source: trunk/src/SDMath.cc@ 339

Last change on this file since 339 was 330, checked in by kil064, 20 years ago

reqork frequency alignment to

  • only make the required numnber of aligners
  • write out a correct frequency table with new FreqIDs
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 48.7 KB
Line 
1//#---------------------------------------------------------------------------
2//# SDMath.cc: A collection of single dish mathematical operations
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:
30//#---------------------------------------------------------------------------
31#include <vector>
32
33#include <casa/aips.h>
34#include <casa/iostream.h>
35#include <casa/iomanip.h>
36#include <casa/BasicSL/String.h>
37#include <casa/Arrays/IPosition.h>
38#include <casa/Arrays/Array.h>
39#include <casa/Arrays/ArrayIter.h>
40#include <casa/Arrays/VectorIter.h>
41#include <casa/Arrays/ArrayMath.h>
42#include <casa/Arrays/ArrayLogical.h>
43#include <casa/Arrays/MaskedArray.h>
44#include <casa/Arrays/MaskArrMath.h>
45#include <casa/Arrays/MaskArrLogi.h>
46#include <casa/Arrays/Matrix.h>
47#include <casa/BasicMath/Math.h>
48#include <casa/Containers/Block.h>
49#include <casa/Exceptions.h>
50#include <casa/Quanta/Quantum.h>
51#include <casa/Quanta/Unit.h>
52#include <casa/Quanta/MVEpoch.h>
53#include <casa/Quanta/QC.h>
54#include <casa/Quanta/MVTime.h>
55#include <casa/Utilities/Assert.h>
56
57#include <coordinates/Coordinates/SpectralCoordinate.h>
58#include <coordinates/Coordinates/CoordinateSystem.h>
59#include <coordinates/Coordinates/CoordinateUtil.h>
60#include <coordinates/Coordinates/FrequencyAligner.h>
61
62#include <lattices/Lattices/LatticeUtilities.h>
63#include <lattices/Lattices/RebinLattice.h>
64
65#include <measures/Measures/MEpoch.h>
66#include <measures/Measures/MDirection.h>
67#include <measures/Measures/MPosition.h>
68
69#include <scimath/Mathematics/VectorKernel.h>
70#include <scimath/Mathematics/Convolver.h>
71#include <scimath/Mathematics/InterpolateArray1D.h>
72#include <scimath/Functionals/Polynomial.h>
73
74#include <tables/Tables/Table.h>
75#include <tables/Tables/ScalarColumn.h>
76#include <tables/Tables/ArrayColumn.h>
77#include <tables/Tables/ReadAsciiTable.h>
78
79#include "MathUtils.h"
80#include "SDDefs.h"
81#include "SDContainer.h"
82#include "SDMemTable.h"
83
84#include "SDMath.h"
85
86using namespace casa;
87using namespace asap;
88
89
90SDMath::SDMath()
91{;}
92
93SDMath::SDMath(const SDMath& other)
94{
95
96// No state
97
98}
99
100SDMath& SDMath::operator=(const SDMath& other)
101{
102 if (this != &other) {
103// No state
104 }
105 return *this;
106}
107
108SDMath::~SDMath()
109{;}
110
111
112
113SDMemTable* SDMath::frequencyAlignment (const SDMemTable& in, const String& refTime, const String& method) const
114{
115
116// Get frame info from Table
117
118 std::vector<std::string> info = in.getCoordInfo();
119
120// Parse frequency system
121
122 String systemStr(info[1]);
123 String baseSystemStr(info[3]);
124 if (baseSystemStr==systemStr) {
125 throw(AipsError("You have not set a frequency frame different from the initial - use function set_freqframe"));
126 }
127//
128 MFrequency::Types freqSystem;
129 MFrequency::getType(freqSystem, systemStr);
130
131// Do it
132
133 return frequencyAlign (in, freqSystem, refTime, method);
134}
135
136
137
138CountedPtr<SDMemTable> SDMath::average(const Block<CountedPtr<SDMemTable> >& in,
139 const Vector<Bool>& mask, Bool scanAv,
140 const String& weightStr, Bool alignFreq) const
141//
142// Weighted averaging of spectra from one or more Tables.
143//
144{
145
146// Convert weight type
147
148 WeightType wtType = NONE;
149 convertWeightString(wtType, weightStr);
150
151// Create output Table by cloning from the first table
152
153 SDMemTable* pTabOut = new SDMemTable(*in[0],True);
154
155// Setup
156
157 IPosition shp = in[0]->rowAsMaskedArray(0).shape(); // Must not change
158 Array<Float> arr(shp);
159 Array<Bool> barr(shp);
160 const Bool useMask = (mask.nelements() == shp(asap::ChanAxis));
161
162// Columns from Tables
163
164 ROArrayColumn<Float> tSysCol;
165 ROScalarColumn<Double> mjdCol;
166 ROScalarColumn<String> srcNameCol;
167 ROScalarColumn<Double> intCol;
168 ROArrayColumn<uInt> fqIDCol;
169
170// Create accumulation MaskedArray. We accumulate for each channel,if,pol,beam
171// Note that the mask of the accumulation array will ALWAYS remain ALL True.
172// The MA is only used so that when data which is masked Bad is added to it,
173// that data does not contribute.
174
175 Array<Float> zero(shp);
176 zero=0.0;
177 Array<Bool> good(shp);
178 good = True;
179 MaskedArray<Float> sum(zero,good);
180
181// Counter arrays
182
183 Array<Float> nPts(shp); // Number of points
184 nPts = 0.0;
185 Array<Float> nInc(shp); // Increment
186 nInc = 1.0;
187
188// Create accumulation Array for variance. We accumulate for
189// each if,pol,beam, but average over channel. So we need
190// a shape with one less axis dropping channels.
191
192 const uInt nAxesSub = shp.nelements() - 1;
193 IPosition shp2(nAxesSub);
194 for (uInt i=0,j=0; i<(nAxesSub+1); i++) {
195 if (i!=asap::ChanAxis) {
196 shp2(j) = shp(i);
197 j++;
198 }
199 }
200 Array<Float> sumSq(shp2);
201 sumSq = 0.0;
202 IPosition pos2(nAxesSub,0); // For indexing
203
204// Time-related accumulators
205
206 Double time;
207 Double timeSum = 0.0;
208 Double intSum = 0.0;
209 Double interval = 0.0;
210
211// To get the right shape for the Tsys accumulator we need to
212// access a column from the first table. The shape of this
213// array must not change
214
215 Array<Float> tSysSum;
216 {
217 const Table& tabIn = in[0]->table();
218 tSysCol.attach(tabIn,"TSYS");
219 tSysSum.resize(tSysCol.shape(0));
220 }
221 tSysSum =0.0;
222 Array<Float> tSys;
223
224// Scan and row tracking
225
226 Int oldScanID = 0;
227 Int outScanID = 0;
228 Int scanID = 0;
229 Int rowStart = 0;
230 Int nAccum = 0;
231 Int tableStart = 0;
232
233// Source and FreqID
234
235 String sourceName, oldSourceName, sourceNameStart;
236 Vector<uInt> freqID, freqIDStart, oldFreqID;
237
238// Loop over tables
239
240 Float fac = 1.0;
241 const uInt nTables = in.nelements();
242 for (uInt iTab=0; iTab<nTables; iTab++) {
243
244// Should check that the frequency tables don't change if doing FreqAlignment
245
246// Attach columns to Table
247
248 const Table& tabIn = in[iTab]->table();
249 tSysCol.attach(tabIn, "TSYS");
250 mjdCol.attach(tabIn, "TIME");
251 srcNameCol.attach(tabIn, "SRCNAME");
252 intCol.attach(tabIn, "INTERVAL");
253 fqIDCol.attach(tabIn, "FREQID");
254
255// Loop over rows in Table
256
257 const uInt nRows = in[iTab]->nRow();
258 for (uInt iRow=0; iRow<nRows; iRow++) {
259
260// Check conformance
261
262 IPosition shp2 = in[iTab]->rowAsMaskedArray(iRow).shape();
263 if (!shp.isEqual(shp2)) {
264 throw (AipsError("Shapes for all rows must be the same"));
265 }
266
267// If we are not doing scan averages, make checks for source and
268// frequency setup and warn if averaging across them
269
270// Get copy of Scan Container for this row
271
272 SDContainer sc = in[iTab]->getSDContainer(iRow);
273 scanID = sc.scanid;
274
275// Get quantities from columns
276
277 srcNameCol.getScalar(iRow, sourceName);
278 mjdCol.get(iRow, time);
279 tSysCol.get(iRow, tSys);
280 intCol.get(iRow, interval);
281 fqIDCol.get(iRow, freqID);
282
283// Initialize first source and freqID
284
285 if (iRow==0 && iTab==0) {
286 sourceNameStart = sourceName;
287 freqIDStart = freqID;
288 }
289
290// If we are doing scan averages, see if we are at the end of an
291// accumulation period (scan). We must check soutce names too,
292// since we might have two tables with one scan each but different
293// source names; we shouldn't average different sources together
294
295 if (scanAv && ( (scanID != oldScanID) ||
296 (iRow==0 && iTab>0 && sourceName!=oldSourceName))) {
297
298// Normalize data in 'sum' accumulation array according to weighting scheme
299
300 normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub);
301
302// Fill scan container. The source and freqID come from the
303// first row of the first table that went into this average (
304// should be the same for all rows in the scan average)
305
306 Float nR(nAccum);
307 fillSDC(sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID,
308 timeSum/nR, intSum, sourceNameStart, freqIDStart);
309
310// Write container out to Table
311
312 pTabOut->putSDContainer(sc);
313
314// Reset accumulators
315
316 sum = 0.0;
317 sumSq = 0.0;
318 nAccum = 0;
319//
320 tSysSum =0.0;
321 timeSum = 0.0;
322 intSum = 0.0;
323 nPts = 0.0;
324
325// Increment
326
327 rowStart = iRow; // First row for next accumulation
328 tableStart = iTab; // First table for next accumulation
329 sourceNameStart = sourceName; // First source name for next accumulation
330 freqIDStart = freqID; // First FreqID for next accumulation
331//
332 oldScanID = scanID;
333 outScanID += 1; // Scan ID for next accumulation period
334 }
335
336// Accumulate
337
338 accumulate(timeSum, intSum, nAccum, sum, sumSq, nPts, tSysSum,
339 tSys, nInc, mask, time, interval, in, iTab, iRow, asap::ChanAxis,
340 nAxesSub, useMask, wtType);
341//
342 oldSourceName = sourceName;
343 oldFreqID = freqID;
344 }
345 }
346
347// OK at this point we have accumulation data which is either
348// - accumulated from all tables into one row
349// or
350// - accumulated from the last scan average
351//
352// Normalize data in 'sum' accumulation array according to weighting scheme
353 normalize(sum, sumSq, nPts, wtType, asap::ChanAxis, nAxesSub);
354
355// Create and fill container. The container we clone will be from
356// the last Table and the first row that went into the current
357// accumulation. It probably doesn't matter that much really...
358
359 Float nR(nAccum);
360 SDContainer sc = in[tableStart]->getSDContainer(rowStart);
361 fillSDC(sc, sum.getMask(), sum.getArray(), tSysSum/nR, outScanID,
362 timeSum/nR, intSum, sourceNameStart, freqIDStart);
363 pTabOut->putSDContainer(sc);
364 pTabOut->resetCursor();
365//
366 return CountedPtr<SDMemTable>(pTabOut);
367}
368
369
370
371CountedPtr<SDMemTable> SDMath::binaryOperate (const CountedPtr<SDMemTable>& left,
372 const CountedPtr<SDMemTable>& right,
373 const String& op, Bool preserve,
374 Bool doTSys) const
375{
376
377// Check operator
378
379 String op2(op);
380 op2.upcase();
381 uInt what = 0;
382 if (op2=="ADD") {
383 what = 0;
384 } else if (op2=="SUB") {
385 what = 1;
386 } else if (op2=="MUL") {
387 what = 2;
388 } else if (op2=="DIV") {
389 what = 3;
390 } else if (op2=="QUOTIENT") {
391 what = 4;
392 doTSys = True;
393 } else {
394 throw( AipsError("Unrecognized operation"));
395 }
396
397// Check rows
398
399 const uInt nRowLeft = left->nRow();
400 const uInt nRowRight = right->nRow();
401 Bool ok = (nRowRight==1&&nRowLeft>0) ||
402 (nRowRight>=1&&nRowLeft==nRowRight);
403 if (!ok) {
404 throw (AipsError("The right Scan Table can have one row or the same number of rows as the left Scan Table"));
405 }
406
407// Input Tables
408
409 const Table& tLeft = left->table();
410 const Table& tRight = right->table();
411
412// TSys columns
413
414 ROArrayColumn<Float> tSysLeftCol, tSysRightCol;
415 if (doTSys) {
416 tSysLeftCol.attach(tLeft, "TSYS");
417 tSysRightCol.attach(tRight, "TSYS");
418 }
419
420// First row for right
421
422 Array<Float> tSysLeftArr, tSysRightArr;
423 if (doTSys) tSysRightCol.get(0, tSysRightArr);
424 MaskedArray<Float>* pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(0));
425 IPosition shpRight = pMRight->shape();
426
427// Output Table cloned from left
428
429 SDMemTable* pTabOut = new SDMemTable(*left, True);
430
431// Loop over rows
432
433 for (uInt i=0; i<nRowLeft; i++) {
434
435// Get data
436
437 MaskedArray<Float> mLeft(left->rowAsMaskedArray(i));
438 IPosition shpLeft = mLeft.shape();
439 if (doTSys) tSysLeftCol.get(i, tSysLeftArr);
440//
441 if (nRowRight>1) {
442 delete pMRight;
443 pMRight = new MaskedArray<Float>(right->rowAsMaskedArray(i));
444 shpRight = pMRight->shape();
445 if (doTSys) tSysRightCol.get(i, tSysRightArr);
446 }
447//
448 if (!shpRight.isEqual(shpLeft)) {
449 throw(AipsError("left and right scan tables are not conformant"));
450 }
451 if (doTSys) {
452 if (!tSysRightArr.shape().isEqual(tSysRightArr.shape())) {
453 throw(AipsError("left and right Tsys data are not conformant"));
454 }
455 if (!shpRight.isEqual(tSysRightArr.shape())) {
456 throw(AipsError("left and right scan tables are not conformant"));
457 }
458 }
459
460// Make container
461
462 SDContainer sc = left->getSDContainer(i);
463
464// Operate on data and TSys
465
466 if (what==0) {
467 MaskedArray<Float> tmp = mLeft + *pMRight;
468 putDataInSDC(sc, tmp.getArray(), tmp.getMask());
469 if (doTSys) sc.putTsys(tSysLeftArr+tSysRightArr);
470 } else if (what==1) {
471 MaskedArray<Float> tmp = mLeft - *pMRight;
472 putDataInSDC(sc, tmp.getArray(), tmp.getMask());
473 if (doTSys) sc.putTsys(tSysLeftArr-tSysRightArr);
474 } else if (what==2) {
475 MaskedArray<Float> tmp = mLeft * *pMRight;
476 putDataInSDC(sc, tmp.getArray(), tmp.getMask());
477 if (doTSys) sc.putTsys(tSysLeftArr*tSysRightArr);
478 } else if (what==3) {
479 MaskedArray<Float> tmp = mLeft / *pMRight;
480 putDataInSDC(sc, tmp.getArray(), tmp.getMask());
481 if (doTSys) sc.putTsys(tSysLeftArr/tSysRightArr);
482 } else if (what==4) {
483 if (preserve) {
484 MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - tSysRightArr;
485 putDataInSDC(sc, tmp.getArray(), tmp.getMask());
486 } else {
487 MaskedArray<Float> tmp = (tSysRightArr * mLeft / *pMRight) - tSysLeftArr;
488 putDataInSDC(sc, tmp.getArray(), tmp.getMask());
489 }
490 sc.putTsys(tSysRightArr);
491 }
492
493// Put new row in output Table
494
495 pTabOut->putSDContainer(sc);
496 }
497 if (pMRight) delete pMRight;
498 pTabOut->resetCursor();
499//
500 return CountedPtr<SDMemTable>(pTabOut);
501}
502
503
504
505std::vector<float> SDMath::statistic(const CountedPtr<SDMemTable>& in,
506 const Vector<Bool>& mask,
507 const String& which, Int row) const
508//
509// Perhaps iteration over pol/beam/if should be in here
510// and inside the nrow iteration ?
511//
512{
513 const uInt nRow = in->nRow();
514
515// Specify cursor location
516
517 IPosition start, end;
518 getCursorLocation(start, end, *in);
519
520// Loop over rows
521
522 const uInt nEl = mask.nelements();
523 uInt iStart = 0;
524 uInt iEnd = in->nRow()-1;
525//
526 if (row>=0) {
527 iStart = row;
528 iEnd = row;
529 }
530//
531 std::vector<float> result(iEnd-iStart+1);
532 for (uInt ii=iStart; ii <= iEnd; ++ii) {
533
534// Get row and deconstruct
535
536 MaskedArray<Float> marr(in->rowAsMaskedArray(ii));
537 Array<Float> arr = marr.getArray();
538 Array<Bool> barr = marr.getMask();
539
540// Access desired piece of data
541
542 Array<Float> v((arr(start,end)).nonDegenerate());
543 Array<Bool> m((barr(start,end)).nonDegenerate());
544
545// Apply OTF mask
546
547 MaskedArray<Float> tmp;
548 if (m.nelements()==nEl) {
549 tmp.setData(v,m&&mask);
550 } else {
551 tmp.setData(v,m);
552 }
553
554// Get statistic
555
556 result[ii-iStart] = mathutil::statistics(which, tmp);
557 }
558//
559 return result;
560}
561
562
563SDMemTable* SDMath::bin(const SDMemTable& in, Int width) const
564{
565 SDHeader sh = in.getSDHeader();
566 SDMemTable* pTabOut = new SDMemTable(in, True);
567
568// Bin up SpectralCoordinates
569
570 IPosition factors(1);
571 factors(0) = width;
572 for (uInt j=0; j<in.nCoordinates(); ++j) {
573 CoordinateSystem cSys;
574 cSys.addCoordinate(in.getSpectralCoordinate(j));
575 CoordinateSystem cSysBin =
576 CoordinateUtil::makeBinnedCoordinateSystem(factors, cSys, False);
577//
578 SpectralCoordinate sCBin = cSysBin.spectralCoordinate(0);
579 pTabOut->setCoordinate(sCBin, j);
580 }
581
582// Use RebinLattice to find shape
583
584 IPosition shapeIn(1,sh.nchan);
585 IPosition shapeOut = RebinLattice<Float>::rebinShape(shapeIn, factors);
586 sh.nchan = shapeOut(0);
587 pTabOut->putSDHeader(sh);
588
589// Loop over rows and bin along channel axis
590
591 for (uInt i=0; i < in.nRow(); ++i) {
592 SDContainer sc = in.getSDContainer(i);
593//
594 Array<Float> tSys(sc.getTsys()); // Get it out before sc changes shape
595
596// Bin up spectrum
597
598 MaskedArray<Float> marr(in.rowAsMaskedArray(i));
599 MaskedArray<Float> marrout;
600 LatticeUtilities::bin(marrout, marr, asap::ChanAxis, width);
601
602// Put back the binned data and flags
603
604 IPosition ip2 = marrout.shape();
605 sc.resize(ip2);
606//
607 putDataInSDC(sc, marrout.getArray(), marrout.getMask());
608
609// Bin up Tsys.
610
611 Array<Bool> allGood(tSys.shape(),True);
612 MaskedArray<Float> tSysIn(tSys, allGood, True);
613//
614 MaskedArray<Float> tSysOut;
615 LatticeUtilities::bin(tSysOut, tSysIn, asap::ChanAxis, width);
616 sc.putTsys(tSysOut.getArray());
617//
618 pTabOut->putSDContainer(sc);
619 }
620 return pTabOut;
621}
622
623SDMemTable* SDMath::resample (const SDMemTable& in, const String& methodStr,
624 Float width) const
625//
626// Should add the possibility of width being specified in km/s. This means
627// that for each freqID (SpectralCoordinate) we will need to convert to an
628// average channel width (say at the reference pixel). Then we would need
629// to be careful to make sure each spectrum (of different freqID)
630// is the same length.
631//
632{
633 Bool doVel = False;
634 if (doVel) {
635 for (uInt j=0; j<in.nCoordinates(); ++j) {
636 SpectralCoordinate sC = in.getSpectralCoordinate(j);
637 }
638 }
639
640// Interpolation method
641
642 InterpolateArray1D<Double,Float>::InterpolationMethod interp;
643 convertInterpString(interp, methodStr);
644 Int interpMethod(interp);
645
646// Make output table
647
648 SDMemTable* pTabOut = new SDMemTable(in, True);
649
650// Resample SpectralCoordinates (one per freqID)
651
652 const uInt nCoord = in.nCoordinates();
653 Vector<Float> offset(1,0.0);
654 Vector<Float> factors(1,1.0/width);
655 Vector<Int> newShape;
656 for (uInt j=0; j<in.nCoordinates(); ++j) {
657 CoordinateSystem cSys;
658 cSys.addCoordinate(in.getSpectralCoordinate(j));
659 CoordinateSystem cSys2 = cSys.subImage(offset, factors, newShape);
660 SpectralCoordinate sC = cSys2.spectralCoordinate(0);
661//
662 pTabOut->setCoordinate(sC, j);
663 }
664
665// Get header
666
667 SDHeader sh = in.getSDHeader();
668
669// Generate resampling vectors
670
671 const uInt nChanIn = sh.nchan;
672 Vector<Float> xIn(nChanIn);
673 indgen(xIn);
674//
675 Int fac = Int(nChanIn/width);
676 Vector<Float> xOut(fac+10); // 10 to be safe - resize later
677 uInt i = 0;
678 Float x = 0.0;
679 Bool more = True;
680 while (more) {
681 xOut(i) = x;
682//
683 i++;
684 x += width;
685 if (x>nChanIn-1) more = False;
686 }
687 const uInt nChanOut = i;
688 xOut.resize(nChanOut,True);
689//
690 IPosition shapeIn(in.rowAsMaskedArray(0).shape());
691 sh.nchan = nChanOut;
692 pTabOut->putSDHeader(sh);
693
694// Loop over rows and resample along channel axis
695
696 Array<Float> valuesOut;
697 Array<Bool> maskOut;
698 Array<Float> tSysOut;
699 Array<Bool> tSysMaskIn(shapeIn,True);
700 Array<Bool> tSysMaskOut;
701 for (uInt i=0; i < in.nRow(); ++i) {
702
703// Get container
704
705 SDContainer sc = in.getSDContainer(i);
706
707// Get data and Tsys
708
709 const Array<Float>& tSysIn = sc.getTsys();
710 const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(i));
711 Array<Float> valuesIn = dataIn.getArray();
712 Array<Bool> maskIn = dataIn.getMask();
713
714// Interpolate data
715
716 InterpolateArray1D<Float,Float>::interpolate(valuesOut, maskOut, xOut,
717 xIn, valuesIn, maskIn,
718 interpMethod, True, True);
719 sc.resize(valuesOut.shape());
720 putDataInSDC(sc, valuesOut, maskOut);
721
722// Interpolate TSys
723
724 InterpolateArray1D<Float,Float>::interpolate(tSysOut, tSysMaskOut, xOut,
725 xIn, tSysIn, tSysMaskIn,
726 interpMethod, True, True);
727 sc.putTsys(tSysOut);
728
729// Put container in output
730
731 pTabOut->putSDContainer(sc);
732 }
733//
734 return pTabOut;
735}
736
737SDMemTable* SDMath::unaryOperate(const SDMemTable& in, Float val, Bool doAll,
738 uInt what, Bool doTSys) const
739//
740// what = 0 Multiply
741// 1 Add
742{
743 SDMemTable* pOut = new SDMemTable(in,False);
744 const Table& tOut = pOut->table();
745 ArrayColumn<Float> specCol(tOut,"SPECTRA");
746 ArrayColumn<Float> tSysCol(tOut,"TSYS");
747 Array<Float> tSysArr;
748//
749 if (doAll) {
750 for (uInt i=0; i < tOut.nrow(); i++) {
751
752// Modify data
753
754 MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i));
755 if (what==0) {
756 dataIn *= val;
757 } else if (what==1) {
758 dataIn += val;
759 }
760 specCol.put(i, dataIn.getArray());
761
762// Modify Tsys
763
764 if (doTSys) {
765 tSysCol.get(i, tSysArr);
766 if (what==0) {
767 tSysArr *= val;
768 } else if (what==1) {
769 tSysArr += val;
770 }
771 tSysCol.put(i, tSysArr);
772 }
773 }
774 } else {
775
776// Get cursor location
777
778 IPosition start, end;
779 getCursorLocation(start, end, in);
780//
781 for (uInt i=0; i < tOut.nrow(); i++) {
782
783// Modify data
784
785 MaskedArray<Float> dataIn(pOut->rowAsMaskedArray(i));
786 MaskedArray<Float> dataIn2 = dataIn(start,end); // Reference
787 if (what==0) {
788 dataIn2 *= val;
789 } else if (what==1) {
790 dataIn2 += val;
791 }
792 specCol.put(i, dataIn.getArray());
793
794// Modify Tsys
795
796 if (doTSys) {
797 tSysCol.get(i, tSysArr);
798 Array<Float> tSysArr2 = tSysArr(start,end); // Reference
799 if (what==0) {
800 tSysArr2 *= val;
801 } else if (what==1) {
802 tSysArr2 += val;
803 }
804 tSysCol.put(i, tSysArr);
805 }
806 }
807 }
808//
809 return pOut;
810}
811
812
813
814SDMemTable* SDMath::averagePol(const SDMemTable& in, const Vector<Bool>& mask,
815 const String& weightStr) const
816//
817// Average all polarizations together, weighted by variance
818//
819{
820 WeightType wtType = NONE;
821 convertWeightString(wtType, weightStr);
822
823 const uInt nRows = in.nRow();
824
825// Create output Table and reshape number of polarizations
826
827 Bool clear=True;
828 SDMemTable* pTabOut = new SDMemTable(in, clear);
829 SDHeader header = pTabOut->getSDHeader();
830 header.npol = 1;
831 pTabOut->putSDHeader(header);
832
833// Shape of input and output data
834
835 const IPosition& shapeIn = in.rowAsMaskedArray(0u, False).shape();
836 IPosition shapeOut(shapeIn);
837 shapeOut(asap::PolAxis) = 1; // Average all polarizations
838 if (shapeIn(asap::PolAxis)==1) {
839 throw(AipsError("The input has only one polarisation"));
840 }
841//
842 const uInt nChan = shapeIn(asap::ChanAxis);
843 const IPosition vecShapeOut(4,1,1,1,nChan); // A multi-dim form of a Vector shape
844 IPosition start(4), end(4);
845
846// Output arrays
847
848 Array<Float> outData(shapeOut, 0.0);
849 Array<Bool> outMask(shapeOut, True);
850 const IPosition axes(2, asap::PolAxis, asap::ChanAxis); // pol-channel plane
851//
852 const Bool useMask = (mask.nelements() == shapeIn(asap::ChanAxis));
853
854// Loop over rows
855
856 for (uInt iRow=0; iRow<nRows; iRow++) {
857
858// Get data for this row
859
860 MaskedArray<Float> marr(in.rowAsMaskedArray(iRow));
861 Array<Float>& arr = marr.getRWArray();
862 const Array<Bool>& barr = marr.getMask();
863
864// Make iterators to iterate by pol-channel planes
865
866 ReadOnlyArrayIterator<Float> itDataPlane(arr, axes);
867 ReadOnlyArrayIterator<Bool> itMaskPlane(barr, axes);
868
869// Accumulations
870
871 Float fac = 1.0;
872 Vector<Float> vecSum(nChan,0.0);
873
874// Iterate through data by pol-channel planes
875
876 while (!itDataPlane.pastEnd()) {
877
878// Iterate through plane by polarization and accumulate Vectors
879
880 Vector<Float> t1(nChan); t1 = 0.0;
881 Vector<Bool> t2(nChan); t2 = True;
882 MaskedArray<Float> vecSum(t1,t2);
883 Float norm = 0.0;
884 {
885 ReadOnlyVectorIterator<Float> itDataVec(itDataPlane.array(), 1);
886 ReadOnlyVectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1);
887 while (!itDataVec.pastEnd()) {
888
889// Create MA of data & mask (optionally including OTF mask) and get variance for this spectrum
890
891 if (useMask) {
892 const MaskedArray<Float> spec(itDataVec.vector(),mask&&itMaskVec.vector());
893 if (wtType==VAR) fac = 1.0 / variance(spec);
894 } else {
895 const MaskedArray<Float> spec(itDataVec.vector(),itMaskVec.vector());
896 if (wtType==VAR) fac = 1.0 / variance(spec);
897 }
898
899// Normalize spectrum (without OTF mask) and accumulate
900
901 const MaskedArray<Float> spec(fac*itDataVec.vector(), itMaskVec.vector());
902 vecSum += spec;
903 norm += fac;
904
905// Next
906
907 itDataVec.next();
908 itMaskVec.next();
909 }
910 }
911
912// Normalize summed spectrum
913
914 vecSum /= norm;
915
916// FInd position in input data array. We are iterating by pol-channel
917// plane so all that will change is beam and IF and that's what we want.
918
919 IPosition pos = itDataPlane.pos();
920
921// Write out data. This is a bit messy. We have to reform the Vector
922// accumulator into an Array of shape (1,1,1,nChan)
923
924 start = pos;
925 end = pos;
926 end(asap::ChanAxis) = nChan-1;
927 outData(start,end) = vecSum.getArray().reform(vecShapeOut);
928 outMask(start,end) = vecSum.getMask().reform(vecShapeOut);
929
930// Step to next beam/IF combination
931
932 itDataPlane.next();
933 itMaskPlane.next();
934 }
935
936// Generate output container and write it to output table
937
938 SDContainer sc = in.getSDContainer();
939 sc.resize(shapeOut);
940//
941 putDataInSDC(sc, outData, outMask);
942 pTabOut->putSDContainer(sc);
943 }
944
945// Set polarization cursor to 0
946
947 pTabOut->setPol(0);
948//
949 return pTabOut;
950}
951
952
953SDMemTable* SDMath::smooth(const SDMemTable& in,
954 const casa::String& kernelType,
955 casa::Float width, Bool doAll) const
956//
957// Should smooth TSys as well
958//
959{
960
961// Number of channels
962
963 SDHeader sh = in.getSDHeader();
964 const uInt nChan = sh.nchan;
965
966// Generate Kernel
967
968 VectorKernel::KernelTypes type = VectorKernel::toKernelType(kernelType);
969 Vector<Float> kernel = VectorKernel::make(type, width, nChan, True, False);
970
971// Generate Convolver
972
973 IPosition shape(1,nChan);
974 Convolver<Float> conv(kernel, shape);
975
976// New Table
977
978 SDMemTable* pTabOut = new SDMemTable(in,True);
979
980// Get cursor location
981
982 IPosition start, end;
983 getCursorLocation(start, end, in);
984//
985 IPosition shapeOut(4,1);
986
987// Output Vectors
988
989 Vector<Float> valuesOut(nChan);
990 Vector<Bool> maskOut(nChan);
991
992// Loop over rows in Table
993
994 for (uInt ri=0; ri < in.nRow(); ++ri) {
995
996// Get copy of data
997
998 const MaskedArray<Float>& dataIn(in.rowAsMaskedArray(ri));
999 AlwaysAssert(dataIn.shape()(asap::ChanAxis)==nChan, AipsError);
1000//
1001 Array<Float> valuesIn = dataIn.getArray();
1002 Array<Bool> maskIn = dataIn.getMask();
1003
1004// Branch depending on whether we smooth all locations or just
1005// those pointed at by the current selection cursor
1006
1007 if (doAll) {
1008 VectorIterator<Float> itValues(valuesIn, asap::ChanAxis);
1009 VectorIterator<Bool> itMask(maskIn, asap::ChanAxis);
1010 while (!itValues.pastEnd()) {
1011
1012// Smooth
1013 if (kernelType==VectorKernel::HANNING) {
1014 mathutil::hanning(valuesOut, maskOut, itValues.vector(), itMask.vector());
1015 itMask.vector() = maskOut;
1016 } else {
1017 mathutil::replaceMaskByZero(itValues.vector(), itMask.vector());
1018 conv.linearConv(valuesOut, itValues.vector());
1019 }
1020//
1021 itValues.vector() = valuesOut;
1022//
1023 itValues.next();
1024 itMask.next();
1025 }
1026 } else {
1027
1028// Set multi-dim Vector shape
1029
1030 shapeOut(asap::ChanAxis) = valuesIn.shape()(asap::ChanAxis);
1031
1032// Stuff about with shapes so that we don't have conformance run-time errors
1033
1034 Vector<Float> valuesIn2 = valuesIn(start,end).nonDegenerate();
1035 Vector<Bool> maskIn2 = maskIn(start,end).nonDegenerate();
1036
1037// Smooth
1038
1039 if (kernelType==VectorKernel::HANNING) {
1040 mathutil::hanning(valuesOut, maskOut, valuesIn2, maskIn2);
1041 maskIn(start,end) = maskOut.reform(shapeOut);
1042 } else {
1043 mathutil::replaceMaskByZero(valuesIn2, maskIn2);
1044 conv.linearConv(valuesOut, valuesIn2);
1045 }
1046//
1047 valuesIn(start,end) = valuesOut.reform(shapeOut);
1048 }
1049
1050// Create and put back
1051
1052 SDContainer sc = in.getSDContainer(ri);
1053 putDataInSDC(sc, valuesIn, maskIn);
1054//
1055 pTabOut->putSDContainer(sc);
1056 }
1057//
1058 return pTabOut;
1059}
1060
1061
1062
1063SDMemTable* SDMath::convertFlux (const SDMemTable& in, Float a, Float eta, Bool doAll) const
1064//
1065// As it is, this function could be implemented with 'simpleOperate'
1066// However, I anticipate that eventually we will look the conversion
1067// values up in a Table and apply them in a frequency dependent way,
1068// so I have implemented it fully here
1069//
1070{
1071 SDHeader sh = in.getSDHeader();
1072 SDMemTable* pTabOut = new SDMemTable(in, True);
1073
1074// FInd out how to convert values into Jy and K (e.g. units might be mJy or mK)
1075// Also automatically find out what we are converting to according to the
1076// flux unit
1077
1078 Unit fluxUnit(sh.fluxunit);
1079 Unit K(String("K"));
1080 Unit JY(String("Jy"));
1081//
1082 Bool toKelvin = True;
1083 Double inFac = 1.0;
1084 if (fluxUnit==JY) {
1085 cerr << "Converting to K" << endl;
1086//
1087 Quantum<Double> t(1.0,fluxUnit);
1088 Quantum<Double> t2 = t.get(JY);
1089 inFac = (t2 / t).getValue();
1090//
1091 toKelvin = True;
1092 sh.fluxunit = "K";
1093 } else if (fluxUnit==K) {
1094 cerr << "Converting to Jy" << endl;
1095//
1096 Quantum<Double> t(1.0,fluxUnit);
1097 Quantum<Double> t2 = t.get(K);
1098 inFac = (t2 / t).getValue();
1099//
1100 toKelvin = False;
1101 sh.fluxunit = "Jy";
1102 } else {
1103 throw(AipsError("Unrecognized brightness units in Table - must be consistent with Jy or K"));
1104 }
1105 pTabOut->putSDHeader(sh);
1106
1107// Compute conversion factor. 'a' and 'eta' are really frequency, time and
1108// telescope dependent and should be looked// up in a table
1109
1110 Float factor = 2.0 * inFac * 1.0e-7 * 1.0e26 *
1111 QC::k.getValue(Unit(String("erg/K"))) / a / eta;
1112 if (toKelvin) {
1113 factor = 1.0 / factor;
1114 }
1115 cerr << "Applying conversion factor = " << factor << endl;
1116
1117// Generate correction vector. Apply same factor regardless
1118// of beam/pol/IF. This will need to change somewhen.
1119
1120 Vector<Float> factors(in.nRow(), factor);
1121
1122// Correct
1123
1124 correctFromVector (pTabOut, in, doAll, factors);
1125//
1126 return pTabOut;
1127}
1128
1129
1130SDMemTable* SDMath::gainElevation (const SDMemTable& in, const Vector<Float>& coeffs,
1131 const String& fileName,
1132 const String& methodStr, Bool doAll) const
1133{
1134
1135// Get header and clone output table
1136
1137 SDHeader sh = in.getSDHeader();
1138 SDMemTable* pTabOut = new SDMemTable(in, True);
1139
1140// Get elevation data from SDMemTable and convert to degrees
1141
1142 const Table& tab = in.table();
1143 ROScalarColumn<Float> elev(tab, "ELEVATION");
1144 Vector<Float> x = elev.getColumn();
1145 x *= Float(180 / C::pi);
1146//
1147 const uInt nC = coeffs.nelements();
1148 if (fileName.length()>0 && nC>0) {
1149 throw(AipsError("You must choose either polynomial coefficients or an ascii file, not both"));
1150 }
1151
1152// Correct
1153
1154 if (nC>0 || fileName.length()==0) {
1155
1156// Find instrument
1157
1158 Bool throwIt = True;
1159 Instrument inst = SDMemTable::convertInstrument (sh.antennaname, throwIt);
1160
1161// Set polynomial
1162
1163 Polynomial<Float>* pPoly = 0;
1164 Vector<Float> coeff;
1165 String msg;
1166 if (nC>0) {
1167 pPoly = new Polynomial<Float>(nC);
1168 coeff = coeffs;
1169 msg = String("user");
1170 } else {
1171 if (inst==ATPKSMB) {
1172 } else if (inst==ATPKSHOH) {
1173 } else if (inst==TIDBINBILLA) {
1174 pPoly = new Polynomial<Float>(3);
1175 coeff.resize(3);
1176 coeff(0) = 3.58788e-1;
1177 coeff(1) = 2.87243e-2;
1178 coeff(2) = -3.219093e-4;
1179 } else if (inst==ATMOPRA) {
1180 } else {
1181 }
1182 msg = String("built in");
1183 }
1184//
1185 if (coeff.nelements()>0) {
1186 pPoly->setCoefficients(coeff);
1187 } else {
1188 throw(AipsError("There is no known gain-el polynomial known for this instrument"));
1189 }
1190//
1191 cerr << "Making polynomial correction with " << msg << " coefficients" << endl;
1192 const uInt nRow = in.nRow();
1193 Vector<Float> factor(nRow);
1194 for (uInt i=0; i<nRow; i++) {
1195 factor[i] = (*pPoly)(x[i]);
1196 }
1197 delete pPoly;
1198//
1199 correctFromVector (pTabOut, in, doAll, factor);
1200 } else {
1201
1202// Indicate which columns to read from ascii file
1203
1204 String col0("ELEVATION");
1205 String col1("FACTOR");
1206
1207// Read and correct
1208
1209 cerr << "Making correction from ascii Table" << endl;
1210 correctFromAsciiTable (pTabOut, in, fileName, col0, col1,
1211 methodStr, doAll, x);
1212 }
1213//
1214 return pTabOut;
1215}
1216
1217
1218
1219SDMemTable* SDMath::opacity (const SDMemTable& in, Float tau, Bool doAll) const
1220{
1221
1222// Get header and clone output table
1223
1224 SDHeader sh = in.getSDHeader();
1225 SDMemTable* pTabOut = new SDMemTable(in, True);
1226
1227// Get elevation data from SDMemTable and convert to degrees
1228
1229 const Table& tab = in.table();
1230 ROScalarColumn<Float> elev(tab, "ELEVATION");
1231 Vector<Float> zDist = elev.getColumn();
1232 zDist = Float(C::pi_2) - zDist;
1233
1234// Generate correction factor
1235
1236 const uInt nRow = in.nRow();
1237 Vector<Float> factor(nRow);
1238 Vector<Float> factor2(nRow);
1239 for (uInt i=0; i<nRow; i++) {
1240 factor[i] = exp(tau)/cos(zDist[i]);
1241 }
1242
1243// Correct
1244
1245 correctFromVector (pTabOut, in, doAll, factor);
1246//
1247 return pTabOut;
1248}
1249
1250
1251
1252
1253// 'private' functions
1254
1255
1256SDMemTable* SDMath::frequencyAlign (const SDMemTable& in,
1257 MFrequency::Types freqSystem,
1258 const String& refTime, const String& methodStr) const
1259{
1260// Get Header
1261
1262 SDHeader sh = in.getSDHeader();
1263 const uInt nChan = sh.nchan;
1264 const uInt nRows = in.nRow();
1265 const uInt nIF = sh.nif;
1266
1267// Get Table reference
1268
1269 const Table& tabIn = in.table();
1270
1271// Get Columns from Table
1272
1273 ROScalarColumn<Double> mjdCol(tabIn, "TIME");
1274 ROScalarColumn<String> srcCol(tabIn, "SRCNAME");
1275 ROArrayColumn<uInt> fqIDCol(tabIn, "FREQID");
1276 Vector<Double> times = mjdCol.getColumn();
1277
1278// Generate DataDesc table
1279
1280 Matrix<uInt> ddIdx;
1281 SDDataDesc dDesc;
1282 generateDataDescTable (ddIdx, dDesc, nIF, in, tabIn, srcCol, fqIDCol);
1283
1284// Get reference Epoch to time of first row or given String
1285
1286 Unit DAY(String("d"));
1287 MEpoch::Ref epochRef(in.getTimeReference());
1288 MEpoch refEpoch;
1289 if (refTime.length()>0) {
1290 refEpoch = epochFromString(refTime, in.getTimeReference());
1291 } else {
1292 refEpoch = in.getEpoch(0);
1293 }
1294 cerr << "Aligning at reference Epoch " << formatEpoch(refEpoch) <<
1295 " in frame " << MFrequency::showType(freqSystem) << endl;
1296
1297// Get Reference Position
1298
1299 MPosition refPos = in.getAntennaPosition();
1300
1301// Create FrequencyAligner Block. One VA for each possible
1302// source/freqID combination
1303
1304 PtrBlock<FrequencyAligner<Float>* > a(dDesc.length());
1305 generateFrequencyAligners (a, dDesc, in, nChan, freqSystem, refPos, refEpoch);
1306
1307// Generate and fill output Frequency Tabke
1308
1309 SDFrequencyTable freqTabOut = in.getSDFreqTable();
1310 freqTabOut.setLength(0);
1311 Vector<String> units(1);
1312 units = String("Hz");
1313 Bool linear=True;
1314//
1315 for (uInt i=0; i<dDesc.length(); i++) {
1316
1317// Get Aligned SC in Hz
1318
1319 SpectralCoordinate sC = a[i]->alignedSpectralCoordinate(linear);
1320 sC.setWorldAxisUnits(units);
1321
1322// Add FreqID
1323
1324 freqTabOut.addFrequency(sC.referencePixel()[0],
1325 sC.referenceValue()[0],
1326 sC.increment()[0]);
1327 }
1328
1329// Interpolation method
1330
1331 InterpolateArray1D<Double,Float>::InterpolationMethod interp;
1332 convertInterpString(interp, methodStr);
1333
1334// New output Table
1335
1336 SDMemTable* pTabOut = new SDMemTable(in,True);
1337 pTabOut->putSDFreqTable(freqTabOut);
1338
1339// Loop over rows in Table
1340
1341 Bool extrapolate=False;
1342 const IPosition polChanAxes(2, asap::PolAxis, asap::ChanAxis);
1343 Bool useCachedAbcissa = False;
1344 Bool first = True;
1345 Bool ok;
1346 Vector<Float> yOut;
1347 Vector<Bool> maskOut;
1348 Vector<uInt> freqID(nIF);
1349 uInt ifIdx, faIdx;
1350//
1351 for (uInt iRow=0; iRow<nRows; ++iRow) {
1352 if (iRow%10==0) {
1353 cerr << "Processing row " << iRow << endl;
1354 }
1355
1356// Get EPoch
1357
1358 Quantum<Double> tQ2(times[iRow],DAY);
1359 MVEpoch mv2(tQ2);
1360 MEpoch epoch(mv2, epochRef);
1361
1362// Get copy of data
1363
1364 const MaskedArray<Float>& mArrIn(in.rowAsMaskedArray(iRow));
1365 Array<Float> values = mArrIn.getArray();
1366 Array<Bool> mask = mArrIn.getMask();
1367
1368// cerr << "values in = " << values(IPosition(4,0,0,0,0),IPosition(4,0,0,0,9)) << endl;
1369
1370// For each row, the Frequency abcissa will be the same regardless
1371// of polarization. For all other axes (IF and BEAM) the abcissa
1372// will change. So we iterate through the data by pol-chan planes
1373// to mimimize the work. Probably won't work for multiple beams
1374// at this point.
1375
1376 ArrayIterator<Float> itValuesPlane(values, polChanAxes);
1377 ArrayIterator<Bool> itMaskPlane(mask, polChanAxes);
1378 while (!itValuesPlane.pastEnd()) {
1379
1380// Find the IF index and then the FA PtrBlock index
1381
1382 const IPosition& pos = itValuesPlane.pos();
1383 ifIdx = pos(asap::IFAxis);
1384 faIdx = ddIdx(iRow,ifIdx);
1385//
1386 VectorIterator<Float> itValuesVec(itValuesPlane.array(), 1);
1387 VectorIterator<Bool> itMaskVec(itMaskPlane.array(), 1);
1388
1389// Iterate through the plane by vector and align
1390
1391 first = True;
1392 useCachedAbcissa=False;
1393 while (!itValuesVec.pastEnd()) {
1394 ok = a[faIdx]->align (yOut, maskOut, itValuesVec.vector(),
1395 itMaskVec.vector(), epoch, useCachedAbcissa,
1396 interp, extrapolate);
1397//
1398 itValuesVec.vector() = yOut;
1399 itMaskVec.vector() = maskOut;
1400//
1401 itValuesVec.next();
1402 itMaskVec.next();
1403//
1404 if (first) {
1405 useCachedAbcissa = True;
1406 first = False;
1407 }
1408 }
1409//
1410 itValuesPlane.next();
1411 itMaskPlane.next();
1412 }
1413
1414// cerr << "values out = " << values(IPosition(4,0,0,0,0),IPosition(4,0,0,0,9)) << endl;
1415
1416// Create SDContainer and put back
1417
1418 SDContainer sc = in.getSDContainer(iRow);
1419 putDataInSDC(sc, values, mask);
1420 for (uInt i=0; i<nIF; i++) {
1421 uInt idx = ddIdx(iRow,i);
1422 freqID(i) = dDesc.freqID(idx);
1423 }
1424 sc.putFreqMap(freqID);
1425//
1426 pTabOut->putSDContainer(sc);
1427 }
1428
1429// Now we must set the base and extra frames to the
1430// input frame
1431
1432 std::vector<string> info = pTabOut->getCoordInfo();
1433 info[1] = MFrequency::showType(freqSystem); // Conversion frame
1434 info[3] = info[1]; // Base frame
1435 pTabOut->setCoordInfo(info);
1436
1437// Clean up PointerBlock
1438
1439 for (uInt i=0; i<a.nelements(); i++) delete a[i];
1440//
1441 return pTabOut;
1442}
1443
1444
1445void SDMath::fillSDC(SDContainer& sc,
1446 const Array<Bool>& mask,
1447 const Array<Float>& data,
1448 const Array<Float>& tSys,
1449 Int scanID, Double timeStamp,
1450 Double interval, const String& sourceName,
1451 const Vector<uInt>& freqID) const
1452{
1453// Data and mask
1454
1455 putDataInSDC(sc, data, mask);
1456
1457// TSys
1458
1459 sc.putTsys(tSys);
1460
1461// Time things
1462
1463 sc.timestamp = timeStamp;
1464 sc.interval = interval;
1465 sc.scanid = scanID;
1466//
1467 sc.sourcename = sourceName;
1468 sc.putFreqMap(freqID);
1469}
1470
1471void SDMath::normalize(MaskedArray<Float>& sum,
1472 const Array<Float>& sumSq,
1473 const Array<Float>& nPts,
1474 WeightType wtType, Int axis,
1475 Int nAxesSub) const
1476{
1477 IPosition pos2(nAxesSub,0);
1478//
1479 if (wtType==NONE) {
1480
1481// We just average by the number of points accumulated.
1482// We need to make a MA out of nPts so that no divide by
1483// zeros occur
1484
1485 MaskedArray<Float> t(nPts, (nPts>Float(0.0)));
1486 sum /= t;
1487 } else if (wtType==VAR) {
1488
1489// Normalize each spectrum by sum(1/var) where the variance
1490// is worked out for each spectrum
1491
1492 Array<Float>& data = sum.getRWArray();
1493 VectorIterator<Float> itData(data, axis);
1494 while (!itData.pastEnd()) {
1495 pos2 = itData.pos().getFirst(nAxesSub);
1496 itData.vector() /= sumSq(pos2);
1497 itData.next();
1498 }
1499 } else if (wtType==TSYS) {
1500 }
1501}
1502
1503
1504void SDMath::accumulate(Double& timeSum, Double& intSum, Int& nAccum,
1505 MaskedArray<Float>& sum, Array<Float>& sumSq,
1506 Array<Float>& nPts, Array<Float>& tSysSum,
1507 const Array<Float>& tSys, const Array<Float>& nInc,
1508 const Vector<Bool>& mask, Double time, Double interval,
1509 const Block<CountedPtr<SDMemTable> >& in,
1510 uInt iTab, uInt iRow, uInt axis,
1511 uInt nAxesSub, Bool useMask,
1512 WeightType wtType) const
1513{
1514
1515// Get data
1516
1517 MaskedArray<Float> dataIn(in[iTab]->rowAsMaskedArray(iRow));
1518 Array<Float>& valuesIn = dataIn.getRWArray(); // writable reference
1519 const Array<Bool>& maskIn = dataIn.getMask(); // RO reference
1520//
1521 if (wtType==NONE) {
1522 const MaskedArray<Float> n(nInc,dataIn.getMask());
1523 nPts += n; // Only accumulates where mask==T
1524 } else if (wtType==VAR) {
1525
1526// We are going to average the data, weighted by the noise for each pol, beam and IF.
1527// So therefore we need to iterate through by spectrum (axis 3)
1528
1529 VectorIterator<Float> itData(valuesIn, axis);
1530 ReadOnlyVectorIterator<Bool> itMask(maskIn, axis);
1531 Float fac = 1.0;
1532 IPosition pos(nAxesSub,0);
1533//
1534 while (!itData.pastEnd()) {
1535
1536// Make MaskedArray of Vector, optionally apply OTF mask, and find scaling factor
1537
1538 if (useMask) {
1539 MaskedArray<Float> tmp(itData.vector(),mask&&itMask.vector());
1540 fac = 1.0/variance(tmp);
1541 } else {
1542 MaskedArray<Float> tmp(itData.vector(),itMask.vector());
1543 fac = 1.0/variance(tmp);
1544 }
1545
1546// Scale data
1547
1548 itData.vector() *= fac; // Writes back into 'dataIn'
1549//
1550// Accumulate variance per if/pol/beam averaged over spectrum
1551// This method to get pos2 from itData.pos() is only valid
1552// because the spectral axis is the last one (so we can just
1553// copy the first nAXesSub positions out)
1554
1555 pos = itData.pos().getFirst(nAxesSub);
1556 sumSq(pos) += fac;
1557//
1558 itData.next();
1559 itMask.next();
1560 }
1561 } else if (wtType==TSYS) {
1562 }
1563
1564// Accumulate sum of (possibly scaled) data
1565
1566 sum += dataIn;
1567
1568// Accumulate Tsys, time, and interval
1569
1570 tSysSum += tSys;
1571 timeSum += time;
1572 intSum += interval;
1573 nAccum += 1;
1574}
1575
1576
1577
1578
1579void SDMath::getCursorLocation(IPosition& start, IPosition& end,
1580 const SDMemTable& in) const
1581{
1582 const uInt nDim = 4;
1583 const uInt i = in.getBeam();
1584 const uInt j = in.getIF();
1585 const uInt k = in.getPol();
1586 const uInt n = in.nChan();
1587//
1588 start.resize(nDim);
1589 start(0) = i;
1590 start(1) = j;
1591 start(2) = k;
1592 start(3) = 0;
1593//
1594 end.resize(nDim);
1595 end(0) = i;
1596 end(1) = j;
1597 end(2) = k;
1598 end(3) = n-1;
1599}
1600
1601
1602void SDMath::convertWeightString(WeightType& wtType, const String& weightStr) const
1603{
1604 String tStr(weightStr);
1605 tStr.upcase();
1606 if (tStr.contains(String("NONE"))) {
1607 wtType = NONE;
1608 } else if (tStr.contains(String("VAR"))) {
1609 wtType = VAR;
1610 } else if (tStr.contains(String("TSYS"))) {
1611 wtType = TSYS;
1612 throw(AipsError("T_sys weighting not yet implemented"));
1613 } else {
1614 throw(AipsError("Unrecognized weighting type"));
1615 }
1616}
1617
1618
1619void SDMath::convertInterpString(casa::InterpolateArray1D<Double,Float>::InterpolationMethod& type,
1620 const casa::String& interp) const
1621{
1622 String tStr(interp);
1623 tStr.upcase();
1624 if (tStr.contains(String("NEAR"))) {
1625 type = InterpolateArray1D<Double,Float>::nearestNeighbour;
1626 } else if (tStr.contains(String("LIN"))) {
1627 type = InterpolateArray1D<Double,Float>::linear;
1628 } else if (tStr.contains(String("CUB"))) {
1629 type = InterpolateArray1D<Double,Float>::cubic;
1630 } else if (tStr.contains(String("SPL"))) {
1631 type = InterpolateArray1D<Double,Float>::spline;
1632 } else {
1633 throw(AipsError("Unrecognized interpolation type"));
1634 }
1635}
1636
1637void SDMath::putDataInSDC(SDContainer& sc, const Array<Float>& data,
1638 const Array<Bool>& mask) const
1639{
1640 sc.putSpectrum(data);
1641//
1642 Array<uChar> outflags(data.shape());
1643 convertArray(outflags,!mask);
1644 sc.putFlags(outflags);
1645}
1646
1647Table SDMath::readAsciiFile (const String& fileName) const
1648{
1649 String formatString;
1650 Table tbl = readAsciiTable (formatString, Table::Memory, fileName, "", "", False);
1651 return tbl;
1652}
1653
1654
1655
1656void SDMath::correctFromAsciiTable(SDMemTable* pTabOut,
1657 const SDMemTable& in, const String& fileName,
1658 const String& col0, const String& col1,
1659 const String& methodStr, Bool doAll,
1660 const Vector<Float>& xOut) const
1661{
1662
1663// Read gain-elevation ascii file data into a Table.
1664
1665 Table geTable = readAsciiFile (fileName);
1666//
1667 correctFromTable (pTabOut, in, geTable, col0, col1, methodStr, doAll, xOut);
1668}
1669
1670void SDMath::correctFromTable(SDMemTable* pTabOut, const SDMemTable& in,
1671 const Table& tTable, const String& col0,
1672 const String& col1,
1673 const String& methodStr, Bool doAll,
1674 const Vector<Float>& xOut) const
1675{
1676
1677// Get data from Table
1678
1679 ROScalarColumn<Float> geElCol(tTable, col0);
1680 ROScalarColumn<Float> geFacCol(tTable, col1);
1681 Vector<Float> xIn = geElCol.getColumn();
1682 Vector<Float> yIn = geFacCol.getColumn();
1683 Vector<Bool> maskIn(xIn.nelements(),True);
1684
1685// Interpolate (and extrapolate) with desired method
1686
1687 InterpolateArray1D<Double,Float>::InterpolationMethod method;
1688 convertInterpString(method, methodStr);
1689 Int intMethod(method);
1690//
1691 Vector<Float> yOut;
1692 Vector<Bool> maskOut;
1693 InterpolateArray1D<Float,Float>::interpolate(yOut, maskOut, xOut,
1694 xIn, yIn, maskIn, intMethod,
1695 True, True);
1696// Apply
1697
1698 correctFromVector (pTabOut, in, doAll, yOut);
1699}
1700
1701
1702void SDMath::correctFromVector (SDMemTable* pTabOut, const SDMemTable& in,
1703 Bool doAll, const Vector<Float>& factor) const
1704{
1705
1706// For operations only on specified cursor location
1707
1708 IPosition start, end;
1709 getCursorLocation(start, end, in);
1710
1711// Loop over rows and apply correction factor
1712
1713 const uInt axis = asap::ChanAxis;
1714 for (uInt i=0; i < in.nRow(); ++i) {
1715
1716// Get data
1717
1718 MaskedArray<Float> dataIn(in.rowAsMaskedArray(i));
1719
1720// Apply factor
1721
1722 if (doAll) {
1723 dataIn *= factor[i];
1724 } else {
1725 MaskedArray<Float> dataIn2 = dataIn(start,end); // reference
1726 dataIn2 *= factor[i];
1727 }
1728
1729// Write out
1730
1731 SDContainer sc = in.getSDContainer(i);
1732 putDataInSDC(sc, dataIn.getArray(), dataIn.getMask());
1733//
1734 pTabOut->putSDContainer(sc);
1735 }
1736}
1737
1738
1739
1740
1741void SDMath::generateDataDescTable (Matrix<uInt>& ddIdx,
1742 SDDataDesc& dDesc,
1743 uInt nIF,
1744 const SDMemTable& in,
1745 const Table& tabIn,
1746 const ROScalarColumn<String>& srcCol,
1747 const ROArrayColumn<uInt>& fqIDCol) const
1748{
1749 const uInt nRows = tabIn.nrow();
1750 ddIdx.resize(nRows,nIF);
1751//
1752 String srcName;
1753 Vector<uInt> freqIDs;
1754 for (uInt iRow=0; iRow<nRows; iRow++) {
1755 srcCol.get(iRow, srcName);
1756 fqIDCol.get(iRow, freqIDs);
1757 const MDirection& dir = in.getDirection(iRow);
1758//
1759 for (uInt iIF=0; iIF<nIF; iIF++) {
1760 uInt idx = dDesc.addEntry(srcName, freqIDs[iIF], dir);
1761 ddIdx(iRow,iIF) = idx;
1762 }
1763 }
1764}
1765
1766MEpoch SDMath::epochFromString (const String& str, MEpoch::Types timeRef) const
1767{
1768 Quantum<Double> qt;
1769 if (MVTime::read(qt,str)) {
1770 MVEpoch mv(qt);
1771 MEpoch me(mv, timeRef);
1772 return me;
1773 } else {
1774 throw(AipsError("Invalid format for Epoch string"));
1775 }
1776}
1777
1778
1779String SDMath::formatEpoch(const MEpoch& epoch) const
1780{
1781 MVTime mvt(epoch.getValue());
1782 return mvt.string(MVTime::YMD) + String(" (") + epoch.getRefString() + String(")");
1783}
1784
1785
1786
1787void SDMath::generateFrequencyAligners (PtrBlock<FrequencyAligner<Float>* >& a,
1788 const SDDataDesc& dDesc,
1789 const SDMemTable& in, uInt nChan,
1790 MFrequency::Types system,
1791 const MPosition& refPos,
1792 const MEpoch& refEpoch) const
1793{
1794 for (uInt i=0; i<dDesc.length(); i++) {
1795 uInt freqID = dDesc.freqID(i);
1796 const MDirection& refDir = dDesc.direction(i);
1797//
1798 SpectralCoordinate sC = in.getSpectralCoordinate(freqID);
1799 a[i] = new FrequencyAligner<Float>(sC, nChan, refEpoch, refDir, refPos, system);
1800 }
1801}
1802
1803
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