of individual Ice slice2xxx programs, e.g. Ice_SLICE2CPP_EXECUTABLE for slice2cpp or Ice_SLICE2JAVA_EXECUTABLE for slice2java. These are typically found in ${ICE_HOME}/bin or on the default PATH. These will not normally require setting.

-DIce_INCLUDE_DIR: Location of Ice headers. This is typically ${ICE_HOME}/include or on the default include search path. This will not normally require setting.

-DIce_SLICE_DIR: Location of Ice slice interface definitions. This is typically ${ICE_HOME}/slice. Use for installations where cmake -DIce_HOME does not contain slice or situations where you wish to build without setting cmake -DIce_HOME. Note that when building using build.py, rather than building directly with cmake, the SLICEPATH environment variable should be used instead (the ant build can’t use the cmake variables since it only runs cmake after a full build of the Java server).

-DIce_<C>_LIBRARIES: Specific libraries for Ice component <C>, where <C> is the uppercased name of the Ice component, e.g. ICE for the Ice component, ICEUTIL for the IceUtil component or GLACIER2 for the Glacier2 component. These libraries are typically found in ${ICE_HOME}/lib or on the default library search path. These will not normally require setting.

-DIce_DEBUG: Set to ON to print detailed diagnostics about the detected Ice installation. Use if there are any problems finding Ice.

cmake offers many additional options. Please refer to the documentation for further details, in particular to the variables which change the behavior of the build.

Visual Studio configuration

Warning

OMERO.cpp will not currently build on Windows due to exceeding DLL symbol limits on this platform, leading to a failure when linking the DLL. It is hoped that this platform limitation can be worked around in a future OMERO release.

cmake has full support for Visual Studio. Use the cmake -G option to set the generator for your Visual Studio version, with a Win64 suffix for an x64 build. The correct Ice programs and libraries for your Ice installation should be automatically discovered.

cmake -G "Visual Studio 11 Win64" [cmake options] /path/to/openmicroscopy

This is for a 64-bit Visual Studio 2012 build. Modify appropriately for other versions and compilers. Running

cmake --help

will list the available generators for your platform (without the Win64 suffix).

Once cmake has finished running, the generated project and solution files may be then opened in Visual Studio, or built directly using the msbuild command-line tool (make sure that the Visual Studio command prompt matches the generator chosen) or by running:

cmake --build .

As for the Unix build, above, it is also possible to build on Windows using build.py or ant, providing that you configure the generator appropriately using the correct cmake options. However, this will not work for all generators reliably, and the Windows shell quoting makes passing nested quotes to ant quite tricky, so running cmake by hand is recommended.

Note

It may be necessary to specify /Zm1000 as an additional compiler setting.

Installing the library

If using make, run:

make [DESTDIR=/path/to/staging/directory] install

If using another build system, please invoke the equivalent install target for that system.

Using the library

To use OMERO C++ language bindings it is necessary to point your compiler and linker at the mentioned directories above. A simple GNU make Makefile might look like this:

#
# MAKEFILE:
#
# Where the OMERO distribution was installed
OMERO_DIST ?= /opt/omero

# Where the Ice lib/ and include/ directories are to be found
ICE_HOME ?= /usr/share/Ice

INCLUDES=-I$(OMERO_DIST)/include -I$(ICE_HOME)/include 

LIBS = -L$(OMERO_DIST)/lib -L$(ICE_HOME)/lib -L$(ICE_HOME)/lib64 \
       -lIce -lIceUtil -lGlacier2 -lomero-client

LIBPATH = $(LD_LIBRARY_PATH):$(ICE_HOME)/lib:$(ICE_HOME)/lib64:$(OMERO_DIST)/lib

.PHONY: clean run

yourcode.o: yourcode.cpp
	$(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDES)

yourcode: yourcode.o
	$(CXX) -o $@ $^ $(LIBS)

run:  yourcode
	LD_LIBRARY_PATH="$(LIBPATH)" ./yourcode --Ice.Config=../etc/ice.config

clean:
	rm -f yourcode *.o *~ core

A trivial example: `yourcode.cpp`

A simple example might look something like the following:

//
// yourcode.cpp:
//

// Domain
#include <omero/client.h>
#include <omero/api/IAdmin.h>
// Std
#include <iostream>
#include <cassert>
#include <vector>
#include <time.h>
#include <map>

using namespace std;

/*
 * Pass "--Ice.Config=your_config_file" to the executable, or
 * set the ICE_CONFIG environment variable.
 */
int main(int argc, char* argv[])
{
    omero::client_ptr omero = new omero::client(argc, argv);
    omero::api::ServiceFactoryPrx sf = omero->createSession();
    sf->closeOnDestroy();

    // IAdmin is responsible for all user/group creation, password changing, etc.
    omero::api::IAdminPrx  admin  = sf->getAdminService();

    // Who you are logged in as.
    cout << admin->getEventContext()->userName << endl;

    // These two services are used for database access
    omero::api::IQueryPrx  query  = sf->getQueryService();
    omero::api::IUpdatePrx update = sf->getUpdateService();

    return 0;
}

This code does not do much. It creates a server session, loads a few services, and prints the user’s name. For serious examples, see Working with OMERO.

Compiling and running your code

To compile and run yourcode, download the two files above (Makefile and yourcode.cpp) and then in a shell:

make OMERO_DIST=dist yourcode
LD_LIBRARY_PATH=dist/lib ./yourcode --Ice.Config=dist/etc/ice.config

where you have edited dist/etc/ice.config to contain the values:

omero.host=localhost
omero.user=your_name
omero.pass=your_password

Alternatively, you can pass these on the command-line:

LD_LIBRARY_PATH=dist/lib ./yourcode omero.host=localhost --omero.user=foo --omero.pass=bar

Note

This example explains how to run on Linux only. For doing the same on MacOS X, change all instances of LD_LIBRARY_PATH to DYLD_LIBRARY_PATH.

Further information

For the details behind writing, configuring, and executing a client, please see Working with OMERO.

OMERO C++ language bindings

Prerequisites

Restrictions

Preparing to build

Building the library

cmake build configuration

Visual Studio configuration

Installing the library

Using the library

A trivial example: yourcode.cpp

Compiling and running your code

Further information

A trivial example: `yourcode.cpp`