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source: trunk/Mars/mcore/fits.h@ 20067

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Last change on this file since 20067 was 20067, checked in by tbretz, 3 years ago
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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	// ROOT_VERSION is not defined in ROOTv5, but special treatment is
19	// needed depending on whether this is to create the disctionary or not
20	// For ROOTv6 now either __CLING__ (dirctionary) or __ROOTv6__ (compiler)
21	// should be defined.
22	#if defined(ROOT_VERSION_CODE)
23	#if ROOT_VERSION_CODE >= ROOT_VERSION(6,00,0)
24	#define __ROOTv6__ 1
25	#endif
26	#endif
27
28	#if !defined(__CINT__) \|\| defined(__CLING__) \|\| defined(__ROOTv6__)
29	#include <unordered_map>
30	#else
31	#define off_t size_t
32	namespace std
33	{
34	template<class T, class S> class unordered_map<T, S>;
35	}
36	#endif
37
38	#if defined(__MARS__) \|\| defined(__CINT__) \|\| defined (__CLING__) \|\| defined (__ROOTv6__)
39	#include "MLog.h"
40	#include "MLogManip.h"
41	#define ___err___ err
42	#define ___warn___ warn
43	#define ___all___ all
44	#else
45	#include <vector>
46	#include <iomanip>
47	#include <iostream>
48	#ifndef gLog
49	#define gLog std::cerr
50	#define ___err___ ""
51	#define ___warn___ ""
52	#define ___all___ ""
53	#endif
54	#endif
55
56	#if defined(HAVE_ZLIB) \|\| defined(__CINT__) \|\| defined(__CLING__) \|\| defined (__ROOTv6__)
57	#include "izstream.h"
58	#else
59	#include <fstream>
60	#define izstream std::ifstream
61	#warning Support for zipped FITS files disabled.
62	#endif
63
64	#include "FITS.h"
65	#include "checksum.h"
66
67	class fits : public izstream
68	{
69	public:
70	//I know I know, you're going to yiell that this does not belong here.
71	//It will belong in the global scope eventually, and it makes the coding of zfits much simpler this way.
72	enum Compression_t
73	{
74	kCompUnknown,
75	kCompFACT
76	};
77
78	enum fitsstate
79	{
80	throwbit = 8
81	};
82
83	struct Entry
84	{
85	char type;
86	std::string value;
87	std::string comment;
88	std::string fitsString;
89
90	template<typename T>
91	T Get() const
92	{
93	T t;
94
95	std::istringstream str(value);
96	str >> t;
97
98	return t;
99	}
100
101	/* Specialization needs to be outside namespace-scope, see below
102	template<>
103	std::string fits::Entry::Get<std::string>() const
104	{
105	return value;
106	}*/
107	};
108
109	struct Table
110	{
111	off_t offset;
112
113	bool is_compressed;
114
115	std::string name;
116	size_t bytes_per_row;
117	size_t num_rows;
118	size_t num_cols;
119	size_t total_bytes; // NAXIS1*NAXIS2
120
121	struct Column
122	{
123	size_t id;
124	size_t offset;
125	size_t num;
126	size_t size;
127	size_t bytes; // num*size
128	char type;
129	std::string unit;
130	std::string comment;
131	Compression_t comp;
132	};
133
134	typedef std::map<std::string, Entry> Keys;
135	typedef std::map<std::string, Column> Columns;
136	typedef std::vector<Column> SortedColumns;
137
138	Columns cols;
139	SortedColumns sorted_cols;
140	Keys keys;
141
142	int64_t datasum;
143
144	std::string Trim(const std::string &str, char c=' ') const
145	{
146	// Trim Both leading and trailing spaces
147	const size_t pstart = str.find_first_not_of(c); // Find the first character position after excluding leading blank spaces
148	const size_t pend = str.find_last_not_of(c); // Find the first character position from reverse af
149
150	// if all spaces or empty return an empty string
151	if (std::string::npos==pstart \|\| std::string::npos==pend)
152	return std::string();
153
154	return str.substr(pstart, pend-pstart+1);
155	}
156
157	bool Check(const std::string &key, char type, const std::string &value="") const
158	{
159	const Keys::const_iterator it = keys.find(key);
160	if (it==keys.end())
161	{
162	std::ostringstream str;
163	str << "Key '" << key << "' not found.";
164	#ifdef __EXCEPTIONS
165	throw std::runtime_error(str.str());
166	#else
167	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
168	return false;
169	#endif
170	}
171
172	if (it->second.type!=type)
173	{
174	std::ostringstream str;
175	str << "Wrong type for key '" << key << "': expected " << type << ", found " << it->second.type << ".";
176	#ifdef __EXCEPTIONS
177	throw std::runtime_error(str.str());
178	#else
179	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
180	return false;
181	#endif
182	}
183
184	if (!value.empty() && it->second.value!=value)
185	{
186	std::ostringstream str;
187	str << "Wrong value for key '" << key << "': expected " << value << ", found " << it->second.value << ".";
188	#ifdef __EXCEPTIONS
189	throw std::runtime_error(str.str());
190	#else
191	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
192	return false;
193	#endif
194	}
195
196	return true;
197	}
198
199	Keys ParseBlock(const std::vector<std::string> &vec) const
200	{
201	Keys rc;
202
203	for (unsigned int i=0; i<vec.size(); i++)
204	{
205	const std::string key = Trim(vec[i].substr(0,8));
206	// Keywords without a value, like COMMENT / HISTORY
207	if (vec[i].substr(8,2)!="= ")
208	continue;
209
210	char type = 0;
211
212	std::string com;
213	std::string val = Trim(vec[i].substr(10));
214
215	if (val[0]=='\'')
216	{
217	// First skip all '' in the string
218	size_t p = 1;
219	while (1)
220	{
221	const size_t pp = val.find_first_of('\'', p);
222	if (pp==std::string::npos)
223	break;
224
225	p = val[pp+1]=='\'' ? pp+2 : pp+1;
226	}
227
228	// Now find the comment
229	const size_t ppp = val.find_first_of('/', p);
230
231	// Set value, comment and type
232	// comments could be just spaces. take care of this.
233	if (ppp!=std::string::npos && val.size()!=ppp+1)
234	com = Trim(val.substr(ppp+1));
235
236	val = Trim(val.substr(1, p-2));
237	type = 'T';
238	}
239	else
240	{
241	const size_t p = val.find_first_of('/');
242
243	if (p!=std::string::npos && val.size()!=p+1)
244	com = Trim(val.substr(p+2));
245
246	val = Trim(val.substr(0, p));
247
248	if (val.empty() \|\| val.find_first_of('T')!=std::string::npos \|\| val.find_first_of('F')!=std::string::npos)
249	type = 'B';
250	else
251	type = val.find_last_of('.')==std::string::npos ? 'I' : 'F';
252	}
253
254	const Entry e = { type, val, com, vec[i] };
255
256	rc[key] = e;
257	}
258
259	return rc;
260	}
261
262	Table() : offset(0), is_compressed(false) { }
263	Table(const std::vector<std::string> &vec, off_t off) : offset(off),
264	keys(ParseBlock(vec))
265	{
266	is_compressed = HasKey("ZTABLE") && Check("ZTABLE", 'B', "T");
267
268	if (!Check("XTENSION", 'T', "BINTABLE") \|\|
269	!Check("NAXIS", 'I', "2") \|\|
270	!Check("BITPIX", 'I', "8") \|\|
271	!Check("GCOUNT", 'I', "1") \|\|
272	!Check("EXTNAME", 'T') \|\|
273	!Check("NAXIS1", 'I') \|\|
274	!Check("NAXIS2", 'I') \|\|
275	!Check("TFIELDS", 'I'))
276	return;
277
278	if (is_compressed)
279	{
280	if (!Check("ZNAXIS1", 'I') \|\|
281	!Check("ZNAXIS2", 'I') \|\|
282	!Check("ZPCOUNT", 'I', "0"))
283	return;
284	}
285	else
286	{
287	if (!Check("PCOUNT", 'I', "0"))
288	return;
289	}
290
291	total_bytes = Get<size_t>("NAXIS1")*Get<size_t>("NAXIS2");
292	bytes_per_row = is_compressed ? Get<size_t>("ZNAXIS1") : Get<size_t>("NAXIS1");
293	num_rows = is_compressed ? Get<size_t>("ZNAXIS2") : Get<size_t>("NAXIS2");
294	num_cols = Get<size_t>("TFIELDS");
295	datasum = Get<int64_t>("DATASUM", -1);
296	size_t bytes = 0;
297
298	const std::string tFormName = is_compressed ? "ZFORM" : "TFORM";
299	for (size_t i=1; i<=num_cols; i++)
300	{
301	const std::string num(std::to_string(i));
302
303	if (!Check("TTYPE"+num, 'T') \|\|
304	!Check(tFormName+num, 'T'))
305	return;
306
307	const std::string id = Get<std::string>("TTYPE"+num);
308	const std::string fmt = Get<std::string>(tFormName+num);
309	const std::string unit = Get<std::string>("TUNIT"+num, "");
310	const std::string comp = Get<std::string>("ZCTYP"+num, "");
311	const std::string comm = Get<std::string>("TCOMM"+num, "");
312
313	Compression_t compress = kCompUnknown;
314	if (comp == "FACT")
315	compress = kCompFACT;
316
317	std::istringstream sin(fmt);
318	size_t n = 0;
319	sin >> n;
320	if (!sin)
321	n = 1;
322
323	const char type = fmt[fmt.length()-1];
324
325	size_t size = 0;
326	switch (type)
327	{
328	// We could use negative values to mark floats
329	// otheriwse we could just cast them to int64_t?
330	case 'L': // logical
331	case 'A': // char
332	case 'B': size = 1; break; // byte
333	case 'I': size = 2; break; // short
334	case 'J': size = 4; break; // int
335	case 'K': size = 8; break; // long long
336	case 'E': size = 4; break; // float
337	case 'D': size = 8; break; // double
338	// case 'X': size = n; break; // bits (n=number of bytes needed to contain all bits)
339	// case 'C': size = 8; break; // complex float
340	// case 'M': size = 16; break; // complex double
341	// case 'P': size = 8; break; // array descriptor (32bit)
342	// case 'Q': size = 16; break; // array descriptor (64bit)
343	default:
344	{
345	std::ostringstream str;
346	str << "FITS format TFORM='" << fmt << "' not yet supported.";
347	#ifdef __EXCEPTIONS
348	throw std::runtime_error(str.str());
349	#else
350	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
351	return;
352	#endif
353	}
354	}
355
356	const Table::Column col = { i, bytes, n, size, n*size, type, unit, comm, compress };
357
358	cols[id] = col;
359	sorted_cols.emplace_back(col);
360	bytes += n*size;
361	}
362
363	if (bytes!=bytes_per_row)
364	{
365	std::ostringstream str;
366	str << "Sum of bytes in columns [" << bytes << "] does not match (Z)NAXIS2 [" << bytes_per_row << "].";
367
368	#ifdef __EXCEPTIONS
369	throw std::runtime_error(str.str());
370	#else
371	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
372	return;
373	#endif
374	}
375
376	name = Get<std::string>("EXTNAME");
377	}
378
379	void PrintKeys(bool display_all=false) const
380	{
381	for (Keys::const_iterator it=keys.cbegin(); it!=keys.cend(); it++)
382	{
383	if (!display_all && FITS::IsReservedKeyWord(it->first))
384	continue;
385
386	gLog << ___all___ << std::setw(2) << it->second.type << '\|' << it->first << '=' << it->second.value << '/' << it->second.comment << '\|' << std::endl;
387	}
388	}
389
390	void PrintColumns() const
391	{
392	typedef std::map<std::pair<size_t, std::string>, Column> Sorted;
393
394	Sorted sorted;
395
396	for (Columns::const_iterator it=cols.cbegin(); it!=cols.cend(); it++)
397	sorted[std::make_pair(it->second.offset, it->first)] = it->second;
398
399	for (Sorted::const_iterator it=sorted.cbegin(); it!=sorted.cend(); it++)
400	{
401	gLog << ___all___ << std::setw(6) << it->second.offset << "\| ";
402	gLog << it->second.num << 'x';
403	switch (it->second.type)
404	{
405	case 'A': gLog << "char(8)"; break;
406	case 'L': gLog << "bool(8)"; break;
407	case 'B': gLog << "byte(8)"; break;
408	case 'I': gLog << "short(16)"; break;
409	case 'J': gLog << "int(32)"; break;
410	case 'K': gLog << "int(64)"; break;
411	case 'E': gLog << "float(32)"; break;
412	case 'D': gLog << "double(64)"; break;
413	}
414	gLog << ": " << it->first.second << " [" << it->second.unit << "]" << std::endl;
415	}
416	}
417
418	operator bool() const { return !name.empty(); }
419
420	bool HasKey(const std::string &key) const
421	{
422	return keys.find(key)!=keys.end();
423	}
424
425	bool HasColumn(const std::string& col) const
426	{
427	return cols.find(col)!=cols.end();
428	}
429
430	const Columns &GetColumns() const
431	{
432	return cols;
433	}
434
435	const Keys &GetKeys() const
436	{
437	return keys;
438	}
439
440	// Values of keys are always signed
441	template<typename T>
442	T Get(const std::string &key) const
443	{
444	const Keys::const_iterator it = keys.find(key);
445	if (it==keys.end())
446	{
447	std::ostringstream str;
448	str << "Key '" << key << "' not found.";
449	#ifdef __EXCEPTIONS
450	throw std::runtime_error(str.str());
451	#else
452	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
453	return T();
454	#endif
455	}
456	return it->second.Get<T>();
457	}
458
459	// Values of keys are always signed
460	template<typename T>
461	T Get(const std::string &key, const T &deflt) const
462	{
463	const Keys::const_iterator it = keys.find(key);
464	return it==keys.end() ? deflt :it->second.Get<T>();
465	}
466
467	size_t GetN(const std::string &key) const
468	{
469	const Columns::const_iterator it = cols.find(key);
470	return it==cols.end() ? 0 : it->second.num;
471	}
472
473
474
475	// There may be a gap between the main table and the start of the heap:
476	// this computes the offset
477	streamoff GetHeapShift() const
478	{
479	if (!HasKey("ZHEAPPTR"))
480	return 0;
481
482	const size_t shift = Get<size_t>("ZHEAPPTR");
483	return shift <= total_bytes ? 0 : shift - total_bytes;
484	}
485
486	// return total number of bytes 'all inclusive'
487	streamoff GetTotalBytes() const
488	{
489	//get offset of special data area from start of main table
490	const streamoff shift = GetHeapShift();
491
492	//and special data area size
493	const streamoff size = HasKey("PCOUNT") ? Get<streamoff>("PCOUNT") : 0;
494
495	// Get the total size
496	const streamoff total = total_bytes + size + shift;
497
498	// check for padding
499	if (total%2880==0)
500	return total;
501
502	// padding necessary
503	return total + (2880 - (total%2880));
504	}
505	};
506
507	void Exception(const std::string &txt)
508	{
509	#ifdef __EXCEPTIONS
510	if (exceptions()&throwbit)
511	throw std::runtime_error(txt);
512	#endif
513	gLog << ___err___ << "ERROR - " << txt << std::endl;
514	}
515
516	// Public for the root dictionary
517	typedef std::pair<void*, Table::Column> Address;
518	typedef std::vector<Address> Addresses;
519	typedef std::unordered_map<std::string, void*> Pointers;
520
521	protected:
522	std::ofstream fCopy;
523	std::vector<std::string> fListOfTables; // List of skipped tables. Last table is open table
524
525	Table fTable;
526
527	//map<void*, Table::Column> fAddresses;
528	Addresses fAddresses;
529
530	Pointers fPointers;
531
532	std::vector<std::vector<char>> fGarbage;
533
534	std::vector<char> fBufferRow;
535	std::vector<char> fBufferDat;
536
537	size_t fRow;
538
539	Checksum fChkHeader;
540	Checksum fChkData;
541
542	bool ReadBlock(std::vector<std::string> &vec)
543	{
544	int endtag = 0;
545	for (int i=0; i<36; i++)
546	{
547	char c[81];
548	c[80] = 0;
549	read(c, 80);
550	if (!good())
551	break;
552
553	fChkHeader.add(c, 80);
554
555	// if (c[0]==0)
556	// return vector<string>();
557
558	std::string str(c);
559
560	// if (!str.empty())
561	// cout << setw(2) << i << "\|" << str << "\|" << (endtag?'-':'+') << endl;
562
563	if (endtag==2 \|\| str=="END ")
564	{
565	endtag = 2; // valid END tag found
566	continue;
567	}
568
569	if (endtag==1 \|\| str==" ")
570	{
571	endtag = 1; // end tag not found, but expected to be there
572	continue;
573	}
574
575	vec.emplace_back(str);
576	}
577
578	// Make sure that no empty vector is returned
579	if (endtag && vec.size()%36==0)
580	vec.emplace_back("END = '' / ");
581
582	return endtag==2;
583	}
584
585	std::string Compile(const std::string &key, int16_t i=-1) const
586	{
587	#if GCC_VERSION < 40603
588	return i<0 ? key : key+std::to_string((long long int)(i));
589	#else
590	return i<0 ? key : key+std::to_string(i);
591	#endif
592	}
593
594	void Constructor(const std::string &fname, std::string fout="", const std::string& tableName="", bool force=false)
595	{
596	char simple[10];
597	read(simple, 10);
598	if (!good())
599	return;
600
601	EnableAddressExceptions();
602
603	if (memcmp(simple, "SIMPLE = ", 10))
604	{
605	clear(rdstate()\|std::ios::badbit);
606	#ifdef __EXCEPTIONS
607	throw std::runtime_error("File is not a FITS file.");
608	#else
609	gLog << ___err___ << "ERROR - File is not a FITS file." << std::endl;
610	return;
611	#endif
612	}
613
614	seekg(0);
615
616	while (good())
617	{
618	std::vector<std::string> block;
619	while (1)
620	{
621	// If we search for a table, we implicitly assume that
622	// not finding the table is not an error. The user
623	// can easily check that by eof() && !bad()
624	peek();
625	if (eof() && !bad() && !tableName.empty())
626	{
627	break;
628	}
629	// FIXME: Set limit on memory consumption
630	const int rc = ReadBlock(block);
631	if (!good())
632	{
633	clear(rdstate()\|std::ios::badbit);
634	#ifdef __EXCEPTIONS
635	throw std::runtime_error("FITS file corrupted.");
636	#else
637	gLog << ___err___ << "ERROR - FITS file corrupted." << std::endl;
638	return;
639	#endif
640	}
641
642	if (block.size()%36)
643	{
644	if (!rc && !force)
645	{
646	clear(rdstate()\|std::ios::badbit);
647	#ifdef __EXCEPTIONS
648	throw std::runtime_error("END keyword missing in FITS header.");
649	#else
650	gLog << ___err___ << "ERROR - END keyword missing in FITS file... file might be corrupted." << std::endl;
651	return;
652	#endif
653	}
654	break;
655	}
656	}
657
658	if (block.empty())
659	break;
660
661	if (block[0].substr(0, 9)=="SIMPLE =")
662	{
663	fChkHeader.reset();
664	continue;
665	}
666
667	if (block[0].substr(0, 9)=="XTENSION=")
668	{
669	fTable = Table(block, tellg());
670	fRow = (size_t)-1;
671
672	if (!fTable)
673	{
674	clear(rdstate()\|std::ios::badbit);
675	return;
676	}
677
678	const std::string &tname = fTable.Get<std::string>("EXTNAME");
679
680	fListOfTables.emplace_back(tname);
681
682	// Check for table name. Skip until eof or requested table are found.
683	// skip the current table?
684	if ((!tableName.empty() && tableName!=tname) \|\| (tableName.empty() && "ZDrsCellOffsets"==tname))
685	{
686	const streamoff skip = fTable.GetTotalBytes();
687	seekg(skip, std::ios_base::cur);
688
689	fChkHeader.reset();
690
691	continue;
692	}
693
694	fBufferRow.resize(fTable.bytes_per_row + 8-fTable.bytes_per_row%4);
695	fBufferDat.resize(fTable.bytes_per_row);
696
697	break;
698	}
699	}
700
701	if (fout.empty())
702	return;
703
704	if (*fout.rbegin()=='/')
705	{
706	const size_t p = fname.find_last_of('/');
707	fout.append(fname.substr(p+1));
708	}
709
710	fCopy.open(fout);
711	if (!fCopy)
712	{
713	clear(rdstate()\|std::ios::badbit);
714	#ifdef __EXCEPTIONS
715	throw std::runtime_error("Could not open output file.");
716	#else
717	gLog << ___err___ << "ERROR - Failed to open output file." << std::endl;
718	return;
719	#endif
720	}
721
722	const streampos p = tellg();
723	seekg(0);
724
725	std::vector<char> buf(p);
726	read(buf.data(), p);
727
728	fCopy.write(buf.data(), p);
729	if (!fCopy)
730	clear(rdstate()\|std::ios::badbit);
731	}
732
733	public:
734	fits(const std::string &fname, const std::string& tableName="", bool force=false) : izstream(fname.c_str())
735	{
736	Constructor(fname, "", tableName, force);
737	if ((fTable.is_compressed \|\|fTable.name=="ZDrsCellOffsets") && !force)
738	{
739	#ifdef __EXCEPTIONS
740	throw std::runtime_error("Trying to read a compressed fits with the base fits class. Use factfits instead.");
741	#else
742	gLog << ___err___ << "ERROR - Trying to read a compressed fits with the base fits class. Use factfits instead." << std::endl;
743	#endif
744	clear(rdstate()\|std::ios::badbit);
745	}
746	}
747
748	fits(const std::string &fname, const std::string &fout, const std::string& tableName, bool force=false) : izstream(fname.c_str())
749	{
750	Constructor(fname, fout, tableName, force);
751	if ((fTable.is_compressed \|\| fTable.name=="ZDrsCellOffsets") && !force)
752	{
753	#ifdef __EXCEPTIONS
754	throw std::runtime_error("Trying to read a compressed fits with the base fits class. Use factfits instead.");
755	#else
756	gLog << ___err___ << "ERROR - Trying to read a compressed fits with the base fits class. Use factfits instead." << std::endl;
757	#endif
758	clear(rdstate()\|std::ios::badbit);
759	}
760	}
761
762	fits() : izstream()
763	{
764
765	}
766
767	~fits()
768	{
769	std::copy(std::istreambuf_iterator<char>(*this),
770	std::istreambuf_iterator<char>(),
771	std::ostreambuf_iterator<char>(fCopy));
772	}
773
774	virtual void StageRow(size_t row, char* dest)
775	{
776	// if (row!=fRow+1) // Fast seeking is ensured by izstream
777	seekg(fTable.offset+row*fTable.bytes_per_row);
778	read(dest, fTable.bytes_per_row);
779	//fin.clear(fin.rdstate()&~ios::eofbit);
780	}
781
782	virtual void WriteRowToCopyFile(size_t row)
783	{
784	if (row==fRow+1)
785	{
786	const uint8_t offset = (row*fTable.bytes_per_row)%4;
787
788	fChkData.add(fBufferRow);
789	if (fCopy.is_open() && fCopy.good())
790	fCopy.write(fBufferRow.data()+offset, fTable.bytes_per_row);
791	if (!fCopy)
792	clear(rdstate()\|std::ios::badbit);
793	}
794	else
795	if (fCopy.is_open())
796	clear(rdstate()\|std::ios::badbit);
797	}
798
799	void ZeroBufferForChecksum(std::vector<char>& vec, const uint64_t extraZeros=0)
800	{
801	auto ib = vec.begin();
802	auto ie = vec.end();
803
804	*ib++ = 0;
805	*ib++ = 0;
806	*ib++ = 0;
807	*ib = 0;
808
809	for (uint64_t i=0;i<extraZeros+8;i++)
810	*--ie = 0;
811	}
812
813	uint8_t ReadRow(size_t row)
814	{
815	// For the checksum we need everything to be correctly aligned
816	const uint8_t offset = (row*fTable.bytes_per_row)%4;
817
818	ZeroBufferForChecksum(fBufferRow);
819
820	StageRow(row, fBufferRow.data()+offset);
821
822	WriteRowToCopyFile(row);
823
824	fRow = row;
825
826	return offset;
827	}
828
829	template<size_t N>
830	void revcpy(char dest, const char src, const int &num)
831	{
832	const char pend = src + numN;
833	for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
834	std::reverse_copy(ptr, ptr+N, dest);
835	}
836
837	virtual void MoveColumnDataToUserSpace(char dest, const char src, const Table::Column& c)
838	{
839	// Let the compiler do some optimization by
840	// knowing that we only have 1, 2, 4 and 8
841	switch (c.size)
842	{
843	case 1: memcpy (dest, src, c.bytes); break;
844	case 2: revcpy<2>(dest, src, c.num); break;
845	case 4: revcpy<4>(dest, src, c.num); break;
846	case 8: revcpy<8>(dest, src, c.num); break;
847	}
848	}
849
850	virtual bool GetRow(size_t row, bool check=true)
851	{
852	if (check && row>=fTable.num_rows)
853	return false;
854
855	const uint8_t offset = ReadRow(row);
856	if (!good())
857	return good();
858
859	const char *ptr = fBufferRow.data() + offset;
860
861	for (Addresses::const_iterator it=fAddresses.cbegin(); it!=fAddresses.cend(); it++)
862	{
863	const Table::Column &c = it->second;
864
865	const char *src = ptr + c.offset;
866	char dest = reinterpret_cast<char>(it->first);
867
868	MoveColumnDataToUserSpace(dest, src, c);
869	}
870
871	return good();
872	}
873
874	bool GetNextRow(bool check=true)
875	{
876	return GetRow(fRow+1, check);
877	}
878
879	virtual bool SkipNextRow()
880	{
881	seekg(fTable.offset+(++fRow)*fTable.bytes_per_row);
882	return good();
883	}
884
885	static bool Compare(const Address &p1, const Address &p2)
886	{
887	return p1.first>p2.first;
888	}
889
890	template<class T, class S>
891	const T &GetAs(const std::string &name)
892	{
893	return reinterpret_cast<S>(fPointers[name]);
894	}
895
896	void EnableAddressExceptions(bool b=true)
897	{
898	if (b)
899	exceptions(iostate(throwbit));
900	else
901	exceptions(iostate(exceptions()&~throwbit));
902	}
903
904	void DisableAddressExceptions()
905	{
906	EnableAddressExceptions(false);
907	}
908
909	void *SetPtrAddress(const std::string &name)
910	{
911	if (fTable.cols.count(name)==0)
912	{
913	std::ostringstream str;
914	str << "SetPtrAddress('" << name << "') - Column not found.";
915	Exception(str.str());
916	return NULL;
917	}
918
919	Pointers::const_iterator it = fPointers.find(name);
920	if (it!=fPointers.end())
921	return it->second;
922
923	fGarbage.emplace_back(fTable.cols[name].bytes);
924
925	void *ptr = fGarbage.back().data();
926
927	fPointers[name] = ptr;
928	fAddresses.emplace_back(ptr, fTable.cols[name]);
929	sort(fAddresses.begin(), fAddresses.end(), Compare);
930	return ptr;
931	}
932
933	template<typename T>
934	bool SetPtrAddress(const std::string &name, T *ptr, size_t cnt)
935	{
936	if (fTable.cols.count(name)==0)
937	{
938	std::ostringstream str;
939	str << "SetPtrAddress('" << name << "') - Column not found.";
940	Exception(str.str());
941	return false;
942	}
943
944	if (sizeof(T)!=fTable.cols[name].size)
945	{
946	std::ostringstream str;
947	str << "SetPtrAddress('" << name << "') - Element size mismatch: expected "
948	<< fTable.cols[name].size << " from header, got " << sizeof(T);
949	Exception(str.str());
950	return false;
951	}
952
953	if (cnt!=fTable.cols[name].num)
954	{
955	std::ostringstream str;
956	str << "SetPtrAddress('" << name << "') - Element count mismatch: expected "
957	<< fTable.cols[name].num << " from header, got " << cnt;
958	Exception(str.str());
959	return false;
960	}
961
962	// if (fAddresses.count(ptr)>0)
963	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
964
965	//fAddresses[ptr] = fTable.cols[name];
966	fPointers[name] = ptr;
967	fAddresses.emplace_back(ptr, fTable.cols[name]);
968	sort(fAddresses.begin(), fAddresses.end(), Compare);
969	return true;
970	}
971
972	template<class T>
973	bool SetRefAddress(const std::string &name, T &ptr)
974	{
975	return SetPtrAddress(name, &ptr, sizeof(ptr)/sizeof(T));
976	}
977
978	template<typename T>
979	bool SetVecAddress(const std::string &name, std::vector<T> &vec)
980	{
981	return SetPtrAddress(name, vec.data(), vec.size());
982	}
983
984	template<typename T>
985	T Get(const std::string &key) const
986	{
987	return fTable.Get<T>(key);
988	}
989
990	template<typename T>
991	T Get(const std::string &key, const std::string &deflt) const
992	{
993	return fTable.Get<T>(key, deflt);
994	}
995
996	bool SetPtrAddress(const std::string &name, void *ptr, size_t cnt=0)
997	{
998	if (fTable.cols.count(name)==0)
999	{
1000	std::ostringstream str;
1001	str <<"SetPtrAddress('" << name << "') - Column not found.";
1002	Exception(str.str());
1003	return false;
1004	}
1005
1006	if (cnt && cnt!=fTable.cols[name].num)
1007	{
1008	std::ostringstream str;
1009	str << "SetPtrAddress('" << name << "') - Element count mismatch: expected "
1010	<< fTable.cols[name].num << " from header, got " << cnt;
1011	Exception(str.str());
1012	return false;
1013	}
1014
1015	// if (fAddresses.count(ptr)>0)
1016	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
1017
1018	//fAddresses[ptr] = fTable.cols[name];
1019	fPointers[name] = ptr;
1020	fAddresses.emplace_back(ptr, fTable.cols[name]);
1021	sort(fAddresses.begin(), fAddresses.end(), Compare);
1022	return true;
1023	}
1024
1025	bool HasKey(const std::string &key) const { return fTable.HasKey(key); }
1026	bool HasColumn(const std::string& col) const { return fTable.HasColumn(col);}
1027	const Table::Columns &GetColumns() const { return fTable.GetColumns();}
1028	const Table::SortedColumns& GetSortedColumns() const { return fTable.sorted_cols;}
1029	const Table::Keys &GetKeys() const { return fTable.GetKeys();}
1030
1031	int64_t GetInt(const std::string &key) const { return fTable.Get<int64_t>(key); }
1032	uint64_t GetUInt(const std::string &key) const { return fTable.Get<uint64_t>(key); }
1033	double GetFloat(const std::string &key) const { return fTable.Get<double>(key); }
1034	std::string GetStr(const std::string &key) const { return fTable.Get<std::string>(key); }
1035
1036	size_t GetN(const std::string &key) const
1037	{
1038	return fTable.GetN(key);
1039	}
1040
1041	// size_t GetNumRows() const { return fTable.num_rows; }
1042	size_t GetRow() const { return fRow==(size_t)-1 ? 0 : fRow; }
1043
1044	operator bool() const { return fTable && fTable.offset!=0; }
1045
1046	void PrintKeys(bool all_keys=false) const { fTable.PrintKeys(all_keys); }
1047	void PrintColumns() const { fTable.PrintColumns(); }
1048
1049	bool IsHeaderOk() const { return fTable.datasum<0?false:(fChkHeader+Checksum(fTable.datasum)).valid(); }
1050	virtual bool IsFileOk() const { return (fChkHeader+fChkData).valid(); }
1051	Checksum GetChecksum() const { return fChkHeader+Checksum(fTable.datasum); }
1052
1053	bool IsCompressedFITS() const { return fTable.is_compressed;}
1054
1055	virtual size_t GetNumRows() const
1056	{
1057	return fTable.Get<size_t>("NAXIS2");
1058	}
1059
1060	virtual size_t GetBytesPerRow() const
1061	{
1062	return fTable.Get<size_t>("NAXIS1");
1063	}
1064
1065	const std::vector<std::string> &GetTables() const
1066	{
1067	return fListOfTables;
1068	}
1069	};
1070
1071	template<>
1072	inline std::string fits::Entry::Get<std::string>() const
1073	{
1074	return value;
1075	}
1076
1077	#endif

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