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source: trunk/Mars/mcore/fits.h@ 13225

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Last change on this file since 13225 was 13225, checked in by tbretz, 13 years ago
Do not read more than the expected number of rows per default.
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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 <sstream>
9	#include <algorithm>
10
11	#ifdef __EXCEPTIONS
12	#include <stdexcept>
13	#endif
14
15	#ifdef __CINT__
16	#define off_t size_t
17	#else
18	#include <unordered_map>
19	#endif
20
21	#ifndef __MARS__
22	#include <vector>
23	#include <iomanip>
24	#include <iostream>
25	#define gLog cerr
26	#define ___err___ ""
27	#define ___all___ ""
28	#else
29	#include "MLog.h"
30	#include "MLogManip.h"
31	#define ___err___ err
32	#define ___all___ all
33	#endif
34
35	#ifdef HAVE_ZLIB
36	#include "izstream.h"
37	#else
38	#include <fstream>
39	#define izstream ifstream
40	#warning Support for zipped FITS files disabled.
41	#endif
42
43	#include "checksum.h"
44
45	namespace std
46	{
47
48	class fits : public izstream
49	{
50	public:
51	struct Entry
52	{
53	char type;
54	string value;
55	string comment;
56
57	template<typename T>
58	T Get() const
59	{
60	T t;
61
62	istringstream str(value);
63	str >> t;
64
65	return t;
66	}
67	};
68
69	struct Table
70	{
71	off_t offset;
72
73	string name;
74	size_t bytes_per_row;
75	size_t num_rows;
76	size_t num_cols;
77
78	struct Column
79	{
80	size_t offset;
81	size_t num;
82	size_t size;
83	char type;
84	string unit;
85	};
86
87	typedef map<string, Entry> Keys;
88	typedef map<string, Column> Columns;
89
90	Columns cols;
91	Keys keys;
92
93	int64_t datasum;
94
95	string Trim(const string &str, char c=' ') const
96	{
97	// Trim Both leading and trailing spaces
98	const size_t pstart = str.find_first_not_of(c); // Find the first character position after excluding leading blank spaces
99	const size_t pend = str.find_last_not_of(c); // Find the first character position from reverse af
100
101	// if all spaces or empty return an empty string
102	if (string::npos==pstart \|\| string::npos==pend)
103	return string();
104
105	return str.substr(pstart, pend-pstart+1);
106	}
107
108	bool Check(const string &key, char type, const string &value="") const
109	{
110	const Keys::const_iterator it = keys.find(key);
111	if (it==keys.end())
112	{
113	ostringstream str;
114	str << "Key '" << key << "' not found.";
115	#ifdef __EXCEPTIONS
116	throw runtime_error(str.str());
117	#else
118	gLog << ___err___ << "ERROR - " << str.str() << endl;
119	return false;
120	#endif
121	}
122
123	if (it->second.type!=type)
124	{
125	ostringstream str;
126	str << "Wrong type for key '" << key << "': expected " << type << ", found " << it->second.type << ".";
127	#ifdef __EXCEPTIONS
128	throw runtime_error(str.str());
129	#else
130	gLog << ___err___ << "ERROR - " << str.str() << endl;
131	return false;
132	#endif
133	}
134
135	if (!value.empty() && it->second.value!=value)
136	{
137	ostringstream str;
138	str << "Wrong value for key '" << key << "': expected " << value << ", found " << it->second.value << ".";
139	#ifdef __EXCEPTIONS
140	throw runtime_error(str.str());
141	#else
142	gLog << ___err___ << "ERROR - " << str.str() << endl;
143	return false;
144	#endif
145	}
146
147	return true;
148	}
149
150	Keys ParseBlock(const vector<string> &vec) const
151	{
152	map<string,Entry> rc;
153
154	for (unsigned int i=0; i<vec.size(); i++)
155	{
156	const string key = Trim(vec[i].substr(0,8));
157	// Keywords without a value, like COMMENT / HISTORY
158	if (vec[i].substr(8,2)!="= ")
159	continue;
160
161	char type = 0;
162
163	string com;
164	string val = Trim(vec[i].substr(10));
165	if (val[0]=='\'')
166	{
167	// First skip all '' in the string
168	size_t p = 1;
169	while (1)
170	{
171	const size_t pp = val.find_first_of('\'', p);
172	if (pp==string::npos)
173	break;
174
175	p = val[pp+1]=='\'' ? pp+2 : pp+1;
176	}
177
178	// Now find the comment
179	const size_t ppp = val.find_first_of('/', p);
180
181	// Set value, comment and type
182	com = ppp==string::npos ? "" : Trim(val.substr(ppp+1));
183	val = Trim(val.substr(1, p-2));
184	type = 'T';
185	}
186	else
187	{
188	const size_t p = val.find_first_of('/');
189
190	com = Trim(val.substr(p+2));
191	val = Trim(val.substr(0, p));
192
193	if (val.empty() \|\| val.find_first_of('T')!=string::npos \|\| val.find_first_of('F')!=string::npos)
194	type = 'B';
195	else
196	type = val.find_last_of('.')==string::npos ? 'I' : 'F';
197	}
198
199	const Entry e = { type, val, com };
200	rc[key] = e;
201	}
202
203	return rc;
204	}
205
206	Table() : offset(0) { }
207	Table(const vector<string> &vec, off_t off) :
208	offset(off), keys(ParseBlock(vec))
209	{
210	if (!Check("XTENSION", 'T', "BINTABLE") \|\|
211	!Check("NAXIS", 'I', "2") \|\|
212	!Check("BITPIX", 'I', "8") \|\|
213	!Check("PCOUNT", 'I', "0") \|\|
214	!Check("GCOUNT", 'I', "1") \|\|
215	!Check("EXTNAME", 'T') \|\|
216	!Check("NAXIS1", 'I') \|\|
217	!Check("NAXIS2", 'I') \|\|
218	!Check("TFIELDS", 'I'))
219	return;
220
221	bytes_per_row = Get<size_t>("NAXIS1");
222	num_rows = Get<size_t>("NAXIS2");
223	num_cols = Get<size_t>("TFIELDS");
224	datasum = Get<int64_t>("DATASUM", -1);
225
226	size_t bytes = 0;
227	for (size_t i=1; i<=num_cols; i++)
228	{
229	ostringstream num;
230	num << i;
231
232	if (!Check("TTYPE"+num.str(), 'T') \|\|
233	!Check("TFORM"+num.str(), 'T'))
234	return;
235
236	const string id = Get<string>("TTYPE"+num.str());
237	const string fmt = Get<string>("TFORM"+num.str());
238	const string unit = Get<string>("TUNIT"+num.str(), "");
239
240	istringstream sin(fmt);
241	int n = 0;
242	sin >> n;
243	if (!sin)
244	n = 1;
245
246	const char type = fmt[fmt.length()-1];
247
248	size_t size = 0;
249	switch (type)
250	{
251	// We could use negative values to mark floats
252	// otheriwse we could just cast them to int64_t?
253	case 'L': // logical
254	case 'A': // char
255	case 'B': size = 1; break; // byte
256	case 'I': size = 2; break; // short
257	case 'J': size = 4; break; // int
258	case 'K': size = 8; break; // long long
259	case 'E': size = 4; break; // float
260	case 'D': size = 8; break; // double
261	// case 'X': size = n; break; // bits (n=number of bytes needed to contain all bits)
262	// case 'C': size = 8; break; // complex float
263	// case 'M': size = 16; break; // complex double
264	// case 'P': size = 8; break; // array descriptor (32bit)
265	// case 'Q': size = 16; break; // array descriptor (64bit)
266	default:
267	{
268	ostringstream str;
269	str << "FITS format TFORM='" << fmt << "' not yet supported.";
270	#ifdef __EXCEPTIONS
271	throw runtime_error(str.str());
272	#else
273	gLog << ___err___ << "ERROR - " << str.str() << endl;
274	return;
275	#endif
276	}
277	}
278
279	const Table::Column col = { bytes, n, size, type, unit };
280
281	cols[id] = col;
282	bytes += n*size;
283	}
284
285	if (bytes!=bytes_per_row)
286	{
287	#ifdef __EXCEPTIONS
288	throw runtime_error("Column size mismatch");
289	#else
290	gLog << ___err___ << "ERROR - Column size mismatch" << endl;
291	return;
292	#endif
293	}
294
295	name = Get<string>("EXTNAME");
296	}
297
298	void PrintKeys(bool display_all=false) const
299	{
300	for (Keys::const_iterator it=keys.begin(); it!=keys.end(); it++)
301	{
302	if (!display_all &&
303	(it->first.substr(0, 6)=="TTYPE" \|\|
304	it->first.substr(0, 6)=="TFORM" \|\|
305	it->first.substr(0, 6)=="TUNIT" \|\|
306	it->first=="TFIELDS" \|\|
307	it->first=="XTENSION" \|\|
308	it->first=="NAXIS" \|\|
309	it->first=="BITPIX" \|\|
310	it->first=="PCOUNT" \|\|
311	it->first=="GCOUNT")
312	)
313	continue;
314
315	gLog << ___all___ << setw(2) << it->second.type << '\|' << it->first << '=' << it->second.value << '/' << it->second.comment << '\|' << endl;
316	}}
317
318	void PrintColumns() const
319	{
320	typedef map<pair<size_t, string>, Column> Sorted;
321
322	Sorted sorted;
323
324	for (Columns::const_iterator it=cols.begin(); it!=cols.end(); it++)
325	sorted[make_pair(it->second.offset, it->first)] = it->second;
326
327	for (Sorted::const_iterator it=sorted.begin(); it!=sorted.end(); it++)
328	{
329	gLog << ___all___ << setw(6) << it->second.offset << "\| ";
330	gLog << it->second.num << 'x';
331	switch (it->second.type)
332	{
333	case 'A': gLog << "char(8)"; break;
334	case 'L': gLog << "bool(8)"; break;
335	case 'B': gLog << "byte(8)"; break;
336	case 'I': gLog << "short(16)"; break;
337	case 'J': gLog << "int(32)"; break;
338	case 'K': gLog << "int(64)"; break;
339	case 'E': gLog << "float(32)"; break;
340	case 'D': gLog << "double(64)"; break;
341	}
342	gLog << ": " << it->first.second << " [" << it->second.unit << "]" << endl;
343	}
344	}
345
346	operator bool() const { return !name.empty(); }
347
348	bool HasKey(const string &key) const
349	{
350	return keys.find(key)!=keys.end();
351	}
352
353	bool HasColumn(const string& col) const
354	{
355	return cols.find(col)!=cols.end();
356	}
357
358	const Columns &GetColumns() const
359	{
360	return cols;
361	}
362
363	const Keys &GetKeys() const
364	{
365	return keys;
366	}
367
368	// Values of keys are always signed
369	template<typename T>
370	T Get(const string &key) const
371	{
372	const map<string,Entry>::const_iterator it = keys.find(key);
373	if (it==keys.end())
374	{
375	ostringstream str;
376	str << "Key '" << key << "' not found." << endl;
377	#ifdef __EXCEPTIONS
378	throw runtime_error(str.str());
379	#else
380	gLog << ___err___ << "ERROR - " << str.str() << endl;
381	return T();
382	#endif
383	}
384	return it->second.Get<T>();
385	}
386
387	// Values of keys are always signed
388	template<typename T>
389	T Get(const string &key, const T &deflt) const
390	{
391	const map<string,Entry>::const_iterator it = keys.find(key);
392	return it==keys.end() ? deflt :it->second.Get<T>();
393	}
394
395	size_t GetN(const string &key) const
396	{
397	const Columns::const_iterator it = cols.find(key);
398	return it==cols.end() ? 0 : it->second.num;
399	}
400	};
401
402	private:
403	Table fTable;
404
405	typedef pair<void*, Table::Column> Address;
406	typedef vector<Address> Addresses;
407	//map<void*, Table::Column> fAddresses;
408	Addresses fAddresses;
409
410	#ifdef __CINT__
411	typedef map<string, void*> Pointers;
412	#else
413	typedef unordered_map<string, void*> Pointers;
414	#endif
415	Pointers fPointers;
416
417	vector<vector<char>> fGarbage;
418
419	vector<char> fBufferRow;
420	vector<char> fBufferDat;
421
422	size_t fRow;
423
424	Checksum fChkHeader;
425	Checksum fChkData;
426
427	bool ReadBlock(vector<string> &vec)
428	{
429	int endtag = 0;
430	for (int i=0; i<36; i++)
431	{
432	char c[81];
433	c[80] = 0;
434	read(c, 80);
435	if (!good())
436	break;
437
438	fChkHeader.add(c, 80);
439
440	// if (c[0]==0)
441	// return vector<string>();
442
443	string str(c);
444
445	// if (!str.empty())
446	// cout << setw(2) << i << "\|" << str << "\|" << (endtag?'-':'+') << endl;
447
448	if (endtag==2 \|\| str=="END ")
449	{
450	endtag = 2; // valid END tag found
451	continue;
452	}
453
454	if (endtag==1 \|\| str==" ")
455	{
456	endtag = 1; // end tag not found, but expected to be there
457	continue;
458	}
459
460	vec.push_back(str);
461	}
462
463	// Make sure that no empty vector is returned
464	if (endtag && vec.size()%36==0)
465	vec.push_back(string("END = '' / "));
466
467	return endtag==2;
468	}
469
470	string Compile(const string &key, int16_t i=-1)
471	{
472	if (i<0)
473	return key;
474
475	ostringstream str;
476	str << key << i;
477	return str.str();
478	}
479
480	public:
481	fits(const string &fname, bool force=false) : izstream(fname.c_str())
482	{
483	char simple[10];
484	read(simple, 10);
485	if (!good())
486	return;
487
488	if (memcmp(simple, "SIMPLE = ", 10))
489	{
490	clear(rdstate()\|ios::badbit);
491	#ifdef __EXCEPTIONS
492	throw runtime_error("File is not a FITS file.");
493	#else
494	gLog << ___err___ << "ERROR - File is not a FITS file." << endl;
495	return;
496	#endif
497	}
498
499	seekg(0);
500
501	while (good())
502	{
503	vector<string> block;
504	while (1)
505	{
506	// FIXME: Set limit on memory consumption
507	const int rc = ReadBlock(block);
508	if (!good())
509	{
510	clear(rdstate()\|ios::badbit);
511	#ifdef __EXCEPTIONS
512	throw runtime_error("FITS file corrupted.");
513	#else
514	gLog << ___err___ << "ERROR - FITS file corrupted." << endl;
515	return;
516	#endif
517	}
518
519	if (block.size()%36)
520	{
521	if (!rc && !force)
522	{
523	clear(rdstate()\|ios::badbit);
524	#ifdef __EXCEPTIONS
525	throw runtime_error("END keyword missing in FITS header.");
526	#else
527	gLog << ___err___ << "ERROR - END keyword missing in FITS file... file might be corrupted." << endl;
528	return;
529	#endif
530	}
531	break;
532	}
533	}
534
535	if (block.size()==0)
536	break;
537
538	if (block[0].substr(0, 9)=="SIMPLE =")
539	{
540	fChkHeader.reset();
541	continue;
542	}
543
544	if (block[0].substr(0, 9)=="XTENSION=")
545	{
546	// FIXME: Check for table name
547
548	fTable = Table(block, tellg());
549	fRow = (size_t)-1;
550
551	//fTable.PrintKeys();
552
553	if (!fTable)
554	{
555	clear(rdstate()\|ios::badbit);
556	return;
557	}
558
559	fBufferRow.resize(fTable.bytes_per_row + 4-fTable.bytes_per_row%4);
560	fBufferDat.resize(fTable.bytes_per_row);
561
562	/*
563	// Next table should start at:
564	const size_t size = fTable.bytes_per_row*fTable.num_rows;
565	const size_t blks = size/(36*80);
566	const size_t rest = size%(36*80);
567
568	seekg((blks+(rest>0?1:0))(3680), ios::cur);
569	if (!good())
570	gLog << ___err___ << "File seems to be incomplete (less data than expected from header)." << endl;
571
572	fRow = fTable.num_rows;
573	*/
574
575	break;
576	}
577	}
578	}
579
580	uint8_t ReadRow(size_t row)
581	{
582	// if (row!=fRow+1) // Fast seeking is ensured by izstream
583	seekg(fTable.offset+row*fTable.bytes_per_row);
584
585	// For the checksum we need everything to be correctly aligned
586	const uint8_t offset = (row*fTable.bytes_per_row)%4;
587
588	auto ib = fBufferRow.begin();
589	auto ie = fBufferRow.end();
590	*ib++ = 0;
591	*ib++ = 0;
592	*ib++ = 0;
593	*ib = 0;
594
595	*--ie = 0;
596	*--ie = 0;
597	*--ie = 0;
598	*--ie = 0;
599
600	fBufferRow.assign(fBufferRow.size(), 0);
601
602	read(fBufferRow.data()+offset, fTable.bytes_per_row);
603	//fin.clear(fin.rdstate()&~ios::eofbit);
604
605	if (row==fRow+1)
606	fChkData.add(fBufferRow);
607
608	fRow = row;
609
610	return offset;
611	}
612
613	template<size_t N>
614	void revcpy(char dest, const char src, int num)
615	{
616	const char pend = src + numN;
617	for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
618	reverse_copy(ptr, ptr+N, dest);
619	}
620
621	bool GetRow(size_t row, bool check=true)
622	{
623	if (check && row>=fTable.num_rows)
624	return false;
625
626	const uint8_t offset = ReadRow(row);
627	if (!good())
628	return good();
629
630	const char *ptr = fBufferRow.data() + offset;
631
632	for (Addresses::const_iterator it=fAddresses.begin(); it!=fAddresses.end(); it++)
633	{
634	const Table::Column &c = it->second;
635
636	const char *src = ptr + c.offset;
637	char dest = reinterpret_cast<char>(it->first);
638
639	// Let the compiler do some optimization by
640	// knowing the we only have 1, 2, 4 and 8
641	switch (c.size)
642	{
643	case 1: memcpy (dest, src, c.num*c.size); break;
644	case 2: revcpy<2>(dest, src, c.num); break;
645	case 4: revcpy<4>(dest, src, c.num); break;
646	case 8: revcpy<8>(dest, src, c.num); break;
647	}
648	}
649
650	return good();
651	}
652
653	bool GetNextRow(bool check=true)
654	{
655	return GetRow(fRow+1, check);
656	}
657
658	bool SkipNextRow()
659	{
660	seekg(fTable.offset+(++fRow)*fTable.bytes_per_row);
661	return good();
662	}
663
664	static bool Compare(const Address &p1, const Address &p2)
665	{
666	return p1.first>p2.first;
667	}
668
669	template<class T, class S>
670	const T &GetAs(const string &name)
671	{
672	return reinterpret_cast<S>(fPointers[name]);
673	}
674
675	void *SetPtrAddress(const string &name)
676	{
677	if (fTable.cols.count(name)==0)
678	{
679	ostringstream str;
680	str <<"SetPtrAddress('" << name << "') - Column not found." << endl;
681	#ifdef __EXCEPTIONS
682	throw runtime_error(str.str());
683	#else
684	gLog << ___err___ << "ERROR - " << str.str() << endl;
685	return NULL;
686	#endif
687	}
688
689	Pointers::const_iterator it = fPointers.find(name);
690	if (it!=fPointers.end())
691	return it->second;
692
693	fGarbage.push_back(vector<char>(fTable.cols[name].size*fTable.cols[name].num));
694
695	void *ptr = fGarbage.back().data();
696
697	fPointers[name] = ptr;
698	fAddresses.push_back(make_pair(ptr, fTable.cols[name]));
699	sort(fAddresses.begin(), fAddresses.end(), Compare);
700	return ptr;
701	}
702
703	template<typename T>
704	bool SetPtrAddress(const string &name, T *ptr, size_t cnt)
705	{
706	if (fTable.cols.count(name)==0)
707	{
708	ostringstream str;
709	str << "SetPtrAddress('" << name << "') - Column not found." << endl;
710	#ifdef __EXCEPTIONS
711	throw runtime_error(str.str());
712	#else
713	gLog << ___err___ << "ERROR - " << str.str() << endl;
714	return false;
715	#endif
716	}
717
718	if (sizeof(T)!=fTable.cols[name].size)
719	{
720	ostringstream str;
721	str << "SetPtrAddress('" << name << "') - Element size mismatch: expected "
722	<< fTable.cols[name].size << " from header, got " << sizeof(T) << endl;
723	#ifdef __EXCEPTIONS
724	throw runtime_error(str.str());
725	#else
726	gLog << ___err___ << "ERROR - " << str.str() << endl;
727	return false;
728	#endif
729	}
730
731	if (cnt!=fTable.cols[name].num)
732	{
733	ostringstream str;
734	str << "SetPtrAddress('" << name << "') - Element count mismatch: expected "
735	<< fTable.cols[name].num << " from header, got " << cnt << endl;
736	#ifdef __EXCEPTIONS
737	throw runtime_error(str.str());
738	#else
739	gLog << ___err___ << "ERROR - " << str.str() << endl;
740	return false;
741	#endif
742	}
743
744	// if (fAddresses.count(ptr)>0)
745	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
746
747	//fAddresses[ptr] = fTable.cols[name];
748	fPointers[name] = ptr;
749	fAddresses.push_back(make_pair(ptr, fTable.cols[name]));
750	sort(fAddresses.begin(), fAddresses.end(), Compare);
751	return true;
752	}
753
754	template<class T>
755	bool SetRefAddress(const string &name, T &ptr)
756	{
757	return SetPtrAddress(name, &ptr, sizeof(ptr)/sizeof(T));
758	}
759
760	template<typename T>
761	bool SetVecAddress(const string &name, vector<T> &vec)
762	{
763	return SetPtrAddress(name, vec.data(), vec.size());
764	}
765
766	template<typename T>
767	T Get(const string &key) const
768	{
769	return fTable.Get<T>(key);
770	}
771
772	template<typename T>
773	T Get(const string &key, const string &deflt) const
774	{
775	return fTable.Get<T>(key, deflt);
776	}
777
778	bool SetPtrAddress(const string &name, void *ptr)
779	{
780	if (fTable.cols.count(name)==0)
781	{
782	ostringstream str;
783	str <<"SetPtrAddress('" << name << "') - Column not found." << endl;
784	#ifdef __EXCEPTIONS
785	throw runtime_error(str.str());
786	#else
787	gLog << ___err___ << "ERROR - " << str.str() << endl;
788	return false;
789	#endif
790	}
791
792	// if (fAddresses.count(ptr)>0)
793	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
794
795	//fAddresses[ptr] = fTable.cols[name];
796	fPointers[name] = ptr;
797	fAddresses.push_back(make_pair(ptr, fTable.cols[name]));
798	sort(fAddresses.begin(), fAddresses.end(), Compare);
799	return true;
800	}
801
802	bool HasKey(const string &key) const { return fTable.HasKey(key); }
803	bool HasColumn(const string& col) const { return fTable.HasColumn(col);}
804	const Table::Columns &GetColumns() const { return fTable.GetColumns();}
805	const Table::Keys &GetKeys() const { return fTable.GetKeys();}
806
807	int64_t GetInt(const string &key) const { return fTable.Get<int64_t>(key); }
808	uint64_t GetUInt(const string &key) const { return fTable.Get<uint64_t>(key); }
809	double GetFloat(const string &key) const { return fTable.Get<double>(key); }
810	string GetStr(const string &key) const { return fTable.Get<string>(key); }
811
812	size_t GetN(const string &key) const
813	{
814	return fTable.GetN(key);
815	}
816
817	size_t GetNumRows() const { return fTable.num_rows; }
818	size_t GetRow() const { return fRow; }
819
820	operator bool() const { return fTable && fTable.offset!=0; }
821
822	void PrintKeys() const { fTable.PrintKeys(); }
823	void PrintColumns() const { fTable.PrintColumns(); }
824
825	bool IsHeaderOk() const { return fTable.datasum<0?false:(fChkHeader+Checksum(fTable.datasum)).valid(); }
826	bool IsFileOk() const { return (fChkHeader+fChkData).valid(); }
827
828	};
829
830	};
831	#endif

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