Context Navigation

source: releases/Mars.2014.05.26/mcore/fits.h@ 20115

Visit:

Last change on this file since 20115 was 17777, checked in by tbretz, 11 years ago
Solved the problem that so far cint does not define __MARS__; added an option to PrintKeys; remove all reserved keywords from the list of printed keys; some minor code cleanup.
File size: 31.4 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	struct Entry
66	{
67	char type;
68	std::string value;
69	std::string comment;
70	std::string fitsString;
71
72	template<typename T>
73	T Get() const
74	{
75	T t;
76
77	std::istringstream str(value);
78	str >> t;
79
80	return t;
81	}
82	};
83
84	struct Table
85	{
86	off_t offset;
87
88	bool is_compressed;
89
90	std::string name;
91	size_t bytes_per_row;
92	size_t num_rows;
93	size_t num_cols;
94	size_t total_bytes; // NAXIS1*NAXIS2
95
96	struct Column
97	{
98	size_t offset;
99	size_t num;
100	size_t size;
101	size_t bytes; // num*size
102	char type;
103	std::string unit;
104	Compression_t comp;
105	};
106
107	typedef std::map<std::string, Entry> Keys;
108	typedef std::map<std::string, Column> Columns;
109	typedef std::vector<Column> SortedColumns;
110
111	Columns cols;
112	SortedColumns sorted_cols;
113	Keys keys;
114
115	int64_t datasum;
116
117	std::string Trim(const std::string &str, char c=' ') const
118	{
119	// Trim Both leading and trailing spaces
120	const size_t pstart = str.find_first_not_of(c); // Find the first character position after excluding leading blank spaces
121	const size_t pend = str.find_last_not_of(c); // Find the first character position from reverse af
122
123	// if all spaces or empty return an empty string
124	if (std::string::npos==pstart \|\| std::string::npos==pend)
125	return std::string();
126
127	return str.substr(pstart, pend-pstart+1);
128	}
129
130	bool Check(const std::string &key, char type, const std::string &value="") const
131	{
132	const Keys::const_iterator it = keys.find(key);
133	if (it==keys.end())
134	{
135	std::ostringstream str;
136	str << "Key '" << key << "' not found.";
137	#ifdef __EXCEPTIONS
138	throw std::runtime_error(str.str());
139	#else
140	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
141	return false;
142	#endif
143	}
144
145	if (it->second.type!=type)
146	{
147	std::ostringstream str;
148	str << "Wrong type for key '" << key << "': expected " << type << ", found " << it->second.type << ".";
149	#ifdef __EXCEPTIONS
150	throw std::runtime_error(str.str());
151	#else
152	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
153	return false;
154	#endif
155	}
156
157	if (!value.empty() && it->second.value!=value)
158	{
159	std::ostringstream str;
160	str << "Wrong value for key '" << key << "': expected " << value << ", found " << it->second.value << ".";
161	#ifdef __EXCEPTIONS
162	throw std::runtime_error(str.str());
163	#else
164	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
165	return false;
166	#endif
167	}
168
169	return true;
170	}
171
172	Keys ParseBlock(const std::vector<std::string> &vec) const
173	{
174	Keys rc;
175
176	for (unsigned int i=0; i<vec.size(); i++)
177	{
178	const std::string key = Trim(vec[i].substr(0,8));
179	// Keywords without a value, like COMMENT / HISTORY
180	if (vec[i].substr(8,2)!="= ")
181	continue;
182
183	char type = 0;
184
185	std::string com;
186	std::string val = Trim(vec[i].substr(10));
187
188	if (val[0]=='\'')
189	{
190	// First skip all '' in the string
191	size_t p = 1;
192	while (1)
193	{
194	const size_t pp = val.find_first_of('\'', p);
195	if (pp==std::string::npos)
196	break;
197
198	p = val[pp+1]=='\'' ? pp+2 : pp+1;
199	}
200
201	// Now find the comment
202	const size_t ppp = val.find_first_of('/', p);
203
204	// Set value, comment and type
205	// comments could be just spaces. take care of this.
206	if (ppp!=std::string::npos && val.size()!=ppp+1)
207	com = Trim(val.substr(ppp+1));
208
209	val = Trim(val.substr(1, p-2));
210	type = 'T';
211	}
212	else
213	{
214	const size_t p = val.find_first_of('/');
215
216	if (p!=std::string::npos && val.size()!=p+1)
217	com = Trim(val.substr(p+2));
218
219	val = Trim(val.substr(0, p));
220
221	if (val.empty() \|\| val.find_first_of('T')!=std::string::npos \|\| val.find_first_of('F')!=std::string::npos)
222	type = 'B';
223	else
224	type = val.find_last_of('.')==std::string::npos ? 'I' : 'F';
225	}
226
227	const Entry e = { type, val, com, vec[i] };
228
229	rc[key] = e;
230	}
231
232	return rc;
233	}
234
235	Table() : offset(0), is_compressed(false) { }
236	Table(const std::vector<std::string> &vec, off_t off) : offset(off),
237	keys(ParseBlock(vec))
238	{
239	is_compressed = HasKey("ZTABLE") && Check("ZTABLE", 'B', "T");
240
241	if (!Check("XTENSION", 'T', "BINTABLE") \|\|
242	!Check("NAXIS", 'I', "2") \|\|
243	!Check("BITPIX", 'I', "8") \|\|
244	!Check("GCOUNT", 'I', "1") \|\|
245	!Check("EXTNAME", 'T') \|\|
246	!Check("NAXIS1", 'I') \|\|
247	!Check("NAXIS2", 'I') \|\|
248	!Check("TFIELDS", 'I'))
249	return;
250
251	if (is_compressed)
252	{
253	if (!Check("ZNAXIS1", 'I') \|\|
254	!Check("ZNAXIS2", 'I') \|\|
255	!Check("ZPCOUNT", 'I', "0"))
256	return;
257	}
258	else
259	{
260	if (!Check("PCOUNT", 'I', "0"))
261	return;
262	}
263
264	total_bytes = Get<size_t>("NAXIS1")*Get<size_t>("NAXIS2");
265	bytes_per_row = is_compressed ? Get<size_t>("ZNAXIS1") : Get<size_t>("NAXIS1");
266	num_rows = is_compressed ? Get<size_t>("ZNAXIS2") : Get<size_t>("NAXIS2");
267	num_cols = Get<size_t>("TFIELDS");
268	datasum = Get<int64_t>("DATASUM", -1);
269	size_t bytes = 0;
270
271	const std::string tFormName = is_compressed ? "ZFORM" : "TFORM";
272	for (long long unsigned int i=1; i<=num_cols; i++)
273	{
274	const std::string num(std::to_string(i));
275
276	if (!Check("TTYPE"+num, 'T') \|\|
277	!Check(tFormName+num, 'T'))
278	return;
279
280	const std::string id = Get<std::string>("TTYPE"+num);
281	const std::string fmt = Get<std::string>(tFormName+num);
282	const std::string unit = Get<std::string>("TUNIT"+num, "");
283	const std::string comp = Get<std::string>("ZCTYP"+num, "");
284
285	Compression_t compress = kCompUnknown;
286	if (comp == "FACT")
287	compress = kCompFACT;
288
289	std::istringstream sin(fmt);
290	int n = 0;
291	sin >> n;
292	if (!sin)
293	n = 1;
294
295	const char type = fmt[fmt.length()-1];
296
297	size_t size = 0;
298	switch (type)
299	{
300	// We could use negative values to mark floats
301	// otheriwse we could just cast them to int64_t?
302	case 'L': // logical
303	case 'A': // char
304	case 'B': size = 1; break; // byte
305	case 'I': size = 2; break; // short
306	case 'J': size = 4; break; // int
307	case 'K': size = 8; break; // long long
308	case 'E': size = 4; break; // float
309	case 'D': size = 8; break; // double
310	// case 'X': size = n; break; // bits (n=number of bytes needed to contain all bits)
311	// case 'C': size = 8; break; // complex float
312	// case 'M': size = 16; break; // complex double
313	// case 'P': size = 8; break; // array descriptor (32bit)
314	// case 'Q': size = 16; break; // array descriptor (64bit)
315	default:
316	{
317	std::ostringstream str;
318	str << "FITS format TFORM='" << fmt << "' not yet supported.";
319	#ifdef __EXCEPTIONS
320	throw std::runtime_error(str.str());
321	#else
322	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
323	return;
324	#endif
325	}
326	}
327
328	const Table::Column col = { bytes, n, size, n*size, type, unit, compress};
329
330	cols[id] = col;
331	sorted_cols.emplace_back(col);
332	bytes += n*size;
333	}
334
335	if (bytes!=bytes_per_row)
336	{
337	std::ostringstream str;
338	str << "Sum of bytes in columns [" << bytes << "] does not match (Z)NAXIS2 [" << bytes_per_row << "].";
339
340	#ifdef __EXCEPTIONS
341	throw std::runtime_error(str.str());
342	#else
343	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
344	return;
345	#endif
346	}
347
348	name = Get<std::string>("EXTNAME");
349	}
350
351	void PrintKeys(bool display_all=false) const
352	{
353	for (Keys::const_iterator it=keys.cbegin(); it!=keys.cend(); it++)
354	{
355	if (!display_all && FITS::IsReservedKeyWord(it->first))
356	continue;
357
358	gLog << ___all___ << std::setw(2) << it->second.type << '\|' << it->first << '=' << it->second.value << '/' << it->second.comment << '\|' << std::endl;
359	}
360	}
361
362	void PrintColumns() const
363	{
364	typedef std::map<std::pair<size_t, std::string>, Column> Sorted;
365
366	Sorted sorted;
367
368	for (Columns::const_iterator it=cols.cbegin(); it!=cols.cend(); it++)
369	sorted[std::make_pair(it->second.offset, it->first)] = it->second;
370
371	for (Sorted::const_iterator it=sorted.cbegin(); it!=sorted.cend(); it++)
372	{
373	gLog << ___all___ << std::setw(6) << it->second.offset << "\| ";
374	gLog << it->second.num << 'x';
375	switch (it->second.type)
376	{
377	case 'A': gLog << "char(8)"; break;
378	case 'L': gLog << "bool(8)"; break;
379	case 'B': gLog << "byte(8)"; break;
380	case 'I': gLog << "short(16)"; break;
381	case 'J': gLog << "int(32)"; break;
382	case 'K': gLog << "int(64)"; break;
383	case 'E': gLog << "float(32)"; break;
384	case 'D': gLog << "double(64)"; break;
385	}
386	gLog << ": " << it->first.second << " [" << it->second.unit << "]" << std::endl;
387	}
388	}
389
390	operator bool() const { return !name.empty(); }
391
392	bool HasKey(const std::string &key) const
393	{
394	return keys.find(key)!=keys.end();
395	}
396
397	bool HasColumn(const std::string& col) const
398	{
399	return cols.find(col)!=cols.end();
400	}
401
402	const Columns &GetColumns() const
403	{
404	return cols;
405	}
406
407	const Keys &GetKeys() const
408	{
409	return keys;
410	}
411
412	// Values of keys are always signed
413	template<typename T>
414	T Get(const std::string &key) const
415	{
416	const Keys::const_iterator it = keys.find(key);
417	if (it==keys.end())
418	{
419	std::ostringstream str;
420	str << "Key '" << key << "' not found.";
421	#ifdef __EXCEPTIONS
422	throw std::runtime_error(str.str());
423	#else
424	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
425	return T();
426	#endif
427	}
428	return it->second.Get<T>();
429	}
430
431	// Values of keys are always signed
432	template<typename T>
433	T Get(const std::string &key, const T &deflt) const
434	{
435	const Keys::const_iterator it = keys.find(key);
436	return it==keys.end() ? deflt :it->second.Get<T>();
437	}
438
439	size_t GetN(const std::string &key) const
440	{
441	const Columns::const_iterator it = cols.find(key);
442	return it==cols.end() ? 0 : it->second.num;
443	}
444
445
446
447	// There may be a gap between the main table and the start of the heap:
448	// this computes the offset
449	streamoff GetHeapShift() const
450	{
451	if (!HasKey("ZHEAPPTR"))
452	return 0;
453
454	const size_t shift = Get<size_t>("ZHEAPPTR");
455	return shift <= total_bytes ? 0 : shift - total_bytes;
456	}
457
458	// return total number of bytes 'all inclusive'
459	streamoff GetTotalBytes() const
460	{
461	//get offset of special data area from start of main table
462	const streamoff shift = GetHeapShift();
463
464	//and special data area size
465	const streamoff size = HasKey("PCOUNT") ? Get<streamoff>("PCOUNT") : 0;
466
467	// Get the total size
468	const streamoff total = total_bytes + size + shift;
469
470	// check for padding
471	if (total%2880==0)
472	return total;
473
474	// padding necessary
475	return total + (2880 - (total%2880));
476	}
477	};
478
479	protected:
480	std::ofstream fCopy;
481	std::vector<std::string> fListOfTables; // List of skipped tables. Last table is open table
482
483	Table fTable;
484
485	typedef std::pair<void*, Table::Column> Address;
486	typedef std::vector<Address> Addresses;
487	//map<void*, Table::Column> fAddresses;
488	Addresses fAddresses;
489
490	typedef std::unordered_map<std::string, void*> Pointers;
491	Pointers fPointers;
492
493	std::vector<std::vector<char>> fGarbage;
494
495	std::vector<char> fBufferRow;
496	std::vector<char> fBufferDat;
497
498	size_t fRow;
499
500	Checksum fChkHeader;
501	Checksum fChkData;
502
503	bool ReadBlock(std::vector<std::string> &vec)
504	{
505	int endtag = 0;
506	for (int i=0; i<36; i++)
507	{
508	char c[81];
509	c[80] = 0;
510	read(c, 80);
511	if (!good())
512	break;
513
514	fChkHeader.add(c, 80);
515
516	// if (c[0]==0)
517	// return vector<string>();
518
519	std::string str(c);
520
521	// if (!str.empty())
522	// cout << setw(2) << i << "\|" << str << "\|" << (endtag?'-':'+') << endl;
523
524	if (endtag==2 \|\| str=="END ")
525	{
526	endtag = 2; // valid END tag found
527	continue;
528	}
529
530	if (endtag==1 \|\| str==" ")
531	{
532	endtag = 1; // end tag not found, but expected to be there
533	continue;
534	}
535
536	vec.emplace_back(str);
537	}
538
539	// Make sure that no empty vector is returned
540	if (endtag && vec.size()%36==0)
541	vec.emplace_back("END = '' / ");
542
543	return endtag==2;
544	}
545
546	std::string Compile(const std::string &key, int16_t i=-1) const
547	{
548	#if GCC_VERSION < 40603
549	return i<0 ? key : key+std::to_string((long long int)(i));
550	#else
551	return i<0 ? key : key+std::to_string(i);
552	#endif
553	}
554
555	void Constructor(const std::string &fname, std::string fout="", const std::string& tableName="", bool force=false)
556	{
557	char simple[10];
558	read(simple, 10);
559	if (!good())
560	return;
561
562	if (memcmp(simple, "SIMPLE = ", 10))
563	{
564	clear(rdstate()\|std::ios::badbit);
565	#ifdef __EXCEPTIONS
566	throw std::runtime_error("File is not a FITS file.");
567	#else
568	gLog << ___err___ << "ERROR - File is not a FITS file." << std::endl;
569	return;
570	#endif
571	}
572
573	seekg(0);
574
575	while (good())
576	{
577	std::vector<std::string> block;
578	while (1)
579	{
580	// If we search for a table, we implicitly assume that
581	// not finding the table is not an error. The user
582	// can easily check that by eof() && !bad()
583	peek();
584	if (eof() && !bad() && !tableName.empty())
585	{
586	break;
587	}
588	// FIXME: Set limit on memory consumption
589	const int rc = ReadBlock(block);
590	if (!good())
591	{
592	clear(rdstate()\|std::ios::badbit);
593	#ifdef __EXCEPTIONS
594	throw std::runtime_error("FITS file corrupted.");
595	#else
596	gLog << ___err___ << "ERROR - FITS file corrupted." << std::endl;
597	return;
598	#endif
599	}
600
601	if (block.size()%36)
602	{
603	if (!rc && !force)
604	{
605	clear(rdstate()\|std::ios::badbit);
606	#ifdef __EXCEPTIONS
607	throw std::runtime_error("END keyword missing in FITS header.");
608	#else
609	gLog << ___err___ << "ERROR - END keyword missing in FITS file... file might be corrupted." << std::endl;
610	return;
611	#endif
612	}
613	break;
614	}
615	}
616
617	if (block.empty())
618	break;
619
620	if (block[0].substr(0, 9)=="SIMPLE =")
621	{
622	fChkHeader.reset();
623	continue;
624	}
625
626	if (block[0].substr(0, 9)=="XTENSION=")
627	{
628	fTable = Table(block, tellg());
629	fRow = (size_t)-1;
630
631	if (!fTable)
632	{
633	clear(rdstate()\|std::ios::badbit);
634	return;
635	}
636
637	const std::string &tname = fTable.Get<std::string>("EXTNAME");
638
639	fListOfTables.emplace_back(tname);
640
641	// Check for table name. Skip until eof or requested table are found.
642	// skip the current table?
643	if ((!tableName.empty() && tableName!=tname) \|\| (tableName.empty() && "ZDrsCellOffsets"==tname))
644	{
645	const streamoff skip = fTable.GetTotalBytes();
646	seekg(skip, std::ios_base::cur);
647
648	fChkHeader.reset();
649
650	continue;
651	}
652
653	fBufferRow.resize(fTable.bytes_per_row + 8-fTable.bytes_per_row%4);
654	fBufferDat.resize(fTable.bytes_per_row);
655
656	break;
657	}
658	}
659
660	if (fout.empty())
661	return;
662
663	if (*fout.rbegin()=='/')
664	{
665	const size_t p = fname.find_last_of('/');
666	fout.append(fname.substr(p+1));
667	}
668
669	fCopy.open(fout);
670	if (!fCopy)
671	{
672	clear(rdstate()\|std::ios::badbit);
673	#ifdef __EXCEPTIONS
674	throw std::runtime_error("Could not open output file.");
675	#else
676	gLog << ___err___ << "ERROR - Failed to open output file." << std::endl;
677	return;
678	#endif
679	}
680
681	const streampos p = tellg();
682	seekg(0);
683
684	std::vector<char> buf(p);
685	read(buf.data(), p);
686
687	fCopy.write(buf.data(), p);
688	if (!fCopy)
689	clear(rdstate()\|std::ios::badbit);
690	}
691
692	public:
693	fits(const std::string &fname, const std::string& tableName="", bool force=false) : izstream(fname.c_str())
694	{
695	Constructor(fname, "", tableName, force);
696	if ((fTable.is_compressed \|\|fTable.name=="ZDrsCellOffsets") && !force)
697	{
698	#ifdef __EXCEPTIONS
699	throw std::runtime_error("You are trying to read a compressed fits with the base fits class. Please use factfits instead.");
700	#else
701	gLog << ___err___ << "ERROR - You are trying to read a compressed fits with the base fits class. Please use factfits instead." << std::endl;
702	#endif
703	clear(rdstate()\|std::ios::badbit);
704	}
705	}
706
707	fits(const std::string &fname, const std::string &fout, const std::string& tableName, bool force=false) : izstream(fname.c_str())
708	{
709	Constructor(fname, fout, tableName, force);
710	if ((fTable.is_compressed \|\| fTable.name=="ZDrsCellOffsets") && !force)
711	{
712	#ifdef __EXCEPTIONS
713	throw std::runtime_error("You are trying to read a compressed fits with the base fits class. Please use factfits instead.");
714	#else
715	gLog << ___err___ << "ERROR - You are trying to read a compressed fits with the base fits class. Please use factfits instead." << std::endl;
716	#endif
717	clear(rdstate()\|std::ios::badbit);
718	}
719	}
720
721	fits() : izstream()
722	{
723
724	}
725
726	~fits()
727	{
728	std::copy(std::istreambuf_iterator<char>(*this),
729	std::istreambuf_iterator<char>(),
730	std::ostreambuf_iterator<char>(fCopy));
731	}
732
733	virtual void StageRow(size_t row, char* dest)
734	{
735	// if (row!=fRow+1) // Fast seeking is ensured by izstream
736	seekg(fTable.offset+row*fTable.bytes_per_row);
737	read(dest, fTable.bytes_per_row);
738	//fin.clear(fin.rdstate()&~ios::eofbit);
739	}
740
741	virtual void WriteRowToCopyFile(size_t row)
742	{
743	if (row==fRow+1)
744	{
745	const uint8_t offset = (row*fTable.bytes_per_row)%4;
746
747	fChkData.add(fBufferRow);
748	if (fCopy.is_open() && fCopy.good())
749	fCopy.write(fBufferRow.data()+offset, fTable.bytes_per_row);
750	if (!fCopy)
751	clear(rdstate()\|std::ios::badbit);
752	}
753	else
754	if (fCopy.is_open())
755	clear(rdstate()\|std::ios::badbit);
756	}
757
758	void ZeroBufferForChecksum(std::vector<char>& vec, const uint64_t extraZeros=0)
759	{
760	auto ib = vec.begin();
761	auto ie = vec.end();
762
763	*ib++ = 0;
764	*ib++ = 0;
765	*ib++ = 0;
766	*ib = 0;
767
768	for (uint64_t i=0;i<extraZeros+8;i++)
769	*--ie = 0;
770	}
771
772	uint8_t ReadRow(size_t row)
773	{
774	// For the checksum we need everything to be correctly aligned
775	const uint8_t offset = (row*fTable.bytes_per_row)%4;
776
777	ZeroBufferForChecksum(fBufferRow);
778
779	StageRow(row, fBufferRow.data()+offset);
780
781	WriteRowToCopyFile(row);
782
783	fRow = row;
784
785	return offset;
786	}
787
788	template<size_t N>
789	void revcpy(char dest, const char src, const int &num)
790	{
791	const char pend = src + numN;
792	for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
793	std::reverse_copy(ptr, ptr+N, dest);
794	}
795
796	virtual void MoveColumnDataToUserSpace(char dest, const char src, const Table::Column& c)
797	{
798	// Let the compiler do some optimization by
799	// knowing that we only have 1, 2, 4 and 8
800	switch (c.size)
801	{
802	case 1: memcpy (dest, src, c.bytes); break;
803	case 2: revcpy<2>(dest, src, c.num); break;
804	case 4: revcpy<4>(dest, src, c.num); break;
805	case 8: revcpy<8>(dest, src, c.num); break;
806	}
807	}
808
809	virtual bool GetRow(size_t row, bool check=true)
810	{
811	if (check && row>=fTable.num_rows)
812	return false;
813
814	const uint8_t offset = ReadRow(row);
815	if (!good())
816	return good();
817
818	const char *ptr = fBufferRow.data() + offset;
819
820	for (Addresses::const_iterator it=fAddresses.cbegin(); it!=fAddresses.cend(); it++)
821	{
822	const Table::Column &c = it->second;
823
824	const char *src = ptr + c.offset;
825	char dest = reinterpret_cast<char>(it->first);
826
827	MoveColumnDataToUserSpace(dest, src, c);
828	}
829
830	return good();
831	}
832
833	bool GetNextRow(bool check=true)
834	{
835	return GetRow(fRow+1, check);
836	}
837
838	virtual bool SkipNextRow()
839	{
840	seekg(fTable.offset+(++fRow)*fTable.bytes_per_row);
841	return good();
842	}
843
844	static bool Compare(const Address &p1, const Address &p2)
845	{
846	return p1.first>p2.first;
847	}
848
849	template<class T, class S>
850	const T &GetAs(const std::string &name)
851	{
852	return reinterpret_cast<S>(fPointers[name]);
853	}
854
855	void *SetPtrAddress(const std::string &name)
856	{
857	if (fTable.cols.count(name)==0)
858	{
859	std::ostringstream str;
860	str << "SetPtrAddress('" << name << "') - Column not found.";
861	#ifdef __EXCEPTIONS
862	throw std::runtime_error(str.str());
863	#else
864	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
865	return NULL;
866	#endif
867	}
868
869	Pointers::const_iterator it = fPointers.find(name);
870	if (it!=fPointers.end())
871	return it->second;
872
873	fGarbage.emplace_back(fTable.cols[name].bytes);
874
875	void *ptr = fGarbage.back().data();
876
877	fPointers[name] = ptr;
878	fAddresses.emplace_back(ptr, fTable.cols[name]);
879	sort(fAddresses.begin(), fAddresses.end(), Compare);
880	return ptr;
881	}
882
883	template<typename T>
884	bool SetPtrAddress(const std::string &name, T *ptr, size_t cnt)
885	{
886	if (fTable.cols.count(name)==0)
887	{
888	std::ostringstream str;
889	str << "SetPtrAddress('" << name << "') - Column not found.";
890	#ifdef __EXCEPTIONS
891	throw std::runtime_error(str.str());
892	#else
893	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
894	return false;
895	#endif
896	}
897
898	if (sizeof(T)!=fTable.cols[name].size)
899	{
900	std::ostringstream str;
901	str << "SetPtrAddress('" << name << "') - Element size mismatch: expected "
902	<< fTable.cols[name].size << " from header, got " << sizeof(T);
903	#ifdef __EXCEPTIONS
904	throw std::runtime_error(str.str());
905	#else
906	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
907	return false;
908	#endif
909	}
910
911	if (cnt!=fTable.cols[name].num)
912	{
913	std::ostringstream str;
914	str << "SetPtrAddress('" << name << "') - Element count mismatch: expected "
915	<< fTable.cols[name].num << " from header, got " << cnt;
916	#ifdef __EXCEPTIONS
917	throw std::runtime_error(str.str());
918	#else
919	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
920	return false;
921	#endif
922	}
923
924	// if (fAddresses.count(ptr)>0)
925	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
926
927	//fAddresses[ptr] = fTable.cols[name];
928	fPointers[name] = ptr;
929	fAddresses.emplace_back(ptr, fTable.cols[name]);
930	sort(fAddresses.begin(), fAddresses.end(), Compare);
931	return true;
932	}
933
934	template<class T>
935	bool SetRefAddress(const std::string &name, T &ptr)
936	{
937	return SetPtrAddress(name, &ptr, sizeof(ptr)/sizeof(T));
938	}
939
940	template<typename T>
941	bool SetVecAddress(const std::string &name, std::vector<T> &vec)
942	{
943	return SetPtrAddress(name, vec.data(), vec.size());
944	}
945
946	template<typename T>
947	T Get(const std::string &key) const
948	{
949	return fTable.Get<T>(key);
950	}
951
952	template<typename T>
953	T Get(const std::string &key, const std::string &deflt) const
954	{
955	return fTable.Get<T>(key, deflt);
956	}
957
958	bool SetPtrAddress(const std::string &name, void *ptr, size_t cnt=0)
959	{
960	if (fTable.cols.count(name)==0)
961	{
962	std::ostringstream str;
963	str <<"SetPtrAddress('" << name << "') - Column not found.";
964	#ifdef __EXCEPTIONS
965	throw std::runtime_error(str.str());
966	#else
967	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
968	return false;
969	#endif
970	}
971
972	if (cnt && cnt!=fTable.cols[name].num)
973	{
974	std::ostringstream str;
975	str << "SetPtrAddress('" << name << "') - Element count mismatch: expected "
976	<< fTable.cols[name].num << " from header, got " << cnt;
977	#ifdef __EXCEPTIONS
978	throw std::runtime_error(str.str());
979	#else
980	gLog << ___err___ << "ERROR - " << str.str() << std::endl;
981	return false;
982	#endif
983	}
984
985	// if (fAddresses.count(ptr)>0)
986	// gLog << warn << "SetPtrAddress('" << name << "') - Pointer " << ptr << " already assigned." << endl;
987
988	//fAddresses[ptr] = fTable.cols[name];
989	fPointers[name] = ptr;
990	fAddresses.emplace_back(ptr, fTable.cols[name]);
991	sort(fAddresses.begin(), fAddresses.end(), Compare);
992	return true;
993	}
994
995	bool HasKey(const std::string &key) const { return fTable.HasKey(key); }
996	bool HasColumn(const std::string& col) const { return fTable.HasColumn(col);}
997	const Table::Columns &GetColumns() const { return fTable.GetColumns();}
998	const Table::SortedColumns& GetSortedColumns() const { return fTable.sorted_cols;}
999	const Table::Keys &GetKeys() const { return fTable.GetKeys();}
1000
1001	int64_t GetInt(const std::string &key) const { return fTable.Get<int64_t>(key); }
1002	uint64_t GetUInt(const std::string &key) const { return fTable.Get<uint64_t>(key); }
1003	double GetFloat(const std::string &key) const { return fTable.Get<double>(key); }
1004	std::string GetStr(const std::string &key) const { return fTable.Get<std::string>(key); }
1005
1006	size_t GetN(const std::string &key) const
1007	{
1008	return fTable.GetN(key);
1009	}
1010
1011	// size_t GetNumRows() const { return fTable.num_rows; }
1012	size_t GetRow() const { return fRow==(size_t)-1 ? 0 : fRow; }
1013
1014	operator bool() const { return fTable && fTable.offset!=0; }
1015
1016	void PrintKeys(bool all_keys=false) const { fTable.PrintKeys(all_keys); }
1017	void PrintColumns() const { fTable.PrintColumns(); }
1018
1019	bool IsHeaderOk() const { return fTable.datasum<0?false:(fChkHeader+Checksum(fTable.datasum)).valid(); }
1020	virtual bool IsFileOk() const { return (fChkHeader+fChkData).valid(); }
1021
1022	bool IsCompressedFITS() const { return fTable.is_compressed;}
1023
1024	virtual size_t GetNumRows() const
1025	{
1026	return fTable.Get<size_t>("NAXIS2");
1027	}
1028
1029	virtual size_t GetBytesPerRow() const
1030	{
1031	return fTable.Get<size_t>("NAXIS1");
1032	}
1033
1034	const std::vector<std::string> &GetTables() const
1035	{
1036	return fListOfTables;
1037	}
1038	};
1039
1040	#endif

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

Download in other formats: