source: trunk/FACT++/src/fitsloader.cc@ 19285

Last change on this file since 19285 was 11578, checked in by tbretz, 14 years ago
Moved some part of the initialization from main to Configure::DoParse
File size: 22.0 KB
Line 
1//****************************************************************
2/** @class FitsLoader
3
4 @brief Load a given Fits file and table, and dump selected columns if requested.
5
6 It derives from StateMachineDim. the first parent is here to enforce
7 a state machine behaviour
8 The possible states and transitions of the machine are:
9 \dot
10 digraph FitsLoader {
11 node [shape=record, fontname=Helvetica, fontsize=10];
12 e [label="Error" color="red"];
13 r [label="Ready"]
14 d [label="FileLoaded"]
15
16 e -> r
17 r -> e
18 r -> d
19 d -> r
20 }
21 \enddot
22 */
23 //****************************************************************
24#include "Event.h"
25#include "StateMachineDim.h"
26#include "WindowLog.h"
27#include "Configuration.h"
28#include "LocalControl.h"
29#include "Description.h"
30
31
32#include <boost/bind.hpp>
33#if BOOST_VERSION < 104400
34#if (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 4))
35#undef BOOST_HAS_RVALUE_REFS
36#endif
37#endif
38#include <boost/thread.hpp>
39
40#include <iostream>
41
42#include <CCfits/CCfits>
43
44class FitsLoader : public StateMachineDim
45{
46
47public:
48 enum
49 {
50 kSM_FileLoaded = 20,
51 } localstates_t;
52
53 FitsLoader(ostream& out);
54 ~FitsLoader();
55
56 ///Define command names
57 static const char* fLoadFits;
58 static const char* fUnloadFits;
59 static const char* fListColumns;
60 static const char* fDumpColumns;
61 static const char* fClearDumpList;
62 static const char* fDoDump;
63 static const char* fConfigFileName;
64 static const char* fConfigTableName;
65 static const char* fConfigPrecName;
66 static const char* fConfigFileOutName;
67
68private:
69 ///Name of the fits file to load
70 string fFileName;
71 ///Name of the table to load from the file
72 string fTableName;
73 ///FITS pointer
74 CCfits::FITS* fFile;
75 ///Table pointer
76 CCfits::Table* fTable;
77 ///Precision of the ofstream. Used to output a given number of significant digits for floats or doubles
78 int fStreamPrecision;
79 ///Name of the output file
80 string fFileOut;
81 ///map between the column names and their CCfits objects
82 map<string, CCfits::Column*> fColMap;
83 ///List of the column names to be dumped
84 vector<string> fDumpList;
85 ///Transition from ready to fileLoaded.
86 int LoadPlease();
87 ///Transition from fileLoaded to ready
88 int UnloadPlease();
89 ///Lists the loaded column names
90 int ListColumnsPlease(const Event&);
91 ///Add a column name to the dump list
92 int AddDumpColumnsPlease(const Event&);
93 ///Clear the dump list
94 int ClearDumpListPlease(const Event&);
95 ///Perform the dumping, based on the current dump list
96 int DoDumpPlease(const Event&);
97 ///Set the name of the Fits file to be loaded
98 int ConfigFileNamePlease(const Event&);
99 ///Set the name of the table to be loaded
100 int ConfigTableNamePlease(const Event&);
101 ///Set the ofstream precision
102 int SetOFStreamPrecisionPlease(const Event&);
103 ///Set the name of the output file
104 int SetFileOutPlease(const Event&);
105 ///Calculate the buffer size required to read a row of the fits table, as well as the offsets to each column
106 vector<int> CalculateBufferSize();
107 ///Write a single row of the selected data
108 void writeValuesFromFits(vector<int>& offsets,ofstream& targetFile, unsigned char* fitsBuffer);
109
110public:
111 ///Configures the fitsLoader from the config file and/or command arguments.
112 void SetupConfig(Configuration& conf);
113};
114
115const char* FitsLoader::fLoadFits = "load";
116const char* FitsLoader::fUnloadFits = "unload";
117const char* FitsLoader::fListColumns = "list_columns";
118const char* FitsLoader::fDumpColumns = "add_dump";
119const char* FitsLoader::fClearDumpList = "clear_dump";
120const char* FitsLoader::fDoDump = "dump";
121const char* FitsLoader::fConfigFileName = "set_file";
122const char* FitsLoader::fConfigTableName = "set_table";
123const char* FitsLoader::fConfigPrecName = "set_prec";
124const char* FitsLoader::fConfigFileOutName = "set_outfile";
125
126// --------------------------------------------------------------------------
127//
128//! Set the name of the output file
129//! @param evt
130//! the event transporting the file name
131//
132int FitsLoader::SetFileOutPlease(const Event& evt)
133{
134 fFileOut = evt.GetText();
135 ostringstream str;
136 str << "Output file is now " << fFileOut;
137 Message(str);
138 return 0;
139}
140// --------------------------------------------------------------------------
141//
142//! Set the precision of the ofstream. So that an appropriate number of significant digits are outputted.
143//! @param evt
144//! the event transporting the precision
145//
146int FitsLoader::SetOFStreamPrecisionPlease(const Event& evt)
147{
148 fStreamPrecision = evt.GetInt();
149 ostringstream str;
150 str << "ofstream precision is now " << fStreamPrecision;
151 Message(str);
152 return 0;
153}
154// --------------------------------------------------------------------------
155//
156//! Writes a single row of the selected FITS data to the output file.
157//! @param offsets
158//! a vector containing the offsets to the columns (in bytes)
159//! @param targetFile
160//! the ofstream where to write to
161//! @param fitsBuffer
162//! the memory were the row has been loaded by cfitsio
163//
164void FitsLoader::writeValuesFromFits(vector<int>& offsets,ofstream& targetFile, unsigned char* fitsBuffer)
165{
166 targetFile.precision(fStreamPrecision);
167 map<string, CCfits::Column*>::iterator it;
168 for (it=fColMap.begin(); it != fColMap.end(); it++)
169 {
170 bool found = false;
171 for (vector<string>::iterator jt=fDumpList.begin(); jt != fDumpList.end(); jt++)
172 {
173 if (it->first == *jt)
174 {
175 found = true;
176 break;
177 }
178 }
179 if (!found)
180 continue;
181 int offset = offsets[it->second->index()-1];
182 const char* charSrc = reinterpret_cast<char*>(&fitsBuffer[offset]);
183 unsigned char copyBuffer[30];//max size of a single variable
184 for (int width = 0; width<it->second->width(); width++)
185 {
186 switch (it->second->type())
187 {
188 case CCfits::Tbyte:
189 targetFile << *charSrc;
190 charSrc += sizeof(char);
191 break;
192 case CCfits::Tushort:
193 targetFile << *reinterpret_cast<const unsigned short*>(charSrc);
194 charSrc += sizeof(char);
195 break;
196 case CCfits::Tshort:
197 targetFile << *reinterpret_cast<const short*>(charSrc);
198 charSrc += sizeof(char);
199 break;
200 case CCfits::Tuint:
201 reverse_copy(charSrc, charSrc+sizeof(unsigned int), copyBuffer);
202 //warning suppressed in gcc4.0.2
203 targetFile << *reinterpret_cast<unsigned int*>(copyBuffer);
204 charSrc += sizeof(int);
205 break;
206 case CCfits::Tint:
207 reverse_copy(charSrc, charSrc+sizeof(int), copyBuffer);
208 targetFile << *reinterpret_cast<int*>(copyBuffer);
209 charSrc += sizeof(int);
210 break;
211 case CCfits::Tulong:
212 reverse_copy(charSrc, charSrc+sizeof(unsigned long), copyBuffer);
213 targetFile << *reinterpret_cast<unsigned long*>(copyBuffer);
214 charSrc += sizeof(int);
215 break;
216 case CCfits::Tlong:
217 reverse_copy(charSrc, charSrc+sizeof(long), copyBuffer);
218 targetFile << *reinterpret_cast<long*>(copyBuffer);
219 charSrc += sizeof(int);
220 break;
221 case CCfits::Tlonglong:
222 reverse_copy(charSrc, charSrc+sizeof(long long), copyBuffer);
223 targetFile << *reinterpret_cast<long long*>(copyBuffer);
224 charSrc += sizeof(long long);
225 break;
226 case CCfits::Tfloat:
227 reverse_copy(charSrc, charSrc+sizeof(float), copyBuffer);
228 targetFile << *reinterpret_cast<float*>(copyBuffer);
229 charSrc += sizeof(float);
230 break;
231 case CCfits::Tdouble:
232 reverse_copy(charSrc, charSrc+sizeof(double), copyBuffer);
233 targetFile << *reinterpret_cast<double*>(copyBuffer);
234 charSrc += sizeof(double);
235 break;
236 case CCfits::Tnull:
237 case CCfits::Tbit:
238 case CCfits::Tlogical:
239 case CCfits::Tstring:
240 case CCfits::Tcomplex:
241 case CCfits::Tdblcomplex:
242 case CCfits::VTbit:
243 case CCfits::VTbyte:
244 case CCfits::VTlogical:
245 case CCfits::VTushort:
246 case CCfits::VTshort:
247 case CCfits::VTuint:
248 case CCfits::VTint:
249 case CCfits::VTulong:
250 case CCfits::VTlong:
251 case CCfits::VTlonglong:
252 case CCfits::VTfloat:
253 case CCfits::VTdouble:
254 case CCfits::VTcomplex:
255 case CCfits::VTdblcomplex:
256 Error("Data type not implemented yet.");
257 return;
258 break;
259 default:
260 Error("THIS SHOULD NEVER BE REACHED");
261 return;
262 }//switch
263 targetFile << " ";
264 }//width loop
265 }//iterator over the columns
266 targetFile << endl;
267}
268
269// --------------------------------------------------------------------------
270//
271//! Calculates the required buffer size for reading one row of the current table.
272//! Also calculates the offsets to all the columns
273//
274vector<int> FitsLoader::CalculateBufferSize()
275{
276 vector<int> result;
277 map<int,int> sizes;
278 int size = 0;
279
280 for (map<string, CCfits::Column*>::iterator it=fColMap.begin(); it != fColMap.end(); it++)
281 {
282 int width = it->second->width();
283 switch (it->second->type())
284 {
285 case CCfits::Tbyte:
286 case CCfits::Tushort:
287 case CCfits::Tshort:
288 Message("short");
289 sizes[it->second->index()] = sizeof(char)*width;
290 break;
291 case CCfits::Tuint:
292 case CCfits::Tint:
293 Message("int");
294 sizes[it->second->index()] = sizeof(int)*width;
295 break;
296 case CCfits::Tulong:
297 case CCfits::Tlong:
298 Message("long");
299 sizes[it->second->index()] = sizeof(int)*width;
300 break;
301 case CCfits::Tlonglong:
302 Message("longlong");
303 sizes[it->second->index()] = sizeof(long long)*width;
304 break;
305 case CCfits::Tfloat:
306 Message("float");
307 sizes[it->second->index()] = sizeof(float)*width;
308 break;
309 case CCfits::Tdouble:
310 Message("double");
311 sizes[it->second->index()] = sizeof(double)*width;
312 break;
313 case CCfits::Tnull:
314 case CCfits::Tbit:
315 case CCfits::Tlogical:
316 case CCfits::Tstring:
317 case CCfits::Tcomplex:
318 case CCfits::Tdblcomplex:
319 case CCfits::VTbit:
320 case CCfits::VTbyte:
321 case CCfits::VTlogical:
322 case CCfits::VTushort:
323 case CCfits::VTshort:
324 case CCfits::VTuint:
325 case CCfits::VTint:
326 case CCfits::VTulong:
327 case CCfits::VTlong:
328 case CCfits::VTlonglong:
329 case CCfits::VTfloat:
330 case CCfits::VTdouble:
331 case CCfits::VTcomplex:
332 case CCfits::VTdblcomplex:
333 Error("Data type not implemented yet.");
334 return vector<int>();
335 break;
336 default:
337 Error("THIS SHOULD NEVER BE REACHED");
338 return vector<int>();
339 }
340 }
341 //calculate the offsets in the vector.
342 int checkIndex = 1;
343 for (map<int,int>::iterator it=sizes.begin(); it != sizes.end(); it++)
344 {
345 result.push_back(size);
346 size += it->second;
347 if (it->first != checkIndex)
348 {
349 ostringstream str;
350 str << "Expected index " << checkIndex << " found " << it->first;
351 Error(str);
352 }
353 checkIndex++;
354 }
355 result.push_back(size);
356 return result;
357}
358// --------------------------------------------------------------------------
359//
360//! Constructor
361//! @param out
362//! the ostream where to redirect the outputs
363//
364FitsLoader::FitsLoader(ostream& out) : StateMachineDim(out, "FITS_LOADER")
365{
366 //Add the existing states
367 AddStateName(kSM_FileLoaded, "FileLoaded", "A Fits file has been loaded");
368
369 //Add the possible transitions
370 AddEvent(kSM_FileLoaded, fLoadFits, kSM_Ready)
371 (boost::bind(&FitsLoader::LoadPlease, this))
372 ("Loads the given Fits file");
373 AddEvent(kSM_Ready, fUnloadFits, kSM_FileLoaded)
374 (boost::bind(&FitsLoader::UnloadPlease, this))
375 ("Unloads the given Fits file");
376
377 //Add the possible configurations
378 AddEvent(fListColumns, "", kSM_FileLoaded)
379 (boost::bind(&FitsLoader::ListColumnsPlease, this, _1))
380 ("List the columns that were loaded from that file");
381 AddEvent(fDumpColumns, "C", kSM_FileLoaded)
382 (boost::bind(&FitsLoader::AddDumpColumnsPlease, this, _1))
383 ("Add a given column to the dumping list");
384 AddEvent(fClearDumpList, "", kSM_FileLoaded)
385 (boost::bind(&FitsLoader::ClearDumpListPlease, this, _1))
386 ("Clear the dumping list");
387 AddEvent(fDoDump, "", kSM_FileLoaded)
388 (boost::bind(&FitsLoader::DoDumpPlease, this, _1))
389 ("Perform the dump of columns data, based on the to dump list");
390 AddEvent(fConfigFileName, "C", kSM_Ready, kSM_FileLoaded)
391 (boost::bind(&FitsLoader::ConfigFileNamePlease, this, _1))
392 ("Gives the name of the Fits file to be loaded");
393 AddEvent(fConfigTableName, "C", kSM_Ready, kSM_FileLoaded)
394 (boost::bind(&FitsLoader::ConfigTableNamePlease, this, _1))
395 ("Gives the name of the Table to be loaded");
396 AddEvent(fConfigPrecName, "I", kSM_Ready, kSM_FileLoaded)
397 (boost::bind(&FitsLoader::SetOFStreamPrecisionPlease, this, _1))
398 ("Set the precision of the ofstream, i.e. the number of significant digits being outputted");
399 AddEvent(fConfigFileOutName, "C", kSM_Ready, kSM_FileLoaded)
400 (boost::bind(&FitsLoader::SetFileOutPlease, this, _1))
401 ("Set the name of the outputted file.");
402
403 fFile = NULL;
404 fStreamPrecision = 20;
405
406}
407// --------------------------------------------------------------------------
408//
409//! Destructor
410//
411FitsLoader::~FitsLoader()
412{
413 if (fFile)
414 delete fFile;
415 fFile = NULL;
416}
417// --------------------------------------------------------------------------
418//
419//! Loads the fits file based on the current parameters
420//
421int FitsLoader::LoadPlease()
422{
423 ostringstream str;
424 try
425 {
426 fFile = new CCfits::FITS(fFileName);
427 }
428 catch (CCfits::FitsException e)
429 {
430 str << "Could not open FITS file " << fFileName << " reason: " << e.message();
431 Error(str);
432 return kSM_Ready;
433 }
434 str.str("");
435 const multimap< string, CCfits::ExtHDU * > extMap = fFile->extension();
436 if (extMap.find(fTableName) == extMap.end())
437 {
438 str.str("");
439 str << "Could not open table " << fTableName << ". Tables in file are: ";
440 for (std::multimap<string, CCfits::ExtHDU*>::const_iterator it=extMap.begin(); it != extMap.end(); it++)
441 str << it->first << " ";
442 Error(str);
443 return kSM_Ready;
444 }
445 else
446 fTable = dynamic_cast<CCfits::Table*>(extMap.find(fTableName)->second);
447 int numRows = fTable->rows();
448 str.str("");
449 str << "Loaded table has " << numRows << " rows";
450 Message(str);
451
452 fColMap = fTable->column();
453 if (fDumpList.size() != 0)
454 {
455 bool should_clear = false;
456 for (vector<string>::iterator it=fDumpList.begin(); it!= fDumpList.end(); it++)
457 {
458 if (fColMap.find(*it) == fColMap.end())
459 {
460 should_clear = true;
461 Error("Config-given dump list contains invalid entry " + *it + " clearing the list");
462 }
463 }
464 if (should_clear)
465 fDumpList.clear();
466 }
467 return kSM_FileLoaded;
468}
469// --------------------------------------------------------------------------
470//
471//! Unloads the Fits file
472//
473int FitsLoader::UnloadPlease()
474{
475 if (fFile)
476 delete fFile;
477 else
478 Error("Error: Fits file is NULL while it should not have been");
479 fFile = NULL;
480 return kSM_Ready;
481}
482// --------------------------------------------------------------------------
483//
484//! List the columns that are in the loaded Fits table
485//
486int FitsLoader::ListColumnsPlease(const Event&)
487{
488 Message("Columns in the loaded table are:");
489 map<string, CCfits::Column*>::iterator it;
490 for (it=fColMap.begin(); it != fColMap.end(); it++)
491 Message(it->first);
492 return GetCurrentState();
493}
494// --------------------------------------------------------------------------
495//
496//! Add a given column name to the list of columns to dump
497//! @param evt
498//! the event transporting the column name
499//
500int FitsLoader::AddDumpColumnsPlease(const Event& evt)
501{
502 string evtText(evt.GetText());
503 //TODO check that this column indeed exist in the file
504 if (fColMap.find(evtText) != fColMap.end())
505 fDumpList.push_back(evtText);
506 else
507 Error("Could not find column " + evtText + " int table");
508 Message("New dump list:");
509 for (vector<string>::iterator it=fDumpList.begin(); it != fDumpList.end(); it++)
510 Message(*it);
511 return GetCurrentState();
512}
513// --------------------------------------------------------------------------
514//
515//! Clear the list of columns to dump
516//
517int FitsLoader::ClearDumpListPlease(const Event&)
518{
519 fDumpList.clear();
520 Message("Dump list is now empty");
521 return GetCurrentState();
522}
523// --------------------------------------------------------------------------
524//
525//! Perform the actual dump, based on the current parameters
526//
527int FitsLoader::DoDumpPlease(const Event&)
528{
529 fTable->makeThisCurrent();
530 vector<int> offsets = CalculateBufferSize();
531 int size = offsets[offsets.size()-1];
532 offsets.pop_back();
533 unsigned char* fitsBuffer = new unsigned char[size];
534
535 ofstream targetFile(fFileOut);
536 int status = 0;
537
538 for (int i=1;i<=fTable->rows(); i++)
539 {
540 fits_read_tblbytes(fFile->fitsPointer(), i, 1, size, fitsBuffer, &status);
541 if (status)
542 {
543 ostringstream str;
544 str << "An error occurred while reading fits row #" << i << " error code: " << status;
545 Error(str);
546 str.str("");
547 for (unsigned int j=0;j<offsets.size(); j++)
548 str << offsets[j] << " ";
549 Error(str);
550 }
551 writeValuesFromFits(offsets, targetFile, fitsBuffer);
552 }
553 delete[] fitsBuffer;
554 return GetCurrentState();
555}
556// --------------------------------------------------------------------------
557//
558//! Set the name of the intput Fits file
559//! @param evt
560//! the event transporting the file name
561//
562int FitsLoader::ConfigFileNamePlease(const Event& evt)
563{
564 fFileName = string(evt.GetText());
565 Message("New Fits file: " + fFileName);
566 return GetCurrentState();
567}
568// --------------------------------------------------------------------------
569//
570//! Set the name of the input table
571//! @param evt
572//! the event transporting the table name
573//
574int FitsLoader::ConfigTableNamePlease(const Event& evt)
575{
576 fTableName = string(evt.GetText());
577 Message("New Fits table: " + fTableName);
578 return GetCurrentState();
579}
580// --------------------------------------------------------------------------
581//
582//! Retrieves the configuration parameters
583//! @param conf
584//! the configuration object
585//
586void FitsLoader::SetupConfig(Configuration& conf)
587{
588 if (conf.Has("outfile"))
589 {
590 fFileOut = conf.Get<string>("outfile");
591 Message("Output file is: " + fFileOut);
592 }
593 if (conf.Has("fitsfile"))
594 {
595 fFileName = conf.Get<string>("fitsfile");
596 Message("Input fits is: " + fFileName);
597 }
598 if (conf.Has("tablename"))
599 {
600 fTableName = conf.Get<string>("tablename");
601 Message("Input Table is: " + fTableName);
602 }
603 if (conf.Has("dump"))
604 {
605 fDumpList = conf.Get<vector<string>>("dump");
606 Message("Dump list is:");
607 for (vector<string>::iterator it=fDumpList.begin(); it != fDumpList.end(); it++)
608 Message(*it);
609 }
610 if (conf.Has("precision"))
611 {
612 fStreamPrecision = conf.Get<int>("precision");
613
614 ostringstream str;
615 str << "OFStream precision is: " << fStreamPrecision;
616 Message(str);
617 }
618}
619void RunThread(FitsLoader* loader)
620{
621 loader->Run(true);
622 Readline::Stop();
623}
624template<class T>
625int RunShell(Configuration& conf)
626{
627 static T shell(conf.GetName().c_str(), conf.Get<int>("console")!=1);
628
629 WindowLog& wout = shell.GetStreamOut();
630
631 FitsLoader loader(wout);
632 loader.SetupConfig(conf);
633 shell.SetReceiver(loader);
634
635 boost::thread t(boost::bind(RunThread, &loader));
636
637 shell.Run();
638
639 loader.Stop();
640
641 t.join();
642
643 return 0;
644}
645void PrintUsage()
646{
647 cout << "This is a usage. to be completed" << endl;
648}
649void PrintHelp()
650{
651 cout << "This is the help. I know, not so helpfull at the moment..." << endl;
652}
653void SetupConfiguration(Configuration& conf)
654{
655 po::options_description configp("Programm options");
656 configp.add_options()
657 ("console,c", var<int>(), "Use console (0=shell, 1=simple buffered, X=simple unbuffered)");
658
659 po::options_description configs("Fits Loader options");
660 configs.add_options()
661 ("outfile,o", var<string>(), "Output file")
662 ("fitsfile,f", var<string>(), "Input Fits file")
663 ("tablename,t", var<string>(), "Input Table")
664 ("dump,d", vars<string>(), "List of columns to dump")
665 ("precision,p", var<int>(), "Precision of ofstream")
666 ;
667// conf.AddEnv("dns", "DIM_DNS_NODE");
668
669 conf.AddOptions(configp);
670 conf.AddOptions(configs);
671}
672int main(int argc, const char** argv)
673{
674 Configuration conf(argv[0]);
675 conf.SetPrintUsage(PrintUsage);
676 SetupConfiguration(conf);
677
678 if (!conf.DoParse(argc, argv, PrintHelp))
679 return -1;
680
681// if (!conf.Has("console"))
682// return Run(conf);
683 if (conf.Get<int>("console")==0)
684 return RunShell<LocalShell>(conf);
685 else
686 return RunShell<LocalConsole>(conf);
687
688 return 0;
689}
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