source: trunk/src/STFITSImageWriter.cpp @ 1500

Last change on this file since 1500 was 1500, checked in by Malte Marquarding, 15 years ago

Fix for ticket #110. Hopefully the last. Using the preferVelocity option in ImageToFITS, which will output a elocity axis if a restfrequency is given, otherwise it will set up a frequency axis hwich looks the same in CLASS and asap
File size: 8.7 KB
Line 
1//#---------------------------------------------------------------------------
2//# STFITSImageWriter.cc: Class to write out single dish spectra as FITS images
3//#---------------------------------------------------------------------------
4//# Copyright (C) 2008
5//# ATNF
6//#
7//# This program is free software; you can redistribute it and/or modify it
8//# under the terms of the GNU General Public License as published by the Free
9//# Software Foundation; either version 2 of the License, or (at your option)
10//# any later version.
11//#
12//# This program is distributed in the hope that it will be useful, but
13//# WITHOUT ANY WARRANTY; without even the implied warranty of
14//# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
15//# Public License for more details.
16//#
17//# You should have received a copy of the GNU General Public License along
18//# with this program; if not, write to the Free Software Foundation, Inc.,
19//# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
20//#
21//# Correspondence concerning this software should be addressed as follows:
22//#        Internet email: Malte.Marquarding@csiro.au
23//#        Postal address: Malte Marquarding,
24//#                        Australia Telescope National Facility,
25//#                        P.O. Box 76,
26//#                        Epping, NSW, 2121,
27//#                        AUSTRALIA
28//#
29//# $Id: $
30//#---------------------------------------------------------------------------
31
32#include <fitsio.h>
33#include <images/Images/TempImage.h>
34
35#include <lattices/Lattices/ArrayLattice.h>
36
37#include <measures/Measures/MEpoch.h>
38#include <measures/Measures/Stokes.h>
39
40#include <tables/Tables/Table.h>
41#include <tables/Tables/TableIter.h>
42#include <tables/Tables/TableRecord.h>
43#include <casa/Containers/RecordField.h>
44#include <tables/Tables/TableRow.h>
45#include <tables/Tables/ScalarColumn.h>
46#include <tables/Tables/ArrayColumn.h>
47
48
49#include <coordinates/Coordinates/CoordinateUtil.h>
50#include <coordinates/Coordinates/CoordinateSystem.h>
51#include <coordinates/Coordinates/SpectralCoordinate.h>
52#include <coordinates/Coordinates/DirectionCoordinate.h>
53#include <coordinates/Coordinates/StokesCoordinate.h>
54#include <coordinates/Coordinates/ObsInfo.h>
55
56#include <images/Images/ImageFITSConverter.h>
57#include <images/Images/TempImage.h>
58
59#include <lattices/Lattices/ArrayLattice.h>
60
61
62//#include "STDefs.h"
63#include "STHeader.h"
64#include "Scantable.h"
65#include "STFITSImageWriter.h"
66
67using namespace casa;
68using namespace asap;
69
70
71STFITSImageWriter::STFITSImageWriter() : isClass_(False)
72{;}
73
74STFITSImageWriter::~STFITSImageWriter()
75{;}
76
77
78Bool STFITSImageWriter::write(const Scantable& stable,
79                              const String& fileName)
80{
81
82// Get global Header from Table
83
84   STHeader hdr = stable.getHeader();
85
86// Column keywords
87
88   Table tab = stable.table();
89
90// Temps
91
92   const Unit RAD(String("rad"));
93
94// Open and write header file
95
96   String rootName(fileName);
97   if (rootName.length()==0) rootName = String("fits");
98   
99   ObsInfo oi;
100   oi.setTelescope(String(hdr.antennaname));
101   oi.setObserver(String(hdr.observer));
102   
103   uInt maxMem = 128;
104   Bool preferVelocity = False;
105   Bool opticalVelocity = False;
106   Int bitPix = -32;                     // FLoating point
107   Float minPix = 1.0;
108   Float maxPix = -1.0;
109   Bool overWrite = True;
110   Bool degLast = False;
111   Bool reallyVerbose = False;
112   String errMsg;
113
114
115  Block<String> cols(5);
116  cols[0] = String("SCANNO");
117  cols[1] = String("CYCLENO");
118  cols[2] = String("BEAMNO");
119  cols[3] = String("IFNO");
120  cols[4] = String("POLNO");
121  TableIterator iter(tab, cols);
122  // Open data file
123  while ( !iter.pastEnd() ) {
124    Table t = iter.table();
125    ROTableRow row(t);
126    const TableRecord& rec = row.get(0);
127    String dirtype = stable.getDirectionRefString();
128    ostringstream onstr;
129    onstr << "SCAN" << rec.asuInt("SCANNO")
130    << "_CYCLE" << rec.asuInt("CYCLENO")
131    << "_BEAM" << rec.asuInt("BEAMNO")
132    << "_IF" << rec.asuInt("IFNO")
133    << "_POL" << rec.asuInt("POLNO");
134    String fileName = rootName + String(onstr) + String(".fits");
135    int row0 = t.rowNumbers(tab)[0];
136
137    const MPosition& mp = stable.getAntennaPosition();
138    const MDirection& md = stable.getDirection(row0);
139    const MEpoch& me = stable.getEpoch(row0);
140    oi.setObsDate(me);
141   
142    const Double& rf = 
143      stable.molecules().getRestFrequency(rec.asuInt("MOLECULE_ID") );
144    SpectralCoordinate sC =
145      stable.frequencies().getSpectralCoordinate(md, mp, me, rf,
146                                                 rec.asuInt("FREQ_ID"));
147
148    Int polno = rec.asuInt("POLNO");
149    Stokes::StokesTypes stokes =
150      Stokes::type(stable.getPolarizationLabel(polno, stable.getPolType()));
151    Vector<Int> whichStokes(1);
152    whichStokes(0) = Int(stokes);
153    StokesCoordinate stC(whichStokes);
154
155
156    CoordinateSystem cSys;
157    Vector<Double> lonlat = md.getAngle().getValue();
158    DirectionCoordinate dC =
159      getDirectionCoordinate(stable.getDirectionRefString(),
160                             lonlat[0], lonlat[1]);
161    cSys.addCoordinate(sC);
162    cSys.addCoordinate(dC);
163    cSys.addCoordinate(stC);
164    cSys.setObsInfo(oi);
165   
166    Vector<Float> spec = rec.asArrayFloat("SPECTRA");
167    Vector<uChar> flag = rec.asArrayuChar("FLAGTRA");
168    Vector<Bool> bflag(flag.shape());
169    convertArray(bflag, flag);
170
171    // Create casacore Image
172    IPosition shp(4, 1);
173    shp(0)= spec.nelements();
174    TempImage<Float> tIm(shp, cSys);
175    tIm.put(spec);
176    ArrayLattice<Bool> latMask(shp);
177    IPosition where(4,0);
178    IPosition stride(4,1);
179    latMask.putSlice(!bflag, where, stride);
180    tIm.attachMask(latMask);
181    if (isClass_) {
182      preferVelocity = True;
183    }
184    Bool ok = ImageFITSConverter::ImageToFITS(errMsg, tIm, fileName,
185                                              maxMem, preferVelocity,
186                                              opticalVelocity, bitPix,
187                                              minPix, maxPix, overWrite,
188                                              degLast, reallyVerbose);
189    if (!ok) {
190      throw(AipsError(errMsg));
191    }
192    if (isClass_) {
193      // Add CLASS specific information
194      // Apply hacks to fits file so it can be read by class
195      // modifications are
196      // CTYPE1 :  FREQ-XYZ -> FREQ
197      // CRVAL1 :  -> CRVAL1-RESTFREQ
198      int status = 0;
199      fitsfile *fptr;     
200      if( fits_open_file(&fptr, fileName.c_str(), READWRITE, &status) )
201        throw AipsError("Coudn't open fits file for CLASS modification");
202
203      // Use preferVelocity which seems to work.
204      // When no restfrequency is given this will set up the correct
205      // frequency axis. Otherwise it uses a velocity axis
206      //       if ( fits_update_key(fptr, TSTRING, "CTYPE1", (char *)"FREQ",
207      //                            NULL, &status) )
208      //         throw AipsError("Couldn't modify CTYPE1.");
209      //       float restf,refval,newfreq;
210      //       fits_read_key(fptr, TFLOAT, "CRVAL1",
211      //                     &refval, NULL, &status);
212      //       fits_read_key(fptr, TFLOAT, "RESTFREQ",
213      //                     &restf, NULL, &status);
214      //       newfreq = refval - restf;
215      //       if ( fits_update_key(fptr, TFLOAT, "CRVAL1", &newfreq,  NULL, &status) )
216      //         throw AipsError("Couldn't modify CRVAL1");
217
218
219      Float tsys = stable.getTsys(row0);
220      if ( fits_update_key(fptr, TFLOAT, "TSYS", &tsys,
221                           "System temperature", &status) ) {
222        throw AipsError("Couldn't modify TSYS");       
223      }
224      Float otime = Float(stable.getIntTime(row0));
225      if ( fits_update_key(fptr, TFLOAT, "OBSTIME", &otime,
226                           "Integration time", &status) ) {
227        throw AipsError("Couldn't modify OBSTIME");       
228      }
229
230      const char* oname = stable.getSourceName(row0).c_str();
231      if ( fits_update_key(fptr, TSTRING, "OBJECT", (char *)oname,
232                           NULL, &status) ) {
233        throw AipsError("Couldn't modify OBJECT");       
234      }
235      fits_close_file(fptr, &status);
236    }
237    //pushLog(String(oss));
238    ++iter;
239  }
240  return True;
241}
242
243DirectionCoordinate
244STFITSImageWriter::getDirectionCoordinate(const String& reff,
245                                          Double lon, Double lat)
246{
247   
248   Projection proj(Projection::SIN);                   // What should we use ?
249   Matrix<Double> xForm(2,2);
250   xForm = 0.0; xForm.diagonal() = 1.0;
251   Vector<Double> incLonLat(2,0.0);
252   Vector<Double> refPixLonLat(2,0.0);
253   MDirection::Types mdt;
254   if (!MDirection::getType(mdt, reff)) {
255     throw(AipsError("Illegal Direction frame."));
256   }
257   return DirectionCoordinate(mdt, proj, lon, lat,
258                              incLonLat[0], incLonLat[1], xForm,
259                              refPixLonLat[0], refPixLonLat[1]);
260   
261}
262
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