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source: trunk/Mars/mcore/ofits.h@ 17581

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Last change on this file since 17581 was 17559, checked in by aparavac, 11 years ago
Added compatibilty for gcc 4.7 and c11 std
File size: 33.6 KB

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1	#ifndef MARS_ofits
2	#define MARS_ofits
3
4	#include <string>
5	#include <string.h>
6	#include <algorithm>
7	#include <sstream>
8	#include <iostream>
9	#include <fstream>
10	#include <iomanip>
11	#include <vector>
12	#include <algorithm>
13	#include <stdexcept>
14
15	#define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
16
17	#ifdef __CINT__
18	#define off_t size_t
19	#endif
20
21	#ifndef __MARS__
22	#ifndef gLog
23	#define gLog std::cerr
24	#define ___err___ ""
25	#define ___warn___ ""
26	#define ___all___ ""
27	#endif
28	#else
29	#include "MLog.h"
30	#include "MLogManip.h"
31	#define ___err___ err
32	#define ___warn___ warn
33	#define ___all___ all
34	#endif
35
36	#include "FITS.h"
37	#include "checksum.h"
38
39	// Sloppy: allow / <--- left
40	// allow all characters (see specs for what is possible)
41
42	// units: m kg s rad sr K A mol cd Hz J W V N Pa C Ohm S F Wb T Hlm lx
43
44	class ofits : public std::ofstream
45	{
46	public:
47	struct Key
48	{
49	std::string key;
50	bool delim;
51	std::string value;
52	std::string comment;
53	std::string fitsString;
54
55	off_t offset; // offset in file
56
57	bool changed; // For closing the file
58
59	Key(const std::string &k="") : key(k), delim(false), fitsString(""), offset(0), changed(true) { }
60
61	std::string Trim(const std::string &str)
62	{
63	// Trim Both leading and trailing spaces
64	const size_t first = str.find_first_not_of(' '); // Find the first character position after excluding leading blank spaces
65	const size_t last = str.find_last_not_of(' '); // Find the first character position from reverse af
66
67	// if all spaces or empty return an empty string
68	if (std::string::npos==first \|\| std::string::npos==last)
69	return std::string();
70
71	return str.substr(first, last-first+1);
72	}
73
74	bool FormatKey()
75	{
76	key = Trim(key);
77	if (key.empty())
78	{
79	#ifdef __EXCEPTIONS
80	throw std::runtime_error("Key name empty.");
81	#else
82	gLog << ___err___ << "ERROR - Key name empty." << std::endl;
83	return false;
84	#endif
85	}
86	if (key.size()>8)
87	{
88	std::ostringstream sout;
89	sout << "Key '" << key << "' exceeds 8 bytes.";
90	#ifdef __EXCEPTIONS
91	throw std::runtime_error(sout.str());
92	#else
93	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
94	return false;
95	#endif
96	}
97
98	//transform(key.begin(), key.end(), key.begin(), toupper);
99	#if GCC_VERSION < 40603
100	for (std::string::const_iterator c=key.begin(); c<key.end(); c++)
101	#else
102	for (std::string::const_iterator c=key.cbegin(); c<key.cend(); c++)
103	#endif
104	if ((c<'A' \|\| c>'Z') && (c<'0' \|\| c>'9') && c!='-' && c!='_')
105	{
106	std::ostringstream sout;
107	sout << "Invalid character '" << *c << "' found in key '" << key << "'";
108	#ifdef __EXCEPTIONS
109	throw std::runtime_error(sout.str());
110	#else
111	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
112	return false;
113	#endif
114	}
115
116	return true;
117	}
118
119	bool FormatComment()
120	{
121	comment = Trim(comment);
122
123	#if GCC_VERSION < 40603
124	for (std::string::const_iterator c=key.begin(); c<key.end(); c++)
125	#else
126	for (std::string::const_iterator c=key.cbegin(); c<key.cend(); c++)
127	#endif
128	if (c<32 \|\| c>126)
129	{
130	std::ostringstream sout;
131	sout << "Invalid character '" << c << "' [" << int(c) << "] found in comment '" << comment << "'";
132	#ifdef __EXCEPTIONS
133	throw std::runtime_error(sout.str());
134	#else
135	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
136	return false;
137	#endif
138	}
139
140	return true;
141	}
142
143	bool check(bool trim=false)
144	{
145	if (!FormatKey())
146	return false;
147
148	if (!FormatComment())
149	return false;
150
151	size_t sz = CalcSize();
152	if (sz<=80)
153	return true;
154
155	if (!trim)
156	{
157	std::ostringstream sout;
158	sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters.";
159	#ifdef __EXCEPTIONS
160	throw std::runtime_error(sout.str());
161	#else
162	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
163	#endif
164	return false;
165	}
166
167	//looks like something went wrong. Maybe entry is too long ?
168	//try to remove the comment
169	comment = "";
170
171	sz = CalcSize();
172	if (sz<=80)
173	{
174	#ifndef __EXCEPTIONS
175	std::ostringstream sout;
176	sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters... removed comment.";
177	gLog << ___warn___ << "WARNING - " << sout.str() << std::endl;
178	#endif
179	return true;
180	}
181
182	std::ostringstream sout;
183	sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters even without comment.";
184	#ifdef __EXCEPTIONS
185	throw std::runtime_error(sout.str());
186	#else
187	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
188	return false;
189	#endif
190	}
191
192	size_t CalcSize() const
193	{
194	if (!delim)
195	return 10+comment.size();
196
197	return 10 + (value.size()<20?20:value.size()) + 3 + comment.size();
198	}
199
200	std::string Compile()
201	{
202
203	if (fitsString != "")
204	return fitsString;
205
206	std::ostringstream sout;
207	sout << std::left << std::setw(8) << key;
208
209	if (!delim)
210	{
211	sout << " " << comment;
212	return sout.str();
213	}
214
215	sout << "= ";
216	sout << (!value.empty() && value[0]=='\''?std::left:std::right);
217	sout << std::setw(20) << value << std::left;
218
219	if (!comment.empty())
220	sout << " / " << comment;
221
222	return sout.str();
223	}
224
225	Checksum checksum;
226
227	void Out(std::ofstream &fout)
228	{
229	if (!changed)
230	return;
231
232	std::string str = Compile();
233	str.insert(str.end(), 80-str.size(), ' ');
234
235	if (offset==0)
236	offset = fout.tellp();
237
238	//cout << "Write[" << offset << "]: " << key << "/" << value << endl;
239
240	fout.seekp(offset);
241	fout << str;
242
243	checksum.reset();
244	checksum.add(str.c_str(), 80);
245
246	changed = false;
247	}
248	/*
249	void Out(ostream &out)
250	{
251	std::string str = Compile();
252
253	str.insert(str.end(), 80-str.size(), ' ');
254
255	out << str;
256	changed = false;
257	}*/
258	};
259
260	private:
261	std::vector<Key> fKeys;
262
263	std::vector<Key>::iterator findkey(const std::string &key)
264	{
265	for (auto it=fKeys.begin(); it!=fKeys.end(); it++)
266	if (key==it->key)
267	return it;
268
269	return fKeys.end();
270	}
271
272	bool Set(const std::string &key="", bool delim=false, const std::string &value="", const std::string &comment="")
273	{
274	// If no delimit add the row no matter if it alread exists
275	if (delim)
276	{
277	// if the row already exists: update it
278	auto it = findkey(key);
279	if (it!=fKeys.end())
280	{
281	it->value = value;
282	it->changed = true;
283	return true;
284	}
285	}
286
287	if (fTable.num_rows>0)
288	{
289	std::ostringstream sout;
290	sout << "No new header key can be defined, rows were already written to the file... ignoring new key '" << key << "'";
291	#ifdef __EXCEPTIONS
292	throw std::runtime_error(sout.str());
293	#else
294	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
295	return false;
296	#endif
297	}
298
299	Key entry;
300
301	entry.key = key;
302	entry.delim = delim;
303	entry.value = value;
304	entry.comment = comment;
305	entry.offset = 0;
306	entry.changed = true;
307
308	if (!entry.check(fCommentTrimming))
309	return false;
310
311	fKeys.push_back(entry);
312	return true;
313	}
314
315	protected:
316	struct Table
317	{
318	off_t offset;
319
320	size_t bytes_per_row;
321	size_t num_rows;
322	size_t num_cols;
323
324	struct Column
325	{
326	std::string name;
327	size_t offset;
328	size_t num;
329	size_t size;
330	char type;
331	};
332
333	std::vector<Column> cols;
334
335	Table() : offset(0), bytes_per_row(0), num_rows(0), num_cols(0)
336	{
337	}
338	};
339
340
341	Table fTable;
342
343	std::vector<char> fOutputBuffer;
344
345	std::vector<Table::Column>::const_iterator findcol(const std::string &name)
346	{
347	for (auto it=fTable.cols.cbegin(); it!=fTable.cols.cend(); it++)
348	if (name==it->name)
349	return it;
350
351	return fTable.cols.cend();
352	}
353
354	Checksum fDataSum;
355	Checksum fHeaderSum;
356
357	bool fCommentTrimming;
358	bool fManualExtName;
359
360	public:
361	ofits() : fCommentTrimming(false),
362	fManualExtName(false)
363	{
364	}
365	ofits(const char *fname) : std::ofstream(),
366	fCommentTrimming(false),
367	fManualExtName(false)
368	{
369	this->open(fname);
370	}
371	virtual ~ofits() { if (is_open()) close(); }
372
373	virtual void open(const char * filename, bool addEXTNAMEKey=true)
374	{
375	fDataSum = 0;
376	fHeaderSum = 0;
377
378	fTable = Table();
379	fKeys.clear();
380
381	SetStr("XTENSION", "BINTABLE", "binary table extension");
382	SetInt("BITPIX", 8, "8-bit bytes");
383	SetInt("NAXIS", 2, "2-dimensional binary table");
384	SetInt("NAXIS1", 0, "width of table in bytes");
385	SetInt("NAXIS2", 0, "number of rows in table");
386	SetInt("PCOUNT", 0, "size of special data area");
387	SetInt("GCOUNT", 1, "one data group (required keyword)");
388	SetInt("TFIELDS", 0, "number of fields in each row");
389	if (addEXTNAMEKey)
390	SetStr("EXTNAME", "", "name of extension table");
391	else
392	fManualExtName = true;
393	SetStr("CHECKSUM", "0000000000000000", "Checksum for the whole HDU");
394	SetStr("DATASUM", " 0", "Checksum for the data block");
395
396	std::ofstream::open(filename);
397	}
398
399	void AllowCommentsTrimming(bool allow)
400	{
401	fCommentTrimming = allow;
402	}
403	//Etienne: required to enable 1 to 1 reconstruction of files
404	bool SetKeyComment(const std::string& key, const std::string& comment)
405	{
406	auto it = findkey(key);
407	if (it==fKeys.end())
408	return false;
409	it->comment = comment;
410	it->changed = true;
411	return true;
412	}
413	bool SetKeyFromFitsString(const std::string& fitsString)
414	{
415	if (fTable.num_rows>0)
416	{
417	std::ostringstream sout;
418	sout << "No new header key can be defined, rows were already written to the file... ignoring new key '" << fitsString << "'";
419	#ifdef __EXCEPTIONS
420	throw std::runtime_error(sout.str());
421	#else
422	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
423	return false;
424	#endif
425	}
426
427	Key entry;
428	entry.fitsString = fitsString;
429	entry.changed = true;
430	fKeys.push_back(entry);
431	return true;
432	}
433	bool SetRaw(const std::string &key, const std::string &val, const std::string &comment)
434	{
435	return Set(key, true, val, comment);
436	}
437
438	bool SetBool(const std::string &key, bool b, const std::string &comment="")
439	{
440	return Set(key, true, b?"T":"F", comment);
441	}
442
443	bool AddEmpty(const std::string &key, const std::string &comment="")
444	{
445	return Set(key, true, "", comment);
446	}
447
448	bool SetStr(const std::string &key, std::string s, const std::string &comment="")
449	{
450	for (uint i=0; i<s.length(); i++)
451	if (s[i]=='\'')
452	s.insert(i++, "\'");
453
454	return Set(key, true, "'"+s+"'", comment);
455	}
456
457	bool SetInt(const std::string &key, int64_t i, const std::string &comment="")
458	{
459	std::ostringstream sout;
460	sout << i;
461
462	return Set(key, true, sout.str(), comment);
463	}
464
465	bool SetFloat(const std::string &key, double f, int p, const std::string &comment="")
466	{
467	std::ostringstream sout;
468
469	if (p<0)
470	sout << std::setprecision(-p) << fixed;
471	if (p>0)
472	sout << std::setprecision(p);
473	if (p==0)
474	sout << std::setprecision(f>1e-100 && f<1e100 ? 15 : 14);
475
476	sout << f;
477
478	std::string str = sout.str();
479
480	replace(str.begin(), str.end(), 'e', 'E');
481
482	if (str.find_first_of('E')==std::string::npos && str.find_first_of('.')==std::string::npos)
483	str += ".";
484
485	return Set(key, true, str, comment);
486	}
487
488	bool SetFloat(const std::string &key, double f, const std::string &comment="")
489	{
490	return SetFloat(key, f, 0, comment);
491	}
492
493	bool SetHex(const std::string &key, uint64_t i, const std::string &comment="")
494	{
495	std::ostringstream sout;
496	sout << std::hex << "0x" << i;
497	return SetStr(key, sout.str(), comment);
498	}
499
500	bool AddComment(const std::string &comment)
501	{
502	return Set("COMMENT", false, "", comment);
503	}
504
505	bool AddHistory(const std::string &comment)
506	{
507	return Set("HISTORY", false, "", comment);
508	}
509
510	void End()
511	{
512	Set("END");
513	while (fKeys.size()%36!=0)
514	fKeys.emplace_back();
515	}
516
517	std::string CommentFromType(char type)
518	{
519	std::string comment;
520
521	switch (type)
522	{
523	case 'L': comment = "[1-byte BOOL]"; break;
524	case 'A': comment = "[1-byte CHAR]"; break;
525	case 'B': comment = "[1-byte BOOL]"; break;
526	case 'I': comment = "[2-byte INT]"; break;
527	case 'J': comment = "[4-byte INT]"; break;
528	case 'K': comment = "[8-byte INT]"; break;
529	case 'E': comment = "[4-byte FLOAT]"; break;
530	case 'D': comment = "[8-byte FLOAT]"; break;
531	case 'Q': comment = "[var. Length]"; break;
532	}
533
534	return comment;
535	}
536
537	uint32_t SizeFromType(char type)
538	{
539	size_t size = 0;
540
541	switch (type)
542	{
543	case 'L': size = 1; break;
544	case 'A': size = 1; break;
545	case 'B': size = 1; break;
546	case 'I': size = 2; break;
547	case 'J': size = 4; break;
548	case 'K': size = 8; break;
549	case 'E': size = 4; break;
550	case 'D': size = 8; break;
551	case 'Q': size = 16; break;
552	}
553
554	return size;
555	}
556	//ETIENNE to be able to restore the file 1 to 1, I must restore the header keys myself
557	virtual bool AddColumn(uint32_t cnt, char typechar, const std::string &name, const std::string &unit, const std::string &comment="", bool addHeaderKeys=true)
558	{
559	if (tellp()<0)
560	{
561	std::ostringstream sout;
562	sout << "File not open... ignoring column '" << name << "'";
563	#ifdef __EXCEPTIONS
564	throw std::runtime_error(sout.str());
565	#else
566	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
567	return false;
568	#endif
569	}
570
571	if (tellp()>0)
572	{
573	std::ostringstream sout;
574	sout << "Header already written, no new column can be defined... ignoring column '" << name << "'";
575	#ifdef __EXCEPTIONS
576	throw std::runtime_error(sout.str());
577	#else
578	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
579	return false;
580	#endif
581	}
582
583	if (findcol(name)!=fTable.cols.cend())
584	{
585	std::ostringstream sout;
586	sout << "A column with the name '" << name << "' already exists.";
587	#ifdef __EXCEPTIONS
588	throw std::runtime_error(sout.str());
589	#else
590	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
591	return false;
592	#endif
593	}
594
595	typechar = toupper(typechar);
596
597	static const std::string allow("LABIJKEDQ");
598	#if GCC_VERSION < 40603
599	if (std::find(allow.begin(), allow.end(), typechar)==allow.end())
600	#else
601	if (std::find(allow.cbegin(), allow.cend(), typechar)==allow.end())
602	#endif
603	{
604	std::ostringstream sout;
605	sout << "Column type '" << typechar << "' not supported.";
606	#ifdef __EXCEPTIONS
607	throw std::runtime_error(sout.str());
608	#else
609	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
610	return false;
611	#endif
612	}
613
614	std::ostringstream type;
615	type << cnt;
616	if (typechar=='Q')
617	type << "QB";
618	else
619	type << typechar;
620
621	fTable.num_cols++;
622
623	if (addHeaderKeys)
624	{
625	#if GCC_VERSION < 40603
626	const std::string nc = std::to_string((long long int)(fTable.num_cols));
627	#else
628	const std::string nc = std::to_string(fTable.num_cols);
629	#endif
630	SetStr("TFORM"+nc, type.str(), "format of "+name+" "+CommentFromType(typechar));
631	SetStr("TTYPE"+nc, name, comment);
632	if (!unit.empty())
633	SetStr("TUNIT"+nc, unit, "unit of "+name);
634	}
635	size_t size = SizeFromType(typechar);
636
637	Table::Column col;
638
639	col.name = name;
640	col.type = typechar;
641	col.num = cnt;
642	col.size = size;
643	col.offset = fTable.bytes_per_row;
644
645	fTable.cols.push_back(col);
646
647	fTable.bytes_per_row += size*cnt;
648
649	// Align to four bytes
650	fOutputBuffer.resize(fTable.bytes_per_row + 4-fTable.bytes_per_row%4);
651
652	return true;
653	}
654
655	virtual bool AddColumn(const FITS::Compression&, uint32_t cnt, char typechar, const std::string& name, const std::string& unit, const std::string& comment="", bool addHeaderKeys=true)
656	{
657	return AddColumn(cnt, typechar, name, unit, comment, addHeaderKeys);
658	}
659
660	bool AddColumnShort(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
661	{ return AddColumn(cnt, 'I', name, unit, comment); }
662	bool AddColumnInt(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
663	{ return AddColumn(cnt, 'J', name, unit, comment); }
664	bool AddColumnLong(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
665	{ return AddColumn(cnt, 'K', name, unit, comment); }
666	bool AddColumnFloat(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
667	{ return AddColumn(cnt, 'E', name, unit, comment); }
668	bool AddColumnDouble(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
669	{ return AddColumn(cnt, 'D', name, unit, comment); }
670	bool AddColumnChar(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
671	{ return AddColumn(cnt, 'A', name, unit, comment); }
672	bool AddColumnByte(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
673	{ return AddColumn(cnt, 'B', name, unit, comment); }
674	bool AddColumnBool(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
675	{ return AddColumn(cnt, 'L', name, unit, comment); }
676
677	bool AddColumnShort(const std::string &name, const std::string &unit="", const std::string &comment="")
678	{ return AddColumn(1, 'I', name, unit, comment); }
679	bool AddColumnInt(const std::string &name, const std::string &unit="", const std::string &comment="")
680	{ return AddColumn(1, 'J', name, unit, comment); }
681	bool AddColumnLong(const std::string &name, const std::string &unit="", const std::string &comment="")
682	{ return AddColumn(1, 'K', name, unit, comment); }
683	bool AddColumnFloat(const std::string &name, const std::string &unit="", const std::string &comment="")
684	{ return AddColumn(1, 'E', name, unit, comment); }
685	bool AddColumnDouble(const std::string &name, const std::string &unit="", const std::string &comment="")
686	{ return AddColumn(1, 'D', name, unit, comment); }
687	bool AddColumnChar(const std::string &name, const std::string &unit="", const std::string &comment="")
688	{ return AddColumn(1, 'A', name, unit, comment); }
689	bool AddColumnByte(const std::string &name, const std::string &unit="", const std::string &comment="")
690	{ return AddColumn(1, 'B', name, unit, comment); }
691	bool AddColumnBool(const std::string &name, const std::string &unit="", const std::string &comment="")
692	{ return AddColumn(1, 'L', name, unit, comment); }
693
694	bool AddColumnShort(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
695	{ return AddColumn(comp, cnt, 'I', name, unit, comment); }
696	bool AddColumnInt(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
697	{ return AddColumn(comp, cnt, 'J', name, unit, comment); }
698	bool AddColumnLong(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
699	{ return AddColumn(comp, cnt, 'K', name, unit, comment); }
700	bool AddColumnFloat(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
701	{ return AddColumn(comp, cnt, 'E', name, unit, comment); }
702	bool AddColumnDouble(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
703	{ return AddColumn(comp, cnt, 'D', name, unit, comment); }
704	bool AddColumnChar(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
705	{ return AddColumn(comp, cnt, 'A', name, unit, comment); }
706	bool AddColumnByte(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
707	{ return AddColumn(comp, cnt, 'B', name, unit, comment); }
708	bool AddColumnBool(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
709	{ return AddColumn(comp, cnt, 'L', name, unit, comment); }
710
711	bool AddColumnShort(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
712	{ return AddColumn(comp, 1, 'I', name, unit, comment); }
713	bool AddColumnInt(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
714	{ return AddColumn(comp, 1, 'J', name, unit, comment); }
715	bool AddColumnLong(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
716	{ return AddColumn(comp, 1, 'K', name, unit, comment); }
717	bool AddColumnFloat(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
718	{ return AddColumn(comp, 1, 'E', name, unit, comment); }
719	bool AddColumnDouble(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
720	{ return AddColumn(comp, 1, 'D', name, unit, comment); }
721	bool AddColumnChar(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
722	{ return AddColumn(comp, 1, 'A', name, unit, comment); }
723	bool AddColumnByte(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
724	{ return AddColumn(comp, 1, 'B', name, unit, comment); }
725	bool AddColumnBool(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
726	{ return AddColumn(comp, 1, 'L', name, unit, comment); }
727
728	/*
729	bool AddKey(string key, double d, const std::string &comment)
730	{
731	ostringstream out;
732	out << d;
733
734	std::string s = out.str();
735
736	replace(s.begin(), s.end(), "e", "E");
737
738	return AddKey(key, s, comment);
739	}*/
740
741
742	Checksum WriteHeader(std::ofstream &fout)
743	{
744	Checksum sum;
745	uint32_t count=0;
746	for (auto it=fKeys.begin(); it!=fKeys.end(); it++)
747	{
748	it->Out(fout);
749	sum += it->checksum;
750	count++;
751	}
752	fout.flush();
753
754	return sum;
755	}
756
757	Checksum WriteHeader()
758	{
759	return WriteHeader(*this);
760	}
761
762	void FlushHeader()
763	{
764	const off_t pos = tellp();
765	WriteHeader();
766	seekp(pos);
767	}
768
769	Checksum WriteFitsHeader()
770	{
771	ofits h;
772
773	h.SetBool("SIMPLE", true, "file does conform to FITS standard");
774	h.SetInt ("BITPIX", 8, "number of bits per data pixel");
775	h.SetInt ("NAXIS", 0, "number of data axes");
776	h.SetBool("EXTEND", true, "FITS dataset may contain extensions");
777	h.SetStr ("CHECKSUM","0000000000000000", "Checksum for the whole HDU");
778	h.SetStr ("DATASUM", " 0", "Checksum for the data block");
779	h.AddComment("FITS (Flexible Image Transport System) format is defined in 'Astronomy");
780	h.AddComment("and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H");
781	h.End();
782
783	const Checksum sum = h.WriteHeader(*this);
784
785	h.SetStr("CHECKSUM", sum.str());
786
787	const size_t offset = tellp();
788	h.WriteHeader(*this);
789	seekp(offset);
790
791	return sum;
792	}
793
794	virtual bool WriteDrsOffsetsTable ()
795	{
796	return true;
797	}
798
799	virtual bool WriteCatalog()
800	{
801	return true;
802	}
803
804	virtual bool WriteTableHeader(const char *name="DATA")
805	{
806	if (tellp()>0)
807	{
808	#ifdef __EXCEPTIONS
809	throw std::runtime_error("File not empty anymore.");
810	#else
811	gLog << ___err___ << "ERROR - File not empty anymore." << std::endl;
812	return false;
813	#endif
814	}
815
816	fHeaderSum = WriteFitsHeader();
817
818	WriteDrsOffsetsTable();
819
820	if (!fManualExtName)
821	SetStr("EXTNAME", name);
822	SetInt("NAXIS1", fTable.bytes_per_row);
823	SetInt("TFIELDS", fTable.cols.size());
824
825	End();
826
827	WriteHeader();
828
829	WriteCatalog();
830
831	return good();
832	}
833
834	template<size_t N>
835	void revcpy(char dest, const char src, int num)
836	{
837	const char pend = src + numN;
838	for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
839	std::reverse_copy(ptr, ptr+N, dest);
840	}
841
842	virtual uint32_t GetBytesPerRow() const { return fTable.bytes_per_row; }
843
844	virtual bool WriteRow(const void *ptr, size_t cnt, bool byte_swap=true)
845	{
846	// FIXME: Make sure that header was already written
847	// or write header now!
848	if (cnt!=fTable.bytes_per_row)
849	{
850	std::ostringstream sout;
851	sout << "WriteRow - Size " << cnt << " does not match expected size " << fTable.bytes_per_row;
852	#ifdef __EXCEPTIONS
853	throw std::runtime_error(sout.str());
854	#else
855	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
856	return false;
857	#endif
858	}
859
860	// For the checksum we need everything to be correctly aligned
861	const uint8_t offset = fTable.offset%4;
862
863	char *buffer = fOutputBuffer.data() + offset;
864
865	auto ib = fOutputBuffer.begin();
866	auto ie = fOutputBuffer.rbegin();
867	*ib++ = 0;
868	*ib++ = 0;
869	*ib++ = 0;
870	*ib = 0;
871
872	*ie++ = 0;
873	*ie++ = 0;
874	*ie++ = 0;
875	*ie = 0;
876
877	if (!byte_swap)
878	memcpy(buffer, ptr, cnt);
879	else
880	{
881	for (auto it=fTable.cols.cbegin(); it!=fTable.cols.cend(); it++)
882	{
883	const char src = reinterpret_cast<const char>(ptr) + it->offset;
884	char *dest = buffer + it->offset;
885
886	// Let the compiler do some optimization by
887	// knowing the we only have 1, 2, 4 and 8
888	switch (it->size)
889	{
890	case 1: memcpy (dest, src, it->num*it->size); break;
891	case 2: revcpy<2>(dest, src, it->num); break;
892	case 4: revcpy<4>(dest, src, it->num); break;
893	case 8: revcpy<8>(dest, src, it->num); break;
894	}
895	}
896	}
897
898	write(buffer, cnt);
899	fDataSum.add(fOutputBuffer);
900
901	fTable.num_rows++;
902	fTable.offset += cnt;
903	return good();
904	}
905
906	template<typename N>
907	bool WriteRow(const std::vector<N> &vec)
908	{
909	return WriteRow(vec.data(), vec.size()*sizeof(N));
910	}
911
912	// Flushes the number of rows to the header on disk
913	virtual void FlushNumRows()
914	{
915	SetInt("NAXIS2", fTable.num_rows);
916	FlushHeader();
917	}
918
919	size_t GetNumRows() const { return fTable.num_rows; }
920
921	void AlignTo2880Bytes()
922	{
923	if (tellp()%(80*36)>0)
924	{
925	std::vector<char> filler(8036-tellp()%(8036));
926	write(filler.data(), filler.size());
927	}
928	}
929
930	Checksum UpdateHeaderChecksum()
931	{
932
933	std::ostringstream dataSumStr;
934	dataSumStr << fDataSum.val();
935	SetStr("DATASUM", dataSumStr.str());
936
937	const Checksum sum = WriteHeader();
938
939	//sum += headersum;
940
941	SetStr("CHECKSUM", (sum+fDataSum).str());
942
943	return WriteHeader();
944	}
945	virtual bool close()
946	{
947	if (tellp()<0)
948	return false;
949
950	AlignTo2880Bytes();
951
952	// We don't have to jump back to the end of the file
953	SetInt("NAXIS2", fTable.num_rows);
954
955
956	const Checksum chk = UpdateHeaderChecksum();
957
958	std::ofstream::close();
959
960	if ((chk+fDataSum).valid())
961	return true;
962
963	std::ostringstream sout;
964	sout << "Checksum (" << std::hex << chk.val() << ") invalid.";
965	#ifdef __EXCEPTIONS
966	throw std::runtime_error(sout.str());
967	#else
968	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
969	return false;
970	#endif
971	}
972
973	std::pair<std::string, int> GetChecksumData()
974	{
975	std::string datasum;
976	std::string checksum;
977	//cannot directly use the Get methods, because they are only in fits.h
978	for (std::vector<Key>::const_iterator it=fKeys.cbegin(); it!= fKeys.cend(); it++)
979	{
980	if (it->key == "CHECKSUM") checksum = it->value;
981	if (it->key == "DATASUM") datasum = it->value;
982	}
983	if (checksum[0] == '\'')
984	checksum = checksum.substr(1,checksum.size()-2);
985	if (datasum[0] == '\'')
986	datasum = datasum.substr(1, datasum.size()-2);
987	return std::make_pair(checksum, atoi(datasum.c_str()));
988	}
989
990	void SetDefaultKeys()
991	{
992	SetStr("TELESCOP", "FACT", "Telescope that acquired this data");
993	SetStr("CREATOR", typeid(*this).name(), "Class that wrote this file");
994	SetFloat("EXTREL", 1.0, "Release Number");
995	SetStr("COMPILED", __DATE__" " __TIME__, "Compile time");
996	SetStr("ORIGIN", "FACT", "Institution that wrote the file");
997	SetStr("TIMESYS", "UTC", "Time system");
998	SetStr("TIMEUNIT", "d", "Time given in days w.r.t. to MJDREF");
999	SetInt("MJDREF", 40587, "MJD to UNIX time (seconds since 1970/1/1)");
1000	SetStr("PACKAGE", PACKAGE_NAME, "Package name");
1001	SetStr("VERSION", PACKAGE_VERSION, "Package description");
1002	SetStr("REVISION", REVISION, "SVN revision");
1003
1004	const time_t t0 = time(NULL);
1005	const struct tm *tmp1 = gmtime(&t0);
1006
1007	std::string str(19, '\0');
1008	if (tmp1 && strftime(const_cast<char*>(str.data()), 20, "%Y-%m-%dT%H:%M:%S", tmp1))
1009	SetStr("DATE", str, "File creation date");
1010	}
1011	};
1012
1013	#if 0
1014	#include "fits.h"
1015
1016	int main()
1017	{
1018	using namespace std;
1019
1020	ofits h2("delme.fits");
1021
1022	h2.SetInt("KEY1", 1, "comment 1");
1023	h2.AddColumnInt(2, "testcol1", "counts", "My comment");
1024	h2.AddColumnInt("testcol2", "counts", "My comment");
1025	//h2.AddColumnInt("testcol2", "counts", "My comment");
1026	h2.SetInt("KEY2", 2, "comment 2");
1027
1028	/*
1029	AddFloat("X0", 0.000123456, "number of fields in each row");
1030	AddFloat("X1", 0, "number of fields in each row");
1031	AddFloat("X2", 12345, "number of fields in each row");
1032	AddFloat("X3", 123456.67890, "number of fields in each row");
1033	AddFloat("X4", 1234567890123456789.12345678901234567890, "number of fields in each row");
1034	AddFloat("X5", 1234567890.1234567890e20, "number of fields in each row");
1035	AddFloat("X6", 1234567890.1234567890e-20, "number of fields in each row");
1036	AddFloat("XB", 1234567890.1234567890e-111, "number of fields in each row");
1037	AddFloat("X7", 1e-5, "number of fields in each row");
1038	AddFloat("X8", 1e-6, "number of fields in each row");
1039	//AddStr("12345678", "123456789012345678", "12345678901234567890123456789012345678901234567");
1040	*/
1041	// -
1042
1043	h2.WriteTableHeader("TABLE_NAME");
1044
1045	for (int i=0; i<10; i++)
1046	{
1047	int j[3] = { i+10, i10, i100 };
1048	h2.WriteRow(j, 3*sizeof(i));
1049	}
1050
1051	//h2.AddColumnInt("testcol2", "counts", "My comment");
1052	//h2.SetInt("KEY3", 2, "comment 2");
1053	h2.SetInt("KEY2", 2, "comment 2xxx");
1054	h2.SetInt("KEY1", 11);
1055
1056	h2.close();
1057
1058	cout << "---" << endl;
1059
1060	fits f("delme.fits");
1061	if (!f)
1062	throw std::runtime_error("xxx");
1063
1064	cout << "Header is valid: " << f.IsHeaderOk() << endl;
1065
1066	while (f.GetNextRow());
1067
1068	cout << "File is valid: " << f.IsFileOk() << endl;
1069
1070	cout << "---" << endl;
1071
1072	return 0;
1073	}
1074	#endif
1075
1076	#endif

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