source: branches/mergetest/src/STFITSImageWriter.cpp @ 1779

Last change on this file since 1779 was 1779, checked in by Kana Sugimoto, 14 years ago

New Development: Yes

JIRA Issue: No (test merging alma branch)

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed:

Test Programs:

Put in Release Notes: No

Module(s):

Description:


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#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
124  while ( !iter.pastEnd() ) {
125    Table t = iter.table();
126    ROTableRow row(t);
127    const TableRecord& rec = row.get(0);
128    String dirtype = stable.getDirectionRefString();
129    ostringstream onstr;
130    if (rootName.length()==0) {
131      rootName = "fits";
132    }
133    if (tab.nrow() > 1) {
134      if (stable.nscan() > 1)
135        onstr << "_SCAN" << rec.asuInt("SCANNO");
136      if (stable.ncycle(rec.asuInt("SCANNO")) > 1)
137        onstr << "_CYCLE" << rec.asuInt("CYCLENO");
138      if (stable.nbeam(rec.asuInt("SCANNO")) > 1)
139        onstr << "_BEAM" << rec.asuInt("BEAMNO");
140      if (stable.nif(rec.asuInt("SCANNO")) > 1)
141        onstr << "_IF" << rec.asuInt("IFNO");
142      if (stable.npol(rec.asuInt("SCANNO")) > 1)
143        onstr << "_POL" << rec.asuInt("POLNO");
144    }
145    String fileName = rootName + String(onstr) + String(".fits");
146    int row0 = t.rowNumbers(tab)[0];
147
148    const MPosition& mp = stable.getAntennaPosition();
149    const MDirection& md = stable.getDirection(row0);
150    const MEpoch& me = stable.getEpoch(row0);
151    oi.setObsDate(me);
152   
153    //const Double& rf = 
154    //  stable.molecules().getRestFrequency(rec.asuInt("MOLECULE_ID") );
155    const std::vector<double>& rf = 
156      stable.molecules().getRestFrequency(rec.asuInt("MOLECULE_ID") );
157    SpectralCoordinate sC =
158      stable.frequencies().getSpectralCoordinate(md, mp, me, rf,
159                                                 rec.asuInt("FREQ_ID"));
160
161    Int polno = rec.asuInt("POLNO");
162    Stokes::StokesTypes stokes =
163      Stokes::type(stable.getPolarizationLabel(polno, stable.getPolType()));
164    Vector<Int> whichStokes(1);
165    whichStokes(0) = Int(stokes);
166    StokesCoordinate stC(whichStokes);
167
168
169    CoordinateSystem cSys;
170    Vector<Double> lonlat = md.getAngle().getValue();
171    DirectionCoordinate dC =
172      getDirectionCoordinate(stable.getDirectionRefString(),
173                             lonlat[0], lonlat[1]);
174    cSys.addCoordinate(sC);
175    cSys.addCoordinate(dC);
176    cSys.addCoordinate(stC);
177    cSys.setObsInfo(oi);
178   
179    Vector<Float> spec = rec.asArrayFloat("SPECTRA");
180    Vector<uChar> flag = rec.asArrayuChar("FLAGTRA");
181    Vector<Bool> bflag(flag.shape());
182    convertArray(bflag, flag);
183
184    // Create casacore Image
185    IPosition shp(4, 1);
186    shp(0)= spec.nelements();
187    TempImage<Float> tIm(shp, cSys);
188    tIm.put(spec);
189    ArrayLattice<Bool> latMask(shp);
190    IPosition where(4,0);
191    IPosition stride(4,1);
192    latMask.putSlice(!bflag, where, stride);
193    tIm.attachMask(latMask);
194    if (isClass_) {
195      preferVelocity = True;
196    }
197    Bool ok = ImageFITSConverter::ImageToFITS(errMsg, tIm, fileName,
198                                              maxMem, preferVelocity,
199                                              opticalVelocity, bitPix,
200                                              minPix, maxPix, overWrite,
201                                              degLast, reallyVerbose);
202    if (!ok) {
203      throw(AipsError(errMsg));
204    }
205   
206    int status = 0;
207    fitsfile *fptr;     
208    if( fits_open_file(&fptr, fileName.c_str(), READWRITE, &status) )
209      throw AipsError("Coudn't open fits file for modification");
210
211    if (isClass_) {
212      // Add CLASS specific information
213      // Apply hacks to fits file so it can be read by class
214      // modifications are
215      // CTYPE1 :  FREQ-XYZ -> FREQ
216      // CRVAL1 :  -> CRVAL1-RESTFREQ
217     
218      // Use preferVelocity which seems to work.
219      // When no restfrequency is given this will set up the correct
220      // frequency axis. Otherwise it uses a velocity axis
221      char ctyp[84];
222      fits_read_key(fptr, TSTRING, "CTYPE1", ctyp, NULL, &status);
223      if (String(ctyp).contains("FREQ", 0)) {
224        float restf,refval;
225        fits_read_key(fptr, TFLOAT, "CRVAL1",
226                      &refval, NULL, &status);
227        restf = 0.0;
228        if ( fits_update_key(fptr, TFLOAT, "CRVAL1", &restf,
229                             NULL, &status) ) {
230          throw AipsError("Couldn't modify CRVAL1");       
231        }
232        if ( fits_update_key(fptr, TFLOAT, "RESTFREQ", &refval,
233                             NULL, &status) ) {
234          throw AipsError("Couldn't modify RESTFREQ");       
235        }
236      } else {
237        float refval = sC.referenceValue()[0];
238        if ( fits_update_key(fptr, TFLOAT, "RESTFREQ", &refval,
239                             NULL, &status) ) {
240          throw AipsError("Couldn't modify RESTFREQ");       
241        }
242       
243      }
244    }
245
246    Float tsys = stable.getTsys(row0);
247    if ( fits_update_key(fptr, TFLOAT, "TSYS", &tsys,
248                         "System temperature", &status) ) {
249      throw AipsError("Couldn't modify TSYS");       
250    }
251    Float otime = Float(stable.getIntTime(row0));
252    if ( fits_update_key(fptr, TFLOAT, "OBSTIME", &otime,
253                         "Integration time", &status) ) {
254      throw AipsError("Couldn't modify OBSTIME");       
255    }
256   
257    const char* oname = stable.getSourceName(row0).c_str();
258    if ( fits_update_key(fptr, TSTRING, "OBJECT", (char *)oname,
259                         NULL, &status) ) {
260      throw AipsError("Couldn't modify OBJECT");       
261    }
262    Float elev = stable.getElevation(row0)/C::pi*180.0;
263    if ( fits_update_key(fptr, TFLOAT, "ELEVATIO", &elev,
264                         "Telescope elevation (degrees)", &status) ) {
265      throw AipsError("Couldn't modify ELEVATIO");       
266    }
267    Float azi = stable.getAzimuth(row0)/C::pi*180.0;
268    if ( fits_update_key(fptr, TFLOAT, "AZIMUTH", &azi,
269                         "Telescope azimuth (degrees)", &status) ) {
270      throw AipsError("Couldn't modify AZIMUTH");       
271    }
272    fits_close_file(fptr, &status);
273    ostringstream oss;
274    oss << "Wrote " << fileName;
275    pushLog(String(oss)); 
276    //pushLog(String(oss));
277    ++iter;
278  }
279  return True;
280}
281
282DirectionCoordinate
283STFITSImageWriter::getDirectionCoordinate(const String& reff,
284                                          Double lon, Double lat)
285{
286   
287   Projection proj(Projection::SIN);                   // What should we use ?
288   Matrix<Double> xForm(2,2);
289   xForm = 0.0; xForm.diagonal() = 1.0;
290   Vector<Double> incLonLat(2,0.0);
291   Vector<Double> refPixLonLat(2,0.0);
292   MDirection::Types mdt;
293   if (!MDirection::getType(mdt, reff)) {
294     throw(AipsError("Illegal Direction frame."));
295   }
296   return DirectionCoordinate(mdt, proj, lon, lat,
297                              incLonLat[0], incLonLat[1], xForm,
298                              refPixLonLat[0], refPixLonLat[1]);
299   
300}
301
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