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source: trunk/Mars/mcore/fits.h@ 19552

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Last change on this file since 19552 was 19405, checked in by tbretz, 6 years ago
n can be of type size_t, no need for a cast. It will not be negative:
File size: 31.8 KB

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1	#ifndef MARS_fits
2	#define MARS_fits
3
4	#include <stdint.h>
5
6	#include <map>
7	#include <string>
8	#include <fstream>
9	#if defined(R__DICTIONARY_FILENAME) && defined(__clang__)
10	#undef private
11	#endif
12	#include <sstream>
13	#include <algorithm>
14	#include <stdexcept>
15
16	#define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
17
18	#ifndef __CINT__
19	#include <unordered_map>
20	#else
21	#define off_t size_t
22	namespace std
23	{
24	template<class T, class S> class unordered_map<T, S>;
25	}
26	#endif
27
28	#if defined(__MARS__) \|\| defined(__CINT__) \|\| defined(__CLING__)
29	#include "MLog.h"
30	#include "MLogManip.h"
31	#define ___err___ err
32	#define ___warn___ warn
33	#define ___all___ all
34	#else
35	#include <vector>
36	#include <iomanip>
37	#include <iostream>
38	#ifndef gLog
39	#define gLog std::cerr
40	#define ___err___ ""
41	#define ___warn___ ""
42	#define ___all___ ""
43	#endif
44	#endif
45
46	#if defined(HAVE_ZLIB) \|\| defined(__CINT__) \|\| defined(__CLING__)
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 "FITS.h"
55	#include "checksum.h"
56
57	class fits : public izstream
58	{
59	public:
60	//I know I know, you're going to yiell that this does not belong here.
61	//It will belong in the global scope eventually, and it makes the coding of zfits much simpler this way.
62	enum Compression_t
63	{
64	kCompUnknown,
65	kCompFACT
66	};
67
68	enum fitsstate
69	{
70	throwbit = 8
71	};
72
73	struct Entry
74	{
75	char type;
76	std::string value;
77	std::string comment;
78	std::string fitsString;
79
80	template<typename T>
81	T Get() const
82	{
83	T t;
84
85	std::istringstream str(value);
86	str >> t;
87
88	return t;
89	}
90
91	/* Specialization needs to be outside namespace-scope, see below
92	template<>
93	std::string fits::Entry::Get<std::string>() const
94	{
95	return value;
96	}*/
97	};
98
99	struct Table
100	{
101	off_t offset;
102
103	bool is_compressed;
104
105	std::string name;
106	size_t bytes_per_row;
107	size_t num_rows;
108	size_t num_cols;
109	size_t total_bytes; // NAXIS1*NAXIS2
110
111	struct Column
112	{
113	size_t id;
114	size_t offset;
115	size_t num;
116	size_t size;
117	size_t bytes; // num*size
118	char type;
119	std::string unit;
120	std::string comment;
121	Compression_t comp;
122	};
123
124	typedef std::map<std::string, Entry> Keys;
125	typedef std::map<std::string, Column> Columns;
126	typedef std::vector<Column> SortedColumns;
127
128	Columns cols;
129	SortedColumns sorted_cols;
130	Keys keys;
131
132	int64_t datasum;
133
134	std::string Trim(const std::string &str, char c=' ') const
135	{
136	// Trim Both leading and trailing spaces
137	const size_t pstart = str.find_first_not_of(c); // Find the first character position after excluding leading blank spaces
138	const size_t pend = str.find_last_not_of(c); // Find the first character position from reverse af
139
140	// if all spaces or empty return an empty string
141	if (std::string::npos==pstart \|\| std::string::npos==pend)
142	return std::string();
143
144	return str.substr(pstart, pend-pstart+1);
145	}
146
147	bool Check(const std::string &key, char type, const std::string &value="") const
148	{
149	const Keys::const_iterator it = keys.find(key);
150	if (it==keys.end())
151	{
152	std::ostringstream str;
153	str << "Key '" << key << "' not found.";
154	#ifdef __EXCEPTIONS
155	throw std::runtime_error(str.str());
156	#else
157	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
158	return false;
159	#endif
160	}
161
162	if (it->second.type!=type)
163	{
164	std::ostringstream str;
165	str << "Wrong type for key '" << key << "': expected " << type << ", found " << it->second.type << ".";
166	#ifdef __EXCEPTIONS
167	throw std::runtime_error(str.str());
168	#else
169	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
170	return false;
171	#endif
172	}
173
174	if (!value.empty() && it->second.value!=value)
175	{
176	std::ostringstream str;
177	str << "Wrong value for key '" << key << "': expected " << value << ", found " << it->second.value << ".";
178	#ifdef __EXCEPTIONS
179	throw std::runtime_error(str.str());
180	#else
181	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
182	return false;
183	#endif
184	}
185
186	return true;
187	}
188
189	Keys ParseBlock(const std::vector<std::string> &vec) const
190	{
191	Keys rc;
192
193	for (unsigned int i=0; i<vec.size(); i++)
194	{
195	const std::string key = Trim(vec[i].substr(0,8));
196	// Keywords without a value, like COMMENT / HISTORY
197	if (vec[i].substr(8,2)!="= ")
198	continue;
199
200	char type = 0;
201
202	std::string com;
203	std::string val = Trim(vec[i].substr(10));
204
205	if (val[0]=='\'')
206	{
207	// First skip all '' in the string
208	size_t p = 1;
209	while (1)
210	{
211	const size_t pp = val.find_first_of('\'', p);
212	if (pp==std::string::npos)
213	break;
214
215	p = val[pp+1]=='\'' ? pp+2 : pp+1;
216	}
217
218	// Now find the comment
219	const size_t ppp = val.find_first_of('/', p);
220
221	// Set value, comment and type
222	// comments could be just spaces. take care of this.
223	if (ppp!=std::string::npos && val.size()!=ppp+1)
224	com = Trim(val.substr(ppp+1));
225
226	val = Trim(val.substr(1, p-2));
227	type = 'T';
228	}
229	else
230	{
231	const size_t p = val.find_first_of('/');
232
233	if (p!=std::string::npos && val.size()!=p+1)
234	com = Trim(val.substr(p+2));
235
236	val = Trim(val.substr(0, p));
237
238	if (val.empty() \|\| val.find_first_of('T')!=std::string::npos \|\| val.find_first_of('F')!=std::string::npos)
239	type = 'B';
240	else
241	type = val.find_last_of('.')==std::string::npos ? 'I' : 'F';
242	}
243
244	const Entry e = { type, val, com, vec[i] };
245
246	rc[key] = e;
247	}
248
249	return rc;
250	}
251
252	Table() : offset(0), is_compressed(false) { }
253	Table(const std::vector<std::string> &vec, off_t off) : offset(off),
254	keys(ParseBlock(vec))
255	{
256	is_compressed = HasKey("ZTABLE") && Check("ZTABLE", 'B', "T");
257
258	if (!Check("XTENSION", 'T', "BINTABLE") \|\|
259	!Check("NAXIS", 'I', "2") \|\|
260	!Check("BITPIX", 'I', "8") \|\|
261	!Check("GCOUNT", 'I', "1") \|\|
262	!Check("EXTNAME", 'T') \|\|
263	!Check("NAXIS1", 'I') \|\|
264	!Check("NAXIS2", 'I') \|\|
265	!Check("TFIELDS", 'I'))
266	return;
267
268	if (is_compressed)
269	{
270	if (!Check("ZNAXIS1", 'I') \|\|
271	!Check("ZNAXIS2", 'I') \|\|
272	!Check("ZPCOUNT", 'I', "0"))
273	return;
274	}
275	else
276	{
277	if (!Check("PCOUNT", 'I', "0"))
278	return;
279	}
280
281	total_bytes = Get<size_t>("NAXIS1")*Get<size_t>("NAXIS2");
282	bytes_per_row = is_compressed ? Get<size_t>("ZNAXIS1") : Get<size_t>("NAXIS1");
283	num_rows = is_compressed ? Get<size_t>("ZNAXIS2") : Get<size_t>("NAXIS2");
284	num_cols = Get<size_t>("TFIELDS");
285	datasum = Get<int64_t>("DATASUM", -1);
286	size_t bytes = 0;
287
288	const std::string tFormName = is_compressed ? "ZFORM" : "TFORM";
289	for (size_t i=1; i<=num_cols; i++)
290	{
291	const std::string num(std::to_string(i));
292
293	if (!Check("TTYPE"+num, 'T') \|\|
294	!Check(tFormName+num, 'T'))
295	return;
296
297	const std::string id = Get<std::string>("TTYPE"+num);
298	const std::string fmt = Get<std::string>(tFormName+num);
299	const std::string unit = Get<std::string>("TUNIT"+num, "");
300	const std::string comp = Get<std::string>("ZCTYP"+num, "");
301	const std::string comm = Get<std::string>("TCOMM"+num, "");
302
303	Compression_t compress = kCompUnknown;
304	if (comp == "FACT")
305	compress = kCompFACT;
306
307	std::istringstream sin(fmt);
308	size_t n = 0;
309	sin >> n;
310	if (!sin)
311	n = 1;
312
313	const char type = fmt[fmt.length()-1];
314
315	size_t size = 0;
316	switch (type)
317	{
318	// We could use negative values to mark floats
319	// otheriwse we could just cast them to int64_t?
320	case 'L': // logical
321	case 'A': // char
322	case 'B': size = 1; break; // byte
323	case 'I': size = 2; break; // short
324	case 'J': size = 4; break; // int
325	case 'K': size = 8; break; // long long
326	case 'E': size = 4; break; // float
327	case 'D': size = 8; break; // double
328	// case 'X': size = n; break; // bits (n=number of bytes needed to contain all bits)
329	// case 'C': size = 8; break; // complex float
330	// case 'M': size = 16; break; // complex double
331	// case 'P': size = 8; break; // array descriptor (32bit)
332	// case 'Q': size = 16; break; // array descriptor (64bit)
333	default:
334	{
335	std::ostringstream str;
336	str << "FITS format TFORM='" << fmt << "' not yet supported.";
337	#ifdef __EXCEPTIONS
338	throw std::runtime_error(str.str());
339	#else
340	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
341	return;
342	#endif
343	}
344	}
345
346	const Table::Column col = { i, bytes, n, size, n*size, type, unit, comm, compress };
347
348	cols[id] = col;
349	sorted_cols.emplace_back(col);
350	bytes += n*size;
351	}
352
353	if (bytes!=bytes_per_row)
354	{
355	std::ostringstream str;
356	str << "Sum of bytes in columns [" << bytes << "] does not match (Z)NAXIS2 [" << bytes_per_row << "].";
357
358	#ifdef __EXCEPTIONS
359	throw std::runtime_error(str.str());
360	#else
361	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
362	return;
363	#endif
364	}
365
366	name = Get<std::string>("EXTNAME");
367	}
368
369	void PrintKeys(bool display_all=false) const
370	{
371	for (Keys::const_iterator it=keys.cbegin(); it!=keys.cend(); it++)
372	{
373	if (!display_all && FITS::IsReservedKeyWord(it->first))
374	continue;
375
376	gLog << ___all___ << std::setw(2) << it->second.type << '\|' << it->first << '=' << it->second.value << '/' << it->second.comment << '\|' << std::endl;
377	}
378	}
379
380	void PrintColumns() const
381	{
382	typedef std::map<std::pair<size_t, std::string>, Column> Sorted;
383
384	Sorted sorted;
385
386	for (Columns::const_iterator it=cols.cbegin(); it!=cols.cend(); it++)
387	sorted[std::make_pair(it->second.offset, it->first)] = it->second;
388
389	for (Sorted::const_iterator it=sorted.cbegin(); it!=sorted.cend(); it++)
390	{
391	gLog << ___all___ << std::setw(6) << it->second.offset << "\| ";
392	gLog << it->second.num << 'x';
393	switch (it->second.type)
394	{
395	case 'A': gLog << "char(8)"; break;
396	case 'L': gLog << "bool(8)"; break;
397	case 'B': gLog << "byte(8)"; break;
398	case 'I': gLog << "short(16)"; break;
399	case 'J': gLog << "int(32)"; break;
400	case 'K': gLog << "int(64)"; break;
401	case 'E': gLog << "float(32)"; break;
402	case 'D': gLog << "double(64)"; break;
403	}
404	gLog << ": " << it->first.second << " [" << it->second.unit << "]" << std::endl;
405	}
406	}
407
408	operator bool() const { return !name.empty(); }
409
410	bool HasKey(const std::string &key) const
411	{
412	return keys.find(key)!=keys.end();
413	}
414
415	bool HasColumn(const std::string& col) const
416	{
417	return cols.find(col)!=cols.end();
418	}
419
420	const Columns &GetColumns() const
421	{
422	return cols;
423	}
424
425	const Keys &GetKeys() const
426	{
427	return keys;
428	}
429
430	// Values of keys are always signed
431	template<typename T>
432	T Get(const std::string &key) const
433	{
434	const Keys::const_iterator it = keys.find(key);
435	if (it==keys.end())
436	{
437	std::ostringstream str;
438	str << "Key '" << key << "' not found.";
439	#ifdef __EXCEPTIONS
440	throw std::runtime_error(str.str());
441	#else
442	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
443	return T();
444	#endif
445	}
446	return it->second.Get<T>();
447	}
448
449	// Values of keys are always signed
450	template<typename T>
451	T Get(const std::string &key, const T &deflt) const
452	{
453	const Keys::const_iterator it = keys.find(key);
454	return it==keys.end() ? deflt :it->second.Get<T>();
455	}
456
457	size_t GetN(const std::string &key) const
458	{
459	const Columns::const_iterator it = cols.find(key);
460	return it==cols.end() ? 0 : it->second.num;
461	}
462
463
464
465	// There may be a gap between the main table and the start of the heap:
466	// this computes the offset
467	streamoff GetHeapShift() const
468	{
469	if (!HasKey("ZHEAPPTR"))
470	return 0;
471
472	const size_t shift = Get<size_t>("ZHEAPPTR");
473	return shift <= total_bytes ? 0 : shift - total_bytes;
474	}
475
476	// return total number of bytes 'all inclusive'
477	streamoff GetTotalBytes() const
478	{
479	//get offset of special data area from start of main table
480	const streamoff shift = GetHeapShift();
481
482	//and special data area size
483	const streamoff size = HasKey("PCOUNT") ? Get<streamoff>("PCOUNT") : 0;
484
485	// Get the total size
486	const streamoff total = total_bytes + size + shift;
487
488	// check for padding
489	if (total%2880==0)
490	return total;
491
492	// padding necessary
493	return total + (2880 - (total%2880));
494	}
495	};
496
497	void Exception(const std::string &txt)
498	{
499	#ifdef __EXCEPTIONS
500	if (exceptions()&throwbit)
501	throw std::runtime_error(txt);
502	#endif
503	gLog << ___err___ << "ERROR - " << txt << std::endl;
504	}
505
506	// Public for the root dictionary
507	typedef std::pair<void*, Table::Column> Address;
508	typedef std::vector<Address> Addresses;
509	typedef std::unordered_map<std::string, void*> Pointers;
510
511	protected:
512	std::ofstream fCopy;
513	std::vector<std::string> fListOfTables; // List of skipped tables. Last table is open table
514
515	Table fTable;
516
517	//map<void*, Table::Column> fAddresses;
518	Addresses fAddresses;
519
520	Pointers fPointers;
521
522	std::vector<std::vector<char>> fGarbage;
523
524	std::vector<char> fBufferRow;
525	std::vector<char> fBufferDat;
526
527	size_t fRow;
528
529	Checksum fChkHeader;
530	Checksum fChkData;
531
532	bool ReadBlock(std::vector<std::string> &vec)
533	{
534	int endtag = 0;
535	for (int i=0; i<36; i++)
536	{
537	char c[81];
538	c[80] = 0;
539	read(c, 80);
540	if (!good())
541	break;
542
543	fChkHeader.add(c, 80);
544
545	// if (c[0]==0)
546	// return vector<string>();
547
548	std::string str(c);
549
550	// if (!str.empty())
551	// cout << setw(2) << i << "\|" << str << "\|" << (endtag?'-':'+') << endl;
552
553	if (endtag==2 \|\| str=="END ")
554	{
555	endtag = 2; // valid END tag found
556	continue;
557	}
558
559	if (endtag==1 \|\| str==" ")
560	{
561	endtag = 1; // end tag not found, but expected to be there
562	continue;
563	}
564
565	vec.emplace_back(str);
566	}
567
568	// Make sure that no empty vector is returned
569	if (endtag && vec.size()%36==0)
570	vec.emplace_back("END = '' / ");
571
572	return endtag==2;
573	}
574
575	std::string Compile(const std::string &key, int16_t i=-1) const
576	{
577	#if GCC_VERSION < 40603
578	return i<0 ? key : key+std::to_string((long long int)(i));
579	#else
580	return i<0 ? key : key+std::to_string(i);
581	#endif
582	}
583
584	void Constructor(const std::string &fname, std::string fout="", const std::string& tableName="", bool force=false)
585	{
586	char simple[10];
587	read(simple, 10);
588	if (!good())
589	return;
590
591	EnableAddressExceptions();
592
593	if (memcmp(simple, "SIMPLE = ", 10))
594	{
595	clear(rdstate()\|std::ios::badbit);
596	#ifdef __EXCEPTIONS
597	throw std::runtime_error("File is not a FITS file.");
598	#else
599	gLog << ___err___ << "ERROR - File is not a FITS file." << std::endl;
600	return;
601	#endif
602	}
603
604	seekg(0);
605
606	while (good())
607	{
608	std::vector<std::string> block;
609	while (1)
610	{
611	// If we search for a table, we implicitly assume that
612	// not finding the table is not an error. The user
613	// can easily check that by eof() && !bad()
614	peek();
615	if (eof() && !bad() && !tableName.empty())
616	{
617	break;
618	}
619	// FIXME: Set limit on memory consumption
620	const int rc = ReadBlock(block);
621	if (!good())
622	{
623	clear(rdstate()\|std::ios::badbit);
624	#ifdef __EXCEPTIONS
625	throw std::runtime_error("FITS file corrupted.");
626	#else
627	gLog << ___err___ << "ERROR - FITS file corrupted." << std::endl;
628	return;
629	#endif
630	}
631
632	if (block.size()%36)
633	{
634	if (!rc && !force)
635	{
636	clear(rdstate()\|std::ios::badbit);
637	#ifdef __EXCEPTIONS
638	throw std::runtime_error("END keyword missing in FITS header.");
639	#else
640	gLog << ___err___ << "ERROR - END keyword missing in FITS file... file might be corrupted." << std::endl;
641	return;
642	#endif
643	}
644	break;
645	}
646	}
647
648	if (block.empty())
649	break;
650
651	if (block[0].substr(0, 9)=="SIMPLE =")
652	{
653	fChkHeader.reset();
654	continue;
655	}
656
657	if (block[0].substr(0, 9)=="XTENSION=")
658	{
659	fTable = Table(block, tellg());
660	fRow = (size_t)-1;
661
662	if (!fTable)
663	{
664	clear(rdstate()\|std::ios::badbit);
665	return;
666	}
667
668	const std::string &tname = fTable.Get<std::string>("EXTNAME");
669
670	fListOfTables.emplace_back(tname);
671
672	// Check for table name. Skip until eof or requested table are found.
673	// skip the current table?
674	if ((!tableName.empty() && tableName!=tname) \|\| (tableName.empty() && "ZDrsCellOffsets"==tname))
675	{
676	const streamoff skip = fTable.GetTotalBytes();
677	seekg(skip, std::ios_base::cur);
678
679	fChkHeader.reset();
680
681	continue;
682	}
683
684	fBufferRow.resize(fTable.bytes_per_row + 8-fTable.bytes_per_row%4);
685	fBufferDat.resize(fTable.bytes_per_row);
686
687	break;
688	}
689	}
690
691	if (fout.empty())
692	return;
693
694	if (*fout.rbegin()=='/')
695	{
696	const size_t p = fname.find_last_of('/');
697	fout.append(fname.substr(p+1));
698	}
699
700	fCopy.open(fout);
701	if (!fCopy)
702	{
703	clear(rdstate()\|std::ios::badbit);
704	#ifdef __EXCEPTIONS
705	throw std::runtime_error("Could not open output file.");
706	#else
707	gLog << ___err___ << "ERROR - Failed to open output file." << std::endl;
708	return;
709	#endif
710	}
711
712	const streampos p = tellg();
713	seekg(0);
714
715	std::vector<char> buf(p);
716	read(buf.data(), p);
717
718	fCopy.write(buf.data(), p);
719	if (!fCopy)
720	clear(rdstate()\|std::ios::badbit);
721	}
722
723	public:
724	fits(const std::string &fname, const std::string& tableName="", bool force=false) : izstream(fname.c_str())
725	{
726	Constructor(fname, "", tableName, force);
727	if ((fTable.is_compressed \|\|fTable.name=="ZDrsCellOffsets") && !force)
728	{
729	#ifdef __EXCEPTIONS
730	throw std::runtime_error("Trying to read a compressed fits with the base fits class. Use factfits instead.");
731	#else
732	gLog << ___err___ << "ERROR - Trying to read a compressed fits with the base fits class. Use factfits instead." << std::endl;
733	#endif
734	clear(rdstate()\|std::ios::badbit);
735	}
736	}
737
738	fits(const std::string &fname, const std::string &fout, const std::string& tableName, bool force=false) : izstream(fname.c_str())
739	{
740	Constructor(fname, fout, tableName, force);
741	if ((fTable.is_compressed \|\| fTable.name=="ZDrsCellOffsets") && !force)
742	{
743	#ifdef __EXCEPTIONS
744	throw std::runtime_error("Trying to read a compressed fits with the base fits class. Use factfits instead.");
745	#else
746	gLog << ___err___ << "ERROR - Trying to read a compressed fits with the base fits class. Use factfits instead." << std::endl;
747	#endif
748	clear(rdstate()\|std::ios::badbit);
749	}
750	}
751
752	fits() : izstream()
753	{
754
755	}
756
757	~fits()
758	{
759	std::copy(std::istreambuf_iterator<char>(*this),
760	std::istreambuf_iterator<char>(),
761	std::ostreambuf_iterator<char>(fCopy));
762	}
763
764	virtual void StageRow(size_t row, char* dest)
765	{
766	// if (row!=fRow+1) // Fast seeking is ensured by izstream
767	seekg(fTable.offset+row*fTable.bytes_per_row);
768	read(dest, fTable.bytes_per_row);
769	//fin.clear(fin.rdstate()&~ios::eofbit);
770	}
771
772	virtual void WriteRowToCopyFile(size_t row)
773	{
774	if (row==fRow+1)
775	{
776	const uint8_t offset = (row*fTable.bytes_per_row)%4;
777
778	fChkData.add(fBufferRow);
779	if (fCopy.is_open() && fCopy.good())
780	fCopy.write(fBufferRow.data()+offset, fTable.bytes_per_row);
781	if (!fCopy)
782	clear(rdstate()\|std::ios::badbit);
783	}
784	else
785	if (fCopy.is_open())
786	clear(rdstate()\|std::ios::badbit);
787	}
788
789	void ZeroBufferForChecksum(std::vector<char>& vec, const uint64_t extraZeros=0)
790	{
791	auto ib = vec.begin();
792	auto ie = vec.end();
793
794	*ib++ = 0;
795	*ib++ = 0;
796	*ib++ = 0;
797	*ib = 0;
798
799	for (uint64_t i=0;i<extraZeros+8;i++)
800	*--ie = 0;
801	}
802
803	uint8_t ReadRow(size_t row)
804	{
805	// For the checksum we need everything to be correctly aligned
806	const uint8_t offset = (row*fTable.bytes_per_row)%4;
807
808	ZeroBufferForChecksum(fBufferRow);
809
810	StageRow(row, fBufferRow.data()+offset);
811
812	WriteRowToCopyFile(row);
813
814	fRow = row;
815
816	return offset;
817	}
818
819	template<size_t N>
820	void revcpy(char dest, const char src, const int &num)
821	{
822	const char pend = src + numN;
823	for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
824	std::reverse_copy(ptr, ptr+N, dest);
825	}
826
827	virtual void MoveColumnDataToUserSpace(char dest, const char src, const Table::Column& c)
828	{
829	// Let the compiler do some optimization by
830	// knowing that we only have 1, 2, 4 and 8
831	switch (c.size)
832	{
833	case 1: memcpy (dest, src, c.bytes); break;
834	case 2: revcpy<2>(dest, src, c.num); break;
835	case 4: revcpy<4>(dest, src, c.num); break;
836	case 8: revcpy<8>(dest, src, c.num); break;
837	}
838	}
839
840	virtual bool GetRow(size_t row, bool check=true)
841	{
842	if (check && row>=fTable.num_rows)
843	return false;
844
845	const uint8_t offset = ReadRow(row);
846	if (!good())
847	return good();
848
849	const char *ptr = fBufferRow.data() + offset;
850
851	for (Addresses::const_iterator it=fAddresses.cbegin(); it!=fAddresses.cend(); it++)
852	{
853	const Table::Column &c = it->second;
854
855	const char *src = ptr + c.offset;
856	char dest = reinterpret_cast<char>(it->first);
857
858	MoveColumnDataToUserSpace(dest, src, c);
859	}
860
861	return good();
862	}
863
864	bool GetNextRow(bool check=true)
865	{
866	return GetRow(fRow+1, check);
867	}
868
869	virtual bool SkipNextRow()
870	{
871	seekg(fTable.offset+(++fRow)*fTable.bytes_per_row);
872	return good();
873	}
874
875	static bool Compare(const Address &p1, const Address &p2)
876	{
877	return p1.first>p2.first;
878	}
879
880	template<class T, class S>
881	const T &GetAs(const std::string &name)
882	{
883	return reinterpret_cast<S>(fPointers[name]);
884	}
885
886	void EnableAddressExceptions(bool b=true)
887	{
888	if (b)
889	exceptions(iostate(throwbit));
890	else
891	exceptions(iostate(exceptions()&~throwbit));
892	}
893
894	void DisableAddressExceptions()
895	{
896	EnableAddressExceptions(false);
897	}
898
899	void *SetPtrAddress(const std::string &name)
900	{
901	if (fTable.cols.count(name)==0)
902	{
903	std::ostringstream str;
904	str << "SetPtrAddress('" << name << "') - Column not found.";
905	Exception(str.str());
906	return NULL;
907	}
908
909	Pointers::const_iterator it = fPointers.find(name);
910	if (it!=fPointers.end())
911	return it->second;
912
913	fGarbage.emplace_back(fTable.cols[name].bytes);
914
915	void *ptr = fGarbage.back().data();
916
917	fPointers[name] = ptr;
918	fAddresses.emplace_back(ptr, fTable.cols[name]);
919	sort(fAddresses.begin(), fAddresses.end(), Compare);
920	return ptr;
921	}
922
923	template<typename T>
924	bool SetPtrAddress(const std::string &name, T *ptr, size_t cnt)
925	{
926	if (fTable.cols.count(name)==0)
927	{
928	std::ostringstream str;
929	str << "SetPtrAddress('" << name << "') - Column not found.";
930	Exception(str.str());
931	return false;
932	}
933
934	if (sizeof(T)!=fTable.cols[name].size)
935	{
936	std::ostringstream str;
937	str << "SetPtrAddress('" << name << "') - Element size mismatch: expected "
938	<< fTable.cols[name].size << " from header, got " << sizeof(T);
939	Exception(str.str());
940	return false;
941	}
942
943	if (cnt!=fTable.cols[name].num)
944	{
945	std::ostringstream str;
946	str << "SetPtrAddress('" << name << "') - Element count mismatch: expected "
947	<< fTable.cols[name].num << " from header, got " << cnt;
948	Exception(str.str());
949	return false;
950	}
951
952	// if (fAddresses.count(ptr)>0)
953	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
954
955	//fAddresses[ptr] = fTable.cols[name];
956	fPointers[name] = ptr;
957	fAddresses.emplace_back(ptr, fTable.cols[name]);
958	sort(fAddresses.begin(), fAddresses.end(), Compare);
959	return true;
960	}
961
962	template<class T>
963	bool SetRefAddress(const std::string &name, T &ptr)
964	{
965	return SetPtrAddress(name, &ptr, sizeof(ptr)/sizeof(T));
966	}
967
968	template<typename T>
969	bool SetVecAddress(const std::string &name, std::vector<T> &vec)
970	{
971	return SetPtrAddress(name, vec.data(), vec.size());
972	}
973
974	template<typename T>
975	T Get(const std::string &key) const
976	{
977	return fTable.Get<T>(key);
978	}
979
980	template<typename T>
981	T Get(const std::string &key, const std::string &deflt) const
982	{
983	return fTable.Get<T>(key, deflt);
984	}
985
986	bool SetPtrAddress(const std::string &name, void *ptr, size_t cnt=0)
987	{
988	if (fTable.cols.count(name)==0)
989	{
990	std::ostringstream str;
991	str <<"SetPtrAddress('" << name << "') - Column not found.";
992	Exception(str.str());
993	return false;
994	}
995
996	if (cnt && cnt!=fTable.cols[name].num)
997	{
998	std::ostringstream str;
999	str << "SetPtrAddress('" << name << "') - Element count mismatch: expected "
1000	<< fTable.cols[name].num << " from header, got " << cnt;
1001	Exception(str.str());
1002	return false;
1003	}
1004
1005	// if (fAddresses.count(ptr)>0)
1006	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
1007
1008	//fAddresses[ptr] = fTable.cols[name];
1009	fPointers[name] = ptr;
1010	fAddresses.emplace_back(ptr, fTable.cols[name]);
1011	sort(fAddresses.begin(), fAddresses.end(), Compare);
1012	return true;
1013	}
1014
1015	bool HasKey(const std::string &key) const { return fTable.HasKey(key); }
1016	bool HasColumn(const std::string& col) const { return fTable.HasColumn(col);}
1017	const Table::Columns &GetColumns() const { return fTable.GetColumns();}
1018	const Table::SortedColumns& GetSortedColumns() const { return fTable.sorted_cols;}
1019	const Table::Keys &GetKeys() const { return fTable.GetKeys();}
1020
1021	int64_t GetInt(const std::string &key) const { return fTable.Get<int64_t>(key); }
1022	uint64_t GetUInt(const std::string &key) const { return fTable.Get<uint64_t>(key); }
1023	double GetFloat(const std::string &key) const { return fTable.Get<double>(key); }
1024	std::string GetStr(const std::string &key) const { return fTable.Get<std::string>(key); }
1025
1026	size_t GetN(const std::string &key) const
1027	{
1028	return fTable.GetN(key);
1029	}
1030
1031	// size_t GetNumRows() const { return fTable.num_rows; }
1032	size_t GetRow() const { return fRow==(size_t)-1 ? 0 : fRow; }
1033
1034	operator bool() const { return fTable && fTable.offset!=0; }
1035
1036	void PrintKeys(bool all_keys=false) const { fTable.PrintKeys(all_keys); }
1037	void PrintColumns() const { fTable.PrintColumns(); }
1038
1039	bool IsHeaderOk() const { return fTable.datasum<0?false:(fChkHeader+Checksum(fTable.datasum)).valid(); }
1040	virtual bool IsFileOk() const { return (fChkHeader+fChkData).valid(); }
1041
1042	bool IsCompressedFITS() const { return fTable.is_compressed;}
1043
1044	virtual size_t GetNumRows() const
1045	{
1046	return fTable.Get<size_t>("NAXIS2");
1047	}
1048
1049	virtual size_t GetBytesPerRow() const
1050	{
1051	return fTable.Get<size_t>("NAXIS1");
1052	}
1053
1054	const std::vector<std::string> &GetTables() const
1055	{
1056	return fListOfTables;
1057	}
1058	};
1059
1060	template<>
1061	inline std::string fits::Entry::Get<std::string>() const
1062	{
1063	return value;
1064	}
1065
1066	#endif

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