Add ADIOS Image class

CMakeLists.txt

@@ -9,6 +9,22 @@ set (CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
+# Is casacore built with ADIOS 2 support ? default is NO
+option(HAVE_ADIOS2 "casacore is built with ADIOS2 support" OFF)
+if (HAVE_ADIOS2)
+    message(STATUS "Casacore is built with ADIOS2 support")
+    add_definitions(-DCASACORE_HAS_ADIOS2)
+else()
+    message(STATUUS "Casacore is NOT built with ADIOS2 support")
+endif()
+
+option(HAVE_MPI "casacore is built with MPI support" OFF)
+if (HAVE_MPI)
+    message(STATUS "Casacore is built with MPI support")
+    add_definitions(-DHAVE_MPI)
+else()
+    message(STATUUS "Casacore is NOT built with MPI support")
+endif()
 
 # rpath setup for libraries
 

synthesis/CMakeLists.txt

@@ -158,6 +158,7 @@ set(synthesis_LIB_SRCS
 
 set(synthesis_PROGRAMS
     lwimager
+    tAdiosImage
 )
 
 
@@ -389,6 +390,8 @@ install (FILES
 Images/ImageFFT.h
 Images/ImageMetaData.h
 Images/ImagePolarimetry.h
+Images/ADIOSImage.h
+Images/ADIOSImage.tcc
 DESTINATION include/casarest/synthesis/Images COMPONENT casa_synthesis
 )
 

synthesis/Images/ADIOSImage.h

@@ -0,0 +1,195 @@
+#ifndef IMAGES_ADIOSIMAGE_H
+#define IMAGES_ADIOSIMAGE_H
+
+//#ifdef CASACORE_HAS_ADIOS2
+
+//# Includes
+#include <casacore/casa/aips.h>
+#include <casacore/images/Images/PagedImage.h>
+#include <casacore/images/Images/ImageInterface.h>
+#include <casacore/images/Images/ImageAttrHandlerCasa.h>
+#include <casacore/tables/Tables/Table.h>
+#include <casacore/casa/Utilities/DataType.h>
+#include <casacore/tables/Tables/TableRecord.h>
+#include <casacore/tables/DataMan/Adios2StMan.h>
+
+//# Forward Declarations
+#include <casacore/casa/iosfwd.h>
+
+// we need to be able to compile without MPI (although this class is not expected to be
+// useful in such circumstances)
+#ifdef HAVE_MPI
+
+#include <mpi.h>
+
+#else
+
+#ifdef MPI_COMM_SELF
+  #error "MPI_COMM_SELF appears to be defined without MPI available - this shouldn't have happened!"
+#endif
+typedef int MPI_Comm;
+// the following can be any number
+#define MPI_COMM_SELF ((MPI_Comm)0x44000001)
+#endif
+
+namespace casacore {
+
+/// @details this class is a subclass of the casacore ImageInterface. It uses
+///          casacore adios2 to read and write image cube from/to file. The 
+///          class utilises the Adios2StMan as a Data Manager and it has two
+///          columns named (1) "map" which stores the pixel value of the image cube
+///          and (2) "mask" that keeps the mask of the image. These column names are
+///          used as ADIOS variables. Also, this class does not support the retrival
+///          of the mask of the image cube because this operation can cause excessive
+///          memory usage on a compute node. However, the mask get/put operation per
+///          image plane is supported.
+template <class T> class ADIOSImage : public casacore::ImageInterface<T>
+{
+public:
+
+    /// @brief create adios image accessor
+    /// @param[in] mapShape of the image
+    /// @param[in] coordinateInfo coordinate of the image
+    /// @param[in] nameOfNewFile filenamee
+    /// @param[in] tolerance used for compression
+    /// @param[in] configname name of configuration file
+    /// @param[in] rowNumber number of rows
+    ADIOSImage(const casacore::TiledShape& mapShape,
+               const casacore::CoordinateSystem& coordinateInfo,
+               const casacore::String& nameOfNewFile,
+               float tolerance = 0.0,
+               casacore::String configname = "", 
+               casacore::uInt rowNumber = 0);
+
+    /// @brief create adios image accessor
+    /// @param[in] comms MPI communicator
+    /// @param[in] mapShape of the image
+    /// @param[in] coordinateInfo coordinate of the image
+    /// @param[in] nameOfNewFile filenamee
+    /// @param[in] tolerance used for compression
+    /// @param[in] configname name of configuration file
+    /// @param[in] rowNumber number of rows
+    ADIOSImage(MPI_Comm comms,
+               const casacore::TiledShape& mapShape,
+               const casacore::CoordinateSystem& coordinateInfo,
+               const casacore::String& nameOfNewFile,
+               float tolerance = 0.0,
+               casacore::String configname = "",
+               casacore::uInt rowNumber = 0);
+
+    /// @brief create adios image accessor
+    /// @param[in] filename name of the file to be created
+    /// @param[in] tolerance used for compression
+    /// @param[in] configname name of configuration file
+    /// @param[in] spec mask value
+    /// @param[in] rowNumber number of rows
+    explicit ADIOSImage(const casacore::String &filename,
+                        float tolerance = 0.0,
+                        casacore::String configname = "",
+                        casacore::uInt rowNumber = 0);
+
+    /// @brief create adios image accessor
+    /// @param[in] comms MPI communicator
+    /// @param[in] filename name of the file to be created
+    /// @param[in] tolerance used for compression
+    /// @param[in] configname name of configuration file
+    /// @param[in] spec mask value
+    /// @param[in] rowNumber number of rows
+    ADIOSImage(MPI_Comm comms,
+               const casacore::String &filename,
+               float tolerance = 0.0,
+               casacore::String configname = "",
+               casacore::uInt rowNumber = 0);
+
+    /// @brief copy constructor
+    /// @param[in] other an instance to copy from
+    ADIOSImage (const ADIOSImage<T>& other);
+
+    casacore::Table& table() { return itsTable; }
+
+    static casacore::String className()
+    { return "ADIOSImage"; }
+
+    /// @brief Create a table that contains an array of columns to be managed by Adios2StMan
+    /// @param[in] shape shape of the array/data
+    /// @param[in] rowNumber number of rows
+    /// @param[in] filename name of the file
+    void makeNewTable (const casacore::TiledShape& shape, casacore::uInt rowNumber, casacore::String filename);
+
+    ///@brief override base abstract methods
+    casacore::ImageInterface<T>* cloneII() const override;
+    casacore::String imageType() const override;
+    void resize (const casacore::TiledShape& newShape) override;
+    const casacore::LatticeRegion* getRegionPtr() const override;
+    casacore::Bool setImageInfo(const casacore::ImageInfo& info) override;
+    casacore::Bool setCoordinateInfo (const casacore::CoordinateSystem& coords);
+    casacore::IPosition shape() const;
+    ///@brief get a slice of the image cube
+    casacore::Bool doGetSlice (casacore::Array<T>& buffer, const casacore::Slicer& theSlice);
+    ///@brief get a slice of the mask.
+    casacore::Bool doGetMaskSlice (casacore::Array<bool>& buffer, const casacore::Slicer& theSlice);
+    ///@brief put a slice of data into the image cube
+    void doPutSlice (const casacore::Array<T>& sourceBuffer, const casacore::IPosition& where, 
+                     const casacore::IPosition& stride);
+    void doPutMaskSlice(const casacore::Array<bool> &mask, const casacore::IPosition& where,
+                        const casacore::IPosition& stride);
+    casacore::Bool setUnits (const casacore::Unit& newUnits) override;
+    casacore::String name(casacore::Bool stripPath=casacore::False) const override;
+
+    ///@brief override base virtual methods
+    casacore::Bool ok() const;
+    casacore::Bool setMiscInfo (const casacore::RecordInterface& newInfo) override;
+    casacore::Bool isPaged() const;
+
+    ///@brief reopen the table column
+    void reopenColumn();
+
+    // masking operation on the whole image cube is not supported
+    bool isMasked() const override { return false; }
+    bool hasPixelMask() const override { return false; }
+    virtual const Lattice<casacore::Bool>& pixelMask() const override;
+    virtual Lattice<casacore::Bool>& pixelMask() override;
+
+    static casacore::Table& getTable(void* imagePtr, casacore::Bool writable);
+// MV: the code seems to build file with the following methods declared private (as they were in the
+// PagedImage interface where it presumably was copied from). Unless there is a good reason not to, it
+// would be better to keep them private. I won't insist on further design improvements for code which 
+// goes into casarest/casacore.
+private:
+    //rewritten PagedImage private functions
+    // @see casacore documentation for more details
+    void attach_logtable();
+    void setTableType();
+    void restoreAll (const casacore::TableRecord& rec);
+    void restoreImageInfo (const casacore::TableRecord& rec);
+    void restoreUnits (const casacore::TableRecord& rec);
+    void restoreMiscInfo (const casacore::TableRecord& rec);
+
+    void reopenRW();
+
+    ///@brief tolerance used for compression
+    float itsTolerance;
+    casacore::ArrayColumn<T> itsDataColumn;
+    casacore::ArrayColumn<bool> itsMaskColumn;
+    casacore::Table itsTable;
+
+    const casacore::uInt itsRow;
+    casacore::String itsConfig;
+    // @brief MPI communicator the default MPI_COMM_SELF is assigned in the constructor (unless proper communicator is provided)
+    MPI_Comm itsIOComms;
+    int rank() const; 
+    void setup(const casacore::TiledShape& shape, casacore::uInt rowNumber, 
+               const casacore::String& filename, const casacore::CoordinateSystem& coordinateInfo);
+    void setup(const casacore::String& filename);
+};
+// The tcc include must be here and not after the namespace
+// otherwise the template definition in the tcc file must have 
+// askap::imageaccess::ADIOSImage<T>::blah(...) instead of
+// ADIOSImage<T>::blah(...)
+#include <synthesis/Images//ADIOSImage.tcc>
+}
+//#else
+//#error "Using ADIOSImage requires building casacore with ADIOS2 support. It also requires building casarest with -DHAVE_ADIOS2=YES"
+//#endif // CASACORE_HAS_ADIOS2
+
+#endif // IMAGES_ADIOSIMAGE_H