Context Navigation

source: trunk/Mars/mcore/ofits.h@ 17766

Visit:

Last change on this file since 17766 was 17761, checked in by tbretz, 11 years ago
Added an semi-automatic setting of PACKAGE_NAME, PACKAGE_VERSION and REVISION
File size: 34.5 KB

Line
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	#ifndef PACKAGE_NAME
18	#define PACKAGE_NAME "n/a"
19	#endif
20
21	#ifndef PACKAGE_VERSION
22	#define PACKAGE_VERSION "n/a"
23	#endif
24
25	#ifndef REVISION
26	#define REVISION "n/a"
27	#endif
28
29	#ifdef __CINT__
30	#define off_t size_t
31	#endif
32
33	#ifndef __MARS__
34	#ifndef gLog
35	#define gLog std::cerr
36	#define ___err___ ""
37	#define ___warn___ ""
38	#define ___all___ ""
39	#endif
40	#else
41	#include "MLog.h"
42	#include "MLogManip.h"
43	#define ___err___ err
44	#define ___warn___ warn
45	#define ___all___ all
46	#endif
47
48	#include "FITS.h"
49	#include "checksum.h"
50
51	// Sloppy: allow / <--- left
52	// allow all characters (see specs for what is possible)
53
54	// units: m kg s rad sr K A mol cd Hz J W V N Pa C Ohm S F Wb T Hlm lx
55
56	class ofits : public std::ostream
57	{
58	protected:
59	std::filebuf fFilebuf;
60
61	public:
62	struct Key
63	{
64	std::string key;
65	bool delim;
66	std::string value;
67	std::string comment;
68	std::string fitsString;
69
70	off_t offset; // offset in file
71
72	bool changed; // For closing the file
73
74	Key(const std::string &k="") : key(k), delim(false), fitsString(""), offset(0), changed(true) { }
75
76	std::string Trim(const std::string &str)
77	{
78	// Trim Both leading and trailing spaces
79	const size_t first = str.find_first_not_of(' '); // Find the first character position after excluding leading blank spaces
80	const size_t last = str.find_last_not_of(' '); // Find the first character position from reverse af
81
82	// if all spaces or empty return an empty string
83	if (std::string::npos==first \|\| std::string::npos==last)
84	return std::string();
85
86	return str.substr(first, last-first+1);
87	}
88
89	bool FormatKey()
90	{
91	key = Trim(key);
92	if (key.empty())
93	{
94	#ifdef __EXCEPTIONS
95	throw std::runtime_error("Key name empty.");
96	#else
97	gLog << ___err___ << "ERROR - Key name empty." << std::endl;
98	return false;
99	#endif
100	}
101	if (key.size()>8)
102	{
103	std::ostringstream sout;
104	sout << "Key '" << key << "' exceeds 8 bytes.";
105	#ifdef __EXCEPTIONS
106	throw std::runtime_error(sout.str());
107	#else
108	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
109	return false;
110	#endif
111	}
112
113	//transform(key.begin(), key.end(), key.begin(), toupper);
114	#if GCC_VERSION < 40603
115	for (std::string::const_iterator c=key.begin(); c<key.end(); c++)
116	#else
117	for (std::string::const_iterator c=key.cbegin(); c<key.cend(); c++)
118	#endif
119	if ((c<'A' \|\| c>'Z') && (c<'0' \|\| c>'9') && c!='-' && c!='_')
120	{
121	std::ostringstream sout;
122	sout << "Invalid character '" << *c << "' found in key '" << key << "'";
123	#ifdef __EXCEPTIONS
124	throw std::runtime_error(sout.str());
125	#else
126	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
127	return false;
128	#endif
129	}
130
131	return true;
132	}
133
134	bool FormatComment()
135	{
136	comment = Trim(comment);
137
138	#if GCC_VERSION < 40603
139	for (std::string::const_iterator c=key.begin(); c<key.end(); c++)
140	#else
141	for (std::string::const_iterator c=key.cbegin(); c<key.cend(); c++)
142	#endif
143	if (c<32 \|\| c>126)
144	{
145	std::ostringstream sout;
146	sout << "Invalid character '" << c << "' [" << int(c) << "] found in comment '" << comment << "'";
147	#ifdef __EXCEPTIONS
148	throw std::runtime_error(sout.str());
149	#else
150	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
151	return false;
152	#endif
153	}
154
155	return true;
156	}
157
158	bool check(bool trim=false)
159	{
160	if (!FormatKey())
161	return false;
162
163	if (!FormatComment())
164	return false;
165
166	size_t sz = CalcSize();
167	if (sz<=80)
168	return true;
169
170	if (!trim)
171	{
172	std::ostringstream sout;
173	sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters.";
174	#ifdef __EXCEPTIONS
175	throw std::runtime_error(sout.str());
176	#else
177	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
178	#endif
179	return false;
180	}
181
182	//looks like something went wrong. Maybe entry is too long ?
183	//try to remove the comment
184	comment = "";
185
186	sz = CalcSize();
187	if (sz<=80)
188	{
189	#ifndef __EXCEPTIONS
190	std::ostringstream sout;
191	sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters... removed comment.";
192	gLog << ___warn___ << "WARNING - " << sout.str() << std::endl;
193	#endif
194	return true;
195	}
196
197	std::ostringstream sout;
198	sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters even without comment.";
199	#ifdef __EXCEPTIONS
200	throw std::runtime_error(sout.str());
201	#else
202	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
203	return false;
204	#endif
205	}
206
207	size_t CalcSize() const
208	{
209	if (!delim)
210	return 10+comment.size();
211
212	return 10 + (value.size()<20?20:value.size()) + 3 + comment.size();
213	}
214
215	std::string Compile()
216	{
217
218	if (fitsString != "")
219	return fitsString;
220
221	std::ostringstream sout;
222	sout << std::left << std::setw(8) << key;
223
224	if (!delim)
225	{
226	sout << " " << comment;
227	return sout.str();
228	}
229
230	sout << "= ";
231	sout << (!value.empty() && value[0]=='\''?std::left:std::right);
232	sout << std::setw(20) << value << std::left;
233
234	if (!comment.empty())
235	sout << " / " << comment;
236
237	return sout.str();
238	}
239
240	Checksum checksum;
241
242	void Out(std::ostream &fout)
243	{
244	if (!changed)
245	return;
246
247	std::string str = Compile();
248	str.insert(str.end(), 80-str.size(), ' ');
249
250	if (offset==0)
251	offset = fout.tellp();
252
253	//cout << "Write[" << offset << "]: " << key << "/" << value << endl;
254
255	fout.seekp(offset);
256	fout << str;
257
258	checksum.reset();
259	checksum.add(str.c_str(), 80);
260
261	changed = false;
262	}
263	/*
264	void Out(ostream &out)
265	{
266	std::string str = Compile();
267
268	str.insert(str.end(), 80-str.size(), ' ');
269
270	out << str;
271	changed = false;
272	}*/
273	};
274
275	private:
276	std::vector<Key> fKeys;
277
278	std::vector<Key>::iterator findkey(const std::string &key)
279	{
280	for (auto it=fKeys.begin(); it!=fKeys.end(); it++)
281	if (key==it->key)
282	return it;
283
284	return fKeys.end();
285	}
286
287	bool Set(const std::string &key="", bool delim=false, const std::string &value="", const std::string &comment="")
288	{
289	// If no delimit add the row no matter if it alread exists
290	if (delim)
291	{
292	// if the row already exists: update it
293	auto it = findkey(key);
294	if (it!=fKeys.end())
295	{
296	it->value = value;
297	it->changed = true;
298	return true;
299	}
300	}
301
302	if (fTable.num_rows>0)
303	{
304	std::ostringstream sout;
305	sout << "No new header key can be defined, rows were already written to the file... ignoring new key '" << key << "'";
306	#ifdef __EXCEPTIONS
307	throw std::runtime_error(sout.str());
308	#else
309	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
310	return false;
311	#endif
312	}
313
314	Key entry;
315
316	entry.key = key;
317	entry.delim = delim;
318	entry.value = value;
319	entry.comment = comment;
320	entry.offset = 0;
321	entry.changed = true;
322
323	if (!entry.check(fCommentTrimming))
324	return false;
325
326	fKeys.push_back(entry);
327	return true;
328	}
329
330	protected:
331	struct Table
332	{
333	off_t offset;
334
335	size_t bytes_per_row;
336	size_t num_rows;
337	size_t num_cols;
338
339	struct Column
340	{
341	std::string name;
342	size_t offset;
343	size_t num;
344	size_t size;
345	char type;
346	};
347
348	std::vector<Column> cols;
349
350	Table() : offset(0), bytes_per_row(0), num_rows(0), num_cols(0)
351	{
352	}
353	};
354
355
356	Table fTable;
357
358	std::vector<char> fOutputBuffer;
359
360	std::vector<Table::Column>::const_iterator findcol(const std::string &name)
361	{
362	for (auto it=fTable.cols.cbegin(); it!=fTable.cols.cend(); it++)
363	if (name==it->name)
364	return it;
365
366	return fTable.cols.cend();
367	}
368
369	Checksum fDataSum;
370	Checksum fHeaderSum;
371
372	bool fCommentTrimming;
373	bool fManualExtName;
374
375	public:
376	ofits()
377	: std::ostream(), fFilebuf(), fCommentTrimming(false), fManualExtName(false)
378	{
379	init(&fFilebuf);
380	}
381
382	ofits(const char *fname)
383	: std::ostream(), fFilebuf(), fCommentTrimming(false), fManualExtName(false)
384	{
385	init(&fFilebuf);
386	open(fname);
387	}
388
389	#ifdef __GXX_EXPERIMENTAL_CXX0X__
390	ofits(const std::string &fname)
391	: std::ostream(), fCommentTrimming(false), fManualExtName(false)
392	{
393	init(&fFilebuf);
394	open(fname);
395	}
396	#endif
397
398	virtual ~ofits()
399	{
400	if (is_open())
401	close();
402	}
403	/*
404	filebuf *rdbuf() const
405	{
406	return const_cast<filebuf*>(&fFilebuf);
407	}
408	*/
409	bool is_open()
410	{
411	return fFilebuf.is_open();
412	}
413
414	bool is_open() const
415	{
416	return fFilebuf.is_open();
417	}
418
419	virtual void open(const char *filename, bool addEXTNAMEKey=true)
420	{
421	fDataSum = 0;
422	fHeaderSum = 0;
423
424	fTable = Table();
425	fKeys.clear();
426
427	SetStr("XTENSION", "BINTABLE", "binary table extension");
428	SetInt("BITPIX", 8, "8-bit bytes");
429	SetInt("NAXIS", 2, "2-dimensional binary table");
430	SetInt("NAXIS1", 0, "width of table in bytes");
431	SetInt("NAXIS2", 0, "number of rows in table");
432	SetInt("PCOUNT", 0, "size of special data area");
433	SetInt("GCOUNT", 1, "one data group (required keyword)");
434	SetInt("TFIELDS", 0, "number of fields in each row");
435	if (addEXTNAMEKey)
436	SetStr("EXTNAME", "", "name of extension table");
437	else
438	fManualExtName = true;
439	SetStr("CHECKSUM", "0000000000000000", "Checksum for the whole HDU");
440	SetStr("DATASUM", " 0", "Checksum for the data block");
441
442	if (!fFilebuf.open(filename, ios_base::out\|ios_base::trunc))
443	setstate(ios_base::failbit);
444	else
445	clear();
446	}
447
448	virtual void open(const std::string &filename, bool addEXTNAMEKey=true)
449	{
450	open(filename.c_str(), addEXTNAMEKey);
451	}
452
453	void AllowCommentsTrimming(bool allow)
454	{
455	fCommentTrimming = allow;
456	}
457	//Etienne: required to enable 1 to 1 reconstruction of files
458	bool SetKeyComment(const std::string& key, const std::string& comment)
459	{
460	auto it = findkey(key);
461	if (it==fKeys.end())
462	return false;
463	it->comment = comment;
464	it->changed = true;
465	return true;
466	}
467	bool SetKeyFromFitsString(const std::string& fitsString)
468	{
469	if (fTable.num_rows>0)
470	{
471	std::ostringstream sout;
472	sout << "No new header key can be defined, rows were already written to the file... ignoring new key '" << fitsString << "'";
473	#ifdef __EXCEPTIONS
474	throw std::runtime_error(sout.str());
475	#else
476	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
477	return false;
478	#endif
479	}
480
481	Key entry;
482	entry.fitsString = fitsString;
483	entry.changed = true;
484	fKeys.push_back(entry);
485	return true;
486	}
487	bool SetRaw(const std::string &key, const std::string &val, const std::string &comment)
488	{
489	return Set(key, true, val, comment);
490	}
491
492	bool SetBool(const std::string &key, bool b, const std::string &comment="")
493	{
494	return Set(key, true, b?"T":"F", comment);
495	}
496
497	bool AddEmpty(const std::string &key, const std::string &comment="")
498	{
499	return Set(key, true, "", comment);
500	}
501
502	bool SetStr(const std::string &key, std::string s, const std::string &comment="")
503	{
504	for (uint i=0; i<s.length(); i++)
505	if (s[i]=='\'')
506	s.insert(i++, "\'");
507
508	return Set(key, true, "'"+s+"'", comment);
509	}
510
511	bool SetInt(const std::string &key, int64_t i, const std::string &comment="")
512	{
513	std::ostringstream sout;
514	sout << i;
515
516	return Set(key, true, sout.str(), comment);
517	}
518
519	bool SetFloat(const std::string &key, double f, int p, const std::string &comment="")
520	{
521	std::ostringstream sout;
522
523	if (p<0)
524	sout << std::setprecision(-p) << fixed;
525	if (p>0)
526	sout << std::setprecision(p);
527	if (p==0)
528	sout << std::setprecision(f>1e-100 && f<1e100 ? 15 : 14);
529
530	sout << f;
531
532	std::string str = sout.str();
533
534	replace(str.begin(), str.end(), 'e', 'E');
535
536	if (str.find_first_of('E')==std::string::npos && str.find_first_of('.')==std::string::npos)
537	str += ".";
538
539	return Set(key, true, str, comment);
540	}
541
542	bool SetFloat(const std::string &key, double f, const std::string &comment="")
543	{
544	return SetFloat(key, f, 0, comment);
545	}
546
547	bool SetHex(const std::string &key, uint64_t i, const std::string &comment="")
548	{
549	std::ostringstream sout;
550	sout << std::hex << "0x" << i;
551	return SetStr(key, sout.str(), comment);
552	}
553
554	bool AddComment(const std::string &comment)
555	{
556	return Set("COMMENT", false, "", comment);
557	}
558
559	bool AddHistory(const std::string &comment)
560	{
561	return Set("HISTORY", false, "", comment);
562	}
563
564	void End()
565	{
566	Set("END");
567	while (fKeys.size()%36!=0)
568	fKeys.emplace_back();
569	}
570
571	std::string CommentFromType(char type)
572	{
573	std::string comment;
574
575	switch (type)
576	{
577	case 'L': comment = "[1-byte BOOL]"; break;
578	case 'A': comment = "[1-byte CHAR]"; break;
579	case 'B': comment = "[1-byte BOOL]"; break;
580	case 'I': comment = "[2-byte INT]"; break;
581	case 'J': comment = "[4-byte INT]"; break;
582	case 'K': comment = "[8-byte INT]"; break;
583	case 'E': comment = "[4-byte FLOAT]"; break;
584	case 'D': comment = "[8-byte FLOAT]"; break;
585	case 'Q': comment = "[var. Length]"; break;
586	}
587
588	return comment;
589	}
590
591	uint32_t SizeFromType(char type)
592	{
593	size_t size = 0;
594
595	switch (type)
596	{
597	case 'L': size = 1; break;
598	case 'A': size = 1; break;
599	case 'B': size = 1; break;
600	case 'I': size = 2; break;
601	case 'J': size = 4; break;
602	case 'K': size = 8; break;
603	case 'E': size = 4; break;
604	case 'D': size = 8; break;
605	case 'Q': size = 16; break;
606	}
607
608	return size;
609	}
610	//ETIENNE to be able to restore the file 1 to 1, I must restore the header keys myself
611	virtual bool AddColumn(uint32_t cnt, char typechar, const std::string &name, const std::string &unit, const std::string &comment="", bool addHeaderKeys=true)
612	{
613	if (tellp()<0)
614	{
615	std::ostringstream sout;
616	sout << "File not open... ignoring column '" << name << "'";
617	#ifdef __EXCEPTIONS
618	throw std::runtime_error(sout.str());
619	#else
620	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
621	return false;
622	#endif
623	}
624
625	if (tellp()>0)
626	{
627	std::ostringstream sout;
628	sout << "Header already written, no new column can be defined... ignoring column '" << name << "'";
629	#ifdef __EXCEPTIONS
630	throw std::runtime_error(sout.str());
631	#else
632	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
633	return false;
634	#endif
635	}
636
637	if (findcol(name)!=fTable.cols.cend())
638	{
639	std::ostringstream sout;
640	sout << "A column with the name '" << name << "' already exists.";
641	#ifdef __EXCEPTIONS
642	throw std::runtime_error(sout.str());
643	#else
644	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
645	return false;
646	#endif
647	}
648
649	typechar = toupper(typechar);
650
651	static const std::string allow("LABIJKEDQ");
652	#if GCC_VERSION < 40603
653	if (std::find(allow.begin(), allow.end(), typechar)==allow.end())
654	#else
655	if (std::find(allow.cbegin(), allow.cend(), typechar)==allow.end())
656	#endif
657	{
658	std::ostringstream sout;
659	sout << "Column type '" << typechar << "' not supported.";
660	#ifdef __EXCEPTIONS
661	throw std::runtime_error(sout.str());
662	#else
663	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
664	return false;
665	#endif
666	}
667
668	std::ostringstream type;
669	type << cnt;
670	if (typechar=='Q')
671	type << "QB";
672	else
673	type << typechar;
674
675	fTable.num_cols++;
676
677	if (addHeaderKeys)
678	{
679	#if GCC_VERSION < 40603
680	const std::string nc = std::to_string((long long int)(fTable.num_cols));
681	#else
682	const std::string nc = std::to_string(fTable.num_cols);
683	#endif
684	SetStr("TFORM"+nc, type.str(), "format of "+name+" "+CommentFromType(typechar));
685	SetStr("TTYPE"+nc, name, comment);
686	if (!unit.empty())
687	SetStr("TUNIT"+nc, unit, "unit of "+name);
688	}
689	size_t size = SizeFromType(typechar);
690
691	Table::Column col;
692
693	col.name = name;
694	col.type = typechar;
695	col.num = cnt;
696	col.size = size;
697	col.offset = fTable.bytes_per_row;
698
699	fTable.cols.push_back(col);
700
701	fTable.bytes_per_row += size*cnt;
702
703	// Align to four bytes
704	fOutputBuffer.resize(fTable.bytes_per_row + 4-fTable.bytes_per_row%4);
705
706	return true;
707	}
708
709	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)
710	{
711	return AddColumn(cnt, typechar, name, unit, comment, addHeaderKeys);
712	}
713
714	bool AddColumnShort(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
715	{ return AddColumn(cnt, 'I', name, unit, comment); }
716	bool AddColumnInt(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
717	{ return AddColumn(cnt, 'J', name, unit, comment); }
718	bool AddColumnLong(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
719	{ return AddColumn(cnt, 'K', name, unit, comment); }
720	bool AddColumnFloat(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
721	{ return AddColumn(cnt, 'E', name, unit, comment); }
722	bool AddColumnDouble(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
723	{ return AddColumn(cnt, 'D', name, unit, comment); }
724	bool AddColumnChar(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
725	{ return AddColumn(cnt, 'A', name, unit, comment); }
726	bool AddColumnByte(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
727	{ return AddColumn(cnt, 'B', name, unit, comment); }
728	bool AddColumnBool(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
729	{ return AddColumn(cnt, 'L', name, unit, comment); }
730
731	bool AddColumnShort(const std::string &name, const std::string &unit="", const std::string &comment="")
732	{ return AddColumn(1, 'I', name, unit, comment); }
733	bool AddColumnInt(const std::string &name, const std::string &unit="", const std::string &comment="")
734	{ return AddColumn(1, 'J', name, unit, comment); }
735	bool AddColumnLong(const std::string &name, const std::string &unit="", const std::string &comment="")
736	{ return AddColumn(1, 'K', name, unit, comment); }
737	bool AddColumnFloat(const std::string &name, const std::string &unit="", const std::string &comment="")
738	{ return AddColumn(1, 'E', name, unit, comment); }
739	bool AddColumnDouble(const std::string &name, const std::string &unit="", const std::string &comment="")
740	{ return AddColumn(1, 'D', name, unit, comment); }
741	bool AddColumnChar(const std::string &name, const std::string &unit="", const std::string &comment="")
742	{ return AddColumn(1, 'A', name, unit, comment); }
743	bool AddColumnByte(const std::string &name, const std::string &unit="", const std::string &comment="")
744	{ return AddColumn(1, 'B', name, unit, comment); }
745	bool AddColumnBool(const std::string &name, const std::string &unit="", const std::string &comment="")
746	{ return AddColumn(1, 'L', name, unit, comment); }
747
748	bool AddColumnShort(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
749	{ return AddColumn(comp, cnt, 'I', name, unit, comment); }
750	bool AddColumnInt(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
751	{ return AddColumn(comp, cnt, 'J', name, unit, comment); }
752	bool AddColumnLong(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
753	{ return AddColumn(comp, cnt, 'K', name, unit, comment); }
754	bool AddColumnFloat(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
755	{ return AddColumn(comp, cnt, 'E', name, unit, comment); }
756	bool AddColumnDouble(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
757	{ return AddColumn(comp, cnt, 'D', name, unit, comment); }
758	bool AddColumnChar(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
759	{ return AddColumn(comp, cnt, 'A', name, unit, comment); }
760	bool AddColumnByte(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
761	{ return AddColumn(comp, cnt, 'B', name, unit, comment); }
762	bool AddColumnBool(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
763	{ return AddColumn(comp, cnt, 'L', name, unit, comment); }
764
765	bool AddColumnShort(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
766	{ return AddColumn(comp, 1, 'I', name, unit, comment); }
767	bool AddColumnInt(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
768	{ return AddColumn(comp, 1, 'J', name, unit, comment); }
769	bool AddColumnLong(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
770	{ return AddColumn(comp, 1, 'K', name, unit, comment); }
771	bool AddColumnFloat(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
772	{ return AddColumn(comp, 1, 'E', name, unit, comment); }
773	bool AddColumnDouble(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
774	{ return AddColumn(comp, 1, 'D', name, unit, comment); }
775	bool AddColumnChar(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
776	{ return AddColumn(comp, 1, 'A', name, unit, comment); }
777	bool AddColumnByte(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
778	{ return AddColumn(comp, 1, 'B', name, unit, comment); }
779	bool AddColumnBool(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
780	{ return AddColumn(comp, 1, 'L', name, unit, comment); }
781
782	/*
783	bool AddKey(string key, double d, const std::string &comment)
784	{
785	ostringstream out;
786	out << d;
787
788	std::string s = out.str();
789
790	replace(s.begin(), s.end(), "e", "E");
791
792	return AddKey(key, s, comment);
793	}*/
794
795
796	Checksum WriteHeader(std::ostream &fout)
797	{
798	Checksum sum;
799	uint32_t count=0;
800	for (auto it=fKeys.begin(); it!=fKeys.end(); it++)
801	{
802	it->Out(fout);
803	sum += it->checksum;
804	count++;
805	}
806	fout.flush();
807
808	return sum;
809	}
810
811	Checksum WriteHeader()
812	{
813	return WriteHeader(*this);
814	}
815
816	void FlushHeader()
817	{
818	const off_t pos = tellp();
819	WriteHeader();
820	seekp(pos);
821	}
822
823	Checksum WriteFitsHeader()
824	{
825	ofits h;
826
827	h.SetBool("SIMPLE", true, "file does conform to FITS standard");
828	h.SetInt ("BITPIX", 8, "number of bits per data pixel");
829	h.SetInt ("NAXIS", 0, "number of data axes");
830	h.SetBool("EXTEND", true, "FITS dataset may contain extensions");
831	h.SetStr ("CHECKSUM","0000000000000000", "Checksum for the whole HDU");
832	h.SetStr ("DATASUM", " 0", "Checksum for the data block");
833	h.AddComment("FITS (Flexible Image Transport System) format is defined in 'Astronomy");
834	h.AddComment("and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H");
835	h.End();
836
837	const Checksum sum = h.WriteHeader(*this);
838
839	h.SetStr("CHECKSUM", sum.str());
840
841	const size_t offset = tellp();
842	h.WriteHeader(*this);
843	seekp(offset);
844
845	return sum;
846	}
847
848	virtual bool WriteDrsOffsetsTable ()
849	{
850	return true;
851	}
852
853	virtual bool WriteCatalog()
854	{
855	return true;
856	}
857
858	virtual bool WriteTableHeader(const char *name="DATA")
859	{
860	if (tellp()>0)
861	{
862	#ifdef __EXCEPTIONS
863	throw std::runtime_error("File not empty anymore.");
864	#else
865	gLog << ___err___ << "ERROR - File not empty anymore." << std::endl;
866	return false;
867	#endif
868	}
869
870	fHeaderSum = WriteFitsHeader();
871
872	WriteDrsOffsetsTable();
873
874	if (!fManualExtName)
875	SetStr("EXTNAME", name);
876	SetInt("NAXIS1", fTable.bytes_per_row);
877	SetInt("TFIELDS", fTable.cols.size());
878
879	End();
880
881	WriteHeader();
882
883	WriteCatalog();
884
885	return good();
886	}
887
888	template<size_t N>
889	void revcpy(char dest, const char src, int num)
890	{
891	const char pend = src + numN;
892	for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
893	std::reverse_copy(ptr, ptr+N, dest);
894	}
895
896	virtual uint32_t GetBytesPerRow() const { return fTable.bytes_per_row; }
897
898	virtual bool WriteRow(const void *ptr, size_t cnt, bool byte_swap=true)
899	{
900	// FIXME: Make sure that header was already written
901	// or write header now!
902	if (cnt!=fTable.bytes_per_row)
903	{
904	std::ostringstream sout;
905	sout << "WriteRow - Size " << cnt << " does not match expected size " << fTable.bytes_per_row;
906	#ifdef __EXCEPTIONS
907	throw std::runtime_error(sout.str());
908	#else
909	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
910	return false;
911	#endif
912	}
913
914	// For the checksum we need everything to be correctly aligned
915	const uint8_t offset = fTable.offset%4;
916
917	char *buffer = fOutputBuffer.data() + offset;
918
919	auto ib = fOutputBuffer.begin();
920	auto ie = fOutputBuffer.rbegin();
921	*ib++ = 0;
922	*ib++ = 0;
923	*ib++ = 0;
924	*ib = 0;
925
926	*ie++ = 0;
927	*ie++ = 0;
928	*ie++ = 0;
929	*ie = 0;
930
931	if (!byte_swap)
932	memcpy(buffer, ptr, cnt);
933	else
934	{
935	for (auto it=fTable.cols.cbegin(); it!=fTable.cols.cend(); it++)
936	{
937	const char src = reinterpret_cast<const char>(ptr) + it->offset;
938	char *dest = buffer + it->offset;
939
940	// Let the compiler do some optimization by
941	// knowing the we only have 1, 2, 4 and 8
942	switch (it->size)
943	{
944	case 1: memcpy (dest, src, it->num*it->size); break;
945	case 2: revcpy<2>(dest, src, it->num); break;
946	case 4: revcpy<4>(dest, src, it->num); break;
947	case 8: revcpy<8>(dest, src, it->num); break;
948	}
949	}
950	}
951
952	write(buffer, cnt);
953	fDataSum.add(fOutputBuffer);
954
955	fTable.num_rows++;
956	fTable.offset += cnt;
957	return good();
958	}
959
960	template<typename N>
961	bool WriteRow(const std::vector<N> &vec)
962	{
963	return WriteRow(vec.data(), vec.size()*sizeof(N));
964	}
965
966	// Flushes the number of rows to the header on disk
967	virtual void FlushNumRows()
968	{
969	SetInt("NAXIS2", fTable.num_rows);
970	FlushHeader();
971	}
972
973	size_t GetNumRows() const { return fTable.num_rows; }
974
975	void AlignTo2880Bytes()
976	{
977	if (tellp()%(80*36)>0)
978	{
979	std::vector<char> filler(8036-tellp()%(8036));
980	write(filler.data(), filler.size());
981	}
982	}
983
984	Checksum UpdateHeaderChecksum()
985	{
986	std::ostringstream dataSumStr;
987	dataSumStr << fDataSum.val();
988	SetStr("DATASUM", dataSumStr.str());
989
990	const Checksum sum = WriteHeader();
991
992	//sum += headersum;
993
994	SetStr("CHECKSUM", (sum+fDataSum).str());
995
996	return WriteHeader();
997	}
998	virtual bool close()
999	{
1000	if (tellp()<0)
1001	return false;
1002
1003	AlignTo2880Bytes();
1004
1005	// We don't have to jump back to the end of the file
1006	SetInt("NAXIS2", fTable.num_rows);
1007
1008	const Checksum chk = UpdateHeaderChecksum();
1009
1010	if (!fFilebuf.close())
1011	setstate(ios_base::failbit);
1012
1013	if ((chk+fDataSum).valid())
1014	return true;
1015
1016	std::ostringstream sout;
1017	sout << "Checksum (" << std::hex << chk.val() << ") invalid.";
1018	#ifdef __EXCEPTIONS
1019	throw std::runtime_error(sout.str());
1020	#else
1021	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
1022	return false;
1023	#endif
1024	}
1025
1026	std::pair<std::string, int> GetChecksumData()
1027	{
1028	std::string datasum;
1029	std::string checksum;
1030	//cannot directly use the Get methods, because they are only in fits.h
1031	for (std::vector<Key>::const_iterator it=fKeys.cbegin(); it!= fKeys.cend(); it++)
1032	{
1033	if (it->key == "CHECKSUM") checksum = it->value;
1034	if (it->key == "DATASUM") datasum = it->value;
1035	}
1036	if (checksum[0] == '\'')
1037	checksum = checksum.substr(1,checksum.size()-2);
1038	if (datasum[0] == '\'')
1039	datasum = datasum.substr(1, datasum.size()-2);
1040	return std::make_pair(checksum, atoi(datasum.c_str()));
1041	}
1042
1043	void SetDefaultKeys()
1044	{
1045	SetStr("TELESCOP", "FACT", "Telescope that acquired this data");
1046	SetStr("CREATOR", typeid(*this).name(), "Class that wrote this file");
1047	SetFloat("EXTREL", 1.0, "Release Number");
1048	SetStr("COMPILED", __DATE__" " __TIME__, "Compile time");
1049	SetStr("ORIGIN", "FACT", "Institution that wrote the file");
1050	SetStr("TIMESYS", "UTC", "Time system");
1051	SetStr("TIMEUNIT", "d", "Time given in days w.r.t. to MJDREF");
1052	SetInt("MJDREF", 40587, "MJD to UNIX time (seconds since 1970/1/1)");
1053	SetStr("PACKAGE", PACKAGE_NAME, "Package name");
1054	SetStr("VERSION", PACKAGE_VERSION, "Package description");
1055	SetStr("REVISION", REVISION, "SVN revision");
1056
1057	const time_t t0 = time(NULL);
1058	const struct tm *tmp1 = gmtime(&t0);
1059
1060	std::string str(19, '\0');
1061	if (tmp1 && strftime(const_cast<char*>(str.data()), 20, "%Y-%m-%dT%H:%M:%S", tmp1))
1062	SetStr("DATE", str, "File creation date");
1063	}
1064	};
1065
1066	#if 0
1067	#include "fits.h"
1068
1069	int main()
1070	{
1071	using namespace std;
1072
1073	ofits h2("delme.fits");
1074
1075	h2.SetInt("KEY1", 1, "comment 1");
1076	h2.AddColumnInt(2, "testcol1", "counts", "My comment");
1077	h2.AddColumnInt("testcol2", "counts", "My comment");
1078	//h2.AddColumnInt("testcol2", "counts", "My comment");
1079	h2.SetInt("KEY2", 2, "comment 2");
1080
1081	/*
1082	AddFloat("X0", 0.000123456, "number of fields in each row");
1083	AddFloat("X1", 0, "number of fields in each row");
1084	AddFloat("X2", 12345, "number of fields in each row");
1085	AddFloat("X3", 123456.67890, "number of fields in each row");
1086	AddFloat("X4", 1234567890123456789.12345678901234567890, "number of fields in each row");
1087	AddFloat("X5", 1234567890.1234567890e20, "number of fields in each row");
1088	AddFloat("X6", 1234567890.1234567890e-20, "number of fields in each row");
1089	AddFloat("XB", 1234567890.1234567890e-111, "number of fields in each row");
1090	AddFloat("X7", 1e-5, "number of fields in each row");
1091	AddFloat("X8", 1e-6, "number of fields in each row");
1092	//AddStr("12345678", "123456789012345678", "12345678901234567890123456789012345678901234567");
1093	*/
1094	// -
1095
1096	h2.WriteTableHeader("TABLE_NAME");
1097
1098	for (int i=0; i<10; i++)
1099	{
1100	int j[3] = { i+10, i10, i100 };
1101	h2.WriteRow(j, 3*sizeof(i));
1102	}
1103
1104	//h2.AddColumnInt("testcol2", "counts", "My comment");
1105	//h2.SetInt("KEY3", 2, "comment 2");
1106	h2.SetInt("KEY2", 2, "comment 2xxx");
1107	h2.SetInt("KEY1", 11);
1108
1109	h2.close();
1110
1111	cout << "---" << endl;
1112
1113	fits f("delme.fits");
1114	if (!f)
1115	throw std::runtime_error("xxx");
1116
1117	cout << "Header is valid: " << f.IsHeaderOk() << endl;
1118
1119	while (f.GetNextRow());
1120
1121	cout << "File is valid: " << f.IsFileOk() << endl;
1122
1123	cout << "---" << endl;
1124
1125	return 0;
1126	}
1127	#endif
1128
1129	#endif

Note: See TracBrowser for help on using the repository browser.

Download in other formats: