hdfio2.h

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/*
 * Author: Steven Ludtke, 04/10/2003 (sludtke@bcm.edu)
 * Copyright (c) 2000-2006 Baylor College of Medicine
 * 
 * This software is issued under a joint BSD/GNU license. You may use the
 * source code in this file under either license. However, note that the
 * complete EMAN2 and SPARX software packages have some GPL dependencies,
 * so you are responsible for compliance with the licenses of these packages
 * if you opt to use BSD licensing. The warranty disclaimer below holds
 * in either instance.
 * 
 * This complete copyright notice must be included in any revised version of the
 * source code. Additional authorship citations may be added, but existing
 * author citations must be preserved.
 * 
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 * 
 * */
 
#ifndef eman__hdfio2_h__
#define eman__hdfio2_h__ 1
 
#ifdef USE_HDF5
 
#define H5_USE_16_API
 
#include "imageio.h"
 
#include <hdf5.h>
#undef __STDINT_H
#ifndef __STDC_LIMIT_MACROS
        #define __STDC_LIMIT_MACROS 1
#endif
#ifndef __STDC_LIMIT_MACROS
        #define __STDC_CONSTANT_MACROS 1
#endif
#include <vector>
 
using std::vector;
 
namespace EMAN
{
        class HdfIO2 : public ImageIO
        {
          public:
                explicit HdfIO2(const string & fname, IOMode rw_mode = READ_ONLY);
                ~HdfIO2();
 
                DEFINE_IMAGEIO_FUNC;
                static bool is_valid(const void *first_block);
 
                bool is_single_image_format() const
                {
                        return false;
                }
        
        /* If this version of init() returns -1, then we have an 
         * old-style HDF5 file 
         * 
         * @return 0 for new HDF5 file, -1 for old-style HDF5 file*/
                int init_test();
                        
                /* Return the number of images in this HDF file
                 * 
                 * @return the number of images in this file*/
                int get_nimg();
 
                int get_num_dataset();
                vector < int >get_image_indices();
 
                /* Write an attribute with specified name to a given open object.
                 * The attribute is opened and closed. returns 0 on success
                 *
                 * @param loc Object (dataset, group, or named datatype) id for this attibute to be attached to
                 * @param name name for this attibute
                 * @param obj value for this attribute
                 * @return 0 on success */
                int write_attr(hid_t loc, const char *name, EMObject obj);
 
                /* Read an already opened attribute and returns the results
                 * as an EMObject. The attribute is not closed.
                 *
                 * @param attr Identifier of an attribute to read
                 * @return attribute value as an EMObject */
                static EMObject read_attr(hid_t attr);
 
                // this one is only defined in classes that implement it
                int read_data_8bit(unsigned char *data, int image_index = 0, const Region * area = 0, bool is_3d = false, float minval = 0.0f, float maxval = 0.0f);
 
                hid_t get_fileid() const {return file;}
 
          private:
                hsize_t nx, ny, nz;
                bool is_exist;  //boolean to tell if the image (group) already exist(to be overwrite)
 
                hid_t file;
                hid_t group;
                hid_t accprop;
                hid_t simple_space;
                
                Dict meta_attr_dict;    //this is used for the meta attributes stored in /MDF/images
 
                /* Erases any existing attributes from the image group
                 * prior to writing a new header. For a new image there
                 * won't be any, so this should be harmless. 
                 * 
                 * @param image_index 
                 * @return 0 for success*/
                int erase_header(int image_index);
 
        // render_min and render_max
            float rendermin;
            float rendermax;
                int renderbits;
                int renderlevel; // compression level
        };
}
 
#endif
 
#endif