source: branches/newfiller/src/STWriter.cpp@ 2038

Last change on this file since 2038 was 1757, checked in by Kana Sugimoto, 14 years ago

New Development: Yes

JIRA Issue: Yes (CAS-2211)

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed: ASAP 3.0.0 interface changes

Test Programs:

Put in Release Notes: Yes

Module(s): all the CASA sd tools and tasks are affected.

Description: Merged ATNF-ASAP 3.0.0 developments to CASA (alma) branch.

Note you also need to update casa/code/atnf.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 13.6 KB
Line 
1//#---------------------------------------------------------------------------
2//# STWriter.cc: ASAP class to write out single dish spectra.
3//#---------------------------------------------------------------------------
4//# Copyright (C) 2004
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: STWriter.cpp 1757 2010-06-09 09:03:06Z KanaSugimoto $
30//#---------------------------------------------------------------------------
31
32#include <string>
33
34#include <casa/aips.h>
35#include <casa/Arrays/Array.h>
36#include <casa/Arrays/Vector.h>
37#include <casa/BasicSL/Complex.h>
38#include <casa/Utilities/CountedPtr.h>
39#include <casa/Utilities/Assert.h>
40
41#include <atnf/PKSIO/PKSrecord.h>
42#include <atnf/PKSIO/PKSMS2writer.h>
43#include <atnf/PKSIO/PKSSDwriter.h>
44#include <atnf/PKSIO/SrcType.h>
45
46#include <tables/Tables/Table.h>
47#include <tables/Tables/TableIter.h>
48#include <tables/Tables/TableRow.h>
49#include <tables/Tables/ArrayColumn.h>
50
51#include "STFITSImageWriter.h"
52#include "STAsciiWriter.h"
53#include "STHeader.h"
54#include "STMath.h"
55
56
57#include "STWriter.h"
58
59using namespace casa;
60namespace asap {
61
62STWriter::STWriter(const std::string &format)
63{
64 format_ = format;
65 String t(format_);
66 t.upcase();
67 if (t == "MS2") {
68 writer_ = new PKSMS2writer();
69 } else if (t == "SDFITS") {
70 writer_ = new PKSSDwriter();
71 } else if (t == "ASCII" || t == "FITS" || t == "CLASS") {
72 writer_ = 0;
73 } else {
74 throw (AipsError("Unrecognized export format"));
75 }
76}
77
78STWriter::~STWriter()
79{
80 if (writer_) {
81 delete writer_;
82 }
83}
84
85Int STWriter::setFormat(const std::string &format)
86{
87 if (format != format_) {
88 if (writer_) delete writer_;
89 }
90
91 format_ = format;
92 String t(format_);
93 t.upcase();
94 if (t== "MS2") {
95 writer_ = new PKSMS2writer();
96 } else if (t== "SDFITS") {
97 writer_ = new PKSSDwriter();
98 } else if (t == "ASCII" || t == "FITS" || t == "CLASS") {
99 writer_ = 0;
100 } else {
101 throw (AipsError("Unrecognized Format"));
102 }
103 return 0;
104}
105
106Int STWriter::write(const CountedPtr<Scantable> in,
107 const std::string &filename)
108{
109 // If we write out foreign formats we have to convert the frequency system
110 // into the output frame, as we do everything related to SPectarlCoordinates
111 // in asap on-the-fly.
112
113 CountedPtr<Scantable> inst = in;
114 if (in->frequencies().getFrame(true) != in->frequencies().getFrame(false)) {
115 STMath stm(false);
116 inst = stm.frequencyAlign(in);
117 }
118
119 if (format_=="ASCII") {
120 STAsciiWriter iw;
121 // ASCII calls SpectralCoordinate::toWorld so no freqAlign use 'in'
122 if (iw.write(*in, filename)) {
123 return 0;
124 } else {
125 return 1;
126 }
127 } else if ( format_ == "FITS" || format_ == "CLASS") {
128 STFITSImageWriter iw;
129 if (format_ == "CLASS") {
130 iw.setClass(True);
131 }
132 if (iw.write(*inst, filename)) {
133 return 0;
134 }
135 }
136
137 // MS or SDFITS
138
139 // Extract the header from the table.
140 // this is a little different from what I have done
141 // before. Need to check with the Offline User Test data
142 STHeader hdr = inst->getHeader();
143 //const Int nPol = hdr.npol;
144 //const Int nChan = hdr.nchan;
145 std::vector<uint> ifs = inst->getIFNos();
146 int nIF = inst->nif();//ifs.size();
147 Vector<uInt> nPol(nIF),nChan(nIF);
148 Vector<Bool> havexpol(nIF);
149 String fluxUnit = hdr.fluxunit;
150 fluxUnit.upcase();
151 nPol = 0;nChan = 0; havexpol = False;
152 for (uint i=0;i<ifs.size();++i) {
153 nPol(ifs[i]) = inst->npol();
154 nChan(ifs[i]) = inst->nchan(ifs[i]);
155 havexpol(ifs[i]) = nPol(ifs[i]) > 2;
156 }
157// Vector<String> obstypes(2);
158// obstypes(0) = "TR";//on
159// obstypes(1) = "RF TR";//off
160 const Table table = inst->table();
161
162
163 // Create the output file and write static data.
164 Int status;
165 status = writer_->create(String(filename), hdr.observer, hdr.project,
166 hdr.antennaname, hdr.antennaposition,
167 hdr.obstype, hdr.fluxunit,
168 hdr.equinox, hdr.freqref,
169 nChan, nPol, havexpol, False);
170 if ( status ) {
171 throw(AipsError("Failed to create output file"));
172 }
173
174 Int count = 0;
175 PKSrecord pksrec;
176 pksrec.scanNo = 1;
177 // use spearate iterators to ensure renumbering of all numbers
178 TableIterator scanit(table, "SCANNO");
179 while (!scanit.pastEnd() ) {
180 Table stable = scanit.table();
181 TableIterator beamit(stable, "BEAMNO");
182 pksrec.beamNo = 1;
183 while (!beamit.pastEnd() ) {
184 Table btable = beamit.table();
185 //MDirection::ScalarColumn dirCol(btable, "DIRECTION");
186 //pksrec.direction = dirCol(0).getAngle("rad").getValue();
187 TableIterator cycit(btable, "CYCLENO");
188 ROArrayColumn<Double> srateCol(btable, "SCANRATE");
189 Vector<Double> sratedbl;
190 srateCol.get(0, sratedbl);
191 Vector<Float> srateflt(sratedbl.nelements());
192 convertArray(srateflt, sratedbl);
193 //pksrec.scanRate = srateflt;
194 pksrec.scanRate = sratedbl;
195 ROArrayColumn<Double> spmCol(btable, "SRCPROPERMOTION");
196 spmCol.get(0, pksrec.srcPM);
197 ROArrayColumn <Double> sdirCol(btable, "SRCDIRECTION");
198 sdirCol.get(0, pksrec.srcDir);
199 ROScalarColumn<Double> svelCol(btable, "SRCVELOCITY");
200 svelCol.get(0, pksrec.srcVel);
201 ROScalarColumn<uInt> bCol(btable, "BEAMNO");
202 pksrec.beamNo = bCol(0)+1;
203 pksrec.cycleNo = 1;
204 while (!cycit.pastEnd() ) {
205 Table ctable = cycit.table();
206 TableIterator ifit(ctable, "IFNO", TableIterator::Ascending, TableIterator::HeapSort);
207 MDirection::ScalarColumn dirCol(ctable, "DIRECTION");
208 pksrec.direction = dirCol(0).getAngle("rad").getValue();
209 pksrec.IFno = 1;
210 while (!ifit.pastEnd() ) {
211 Table itable = ifit.table();
212 TableRow row(itable);
213 // use the first row to fill in all the "metadata"
214 const TableRecord& rec = row.get(0);
215 ROArrayColumn<Float> specCol(itable, "SPECTRA");
216 pksrec.IFno = rec.asuInt("IFNO")+1;
217 uInt nchan = specCol(0).nelements();
218 Double crval,crpix;
219 //Vector<Double> restfreq;
220 Float tmp0,tmp1,tmp2,tmp3,tmp4;
221 String tcalt;
222 Vector<String> stmp0, stmp1;
223 inst->frequencies().getEntry(crpix,crval, pksrec.freqInc,
224 rec.asuInt("FREQ_ID"));
225 inst->focus().getEntry(pksrec.parAngle, pksrec.focusAxi, pksrec.focusTan,
226 pksrec.focusRot, tmp0,tmp1,tmp2,tmp3,tmp4,
227 rec.asuInt("FOCUS_ID"));
228 inst->molecules().getEntry(pksrec.restFreq,stmp0,stmp1,
229 rec.asuInt("MOLECULE_ID"));
230 inst->tcal().getEntry(pksrec.tcalTime, pksrec.tcal,
231 rec.asuInt("TCAL_ID"));
232 inst->weather().getEntry(pksrec.temperature, pksrec.pressure,
233 pksrec.humidity, pksrec.windSpeed,
234 pksrec.windAz, rec.asuInt("WEATHER_ID"));
235 Double pixel = Double(nchan/2);
236 pksrec.refFreq = (pixel-crpix)*pksrec.freqInc + crval;
237 // ok, now we have nrows for the n polarizations in this table
238 polConversion(pksrec.spectra, pksrec.flagged, pksrec.xPol, itable);
239 pksrec.tsys = tsysFromTable(itable);
240 // dummy data
241 uInt npol = pksrec.spectra.ncolumn();
242
243 pksrec.mjd = rec.asDouble("TIME");
244 pksrec.interval = rec.asDouble("INTERVAL");
245 pksrec.fieldName = rec.asString("FIELDNAME");
246 pksrec.srcName = rec.asString("SRCNAME");
247 //pksrec.obsType = obstypes[rec.asInt("SRCTYPE")];
248 pksrec.obsType = getObsTypes( rec.asInt("SRCTYPE") ) ;
249 pksrec.bandwidth = nchan * abs(pksrec.freqInc);
250 pksrec.azimuth = rec.asFloat("AZIMUTH");
251 pksrec.elevation = rec.asFloat("ELEVATION");
252 pksrec.refBeam = rec.asInt("REFBEAMNO") + 1;
253 pksrec.sigma.resize(npol);
254 pksrec.sigma = 0.0f;
255 pksrec.calFctr.resize(npol);
256 pksrec.calFctr = 0.0f;
257 pksrec.baseLin.resize(npol,2);
258 pksrec.baseLin = 0.0f;
259 pksrec.baseSub.resize(npol,9);
260 pksrec.baseSub = 0.0f;
261 pksrec.xCalFctr = 0.0;
262 pksrec.flagrow = rec.asuInt("FLAGROW");
263
264 status = writer_->write(pksrec);
265 if ( status ) {
266 writer_->close();
267 throw(AipsError("STWriter: Failed to export Scantable."));
268 }
269 ++count;
270 //++pksrec.IFno;
271 ++ifit;
272 }
273 ++pksrec.cycleNo;
274 ++cycit;
275 }
276 //++pksrec.beamNo;
277 ++beamit;
278 }
279 ++pksrec.scanNo;
280 ++scanit;
281 }
282 ostringstream oss;
283 oss << "STWriter: wrote " << count << " rows to " << filename;
284 pushLog(String(oss));
285 writer_->close();
286 //if MS2 delete POINTING table exists and copy the one in the keyword
287 if ( format_ == "MS2" ) {
288 replacePtTab(table, filename);
289 }
290 return 0;
291}
292
293Vector<Float> STWriter::tsysFromTable(const Table& tab)
294{
295 ROArrayColumn<Float> tsysCol(tab, "TSYS");
296 Vector<Float> out(tab.nrow());
297 Vector<Float> tmp;
298 for (uInt i=0; i<tab.nrow(); ++i) {
299 tmp.resize();
300 tmp = tsysCol(i);
301 out[i] = tmp[0];
302 }
303 return out;
304}
305
306void STWriter::polConversion( Matrix< Float >& specs, Matrix< uChar >& flags,
307 Vector< Complex > & xpol, const Table & tab )
308{
309 String poltype = tab.keywordSet().asString("POLTYPE");
310// Full stokes is not supported. Just allow stokes I
311 if ( poltype == "stokes" && tab.nrow() != 1) {
312 String msg = "poltype = " + poltype + " not yet supported in output.";
313 throw(AipsError(msg));
314 }
315 ROArrayColumn<Float> specCol(tab, "SPECTRA");
316 ROArrayColumn<uChar> flagCol(tab, "FLAGTRA");
317 uInt nchan = specCol(0).nelements();
318 uInt ncol = (tab.nrow()==1 ? 1: 2 );
319 specs.resize(nchan, ncol);
320 flags.resize(nchan, ncol);
321 // the linears
322 for (uInt i=0; i<ncol; ++i) {
323 specs.column(i) = specCol(i);
324 flags.column(i) = flagCol(i);
325 }
326 // now the complex if exists
327 Bool hasxpol = False;
328 xpol.resize();
329 if ( tab.nrow() == 4 ) {
330 hasxpol = True;
331 xpol.resize(nchan);
332 Vector<Float> reals, imags;
333 reals = specCol(2); imags = specCol(3);
334 for (uInt k=0; k < nchan; ++k) {
335 xpol[k] = Complex(reals[k], imags[k]);
336 }
337 }
338}
339
340// For writing MS data, if there is the reference to
341// original pointing table it replace it by it.
342void STWriter::replacePtTab (const Table& tab, const std::string& fname)
343{
344 String oldPtTabName = fname;
345 oldPtTabName.append("/POINTING");
346 if ( tab.keywordSet().isDefined("POINTING") ) {
347 String PointingTab = tab.keywordSet().asString("POINTING");
348 if ( Table::isReadable(PointingTab) ) {
349 Table newPtTab(PointingTab, Table::Old);
350 newPtTab.copy(oldPtTabName, Table::New);
351 ostringstream oss;
352 oss << "STWriter: copied " <<PointingTab << " to " << fname;
353 pushLog(String(oss));
354 }
355 }
356}
357
358// get obsType string from SRCTYPE value
359String STWriter::getObsTypes( Int srctype )
360{
361 String obsType ;
362 switch( srctype ) {
363 case Int(SrcType::PSON):
364 obsType = "PSON" ;
365 break ;
366 case Int(SrcType::PSOFF):
367 obsType = "PSOFF" ;
368 break ;
369 case Int(SrcType::NOD):
370 obsType = "NOD" ;
371 break ;
372 case Int(SrcType::FSON):
373 obsType = "FSON" ;
374 break ;
375 case Int(SrcType::FSOFF):
376 obsType = "FSOFF" ;
377 break ;
378 case Int(SrcType::SKY):
379 obsType = "SKY" ;
380 break ;
381 case Int(SrcType::HOT):
382 obsType = "HOT" ;
383 break ;
384 case Int(SrcType::WARM):
385 obsType = "WARM" ;
386 break ;
387 case Int(SrcType::COLD):
388 obsType = "COLD" ;
389 break ;
390 case Int(SrcType::PONCAL):
391 obsType = "PSON:CALON" ;
392 break ;
393 case Int(SrcType::POFFCAL):
394 obsType = "PSOFF:CALON" ;
395 break ;
396 case Int(SrcType::NODCAL):
397 obsType = "NOD:CALON" ;
398 break ;
399 case Int(SrcType::FONCAL):
400 obsType = "FSON:CALON" ;
401 break ;
402 case Int(SrcType::FOFFCAL):
403 obsType = "FSOFF:CALOFF" ;
404 break ;
405 case Int(SrcType::FSLO):
406 obsType = "FSLO" ;
407 break ;
408 case Int(SrcType::FLOOFF):
409 obsType = "FS:LOWER:OFF" ;
410 break ;
411 case Int(SrcType::FLOSKY):
412 obsType = "FS:LOWER:SKY" ;
413 break ;
414 case Int(SrcType::FLOHOT):
415 obsType = "FS:LOWER:HOT" ;
416 break ;
417 case Int(SrcType::FLOWARM):
418 obsType = "FS:LOWER:WARM" ;
419 break ;
420 case Int(SrcType::FLOCOLD):
421 obsType = "FS:LOWER:COLD" ;
422 break ;
423 case Int(SrcType::FSHI):
424 obsType = "FSHI" ;
425 break ;
426 case Int(SrcType::FHIOFF):
427 obsType = "FS:HIGHER:OFF" ;
428 break ;
429 case Int(SrcType::FHISKY):
430 obsType = "FS:HIGHER:SKY" ;
431 break ;
432 case Int(SrcType::FHIHOT):
433 obsType = "FS:HIGHER:HOT" ;
434 break ;
435 case Int(SrcType::FHIWARM):
436 obsType = "FS:HIGHER:WARM" ;
437 break ;
438 case Int(SrcType::FHICOLD):
439 obsType = "FS:HIGHER:COLD" ;
440 break ;
441 default:
442 obsType = "NOTYPE" ;
443 }
444
445 return obsType ;
446}
447
448}
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