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 2577 2012-06-27 02:58:28Z TakeshiNakazato $ |
---|
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 | #ifndef NOPKSMS |
---|
43 | #include <atnf/PKSIO/PKSMS2writer.h> |
---|
44 | #endif |
---|
45 | #include <atnf/PKSIO/PKSSDwriter.h> |
---|
46 | #include <atnf/PKSIO/SrcType.h> |
---|
47 | |
---|
48 | #include <tables/Tables/Table.h> |
---|
49 | #include <tables/Tables/TableIter.h> |
---|
50 | #include <tables/Tables/TableRow.h> |
---|
51 | #include <tables/Tables/ArrayColumn.h> |
---|
52 | |
---|
53 | #include "STFITSImageWriter.h" |
---|
54 | #include "STAsciiWriter.h" |
---|
55 | #include "STHeader.h" |
---|
56 | #include "STMath.h" |
---|
57 | |
---|
58 | |
---|
59 | #include "STWriter.h" |
---|
60 | |
---|
61 | using namespace casa; |
---|
62 | namespace asap { |
---|
63 | |
---|
64 | STWriter::STWriter(const std::string &format) |
---|
65 | { |
---|
66 | format_ = format; |
---|
67 | String t(format_); |
---|
68 | t.upcase(); |
---|
69 | if (t == "MS2") { |
---|
70 | #ifdef NOPKSMS |
---|
71 | throw (AipsError("MS2 OUTPUT FORMAT IS NO LONGER SUPPORTED")); |
---|
72 | #else |
---|
73 | writer_ = new PKSMS2writer(); |
---|
74 | #endif |
---|
75 | } else if (t == "SDFITS") { |
---|
76 | writer_ = new PKSSDwriter(); |
---|
77 | } else if (t == "ASCII" || t == "FITS" || t == "CLASS") { |
---|
78 | writer_ = 0; |
---|
79 | } else { |
---|
80 | throw (AipsError("Unrecognized export format")); |
---|
81 | } |
---|
82 | } |
---|
83 | |
---|
84 | STWriter::~STWriter() |
---|
85 | { |
---|
86 | if (writer_) { |
---|
87 | delete writer_; |
---|
88 | } |
---|
89 | } |
---|
90 | |
---|
91 | Int STWriter::setFormat(const std::string &format) |
---|
92 | { |
---|
93 | if (format != format_) { |
---|
94 | if (writer_) delete writer_; |
---|
95 | } |
---|
96 | |
---|
97 | format_ = format; |
---|
98 | String t(format_); |
---|
99 | t.upcase(); |
---|
100 | if (t== "MS2") { |
---|
101 | #ifdef NOPKSMS |
---|
102 | throw (AipsError("MS2 OUTPUT FORMAT IS NO LONGER SUPPORTED")); |
---|
103 | #else |
---|
104 | writer_ = new PKSMS2writer(); |
---|
105 | #endif |
---|
106 | } else if (t== "SDFITS") { |
---|
107 | writer_ = new PKSSDwriter(); |
---|
108 | } else if (t == "ASCII" || t == "FITS" || t == "CLASS") { |
---|
109 | writer_ = 0; |
---|
110 | } else { |
---|
111 | throw (AipsError("Unrecognized Format")); |
---|
112 | } |
---|
113 | return 0; |
---|
114 | } |
---|
115 | |
---|
116 | Int STWriter::write(const CountedPtr<Scantable> in, |
---|
117 | const std::string &filename) |
---|
118 | { |
---|
119 | // If we write out foreign formats we have to convert the frequency system |
---|
120 | // into the output frame, as we do everything related to SPectarlCoordinates |
---|
121 | // in asap on-the-fly. |
---|
122 | |
---|
123 | CountedPtr<Scantable> inst = in; |
---|
124 | if (in->frequencies().getFrame(true) != in->frequencies().getFrame(false)) { |
---|
125 | STMath stm(false); |
---|
126 | inst = stm.frequencyAlign(in); |
---|
127 | } |
---|
128 | |
---|
129 | if (format_=="ASCII") { |
---|
130 | STAsciiWriter iw; |
---|
131 | // ASCII calls SpectralCoordinate::toWorld so no freqAlign use 'in' |
---|
132 | if (iw.write(*in, filename)) { |
---|
133 | return 0; |
---|
134 | } else { |
---|
135 | return 1; |
---|
136 | } |
---|
137 | } else if ( format_ == "FITS" || format_ == "CLASS") { |
---|
138 | STFITSImageWriter iw; |
---|
139 | if (format_ == "CLASS") { |
---|
140 | iw.setClass(True); |
---|
141 | } |
---|
142 | if (iw.write(*inst, filename)) { |
---|
143 | return 0; |
---|
144 | } |
---|
145 | } |
---|
146 | |
---|
147 | // MS or SDFITS |
---|
148 | |
---|
149 | // Extract the header from the table. |
---|
150 | // this is a little different from what I have done |
---|
151 | // before. Need to check with the Offline User Test data |
---|
152 | STHeader hdr = inst->getHeader(); |
---|
153 | //const Int nPol = hdr.npol; |
---|
154 | //const Int nChan = hdr.nchan; |
---|
155 | std::vector<uint> ifs = inst->getIFNos(); |
---|
156 | int nIF = inst->nif();//ifs.size(); |
---|
157 | Vector<uInt> nPol(nIF),nChan(nIF); |
---|
158 | Vector<Bool> havexpol(nIF); |
---|
159 | String fluxUnit = hdr.fluxunit; |
---|
160 | fluxUnit.upcase(); |
---|
161 | nPol = 0;nChan = 0; havexpol = False; |
---|
162 | for (uint i=0;i<ifs.size();++i) { |
---|
163 | nPol(ifs[i]) = inst->npol(); |
---|
164 | nChan(ifs[i]) = inst->nchan(ifs[i]); |
---|
165 | havexpol(ifs[i]) = nPol(ifs[i]) > 2; |
---|
166 | } |
---|
167 | // Vector<String> obstypes(2); |
---|
168 | // obstypes(0) = "TR";//on |
---|
169 | // obstypes(1) = "RF TR";//off |
---|
170 | const Table table = inst->table(); |
---|
171 | |
---|
172 | |
---|
173 | // Create the output file and write static data. |
---|
174 | Int status; |
---|
175 | // status = writer_->create(String(filename), hdr.observer, hdr.project, |
---|
176 | // hdr.antennaname, hdr.antennaposition, |
---|
177 | // hdr.obstype, hdr.fluxunit, |
---|
178 | // hdr.equinox, hdr.freqref, |
---|
179 | // nChan, nPol, havexpol, False); |
---|
180 | status = writer_->create(String(filename), hdr.observer, hdr.project, |
---|
181 | inst->getAntennaName(), hdr.antennaposition, |
---|
182 | hdr.obstype, hdr.fluxunit, |
---|
183 | hdr.equinox, hdr.freqref, |
---|
184 | nChan, nPol, havexpol, False); |
---|
185 | if ( status ) { |
---|
186 | throw(AipsError("Failed to create output file")); |
---|
187 | } |
---|
188 | |
---|
189 | Int count = 0; |
---|
190 | PKSrecord pksrec; |
---|
191 | pksrec.scanNo = 1; |
---|
192 | // use spearate iterators to ensure renumbering of all numbers |
---|
193 | TableIterator scanit(table, "SCANNO"); |
---|
194 | while (!scanit.pastEnd() ) { |
---|
195 | Table stable = scanit.table(); |
---|
196 | TableIterator beamit(stable, "BEAMNO"); |
---|
197 | pksrec.beamNo = 1; |
---|
198 | while (!beamit.pastEnd() ) { |
---|
199 | Table btable = beamit.table(); |
---|
200 | //MDirection::ScalarColumn dirCol(btable, "DIRECTION"); |
---|
201 | //pksrec.direction = dirCol(0).getAngle("rad").getValue(); |
---|
202 | TableIterator cycit(btable, "CYCLENO"); |
---|
203 | ROArrayColumn<Double> srateCol(btable, "SCANRATE"); |
---|
204 | Vector<Double> sratedbl; |
---|
205 | srateCol.get(0, sratedbl); |
---|
206 | Vector<Float> srateflt(sratedbl.nelements()); |
---|
207 | convertArray(srateflt, sratedbl); |
---|
208 | //pksrec.scanRate = srateflt; |
---|
209 | pksrec.scanRate = sratedbl; |
---|
210 | ROArrayColumn<Double> spmCol(btable, "SRCPROPERMOTION"); |
---|
211 | spmCol.get(0, pksrec.srcPM); |
---|
212 | ROArrayColumn <Double> sdirCol(btable, "SRCDIRECTION"); |
---|
213 | sdirCol.get(0, pksrec.srcDir); |
---|
214 | ROScalarColumn<Double> svelCol(btable, "SRCVELOCITY"); |
---|
215 | svelCol.get(0, pksrec.srcVel); |
---|
216 | ROScalarColumn<uInt> bCol(btable, "BEAMNO"); |
---|
217 | pksrec.beamNo = bCol(0)+1; |
---|
218 | pksrec.cycleNo = 1; |
---|
219 | while (!cycit.pastEnd() ) { |
---|
220 | Table ctable = cycit.table(); |
---|
221 | TableIterator typeit( ctable, "SRCTYPE" ) ; |
---|
222 | while(!typeit.pastEnd() ) { |
---|
223 | Table ttable = typeit.table() ; |
---|
224 | TableIterator ifit(ttable, "IFNO", TableIterator::Ascending, TableIterator::HeapSort); |
---|
225 | MDirection::ScalarColumn dirCol(ctable, "DIRECTION"); |
---|
226 | pksrec.direction = dirCol(0).getAngle("rad").getValue(); |
---|
227 | pksrec.IFno = 1; |
---|
228 | while (!ifit.pastEnd() ) { |
---|
229 | Table itable = ifit.table(); |
---|
230 | TableRow row(itable); |
---|
231 | // use the first row to fill in all the "metadata" |
---|
232 | const TableRecord& rec = row.get(0); |
---|
233 | ROArrayColumn<Float> specCol(itable, "SPECTRA"); |
---|
234 | pksrec.IFno = rec.asuInt("IFNO")+1; |
---|
235 | uInt nchan = specCol(0).nelements(); |
---|
236 | Double crval,crpix; |
---|
237 | //Vector<Double> restfreq; |
---|
238 | Float tmp0,tmp1,tmp2,tmp3,tmp4; |
---|
239 | String tcalt; |
---|
240 | Vector<String> stmp0, stmp1; |
---|
241 | inst->frequencies().getEntry(crpix,crval, pksrec.freqInc, |
---|
242 | rec.asuInt("FREQ_ID")); |
---|
243 | inst->focus().getEntry(pksrec.parAngle, pksrec.focusAxi, pksrec.focusTan, |
---|
244 | pksrec.focusRot, tmp0,tmp1,tmp2,tmp3,tmp4, |
---|
245 | rec.asuInt("FOCUS_ID")); |
---|
246 | inst->molecules().getEntry(pksrec.restFreq,stmp0,stmp1, |
---|
247 | rec.asuInt("MOLECULE_ID")); |
---|
248 | // inst->tcal().getEntry(pksrec.tcalTime, pksrec.tcal, |
---|
249 | // rec.asuInt("TCAL_ID")); |
---|
250 | inst->weather().getEntry(pksrec.temperature, pksrec.pressure, |
---|
251 | pksrec.humidity, pksrec.windSpeed, |
---|
252 | pksrec.windAz, rec.asuInt("WEATHER_ID")); |
---|
253 | Double pixel = Double(nchan/2); |
---|
254 | pksrec.refFreq = (pixel-crpix)*pksrec.freqInc + crval; |
---|
255 | // ok, now we have nrows for the n polarizations in this table |
---|
256 | polConversion(pksrec.spectra, pksrec.flagged, pksrec.xPol, itable); |
---|
257 | pksrec.tsys = tsysFromTable(itable); |
---|
258 | // dummy data |
---|
259 | uInt npol = pksrec.spectra.ncolumn(); |
---|
260 | |
---|
261 | // TCAL |
---|
262 | inst->tcal().getEntry( pksrec.tcalTime, pksrec.tcal, |
---|
263 | rec.asuInt("TCAL_ID") ) ; |
---|
264 | if ( pksrec.tcal.nelements() == 1 ) { |
---|
265 | ROScalarColumn<uInt> uintCol( itable, "TCAL_ID" ) ; |
---|
266 | Vector<uInt> tcalids = uintCol.getColumn() ; |
---|
267 | pksrec.tcal.resize( npol ) ; |
---|
268 | Vector<Float> dummyA ; |
---|
269 | String dummyS ; |
---|
270 | for ( uInt ipol = 0 ; ipol < npol ; ipol++ ) { |
---|
271 | inst->tcal().getEntry( dummyS, dummyA, tcalids[ipol] ) ; |
---|
272 | pksrec.tcal[ipol] = dummyA[0] ; |
---|
273 | } |
---|
274 | } |
---|
275 | else if ( pksrec.tcal.nelements() == nchan ) { |
---|
276 | ROScalarColumn<uInt> uintCol( itable, "TCAL_ID" ) ; |
---|
277 | Vector<uInt> tcalids = uintCol.getColumn() ; |
---|
278 | pksrec.tcal.resize( npol ) ; |
---|
279 | Vector<Float> dummyA ; |
---|
280 | String dummyS ; |
---|
281 | for ( uInt ipol = 0 ; ipol < npol ; ipol++ ) { |
---|
282 | inst->tcal().getEntry( dummyS, dummyA, tcalids[ipol] ) ; |
---|
283 | pksrec.tcal[ipol] = mean( dummyA ) ; |
---|
284 | } |
---|
285 | } |
---|
286 | //LogIO os ; |
---|
287 | //os << "npol = " << npol << " pksrec.tcal = " << pksrec.tcal << LogIO::POST ; |
---|
288 | |
---|
289 | pksrec.mjd = rec.asDouble("TIME"); |
---|
290 | pksrec.interval = rec.asDouble("INTERVAL"); |
---|
291 | pksrec.fieldName = rec.asString("FIELDNAME"); |
---|
292 | pksrec.srcName = rec.asString("SRCNAME"); |
---|
293 | //pksrec.obsType = obstypes[rec.asInt("SRCTYPE")]; |
---|
294 | pksrec.obsType = getObsTypes( rec.asInt("SRCTYPE") ) ; |
---|
295 | pksrec.bandwidth = nchan * abs(pksrec.freqInc); |
---|
296 | pksrec.azimuth = rec.asFloat("AZIMUTH"); |
---|
297 | pksrec.elevation = rec.asFloat("ELEVATION"); |
---|
298 | pksrec.refBeam = rec.asInt("REFBEAMNO") + 1; |
---|
299 | pksrec.sigma.resize(npol); |
---|
300 | pksrec.sigma = 0.0f; |
---|
301 | pksrec.calFctr.resize(npol); |
---|
302 | pksrec.calFctr = 0.0f; |
---|
303 | pksrec.baseLin.resize(npol,2); |
---|
304 | pksrec.baseLin = 0.0f; |
---|
305 | pksrec.baseSub.resize(npol,9); |
---|
306 | pksrec.baseSub = 0.0f; |
---|
307 | pksrec.xCalFctr = 0.0; |
---|
308 | pksrec.flagrow = rec.asuInt("FLAGROW"); |
---|
309 | |
---|
310 | status = writer_->write(pksrec); |
---|
311 | if ( status ) { |
---|
312 | writer_->close(); |
---|
313 | throw(AipsError("STWriter: Failed to export Scantable.")); |
---|
314 | } |
---|
315 | ++count; |
---|
316 | //++pksrec.IFno; |
---|
317 | ++ifit; |
---|
318 | } |
---|
319 | ++typeit ; |
---|
320 | } |
---|
321 | ++pksrec.cycleNo; |
---|
322 | ++cycit; |
---|
323 | } |
---|
324 | //++pksrec.beamNo; |
---|
325 | ++beamit; |
---|
326 | } |
---|
327 | ++pksrec.scanNo; |
---|
328 | ++scanit; |
---|
329 | } |
---|
330 | ostringstream oss; |
---|
331 | oss << "STWriter: wrote " << count << " rows to " << filename; |
---|
332 | pushLog(String(oss)); |
---|
333 | |
---|
334 | writer_->close(); |
---|
335 | //if MS2 delete POINTING table exists and copy the one in the keyword |
---|
336 | if ( format_ == "MS2" ) { |
---|
337 | replacePtTab(table, filename); |
---|
338 | } |
---|
339 | return 0; |
---|
340 | } |
---|
341 | |
---|
342 | Vector<Float> STWriter::tsysFromTable(const Table& tab) |
---|
343 | { |
---|
344 | ROArrayColumn<Float> tsysCol(tab, "TSYS"); |
---|
345 | Vector<Float> out(tab.nrow()); |
---|
346 | Vector<Float> tmp; |
---|
347 | for (uInt i=0; i<tab.nrow(); ++i) { |
---|
348 | tmp.resize(); |
---|
349 | tmp = tsysCol(i); |
---|
350 | out[i] = tmp[0]; |
---|
351 | } |
---|
352 | return out; |
---|
353 | } |
---|
354 | |
---|
355 | void STWriter::polConversion( Matrix< Float >& specs, Matrix< uChar >& flags, |
---|
356 | Vector< Complex > & xpol, const Table & tab ) |
---|
357 | { |
---|
358 | String poltype = tab.keywordSet().asString("POLTYPE"); |
---|
359 | // Full stokes is not supported. Just allow stokes I |
---|
360 | if ( poltype == "stokes" && tab.nrow() != 1) { |
---|
361 | String msg = "poltype = " + poltype + " not yet supported in output."; |
---|
362 | throw(AipsError(msg)); |
---|
363 | } |
---|
364 | ROArrayColumn<Float> specCol(tab, "SPECTRA"); |
---|
365 | ROArrayColumn<uChar> flagCol(tab, "FLAGTRA"); |
---|
366 | uInt nchan = specCol(0).nelements(); |
---|
367 | uInt ncol = (tab.nrow()==1 ? 1: 2 ); |
---|
368 | specs.resize(nchan, ncol); |
---|
369 | flags.resize(nchan, ncol); |
---|
370 | // the linears |
---|
371 | for (uInt i=0; i<ncol; ++i) { |
---|
372 | specs.column(i) = specCol(i); |
---|
373 | flags.column(i) = flagCol(i); |
---|
374 | } |
---|
375 | // now the complex if exists |
---|
376 | Bool hasxpol = False; |
---|
377 | xpol.resize(); |
---|
378 | if ( tab.nrow() == 4 ) { |
---|
379 | hasxpol = True; |
---|
380 | xpol.resize(nchan); |
---|
381 | Vector<Float> reals, imags; |
---|
382 | reals = specCol(2); imags = specCol(3); |
---|
383 | for (uInt k=0; k < nchan; ++k) { |
---|
384 | xpol[k] = Complex(reals[k], imags[k]); |
---|
385 | } |
---|
386 | } |
---|
387 | } |
---|
388 | |
---|
389 | // For writing MS data, if there is the reference to |
---|
390 | // original pointing table it replace it by it. |
---|
391 | void STWriter::replacePtTab (const Table& tab, const std::string& fname) |
---|
392 | { |
---|
393 | String oldPtTabName = fname; |
---|
394 | oldPtTabName.append("/POINTING"); |
---|
395 | if ( tab.keywordSet().isDefined("POINTING") ) { |
---|
396 | String PointingTab = tab.keywordSet().asString("POINTING"); |
---|
397 | if ( Table::isReadable(PointingTab) ) { |
---|
398 | Table newPtTab(PointingTab, Table::Old); |
---|
399 | newPtTab.copy(oldPtTabName, Table::New); |
---|
400 | ostringstream oss; |
---|
401 | oss << "STWriter: copied " <<PointingTab << " to " << fname; |
---|
402 | pushLog(String(oss)); |
---|
403 | } |
---|
404 | } |
---|
405 | } |
---|
406 | |
---|
407 | // get obsType string from SRCTYPE value |
---|
408 | String STWriter::getObsTypes( Int srctype ) |
---|
409 | { |
---|
410 | return SrcType::getName(srctype) ; |
---|
411 | } |
---|
412 | |
---|
413 | } |
---|