source: trunk/external/atnf/PKSIO/SDFITSreader.cc @ 1427

Last change on this file since 1427 was 1427, checked in by Malte Marquarding, 16 years ago

sync with livedata/implement/atnf

File size: 50.9 KB
Line 
1//#---------------------------------------------------------------------------
2//# SDFITSreader.cc: ATNF CFITSIO interface class for SDFITS input.
3//#---------------------------------------------------------------------------
4//# Copyright (C) 2000-2008
5//# Associated Universities, Inc. Washington DC, USA.
6//#
7//# This library is free software; you can redistribute it and/or modify it
8//# under the terms of the GNU Library General Public License as published by
9//# the Free Software Foundation; either version 2 of the License, or (at your
10//# option) any later version.
11//#
12//# This library is distributed in the hope that it will be useful, but WITHOUT
13//# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
14//# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Library General Public
15//# License for more details.
16//#
17//# You should have received a copy of the GNU Library General Public License
18//# along with this library; if not, write to the Free Software Foundation,
19//# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA.
20//#
21//# Correspondence concerning this software should be addressed as follows:
22//#        Internet email: aips2-request@nrao.edu.
23//#        Postal address: AIPS++ Project Office
24//#                        National Radio Astronomy Observatory
25//#                        520 Edgemont Road
26//#                        Charlottesville, VA 22903-2475 USA
27//#
28//# $Id: SDFITSreader.cc,v 19.24 2008-06-26 02:13:11 cal103 Exp $
29//#---------------------------------------------------------------------------
30//# The SDFITSreader class reads single dish FITS files such as those written
31//# by SDFITSwriter containing Parkes Multibeam data.
32//#
33//# Original: 2000/08/09, Mark Calabretta, ATNF
34//#---------------------------------------------------------------------------
35
36#include <algorithm>
37#include <strings.h>
38
39// AIPS++ includes.
40#include <casa/iostream.h>
41#include <casa/math.h>
42#include <casa/stdio.h>
43
44// ATNF includes.
45#include <atnf/pks/pks_maths.h>
46#include <atnf/PKSIO/PKSMBrecord.h>
47#include <atnf/PKSIO/SDFITSreader.h>
48
49
50class FITSparm
51{
52  public:
53    char *name;         // Keyword or column name.
54    int  type;          // Expected keyvalue or column data type.
55    int  colnum;        // Column number; 0 for keyword; -1 absent.
56    int  coltype;       // Column data type, as found.
57    long nelem;         // Column data repeat count; < 0 for vardim.
58    int  tdimcol;       // TDIM column number; 0 for keyword; -1 absent.
59    char units[32];     // Units from TUNITn keyword.
60};
61
62// Numerical constants.
63const double PI  = 3.141592653589793238462643;
64
65// Factor to convert radians to degrees.
66const double D2R = PI / 180.0;
67
68//------------------------------------------------- SDFITSreader::SDFITSreader
69
70SDFITSreader::SDFITSreader()
71{
72  // Default constructor.
73  cSDptr = 0;
74
75  // Allocate space for data descriptors.
76  cData = new FITSparm[NDATA];
77
78  for (int iData = 0; iData < NDATA; iData++) {
79    cData[iData].colnum = -1;
80  }
81
82  // Initialize pointers.
83  cBeams     = 0x0;
84  cIFs       = 0x0;
85  cStartChan = 0x0;
86  cEndChan   = 0x0;
87  cRefChan   = 0x0;
88}
89
90//------------------------------------------------ SDFITSreader::~SDFITSreader
91
92SDFITSreader::~SDFITSreader()
93{
94  close();
95
96  delete [] cData;
97}
98
99//--------------------------------------------------------- SDFITSreader::open
100
101// Open an SDFITS file for reading.
102
103int SDFITSreader::open(
104        char*  sdName,
105        int    &nBeam,
106        int*   &beams,
107        int    &nIF,
108        int*   &IFs,
109        int*   &nChan,
110        int*   &nPol,
111        int*   &haveXPol,
112        int    &haveBase,
113        int    &haveSpectra,
114        int    &extraSysCal)
115{
116  if (cSDptr) {
117    close();
118  }
119
120  // Open the SDFITS file.
121  cStatus = 0;
122  if (fits_open_file(&cSDptr, sdName, READONLY, &cStatus)) {
123    cerr << "Failed to open SDFITS file: " << sdName << endl;
124    reportError();
125    return 1;
126  }
127
128  // Move to the SDFITS extension.
129  cALFA = cALFA_BD = cALFA_CIMA = 0;
130  if (fits_movnam_hdu(cSDptr, BINARY_TBL, "SINGLE DISH", 0, &cStatus)) {
131    // No SDFITS table, look for BDFITS or CIMAFITS.
132    cStatus = 0;
133    if (fits_movnam_hdu(cSDptr, BINARY_TBL, "BDFITS", 0, &cStatus) == 0) {
134      cALFA_BD = 1;
135
136    } else {
137      cStatus = 0;
138      if (fits_movnam_hdu(cSDptr, BINARY_TBL, "CIMAFITS", 0, &cStatus) == 0) {
139        cALFA_CIMA = 1;
140
141      } else {
142        cerr << "Failed to locate SDFITS binary table." << endl;
143        reportError();
144        close();
145        return 1;
146      }
147    }
148
149    // Arecibo ALFA data of some kind.
150    cALFA = 1;
151    for (int iBeam = 0; iBeam < 8; iBeam++) {
152      for (int iPol = 0; iPol < 2; iPol++) {
153        cALFAcalOn[iBeam][iPol]  = 0.0f;
154        cALFAcalOff[iBeam][iPol] = 0.0f;
155
156        // Nominal factor to calibrate spectra in Jy.
157        cALFAcal[iBeam][iPol] = 3.0f;
158      }
159    }
160  }
161
162  // GBT data.
163  char telescope[32];
164  readParm("TELESCOP", TSTRING, telescope);      // Core.
165  cGBT = strncmp(telescope, "GBT", 3) == 0 ||
166         strncmp(telescope, "NRAO_GBT", 8) == 0;
167
168  cRow = 0;
169
170
171  // Check that the DATA array column is present.
172  findData(DATA, "DATA", TFLOAT);
173  haveSpectra = cHaveSpectra = cData[DATA].colnum > 0;
174
175  if (cHaveSpectra) {
176    // Find the number of data axes (must be the same for each IF).
177    cNAxis = 5;
178    if (readDim(DATA, 1, &cNAxis, cNAxes)) {
179      reportError();
180      close();
181      return 1;
182    }
183
184    if (cALFA_BD) {
185      // ALFA BDFITS: variable length arrays don't actually vary and there is
186      // no TDIM (or MAXISn) card; use the LAGS_IN value.
187      cNAxis = 5;
188      readParm("LAGS_IN", TLONG, cNAxes);
189      cNAxes[1] = 1;
190      cNAxes[2] = 1;
191      cNAxes[3] = 1;
192      cNAxes[4] = 1;
193      cData[DATA].nelem = cNAxes[0];
194    }
195
196    if (cNAxis < 4) {
197      // Need at least four axes (for now).
198      cerr << "DATA array contains fewer than four axes." << endl;
199      close();
200      return 1;
201    } else if (cNAxis > 5) {
202      // We support up to five axes.
203      cerr << "DATA array contains more than five axes." << endl;
204      close();
205      return 1;
206    }
207
208    findData(FLAGGED, "FLAGGED", TBYTE);
209
210  } else {
211    // DATA column not present, check for a DATAXED keyword.
212    findData(DATAXED, "DATAXED", TSTRING);
213    if (cData[DATAXED].colnum < 0) {
214      cerr << "DATA array column absent from binary table." << endl;
215      close();
216      return 1;
217    }
218
219    // Determine the number of axes and their length.
220    char dataxed[32];
221    readParm("DATAXED", TSTRING, dataxed);
222
223    for (int iaxis = 0; iaxis < 5; iaxis++) cNAxes[iaxis] = 0;
224    sscanf(dataxed, "(%ld,%ld,%ld,%ld,%ld)", cNAxes, cNAxes+1, cNAxes+2,
225      cNAxes+3, cNAxes+4);
226    for (int iaxis = 4; iaxis > -1; iaxis--) {
227      if (cNAxes[iaxis] == 0) cNAxis = iaxis;
228    }
229  }
230
231  char  *CTYPE[5] = {"CTYPE1", "CTYPE2", "CTYPE3", "CTYPE4", "CTYPE5"};
232  char  *CRPIX[5] = {"CRPIX1", "CRPIX2", "CRPIX3", "CRPIX4", "CRPIX5"};
233  char  *CRVAL[5] = {"CRVAL1", "CRVAL2", "CRVAL3", "CRVAL4", "CRVAL5"};
234  char  *CDELT[5] = {"CDELT1", "CDELT2", "CDELT3", "CDELT4", "CDELT5"};
235
236  // Find required DATA array axes.
237  char ctype[5][72];
238  for (int iaxis = 0; iaxis < cNAxis; iaxis++) {
239    strcpy(ctype[iaxis], "");
240    readParm(CTYPE[iaxis], TSTRING, ctype[iaxis]);      // Core.
241  }
242
243  if (cStatus) {
244    reportError();
245    close();
246    return 1;
247  }
248
249  char *fqCRPIX  = 0;
250  char *fqCRVAL  = 0;
251  char *fqCDELT  = 0;
252  char *raCRVAL  = 0;
253  char *decCRVAL = 0;
254  char *timeCRVAL = 0;
255  char *beamCRVAL = 0;
256
257  for (int iaxis = 0; iaxis < cNAxis; iaxis++) {
258    if (strncmp(ctype[iaxis], "FREQ", 4) == 0) {
259      cReqax[0] = iaxis;
260      fqCRPIX  = CRPIX[iaxis];
261      fqCRVAL  = CRVAL[iaxis];
262      fqCDELT  = CDELT[iaxis];
263
264    } else if (strncmp(ctype[iaxis], "STOKES", 6) == 0) {
265      cReqax[1] = iaxis;
266
267    } else if (strncmp(ctype[iaxis], "RA", 2) == 0) {
268      cReqax[2] = iaxis;
269      raCRVAL  = CRVAL[iaxis];
270
271    } else if (strncmp(ctype[iaxis], "DEC", 3) == 0) {
272      cReqax[3] = iaxis;
273      decCRVAL = CRVAL[iaxis];
274
275    } else if (strcmp(ctype[iaxis], "TIME") == 0) {
276      // TIME (UTC seconds since midnight) can be a keyword or axis type.
277      timeCRVAL = CRVAL[iaxis];
278
279    } else if (strcmp(ctype[iaxis], "BEAM") == 0) {
280      // BEAM can be a keyword or axis type.
281      beamCRVAL = CRVAL[iaxis];
282    }
283  }
284
285  if (cALFA_BD) {
286    // Fixed in ALFA CIMAFITS.
287    cReqax[2] = 2;
288    raCRVAL = "CRVAL2A";
289
290    cReqax[3] = 3;
291    decCRVAL = "CRVAL3A";
292  }
293
294  // Check that all are present.
295  for (int iaxis = 0; iaxis < 4; iaxis++) {
296    if (cReqax[iaxis] < 0) {
297      cerr << "Could not find required DATA array axes." << endl;
298      close();
299      return 1;
300    }
301  }
302
303  // Set up machinery for data retrieval.
304  findData(SCAN,     "SCAN",     TINT);         // Shared.
305  findData(CYCLE,    "CYCLE",    TINT);         // Additional.
306  findData(DATE_OBS, "DATE-OBS", TSTRING);      // Core.
307  findData(TIME,     "TIME",     TDOUBLE);      // Core.
308  findData(EXPOSURE, "EXPOSURE", TFLOAT);       // Core.
309  findData(OBJECT,   "OBJECT",   TSTRING);      // Core.
310  findData(OBJ_RA,   "OBJ-RA",   TDOUBLE);      // Additional.
311  findData(OBJ_DEC,  "OBJ-DEC",  TDOUBLE);      // Additional.
312  findData(RESTFRQ,  "RESTFRQ",  TDOUBLE);      // Additional.
313  findData(OBSMODE,  "OBSMODE",  TSTRING);      // Shared.
314
315  findData(BEAM,     "BEAM",     TSHORT);       // Additional.
316  findData(IF,       "IF",       TSHORT);       // Additional.
317  findData(FqRefPix,  fqCRPIX,   TFLOAT);       // Frequency reference pixel.
318  findData(FqRefVal,  fqCRVAL,   TDOUBLE);      // Frequency reference value.
319  findData(FqDelt,    fqCDELT,   TDOUBLE);      // Frequency increment.
320  findData(RA,        raCRVAL,   TDOUBLE);      // Right ascension.
321  findData(DEC,      decCRVAL,   TDOUBLE);      // Declination.
322  findData(SCANRATE, "SCANRATE", TFLOAT);       // Additional.
323
324  findData(TSYS,     "TSYS",     TFLOAT);       // Core.
325  findData(CALFCTR,  "CALFCTR",  TFLOAT);       // Additional.
326  findData(XCALFCTR, "XCALFCTR", TFLOAT);       // Additional.
327  findData(BASELIN,  "BASELIN",  TFLOAT);       // Additional.
328  findData(BASESUB,  "BASESUB",  TFLOAT);       // Additional.
329  findData(XPOLDATA, "XPOLDATA", TFLOAT);       // Additional.
330
331  findData(REFBEAM,  "REFBEAM",  TSHORT);       // Additional.
332  findData(TCAL,     "TCAL",     TFLOAT);       // Shared.
333  findData(TCALTIME, "TCALTIME", TSTRING);      // Additional.
334  findData(AZIMUTH,  "AZIMUTH",  TFLOAT);       // Shared.
335  findData(ELEVATIO, "ELEVATIO", TFLOAT);       // Shared.
336  findData(PARANGLE, "PARANGLE", TFLOAT);       // Additional.
337  findData(FOCUSAXI, "FOCUSAXI", TFLOAT);       // Additional.
338  findData(FOCUSTAN, "FOCUSTAN", TFLOAT);       // Additional.
339  findData(FOCUSROT, "FOCUSROT", TFLOAT);       // Additional.
340  findData(TAMBIENT, "TAMBIENT", TFLOAT);       // Shared.
341  findData(PRESSURE, "PRESSURE", TFLOAT);       // Shared.
342  findData(HUMIDITY, "HUMIDITY", TFLOAT);       // Shared.
343  findData(WINDSPEE, "WINDSPEE", TFLOAT);       // Shared.
344  findData(WINDDIRE, "WINDDIRE", TFLOAT);       // Shared.
345
346  if (cStatus) {
347    reportError();
348    close();
349    return 1;
350  }
351
352
353  // Check for alternative column names.
354  if (cALFA) {
355    // ALFA data.
356    cALFAscan = 0;
357    cScanNo = 0;
358    if (cALFA_BD) {
359      findData(SCAN,  "SCAN_NUMBER", TINT);
360      findData(CYCLE, "PATTERN_NUMBER", TINT);
361    } else if (cALFA_CIMA) {
362      findData(SCAN,  "SCAN_ID", TINT);
363      findData(CYCLE, "SUBSCAN", TINT);
364    }
365  } else {
366    readData(SCAN, 1, &cFirstScanNo);
367  }
368
369  cCycleNo = 0;
370  cLastUTC = 0.0;
371
372  // Beam number, 1-relative by default.
373  cBeam_1rel = 1;
374  if (cData[BEAM].colnum < 0) {
375    if (beamCRVAL) {
376      // There is a BEAM axis.
377      findData(BEAM, beamCRVAL, TDOUBLE);
378
379    } else {
380      if (cALFA) {
381        // ALFA data, 0-relative.
382        findData(BEAM, "INPUT_ID", TSHORT);
383      } else {
384        // ms2sdfits output, 0-relative "feed" number.
385        findData(BEAM, "MAIN_FEED1", TSHORT);
386      }
387
388      cBeam_1rel = 0;
389    }
390  }
391
392  // IF number, 1-relative by default.
393  cIF_1rel = 1;
394  if (cALFA && cData[IF].colnum < 0) {
395    // ALFA data, 0-relative.
396    findData(IF, "IFVAL", TSHORT);
397    cIF_1rel = 0;
398  }
399
400  if (cData[TIME].colnum < 0) {
401    if (timeCRVAL) {
402      // There is a TIME axis.
403      findData(TIME, timeCRVAL, TDOUBLE);
404    }
405  }
406
407  // ms2sdfits writes a scalar "TSYS" column that averages the polarizations.
408  int colnum;
409  findCol("SYSCAL_TSYS", &colnum);
410  if (colnum > 0) {
411    // This contains the vector Tsys.
412    findData(TSYS, "SYSCAL_TSYS", TFLOAT);
413  }
414
415  // XPOLDATA?
416
417  if (cData[SCANRATE].colnum < 0) {
418    findData(SCANRATE, "FIELD_POINTING_DIR_RATE", TFLOAT);
419  }
420
421  if (cData[RESTFRQ].colnum < 0) {
422    findData(RESTFRQ, "RESTFREQ", TDOUBLE);
423    if (cData[RESTFRQ].colnum < 0) {
424      findData(RESTFRQ, "SPECTRAL_WINDOW_REST_FREQUENCY", TDOUBLE);
425    }
426  }
427
428  if (cData[OBJ_RA].colnum < 0) {
429    findData(OBJ_RA, "SOURCE_DIRECTION", TDOUBLE);
430  }
431  if (cData[OBJ_DEC].colnum < 0) {
432    findData(OBJ_DEC, "SOURCE_DIRECTION", TDOUBLE);
433  }
434
435  // REFBEAM?
436
437  if (cData[TCAL].colnum < 0) {
438    findData(TCAL, "SYSCAL_TCAL", TFLOAT);
439  } else if (cALFA_BD) {
440    // ALFA BDFITS has a different TCAL with 64 elements - kill it!
441    findData(TCAL, "NO NO NO", TFLOAT);
442  }
443
444  if (cALFA_BD) {
445    // ALFA BDFITS.
446    findData(AZIMUTH, "CRVAL2B", TFLOAT);
447    findData(ELEVATIO, "CRVAL3B", TFLOAT);
448  }
449
450  if (cALFA) {
451    // ALFA data.
452    findData(PARANGLE, "PARA_ANG", TFLOAT);
453  }
454
455  if (cData[TAMBIENT].colnum < 0) {
456    findData(TAMBIENT, "WEATHER_TEMPERATURE", TFLOAT);
457  }
458
459  if (cData[PRESSURE].colnum < 0) {
460    findData(PRESSURE, "WEATHER_PRESSURE", TFLOAT);
461  }
462
463  if (cData[HUMIDITY].colnum < 0) {
464    findData(HUMIDITY, "WEATHER_REL_HUMIDITY", TFLOAT);
465  }
466
467  if (cData[WINDSPEE].colnum < 0) {
468    findData(WINDSPEE, "WEATHER_WIND_SPEED", TFLOAT);
469  }
470
471  if (cData[WINDDIRE].colnum < 0) {
472    findData(WINDDIRE, "WEATHER_WIND_DIRECTION", TFLOAT);
473  }
474
475
476  // Find the number of rows.
477  fits_get_num_rows(cSDptr, &cNRow, &cStatus);
478  if (!cNRow) {
479    cerr << "Table contains no entries." << endl;
480    close();
481    return 1;
482  }
483
484
485  // Determine which beams are present in the data.
486  if (cData[BEAM].colnum > 0) {
487    short *beamCol = new short[cNRow];
488    short beamNul = 1;
489    int   anynul;
490    if (fits_read_col(cSDptr, TSHORT, cData[BEAM].colnum, 1, 1, cNRow,
491                      &beamNul, beamCol, &anynul, &cStatus)) {
492      reportError();
493      delete [] beamCol;
494      close();
495      return 1;
496    }
497
498    // Find the maximum beam number.
499    cNBeam = cBeam_1rel - 1;
500    for (int irow = 0; irow < cNRow; irow++) {
501      if (beamCol[irow] > cNBeam) {
502        cNBeam = beamCol[irow];
503      }
504
505      // Check validity.
506      if (beamCol[irow] < cBeam_1rel) {
507        cerr << "SDFITS file contains invalid beam number." << endl;
508        delete [] beamCol;
509        close();
510        return 1;
511      }
512    }
513
514    if (!cBeam_1rel) cNBeam++;
515
516    // Find all beams present in the data.
517    cBeams = new int[cNBeam];
518    for (int ibeam = 0; ibeam < cNBeam; ibeam++) {
519      cBeams[ibeam] = 0;
520    }
521
522    for (int irow = 0; irow < cNRow; irow++) {
523      cBeams[beamCol[irow] - cBeam_1rel] = 1;
524    }
525
526    delete [] beamCol;
527
528  } else {
529    // No BEAM column.
530    cNBeam = 1;
531    cBeams = new int[1];
532    cBeams[0] = 1;
533  }
534
535  // Passing back the address of the array allows PKSFITSreader::select() to
536  // modify its elements directly.
537  nBeam = cNBeam;
538  beams = cBeams;
539
540
541  // Determine which IFs are present in the data.
542  if (cData[IF].colnum > 0) {
543    short *IFCol = new short[cNRow];
544    short IFNul = 1;
545    int   anynul;
546    if (fits_read_col(cSDptr, TSHORT, cData[IF].colnum, 1, 1, cNRow,
547                      &IFNul, IFCol, &anynul, &cStatus)) {
548      reportError();
549      delete [] IFCol;
550      close();
551      return 1;
552    }
553
554    // Find the maximum IF number.
555    cNIF = cIF_1rel - 1;
556    for (int irow = 0; irow < cNRow; irow++) {
557      if (IFCol[irow] > cNIF) {
558        cNIF = IFCol[irow];
559      }
560
561      // Check validity.
562      if (IFCol[irow] < cIF_1rel) {
563        cerr << "SDFITS file contains invalid IF number." << endl;
564        delete [] IFCol;
565        close();
566        return 1;
567      }
568    }
569
570    if (!cIF_1rel) cNIF++;
571
572    // Find all IFs present in the data.
573    cIFs      = new int[cNIF];
574    cNChan    = new int[cNIF];
575    cNPol     = new int[cNIF];
576    cHaveXPol = new int[cNIF];
577    cGetXPol  = 0;
578
579    for (int iIF = 0; iIF < cNIF; iIF++) {
580      cIFs[iIF]   = 0;
581      cNChan[iIF] = 0;
582      cNPol[iIF]  = 0;
583      cHaveXPol[iIF] = 0;
584    }
585
586    for (int irow = 0; irow < cNRow; irow++) {
587      int iIF = IFCol[irow] - cIF_1rel;
588      if (cIFs[iIF] == 0) {
589        cIFs[iIF] = 1;
590
591        // Find the axis lengths.
592        if (cHaveSpectra) {
593          if (cData[DATA].nelem < 0) {
594            // Variable dimension array.
595            if (readDim(DATA, irow+1, &cNAxis, cNAxes)) {
596              reportError();
597              close();
598              return 1;
599            }
600          }
601
602        } else {
603          if (cData[DATAXED].colnum > 0) {
604            char dataxed[32];
605            readParm("DATAXED", TSTRING, dataxed);
606
607            sscanf(dataxed, "(%ld,%ld,%ld,%ld,%ld)", cNAxes, cNAxes+1,
608              cNAxes+2, cNAxes+3, cNAxes+4);
609          }
610        }
611
612        // Number of channels and polarizations.
613        cNChan[iIF]    = cNAxes[cReqax[0]];
614        cNPol[iIF]     = cNAxes[cReqax[1]];
615        cHaveXPol[iIF] = 0;
616
617        // Is cross-polarization data present?
618        if (cData[XPOLDATA].colnum > 0) {
619          // Check that it conforms.
620          int  nAxis;
621          long nAxes[2];
622
623          if (readDim(XPOLDATA, irow+1, &nAxis, nAxes)) {
624            reportError();
625            close();
626            return 1;
627          }
628
629          // Default is to get it if we have it.
630          if (nAxis    == 2 &&
631              nAxes[0] == 2 &&
632              nAxes[1] == cNChan[iIF]) {
633            cGetXPol = cHaveXPol[iIF] = 1;
634          }
635        }
636      }
637    }
638
639    delete [] IFCol;
640
641  } else {
642    // No IF column.
643    cNIF = 1;
644    cIFs = new int[1];
645    cIFs[0] = 1;
646
647    cNChan    = new int[1];
648    cNPol     = new int[1];
649    cHaveXPol = new int[1];
650    cGetXPol  = 0;
651
652    // Number of channels and polarizations.
653    cNChan[0] = cNAxes[cReqax[0]];
654    cNPol[0]  = cNAxes[cReqax[1]];
655    cHaveXPol[0] = 0;
656  }
657
658  if (cALFA) {
659    // ALFA labels each polarization as a separate IF.
660    cNPol[0] = cNIF;
661    cNIF = 1;
662  }
663
664  // Passing back the address of the array allows PKSFITSreader::select() to
665  // modify its elements directly.
666  nIF = cNIF;
667  IFs = cIFs;
668
669  nChan    = cNChan;
670  nPol     = cNPol;
671  haveXPol = cHaveXPol;
672
673
674  // Default channel range selection.
675  cStartChan = new int[cNIF];
676  cEndChan   = new int[cNIF];
677  cRefChan   = new int[cNIF];
678
679  for (int iIF = 0; iIF < cNIF; iIF++) {
680    cStartChan[iIF] = 1;
681    cEndChan[iIF] = cNChan[iIF];
682    cRefChan[iIF] = cNChan[iIF]/2 + 1;
683  }
684
685  // Default is to get it if we have it.
686  cGetSpectra = cHaveSpectra;
687
688
689  // Are baseline parameters present?
690  cHaveBase = 0;
691  if (cData[BASELIN].colnum) {
692    // Check that it conforms.
693    int  nAxis, status = 0;
694    long nAxes[2];
695
696    if (fits_read_tdim(cSDptr, cData[BASELIN].colnum, 2, &nAxis, nAxes,
697                       &status) == 0) {
698      cHaveBase = (nAxis == 2);
699    }
700  }
701  haveBase = cHaveBase;
702
703
704  // Is extra system calibration data available?
705  cExtraSysCal = 0;
706  for (int iparm = REFBEAM; iparm < NDATA; iparm++) {
707    if (cData[iparm].colnum >= 0) {
708      cExtraSysCal = 1;
709      break;
710    }
711  }
712
713  extraSysCal = cExtraSysCal;
714
715  return 0;
716}
717
718//---------------------------------------------------- SDFITSreader::getHeader
719
720// Get parameters describing the data.
721
722int SDFITSreader::getHeader(
723        char   observer[32],
724        char   project[32],
725        char   telescope[32],
726        double antPos[3],
727        char   obsMode[32],
728        char   bunit[32],
729        float  &equinox,
730        char   radecsys[32],
731        char   dopplerFrame[32],
732        char   datobs[32],
733        double &utc,
734        double &refFreq,
735        double &bandwidth)
736{
737  // Has the file been opened?
738  if (!cSDptr) {
739    return 1;
740  }
741
742  // Read parameter values.
743  readParm("OBSERVER", TSTRING, observer);              // Shared.
744  readParm("PROJID",   TSTRING, project);               // Shared.
745  readParm("TELESCOP", TSTRING, telescope);             // Core.
746
747  antPos[0] = 0.0;
748  antPos[1] = 0.0;
749  antPos[2] = 0.0;
750  if (readParm("ANTENNA_POSITION", TDOUBLE, antPos)) {
751    readParm("OBSGEO-X",  TDOUBLE, antPos);             // Additional.
752    readParm("OBSGEO-Y",  TDOUBLE, antPos + 1);         // Additional.
753    readParm("OBSGEO-Z",  TDOUBLE, antPos + 2);         // Additional.
754  }
755
756  if (antPos[0] == 0.0) {
757    if (strncmp(telescope, "ATPKS", 5) == 0) {
758      // Parkes coordinates.
759      antPos[0] = -4554232.087;
760      antPos[1] =  2816759.046;
761      antPos[2] = -3454035.950;
762    } else if (strncmp(telescope, "ATMOPRA", 7) == 0) {
763      // Mopra coordinates.
764      antPos[0] = -4682768.630;
765      antPos[1] =  2802619.060;
766      antPos[2] = -3291759.900;
767    } else if (strncmp(telescope, "ARECIBO", 7) == 0) {
768      // Arecibo coordinates.
769      antPos[0] =  2390486.900;
770      antPos[1] = -5564731.440;
771      antPos[2] =  1994720.450;
772    }
773  }
774
775  readData(OBSMODE, 1, obsMode);                        // Shared.
776
777  // Brightness unit.
778  strcpy(bunit, cData[DATA].units);
779  if (strcmp(bunit, "JY") == 0) {
780    bunit[1] = 'y';
781  } else if (strcmp(bunit, "JY/BEAM") == 0) {
782    strcpy(bunit, "Jy/beam");
783  }
784
785  readParm("EQUINOX",  TFLOAT,  &equinox);              // Shared.
786  if (cStatus == 405) {
787    // EQUINOX was written as string value in early versions.
788    cStatus = 0;
789    char strtmp[32];
790    readParm("EQUINOX", TSTRING, strtmp);
791    sscanf(strtmp, "%f", &equinox);
792  }
793
794  if (readParm("RADESYS", TSTRING, radecsys)) {         // Additional.
795    if (readParm("RADECSYS", TSTRING, radecsys)) {      // Additional.
796      strcpy(radecsys, "");
797    }
798  }
799
800  if (readParm("SPECSYS", TSTRING, dopplerFrame)) {     // Additional.
801    // Fallback value.
802    strcpy(dopplerFrame, "TOPOCENT");
803
804    // Look for VELFRAME, written by earlier versions of Livedata.
805    if (readParm("VELFRAME", TSTRING, dopplerFrame)) {  // Additional.
806      // No, try digging it out of the CTYPE card (AIPS convention).
807      char keyw[9], ctype[9];
808      sprintf(keyw, "CTYPE%ld", cReqax[0]+1);
809      readParm(keyw, TSTRING, ctype);
810
811      if (strncmp(ctype, "FREQ-", 5) == 0) {
812        strcpy(dopplerFrame, ctype+5);
813        if (strcmp(dopplerFrame, "LSR") == 0) {
814          // LSR unqualified usually means LSR (kinematic).
815          strcpy(dopplerFrame, "LSRK");
816        } else if (strcmp(dopplerFrame, "HEL") == 0) {
817          // Almost certainly barycentric.
818          strcpy(dopplerFrame, "BARYCENT");
819        }
820      } else {
821        strcpy(dopplerFrame, "");
822      }
823    }
824
825    // Translate to FITS standard names.
826    if (strncmp(dopplerFrame, "TOP", 3) == 0) {
827      strcpy(dopplerFrame, "TOPOCENT");
828    } else if (strncmp(dopplerFrame, "GEO", 3) == 0) {
829      strcpy(dopplerFrame, "GEOCENTR");
830    } else if (strncmp(dopplerFrame, "HEL", 3) == 0) {
831      strcpy(dopplerFrame, "HELIOCEN");
832    } else if (strncmp(dopplerFrame, "BARY", 4) == 0) {
833      strcpy(dopplerFrame, "BARYCENT");
834    }
835  }
836
837  if (cStatus) {
838    reportError();
839    return 1;
840  }
841
842  // Get parameters from first row of table.
843  readData(DATE_OBS, 1, datobs);
844  readData(TIME,     1, &utc);
845  readData(FqRefVal, 1, &refFreq);
846  readParm("BANDWID", TDOUBLE, &bandwidth);             // Core.
847
848  if (cALFA_BD) utc *= 3600.0;
849
850  if (cStatus) {
851    reportError();
852    return 1;
853  }
854
855  // Check DATE-OBS format.
856  if (datobs[2] == '/') {
857    // Translate an old-format DATE-OBS.
858    datobs[9] = datobs[1];
859    datobs[8] = datobs[0];
860    datobs[2] = datobs[6];
861    datobs[5] = datobs[3];
862    datobs[3] = datobs[7];
863    datobs[6] = datobs[4];
864    datobs[7] = '-';
865    datobs[4] = '-';
866    datobs[1] = '9';
867    datobs[0] = '1';
868    datobs[10] = '\0';
869
870  } else if (datobs[10] == 'T' && cData[TIME].colnum < 0) {
871    // Dig UTC out of a new-format DATE-OBS.
872    int   hh, mm;
873    float ss;
874    sscanf(datobs+11, "%d:%d:%f", &hh, &mm, &ss);
875    utc = (hh*60 + mm)*60 + ss;
876    datobs[10] = '\0';
877  }
878
879  return 0;
880}
881
882//-------------------------------------------------- SDFITSreader::getFreqInfo
883
884// Get frequency parameters for each IF.
885
886int SDFITSreader::getFreqInfo(
887        int     &nIF,
888        double* &startFreq,
889        double* &endFreq)
890{
891  float  fqRefPix;
892  double fqDelt, fqRefVal;
893
894  nIF = cNIF;
895  startFreq = new double[nIF];
896  endFreq   = new double[nIF];
897
898  if (cData[IF].colnum > 0) {
899    short *IFCol = new short[cNRow];
900    short IFNul = 1;
901    int   anynul;
902    if (fits_read_col(cSDptr, TSHORT, cData[IF].colnum, 1, 1, cNRow,
903                      &IFNul, IFCol, &anynul, &cStatus)) {
904      reportError();
905      delete [] IFCol;
906      close();
907      return 1;
908    }
909
910    for (int iIF = 0; iIF < nIF; iIF++) {
911      if (cIFs[iIF]) {
912        // Find the first occurrence of this IF in the table.
913        int IFno = iIF + cIF_1rel;
914        for (int irow = 0; irow < cNRow;) {
915          if (IFCol[irow++] == IFno) {
916            readData(FqRefPix, irow, &fqRefPix);
917            readData(FqRefVal, irow, &fqRefVal);
918            readData(FqDelt,   irow, &fqDelt);
919
920            if (cALFA_BD) {
921              unsigned char invert;
922              readData("UPPERSB", TBYTE, irow, &invert);
923
924              if (invert) {
925                fqDelt = -fqDelt;
926              }
927            }
928
929            startFreq[iIF] = fqRefVal + (          1 - fqRefPix) * fqDelt;
930            endFreq[iIF]   = fqRefVal + (cNChan[iIF] - fqRefPix) * fqDelt;
931
932            break;
933          }
934        }
935
936      } else {
937        startFreq[iIF] = 0.0;
938        endFreq[iIF]   = 0.0;
939      }
940    }
941
942    delete [] IFCol;
943
944  } else {
945    // No IF column, read the first table entry.
946    readData(FqRefPix, 1, &fqRefPix);
947    readData(FqRefVal, 1, &fqRefVal);
948    readData(FqDelt,   1, &fqDelt);
949
950    startFreq[0] = fqRefVal + (        1 - fqRefPix) * fqDelt;
951    endFreq[0]   = fqRefVal + (cNChan[0] - fqRefPix) * fqDelt;
952  }
953
954  return cStatus;
955}
956
957//---------------------------------------------------- SDFITSreader::findRange
958
959// Find the range of the data in time and position.
960
961int SDFITSreader::findRange(
962        int    &nRow,
963        int    &nSel,
964        char   dateSpan[2][32],
965        double utcSpan[2],
966        double* &positions)
967{
968  int anynul;
969
970  // Has the file been opened?
971  if (!cSDptr) {
972    return 1;
973  }
974
975  nRow = cNRow;
976
977  // Find the number of rows selected.
978  short *sel = new short[nRow];
979  for (int irow = 0; irow < nRow; irow++) {
980    sel[irow] = 1;
981  }
982
983  if (cData[BEAM].colnum > 0) {
984    short *beamCol = new short[cNRow];
985    short beamNul = 1;
986    if (fits_read_col(cSDptr, TSHORT, cData[BEAM].colnum, 1, 1, cNRow,
987                      &beamNul, beamCol, &anynul, &cStatus)) {
988      reportError();
989      delete [] beamCol;
990      delete [] sel;
991      return 1;
992    }
993
994    for (int irow = 0; irow < nRow; irow++) {
995      if (!cBeams[beamCol[irow]-cBeam_1rel]) {
996        sel[irow] = 0;
997      }
998    }
999
1000    delete [] beamCol;
1001  }
1002
1003  if (cData[IF].colnum > 0) {
1004    short *IFCol = new short[cNRow];
1005    short IFNul = 1;
1006    if (fits_read_col(cSDptr, TSHORT, cData[IF].colnum, 1, 1, cNRow,
1007                      &IFNul, IFCol, &anynul, &cStatus)) {
1008      reportError();
1009      delete [] IFCol;
1010      delete [] sel;
1011      return 1;
1012    }
1013
1014    for (int irow = 0; irow < nRow; irow++) {
1015      if (!cIFs[IFCol[irow]-cIF_1rel]) {
1016        sel[irow] = 0;
1017      }
1018    }
1019
1020    delete [] IFCol;
1021  }
1022
1023  nSel = 0;
1024  for (int irow = 0; irow < nRow; irow++) {
1025    nSel += sel[irow];
1026  }
1027
1028
1029  // Find the time range assuming the data is in chronological order.
1030  readData(DATE_OBS, 1,    dateSpan[0]);
1031  readData(DATE_OBS, nRow, dateSpan[1]);
1032  readData(TIME, 1,    utcSpan);
1033  readData(TIME, nRow, utcSpan+1);
1034
1035  if (cALFA_BD) {
1036    utcSpan[0] *= 3600.0;
1037    utcSpan[1] *= 3600.0;
1038  }
1039
1040  // Check DATE-OBS format.
1041  for (int i = 0; i < 2; i++) {
1042    if (dateSpan[0][2] == '/') {
1043      // Translate an old-format DATE-OBS.
1044      dateSpan[i][9] = dateSpan[i][1];
1045      dateSpan[i][8] = dateSpan[i][0];
1046      dateSpan[i][2] = dateSpan[i][6];
1047      dateSpan[i][5] = dateSpan[i][3];
1048      dateSpan[i][3] = dateSpan[i][7];
1049      dateSpan[i][6] = dateSpan[i][4];
1050      dateSpan[i][7] = '-';
1051      dateSpan[i][4] = '-';
1052      dateSpan[i][1] = '9';
1053      dateSpan[i][0] = '1';
1054      dateSpan[i][10] = '\0';
1055    }
1056
1057    if (dateSpan[i][10] == 'T' && cData[TIME].colnum < 0) {
1058      // Dig UTC out of a new-format DATE-OBS.
1059      int   hh, mm;
1060      float ss;
1061      sscanf(dateSpan[i]+11, "%d:%d:%f", &hh, &mm, &ss);
1062      utcSpan[i] = (hh*60 + mm)*60 + ss;
1063    }
1064  }
1065
1066
1067  // Retrieve positions for selected data.
1068  double *ra  = new double[cNRow];
1069  double *dec = new double[cNRow];
1070  fits_read_col(cSDptr, TDOUBLE, cData[RA].colnum,  1, 1, nRow, 0, ra,
1071                &anynul, &cStatus);
1072  fits_read_col(cSDptr, TDOUBLE, cData[DEC].colnum, 1, 1, nRow, 0, dec,
1073                &anynul, &cStatus);
1074
1075  if (cALFA_BD) {
1076    for (int irow = 0; irow < nRow; irow++) {
1077      // Convert hours to degrees.
1078      ra[irow] *= 15.0;
1079    }
1080  }
1081
1082  int isel = 0;
1083  positions = new double[2*nSel];
1084
1085  // Parameters needed to compute feed-plane coordinates.
1086  double *srcRA, *srcDec;
1087  float  *par, *rot;
1088  if (cGetFeedPos) {
1089    srcRA  = new double[cNRow];
1090    srcDec = new double[cNRow];
1091    par    = new float[cNRow];
1092    rot    = new float[cNRow];
1093    fits_read_col(cSDptr, TDOUBLE, cData[OBJ_RA].colnum,   1, 1, nRow, 0,
1094                  srcRA,  &anynul, &cStatus);
1095    fits_read_col(cSDptr, TDOUBLE, cData[OBJ_DEC].colnum,  1, 1, nRow, 0,
1096                  srcDec, &anynul, &cStatus);
1097    fits_read_col(cSDptr, TFLOAT,  cData[PARANGLE].colnum, 1, 1, nRow, 0,
1098                  par,    &anynul, &cStatus);
1099    fits_read_col(cSDptr, TFLOAT,  cData[FOCUSROT].colnum, 1, 1, nRow, 0,
1100                  rot,    &anynul, &cStatus);
1101
1102    for (int irow = 0; irow < nRow; irow++) {
1103      if (sel[irow]) {
1104        // Convert to feed-plane coordinates.
1105        Double dist, pa;
1106        distPA(ra[irow]*D2R, dec[irow]*D2R, srcRA[irow]*D2R, srcDec[irow]*D2R,
1107               dist, pa);
1108
1109        Double spin = (par[irow] + rot[irow])*D2R - pa + PI;
1110        if (spin > 2.0*PI) spin -= 2.0*PI;
1111        Double squint = PI/2.0 - dist;
1112
1113        positions[isel++] = spin;
1114        positions[isel++] = squint;
1115      }
1116    }
1117
1118    delete [] srcRA;
1119    delete [] srcDec;
1120    delete [] par;
1121    delete [] rot;
1122
1123  } else {
1124    for (int irow = 0; irow < nRow; irow++) {
1125      if (sel[irow]) {
1126        positions[isel++] =  ra[irow] * D2R;
1127        positions[isel++] = dec[irow] * D2R;
1128      }
1129    }
1130  }
1131
1132  delete [] sel;
1133  delete [] ra;
1134  delete [] dec;
1135
1136  return cStatus;
1137}
1138
1139
1140//--------------------------------------------------------- SDFITSreader::read
1141
1142// Read the next data record.
1143
1144int SDFITSreader::read(
1145        PKSMBrecord &mbrec)
1146{
1147  // Has the file been opened?
1148  if (!cSDptr) {
1149    return 1;
1150  }
1151
1152  // Find the next selected beam and IF.
1153  short iBeam = 0, iIF = 0;
1154  while (++cRow <= cNRow) {
1155    if (cData[BEAM].colnum > 0) {
1156      readData(BEAM, cRow, &iBeam);
1157
1158      // Convert to 0-relative.
1159      if (cBeam_1rel) iBeam--;
1160    }
1161
1162
1163    if (cBeams[iBeam]) {
1164      if (cData[IF].colnum > 0) {
1165        readData(IF, cRow, &iIF);
1166
1167        // Convert to 0-relative.
1168        if (cIF_1rel) iIF--;
1169      }
1170
1171      if (cIFs[iIF]) {
1172        if (cALFA) {
1173          // ALFA data, check for calibration data.
1174          char chars[32];
1175          readData(OBSMODE, cRow, chars);
1176          if (strcmp(chars, "CAL") == 0) {
1177            // iIF is really the polarization in ALFA data.
1178            alfaCal(iBeam, iIF);
1179            continue;
1180          }
1181        }
1182
1183        break;
1184      }
1185    }
1186  }
1187
1188  // EOF?
1189  if (cRow > cNRow) {
1190    return -1;
1191  }
1192
1193
1194  if (cALFA) {
1195    int scanNo;
1196    readData(SCAN, cRow, &scanNo);
1197    if (scanNo != cALFAscan) {
1198      cScanNo++;
1199      cALFAscan = scanNo;
1200    }
1201    mbrec.scanNo = cScanNo;
1202
1203  } else {
1204    readData(SCAN, cRow, &mbrec.scanNo);
1205
1206    // Ensure that scan number is 1-relative.
1207    mbrec.scanNo -= (cFirstScanNo - 1);
1208  }
1209
1210  // Times.
1211  char datobs[32];
1212  readData(DATE_OBS, cRow,  datobs);
1213  readData(TIME,     cRow, &mbrec.utc);
1214  if (cALFA_BD) mbrec.utc *= 3600.0;
1215
1216  if (datobs[2] == '/') {
1217    // Translate an old-format DATE-OBS.
1218    datobs[9] = datobs[1];
1219    datobs[8] = datobs[0];
1220    datobs[2] = datobs[6];
1221    datobs[5] = datobs[3];
1222    datobs[3] = datobs[7];
1223    datobs[6] = datobs[4];
1224    datobs[7] = '-';
1225    datobs[4] = '-';
1226    datobs[1] = '9';
1227    datobs[0] = '1';
1228
1229  } else if (datobs[10] == 'T' && cData[TIME].colnum < 0) {
1230    // Dig UTC out of a new-format DATE-OBS.
1231    int   hh, mm;
1232    float ss;
1233    sscanf(datobs+11, "%d:%d:%f", &hh, &mm, &ss);
1234    mbrec.utc = (hh*60 + mm)*60 + ss;
1235  }
1236
1237  datobs[10] = '\0';
1238  strcpy(mbrec.datobs, datobs);
1239
1240  if (cData[CYCLE].colnum > 0) {
1241    readData(CYCLE, cRow, &mbrec.cycleNo);
1242    if (cALFA_BD) mbrec.cycleNo++;
1243  } else {
1244    // Cycle number not recorded, must do our own bookkeeping.
1245    if (mbrec.utc != cLastUTC) {
1246      mbrec.cycleNo = ++cCycleNo;
1247      cLastUTC = mbrec.utc;
1248    }
1249  }
1250
1251  readData(EXPOSURE, cRow, &mbrec.exposure);
1252
1253  // Source identification.
1254  readData(OBJECT, cRow, mbrec.srcName);
1255
1256  readData(OBJ_RA,  cRow, &mbrec.srcRA);
1257  if (strcmp(cData[OBJ_RA].name, "OBJ-RA") == 0) {
1258    mbrec.srcRA  *= D2R;
1259  }
1260
1261  if (strcmp(cData[OBJ_DEC].name, "OBJ-DEC") == 0) {
1262    readData(OBJ_DEC, cRow, &mbrec.srcDec);
1263    mbrec.srcDec *= D2R;
1264  }
1265
1266  // Line rest frequency (Hz).
1267  readData(RESTFRQ, cRow, &mbrec.restFreq);
1268  if (mbrec.restFreq == 0.0 && cALFA_BD) {
1269    mbrec.restFreq = 1420.40575e6;
1270  }
1271
1272  // Observation mode.
1273  readData(OBSMODE, cRow, mbrec.obsType);
1274
1275  // Beam-dependent parameters.
1276  mbrec.beamNo = iBeam + 1;
1277
1278  readData(RA,  cRow, &mbrec.ra);
1279  readData(DEC, cRow, &mbrec.dec);
1280  mbrec.ra  *= D2R;
1281  mbrec.dec *= D2R;
1282
1283  if (cALFA_BD) mbrec.ra *= 15.0;
1284
1285  float scanrate[2];
1286  readData(SCANRATE, cRow, &scanrate);
1287  if (strcmp(cData[SCANRATE].name, "SCANRATE") == 0) {
1288    mbrec.raRate  = scanrate[0] * D2R;
1289    mbrec.decRate = scanrate[1] * D2R;
1290  }
1291  mbrec.rateAge = 0;
1292  mbrec.rateson = 0;
1293
1294  // IF-dependent parameters.
1295  int startChan = cStartChan[iIF];
1296  int endChan   = cEndChan[iIF];
1297  int refChan   = cRefChan[iIF];
1298
1299  // Allocate data storage.
1300  int nChan = abs(endChan - startChan) + 1;
1301  int nPol = cNPol[iIF];
1302
1303  if (cGetSpectra || cGetXPol) {
1304    int nxpol = cGetXPol ? 2*nChan : 0;
1305    mbrec.allocate(0, nChan*nPol, nxpol);
1306  }
1307
1308  mbrec.nIF = 1;
1309  mbrec.IFno[0]  = iIF + 1;
1310  mbrec.nChan[0] = nChan;
1311  mbrec.nPol[0]  = nPol;
1312
1313  readData(FqRefPix, cRow, mbrec.fqRefPix);
1314  readData(FqRefVal, cRow, mbrec.fqRefVal);
1315  readData(FqDelt,   cRow, mbrec.fqDelt);
1316
1317  if (cALFA_BD) {
1318    unsigned char invert;
1319    int anynul, colnum;
1320    findCol("UPPERSB", &colnum);
1321    fits_read_col(cSDptr, TBYTE, colnum, cRow, 1, 1, 0, &invert, &anynul,
1322                  &cStatus);
1323
1324    if (invert) {
1325      mbrec.fqDelt[0] = -mbrec.fqDelt[0];
1326    }
1327  }
1328
1329  if (cStatus) {
1330    reportError();
1331    return 1;
1332  }
1333
1334  // Adjust for channel selection.
1335  if (mbrec.fqRefPix[0] != refChan) {
1336    mbrec.fqRefVal[0] += (refChan - mbrec.fqRefPix[0]) * mbrec.fqDelt[0];
1337    mbrec.fqRefPix[0]  =  refChan;
1338  }
1339
1340  if (endChan < startChan) {
1341    mbrec.fqDelt[0] = -mbrec.fqDelt[0];
1342  }
1343
1344  // The data may only have a scalar Tsys value.
1345  mbrec.tsys[0][0] = 0.0f;
1346  mbrec.tsys[0][1] = 0.0f;
1347  if (cData[TSYS].nelem >= nPol) {
1348    readData(TSYS, cRow, mbrec.tsys[0]);
1349  }
1350
1351  for (int j = 0; j < 2; j++) {
1352    mbrec.calfctr[0][j] = 0.0f;
1353  }
1354  if (cData[CALFCTR].colnum > 0) {
1355    readData(CALFCTR, cRow, mbrec.calfctr);
1356  }
1357
1358  if (cHaveBase) {
1359    mbrec.haveBase = 1;
1360    readData(BASELIN, cRow, mbrec.baseLin);
1361    readData(BASESUB, cRow, mbrec.baseSub);
1362  } else {
1363    mbrec.haveBase = 0;
1364  }
1365
1366  if (cStatus) {
1367    reportError();
1368    return 1;
1369  }
1370
1371  // Read data, sectioning and transposing it in the process.
1372  long *blc = new long[cNAxis+1];
1373  long *trc = new long[cNAxis+1];
1374  long *inc = new long[cNAxis+1];
1375  for (int iaxis = 0; iaxis <= cNAxis; iaxis++) {
1376    blc[iaxis] = 1;
1377    trc[iaxis] = 1;
1378    inc[iaxis] = 1;
1379  }
1380
1381  blc[cReqax[0]] = std::min(startChan, endChan);
1382  trc[cReqax[0]] = std::max(startChan, endChan);
1383  blc[cNAxis] = cRow;
1384  trc[cNAxis] = cRow;
1385
1386  mbrec.haveSpectra = cGetSpectra;
1387  if (cGetSpectra) {
1388    int  anynul;
1389
1390    for (int ipol = 0; ipol < nPol; ipol++) {
1391      blc[cReqax[1]] = ipol+1;
1392      trc[cReqax[1]] = ipol+1;
1393
1394      if (cALFA) {
1395        // ALFA data: polarizations are stored in successive rows.
1396        blc[cReqax[1]] = 1;
1397        trc[cReqax[1]] = 1;
1398
1399        if (ipol) {
1400          if (++cRow > cNRow) {
1401            return -1;
1402          }
1403
1404          blc[cNAxis] = cRow;
1405          trc[cNAxis] = cRow;
1406        }
1407
1408      } else if (cData[DATA].nelem < 0) {
1409        // Variable dimension array; get axis lengths.
1410        int  naxis = 5, status;
1411
1412        if ((status = readDim(DATA, cRow, &naxis, cNAxes))) {
1413          reportError();
1414
1415        } else if ((status = (naxis != cNAxis))) {
1416          cerr << "DATA array dimensions changed." << endl;
1417        }
1418
1419        if (status) {
1420          delete [] blc;
1421          delete [] trc;
1422          delete [] inc;
1423          return 1;
1424        }
1425      }
1426
1427      if (fits_read_subset_flt(cSDptr, cData[DATA].colnum, cNAxis, cNAxes,
1428          blc, trc, inc, 0, mbrec.spectra[0] + ipol*nChan, &anynul,
1429          &cStatus)) {
1430        reportError();
1431        delete [] blc;
1432        delete [] trc;
1433        delete [] inc;
1434        return 1;
1435      }
1436
1437      if (endChan < startChan) {
1438        // Reverse the spectrum.
1439        float *iptr = mbrec.spectra[0] + ipol*nChan;
1440        float *jptr = iptr + nChan - 1;
1441        float *mid  = iptr + nChan/2;
1442        while (iptr < mid) {
1443          float tmp = *iptr;
1444          *(iptr++) = *jptr;
1445          *(jptr--) = tmp;
1446        }
1447      }
1448
1449      if (cALFA) {
1450        // ALFA data, rescale the spectrum.
1451        float *chan  = mbrec.spectra[0] + ipol*nChan;
1452        float *chanN = chan + nChan;
1453        while (chan < chanN) {
1454          // Approximate conversion to Jy.
1455          *(chan++) *= cALFAcal[iBeam][iIF];
1456        }
1457      }
1458
1459      if (mbrec.tsys[0][ipol] == 0.0) {
1460        // Compute Tsys as the average across the spectrum.
1461        float *chan  = mbrec.spectra[0] + ipol*nChan;
1462        float *chanN = chan + nChan;
1463        float *tsys = mbrec.tsys[0] + ipol;
1464        while (chan < chanN) {
1465          *tsys += *(chan++);
1466        }
1467
1468        *tsys /= nChan;
1469      }
1470
1471      // Read data flags.
1472      if (cData[FLAGGED].colnum > 0) {
1473        if (fits_read_subset_byt(cSDptr, cData[FLAGGED].colnum, cNAxis,
1474            cNAxes, blc, trc, inc, 0, mbrec.flagged[0] + ipol*nChan, &anynul,
1475            &cStatus)) {
1476          reportError();
1477          delete [] blc;
1478          delete [] trc;
1479          delete [] inc;
1480          return 1;
1481        }
1482
1483        if (endChan < startChan) {
1484          // Reverse the flag vector.
1485          unsigned char *iptr = mbrec.flagged[0] + ipol*nChan;
1486          unsigned char *jptr = iptr + nChan - 1;
1487          for (int ichan = 0; ichan < nChan/2; ichan++) {
1488            unsigned char tmp = *iptr;
1489            *(iptr++) = *jptr;
1490            *(jptr--) = tmp;
1491          }
1492        }
1493
1494      } else {
1495        // All channels are unflagged by default.
1496        unsigned char *iptr = mbrec.flagged[0] + ipol*nChan;
1497        for (int ichan = 0; ichan < nChan; ichan++) {
1498          *(iptr++) = 0;
1499        }
1500      }
1501    }
1502  }
1503
1504
1505  // Read cross-polarization data.
1506  if (cGetXPol) {
1507    int anynul;
1508    for (int j = 0; j < 2; j++) {
1509      mbrec.xcalfctr[0][j] = 0.0f;
1510    }
1511    if (cData[XCALFCTR].colnum > 0) {
1512      readData(XCALFCTR, cRow, mbrec.xcalfctr);
1513    }
1514
1515    blc[0] = 1;
1516    trc[0] = 2;
1517    blc[1] = std::min(startChan, endChan);
1518    trc[1] = std::max(startChan, endChan);
1519    blc[2] = cRow;
1520    trc[2] = cRow;
1521
1522    int  nAxis = 2;
1523    long nAxes[] = {2, nChan};
1524
1525    if (fits_read_subset_flt(cSDptr, cData[XPOLDATA].colnum, nAxis, nAxes,
1526        blc, trc, inc, 0, mbrec.xpol[0], &anynul, &cStatus)) {
1527      reportError();
1528      delete [] blc;
1529      delete [] trc;
1530      delete [] inc;
1531      return 1;
1532    }
1533
1534    if (endChan < startChan) {
1535      // Invert the cross-polarization spectrum.
1536      float *iptr = mbrec.xpol[0];
1537      float *jptr = iptr + nChan - 2;
1538      for (int ichan = 0; ichan < nChan/2; ichan++) {
1539        float tmp = *iptr;
1540        *iptr = *jptr;
1541        *jptr = tmp;
1542
1543        tmp = *(iptr+1);
1544        *(iptr+1) = *(jptr+1);
1545        *(jptr+1) = tmp;
1546
1547        iptr += 2;
1548        jptr -= 2;
1549      }
1550    }
1551  }
1552
1553  delete [] blc;
1554  delete [] trc;
1555  delete [] inc;
1556
1557  if (cStatus) {
1558    reportError();
1559    return 1;
1560  }
1561
1562  mbrec.extraSysCal = cExtraSysCal;
1563  readData(REFBEAM,  cRow, &mbrec.refBeam);
1564  readData(TCAL,     cRow, &mbrec.tcal[0]);
1565  readData(TCALTIME, cRow,  mbrec.tcalTime);
1566  readData(AZIMUTH,  cRow, &mbrec.azimuth);
1567  readData(ELEVATIO, cRow, &mbrec.elevation);
1568  readData(PARANGLE, cRow, &mbrec.parAngle);
1569  readData(FOCUSAXI, cRow, &mbrec.focusAxi);
1570  readData(FOCUSTAN, cRow, &mbrec.focusTan);
1571  readData(FOCUSROT, cRow, &mbrec.focusRot);
1572  readData(TAMBIENT, cRow, &mbrec.temp);
1573  readData(PRESSURE, cRow, &mbrec.pressure);
1574  readData(HUMIDITY, cRow, &mbrec.humidity);
1575  readData(WINDSPEE, cRow, &mbrec.windSpeed);
1576  readData(WINDDIRE, cRow, &mbrec.windAz);
1577
1578  if (cALFA_BD) {
1579    // ALFA BDFITS stores zenith angle rather than elevation.
1580    mbrec.elevation = 90.0 - mbrec.elevation;
1581  }
1582
1583  mbrec.azimuth   *= D2R;
1584  mbrec.elevation *= D2R;
1585  mbrec.parAngle  *= D2R;
1586  mbrec.focusRot  *= D2R;
1587  mbrec.windAz    *= D2R;
1588
1589  if (cStatus) {
1590    reportError();
1591    return 1;
1592  }
1593
1594  return 0;
1595}
1596
1597
1598//------------------------------------------------------ SDFITSreader::alfaCal
1599
1600// Process ALFA calibration data.
1601
1602int SDFITSreader::alfaCal(
1603        short iBeam,
1604        short iPol)
1605{
1606  int  calOn;
1607  char chars[32];
1608  if (cALFA_BD) {
1609    readData("OBS_NAME", TSTRING, cRow, chars);
1610  } else {
1611    readData("SCANTYPE", TSTRING, cRow, chars);
1612  }
1613
1614  if (strcmp(chars, "ON") == 0) {
1615    calOn = 1;
1616  } else if (strcmp(chars, "OFF") == 0) {
1617    calOn = 0;
1618  } else {
1619    return 1;
1620  }
1621
1622  // Read cal data.
1623  long *blc = new long[cNAxis+1];
1624  long *trc = new long[cNAxis+1];
1625  long *inc = new long[cNAxis+1];
1626  for (int iaxis = 0; iaxis <= cNAxis; iaxis++) {
1627    blc[iaxis] = 1;
1628    trc[iaxis] = 1;
1629    inc[iaxis] = 1;
1630  }
1631
1632  // User channel selection.
1633  int startChan = cStartChan[0];
1634  int endChan   = cEndChan[0];
1635
1636  blc[cNAxis] = cRow;
1637  trc[cNAxis] = cRow;
1638  blc[cReqax[0]] = std::min(startChan, endChan);
1639  trc[cReqax[0]] = std::max(startChan, endChan);
1640  blc[cReqax[1]] = 1;
1641  trc[cReqax[1]] = 1;
1642
1643  float spectrum[endChan];
1644  int anynul;
1645  if (fits_read_subset_flt(cSDptr, cData[DATA].colnum, cNAxis, cNAxes,
1646      blc, trc, inc, 0, spectrum, &anynul, &cStatus)) {
1647    reportError();
1648    delete [] blc;
1649    delete [] trc;
1650    delete [] inc;
1651    return 1;
1652  }
1653
1654  // Average the spectrum.
1655  float mean = 1e9f;
1656  for (int k = 0; k < 2; k++) {
1657    float discrim = 2.0f * mean;
1658
1659    int nChan = 0;
1660    float sum = 0.0f;
1661
1662    float *chanN = spectrum + abs(endChan - startChan) + 1;
1663    for (float *chan = spectrum; chan < chanN; chan++) {
1664      // Simple discriminant that eliminates strong radar interference.
1665      if (*chan < discrim) {
1666        nChan++;
1667        sum += *chan;
1668      }
1669    }
1670
1671    mean = sum / nChan;
1672  }
1673
1674  if (calOn) {
1675    cALFAcalOn[iBeam][iPol]  += mean;
1676  } else {
1677    cALFAcalOff[iBeam][iPol] += mean;
1678  }
1679
1680  if (cALFAcalOn[iBeam][iPol] != 0.0f &&
1681      cALFAcalOff[iBeam][iPol] != 0.0f) {
1682    // Tcal should come from the TCAL table, it varies weakly with beam,
1683    // polarization, and frequency.  However, TCAL is not written properly.
1684    float Tcal = 12.0f;
1685    cALFAcal[iBeam][iPol] = Tcal / (cALFAcalOn[iBeam][iPol] -
1686                                    cALFAcalOff[iBeam][iPol]);
1687
1688    // Scale from K to Jy; the gain also varies weakly with beam,
1689    // polarization, frequency, and zenith angle.
1690    float fluxCal = 10.0f;
1691    cALFAcal[iBeam][iPol] /= fluxCal;
1692
1693    cALFAcalOn[iBeam][iPol]  = 0.0f;
1694    cALFAcalOff[iBeam][iPol] = 0.0f;
1695  }
1696
1697  return 0;
1698}
1699
1700
1701//-------------------------------------------------- SDFITSreader::reportError
1702
1703// Print the error message corresponding to the input status value and all the
1704// messages on the CFITSIO error stack to stderr.
1705
1706void SDFITSreader::reportError()
1707{
1708  fits_report_error(stderr, cStatus);
1709}
1710
1711//-------------------------------------------------------- SDFITSreader::close
1712
1713// Close the SDFITS file.
1714
1715void SDFITSreader::close()
1716{
1717  if (cSDptr) {
1718    int status = 0;
1719    fits_close_file(cSDptr, &status);
1720    cSDptr = 0;
1721
1722    if (cBeams)     delete [] cBeams;
1723    if (cIFs)       delete [] cIFs;
1724    if (cStartChan) delete [] cStartChan;
1725    if (cEndChan)   delete [] cEndChan;
1726    if (cRefChan)   delete [] cRefChan;
1727  }
1728}
1729
1730//----------------------------------------------------- SDFITSreader::findData
1731
1732// Locate a data item in the SDFITS file.
1733
1734void SDFITSreader::findData(
1735        int  iData,
1736        char *name,
1737        int  type)
1738{
1739  cData[iData].name = name;
1740  cData[iData].type = type;
1741
1742  int colnum;
1743  findCol(name, &colnum);
1744  cData[iData].colnum = colnum;
1745
1746  // Determine the number of data elements.
1747  if (colnum > 0) {
1748    int  coltype;
1749    long nelem, width;
1750    fits_get_coltype(cSDptr, colnum, &coltype, &nelem, &width, &cStatus);
1751    fits_get_bcolparms(cSDptr, colnum, 0x0, cData[iData].units, 0x0, 0x0, 0x0,
1752      0x0, 0x0, 0x0, &cStatus);
1753
1754    // Look for a TDIMnnn keyword or column.
1755    char tdim[8];
1756    sprintf(tdim, "TDIM%d", colnum);
1757    findCol(tdim, &cData[iData].tdimcol);
1758
1759    if (coltype < 0) {
1760      // CFITSIO returns coltype < 0 for variable length arrays.
1761      cData[iData].coltype = -coltype;
1762      cData[iData].nelem   = -nelem;
1763
1764    } else {
1765      cData[iData].coltype = coltype;
1766
1767      // Is there a TDIMnnn column?
1768      if (cData[iData].tdimcol > 0) {
1769        // Yes, dimensions of the fixed-length array could still vary.
1770        cData[iData].nelem = -nelem;
1771      } else {
1772        cData[iData].nelem =  nelem;
1773      }
1774    }
1775
1776  } else if (colnum == 0) {
1777    // Keyword.
1778    cData[iData].coltype =  0;
1779    cData[iData].nelem   =  1;
1780    cData[iData].tdimcol = -1;
1781  }
1782}
1783
1784//------------------------------------------------------ SDFITSreader::readDim
1785
1786// Determine the dimensions of an array in the SDFITS file.
1787
1788int SDFITSreader::readDim(
1789        int  iData,
1790        long iRow,
1791        int *naxis,
1792        long naxes[])
1793{
1794  int colnum = cData[iData].colnum;
1795  if (colnum <= 0) {
1796    return 1;
1797  }
1798
1799  int maxdim = *naxis;
1800  if (cData[iData].tdimcol < 0) {
1801    // No TDIMnnn column for this array.
1802    if (cData[iData].nelem < 0) {
1803      // Variable length array; read the array descriptor.
1804      *naxis = 1;
1805      long dummy;
1806      if (fits_read_descript(cSDptr, colnum, iRow, naxes, &dummy, &cStatus)) {
1807        return 1;
1808      }
1809
1810    } else {
1811      // Read the repeat count from TFORMnnn.
1812      if (fits_read_tdim(cSDptr, colnum, maxdim, naxis, naxes, &cStatus)) {
1813        return 1;
1814      }
1815    }
1816
1817  } else {
1818    // Read the TDIMnnn value from the header or table.
1819    char tdim[8], tdimval[64];
1820    sprintf(tdim, "TDIM%d", colnum);
1821    readData(tdim, TSTRING, iRow, tdimval);
1822
1823    // fits_decode_tdim() checks that the TDIMnnn value is within the length
1824    // of the array in the specified column number but unfortunately doesn't
1825    // recognize variable-length arrays.  Hence we must decode it here.
1826    char *tp = tdimval;
1827    if (*tp != '(') return 1;
1828
1829    tp++;
1830    *naxis = 0;
1831    for (size_t j = 1; j < strlen(tdimval); j++) {
1832      if (tdimval[j] == ',' || tdimval[j] == ')') {
1833        sscanf(tp, "%ld", naxes + (*naxis)++);
1834        if (tdimval[j] == ')') break;
1835        tp = tdimval + j + 1;
1836      }
1837    }
1838  }
1839
1840  return 0;
1841}
1842
1843//----------------------------------------------------- SDFITSreader::readParm
1844
1845// Read a parameter value from the SDFITS file.
1846
1847int SDFITSreader::readParm(
1848        char *name,
1849        int  type,
1850        void *value)
1851{
1852  return readData(name, type, 1, value);
1853}
1854
1855//----------------------------------------------------- SDFITSreader::readData
1856
1857// Read a data value from the SDFITS file.
1858
1859int SDFITSreader::readData(
1860        char *name,
1861        int  type,
1862        long iRow,
1863        void *value)
1864{
1865  int colnum;
1866  findCol(name, &colnum);
1867
1868  if (colnum > 0) {
1869    // Read the first value from the specified row of the table.
1870    int  coltype;
1871    long nelem, width;
1872    fits_get_coltype(cSDptr, colnum, &coltype, &nelem, &width, &cStatus);
1873
1874    int anynul;
1875    if (type == TSTRING) {
1876      if (nelem) {
1877        fits_read_col(cSDptr, type, colnum, iRow, 1, 1, 0, &value, &anynul,
1878                      &cStatus);
1879      } else {
1880        strcpy((char *)value, "");
1881      }
1882
1883    } else {
1884      if (nelem) {
1885        fits_read_col(cSDptr, type, colnum, iRow, 1, 1, 0, value, &anynul,
1886                      &cStatus);
1887      } else {
1888        if (type == TSHORT) {
1889          *((short *)value) = 0;
1890        } else if (type == TINT) {
1891          *((int *)value) = 0;
1892        } else if (type == TFLOAT) {
1893          *((float *)value) = 0.0f;
1894        } else if (type == TDOUBLE) {
1895          *((double *)value) = 0.0;
1896        }
1897      }
1898    }
1899
1900  } else if (colnum == 0) {
1901    // Read keyword value.
1902    fits_read_key(cSDptr, type, name, value, 0, &cStatus);
1903
1904  } else {
1905    // Not present.
1906    if (type == TSTRING) {
1907      strcpy((char *)value, "");
1908    } else if (type == TSHORT) {
1909      *((short *)value) = 0;
1910    } else if (type == TINT) {
1911      *((int *)value) = 0;
1912    } else if (type == TFLOAT) {
1913      *((float *)value) = 0.0f;
1914    } else if (type == TDOUBLE) {
1915      *((double *)value) = 0.0;
1916    }
1917  }
1918
1919  return colnum < 0;
1920}
1921
1922//----------------------------------------------------- SDFITSreader::readData
1923
1924// Read data from the SDFITS file.
1925
1926int SDFITSreader::readData(
1927        int  iData,
1928        long iRow,
1929        void *value)
1930{
1931  char *name  = cData[iData].name;
1932  int  type   = cData[iData].type;
1933  int  colnum = cData[iData].colnum;
1934  long nelem  = cData[iData].nelem;
1935
1936  if (colnum > 0) {
1937    // Read the required number of values from the specified row of the table.
1938    int anynul;
1939    if (type == TSTRING) {
1940      if (nelem) {
1941        fits_read_col(cSDptr, type, colnum, iRow, 1, 1, 0, &value, &anynul,
1942                      &cStatus);
1943      } else {
1944        strcpy((char *)value, "");
1945      }
1946
1947    } else {
1948      if (nelem) {
1949        fits_read_col(cSDptr, type, colnum, iRow, 1, abs(nelem), 0, value,
1950                      &anynul, &cStatus);
1951      } else {
1952        if (type == TSHORT) {
1953          *((short *)value) = 0;
1954        } else if (type == TINT) {
1955          *((int *)value) = 0;
1956        } else if (type == TFLOAT) {
1957          *((float *)value) = 0.0f;
1958        } else if (type == TDOUBLE) {
1959          *((double *)value) = 0.0;
1960        }
1961      }
1962    }
1963
1964  } else if (colnum == 0) {
1965    // Read keyword value.
1966    fits_read_key(cSDptr, type, name, value, 0, &cStatus);
1967
1968  } else {
1969    // Not present.
1970    if (type == TSTRING) {
1971      strcpy((char *)value, "");
1972    } else if (type == TSHORT) {
1973      *((short *)value) = 0;
1974    } else if (type == TINT) {
1975      *((int *)value) = 0;
1976    } else if (type == TFLOAT) {
1977      *((float *)value) = 0.0f;
1978    } else if (type == TDOUBLE) {
1979      *((double *)value) = 0.0;
1980    }
1981  }
1982
1983  return colnum < 0;
1984}
1985
1986//------------------------------------------------------ SDFITSreader::findCol
1987
1988// Locate a parameter in the SDFITS file.
1989
1990void SDFITSreader::findCol(
1991        char *name,
1992        int *colnum)
1993{
1994  *colnum = 0;
1995  int status = 0;
1996  fits_get_colnum(cSDptr, CASESEN, name, colnum, &status);
1997
1998  if (status) {
1999    // Not a real column - maybe it's virtual.
2000    char card[81];
2001
2002    status = 0;
2003    fits_read_card(cSDptr, name, card, &status);
2004    if (status) {
2005      // Not virtual either.
2006      *colnum = -1;
2007    }
2008
2009    // Clear error messages.
2010    fits_clear_errmsg();
2011  }
2012}
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