Context Navigation

source: branches/removing_cpp11_features/mcore/fits.h@ 20076

Visit:

Last change on this file since 20076 was 18049, checked in by tbretz, 10 years ago

File size: 31.3 KB

Line
1	#ifndef MARS_fits
2	#define MARS_fits
3
4	#include <stdint.h>
5
6	#include <map>
7	#include <string>
8	#include <fstream>
9	#include <sstream>
10	#include <algorithm>
11	#include <stdexcept>
12
13	#define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
14
15	#ifndef __CINT__
16	#include <unordered_map>
17	#else
18	#define off_t size_t
19	namespace std
20	{
21	template<class T, class S> class unordered_map<T, S>;
22	}
23	#endif
24
25	#if defined(__MARS__) \|\| defined(__CINT__)
26	#include "MLog.h"
27	#include "MLogManip.h"
28	#define ___err___ err
29	#define ___warn___ warn
30	#define ___all___ all
31	#else
32	#include <vector>
33	#include <iomanip>
34	#include <iostream>
35	#ifndef gLog
36	#define gLog std::cerr
37	#define ___err___ ""
38	#define ___warn___ ""
39	#define ___all___ ""
40	#endif
41	#endif
42
43	#if defined(HAVE_ZLIB) \|\| defined(__CINT__)
44	#include "izstream.h"
45	#else
46	#include <fstream>
47	#define izstream ifstream
48	#warning Support for zipped FITS files disabled.
49	#endif
50
51	#include "FITS.h"
52	#include "checksum.h"
53
54	class fits : public izstream
55	{
56	public:
57	//I know I know, you're going to yiell that this does not belong here.
58	//It will belong in the global scope eventually, and it makes the coding of zfits much simpler this way.
59	enum Compression_t
60	{
61	kCompUnknown,
62	kCompFACT
63	};
64
65	enum fitsstate
66	{
67	throwbit = 8
68	};
69
70	struct Entry
71	{
72	char type;
73	std::string value;
74	std::string comment;
75	std::string fitsString;
76
77	template<typename T>
78	T Get() const
79	{
80	T t;
81
82	std::istringstream str(value);
83	str >> t;
84
85	return t;
86	}
87	};
88
89	struct Table
90	{
91	off_t offset;
92
93	bool is_compressed;
94
95	std::string name;
96	size_t bytes_per_row;
97	size_t num_rows;
98	size_t num_cols;
99	size_t total_bytes; // NAXIS1*NAXIS2
100
101	struct Column
102	{
103	size_t offset;
104	size_t num;
105	size_t size;
106	size_t bytes; // num*size
107	char type;
108	std::string unit;
109	Compression_t comp;
110	};
111
112	typedef std::map<std::string, Entry> Keys;
113	typedef std::map<std::string, Column> Columns;
114	typedef std::vector<Column> SortedColumns;
115
116	Columns cols;
117	SortedColumns sorted_cols;
118	Keys keys;
119
120	int64_t datasum;
121
122	std::string Trim(const std::string &str, char c=' ') const
123	{
124	// Trim Both leading and trailing spaces
125	const size_t pstart = str.find_first_not_of(c); // Find the first character position after excluding leading blank spaces
126	const size_t pend = str.find_last_not_of(c); // Find the first character position from reverse af
127
128	// if all spaces or empty return an empty string
129	if (std::string::npos==pstart \|\| std::string::npos==pend)
130	return std::string();
131
132	return str.substr(pstart, pend-pstart+1);
133	}
134
135	bool Check(const std::string &key, char type, const std::string &value="") const
136	{
137	const Keys::const_iterator it = keys.find(key);
138	if (it==keys.end())
139	{
140	std::ostringstream str;
141	str << "Key '" << key << "' not found.";
142	#ifdef __EXCEPTIONS
143	throw std::runtime_error(str.str());
144	#else
145	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
146	return false;
147	#endif
148	}
149
150	if (it->second.type!=type)
151	{
152	std::ostringstream str;
153	str << "Wrong type for key '" << key << "': expected " << type << ", found " << it->second.type << ".";
154	#ifdef __EXCEPTIONS
155	throw std::runtime_error(str.str());
156	#else
157	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
158	return false;
159	#endif
160	}
161
162	if (!value.empty() && it->second.value!=value)
163	{
164	std::ostringstream str;
165	str << "Wrong value for key '" << key << "': expected " << value << ", found " << it->second.value << ".";
166	#ifdef __EXCEPTIONS
167	throw std::runtime_error(str.str());
168	#else
169	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
170	return false;
171	#endif
172	}
173
174	return true;
175	}
176
177	Keys ParseBlock(const std::vector<std::string> &vec) const
178	{
179	Keys rc;
180
181	for (unsigned int i=0; i<vec.size(); i++)
182	{
183	const std::string key = Trim(vec[i].substr(0,8));
184	// Keywords without a value, like COMMENT / HISTORY
185	if (vec[i].substr(8,2)!="= ")
186	continue;
187
188	char type = 0;
189
190	std::string com;
191	std::string val = Trim(vec[i].substr(10));
192
193	if (val[0]=='\'')
194	{
195	// First skip all '' in the string
196	size_t p = 1;
197	while (1)
198	{
199	const size_t pp = val.find_first_of('\'', p);
200	if (pp==std::string::npos)
201	break;
202
203	p = val[pp+1]=='\'' ? pp+2 : pp+1;
204	}
205
206	// Now find the comment
207	const size_t ppp = val.find_first_of('/', p);
208
209	// Set value, comment and type
210	// comments could be just spaces. take care of this.
211	if (ppp!=std::string::npos && val.size()!=ppp+1)
212	com = Trim(val.substr(ppp+1));
213
214	val = Trim(val.substr(1, p-2));
215	type = 'T';
216	}
217	else
218	{
219	const size_t p = val.find_first_of('/');
220
221	if (p!=std::string::npos && val.size()!=p+1)
222	com = Trim(val.substr(p+2));
223
224	val = Trim(val.substr(0, p));
225
226	if (val.empty() \|\| val.find_first_of('T')!=std::string::npos \|\| val.find_first_of('F')!=std::string::npos)
227	type = 'B';
228	else
229	type = val.find_last_of('.')==std::string::npos ? 'I' : 'F';
230	}
231
232	const Entry e = { type, val, com, vec[i] };
233
234	rc[key] = e;
235	}
236
237	return rc;
238	}
239
240	Table() : offset(0), is_compressed(false) { }
241	Table(const std::vector<std::string> &vec, off_t off) : offset(off),
242	keys(ParseBlock(vec))
243	{
244	is_compressed = HasKey("ZTABLE") && Check("ZTABLE", 'B', "T");
245
246	if (!Check("XTENSION", 'T', "BINTABLE") \|\|
247	!Check("NAXIS", 'I', "2") \|\|
248	!Check("BITPIX", 'I', "8") \|\|
249	!Check("GCOUNT", 'I', "1") \|\|
250	!Check("EXTNAME", 'T') \|\|
251	!Check("NAXIS1", 'I') \|\|
252	!Check("NAXIS2", 'I') \|\|
253	!Check("TFIELDS", 'I'))
254	return;
255
256	if (is_compressed)
257	{
258	if (!Check("ZNAXIS1", 'I') \|\|
259	!Check("ZNAXIS2", 'I') \|\|
260	!Check("ZPCOUNT", 'I', "0"))
261	return;
262	}
263	else
264	{
265	if (!Check("PCOUNT", 'I', "0"))
266	return;
267	}
268
269	total_bytes = Get<size_t>("NAXIS1")*Get<size_t>("NAXIS2");
270	bytes_per_row = is_compressed ? Get<size_t>("ZNAXIS1") : Get<size_t>("NAXIS1");
271	num_rows = is_compressed ? Get<size_t>("ZNAXIS2") : Get<size_t>("NAXIS2");
272	num_cols = Get<size_t>("TFIELDS");
273	datasum = Get<int64_t>("DATASUM", -1);
274	size_t bytes = 0;
275
276	const std::string tFormName = is_compressed ? "ZFORM" : "TFORM";
277	for (long long unsigned int i=1; i<=num_cols; i++)
278	{
279	const std::string num(std::to_string(i));
280
281	if (!Check("TTYPE"+num, 'T') \|\|
282	!Check(tFormName+num, 'T'))
283	return;
284
285	const std::string id = Get<std::string>("TTYPE"+num);
286	const std::string fmt = Get<std::string>(tFormName+num);
287	const std::string unit = Get<std::string>("TUNIT"+num, "");
288	const std::string comp = Get<std::string>("ZCTYP"+num, "");
289
290	Compression_t compress = kCompUnknown;
291	if (comp == "FACT")
292	compress = kCompFACT;
293
294	std::istringstream sin(fmt);
295	int n = 0;
296	sin >> n;
297	if (!sin)
298	n = 1;
299
300	const char type = fmt[fmt.length()-1];
301
302	size_t size = 0;
303	switch (type)
304	{
305	// We could use negative values to mark floats
306	// otheriwse we could just cast them to int64_t?
307	case 'L': // logical
308	case 'A': // char
309	case 'B': size = 1; break; // byte
310	case 'I': size = 2; break; // short
311	case 'J': size = 4; break; // int
312	case 'K': size = 8; break; // long long
313	case 'E': size = 4; break; // float
314	case 'D': size = 8; break; // double
315	// case 'X': size = n; break; // bits (n=number of bytes needed to contain all bits)
316	// case 'C': size = 8; break; // complex float
317	// case 'M': size = 16; break; // complex double
318	// case 'P': size = 8; break; // array descriptor (32bit)
319	// case 'Q': size = 16; break; // array descriptor (64bit)
320	default:
321	{
322	std::ostringstream str;
323	str << "FITS format TFORM='" << fmt << "' not yet supported.";
324	#ifdef __EXCEPTIONS
325	throw std::runtime_error(str.str());
326	#else
327	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
328	return;
329	#endif
330	}
331	}
332
333	const Table::Column col = { bytes, size_t(n), size, n*size, type, unit, compress};
334
335	cols[id] = col;
336	sorted_cols.emplace_back(col);
337	bytes += n*size;
338	}
339
340	if (bytes!=bytes_per_row)
341	{
342	std::ostringstream str;
343	str << "Sum of bytes in columns [" << bytes << "] does not match (Z)NAXIS2 [" << bytes_per_row << "].";
344
345	#ifdef __EXCEPTIONS
346	throw std::runtime_error(str.str());
347	#else
348	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
349	return;
350	#endif
351	}
352
353	name = Get<std::string>("EXTNAME");
354	}
355
356	void PrintKeys(bool display_all=false) const
357	{
358	for (Keys::const_iterator it=keys.cbegin(); it!=keys.cend(); it++)
359	{
360	if (!display_all && FITS::IsReservedKeyWord(it->first))
361	continue;
362
363	gLog << ___all___ << std::setw(2) << it->second.type << '\|' << it->first << '=' << it->second.value << '/' << it->second.comment << '\|' << std::endl;
364	}
365	}
366
367	void PrintColumns() const
368	{
369	typedef std::map<std::pair<size_t, std::string>, Column> Sorted;
370
371	Sorted sorted;
372
373	for (Columns::const_iterator it=cols.cbegin(); it!=cols.cend(); it++)
374	sorted[std::make_pair(it->second.offset, it->first)] = it->second;
375
376	for (Sorted::const_iterator it=sorted.cbegin(); it!=sorted.cend(); it++)
377	{
378	gLog << ___all___ << std::setw(6) << it->second.offset << "\| ";
379	gLog << it->second.num << 'x';
380	switch (it->second.type)
381	{
382	case 'A': gLog << "char(8)"; break;
383	case 'L': gLog << "bool(8)"; break;
384	case 'B': gLog << "byte(8)"; break;
385	case 'I': gLog << "short(16)"; break;
386	case 'J': gLog << "int(32)"; break;
387	case 'K': gLog << "int(64)"; break;
388	case 'E': gLog << "float(32)"; break;
389	case 'D': gLog << "double(64)"; break;
390	}
391	gLog << ": " << it->first.second << " [" << it->second.unit << "]" << std::endl;
392	}
393	}
394
395	operator bool() const { return !name.empty(); }
396
397	bool HasKey(const std::string &key) const
398	{
399	return keys.find(key)!=keys.end();
400	}
401
402	bool HasColumn(const std::string& col) const
403	{
404	return cols.find(col)!=cols.end();
405	}
406
407	const Columns &GetColumns() const
408	{
409	return cols;
410	}
411
412	const Keys &GetKeys() const
413	{
414	return keys;
415	}
416
417	// Values of keys are always signed
418	template<typename T>
419	T Get(const std::string &key) const
420	{
421	const Keys::const_iterator it = keys.find(key);
422	if (it==keys.end())
423	{
424	std::ostringstream str;
425	str << "Key '" << key << "' not found.";
426	#ifdef __EXCEPTIONS
427	throw std::runtime_error(str.str());
428	#else
429	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
430	return T();
431	#endif
432	}
433	return it->second.Get<T>();
434	}
435
436	// Values of keys are always signed
437	template<typename T>
438	T Get(const std::string &key, const T &deflt) const
439	{
440	const Keys::const_iterator it = keys.find(key);
441	return it==keys.end() ? deflt :it->second.Get<T>();
442	}
443
444	size_t GetN(const std::string &key) const
445	{
446	const Columns::const_iterator it = cols.find(key);
447	return it==cols.end() ? 0 : it->second.num;
448	}
449
450
451
452	// There may be a gap between the main table and the start of the heap:
453	// this computes the offset
454	streamoff GetHeapShift() const
455	{
456	if (!HasKey("ZHEAPPTR"))
457	return 0;
458
459	const size_t shift = Get<size_t>("ZHEAPPTR");
460	return shift <= total_bytes ? 0 : shift - total_bytes;
461	}
462
463	// return total number of bytes 'all inclusive'
464	streamoff GetTotalBytes() const
465	{
466	//get offset of special data area from start of main table
467	const streamoff shift = GetHeapShift();
468
469	//and special data area size
470	const streamoff size = HasKey("PCOUNT") ? Get<streamoff>("PCOUNT") : 0;
471
472	// Get the total size
473	const streamoff total = total_bytes + size + shift;
474
475	// check for padding
476	if (total%2880==0)
477	return total;
478
479	// padding necessary
480	return total + (2880 - (total%2880));
481	}
482	};
483
484	void Exception(const std::string &txt)
485	{
486	#ifdef __EXCEPTIONS
487	if (exceptions()&throwbit)
488	throw std::runtime_error(txt);
489	#endif
490	gLog << ___err___ << "ERROR - " << txt << std::endl;
491	}
492
493	protected:
494	std::ofstream fCopy;
495	std::vector<std::string> fListOfTables; // List of skipped tables. Last table is open table
496
497	Table fTable;
498
499	typedef std::pair<void*, Table::Column> Address;
500	typedef std::vector<Address> Addresses;
501	//map<void*, Table::Column> fAddresses;
502	Addresses fAddresses;
503
504	typedef std::unordered_map<std::string, void*> Pointers;
505	Pointers fPointers;
506
507	std::vector<std::vector<char>> fGarbage;
508
509	std::vector<char> fBufferRow;
510	std::vector<char> fBufferDat;
511
512	size_t fRow;
513
514	Checksum fChkHeader;
515	Checksum fChkData;
516
517	bool ReadBlock(std::vector<std::string> &vec)
518	{
519	int endtag = 0;
520	for (int i=0; i<36; i++)
521	{
522	char c[81];
523	c[80] = 0;
524	read(c, 80);
525	if (!good())
526	break;
527
528	fChkHeader.add(c, 80);
529
530	// if (c[0]==0)
531	// return vector<string>();
532
533	std::string str(c);
534
535	// if (!str.empty())
536	// cout << setw(2) << i << "\|" << str << "\|" << (endtag?'-':'+') << endl;
537
538	if (endtag==2 \|\| str=="END ")
539	{
540	endtag = 2; // valid END tag found
541	continue;
542	}
543
544	if (endtag==1 \|\| str==" ")
545	{
546	endtag = 1; // end tag not found, but expected to be there
547	continue;
548	}
549
550	vec.emplace_back(str);
551	}
552
553	// Make sure that no empty vector is returned
554	if (endtag && vec.size()%36==0)
555	vec.emplace_back("END = '' / ");
556
557	return endtag==2;
558	}
559
560	std::string Compile(const std::string &key, int16_t i=-1) const
561	{
562	#if GCC_VERSION < 40603
563	return i<0 ? key : key+std::to_string((long long int)(i));
564	#else
565	return i<0 ? key : key+std::to_string(i);
566	#endif
567	}
568
569	void Constructor(const std::string &fname, std::string fout="", const std::string& tableName="", bool force=false)
570	{
571	char simple[10];
572	read(simple, 10);
573	if (!good())
574	return;
575
576	EnableAddressExceptions();
577
578	if (memcmp(simple, "SIMPLE = ", 10))
579	{
580	clear(rdstate()\|std::ios::badbit);
581	#ifdef __EXCEPTIONS
582	throw std::runtime_error("File is not a FITS file.");
583	#else
584	gLog << ___err___ << "ERROR - File is not a FITS file." << std::endl;
585	return;
586	#endif
587	}
588
589	seekg(0);
590
591	while (good())
592	{
593	std::vector<std::string> block;
594	while (1)
595	{
596	// If we search for a table, we implicitly assume that
597	// not finding the table is not an error. The user
598	// can easily check that by eof() && !bad()
599	peek();
600	if (eof() && !bad() && !tableName.empty())
601	{
602	break;
603	}
604	// FIXME: Set limit on memory consumption
605	const int rc = ReadBlock(block);
606	if (!good())
607	{
608	clear(rdstate()\|std::ios::badbit);
609	#ifdef __EXCEPTIONS
610	throw std::runtime_error("FITS file corrupted.");
611	#else
612	gLog << ___err___ << "ERROR - FITS file corrupted." << std::endl;
613	return;
614	#endif
615	}
616
617	if (block.size()%36)
618	{
619	if (!rc && !force)
620	{
621	clear(rdstate()\|std::ios::badbit);
622	#ifdef __EXCEPTIONS
623	throw std::runtime_error("END keyword missing in FITS header.");
624	#else
625	gLog << ___err___ << "ERROR - END keyword missing in FITS file... file might be corrupted." << std::endl;
626	return;
627	#endif
628	}
629	break;
630	}
631	}
632
633	if (block.empty())
634	break;
635
636	if (block[0].substr(0, 9)=="SIMPLE =")
637	{
638	fChkHeader.reset();
639	continue;
640	}
641
642	if (block[0].substr(0, 9)=="XTENSION=")
643	{
644	fTable = Table(block, tellg());
645	fRow = (size_t)-1;
646
647	if (!fTable)
648	{
649	clear(rdstate()\|std::ios::badbit);
650	return;
651	}
652
653	const std::string &tname = fTable.Get<std::string>("EXTNAME");
654
655	fListOfTables.emplace_back(tname);
656
657	// Check for table name. Skip until eof or requested table are found.
658	// skip the current table?
659	if ((!tableName.empty() && tableName!=tname) \|\| (tableName.empty() && "ZDrsCellOffsets"==tname))
660	{
661	const streamoff skip = fTable.GetTotalBytes();
662	seekg(skip, std::ios_base::cur);
663
664	fChkHeader.reset();
665
666	continue;
667	}
668
669	fBufferRow.resize(fTable.bytes_per_row + 8-fTable.bytes_per_row%4);
670	fBufferDat.resize(fTable.bytes_per_row);
671
672	break;
673	}
674	}
675
676	if (fout.empty())
677	return;
678
679	if (*fout.rbegin()=='/')
680	{
681	const size_t p = fname.find_last_of('/');
682	fout.append(fname.substr(p+1));
683	}
684
685	fCopy.open(fout);
686	if (!fCopy)
687	{
688	clear(rdstate()\|std::ios::badbit);
689	#ifdef __EXCEPTIONS
690	throw std::runtime_error("Could not open output file.");
691	#else
692	gLog << ___err___ << "ERROR - Failed to open output file." << std::endl;
693	return;
694	#endif
695	}
696
697	const streampos p = tellg();
698	seekg(0);
699
700	std::vector<char> buf(p);
701	read(buf.data(), p);
702
703	fCopy.write(buf.data(), p);
704	if (!fCopy)
705	clear(rdstate()\|std::ios::badbit);
706	}
707
708	public:
709	fits(const std::string &fname, const std::string& tableName="", bool force=false) : izstream(fname.c_str())
710	{
711	Constructor(fname, "", tableName, force);
712	if ((fTable.is_compressed \|\|fTable.name=="ZDrsCellOffsets") && !force)
713	{
714	#ifdef __EXCEPTIONS
715	throw std::runtime_error("Trying to read a compressed fits with the base fits class. Use factfits instead.");
716	#else
717	gLog << ___err___ << "ERROR - Trying to read a compressed fits with the base fits class. Use factfits instead." << std::endl;
718	#endif
719	clear(rdstate()\|std::ios::badbit);
720	}
721	}
722
723	fits(const std::string &fname, const std::string &fout, const std::string& tableName, bool force=false) : izstream(fname.c_str())
724	{
725	Constructor(fname, fout, tableName, force);
726	if ((fTable.is_compressed \|\| fTable.name=="ZDrsCellOffsets") && !force)
727	{
728	#ifdef __EXCEPTIONS
729	throw std::runtime_error("Trying to read a compressed fits with the base fits class. Use factfits instead.");
730	#else
731	gLog << ___err___ << "ERROR - Trying to read a compressed fits with the base fits class. Use factfits instead." << std::endl;
732	#endif
733	clear(rdstate()\|std::ios::badbit);
734	}
735	}
736
737	fits() : izstream()
738	{
739
740	}
741
742	~fits()
743	{
744	std::copy(std::istreambuf_iterator<char>(*this),
745	std::istreambuf_iterator<char>(),
746	std::ostreambuf_iterator<char>(fCopy));
747	}
748
749	virtual void StageRow(size_t row, char* dest)
750	{
751	// if (row!=fRow+1) // Fast seeking is ensured by izstream
752	seekg(fTable.offset+row*fTable.bytes_per_row);
753	read(dest, fTable.bytes_per_row);
754	//fin.clear(fin.rdstate()&~ios::eofbit);
755	}
756
757	virtual void WriteRowToCopyFile(size_t row)
758	{
759	if (row==fRow+1)
760	{
761	const uint8_t offset = (row*fTable.bytes_per_row)%4;
762
763	fChkData.add(fBufferRow);
764	if (fCopy.is_open() && fCopy.good())
765	fCopy.write(fBufferRow.data()+offset, fTable.bytes_per_row);
766	if (!fCopy)
767	clear(rdstate()\|std::ios::badbit);
768	}
769	else
770	if (fCopy.is_open())
771	clear(rdstate()\|std::ios::badbit);
772	}
773
774	void ZeroBufferForChecksum(std::vector<char>& vec, const uint64_t extraZeros=0)
775	{
776	auto ib = vec.begin();
777	auto ie = vec.end();
778
779	*ib++ = 0;
780	*ib++ = 0;
781	*ib++ = 0;
782	*ib = 0;
783
784	for (uint64_t i=0;i<extraZeros+8;i++)
785	*--ie = 0;
786	}
787
788	uint8_t ReadRow(size_t row)
789	{
790	// For the checksum we need everything to be correctly aligned
791	const uint8_t offset = (row*fTable.bytes_per_row)%4;
792
793	ZeroBufferForChecksum(fBufferRow);
794
795	StageRow(row, fBufferRow.data()+offset);
796
797	WriteRowToCopyFile(row);
798
799	fRow = row;
800
801	return offset;
802	}
803
804	template<size_t N>
805	void revcpy(char dest, const char src, const int &num)
806	{
807	const char pend = src + numN;
808	for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
809	std::reverse_copy(ptr, ptr+N, dest);
810	}
811
812	virtual void MoveColumnDataToUserSpace(char dest, const char src, const Table::Column& c)
813	{
814	// Let the compiler do some optimization by
815	// knowing that we only have 1, 2, 4 and 8
816	switch (c.size)
817	{
818	case 1: memcpy (dest, src, c.bytes); break;
819	case 2: revcpy<2>(dest, src, c.num); break;
820	case 4: revcpy<4>(dest, src, c.num); break;
821	case 8: revcpy<8>(dest, src, c.num); break;
822	}
823	}
824
825	virtual bool GetRow(size_t row, bool check=true)
826	{
827	if (check && row>=fTable.num_rows)
828	return false;
829
830	const uint8_t offset = ReadRow(row);
831	if (!good())
832	return good();
833
834	const char *ptr = fBufferRow.data() + offset;
835
836	for (Addresses::const_iterator it=fAddresses.cbegin(); it!=fAddresses.cend(); it++)
837	{
838	const Table::Column &c = it->second;
839
840	const char *src = ptr + c.offset;
841	char dest = reinterpret_cast<char>(it->first);
842
843	MoveColumnDataToUserSpace(dest, src, c);
844	}
845
846	return good();
847	}
848
849	bool GetNextRow(bool check=true)
850	{
851	return GetRow(fRow+1, check);
852	}
853
854	virtual bool SkipNextRow()
855	{
856	seekg(fTable.offset+(++fRow)*fTable.bytes_per_row);
857	return good();
858	}
859
860	static bool Compare(const Address &p1, const Address &p2)
861	{
862	return p1.first>p2.first;
863	}
864
865	template<class T, class S>
866	const T &GetAs(const std::string &name)
867	{
868	return reinterpret_cast<S>(fPointers[name]);
869	}
870
871	void EnableAddressExceptions(bool b=true)
872	{
873	if (b)
874	exceptions(iostate(throwbit));
875	else
876	exceptions(iostate(exceptions()&~throwbit));
877	}
878
879	void DisableAddressExceptions()
880	{
881	EnableAddressExceptions(false);
882	}
883
884	void *SetPtrAddress(const std::string &name)
885	{
886	if (fTable.cols.count(name)==0)
887	{
888	std::ostringstream str;
889	str << "SetPtrAddress('" << name << "') - Column not found.";
890	Exception(str.str());
891	return NULL;
892	}
893
894	Pointers::const_iterator it = fPointers.find(name);
895	if (it!=fPointers.end())
896	return it->second;
897
898	fGarbage.emplace_back(fTable.cols[name].bytes);
899
900	void *ptr = fGarbage.back().data();
901
902	fPointers[name] = ptr;
903	fAddresses.emplace_back(ptr, fTable.cols[name]);
904	sort(fAddresses.begin(), fAddresses.end(), Compare);
905	return ptr;
906	}
907
908	template<typename T>
909	bool SetPtrAddress(const std::string &name, T *ptr, size_t cnt)
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 false;
917	}
918
919	if (sizeof(T)!=fTable.cols[name].size)
920	{
921	std::ostringstream str;
922	str << "SetPtrAddress('" << name << "') - Element size mismatch: expected "
923	<< fTable.cols[name].size << " from header, got " << sizeof(T);
924	Exception(str.str());
925	return false;
926	}
927
928	if (cnt!=fTable.cols[name].num)
929	{
930	std::ostringstream str;
931	str << "SetPtrAddress('" << name << "') - Element count mismatch: expected "
932	<< fTable.cols[name].num << " from header, got " << cnt;
933	Exception(str.str());
934	return false;
935	}
936
937	// if (fAddresses.count(ptr)>0)
938	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
939
940	//fAddresses[ptr] = fTable.cols[name];
941	fPointers[name] = ptr;
942	fAddresses.emplace_back(ptr, fTable.cols[name]);
943	sort(fAddresses.begin(), fAddresses.end(), Compare);
944	return true;
945	}
946
947	template<class T>
948	bool SetRefAddress(const std::string &name, T &ptr)
949	{
950	return SetPtrAddress(name, &ptr, sizeof(ptr)/sizeof(T));
951	}
952
953	template<typename T>
954	bool SetVecAddress(const std::string &name, std::vector<T> &vec)
955	{
956	return SetPtrAddress(name, vec.data(), vec.size());
957	}
958
959	template<typename T>
960	T Get(const std::string &key) const
961	{
962	return fTable.Get<T>(key);
963	}
964
965	template<typename T>
966	T Get(const std::string &key, const std::string &deflt) const
967	{
968	return fTable.Get<T>(key, deflt);
969	}
970
971	bool SetPtrAddress(const std::string &name, void *ptr, size_t cnt=0)
972	{
973	if (fTable.cols.count(name)==0)
974	{
975	std::ostringstream str;
976	str <<"SetPtrAddress('" << name << "') - Column not found.";
977	Exception(str.str());
978	return false;
979	}
980
981	if (cnt && cnt!=fTable.cols[name].num)
982	{
983	std::ostringstream str;
984	str << "SetPtrAddress('" << name << "') - Element count mismatch: expected "
985	<< fTable.cols[name].num << " from header, got " << cnt;
986	Exception(str.str());
987	return false;
988	}
989
990	// if (fAddresses.count(ptr)>0)
991	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
992
993	//fAddresses[ptr] = fTable.cols[name];
994	fPointers[name] = ptr;
995	fAddresses.emplace_back(ptr, fTable.cols[name]);
996	sort(fAddresses.begin(), fAddresses.end(), Compare);
997	return true;
998	}
999
1000	bool HasKey(const std::string &key) const { return fTable.HasKey(key); }
1001	bool HasColumn(const std::string& col) const { return fTable.HasColumn(col);}
1002	const Table::Columns &GetColumns() const { return fTable.GetColumns();}
1003	const Table::SortedColumns& GetSortedColumns() const { return fTable.sorted_cols;}
1004	const Table::Keys &GetKeys() const { return fTable.GetKeys();}
1005
1006	int64_t GetInt(const std::string &key) const { return fTable.Get<int64_t>(key); }
1007	uint64_t GetUInt(const std::string &key) const { return fTable.Get<uint64_t>(key); }
1008	double GetFloat(const std::string &key) const { return fTable.Get<double>(key); }
1009	std::string GetStr(const std::string &key) const { return fTable.Get<std::string>(key); }
1010
1011	size_t GetN(const std::string &key) const
1012	{
1013	return fTable.GetN(key);
1014	}
1015
1016	// size_t GetNumRows() const { return fTable.num_rows; }
1017	size_t GetRow() const { return fRow==(size_t)-1 ? 0 : fRow; }
1018
1019	operator bool() const { return fTable && fTable.offset!=0; }
1020
1021	void PrintKeys(bool all_keys=false) const { fTable.PrintKeys(all_keys); }
1022	void PrintColumns() const { fTable.PrintColumns(); }
1023
1024	bool IsHeaderOk() const { return fTable.datasum<0?false:(fChkHeader+Checksum(fTable.datasum)).valid(); }
1025	virtual bool IsFileOk() const { return (fChkHeader+fChkData).valid(); }
1026
1027	bool IsCompressedFITS() const { return fTable.is_compressed;}
1028
1029	virtual size_t GetNumRows() const
1030	{
1031	return fTable.Get<size_t>("NAXIS2");
1032	}
1033
1034	virtual size_t GetBytesPerRow() const
1035	{
1036	return fTable.Get<size_t>("NAXIS1");
1037	}
1038
1039	const std::vector<std::string> &GetTables() const
1040	{
1041	return fListOfTables;
1042	}
1043	};
1044
1045	#endif

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

Download in other formats: