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source: trunk/Mars/mcore/fits.h@ 14860

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Last change on this file since 14860 was 14860, checked in by tbretz, 12 years ago
Added a complete list of stdint.h members for CITN.
File size: 24.2 KB

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1	#ifndef MARS_fits
2	#define MARS_fits
3
4	#ifdef __CINT__
5	#define int8_t Char_t
6	#define int16_t Short_t
7	#define int32_t Int_t
8	#define int64_t Long64_t
9	#define uint8_t UChar_t
10	#define uint16_t UShort_t
11	#define uint32_t UInt_t
12	#define uint64_t ULong64_t
13	#else
14	#include <stdint.h>
15	#endif
16
17	#include <map>
18	#include <string>
19	#include <sstream>
20	#include <algorithm>
21
22	#ifdef __EXCEPTIONS
23	#include <stdexcept>
24	#endif
25
26	#ifdef __CINT__
27	#define off_t size_t
28	#else
29	#include <unordered_map>
30	#endif
31
32	#ifndef __MARS__
33	#include <vector>
34	#include <iomanip>
35	#include <iostream>
36	#define gLog cerr
37	#define ___err___ ""
38	#define ___all___ ""
39	#else
40	#include "MLog.h"
41	#include "MLogManip.h"
42	#define ___err___ err
43	#define ___all___ all
44	#endif
45
46	#ifdef HAVE_ZLIB
47	#include "izstream.h"
48	#else
49	#include <fstream>
50	#define izstream ifstream
51	#warning Support for zipped FITS files disabled.
52	#endif
53
54	#include "checksum.h"
55
56	namespace std
57	{
58
59	class fits : public izstream
60	{
61	public:
62	struct Entry
63	{
64	char type;
65	string value;
66	string comment;
67
68	template<typename T>
69	T Get() const
70	{
71	T t;
72
73	istringstream str(value);
74	str >> t;
75
76	return t;
77	}
78	};
79
80	struct Table
81	{
82	off_t offset;
83
84	string name;
85	size_t bytes_per_row;
86	size_t num_rows;
87	size_t num_cols;
88
89	struct Column
90	{
91	size_t offset;
92	size_t num;
93	size_t size;
94	char type;
95	string unit;
96	};
97
98	typedef map<string, Entry> Keys;
99	typedef map<string, Column> Columns;
100
101	Columns cols;
102	Keys keys;
103
104	int64_t datasum;
105
106	string Trim(const string &str, char c=' ') const
107	{
108	// Trim Both leading and trailing spaces
109	const size_t pstart = str.find_first_not_of(c); // Find the first character position after excluding leading blank spaces
110	const size_t pend = str.find_last_not_of(c); // Find the first character position from reverse af
111
112	// if all spaces or empty return an empty string
113	if (string::npos==pstart \|\| string::npos==pend)
114	return string();
115
116	return str.substr(pstart, pend-pstart+1);
117	}
118
119	bool Check(const string &key, char type, const string &value="") const
120	{
121	const Keys::const_iterator it = keys.find(key);
122	if (it==keys.end())
123	{
124	ostringstream str;
125	str << "Key '" << key << "' not found.";
126	#ifdef __EXCEPTIONS
127	throw runtime_error(str.str());
128	#else
129	gLog << ___err___ << "ERROR - " << str.str() << endl;
130	return false;
131	#endif
132	}
133
134	if (it->second.type!=type)
135	{
136	ostringstream str;
137	str << "Wrong type for key '" << key << "': expected " << type << ", found " << it->second.type << ".";
138	#ifdef __EXCEPTIONS
139	throw runtime_error(str.str());
140	#else
141	gLog << ___err___ << "ERROR - " << str.str() << endl;
142	return false;
143	#endif
144	}
145
146	if (!value.empty() && it->second.value!=value)
147	{
148	ostringstream str;
149	str << "Wrong value for key '" << key << "': expected " << value << ", found " << it->second.value << ".";
150	#ifdef __EXCEPTIONS
151	throw runtime_error(str.str());
152	#else
153	gLog << ___err___ << "ERROR - " << str.str() << endl;
154	return false;
155	#endif
156	}
157
158	return true;
159	}
160
161	Keys ParseBlock(const vector<string> &vec) const
162	{
163	map<string,Entry> rc;
164
165	for (unsigned int i=0; i<vec.size(); i++)
166	{
167	const string key = Trim(vec[i].substr(0,8));
168	// Keywords without a value, like COMMENT / HISTORY
169	if (vec[i].substr(8,2)!="= ")
170	continue;
171
172	char type = 0;
173
174	string com;
175	string val = Trim(vec[i].substr(10));
176	if (val[0]=='\'')
177	{
178	// First skip all '' in the string
179	size_t p = 1;
180	while (1)
181	{
182	const size_t pp = val.find_first_of('\'', p);
183	if (pp==string::npos)
184	break;
185
186	p = val[pp+1]=='\'' ? pp+2 : pp+1;
187	}
188
189	// Now find the comment
190	const size_t ppp = val.find_first_of('/', p);
191
192	// Set value, comment and type
193	com = ppp==string::npos ? "" : Trim(val.substr(ppp+1));
194	val = Trim(val.substr(1, p-2));
195	type = 'T';
196	}
197	else
198	{
199	const size_t p = val.find_first_of('/');
200
201	com = Trim(val.substr(p+2));
202	val = Trim(val.substr(0, p));
203
204	if (val.empty() \|\| val.find_first_of('T')!=string::npos \|\| val.find_first_of('F')!=string::npos)
205	type = 'B';
206	else
207	type = val.find_last_of('.')==string::npos ? 'I' : 'F';
208	}
209
210	const Entry e = { type, val, com };
211	rc[key] = e;
212	}
213
214	return rc;
215	}
216
217	Table() : offset(0) { }
218	Table(const vector<string> &vec, off_t off) :
219	offset(off), keys(ParseBlock(vec))
220	{
221	if (!Check("XTENSION", 'T', "BINTABLE") \|\|
222	!Check("NAXIS", 'I', "2") \|\|
223	!Check("BITPIX", 'I', "8") \|\|
224	!Check("PCOUNT", 'I', "0") \|\|
225	!Check("GCOUNT", 'I', "1") \|\|
226	!Check("EXTNAME", 'T') \|\|
227	!Check("NAXIS1", 'I') \|\|
228	!Check("NAXIS2", 'I') \|\|
229	!Check("TFIELDS", 'I'))
230	return;
231
232	bytes_per_row = Get<size_t>("NAXIS1");
233	num_rows = Get<size_t>("NAXIS2");
234	num_cols = Get<size_t>("TFIELDS");
235	datasum = Get<int64_t>("DATASUM", -1);
236
237	size_t bytes = 0;
238	for (size_t i=1; i<=num_cols; i++)
239	{
240	ostringstream num;
241	num << i;
242
243	if (!Check("TTYPE"+num.str(), 'T') \|\|
244	!Check("TFORM"+num.str(), 'T'))
245	return;
246
247	const string id = Get<string>("TTYPE"+num.str());
248	const string fmt = Get<string>("TFORM"+num.str());
249	const string unit = Get<string>("TUNIT"+num.str(), "");
250
251	istringstream sin(fmt);
252	int n = 0;
253	sin >> n;
254	if (!sin)
255	n = 1;
256
257	const char type = fmt[fmt.length()-1];
258
259	size_t size = 0;
260	switch (type)
261	{
262	// We could use negative values to mark floats
263	// otheriwse we could just cast them to int64_t?
264	case 'L': // logical
265	case 'A': // char
266	case 'B': size = 1; break; // byte
267	case 'I': size = 2; break; // short
268	case 'J': size = 4; break; // int
269	case 'K': size = 8; break; // long long
270	case 'E': size = 4; break; // float
271	case 'D': size = 8; break; // double
272	// case 'X': size = n; break; // bits (n=number of bytes needed to contain all bits)
273	// case 'C': size = 8; break; // complex float
274	// case 'M': size = 16; break; // complex double
275	// case 'P': size = 8; break; // array descriptor (32bit)
276	// case 'Q': size = 16; break; // array descriptor (64bit)
277	default:
278	{
279	ostringstream str;
280	str << "FITS format TFORM='" << fmt << "' not yet supported.";
281	#ifdef __EXCEPTIONS
282	throw runtime_error(str.str());
283	#else
284	gLog << ___err___ << "ERROR - " << str.str() << endl;
285	return;
286	#endif
287	}
288	}
289
290	const Table::Column col = { bytes, n, size, type, unit };
291
292	cols[id] = col;
293	bytes += n*size;
294	}
295
296	if (bytes!=bytes_per_row)
297	{
298	#ifdef __EXCEPTIONS
299	throw runtime_error("Column size mismatch");
300	#else
301	gLog << ___err___ << "ERROR - Column size mismatch" << endl;
302	return;
303	#endif
304	}
305
306	name = Get<string>("EXTNAME");
307	}
308
309	void PrintKeys(bool display_all=false) const
310	{
311	for (Keys::const_iterator it=keys.begin(); it!=keys.end(); it++)
312	{
313	if (!display_all &&
314	(it->first.substr(0, 6)=="TTYPE" \|\|
315	it->first.substr(0, 6)=="TFORM" \|\|
316	it->first.substr(0, 6)=="TUNIT" \|\|
317	it->first=="TFIELDS" \|\|
318	it->first=="XTENSION" \|\|
319	it->first=="NAXIS" \|\|
320	it->first=="BITPIX" \|\|
321	it->first=="PCOUNT" \|\|
322	it->first=="GCOUNT")
323	)
324	continue;
325
326	gLog << ___all___ << setw(2) << it->second.type << '\|' << it->first << '=' << it->second.value << '/' << it->second.comment << '\|' << endl;
327	}}
328
329	void PrintColumns() const
330	{
331	typedef map<pair<size_t, string>, Column> Sorted;
332
333	Sorted sorted;
334
335	for (Columns::const_iterator it=cols.begin(); it!=cols.end(); it++)
336	sorted[make_pair(it->second.offset, it->first)] = it->second;
337
338	for (Sorted::const_iterator it=sorted.begin(); it!=sorted.end(); it++)
339	{
340	gLog << ___all___ << setw(6) << it->second.offset << "\| ";
341	gLog << it->second.num << 'x';
342	switch (it->second.type)
343	{
344	case 'A': gLog << "char(8)"; break;
345	case 'L': gLog << "bool(8)"; break;
346	case 'B': gLog << "byte(8)"; break;
347	case 'I': gLog << "short(16)"; break;
348	case 'J': gLog << "int(32)"; break;
349	case 'K': gLog << "int(64)"; break;
350	case 'E': gLog << "float(32)"; break;
351	case 'D': gLog << "double(64)"; break;
352	}
353	gLog << ": " << it->first.second << " [" << it->second.unit << "]" << endl;
354	}
355	}
356
357	operator bool() const { return !name.empty(); }
358
359	bool HasKey(const string &key) const
360	{
361	return keys.find(key)!=keys.end();
362	}
363
364	bool HasColumn(const string& col) const
365	{
366	return cols.find(col)!=cols.end();
367	}
368
369	const Columns &GetColumns() const
370	{
371	return cols;
372	}
373
374	const Keys &GetKeys() const
375	{
376	return keys;
377	}
378
379	// Values of keys are always signed
380	template<typename T>
381	T Get(const string &key) const
382	{
383	const map<string,Entry>::const_iterator it = keys.find(key);
384	if (it==keys.end())
385	{
386	ostringstream str;
387	str << "Key '" << key << "' not found." << endl;
388	#ifdef __EXCEPTIONS
389	throw runtime_error(str.str());
390	#else
391	gLog << ___err___ << "ERROR - " << str.str() << endl;
392	return T();
393	#endif
394	}
395	return it->second.Get<T>();
396	}
397
398	// Values of keys are always signed
399	template<typename T>
400	T Get(const string &key, const T &deflt) const
401	{
402	const map<string,Entry>::const_iterator it = keys.find(key);
403	return it==keys.end() ? deflt :it->second.Get<T>();
404	}
405
406	size_t GetN(const string &key) const
407	{
408	const Columns::const_iterator it = cols.find(key);
409	return it==cols.end() ? 0 : it->second.num;
410	}
411	};
412
413	private:
414	Table fTable;
415
416	typedef pair<void*, Table::Column> Address;
417	typedef vector<Address> Addresses;
418	//map<void*, Table::Column> fAddresses;
419	Addresses fAddresses;
420
421	#ifdef __CINT__
422	typedef char Pointers[56];
423	#else
424	typedef unordered_map<string, void*> Pointers;
425	#endif
426	Pointers fPointers;
427
428	vector<vector<char>> fGarbage;
429
430	vector<char> fBufferRow;
431	vector<char> fBufferDat;
432
433	size_t fRow;
434
435	Checksum fChkHeader;
436	Checksum fChkData;
437
438	bool ReadBlock(vector<string> &vec)
439	{
440	int endtag = 0;
441	for (int i=0; i<36; i++)
442	{
443	char c[81];
444	c[80] = 0;
445	read(c, 80);
446	if (!good())
447	break;
448
449	fChkHeader.add(c, 80);
450
451	// if (c[0]==0)
452	// return vector<string>();
453
454	string str(c);
455
456	// if (!str.empty())
457	// cout << setw(2) << i << "\|" << str << "\|" << (endtag?'-':'+') << endl;
458
459	if (endtag==2 \|\| str=="END ")
460	{
461	endtag = 2; // valid END tag found
462	continue;
463	}
464
465	if (endtag==1 \|\| str==" ")
466	{
467	endtag = 1; // end tag not found, but expected to be there
468	continue;
469	}
470
471	vec.push_back(str);
472	}
473
474	// Make sure that no empty vector is returned
475	if (endtag && vec.size()%36==0)
476	vec.push_back(string("END = '' / "));
477
478	return endtag==2;
479	}
480
481	string Compile(const string &key, int16_t i=-1)
482	{
483	if (i<0)
484	return key;
485
486	ostringstream str;
487	str << key << i;
488	return str.str();
489	}
490
491	public:
492	fits(const string &fname, bool force=false) : izstream(fname.c_str())
493	{
494	char simple[10];
495	read(simple, 10);
496	if (!good())
497	return;
498
499	if (memcmp(simple, "SIMPLE = ", 10))
500	{
501	clear(rdstate()\|ios::badbit);
502	#ifdef __EXCEPTIONS
503	throw runtime_error("File is not a FITS file.");
504	#else
505	gLog << ___err___ << "ERROR - File is not a FITS file." << endl;
506	return;
507	#endif
508	}
509
510	seekg(0);
511
512	while (good())
513	{
514	vector<string> block;
515	while (1)
516	{
517	// FIXME: Set limit on memory consumption
518	const int rc = ReadBlock(block);
519	if (!good())
520	{
521	clear(rdstate()\|ios::badbit);
522	#ifdef __EXCEPTIONS
523	throw runtime_error("FITS file corrupted.");
524	#else
525	gLog << ___err___ << "ERROR - FITS file corrupted." << endl;
526	return;
527	#endif
528	}
529
530	if (block.size()%36)
531	{
532	if (!rc && !force)
533	{
534	clear(rdstate()\|ios::badbit);
535	#ifdef __EXCEPTIONS
536	throw runtime_error("END keyword missing in FITS header.");
537	#else
538	gLog << ___err___ << "ERROR - END keyword missing in FITS file... file might be corrupted." << endl;
539	return;
540	#endif
541	}
542	break;
543	}
544	}
545
546	if (block.size()==0)
547	break;
548
549	if (block[0].substr(0, 9)=="SIMPLE =")
550	{
551	fChkHeader.reset();
552	continue;
553	}
554
555	if (block[0].substr(0, 9)=="XTENSION=")
556	{
557	// FIXME: Check for table name
558
559	fTable = Table(block, tellg());
560	fRow = (size_t)-1;
561
562	//fTable.PrintKeys();
563
564	if (!fTable)
565	{
566	clear(rdstate()\|ios::badbit);
567	return;
568	}
569
570	fBufferRow.resize(fTable.bytes_per_row + 4-fTable.bytes_per_row%4);
571	fBufferDat.resize(fTable.bytes_per_row);
572
573	/*
574	// Next table should start at:
575	const size_t size = fTable.bytes_per_row*fTable.num_rows;
576	const size_t blks = size/(36*80);
577	const size_t rest = size%(36*80);
578
579	seekg((blks+(rest>0?1:0))(3680), ios::cur);
580	if (!good())
581	gLog << ___err___ << "File seems to be incomplete (less data than expected from header)." << endl;
582
583	fRow = fTable.num_rows;
584	*/
585
586	break;
587	}
588	}
589	}
590
591	uint8_t ReadRow(size_t row)
592	{
593	// if (row!=fRow+1) // Fast seeking is ensured by izstream
594	seekg(fTable.offset+row*fTable.bytes_per_row);
595
596	// For the checksum we need everything to be correctly aligned
597	const uint8_t offset = (row*fTable.bytes_per_row)%4;
598
599	auto ib = fBufferRow.begin();
600	auto ie = fBufferRow.end();
601	*ib++ = 0;
602	*ib++ = 0;
603	*ib++ = 0;
604	*ib = 0;
605
606	*--ie = 0;
607	*--ie = 0;
608	*--ie = 0;
609	*--ie = 0;
610
611	fBufferRow.assign(fBufferRow.size(), 0);
612
613	read(fBufferRow.data()+offset, fTable.bytes_per_row);
614	//fin.clear(fin.rdstate()&~ios::eofbit);
615
616	if (row==fRow+1)
617	fChkData.add(fBufferRow);
618
619	fRow = row;
620
621	return offset;
622	}
623
624	template<size_t N>
625	void revcpy(char dest, const char src, int num)
626	{
627	const char pend = src + numN;
628	for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
629	reverse_copy(ptr, ptr+N, dest);
630	}
631
632	bool GetRow(size_t row, bool check=true)
633	{
634	if (check && row>=fTable.num_rows)
635	return false;
636
637	const uint8_t offset = ReadRow(row);
638	if (!good())
639	return good();
640
641	const char *ptr = fBufferRow.data() + offset;
642
643	for (Addresses::const_iterator it=fAddresses.begin(); it!=fAddresses.end(); it++)
644	{
645	const Table::Column &c = it->second;
646
647	const char *src = ptr + c.offset;
648	char dest = reinterpret_cast<char>(it->first);
649
650	// Let the compiler do some optimization by
651	// knowing the we only have 1, 2, 4 and 8
652	switch (c.size)
653	{
654	case 1: memcpy (dest, src, c.num*c.size); break;
655	case 2: revcpy<2>(dest, src, c.num); break;
656	case 4: revcpy<4>(dest, src, c.num); break;
657	case 8: revcpy<8>(dest, src, c.num); break;
658	}
659	}
660
661	return good();
662	}
663
664	bool GetNextRow(bool check=true)
665	{
666	return GetRow(fRow+1, check);
667	}
668
669	bool SkipNextRow()
670	{
671	seekg(fTable.offset+(++fRow)*fTable.bytes_per_row);
672	return good();
673	}
674
675	static bool Compare(const Address &p1, const Address &p2)
676	{
677	return p1.first>p2.first;
678	}
679
680	template<class T, class S>
681	const T &GetAs(const string &name)
682	{
683	return reinterpret_cast<S>(fPointers[name]);
684	}
685
686	void *SetPtrAddress(const string &name)
687	{
688	if (fTable.cols.count(name)==0)
689	{
690	ostringstream str;
691	str <<"SetPtrAddress('" << name << "') - Column not found." << endl;
692	#ifdef __EXCEPTIONS
693	throw runtime_error(str.str());
694	#else
695	gLog << ___err___ << "ERROR - " << str.str() << endl;
696	return NULL;
697	#endif
698	}
699
700	Pointers::const_iterator it = fPointers.find(name);
701	if (it!=fPointers.end())
702	return it->second;
703
704	fGarbage.push_back(vector<char>(fTable.cols[name].size*fTable.cols[name].num));
705
706	void *ptr = fGarbage.back().data();
707
708	fPointers[name] = ptr;
709	fAddresses.push_back(make_pair(ptr, fTable.cols[name]));
710	sort(fAddresses.begin(), fAddresses.end(), Compare);
711	return ptr;
712	}
713
714	template<typename T>
715	bool SetPtrAddress(const string &name, T *ptr, size_t cnt)
716	{
717	if (fTable.cols.count(name)==0)
718	{
719	ostringstream str;
720	str << "SetPtrAddress('" << name << "') - Column not found." << endl;
721	#ifdef __EXCEPTIONS
722	throw runtime_error(str.str());
723	#else
724	gLog << ___err___ << "ERROR - " << str.str() << endl;
725	return false;
726	#endif
727	}
728
729	if (sizeof(T)!=fTable.cols[name].size)
730	{
731	ostringstream str;
732	str << "SetPtrAddress('" << name << "') - Element size mismatch: expected "
733	<< fTable.cols[name].size << " from header, got " << sizeof(T) << endl;
734	#ifdef __EXCEPTIONS
735	throw runtime_error(str.str());
736	#else
737	gLog << ___err___ << "ERROR - " << str.str() << endl;
738	return false;
739	#endif
740	}
741
742	if (cnt!=fTable.cols[name].num)
743	{
744	ostringstream str;
745	str << "SetPtrAddress('" << name << "') - Element count mismatch: expected "
746	<< fTable.cols[name].num << " from header, got " << cnt << endl;
747	#ifdef __EXCEPTIONS
748	throw runtime_error(str.str());
749	#else
750	gLog << ___err___ << "ERROR - " << str.str() << endl;
751	return false;
752	#endif
753	}
754
755	// if (fAddresses.count(ptr)>0)
756	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
757
758	//fAddresses[ptr] = fTable.cols[name];
759	fPointers[name] = ptr;
760	fAddresses.push_back(make_pair(ptr, fTable.cols[name]));
761	sort(fAddresses.begin(), fAddresses.end(), Compare);
762	return true;
763	}
764
765	template<class T>
766	bool SetRefAddress(const string &name, T &ptr)
767	{
768	return SetPtrAddress(name, &ptr, sizeof(ptr)/sizeof(T));
769	}
770
771	template<typename T>
772	bool SetVecAddress(const string &name, vector<T> &vec)
773	{
774	return SetPtrAddress(name, vec.data(), vec.size());
775	}
776
777	template<typename T>
778	T Get(const string &key) const
779	{
780	return fTable.Get<T>(key);
781	}
782
783	template<typename T>
784	T Get(const string &key, const string &deflt) const
785	{
786	return fTable.Get<T>(key, deflt);
787	}
788
789	bool SetPtrAddress(const string &name, void *ptr)
790	{
791	if (fTable.cols.count(name)==0)
792	{
793	ostringstream str;
794	str <<"SetPtrAddress('" << name << "') - Column not found." << endl;
795	#ifdef __EXCEPTIONS
796	throw runtime_error(str.str());
797	#else
798	gLog << ___err___ << "ERROR - " << str.str() << endl;
799	return false;
800	#endif
801	}
802
803	// if (fAddresses.count(ptr)>0)
804	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
805
806	//fAddresses[ptr] = fTable.cols[name];
807	fPointers[name] = ptr;
808	fAddresses.push_back(make_pair(ptr, fTable.cols[name]));
809	sort(fAddresses.begin(), fAddresses.end(), Compare);
810	return true;
811	}
812
813	bool HasKey(const string &key) const { return fTable.HasKey(key); }
814	bool HasColumn(const string& col) const { return fTable.HasColumn(col);}
815	const Table::Columns &GetColumns() const { return fTable.GetColumns();}
816	const Table::Keys &GetKeys() const { return fTable.GetKeys();}
817
818	int64_t GetInt(const string &key) const { return fTable.Get<int64_t>(key); }
819	uint64_t GetUInt(const string &key) const { return fTable.Get<uint64_t>(key); }
820	double GetFloat(const string &key) const { return fTable.Get<double>(key); }
821	string GetStr(const string &key) const { return fTable.Get<string>(key); }
822
823	size_t GetN(const string &key) const
824	{
825	return fTable.GetN(key);
826	}
827
828	size_t GetNumRows() const { return fTable.num_rows; }
829	size_t GetRow() const { return fRow==(size_t)-1 ? 0 : fRow; }
830
831	operator bool() const { return fTable && fTable.offset!=0; }
832
833	void PrintKeys() const { fTable.PrintKeys(); }
834	void PrintColumns() const { fTable.PrintColumns(); }
835
836	bool IsHeaderOk() const { return fTable.datasum<0?false:(fChkHeader+Checksum(fTable.datasum)).valid(); }
837	bool IsFileOk() const { return (fChkHeader+fChkData).valid(); }
838
839	};
840
841	};
842	#endif

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