00001 00005 /* 00006 * Author: Steven Ludtke, 04/10/2003 (sludtke@bcm.edu) 00007 * Copyright (c) 2000-2006 Baylor College of Medicine 00008 * 00009 * This software is issued under a joint BSD/GNU license. You may use the 00010 * source code in this file under either license. However, note that the 00011 * complete EMAN2 and SPARX software packages have some GPL dependencies, 00012 * so you are responsible for compliance with the licenses of these packages 00013 * if you opt to use BSD licensing. The warranty disclaimer below holds 00014 * in either instance. 00015 * 00016 * This complete copyright notice must be included in any revised version of the 00017 * source code. Additional authorship citations may be added, but existing 00018 * author citations must be preserved. 00019 * 00020 * This program is free software; you can redistribute it and/or modify 00021 * it under the terms of the GNU General Public License as published by 00022 * the Free Software Foundation; either version 2 of the License, or 00023 * (at your option) any later version. 00024 * 00025 * This program is distributed in the hope that it will be useful, 00026 * but WITHOUT ANY WARRANTY; without even the implied warranty of 00027 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00028 * GNU General Public License for more details. 00029 * 00030 * You should have received a copy of the GNU General Public License 00031 * along with this program; if not, write to the Free Software 00032 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 00033 * 00034 * */ 00035 00036 #ifndef eman__hdfio2_h__ 00037 #define eman__hdfio2_h__ 1 00038 00039 #ifdef EM_HDF5 00040 00041 #define H5_USE_16_API 00042 00043 #include "imageio.h" 00044 00045 #include <hdf5.h> 00046 #include <vector> 00047 00048 using std::vector; 00049 00050 namespace EMAN 00051 { 00064 class HdfIO2:public ImageIO 00065 { 00066 public: 00067 explicit HdfIO2(const string & filename, IOMode rw_mode = READ_ONLY); 00068 ~HdfIO2(); 00069 00070 DEFINE_IMAGEIO_FUNC; 00071 static bool is_valid(const void *first_block); 00072 00073 bool is_single_image_format() const 00074 { 00075 return false; 00076 } 00077 00078 /* If this version of init() returns -1, then we have an 00079 * old-style HDF5 file 00080 * 00081 * @return 0 for new HDF5 file, -1 for old-style HDF5 file*/ 00082 int init_test(); 00083 00084 /* Return the number of images in this HDF file 00085 * 00086 * @return the number of images in this file*/ 00087 int get_nimg(); 00088 00089 int get_num_dataset(); 00090 vector < int >get_image_indices(); 00091 00092 /* Write an attribute with specified name to a given open object. 00093 * The attribute is opened and closed. returns 0 on success 00094 * 00095 * @param loc Object (dataset, group, or named datatype) id for this attibute to be attached to 00096 * @param name name for this attibute 00097 * @param obj value for this attribute 00098 * @return 0 on success */ 00099 int write_attr(hid_t loc, const char *name, EMObject obj); 00100 00101 /* Read an already opened attribute and returns the results 00102 * as an EMObject. The attribute is not closed. 00103 * 00104 * @param attr Identifier of an attribute to read 00105 * @return attribute value as an EMObject */ 00106 EMObject read_attr(hid_t attr); 00107 00110 hid_t get_fileid() const {return file;} 00111 00112 private: 00113 hsize_t nx, ny, nz; 00114 bool is_exist; //boolean to tell if the image (group) already exist(to be overwrite) 00115 00116 hid_t file; 00117 hid_t group; 00118 hid_t accprop; 00119 hid_t simple_space; 00120 string filename; 00121 IOMode rw_mode; 00122 bool initialized; 00123 00124 Dict meta_attr_dict; //this is used for the meta attributes stored in /MDF/images 00125 00126 /* Erases any existing attributes from the image group 00127 * prior to writing a new header. For a new image there 00128 * won't be any, so this should be harmless. 00129 * 00130 * @param image_index 00131 * @return 0 for success*/ 00132 int erase_header(int image_index); 00133 00134 // render_min and render_max 00135 float rendermin; 00136 float rendermax; 00137 }; 00138 } 00139 00140 #endif 00141 00142 #endif