libnexus0-dev 4.3.2-svn1919-1 / usr / include / nexus / NeXusFile.hpp

#ifndef NEXUSFILE_HPP
#define NEXUSFILE_HPP 1

#include <map>
#include <string>
#include <utility>
#include <vector>
#include "napi.h"

#ifdef _WIN32

#ifndef _MSC_VER 
#  define NXDLL_EXPORT
#else
#  if IN_NEXUS_CPP_LIBRARY
#    define NXDLL_EXPORT __declspec(dllexport)
#  else
#    define NXDLL_EXPORT __declspec(dllimport)
#  endif
#endif /* _MSC_VER */

#else /* _WIN32 */
#  define NXDLL_EXPORT 
#endif /* _WIN32 */

/**
 * \file NeXusFile.hpp Definition of the NeXus C++ API.
 * \defgroup cpp_types C++ Types
 * \defgroup cpp_core C++ Core
 * \ingroup cpp_main
 */

namespace NeXus {
  /**
   * The primitive types published by this API.
   * \li FLOAT32 float.
   * \li FLOAT64 double
   * \li INT8 int8_t
   * \li UINT8 uint8_t
   * \li INT16 int16_t
   * \li UINT16 uint16_t
   * \li INT32 int32_t
   * \li UINT32 uint32_t
   * \li INT64 int8_t if available on the machine
   * \li UINT64 uint8_t if available on the machine
   * \ingroup cpp_types
   */
  enum NXnumtype {
    FLOAT32 = NX_FLOAT32,
    FLOAT64 = NX_FLOAT64,
    INT8 = NX_INT8,
    UINT8 = NX_UINT8,
    // BOOLEAN = NX_BOOLEAN, // NX_BOOLEAN is currently broken
    INT16 = NX_INT16,
    UINT16 = NX_UINT16,
    INT32 = NX_INT32,
    UINT32 = NX_UINT32,
    INT64 = NX_INT64,
    UINT64 = NX_UINT64,
    CHAR = NX_CHAR,
    BINARY = NX_BINARY
  };

  /**
   * The available compression types. These are all ignored in xml files.
   * \li NONE no compression
   * \li LZW Lossless Lempel Ziv Welch compression (recommended)
   * \li RLE Run length encoding (only HDF-4)
   * \li HUF Huffmann encoding (only HDF-4)
   * \ingroup cpp_types
   */
  enum NXcompression {
    CHUNK = NX_CHUNK,
    NONE = NX_COMP_NONE,
    LZW = NX_COMP_LZW,
    RLE = NX_COMP_RLE,
    HUF = NX_COMP_HUF
  };

  /**
   * Type definition for a type-keyed multimap
   */
  typedef std::multimap<std::string, std::string> TypeMap;

  /**
   * This structure holds the type and dimensions of a primative field/array.
   */
  struct Info{
    /** The primative type for the field. */
    NXnumtype type;
    /** The dimensions of the file. */
    std::vector<int64_t> dims;
  };

  /** Information about an attribute. */
  struct AttrInfo{
    /** The primative type for the attribute. */
    NXnumtype type;
    /** The length of the attribute. */
    unsigned length;
    /** The name of the attribute. */
    std::string name;
  };

  /**
   * The Object that allows access to the information in the file.
   * \ingroup cpp_core
   */
  class NXDLL_EXPORT File
  {
  private:
    /** The handle for the C-API. */
    NXhandle m_file_id;
    /** should be close handle on exit */
    bool m_close_handle;

  public:
    /**
     * \return A pair of the next entry available in a listing.
     */
    std::pair<std::string, std::string> getNextEntry();
    /**
     * \return Information about the next attribute.
     */
    AttrInfo getNextAttr();

  private:
    /**
     * This is a deprecated function.
     * \param com The compression type.
     */
    void compress(NXcompression comp);

    /**
     * Initialize the pending group search to start again.
     */
    void initGroupDir();

    /**
     * Initialize the pending attribute search to start again.
     */
    void initAttrDir();

    /**
     * Function to walk the file tree and fill in the TypeMap.
     *
     * \param path the current path in the file
     * \param class_name the current NX class name
     * \param tmap the typemap being constructed
     */
    void walkFileForTypeMap(const std::string path, const std::string class_name, TypeMap &tmap);

    /**
     * Function to append new path to current one.
     * \param currpath the current path to append to
     * \param subpath the path to append to the current path
     * \return the newly joined path
     */
    const std::string makeCurrentPath(const std::string currpath, const std::string subpath);

    /**
     * Function to consolidate the file opening code for the various constructors
     * \param filename The name of the file to open.
     * \param access How to access the file.
     */
    void initOpenFile(const std::string& filename, const NXaccess access = NXACC_READ);

  public:
    /**
     * Create a new File.
     *
     * \param filename The name of the file to open.
     * \param access How to access the file.
     */
    File(const std::string& filename, const NXaccess access = NXACC_READ);

    /**
     * Create a new File.
     *
     * \param filename The name of the file to open.
     * \param access How to access the file.
     */
    File(const char *filename, const NXaccess access = NXACC_READ);

    /**
     * Use an existing handle returned from NXopen()
     *
     * \param handle Handle to connect to
     * \param close_handle Should the handle be closed on destruction
     */
    File(NXhandle handle, bool close_handle = false);

    /** Destructor. This does close the file. */
    ~File();

    /** Close the file before the constructor is called. */
    void close();

    /** Flush the file. */
    void flush();

    template<typename NumT>
    void malloc(NumT*& data, const Info& info);

    template<typename NumT>
    void free(NumT*& data);

    /**
     * Create a new group.
     *
     * \param name The name of the group to create (i.e. "entry").
     * \param class_name The type of group to create (i.e. "NXentry").
     * \param open_group Whether or not to automatically open the group after 
     * creating it.
     */
    void makeGroup(const std::string& name, const std::string& class_name,
                   bool open_group = false);

    /**
     * Open an existing group.
     *
     * \param name The name of the group to create (i.e. "entry").
     * \param class_name The type of group to create (i.e. "NXentry").
     */
    void openGroup(const std::string& name, const std::string& class_name);

    /**
     * Open the NeXus object with the path specified.
     *
     * \param path A unix like path string to a group or field. The path 
     * string is a list of group names and SDS names separated with a slash,
     * '/' (i.e. "/entry/sample/name").
     */
    void openPath(const std::string& path);

    /**
     * Open the group in which the NeXus object with the specified path exists.
     *
     * \param path A unix like path string to a group or field. The path 
     * string is a list of group names and SDS names separated with a slash,
     * '/' (i.e. "/entry/sample/name").
     */
    void openGroupPath(const std::string& path);
    /**
     * Get the path into the current file
     * \return A unix like path string pointing to the current 
     *         position in the file
     */
    std::string  getPath();

    /**
     * Close the currently open group.
     */
    void closeGroup();

    /**
     * \copydoc NeXus::File::makeData(const std::string&, NXnumtype,
     *                              const std::vector<int64_t>&, bool);
     */
    void makeData(const std::string& name, NXnumtype type,
                  const std::vector<int>& dims, bool open_data = false);

    /**
     * Create a data field with the specified information.
     *
     * \param name The name of the field to create (i.e. "distance").
     * \param type The primative type of the field (i.e. "NeXus::FLOAT32").
     * \param dims The dimensions of the field.
     * \param open_data Whether or not to open the data after creating it.
     */
    void makeData(const std::string& name, NXnumtype type,
                  const std::vector<int64_t>& dims, bool open_data = false);

    /**
     * Create a 1D data field with the specified information.
     *
     * \param name The name of the field to create (i.e. "distance").
     * \param type The primative type of the field (i.e. "NeXus::FLOAT32").
     * \param length The number of elements in the field.
     * \param open_data Whether or not to open the data after creating it.
     */
    template <typename NumT>
    void makeData(const std::string& name, const NXnumtype type,
                  const NumT length, bool open_data = false);

    /**
     * Create a 1D data field, insert the data, and close the data.
     *
     * \param name The name of the field to create.
     * \param value The string to put into the file.
     */
    void writeData(const std::string& name, const std::string& value);

    /**
     * Create a 1D data field, insert the data, and close the data.
     *
     * \param name The name of the field to create.
     * \param value The string to put into the file.
     */
    void writeData(const std::string& name, const char* value);

    /**
     * Create a 1D data field, insert the data, and close the data.
     *
     * \tparam NumT numeric data type of \a value
     * \param name The name of the field to create.
     * \param value The vector to put into the file.
     */
    template <typename NumT>
    void writeData(const std::string& name, const std::vector<NumT>& value);

    /**
     * Create a 1D data field, insert the data, and close the data.
     *
     * \tparam NumT numeric data type of \a value
     * \param name The name of the field to create.
     * \param value The value to put into the file.
     */
    template <typename NumT>
    void writeData(const std::string& name, const NumT& value);

    /**
     * Create a n-dimension data field, insert the data, and close the data.
     *
     * \param name The name of the field to create.
     * \param value The data to put into the file.
     * \param dims The dimensions of the data.
     * \tparam NumT numeric data type of \a value
     */
    template <typename NumT>
    void writeData(const std::string& name, const std::vector<NumT>& value,
                   const std::vector<int>& dims);

	/**
     * Create a n-dimension data field, insert the data, and close the data.
     *
     * \param name The name of the field to create.
     * \param value The data to put into the file.
     * \param dims The dimensions of the data.
     * \tparam NumT numeric data type of \a value
     */
    template <typename NumT>
    void writeData(const std::string& name, const std::vector<NumT>& value,
                   const std::vector<int64_t>& dims);

    /** Create a 1D data field with an unlimited dimension, insert the data, and close the data.
     *
     * \tparam NumT numeric data type of \a value
     * \param name :: The name of the field to create.
     * \param value :: The vector to put into the file.
     */
    template <typename NumT>
    void writeExtendibleData(const std::string& name, std::vector<NumT>& value);

    /** Create a 1D data field with an unlimited dimension, insert the data, and close the data.
     *
     * \tparam NumT numeric data type of \a value
     * \param name :: The name of the field to create.
     * \param value :: The vector to put into the file.
     * \param chunkSize :: chunk size to use when writing
     */
    template <typename NumT>
    void writeExtendibleData(const std::string& name, std::vector<NumT>& value, const int64_t chunk);

    /** Create a 1D data field with an unlimited dimension, insert the data, and close the data.
     *
     * \tparam NumT numeric data type of \a value
     * \param name :: The name of the field to create.
     * \param value :: The vector to put into the file.
     * \param dims :: The dimensions of the data.
     * \param chunk :: chunk size to use when writing
     */
    template <typename NumT>
    void writeExtendibleData(const std::string& name, std::vector<NumT>& value,
                             std::vector<int64_t>& dims, std::vector<int64_t> & chunk);


    /** Updates the data written into an already-created
     * data vector. If the data was created as extendible, it will be resized.
     *
     * \tparam NumT numeric data type of \a value
     * \param name :: The name of the field to create.
     * \param value :: The vector to put into the file.
     */
    template <typename NumT>
    void writeUpdatedData(const std::string& name, std::vector<NumT>& value);

    /** Updates the data written into an already-created
     * data vector. If the data was created as extendible, it will be resized.
     *
     * \tparam NumT numeric data type of \a value
     * \param name :: The name of the field to create.
     * \param value :: The vector to put into the file.
     * \param dims :: The dimensions of the data.
     */
    template <typename NumT>
    void writeUpdatedData(const std::string& name, std::vector<NumT>& value,
                          std::vector<int64_t>& dims);

    /**
     * \copydoc makeCompData(const std::string&, const NXnumtype,
     *                       const std::vector<int64_t>&, const NXcompression,
     *                       const std::vector<int64_t>&, bool)
     */
    void makeCompData(const std::string& name, const NXnumtype type,
                      const std::vector<int>& dims, const NXcompression comp,
                      const std::vector<int>& bufsize, bool open_data = false);

    /**
     * Create a field with compression.
     *
     * \param name The name of the data to create.
     * \param type The primitive type for the data.
     * \param dims The dimensions of the data.
     * \param comp The compression algorithm to use.
     * \param bufsize The size of the compression buffer to use.
     * \param open_data Whether or not to open the data after creating it.
     */
    void makeCompData(const std::string& name, const NXnumtype type,
                      const std::vector<int64_t>& dims, const NXcompression comp,
                      const std::vector<int64_t>& bufsize, bool open_data = false);

    /**
     * \copydoc writeCompData(const std::string & name,
     *                        const std::vector<NumT> & value,
     *                        const std::vector<int64_t> & dims, const NXcompression comp,
     *                        const std::vector<int64_t> & bufsize)
     */
    template <typename NumT>
    void writeCompData(const std::string & name,
                       const std::vector<NumT> & value,
                       const std::vector<int> & dims, const NXcompression comp,
                       const std::vector<int> & bufsize);

    /**
     * Create a compressed data, insert the data, and close it.
     *
     * \param name The name of the data to create.
     * \param value The vector to put into the file.
     * \param dims The dimensions of the data.
     * \param comp The compression algorithm to use.
     * \param bufsize The size of the compression buffer to use.
     * \tparam NumT numeric data type of \a value
     */
    template <typename NumT>
    void writeCompData(const std::string & name,
                       const std::vector<NumT> & value,
                       const std::vector<int64_t> & dims, const NXcompression comp,
                       const std::vector<int64_t> & bufsize);

    /**
     * \param name The name of the data to open.
     */
    void openData(const std::string& name);

    /**
     * Close the currently open data.
     */
    void closeData();

    /**
     * \param data The data to put in the file.
     */
    void putData(const void* data);

    /**
     * \param data The data to put in the file.
     * \tparam NumT numeric data type of \a data
     */
    template <typename NumT>
    void putData(const std::vector<NumT>& data);

    /**
     * Put the supplied data as an attribute into the currently open data.
     *
     * \param info Description of the attribute to add.
     * \param data The attribute value.
     */
    void putAttr(const AttrInfo& info, const void* data);

    /**
     * Put the supplied data as an attribute into the currently open data.
     *
     * \param name Name of the attribute to add.
     * \param value The attribute value.
     * \tparam NumT numeric data type of \a value
     */
    template <typename NumT>
    void putAttr(const std::string& name, const NumT value);

    /**
     * Put a string as an attribute in the file.
     *
     * \param name Name of the attribute to add.
     * \param value The attribute value.
     */
    void putAttr(const char* name, const char* value);

    /**
     * Put a string as an attribute in the file.
     *
     * \param name Name of the attribute to add.
     * \param value The attribute value.
     */
    void putAttr(const std::string& name, const std::string value);

    /**
     * \copydoc NeXus::File::putSlab(void* data, std::vector<int64_t>& start,
     *                                std::vector<int64_t>& size)
     */
    void putSlab(void* data, std::vector<int>& start,
                 std::vector<int>& size);

    /**
     * Insert an array as part of a data in the final file.
     *
     * \param data The array to put in the file.
     * \param start The starting index to insert the data.
     * \param size The size of the array to put in the file.
     */
    void putSlab(void* data, std::vector<int64_t>& start,
                 std::vector<int64_t>& size);

    /**
     * \copydoc NeXus::File::putSlab(std::vector<NumT>& data, std::vector<int64_t>&,
     *                               std::vector<int64_t>&)
     */
    template <typename NumT>
    void putSlab(std::vector<NumT>& data, std::vector<int>& start,
                 std::vector<int>& size);

    /**
     * Insert an array as part of a data in the final file.
     *
     * \param data The array to put in the file.
     * \param start The starting index to insert the data.
     * \param size The size of the array to put in the file.
     * \tparam NumT numeric data type of \a data
     */
    template <typename NumT>
    void putSlab(std::vector<NumT>& data, std::vector<int64_t>& start,
                 std::vector<int64_t>& size);

    /**
     * \copydoc NeXus::File::putSlab(std::vector<NumT>&, int64_t, int64_t)
     */
    template <typename NumT>
    void putSlab(std::vector<NumT>& data, int start, int size);

    /**
     * Insert a number as part of a data in the final file.
     *
     * \param data The array to put in the file.
     * \param start The starting index to insert the data.
     * \param size The size of the array to put in the file.
     * \tparam NumT numeric data type of \a data
     */
    template <typename NumT>
    void putSlab(std::vector<NumT>& data, int64_t start, int64_t size);

    /**
     * \return The id of the data used for linking.
     */
    NXlink getDataID();

    /**
     * Create a link in the current location to the supplied id.
     *
     * \param link The object (group or data) in the file to link to.
     */
    void makeLink(NXlink& link);

    /**
     * Create a link with a new name.
     *
     * \param name The name of this copy of the link.
     * \param link The object (group or data) in the file to link to.
     */
    void makeNamedLink(const std::string& name, NXlink& link);

    /**
     * Open the original copy of this group or data as declared by the
     * "target" attribute.
     */
    void openSourceGroup();

    /**
     * Put the currently open data in the supplied pointer.
     *
     * \param data The pointer to copy the data to.
     */
    void getData(void* data);

    /**
     * Allocate memory and return the data as a vector. Since this
     * does call "new vector<NumT>" the caller is responsible for
     * calling "delete".
     * \tparam NumT numeric data type of result
     *
     * \return The data as a vector.
     */
    template <typename NumT>
    std::vector<NumT> * getData();

    /**
     * Put data into the supplied vector. The vector does not need to
     * be the correct size, just the correct type as it is resized to
     * the appropriate value.
     *
     * \param data Where to put the data.
     * \tparam NumT numeric data type of \a data
     */
    template <typename NumT>
    void getData(std::vector<NumT>& data);

    /** Get data and coerce into an int vector.
     *
     * @throw Exception if the data is actually a float or
     *    another type that cannot be coerced to an int.
     * @param data :: vector to be filled.
     */
    void getDataCoerce(std::vector<int> &data);

    /** Get data and coerce into a vector of doubles.
     *
     * @throw Exception if the data cannot be coerced to a double.
     * @param data :: vector to be filled.
     */
    void getDataCoerce(std::vector<double> &data);

    /** Return true if the data opened is of one of the
     * int data types, 32 bits or less.
     */
    bool isDataInt();

    /** Put data into the supplied vector. The vector does not need to
     * be the correct size, just the correct type as it is resized to
     * the appropriate value.
     *
     * The named data object is opened, loaded, then closed.
     *
     * @param dataName :: name of the data to open.
     * @param data :: Where to put the data.
     * \tparam NumT numeric data type of \a data
     */
    template <typename NumT>
    void readData(const std::string & dataName, std::vector<NumT>& data);

    /** Put data into the supplied value.
     *
     * The named data object is opened, loaded, then closed.
     *
     * \param dataName :: name of the data to open.
     * \param data :: Where to put the data.
     * \tparam NumT numeric data type of \a data
     */
    template <typename NumT>
    void readData(const std::string & dataName, NumT & data);

    /** Put data into the supplied string. The vector does not need to
     * be the correct size, just the correct type as it is resized to
     * the appropriate value.
     *
     * The named data object is opened, loaded, then closed.
     *
     * @param dataName :: name of the data to open.
     * @param data :: Where to put the data.
     */
    void readData(const std::string & dataName, std::string & data);

    /**
     * \return String data from the file.
     */
    std::string getStrData();

    /**
     * \return The Info structure that describes the currently open data.
     */
    Info getInfo();

    /**
     * Return the entries available in the current place in the file.
     */
    std::map<std::string, std::string> getEntries();

    /** Return the entries available in the current place in the file,
     * but avoids the map copy of getEntries().
     *
     * \param result The map that will be filled with the entries
     */
    void getEntries(std::map<std::string, std::string> & result);

    /**
     * \copydoc NeXus::File::getSlab(void*, const std::vector<int64_t>&,
     *                               const std::vector<int64_t>&)
     */
    void getSlab(void* data, const std::vector<int>& start,
                 const std::vector<int>& size);

    /**
     * Get a section of data from the file.
     *
     * \param data The pointer to insert that data into.
     * \param start The offset into the file's data block to start the read 
     * from.
     * \param size The size of the block to read from the file.
     */
    void getSlab(void* data, const std::vector<int64_t>& start,
                 const std::vector<int64_t>& size);

    /**
     * \return Information about all attributes on the data that is
     * currently open.
     */
    std::vector<AttrInfo> getAttrInfos();

    /**
     *  \return true if the current point in the file has the named attribute
     *  \param name the name of the attribute to look for.
     */
    bool hasAttr(const std::string & name);

    /**
     * Get the value of the attribute specified by the AttrInfo supplied.
     *
     * \param info Designation of which attribute to read.
     * \param data The pointer to put the attribute value in.
     * \param length The length of the attribute. If this is "-1" then the 
     * information in the supplied AttrInfo object will be used.
     */
    void getAttr(const AttrInfo& info, void* data, int length = -1);

    /**
     * Get the value of an attribute that is a scalar number.
     *
     * \param info Designation of which attribute to read.
     * \tparam NumT numeric data type of result
     *
     * \return The attribute value.
     */
    template <typename NumT>
    NumT getAttr(const AttrInfo& info);


    /**
     * Get the value of an attribute that is a scalar number.
     *
     * \param[in] name Name of attribute to read
     * \param[out] value The read attribute value.
     * \tparam NumT numeric data type of \a value
     */
    template <typename NumT>
        void getAttr(const std::string& name, NumT& value);


    /**
     * Get the value of a string attribute.
     *
     * \param info Which attribute to read.
     *
     * \return The value of the attribute.
     */
    std::string getStrAttr(const AttrInfo & info);

    /**
     * \return The id of the group used for linking.
     */
    NXlink getGroupID();

    /**
     * Determine whether or not two links refer to the same data or group.
     *
     * \param first The first link information to compare.
     * \param second The second link information to compare.
     *
     * \return True if the two point at the same data or group.
     */
    bool sameID(NXlink& first, NXlink& second);

    /**
     * Diagnostic print of the link information.
     *
     * \param link The link to print to stdout.
     */
    void printLink(NXlink & link);

    /**
     * Set the number format used for a particular type when using the
     * xml base. This is ignore in the other bases.
     *
     * \param type The primitive type to set the format for.
     * \param format The format to use.
     */
    void setNumberFormat(NXnumtype& type, const std::string& format);

    /**
     * Find out the name of the file this object is holding onto.
     *
     * \param buff_length The size of the buffer to use for reading the name.
     *
     * \return The name of the file.
     */
    std::string inquireFile(const int buff_length = NX_MAXPATHLEN);

    /**
     * Determine Whether or not a supplied group is external.
     *
     * \param name The name of the group to check.
     * \param type The type of the group to check.
     * \param buff_length The size of the buffer to use for reading the url.
     *
     * \return The url to the external group.
     */
    std::string isExternalGroup(const std::string& name,
                                const std::string& type,
                                const unsigned buff_length = NX_MAXNAMELEN);

    /**
     * Create a link to a group in an external file.
     *
     * \param name The name for the group in this file.
     * \param type The type for the group in this file.
     * \param url The url to the group in the external file.
     */
    void linkExternal(const std::string& name, const std::string& type,
                      const std::string& url);
    /**
     * This function checksi if we are in an open dataset
     * \returns true if we are currently in an open dataset else false
     */
    bool isDataSetOpen();

    /**
     * Create a multimap with the data types as keys and the associated paths as values.
     *
     * \return The multimap of the opened file.
     */
    TypeMap *getTypeMap();
  };

  /**
   * This function returns the NXnumtype given a concrete number.
   * \tparam NumT numeric data type of \a number to check
   */
   template <typename NumT>
     NXDLL_EXPORT NXnumtype getType(NumT number = NumT());


};

#include "NeXusStream.hpp"

#endif