source: trunk/FACT++/src/fitsdump.cc@ 10978

Last change on this file since 10978 was 10837, checked in by tbretz, 13 years ago
Some performance improvements; added some comments with code to fill just a histogram or a graph - maybe for later use.
File size: 20.5 KB
Line 
1//****************************************************************
2/** @class FitsDumper
3
4 @brief Dumps contents of fits tables to stdout or a file
5
6 */
7 //****************************************************************
8#include "Configuration.h"
9
10#include <map>
11#include <fstream>
12
13#include <CCfits/CCfits>
14
15using namespace std;
16
17class FitsDumper
18{
19public:
20 FitsDumper();
21 ~FitsDumper();
22
23private:
24
25 CCfits::FITS *fFile; /// FITS pointer
26 CCfits::Table *fTable; /// Table pointer
27 map<string, CCfits::Column*> fColMap; /// map between the column names and their CCfits objects
28
29 // Convert CCfits::ValueType into a human readable string
30 string ValueTypeToStr(CCfits::ValueType type) const;
31
32 // Convert CCfits::ValueType into a number of associated bytes
33 int ValueTypeToSize(CCfits::ValueType type) const;
34
35 /// Calculate the buffer size required to read a row of the fits table, as well as the offsets to each column
36 vector<int> CalculateOffsets() const;
37
38 template<class T>
39 T PtrToValue(const unsigned char* &ptr) const;
40// template<class T>
41// double PtrToDouble(const unsigned char *ptr) const;
42// double PtrToDouble(const unsigned char *ptr, CCfits::ValueType type) const;
43
44 /// Write a single row of the selected data
45 int WriteRow(ostream &, const vector<CCfits::Column*> &, const vector<int> &, unsigned char *) const;
46
47 bool OpenFile(const string &); /// Open a file
48 bool OpenTable(const string &); /// Open a table
49
50 /// Lists all columns of an open file
51 void List();
52 void ListHeader();
53 void ListKeywords(ostream &);
54
55 /// Perform the dumping, based on the current dump list
56 bool Dump(const string &, const vector<string> &list, int);
57
58// bool Plot(const vector<string> &list);
59
60public:
61 ///Configures the fitsLoader from the config file and/or command arguments.
62 int ExecConfig(Configuration& conf);
63};
64
65// --------------------------------------------------------------------------
66//
67//! Constructor
68//! @param out
69//! the ostream where to redirect the outputs
70//
71FitsDumper::FitsDumper() : fFile(0), fTable(0)
72{
73}
74
75// --------------------------------------------------------------------------
76//
77//! Destructor
78//
79FitsDumper::~FitsDumper()
80{
81 if (fFile)
82 delete fFile;
83}
84
85
86string FitsDumper::ValueTypeToStr(CCfits::ValueType type) const
87{
88 switch (type)
89 {
90 case CCfits::Tbyte: return "uint8_t";
91 case CCfits::Tushort: return "uint16_t";
92 case CCfits::Tshort: return "int16_t";
93 case CCfits::Tuint: return "uint32_t";
94 case CCfits::Tint: return "int32_t";
95 case CCfits::Tulong: return "uint32_t";
96 case CCfits::Tlong: return "int32_t";
97 case CCfits::Tlonglong: return "int64_t";
98 case CCfits::Tfloat: return "float";
99 case CCfits::Tdouble: return "double";
100
101 default:
102 return "unknwown";
103 }
104}
105
106int FitsDumper::ValueTypeToSize(CCfits::ValueType type) const
107{
108 switch (type)
109 {
110 case CCfits::Tbyte: return sizeof(uint8_t);
111 case CCfits::Tushort:
112 case CCfits::Tshort: return sizeof(uint16_t);
113 case CCfits::Tuint:
114 case CCfits::Tint:
115 case CCfits::Tulong:
116 case CCfits::Tlong: return sizeof(uint32_t);
117 case CCfits::Tlonglong: return sizeof(uint64_t);
118 case CCfits::Tfloat: return sizeof(float);
119 case CCfits::Tdouble: return sizeof(double);
120
121 default:
122 return 0;
123 }
124}
125
126template<class T>
127T FitsDumper::PtrToValue(const unsigned char* &ptr) const
128{
129 T t;
130 reverse_copy(ptr, ptr+sizeof(T), reinterpret_cast<unsigned char*>(&t));
131 ptr += sizeof(T);
132
133 return t;
134}
135/*
136template<class T>
137double FitsDumper::PtrToDouble(const unsigned char *ptr) const
138{
139 T t;
140 reverse_copy(ptr, ptr+sizeof(T), reinterpret_cast<unsigned char*>(&t));
141 return t;
142}
143
144double FitsDumper::PtrToDouble(const unsigned char *ptr, CCfits::ValueType type) const
145{
146 switch (type)
147 {
148 case CCfits::Tbyte: return PtrToDouble<uint8_t> (ptr);
149 case CCfits::Tushort: return PtrToDouble<uint16_t>(ptr);
150 case CCfits::Tuint:
151 case CCfits::Tulong: return PtrToDouble<uint32_t>(ptr);
152 case CCfits::Tshort: return PtrToDouble<int16_t> (ptr);
153 case CCfits::Tint:
154 case CCfits::Tlong: return PtrToDouble<int32_t> (ptr);
155 case CCfits::Tlonglong: return PtrToDouble<int64_t> (ptr);
156 case CCfits::Tfloat: return PtrToDouble<float> (ptr);
157 case CCfits::Tdouble: return PtrToDouble<double> (ptr);
158
159 default:
160 throw runtime_error("Data type not implemented yet.");
161 }
162}
163*/
164
165// --------------------------------------------------------------------------
166//
167//! Writes a single row of the selected FITS data to the output file.
168//!
169//! Data type \b not yet implemented:
170//! CCfits::Tnull, CCfits::Tbit, CCfits::Tlogical, CCfits::Tstring,
171//! CCfits::Tcomplex, CCfits::Tdblcomplex, CCfits::VTbit,
172//! CCfits::VTbyte, CCfits::VTlogical, CCfits::VTushort,
173//! CCfits::VTshort, CCfits::VTuint, CCfits::VTint, CCfits::VTulong,
174//! CCfits::VTlong, CCfits::VTlonglong, CCfits::VTfloat,
175//! CCfits::VTdouble, CCfits::VTcomplex, CCfits::VTdblcomplex
176//!
177//! @param offsets
178//! a vector containing the offsets to the columns (in bytes)
179//! @param targetFile
180//! the ofstream where to write to
181//! @param fitsBuffer
182//! the memory were the row has been loaded by cfitsio
183//
184int FitsDumper::WriteRow(ostream &out, const vector<CCfits::Column*> &list, const vector<int> &offsets, unsigned char* fitsBuffer) const
185{
186 int cnt = 0;
187
188 for (vector<CCfits::Column*>::const_iterator it=list.begin(); it!=list.end(); it++)
189 {
190 const CCfits::Column *col = *it;
191
192 // CCfits starts counting at 1 not 0
193 const int offset = offsets[col->index()-1];
194
195 // Get the pointer to the array which we are supposed to print
196 const unsigned char *ptr = fitsBuffer + offset;
197
198 // Loop over all array entries
199 for (int width=0; width<col->width(); width++)
200 {
201 switch (col->type())
202 {
203 case CCfits::Tbyte: out << PtrToValue<uint8_t> (ptr); break;
204 case CCfits::Tushort: out << PtrToValue<uint16_t>(ptr); break;
205 case CCfits::Tuint:
206 case CCfits::Tulong: out << PtrToValue<uint32_t>(ptr); break;
207 case CCfits::Tshort: out << PtrToValue<int16_t> (ptr); break;
208 case CCfits::Tint:
209 case CCfits::Tlong: out << PtrToValue<int32_t> (ptr); break;
210 case CCfits::Tlonglong: out << PtrToValue<int64_t> (ptr); break;
211 case CCfits::Tfloat: out << PtrToValue<float> (ptr); break;
212 case CCfits::Tdouble: out << PtrToValue<double> (ptr); break;
213
214 default:
215 cerr << "Data type not implemented yet." << endl;
216 return 0;
217 }
218
219 out << " ";
220 cnt++;
221 }
222 }
223
224 if (cnt>0)
225 out << endl;
226
227 if (out.fail())
228 {
229 cerr << "ERROR - writing output: " << strerror(errno) << endl;
230 return -1;
231 }
232
233 return cnt;
234}
235
236// --------------------------------------------------------------------------
237//
238//! Calculates the required buffer size for reading one row of the current
239//! table. Also calculates the offsets to all the columns
240//
241vector<int> FitsDumper::CalculateOffsets() const
242{
243 map<int,int> sizes;
244
245 for (map<string, CCfits::Column*>::const_iterator it=fColMap.begin();
246 it!=fColMap.end(); it++)
247 {
248 const int &width = it->second->width();
249 const int &idx = it->second->index();
250
251 const int size = ValueTypeToSize(it->second->type());
252 if (size==0)
253 {
254 cerr << "Data type " << (int)it->second->type() << " not implemented yet." << endl;
255 return vector<int>();
256 }
257
258 sizes[idx] = size*width;
259 }
260
261 //calculate the offsets in the vector.
262 vector<int> result(1, 0);
263
264 int size = 0;
265 int idx = 0;
266
267 for (map<int,int>::const_iterator it=sizes.begin(); it!=sizes.end(); it++)
268 {
269 size += it->second;
270 result.push_back(size);
271
272 if (it->first == ++idx)
273 continue;
274
275 cerr << "Expected index " << idx << ", but found " << it->first << endl;
276 return vector<int>();
277 }
278
279 return result;
280}
281
282// --------------------------------------------------------------------------
283//
284//! Loads the fits file based on the current parameters
285//
286bool FitsDumper::OpenFile(const string &filename)
287{
288 if (fFile)
289 delete fFile;
290
291 ostringstream str;
292 try
293 {
294 fFile = new CCfits::FITS(filename);
295 }
296 catch (CCfits::FitsException e)
297 {
298 cerr << "Could not open FITS file " << filename << " reason: " << e.message() << endl;
299 return false;
300 }
301
302 return true;
303}
304
305bool FitsDumper::OpenTable(const string &tablename)
306{
307 if (!fFile)
308 {
309 cerr << "No file open." << endl;
310 return false;
311 }
312
313 const multimap< string, CCfits::ExtHDU * > extMap = fFile->extension();
314 if (extMap.find(tablename) == extMap.end())
315 {
316 cerr << "Table '" << tablename << "' not found." << endl;
317 return false;
318 }
319
320 fTable = dynamic_cast<CCfits::Table*>(extMap.find(tablename)->second);
321 if (!fTable)
322 {
323 cerr << "Object '" << tablename << "' returned not a CCfits::Table." << endl;
324 return false;
325 }
326
327 fColMap = fTable->column();
328
329 fTable->makeThisCurrent();
330
331 fTable->getComments();
332 fTable->getHistory();
333 fTable->readAllKeys();
334
335 return true;
336}
337
338class MyColumn : public CCfits::Column
339{
340public:
341 const string &comment() const { return CCfits::Column::comment(); }
342};
343
344void FitsDumper::List()
345{
346 if (!fFile)
347 {
348 cerr << "No file open." << endl;
349 return;
350 }
351
352 cout << "\nFile: " << fFile->name() << "\n";
353
354 const multimap< string, CCfits::ExtHDU * > extMap = fFile->extension();
355 for (std::multimap<string, CCfits::ExtHDU*>::const_iterator it=extMap.begin(); it != extMap.end(); it++)
356 {
357
358 CCfits::Table *table = dynamic_cast<CCfits::Table*>(extMap.find(it->first)->second);
359
360 cout << " " << it->first << " [" << table->rows() << "]\n";
361
362 const map<string, CCfits::Column*> &cols = table->column();
363
364 for (map<string, CCfits::Column*>::const_iterator ic=cols.begin();
365 ic != cols.end(); ic++)
366 {
367 const MyColumn *col = static_cast<MyColumn*>(ic->second);
368
369 cout << " " << col->name() << "[" << col->width() << "] * " << col->scale() << " (" << col->unit() << ":" << ValueTypeToStr(col->type())<< ") " << col->comment() << "\n";
370 /*
371 inline size_t Column::repeat () const
372 inline bool Column::varLength () const
373 inline double Column::zero () const
374 inline const String& Column::display () const
375 inline const String& Column::dimen () const
376 inline const String& Column::TBCOL ()
377 inline const String& Column::TTYPE ()
378 inline const String& Column::TFORM ()
379 inline const String& Column::TDISP ()
380 inline const String& Column::TZERO ()
381 inline const String& Column::TDIM ()
382 inline const String& Column::TNULL ()
383 inline const String& Column::TLMIN ()
384 inline const String& Column::TLMAX ()
385 inline const String& Column::TDMAX ()
386 inline const String& Column::TDMIN ()
387 */
388 }
389 cout << '\n';
390 }
391 cout << flush;
392}
393
394class MyKeyword : public CCfits::Keyword
395{
396public:
397 CCfits::ValueType keytype() const { return CCfits::Keyword::keytype(); }
398};
399
400void FitsDumper::ListKeywords(ostream &out)
401{
402 map<string,CCfits::Keyword*> keys = fTable->keyWord();
403 for (map<string,CCfits::Keyword*>::const_iterator it=keys.begin();
404 it!=keys.end(); it++)
405 {
406 string str;
407 double d;
408
409 const MyKeyword *kw = static_cast<MyKeyword*>(it->second);
410 kw->keytype();
411 out << "## " << setw(8) << kw->name() << "='";
412 if (kw->keytype()==16)
413 out << kw->value(str);
414 if (kw->keytype()==82)
415 out << kw->value(d);
416 out << "' \t(" << kw->comment() << ")" << endl;
417 }
418}
419
420void FitsDumper::ListHeader()
421{
422 if (!fTable)
423 {
424 cerr << "No table open." << endl;
425 return;
426 }
427
428 cout << "\nTable: " << fTable->name() << " (rows=" << fTable->rows() << ")\n";
429 if (!fTable->comment().empty())
430 cout << "Comment: \t" << fTable->comment() << '\n';
431 if (!fTable->history().empty())
432 cout << "History: \t" << fTable->history() << '\n';
433
434 ListKeywords(cout);
435 cout << endl;
436}
437
438
439// --------------------------------------------------------------------------
440//
441//! Perform the actual dump, based on the current parameters
442//
443bool FitsDumper::Dump(const string &filename, const vector<string> &list, int precision)
444{
445 for (vector<string>::const_iterator it=list.begin(); it!=list.end(); it++)
446 if (fColMap.find(*it) == fColMap.end())
447 {
448 cerr << "WARNING - Column '" << *it << "' not found in table." << endl;
449 return false;
450 }
451
452 // FIXME: Maybe do this when opening a table?
453 const vector<int> offsets = CalculateOffsets();
454 if (offsets.size()==0)
455 return false;
456
457 ofstream out(filename=="-"?"/dev/stdout":filename);
458 if (!out)
459 {
460 cerr << "Cannot open file " << filename << ": " << strerror(errno) << endl;
461 return false;
462 }
463
464 out.precision(precision);
465
466 out << "## --------------------------------------------------------------------------\n";
467 if (filename!="-")
468 out << "## File: \t" << filename << '\n';
469 out << "## Table: \t" << fTable->name() << '\n';
470 if (!fTable->comment().empty())
471 out << "## Comment: \t" << fTable->comment() << '\n';
472 if (!fTable->history().empty())
473 out << "## History: \t" << fTable->history() << '\n';
474 out << "## NumRows: \t" << fTable->rows() << '\n';
475 out << "## --------------------------------------------------------------------------\n";
476 ListKeywords(out);
477 out << "## --------------------------------------------------------------------------\n";
478 out << "#\n";
479 for (vector<string>::const_iterator it=list.begin(); it!=list.end(); it++)
480 {
481 const MyColumn *col = static_cast<MyColumn*>(fTable->column()[*it]);
482 out << "# " << col->name() << "[" << col->width() << "]: " << col->unit();
483 if (!col->comment().empty())
484 out << " (" <<col->comment() << ")";
485 out << '\n';
486 }
487 out << "#" << endl;
488
489
490 // Loop over all columns in our list of requested columns
491 vector<CCfits::Column*> columns;
492 for (vector<string>::const_iterator it=list.begin(); it!=list.end(); it++)
493 columns.push_back(fColMap.find(*it)->second);
494
495
496 const int size = offsets[offsets.size()-1];
497 unsigned char* fitsBuffer = new unsigned char[size];
498
499 int status = 0;
500 for (int i=1; i<=fTable->rows(); i++)
501 {
502 fits_read_tblbytes(fFile->fitsPointer(), i, 1, size, fitsBuffer, &status);
503 if (status)
504 {
505 cerr << "An error occurred while reading fits row #" << i << " error code: " << status << endl;
506 break;
507 }
508 if (WriteRow(out, columns, offsets, fitsBuffer)<0)
509 {
510 status=1;
511 break;
512 }
513 }
514 delete[] fitsBuffer;
515
516 return status==0;
517}
518
519// --------------------------------------------------------------------------
520//
521//! Perform the actual dump, based on the current parameters
522//
523/*
524bool FitsDumper::Plot(const vector<string> &list)
525{
526 for (vector<string>::const_iterator it=list.begin(); it!=list.end(); it++)
527 if (fColMap.find(*it) == fColMap.end())
528 {
529 cerr << "WARNING - Column '" << *it << "' not found in table." << endl;
530 return false;
531 }
532
533 // FIXME: Maybe do this when opening a table?
534 const vector<int> offsets = CalculateOffsets();
535 if (offsets.size()==0)
536 return false;
537
538 // Loop over all columns in our list of requested columns
539 const CCfits::Column *col[3] =
540 {
541 list.size()>0 ? fColMap.find(list[0])->second : 0,
542 list.size()>1 ? fColMap.find(list[1])->second : 0,
543 list.size()>2 ? fColMap.find(list[2])->second : 0
544 };
545
546 const int size = offsets[offsets.size()-1];
547 unsigned char* fitsBuffer = new unsigned char[size];
548
549 const int idx = 0;
550
551 // CCfits starts counting at 1 not 0
552 const size_t pos[3] =
553 {
554 col[0] ? offsets[col[0]->index()-1] + idx*col[0]->width()*ValueTypeToSize(col[0]->type()) : 0,
555 col[1] ? offsets[col[1]->index()-1] + idx*col[1]->width()*ValueTypeToSize(col[1]->type()) : 0,
556 col[2] ? offsets[col[2]->index()-1] + idx*col[2]->width()*ValueTypeToSize(col[2]->type()) : 0
557 };
558
559 int status = 0;
560 for (int i=1; i<=fTable->rows(); i++)
561 {
562 fits_read_tblbytes(fFile->fitsPointer(), i, 1, size, fitsBuffer, &status);
563 if (status)
564 {
565 cerr << "An error occurred while reading fits row #" << i << " error code: " << status << endl;
566 break;
567 }
568
569 try
570 {
571 const double x[3] =
572 {
573 col[0] ? PtrToDouble(fitsBuffer+pos[0], col[0]->type()) : 0,
574 col[1] ? PtrToDouble(fitsBuffer+pos[1], col[1]->type()) : 0,
575 col[2] ? PtrToDouble(fitsBuffer+pos[2], col[2]->type()) : 0
576 };
577 }
578 catch (const runtime_error &e)
579 {
580 cerr << e.what() << endl;
581 status=1;
582 break;
583 }
584 }
585 delete[] fitsBuffer;
586
587 return status==0;
588}
589*/
590
591// --------------------------------------------------------------------------
592//
593//! Retrieves the configuration parameters
594//! @param conf
595//! the configuration object
596//
597int FitsDumper::ExecConfig(Configuration& conf)
598{
599 if (conf.Has("fitsfile"))
600 {
601 if (!OpenFile(conf.Get<string>("fitsfile")))
602 return -1;
603 }
604
605 if (conf.Get<bool>("list"))
606 List();
607
608 if (conf.Has("tablename"))
609 {
610 if (!OpenTable(conf.Get<string>("tablename")))
611 return -1;
612 }
613
614 if (conf.Get<bool>("header"))
615 ListHeader();
616
617 if (conf.Get<bool>("header") || conf.Get<bool>("list"))
618 return 1;
619
620 if (conf.Has("outfile"))
621 {
622 if (!Dump(conf.Get<string>("outfile"),
623 conf.Get<vector<string>>("col"),
624 conf.Get<int>("precision")))
625 return -1;
626 }
627
628 return 0;
629}
630
631void PrintUsage()
632{
633 cout <<
634 "fitsdump is a tool to dump data from a FITS table as ascii.\n"
635 "\n"
636 "Usage: fitsdump [OPTIONS] fitsfile col col ... \n"
637 " or: fitsdump [OPTIONS]\n";
638 cout << endl;
639}
640
641void PrintHelp()
642{
643 //
644}
645
646void SetupConfiguration(Configuration& conf)
647{
648 po::options_description configs("Fitsdump options");
649 configs.add_options()
650 ("fitsfile,f", var<string>()
651#if BOOST_VERSION >= 104200
652 ->required()
653#endif
654 , "Name of FITS file")
655 ("tablename,t", var<string>("DATA")
656#if BOOST_VERSION >= 104200
657 ->required()
658#endif
659 , "Name of input table")
660 ("col,c", vars<string>(), "List of columns to dump")
661 ("outfile,o", var<string>("/dev/stdout"), "Name of output file (-:/dev/stdout)")
662 ("precision,p", var<int>(20), "Precision of ofstream")
663 ("list,l", po_switch(), "List all tables and columns in file")
664 ("header,h", po_switch(), "Dump header of given table")
665 ;
666
667 po::positional_options_description p;
668 p.add("fitsfile", 1); // The first positional options
669 p.add("col", -1); // All others
670
671 conf.AddOptions(configs);
672 conf.SetArgumentPositions(p);
673}
674
675int main(int argc, const char** argv)
676{
677 Configuration conf(argv[0]);
678 conf.SetPrintUsage(PrintUsage);
679 SetupConfiguration(conf);
680
681 po::variables_map vm;
682 try
683 {
684 vm = conf.Parse(argc, argv);
685 }
686#if BOOST_VERSION > 104000
687 catch (po::multiple_occurrences &e)
688 {
689 cerr << "Program options invalid due to: " << e.what() << " of option '" << e.get_option_name() << "'." << endl;
690 return -1;
691 }
692#endif
693 catch (exception& e)
694 {
695 cerr << "Program options invalid due to: " << e.what() << endl;
696 return -1;
697 }
698
699 if (conf.HasVersion() || conf.HasPrint())
700 return -1;
701
702 if (conf.HasHelp())
703 {
704 PrintHelp();
705 return -1;
706 }
707
708 FitsDumper loader;
709 return loader.ExecConfig(conf);
710}
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