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1 // Copyright (C) 2010, Guy Barrand. All rights 1 // Copyright (C) 2010, Guy Barrand. All rights reserved.
2 // See the file tools.license for terms. 2 // See the file tools.license for terms.
3 3
4 #ifndef toolx_hdf5_pages 4 #ifndef toolx_hdf5_pages
5 #define toolx_hdf5_pages 5 #define toolx_hdf5_pages
6 6
7 #include "T_tools" 7 #include "T_tools"
8 #include "tools" 8 #include "tools"
9 9
10 #include <tools/S_STRING> 10 #include <tools/S_STRING>
11 11
12 #ifdef TOOLS_MEM 12 #ifdef TOOLS_MEM
13 #include <tools/mem> 13 #include <tools/mem>
14 #endif 14 #endif
15 15
16 #include <ostream> 16 #include <ostream>
17 17
18 namespace toolx { 18 namespace toolx {
19 namespace hdf5 { 19 namespace hdf5 {
20 20
21 TOOLS_GLOBAL_STRING(pages) 21 TOOLS_GLOBAL_STRING(pages)
22 TOOLS_GLOBAL_STRING(entries) 22 TOOLS_GLOBAL_STRING(entries)
23 TOOLS_GLOBAL_STRING(columns) 23 TOOLS_GLOBAL_STRING(columns)
24 TOOLS_GLOBAL_STRING(names) 24 TOOLS_GLOBAL_STRING(names)
25 TOOLS_GLOBAL_STRING(forms) 25 TOOLS_GLOBAL_STRING(forms)
26 26
27 class pages { 27 class pages {
28 TOOLS_SCLASS(toolx::hdf5::pages) 28 TOOLS_SCLASS(toolx::hdf5::pages)
29 public: 29 public:
30 pages(std::ostream& a_out, 30 pages(std::ostream& a_out,
31 hid_t a_group,const std::string& a_nam 31 hid_t a_group,const std::string& a_name,const std::string& a_form,
32 bool a_write,unsigned int a_compress) 32 bool a_write,unsigned int a_compress)
33 :m_out(a_out),m_name(a_name),m_form(a_form) 33 :m_out(a_out),m_name(a_name),m_form(a_form)
34 //,m_type(0),m_size(0) 34 //,m_type(0),m_size(0)
35 ,m_group(-1),m_dataset(-1),m_write(a_write), 35 ,m_group(-1),m_dataset(-1),m_write(a_write),m_compress(a_compress),m_entries(0),m_pos(0){
36 #ifdef TOOLS_MEM 36 #ifdef TOOLS_MEM
37 tools::mem::increment(s_class().c_str()); 37 tools::mem::increment(s_class().c_str());
38 #endif 38 #endif
39 if(m_write) { 39 if(m_write) {
40 m_group = toolx_H5Gcreate(a_group,m_name 40 m_group = toolx_H5Gcreate(a_group,m_name.c_str(),0);
41 if(m_group<0) { 41 if(m_group<0) {
42 m_out << "pages::pages : can't create 42 m_out << "pages::pages : can't create group for column " << m_name << "." << std::endl;
43 m_group = -1; 43 m_group = -1;
44 return; 44 return;
45 } 45 }
46 if(!write_atb(m_group,"class",s_class()) 46 if(!write_atb(m_group,"class",s_class())) {
47 m_out << "pages::pages : write_atb(cla 47 m_out << "pages::pages : write_atb(class) failed." << std::endl;
48 ::H5Gclose(m_group); 48 ::H5Gclose(m_group);
49 m_group = -1; 49 m_group = -1;
50 return; 50 return;
51 } 51 }
52 int v = 1; 52 int v = 1;
53 if (!write_scalar_atb<int>(m_group,"vers 53 if (!write_scalar_atb<int>(m_group,"version",v)) {
54 m_out << "pages::pages : write_scalar_ 54 m_out << "pages::pages : write_scalar_atb(version) failed." << std::endl;
55 ::H5Gclose(m_group); 55 ::H5Gclose(m_group);
56 m_group = -1; 56 m_group = -1;
57 return; 57 return;
58 } 58 }
59 } else { 59 } else {
60 m_group = toolx_H5Gopen(a_group,m_name.c 60 m_group = toolx_H5Gopen(a_group,m_name.c_str());
61 if(m_group<0) { 61 if(m_group<0) {
62 m_out << "pages::pages : can't open gr 62 m_out << "pages::pages : can't open group for column " << m_name << "." << std::endl;
63 m_group = -1; 63 m_group = -1;
64 return; 64 return;
65 } 65 }
66 if(!read_scalar<tools::uint64>(m_group,s 66 if(!read_scalar<tools::uint64>(m_group,s_entries(),m_entries)) {
67 m_out << "pages::pages : read_scalar(e 67 m_out << "pages::pages : read_scalar(entries) failed." << std::endl;
68 ::H5Gclose(m_group); 68 ::H5Gclose(m_group);
69 m_group = -1; 69 m_group = -1;
70 return; 70 return;
71 } 71 }
72 } 72 }
73 } 73 }
74 virtual ~pages(){ 74 virtual ~pages(){
75 if(m_write) { 75 if(m_write) {
76 if(!write_scalar<tools::uint64>(m_group, 76 if(!write_scalar<tools::uint64>(m_group,s_entries(),m_entries)) {
77 m_out << "pages::~pages : write_scalar 77 m_out << "pages::~pages : write_scalar(entries) failed." << std::endl;
78 } 78 }
79 if(m_dataset>=0) ::H5Dclose(m_dataset); 79 if(m_dataset>=0) ::H5Dclose(m_dataset);
80 } 80 }
81 ::H5Gclose(m_group); 81 ::H5Gclose(m_group);
82 #ifdef TOOLS_MEM 82 #ifdef TOOLS_MEM
83 tools::mem::decrement(s_class().c_str()); 83 tools::mem::decrement(s_class().c_str());
84 #endif 84 #endif
85 } 85 }
86 protected: 86 protected:
87 pages(const pages& a_from):m_out(a_from.m_ou 87 pages(const pages& a_from):m_out(a_from.m_out){
88 #ifdef TOOLS_MEM 88 #ifdef TOOLS_MEM
89 tools::mem::increment(s_class().c_str()); 89 tools::mem::increment(s_class().c_str());
90 #endif 90 #endif
91 } 91 }
92 pages& operator=(const pages&){return *this; 92 pages& operator=(const pages&){return *this;}
93 public: 93 public:
94 bool is_valid() const {return m_group<0?fals 94 bool is_valid() const {return m_group<0?false:true;}
95 95
96 const std::string& name() const {return m_na 96 const std::string& name() const {return m_name;}
97 const std::string& form() const {return m_fo 97 const std::string& form() const {return m_form;}
98 //int type() const {return m_type;} 98 //int type() const {return m_type;}
99 //unsigned int size() const {return m_size;} 99 //unsigned int size() const {return m_size;}
100 tools::uint64 entries() const {return m_entr 100 tools::uint64 entries() const {return m_entries;}
101 tools::uint64 pos() const {return m_pos;} 101 tools::uint64 pos() const {return m_pos;}
102 void reset_pos() {m_pos = 0;} 102 void reset_pos() {m_pos = 0;}
103 103
104 template <class TYPE> 104 template <class TYPE>
105 bool write_page(size_t a_size,const TYPE* a_ 105 bool write_page(size_t a_size,const TYPE* a_array) {
106 if(!m_pos) { 106 if(!m_pos) {
107 if(!write_array<TYPE>(m_group,s_pages(), 107 if(!write_array<TYPE>(m_group,s_pages(),a_size,a_array,a_size?a_size:32,m_compress)) {
108 m_out << "pages::write_page : write_ar 108 m_out << "pages::write_page : write_array<TYPE>() failed. Pos " << m_pos << std::endl;
109 return false; 109 return false;
110 } 110 }
111 m_dataset = toolx_H5Dopen(m_group,s_page 111 m_dataset = toolx_H5Dopen(m_group,s_pages().c_str());
112 if(m_dataset<0) { 112 if(m_dataset<0) {
113 m_out << "pages::write_page : H5Dopen 113 m_out << "pages::write_page : H5Dopen failed. Pos " << m_pos << std::endl;
114 return false; 114 return false;
115 } 115 }
116 } else { 116 } else {
117 if(!write_append_array_dataset<TYPE>(m_d 117 if(!write_append_array_dataset<TYPE>(m_dataset,a_size,a_array)) {
118 m_out << "pages::write_page : write_ap 118 m_out << "pages::write_page : write_append_array_dataset<TYPE>() failed. Pos " << m_pos << std::endl;
119 return false; 119 return false;
120 } 120 }
121 } 121 }
122 m_pos += a_size; 122 m_pos += a_size;
123 m_entries = m_pos; 123 m_entries = m_pos;
124 return true; 124 return true;
125 } 125 }
126 126
127 template <class TYPE> 127 template <class TYPE>
128 bool read_page(size_t a_size,TYPE* a_array) 128 bool read_page(size_t a_size,TYPE* a_array) {
129 //it is assumed that a_array can contain a 129 //it is assumed that a_array can contain a_size*sizeof(TYPE) bytes.
130 unsigned int _size = a_size; 130 unsigned int _size = a_size;
131 unsigned int n = 0; 131 unsigned int n = 0;
132 TYPE* array = 0; 132 TYPE* array = 0;
133 if(!read_sub_array<TYPE>(m_group,s_pages() 133 if(!read_sub_array<TYPE>(m_group,s_pages(),(unsigned int)m_pos,(unsigned int)_size,n,array)) {
134 m_out << "pages::read_page : read_sub_ar 134 m_out << "pages::read_page : read_sub_array<TYPE>() failed." << std::endl;
135 return false; 135 return false;
136 } 136 }
137 if(n!=_size) { 137 if(n!=_size) {
138 m_out << "pages::read_page : size mismat 138 m_out << "pages::read_page : size mismatch. Requested " << _size << ", got "<< n << "." << std::endl;
139 delete [] array; 139 delete [] array;
140 return false; 140 return false;
141 } 141 }
142 142
143 {TYPE* rpos = (TYPE*)array; 143 {TYPE* rpos = (TYPE*)array;
144 TYPE* wpos = (TYPE*)a_array; 144 TYPE* wpos = (TYPE*)a_array;
145 for(size_t i=0;i<n;i++,rpos++,wpos++) *wpo 145 for(size_t i=0;i<n;i++,rpos++,wpos++) *wpos = *rpos;
146 for(size_t i=n;i<_size;i++,rpos++,wpos++) 146 for(size_t i=n;i<_size;i++,rpos++,wpos++) *wpos = TYPE();}
147 147
148 delete [] array; 148 delete [] array;
149 149
150 m_pos += n; 150 m_pos += n;
151 return true; 151 return true;
152 } 152 }
153 153
154 template <class TYPE> 154 template <class TYPE>
155 bool write_vlen(size_t a_size,const TYPE* a_ 155 bool write_vlen(size_t a_size,const TYPE* a_array) {
156 if(!m_pos) { 156 if(!m_pos) {
157 if(!hdf5::write_vlen<TYPE>(m_group,s_pag 157 if(!hdf5::write_vlen<TYPE>(m_group,s_pages(),a_size,a_array,a_size?a_size:32,m_compress)) {
158 m_out << "pages::write_vlen : write_vl 158 m_out << "pages::write_vlen : write_vlen<TYPE>() failed. Pos " << m_pos << std::endl;
159 return false; 159 return false;
160 } 160 }
161 m_dataset = toolx_H5Dopen(m_group,s_page 161 m_dataset = toolx_H5Dopen(m_group,s_pages().c_str());
162 if(m_dataset<0) { 162 if(m_dataset<0) {
163 m_out << "pages::write_vlen : H5Dopen 163 m_out << "pages::write_vlen : H5Dopen failed. Pos " << m_pos << std::endl;
164 return false; 164 return false;
165 } 165 }
166 } else { 166 } else {
167 if(!write_append_vlen_dataset<TYPE>(m_da 167 if(!write_append_vlen_dataset<TYPE>(m_dataset,a_size,a_array)) {
168 m_out << "pages::write_vlen : write_ap 168 m_out << "pages::write_vlen : write_append_vlen_dataset<TYPE>() failed. Pos " << m_pos << std::endl;
169 return false; 169 return false;
170 } 170 }
171 } 171 }
172 m_pos++; 172 m_pos++;
173 m_entries++; 173 m_entries++;
174 return true; 174 return true;
175 } 175 }
176 176
177 template <class TYPE> 177 template <class TYPE>
178 bool read_vlen(size_t& a_size,TYPE*& a_array 178 bool read_vlen(size_t& a_size,TYPE*& a_array) {
179 //it is assumed that a_array can contain a 179 //it is assumed that a_array can contain a_size*sizeof(TYPE) bytes.
180 unsigned int sz; 180 unsigned int sz;
181 if(!read_sub_vlen<TYPE>(m_group,s_pages(), 181 if(!read_sub_vlen<TYPE>(m_group,s_pages(),(unsigned int)m_pos,sz,a_array)) {
182 m_out << "pages::read_vlen : read_sub_vl 182 m_out << "pages::read_vlen : read_sub_vlen<TYPE>() failed." << std::endl;
183 a_size = 0; 183 a_size = 0;
184 a_array = 0; 184 a_array = 0;
185 return false; 185 return false;
186 } 186 }
187 a_size = sz; 187 a_size = sz;
188 m_pos++; 188 m_pos++;
189 m_entries++; 189 m_entries++;
190 return true; 190 return true;
191 } 191 }
192 192
193 bool write_string(const std::string& a_strin 193 bool write_string(const std::string& a_string) {
194 if(!m_pos) { 194 if(!m_pos) {
195 if(!hdf5::write_string_dataset(m_group,s 195 if(!hdf5::write_string_dataset(m_group,s_pages(),a_string,128,m_compress)) { //32=>enforce extendable.
196 m_out << "pages::write_string : hdf5:: 196 m_out << "pages::write_string : hdf5::write_string() failed. Pos " << m_pos << std::endl;
197 return false; 197 return false;
198 } 198 }
199 m_dataset = toolx_H5Dopen(m_group,s_page 199 m_dataset = toolx_H5Dopen(m_group,s_pages().c_str());
200 if(m_dataset<0) { 200 if(m_dataset<0) {
201 m_out << "pages::write_string : H5Dope 201 m_out << "pages::write_string : H5Dopen failed. Pos " << m_pos << std::endl;
202 return false; 202 return false;
203 } 203 }
204 } else { 204 } else {
205 if(!write_append_string_dataset(m_datase 205 if(!write_append_string_dataset(m_dataset,a_string)) {
206 m_out << "pages::write_string : write_ 206 m_out << "pages::write_string : write_append_string_dataset() failed. Pos " << m_pos << std::endl;
207 return false; 207 return false;
208 } 208 }
209 } 209 }
210 m_pos++; 210 m_pos++;
211 m_entries++; 211 m_entries++;
212 return true; 212 return true;
213 } 213 }
214 214
215 bool read_string(std::string& a_string) { 215 bool read_string(std::string& a_string) {
216 if(!read_sub_string(m_group,s_pages(),(uns 216 if(!read_sub_string(m_group,s_pages(),(unsigned int)m_pos,a_string)) {
217 m_out << "pages::read_string : read_sub_ 217 m_out << "pages::read_string : read_sub_string() failed." << std::endl;
218 a_string.clear(); 218 a_string.clear();
219 return false; 219 return false;
220 } 220 }
221 m_pos++; 221 m_pos++;
222 m_entries++; 222 m_entries++;
223 return true; 223 return true;
224 } 224 }
225 225
226 /* 226 /*
227 bool write_string(const std::string& a_strin 227 bool write_string(const std::string& a_string) {return write_vlen<char>(a_string.size(),a_string.c_str());}
228 228
229 bool read_string(std::string& a_string) { 229 bool read_string(std::string& a_string) {
230 size_t sz;char* _data; 230 size_t sz;char* _data;
231 if(!read_vlen<char>(sz,_data)) {a_string.c 231 if(!read_vlen<char>(sz,_data)) {a_string.clear();return false;}
232 a_string.resize(sz); 232 a_string.resize(sz);
233 for(size_t index=0;index<sz;index++) a_str 233 for(size_t index=0;index<sz;index++) a_string[index] = _data[index];
234 delete [] _data; 234 delete [] _data;
235 return true; 235 return true;
236 } 236 }
237 */ 237 */
238 238
239 /* 239 /*
240 bool write_strings(size_t a_number,void* a_a 240 bool write_strings(size_t a_number,void* a_array) {
241 size_t sz = m_size*a_number; 241 size_t sz = m_size*a_number;
242 char* buffer = new char[sz]; 242 char* buffer = new char[sz];
243 {char* pos = buffer; 243 {char* pos = buffer;
244 for(size_t index=0;index<sz;index++,pos++) 244 for(size_t index=0;index<sz;index++,pos++) *pos = ' ';}
245 245
246 {char** strings = (char**)a_array; 246 {char** strings = (char**)a_array;
247 char* pos = buffer; 247 char* pos = buffer;
248 size_t ls; 248 size_t ls;
249 for(size_t index=0;index<a_number;index++) 249 for(size_t index=0;index<a_number;index++) {
250 char* ss = strings[index]; 250 char* ss = strings[index];
251 ls = ::strlen(ss); 251 ls = ::strlen(ss);
252 ::memcpy(pos,ss,ls); //do not copy the e 252 ::memcpy(pos,ss,ls); //do not copy the ending 0.
253 *(pos+m_size-1) = 0; 253 *(pos+m_size-1) = 0;
254 pos += m_size; 254 pos += m_size;
255 }} 255 }}
256 256
257 if(!m_pos) { 257 if(!m_pos) {
258 unsigned int chunked = 32*m_size; //<siz 258 unsigned int chunked = 32*m_size; //<size>A strings.
259 if(!write_array<char>(m_group,s_pages(), 259 if(!write_array<char>(m_group,s_pages(),sz,buffer,chunked,m_compress)) {
260 m_out << "pages::write_strings : write 260 m_out << "pages::write_strings : write_strings() failed. Pos " << m_pos << std::endl;
261 return false; 261 return false;
262 } 262 }
263 m_dataset = toolx_H5Dopen(m_group,s_page 263 m_dataset = toolx_H5Dopen(m_group,s_pages().c_str());
264 if(m_dataset<0) { 264 if(m_dataset<0) {
265 m_out << "pages::write_strings : H5Dop 265 m_out << "pages::write_strings : H5Dopen failed. Pos " << m_pos << std::endl;
266 return false; 266 return false;
267 } 267 }
268 } else { 268 } else {
269 if(!write_append_array_dataset<char>(m_d 269 if(!write_append_array_dataset<char>(m_dataset,sz,buffer)) {
270 m_out << "pages::write_strings : write 270 m_out << "pages::write_strings : write_append_strings() failed. Pos " << m_pos << std::endl;
271 return false; 271 return false;
272 } 272 }
273 } 273 }
274 m_pos += a_number; 274 m_pos += a_number;
275 m_entries = m_pos; 275 m_entries = m_pos;
276 return true; 276 return true;
277 } 277 }
278 278
279 bool read_strings(size_t a_size,char* a_arra 279 bool read_strings(size_t a_size,char* a_array) {
280 unsigned int _size = a_size*m_size; 280 unsigned int _size = a_size*m_size;
281 unsigned int n = 0; 281 unsigned int n = 0;
282 char* array = 0; 282 char* array = 0;
283 if(!read_sub_array<char>(m_group,s_pages() 283 if(!read_sub_array<char>(m_group,s_pages(),m_pos,_size,n,array)) {
284 m_out << "pages::read_strings : read_sub 284 m_out << "pages::read_strings : read_sub_array<char>() failed." << std::endl;
285 return false; 285 return false;
286 } 286 }
287 if(n!=_size) { 287 if(n!=_size) {
288 m_out << "pages::read_strings : size mis 288 m_out << "pages::read_strings : size mismatch. Requested " << _size << ", got "<< n << "." << std::endl;
289 delete [] array; 289 delete [] array;
290 return false; 290 return false;
291 } 291 }
292 char* pos = array; 292 char* pos = array;
293 {char** strings = (char**)a_array; 293 {char** strings = (char**)a_array;
294 for(size_t index=0;index<a_size;index++) { 294 for(size_t index=0;index<a_size;index++) {
295 ::memcpy(strings[index],pos,m_size*sizeo 295 ::memcpy(strings[index],pos,m_size*sizeof(char));
296 pos += m_size; 296 pos += m_size;
297 }} 297 }}
298 delete [] array; 298 delete [] array;
299 m_pos += n; 299 m_pos += n;
300 return true; 300 return true;
301 } 301 }
302 */ 302 */
303 protected: 303 protected:
304 std::ostream& m_out; 304 std::ostream& m_out;
305 std::string m_name; 305 std::string m_name;
306 std::string m_form; 306 std::string m_form;
307 //int m_type; 307 //int m_type;
308 //unsigned int m_size; 308 //unsigned int m_size;
309 hid_t m_group; 309 hid_t m_group;
310 hid_t m_dataset; 310 hid_t m_dataset;
311 bool m_write; 311 bool m_write;
312 unsigned int m_compress; //if write. 312 unsigned int m_compress; //if write.
313 tools::uint64 m_entries; 313 tools::uint64 m_entries;
314 tools::uint64 m_pos; 314 tools::uint64 m_pos;
315 }; 315 };
316 316
317 }} 317 }}
318 318
319 #endif 319 #endif