source: trunk/src/STFITSImageWriter.cpp @ 3106

Last change on this file since 3106 was 3106, checked in by Takeshi Nakazato, 8 years ago

New Development: No

JIRA Issue: No

Ready for Test: Yes/No?

Interface Changes: Yes/No?

What Interface Changed: Please list interface changes

Test Programs: List test programs

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Module(s): Module Names change impacts.

Description: Describe your changes here...


Check-in asap modifications from Jim regarding casacore namespace conversion.
File size: 9.9 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
33#include <fitsio.h>
34#include <casa/Containers/RecordField.h>
35#include <casa/Logging/LogIO.h>
36
37#include <lattices/Lattices/ArrayLattice.h>
38
39#include <measures/Measures/MEpoch.h>
40#include <measures/Measures/Stokes.h>
41
42#include <tables/Tables/Table.h>
43#include <tables/Tables/TableIter.h>
44#include <tables/Tables/TableRecord.h>
45
46#include <tables/Tables/TableRow.h>
47#include <tables/Tables/ScalarColumn.h>
48#include <tables/Tables/ArrayColumn.h>
49
50
51#include <coordinates/Coordinates/CoordinateUtil.h>
52#include <coordinates/Coordinates/CoordinateSystem.h>
53#include <coordinates/Coordinates/SpectralCoordinate.h>
54#include <coordinates/Coordinates/DirectionCoordinate.h>
55#include <coordinates/Coordinates/StokesCoordinate.h>
56#include <coordinates/Coordinates/ObsInfo.h>
57
58#include <images/Images/ImageFITSConverter.h>
59#include <images/Images/TempImage.h>
60
61#include <lattices/Lattices/ArrayLattice.h>
62
63
64//#include "STDefs.h"
65#include "STHeader.h"
66#include "Scantable.h"
67#include "STFITSImageWriter.h"
68
69using namespace casacore;
70using namespace asap;
71
72
73STFITSImageWriter::STFITSImageWriter() : isClass_(False)
74{;}
75
76STFITSImageWriter::~STFITSImageWriter()
77{;}
78
79
80Bool STFITSImageWriter::write(const Scantable& stable,
81                              const String& fileName)
82{
83
84// Get global Header from Table
85
86   STHeader hdr = stable.getHeader();
87
88// Column keywords
89
90   Table tab = stable.table();
91
92// Temps
93
94   const Unit RAD(String("rad"));
95
96// Open and write header file
97
98   String rootName(fileName);
99   if (rootName.length()==0) rootName = String("fits");
100   
101   ObsInfo oi;
102   oi.setTelescope(String(hdr.antennaname));
103   oi.setObserver(String(hdr.observer));
104   
105   uInt maxMem = 128;
106   Bool preferVelocity = False;
107   Bool opticalVelocity = False;
108   Int bitPix = -32;                     // FLoating point
109   Float minPix = 1.0;
110   Float maxPix = -1.0;
111   Bool overWrite = True;
112   Bool degLast = False;
113   Bool reallyVerbose = False;
114   String errMsg;
115
116
117  Block<String> cols(5);
118  cols[0] = String("SCANNO");
119  cols[1] = String("CYCLENO");
120  cols[2] = String("BEAMNO");
121  cols[3] = String("IFNO");
122  cols[4] = String("POLNO");
123  TableIterator iter(tab, cols);
124  // Open data file
125
126  while ( !iter.pastEnd() ) {
127    Table t = iter.table();
128    ROTableRow row(t);
129    const TableRecord& rec = row.get(0);
130    String dirtype = stable.getDirectionRefString();
131    ostringstream onstr;
132    if (rootName.length()==0) {
133      rootName = "fits";
134    }
135    if (tab.nrow() > 1) {
136      if (stable.nscan() > 1)
137        onstr << "_SCAN" << rec.asuInt("SCANNO");
138      if (stable.ncycle(rec.asuInt("SCANNO")) > 1)
139        onstr << "_CYCLE" << rec.asuInt("CYCLENO");
140      if (stable.nbeam(rec.asuInt("SCANNO")) > 1)
141        onstr << "_BEAM" << rec.asuInt("BEAMNO");
142      if (stable.nif(rec.asuInt("SCANNO")) > 1)
143        onstr << "_IF" << rec.asuInt("IFNO");
144      if (stable.npol(rec.asuInt("SCANNO")) > 1)
145        onstr << "_POL" << rec.asuInt("POLNO");
146    }
147    String fileName = rootName + String(onstr) + String(".fits");
148    int row0 = t.rowNumbers(tab)[0];
149
150    const MPosition& mp = stable.getAntennaPosition();
151    const MDirection& md = stable.getDirection(row0);
152    const MEpoch& me = stable.getEpoch(row0);
153    oi.setObsDate(me);
154   
155    //const Double& rf = 
156    //  stable.molecules().getRestFrequency(rec.asuInt("MOLECULE_ID") );
157    const std::vector<double>& rf =
158      stable.molecules().getRestFrequency(rec.asuInt("MOLECULE_ID") );
159    SpectralCoordinate sC =
160      stable.frequencies().getSpectralCoordinate(md, mp, me, rf,
161                                                 rec.asuInt("FREQ_ID"));
162
163    Int polno = rec.asuInt("POLNO");
164    Stokes::StokesTypes stokes =
165      Stokes::type(stable.getPolarizationLabel(polno, stable.getPolType()));
166    Vector<Int> whichStokes(1);
167    whichStokes(0) = Int(stokes);
168    StokesCoordinate stC(whichStokes);
169
170
171    CoordinateSystem cSys;
172    Vector<Double> lonlat = md.getAngle().getValue();
173    DirectionCoordinate dC =
174      getDirectionCoordinate(stable.getDirectionRefString(),
175                             lonlat[0], lonlat[1]);
176    cSys.addCoordinate(sC);
177    cSys.addCoordinate(dC);
178    cSys.addCoordinate(stC);
179    cSys.setObsInfo(oi);
180   
181    Vector<Float> spec = rec.asArrayFloat("SPECTRA");
182    Vector<uChar> flag = rec.asArrayuChar("FLAGTRA");
183    Vector<Bool> bflag(flag.shape());
184    convertArray(bflag, flag);
185
186    // Create casacore Image
187    IPosition shp(4, 1);
188    shp(0)= spec.nelements();
189    TempImage<Float> tIm(shp, cSys);
190    tIm.put(spec);
191    ArrayLattice<Bool> latMask(shp);
192    IPosition where(4,0);
193    IPosition stride(4,1);
194    latMask.putSlice(!bflag, where, stride);
195    tIm.attachMask(latMask);
196    if (isClass_) {
197      preferVelocity = True;
198    }
199    Bool ok = ImageFITSConverter::ImageToFITS(errMsg, tIm, fileName,
200                                              maxMem, preferVelocity,
201                                              opticalVelocity, bitPix,
202                                              minPix, maxPix, overWrite,
203                                              degLast, reallyVerbose);
204    if (!ok) {
205      throw(AipsError(errMsg));
206    }
207   
208    int status = 0;
209    fitsfile *fptr;     
210    if( fits_open_file(&fptr, fileName.c_str(), READWRITE, &status) )
211      throw AipsError("Coudn't open fits file for modification");
212
213    if (isClass_) {
214      // Add CLASS specific information
215      // Apply hacks to fits file so it can be read by class
216      // modifications are
217      // CTYPE1 :  FREQ-XYZ -> FREQ
218      // CRVAL1 :  -> CRVAL1-RESTFREQ
219     
220      // Use preferVelocity which seems to work.
221      // When no restfrequency is given this will set up the correct
222      // frequency axis. Otherwise it uses a velocity axis
223      char ctyp[84];
224      fits_read_key(fptr, TSTRING, "CTYPE1", ctyp, NULL, &status);
225      if (String(ctyp).contains("FREQ", 0)) {
226        float restf,refval;
227        fits_read_key(fptr, TFLOAT, "CRVAL1",
228                      &refval, NULL, &status);
229        restf = 0.0;
230        if ( fits_update_key(fptr, TFLOAT, "CRVAL1", &restf,
231                             NULL, &status) ) {
232          throw AipsError("Couldn't modify CRVAL1");       
233        }
234        if ( fits_update_key(fptr, TFLOAT, "RESTFREQ", &refval,
235                             NULL, &status) ) {
236          throw AipsError("Couldn't modify RESTFREQ");       
237        }
238      } else {
239        float refval = sC.referenceValue()[0];
240        if ( fits_update_key(fptr, TFLOAT, "RESTFREQ", &refval,
241                             NULL, &status) ) {
242          throw AipsError("Couldn't modify RESTFREQ");       
243        }
244       
245      }
246    }
247
248    Float tsys = stable.getTsys(row0);
249    if ( fits_update_key(fptr, TFLOAT, "TSYS", &tsys,
250                         "System temperature", &status) ) {
251      throw AipsError("Couldn't modify TSYS");       
252    }
253    Float otime = Float(stable.getIntTime(row0));
254    if ( fits_update_key(fptr, TFLOAT, "OBSTIME", &otime,
255                         "Integration time", &status) ) {
256      throw AipsError("Couldn't modify OBSTIME");       
257    }
258   
259    const char* oname = stable.getSourceName(row0).c_str();
260    if ( fits_update_key(fptr, TSTRING, "OBJECT", (char *)oname,
261                         NULL, &status) ) {
262      throw AipsError("Couldn't modify OBJECT");       
263    }
264    Float elev = stable.getElevation(row0)/C::pi*180.0;
265    if ( fits_update_key(fptr, TFLOAT, "ELEVATIO", &elev,
266                         "Telescope elevation (degrees)", &status) ) {
267      throw AipsError("Couldn't modify ELEVATIO");       
268    }
269    Float azi = stable.getAzimuth(row0)/C::pi*180.0;
270    if ( fits_update_key(fptr, TFLOAT, "AZIMUTH", &azi,
271                         "Telescope azimuth (degrees)", &status) ) {
272      throw AipsError("Couldn't modify AZIMUTH");       
273    }
274    fits_close_file(fptr, &status);
275   
276    LogIO os( casacore::LogOrigin("STFITSImageWriter"));
277    os << "Wrote " << fileName << LogIO::POST;
278    ++iter;
279  }
280  return True;
281}
282
283DirectionCoordinate
284STFITSImageWriter::getDirectionCoordinate(const String& reff,
285                                          Double lon, Double lat)
286{
287   
288   Projection proj(Projection::SIN);                   // What should we use ?
289   Matrix<Double> xForm(2,2);
290   xForm = 0.0; xForm.diagonal() = 1.0;
291   Vector<Double> incLonLat(2,0.0);
292   Vector<Double> refPixLonLat(2,0.0);
293   MDirection::Types mdt;
294   if (!MDirection::getType(mdt, reff)) {
295     throw(AipsError("Illegal Direction frame."));
296   }
297   return DirectionCoordinate(mdt, proj, lon, lat,
298                              incLonLat[0], incLonLat[1], xForm,
299                              refPixLonLat[0], refPixLonLat[1]);
300   
301}
302
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