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