source: trunk/FACT++/src/fitsdump.cc@ 11607

Last change on this file since 11607 was 11578, checked in by tbretz, 13 years ago
Moved some part of the initialization from main to Configure::DoParse
File size: 20.1 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 int l;
409
410 const MyKeyword *kw = static_cast<MyKeyword*>(it->second);
411 kw->keytype();
412 out << "## " << setw(8) << kw->name() << " = " << setw(10);
413 if (kw->keytype()==16)
414 out << ("'"+kw->value(str)+"'");
415 if (kw->keytype()==31)
416 out << kw->value(l);
417 if (kw->keytype()==82)
418 out << kw->value(d);
419 out << " / " << kw->comment() << endl;
420 }
421}
422
423void FitsDumper::ListHeader()
424{
425 if (!fTable)
426 {
427 cerr << "No table open." << endl;
428 return;
429 }
430
431 cout << "\nTable: " << fTable->name() << " (rows=" << fTable->rows() << ")\n";
432 if (!fTable->comment().empty())
433 cout << "Comment: \t" << fTable->comment() << '\n';
434 if (!fTable->history().empty())
435 cout << "History: \t" << fTable->history() << '\n';
436
437 ListKeywords(cout);
438 cout << endl;
439}
440
441
442// --------------------------------------------------------------------------
443//
444//! Perform the actual dump, based on the current parameters
445//
446bool FitsDumper::Dump(const string &filename, const vector<string> &list, int precision)
447{
448 for (vector<string>::const_iterator it=list.begin(); it!=list.end(); it++)
449 if (fColMap.find(*it) == fColMap.end())
450 {
451 cerr << "WARNING - Column '" << *it << "' not found in table." << endl;
452 return false;
453 }
454
455 // FIXME: Maybe do this when opening a table?
456 const vector<int> offsets = CalculateOffsets();
457 if (offsets.size()==0)
458 return false;
459
460 ofstream out(filename=="-"?"/dev/stdout":filename);
461 if (!out)
462 {
463 cerr << "Cannot open file " << filename << ": " << strerror(errno) << endl;
464 return false;
465 }
466
467 out.precision(precision);
468
469 out << "## --------------------------------------------------------------------------\n";
470 if (filename!="-")
471 out << "## File: \t" << filename << '\n';
472 out << "## Table: \t" << fTable->name() << '\n';
473 if (!fTable->comment().empty())
474 out << "## Comment: \t" << fTable->comment() << '\n';
475 if (!fTable->history().empty())
476 out << "## History: \t" << fTable->history() << '\n';
477 out << "## NumRows: \t" << fTable->rows() << '\n';
478 out << "## --------------------------------------------------------------------------\n";
479 ListKeywords(out);
480 out << "## --------------------------------------------------------------------------\n";
481 out << "#\n";
482 for (vector<string>::const_iterator it=list.begin(); it!=list.end(); it++)
483 {
484 const MyColumn *col = static_cast<MyColumn*>(fTable->column()[*it]);
485 out << "# " << col->name() << "[" << col->width() << "]: " << col->unit();
486 if (!col->comment().empty())
487 out << " (" <<col->comment() << ")";
488 out << '\n';
489 }
490 out << "#" << endl;
491
492
493 // Loop over all columns in our list of requested columns
494 vector<CCfits::Column*> columns;
495 for (vector<string>::const_iterator it=list.begin(); it!=list.end(); it++)
496 columns.push_back(fColMap.find(*it)->second);
497
498
499 const int size = offsets[offsets.size()-1];
500 unsigned char* fitsBuffer = new unsigned char[size];
501
502 int status = 0;
503 for (int i=1; i<=fTable->rows(); i++)
504 {
505 fits_read_tblbytes(fFile->fitsPointer(), i, 1, size, fitsBuffer, &status);
506 if (status)
507 {
508 cerr << "An error occurred while reading fits row #" << i << " error code: " << status << endl;
509 break;
510 }
511 if (WriteRow(out, columns, offsets, fitsBuffer)<0)
512 {
513 status=1;
514 break;
515 }
516 }
517 delete[] fitsBuffer;
518
519 return status==0;
520}
521
522// --------------------------------------------------------------------------
523//
524//! Perform the actual dump, based on the current parameters
525//
526/*
527bool FitsDumper::Plot(const vector<string> &list)
528{
529 for (vector<string>::const_iterator it=list.begin(); it!=list.end(); it++)
530 if (fColMap.find(*it) == fColMap.end())
531 {
532 cerr << "WARNING - Column '" << *it << "' not found in table." << endl;
533 return false;
534 }
535
536 // FIXME: Maybe do this when opening a table?
537 const vector<int> offsets = CalculateOffsets();
538 if (offsets.size()==0)
539 return false;
540
541 // Loop over all columns in our list of requested columns
542 const CCfits::Column *col[3] =
543 {
544 list.size()>0 ? fColMap.find(list[0])->second : 0,
545 list.size()>1 ? fColMap.find(list[1])->second : 0,
546 list.size()>2 ? fColMap.find(list[2])->second : 0
547 };
548
549 const int size = offsets[offsets.size()-1];
550 unsigned char* fitsBuffer = new unsigned char[size];
551
552 const int idx = 0;
553
554 // CCfits starts counting at 1 not 0
555 const size_t pos[3] =
556 {
557 col[0] ? offsets[col[0]->index()-1] + idx*col[0]->width()*ValueTypeToSize(col[0]->type()) : 0,
558 col[1] ? offsets[col[1]->index()-1] + idx*col[1]->width()*ValueTypeToSize(col[1]->type()) : 0,
559 col[2] ? offsets[col[2]->index()-1] + idx*col[2]->width()*ValueTypeToSize(col[2]->type()) : 0
560 };
561
562 int status = 0;
563 for (int i=1; i<=fTable->rows(); i++)
564 {
565 fits_read_tblbytes(fFile->fitsPointer(), i, 1, size, fitsBuffer, &status);
566 if (status)
567 {
568 cerr << "An error occurred while reading fits row #" << i << " error code: " << status << endl;
569 break;
570 }
571
572 try
573 {
574 const double x[3] =
575 {
576 col[0] ? PtrToDouble(fitsBuffer+pos[0], col[0]->type()) : 0,
577 col[1] ? PtrToDouble(fitsBuffer+pos[1], col[1]->type()) : 0,
578 col[2] ? PtrToDouble(fitsBuffer+pos[2], col[2]->type()) : 0
579 };
580 }
581 catch (const runtime_error &e)
582 {
583 cerr << e.what() << endl;
584 status=1;
585 break;
586 }
587 }
588 delete[] fitsBuffer;
589
590 return status==0;
591}
592*/
593
594// --------------------------------------------------------------------------
595//
596//! Retrieves the configuration parameters
597//! @param conf
598//! the configuration object
599//
600int FitsDumper::ExecConfig(Configuration& conf)
601{
602 if (conf.Has("fitsfile"))
603 {
604 if (!OpenFile(conf.Get<string>("fitsfile")))
605 return -1;
606 }
607
608 if (conf.Get<bool>("list"))
609 List();
610
611 if (conf.Has("tablename"))
612 {
613 if (!OpenTable(conf.Get<string>("tablename")))
614 return -1;
615 }
616
617 if (conf.Get<bool>("header"))
618 ListHeader();
619
620 if (conf.Get<bool>("header") || conf.Get<bool>("list"))
621 return 1;
622
623 if (conf.Has("outfile"))
624 {
625 if (!Dump(conf.Get<string>("outfile"),
626 conf.Get<vector<string>>("col"),
627 conf.Get<int>("precision")))
628 return -1;
629 }
630
631 return 0;
632}
633
634void PrintUsage()
635{
636 cout <<
637 "fitsdump is a tool to dump data from a FITS table as ascii.\n"
638 "\n"
639 "Usage: fitsdump [OPTIONS] fitsfile col col ... \n"
640 " or: fitsdump [OPTIONS]\n";
641 cout << endl;
642}
643
644void PrintHelp()
645{
646 //
647}
648
649void SetupConfiguration(Configuration& conf)
650{
651 po::options_description configs("Fitsdump options");
652 configs.add_options()
653 ("fitsfile,f", var<string>()
654#if BOOST_VERSION >= 104200
655 ->required()
656#endif
657 , "Name of FITS file")
658 ("tablename,t", var<string>("DATA")
659#if BOOST_VERSION >= 104200
660 ->required()
661#endif
662 , "Name of input table")
663 ("col,c", vars<string>(), "List of columns to dump")
664 ("outfile,o", var<string>("/dev/stdout"), "Name of output file (-:/dev/stdout)")
665 ("precision,p", var<int>(20), "Precision of ofstream")
666 ("list,l", po_switch(), "List all tables and columns in file")
667 ("header,h", po_switch(), "Dump header of given table")
668 ;
669
670 po::positional_options_description p;
671 p.add("fitsfile", 1); // The first positional options
672 p.add("col", -1); // All others
673
674 conf.AddOptions(configs);
675 conf.SetArgumentPositions(p);
676}
677
678int main(int argc, const char** argv)
679{
680 Configuration conf(argv[0]);
681 conf.SetPrintUsage(PrintUsage);
682 SetupConfiguration(conf);
683
684 if (!conf.DoParse(argc, argv, PrintHelp))
685 return -1;
686
687 FitsDumper loader;
688 return loader.ExecConfig(conf);
689}
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