Ignore:
Timestamp:
02/16/06 12:02:18 (18 years ago)
Author:
mar637
Message:

Code replacemnts after the rename

File:
1 edited

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  • trunk/src/Scantable.cpp

    r804 r805  
    1 //#---------------------------------------------------------------------------
    2 //# SDMemTable.cc: A MemoryTable container for single dish integrations
    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 
     1//
     2// C++ Implementation: Scantable
     3//
     4// Description:
     5//
     6//
     7// Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005
     8//
     9// Copyright: See COPYING file that comes with this distribution
     10//
     11//
    3212#include <map>
    3313
    … …  
    3515#include <casa/iostream.h>
    3616#include <casa/iomanip.h>
     17#include <casa/OS/Path.h>
     18#include <casa/OS/File.h>
    3719#include <casa/Arrays/Array.h>
    3820#include <casa/Arrays/ArrayMath.h>
    … …  
    4527#include <casa/BasicSL/Constants.h>
    4628#include <casa/Quanta/MVAngle.h>
     29#include <casa/Containers/RecordField.h>
    4730
    4831#include <tables/Tables/TableParse.h>
    … …  
    5235#include <tables/Tables/ScaColDesc.h>
    5336#include <tables/Tables/ArrColDesc.h>
     37#include <tables/Tables/TableRow.h>
     38#include <tables/Tables/TableVector.h>
     39#include <tables/Tables/TableIter.h>
    5440
    5541#include <tables/Tables/ExprNode.h>
    5642#include <tables/Tables/TableRecord.h>
    5743#include <measures/Measures/MFrequency.h>
     44#include <measures/Measures/MEpoch.h>
    5845#include <measures/Measures/MeasTable.h>
     46#include <measures/Measures/MeasRef.h>
     47#include <measures/TableMeasures/TableMeasRefDesc.h>
     48#include <measures/TableMeasures/TableMeasValueDesc.h>
     49#include <measures/TableMeasures/TableMeasDesc.h>
     50#include <measures/TableMeasures/ScalarMeasColumn.h>
    5951#include <coordinates/Coordinates/CoordinateUtil.h>
    6052#include <casa/Quanta/MVTime.h>
    6153#include <casa/Quanta/MVAngle.h>
    6254
    63 #include "SDDefs.h"
    64 #include "SDContainer.h"
    65 #include "MathUtils.h"
    66 #include "SDPol.h"
     55#include "Scantable.h"
    6756#include "SDAttr.h"
    6857
    69 #include "SDMemTable.h"
    70 
    7158using namespace casa;
    72 using namespace asap;
    73 
    74 SDMemTable::SDMemTable() :
    75   IFSel_(0),
    76   beamSel_(0),
    77   polSel_(0)
    78 {
    79   setup();
     59
     60namespace asap {
     61
     62Scantable::Scantable(Table::TableType ttype) :
     63  type_(ttype),
     64  freqTable_(ttype),
     65  focusTable_(ttype),
     66  weatherTable_(ttype),
     67  tcalTable_(ttype),
     68  moleculeTable_(ttype)
     69{
     70  setupMainTable();
     71  table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table());
     72  table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table());
     73  table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table());
     74  table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table());
     75  table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table());
     76  setupHistoryTable();
     77  setupFitTable();
     78
     79  originalTable_ = table_;
    8080  attach();
    8181}
    8282
    83 SDMemTable::SDMemTable(const std::string& name) :
    84   IFSel_(0),
    85   beamSel_(0),
    86   polSel_(0)
     83Scantable::Scantable(const std::string& name, Table::TableType ttype) :
     84  type_(ttype),
     85  freqTable_(ttype)
    8786{
    8887  Table tab(name);
    … …  
    9291    throw(AipsError("Unsupported version of ASAP file."));
    9392  }
    94   table_ = tab.copyToMemoryTable("dummy");
     93  if ( type_ == Table::Memory )
     94    table_ = tab.copyToMemoryTable("dummy");
     95  else
     96    table_ = tab;
     97
     98  originalTable_ = table_;
    9599  attach();
    96100}
    97101
    98 SDMemTable::SDMemTable(const SDMemTable& other, Bool clear)
    99 {
    100   table_ = other.table_.copyToMemoryTable(String("dummy"));
    101   // clear all rows()
     102
     103Scantable::Scantable( const Scantable& other, bool clear )
     104{
     105  // with or without data
    102106  if (clear) {
    103     table_.removeRow(this->table_.rowNumbers());
    104     IFSel_= 0;
    105     beamSel_= 0;
    106     polSel_= 0;
    107   } else {
    108     IFSel_= other.IFSel_;
    109     beamSel_= other.beamSel_;
    110     polSel_= other.polSel_;
    111   }
    112 
     107    table_ = TableCopy::makeEmptyMemoryTable(String("dummy"), other.table_,
     108                                             True);
     109  } else {
     110    table_ = other.table_.copyToMemoryTable(String("dummy"));
     111  }
     112
     113  originalTable_ = table_;
    113114  attach();
    114115}
    115116
    116 SDMemTable::SDMemTable(const Table& tab, const std::string& exprs) :
    117   IFSel_(0),
    118   beamSel_(0),
    119   polSel_(0)
    120 {
    121   Table t = tableCommand(exprs,tab);
    122   if (t.nrow() == 0)
    123       throw(AipsError("Query unsuccessful."));
    124   table_ = t.copyToMemoryTable("dummy");
    125   attach();
    126   renumber();
    127 }
    128 
    129 SDMemTable::~SDMemTable()
    130 {
    131   //cerr << "goodbye from SDMemTable @ " << this << endl;
    132 }
    133 
    134 SDMemTable SDMemTable::getScan(Int scanID) const
    135 {
    136   String cond("SELECT * from $1 WHERE SCANID == ");
    137   cond += String::toString(scanID);
    138   return SDMemTable(table_, cond);
    139 }
    140 
    141 SDMemTable &SDMemTable::operator=(const SDMemTable& other)
    142 {
    143   if (this != &other) {
    144      IFSel_= other.IFSel_;
    145      beamSel_= other.beamSel_;
    146      polSel_= other.polSel_;
    147      table_ = other.table_.copyToMemoryTable(String("dummy"));
    148      attach();
    149   }
    150   return *this;
    151 }
    152 
    153 SDMemTable SDMemTable::getSource(const std::string& source) const
    154 {
    155   String cond("SELECT * from $1 WHERE SRCNAME == ");
    156   cond += source;
    157   return SDMemTable(table_, cond);
    158 }
    159 
    160 void SDMemTable::setup()
     117Scantable::~Scantable()
     118{
     119  cout << "~Scantable() " << this << endl;
     120}
     121
     122void Scantable::setupMainTable()
    161123{
    162124  TableDesc td("", "1", TableDesc::Scratch);
    163   td.comment() = "A SDMemTable";
     125  td.comment() = "An ASAP Scantable";
    164126  td.rwKeywordSet().define("VERSION", Int(version_));
    165127
     128  // n Cycles
     129  td.addColumn(ScalarColumnDesc<uInt>("SCANNO"));
     130  // new index every nBeam x nIF x nPol
     131  td.addColumn(ScalarColumnDesc<uInt>("CYCLENO"));
     132
     133  td.addColumn(ScalarColumnDesc<uInt>("BEAMNO"));
     134  td.addColumn(ScalarColumnDesc<uInt>("IFNO"));
     135  td.rwKeywordSet().define("POLTYPE", String("linear"));
     136  td.addColumn(ScalarColumnDesc<uInt>("POLNO"));
     137
     138  td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID"));
     139  td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID"));
     140  // linear, circular, stokes [I Q U V], stokes1 [I Plinear Pangle V]
     141  td.addColumn(ScalarColumnDesc<Int>("REFBEAMNO"));
     142
    166143  td.addColumn(ScalarColumnDesc<Double>("TIME"));
     144  TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default
     145  TableMeasValueDesc measVal(td, "TIME");
     146  TableMeasDesc<MEpoch> mepochCol(measVal, measRef);
     147  mepochCol.write(td);
     148
     149  td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
     150
    167151  td.addColumn(ScalarColumnDesc<String>("SRCNAME"));
     152  // Type of source (on=0, off=1, other=-1)
     153  td.addColumn(ScalarColumnDesc<Int>("SRCTYPE", Int(-1)));
     154  td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
     155
     156  //The actual Data Vectors
    168157  td.addColumn(ArrayColumnDesc<Float>("SPECTRA"));
    169158  td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA"));
    170159  td.addColumn(ArrayColumnDesc<Float>("TSYS"));
    171   td.addColumn(ArrayColumnDesc<Float>("STOKES"));
    172   td.addColumn(ScalarColumnDesc<Int>("SCANID"));
    173   td.addColumn(ScalarColumnDesc<Double>("INTERVAL"));
    174   td.addColumn(ArrayColumnDesc<uInt>("FREQID"));
    175   td.addColumn(ArrayColumnDesc<uInt>("RESTFREQID"));
    176   td.addColumn(ArrayColumnDesc<Double>("DIRECTION"));
    177   td.addColumn(ScalarColumnDesc<String>("FIELDNAME"));
    178   td.addColumn(ScalarColumnDesc<String>("TCALTIME"));
    179   td.addColumn(ArrayColumnDesc<Float>("TCAL"));
    180   td.addColumn(ScalarColumnDesc<Float>("AZIMUTH"));
    181   td.addColumn(ScalarColumnDesc<Float>("ELEVATION"));
     160
     161  td.addColumn(ArrayColumnDesc<Double>("DIRECTION",
     162                                       IPosition(1,2),
     163                                       ColumnDesc::Direct));
     164  TableMeasRefDesc mdirRef(MDirection::J2000); // default
     165  TableMeasValueDesc tmvdMDir(td, "DIRECTION");
     166  // the TableMeasDesc gives the column a type
     167  TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef);
     168  // writing create the measure column
     169  mdirCol.write(td);
     170  td.addColumn(ScalarColumnDesc<Double>("AZIMUTH"));
     171  td.addColumn(ScalarColumnDesc<Double>("ELEVATION"));
    182172  td.addColumn(ScalarColumnDesc<Float>("PARANGLE"));
    183   td.addColumn(ScalarColumnDesc<Int>("REFBEAM"));
    184   td.addColumn(ArrayColumnDesc<Int>("FITID"));
     173
     174  td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID"));
     175  td.addColumn(ScalarColumnDesc<uInt>("FIT_ID"));
     176
     177  td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID"));
     178  td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID"));
     179
     180  td.rwKeywordSet().define("OBSMODE", String(""));
    185181
    186182  // Now create Table SetUp from the description.
    187183  SetupNewTable aNewTab("dummy", td, Table::New);
    188 
    189   // Bind the Stokes Virtual machine to the STOKES column Because we
    190   // don't know how many polarizations will be in the data at this
    191   // point, we must bind the Virtual Engine regardless.  The STOKES
    192   // column won't be accessed if not appropriate (nPol=4)
    193   SDStokesEngine::registerClass();
    194   SDStokesEngine stokesEngine(String("STOKES"), String("SPECTRA"));
    195   aNewTab.bindColumn("STOKES", stokesEngine);
    196 
    197   // Create Table
    198184  table_ = Table(aNewTab, Table::Memory, 0);
    199   // add subtable
    200   TableDesc tdf("", "1", TableDesc::Scratch);
    201   tdf.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
    202   tdf.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
    203   tdf.addColumn(ArrayColumnDesc<Double>("PARAMETERS"));
    204   tdf.addColumn(ArrayColumnDesc<Bool>("PARMASK"));
    205   tdf.addColumn(ArrayColumnDesc<String>("FRAMEINFO"));
    206   SetupNewTable fittab("fits", tdf, Table::New);
    207   Table fitTable(fittab, Table::Memory);
    208   table_.rwKeywordSet().defineTable("FITS", fitTable);
    209 
     185
     186  originalTable_ = table_;
     187
     188}
     189
     190void asap::Scantable::setupHistoryTable( )
     191{
    210192  TableDesc tdh("", "1", TableDesc::Scratch);
    211193  tdh.addColumn(ScalarColumnDesc<String>("ITEM"));
    212   SetupNewTable histtab("hist", tdh, Table::New);
     194  SetupNewTable histtab("history", tdh, Table::New);
    213195  Table histTable(histtab, Table::Memory);
    214196  table_.rwKeywordSet().defineTable("HISTORY", histTable);
    215197}
    216198
    217 void SDMemTable::attach()
    218 {
    219   timeCol_.attach(table_, "TIME");
    220   srcnCol_.attach(table_, "SRCNAME");
    221   specCol_.attach(table_, "SPECTRA");
    222   flagsCol_.attach(table_, "FLAGTRA");
    223   tsCol_.attach(table_, "TSYS");
    224   stokesCol_.attach(table_, "STOKES");
    225   scanCol_.attach(table_, "SCANID");
    226   integrCol_.attach(table_, "INTERVAL");
    227   freqidCol_.attach(table_, "FREQID");
    228   restfreqidCol_.attach(table_, "RESTFREQID");
    229   dirCol_.attach(table_, "DIRECTION");
    230   fldnCol_.attach(table_, "FIELDNAME");
    231   tcaltCol_.attach(table_, "TCALTIME");
    232   tcalCol_.attach(table_, "TCAL");
    233   azCol_.attach(table_, "AZIMUTH");
    234   elCol_.attach(table_, "ELEVATION");
    235   paraCol_.attach(table_, "PARANGLE");
    236   rbeamCol_.attach(table_, "REFBEAM");
    237   fitCol_.attach(table_,"FITID");
    238 }
    239 
    240 
    241 std::string SDMemTable::getSourceName(Int whichRow) const
    242 {
    243   String name;
    244   srcnCol_.get(whichRow, name);
    245   return name;
    246 }
    247 
    248 float SDMemTable::getElevation(Int whichRow) const
    249 {
    250   float elevation;
    251   elCol_.get(whichRow, elevation);
    252   return elevation;
    253 }
    254 
    255 float SDMemTable::getAzimuth(Int whichRow) const
    256 {
    257   float azimuth;
    258   azCol_.get(whichRow, azimuth);
    259   return azimuth;
    260 }
    261 
    262 float SDMemTable::getParAngle(Int whichRow) const
    263 {
    264   float parangle;
    265   paraCol_.get(whichRow, parangle);
    266   return parangle;
    267 }
    268 
    269 std::string SDMemTable::getTime(Int whichRow, Bool showDate) const
    270 {
    271   Double tm;
    272   if (whichRow > -1) {
    273     timeCol_.get(whichRow, tm);
    274   } else {
    275     table_.keywordSet().get("UTC",tm);
    276   }
    277   MVTime mvt(tm);
    278   if (showDate)
    279     mvt.setFormat(MVTime::YMD);
    280   else
    281     mvt.setFormat(MVTime::TIME);
    282   ostringstream oss;
    283   oss << mvt;
    284   return String(oss);
    285 }
    286 
    287 double SDMemTable::getInterval(Int whichRow) const
    288 {
    289   Double intval;
    290   integrCol_.get(whichRow, intval);
    291   return intval;
    292 }
    293 
    294 bool SDMemTable::setIF(Int whichIF)
    295 {
    296   if ( whichIF >= 0 && whichIF < nIF()) {
    297     IFSel_ = whichIF;
    298     return true;
    299   }
    300   return false;
    301 }
    302 
    303 bool SDMemTable::setBeam(Int whichBeam)
    304 {
    305   if ( whichBeam >= 0 && whichBeam < nBeam()) {
    306     beamSel_ = whichBeam;
    307     return true;
    308   }
    309   return false;
    310 }
    311 
    312 bool SDMemTable::setPol(Int whichPol)
    313 {
    314   if ( whichPol >= 0 && whichPol < nPol()) {
    315     polSel_ = whichPol;
    316     return true;
    317   }
    318   return false;
    319 }
    320 
    321 void SDMemTable::resetCursor()
    322 {
    323    polSel_ = 0;
    324    IFSel_ = 0;
    325    beamSel_ = 0;
    326 }
    327 
    328 std::vector<bool> SDMemTable::getMask(Int whichRow) const
    329 {
    330 
    331   std::vector<bool> mask;
    332 
    333   Array<uChar> arr;
    334   flagsCol_.get(whichRow, arr);
    335 
    336   ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
    337   aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
    338   ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
    339   aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
    340   ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
    341   aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
    342 
    343   for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
    344     bool out =!static_cast<bool>(*i);
    345     mask.push_back(out);
    346   }
    347   return mask;
    348 }
    349 
    350 
    351 
    352 std::vector<float> SDMemTable::getSpectrum(Int whichRow) const
    353 {
    354   Array<Float> arr;
    355   specCol_.get(whichRow, arr);
    356   return getFloatSpectrum(arr);
    357 }
    358 
    359 
    360 int SDMemTable::nStokes() const
    361 {
    362    return stokesCol_.shape(0).nelements();        // All rows same shape
    363 }
    364 
    365 
    366 std::vector<float> SDMemTable::getStokesSpectrum(Int whichRow,
    367                                                  Bool doPol) const
    368   //
    369   // Gets one STokes parameter depending on cursor polSel location
    370   //  doPol=False  : I,Q,U,V
    371   //  doPol=True   : I,P,PA,V   ; P = sqrt(Q**2+U**2), PA = 0.5*atan2(Q,U)
    372   //
    373 {
    374   AlwaysAssert(asap::nAxes==4,AipsError);
    375   if (nPol()!=1 && nPol()!=2 && nPol()!=4) {
    376     throw (AipsError("You must have 1,2 or 4 polarizations to get the Stokes parameters"));
    377   }
    378 
    379   // For full conversion we are only supporting linears at the moment
    380 
    381   if (nPol() > 2) {
    382     String antName;
    383     table_.keywordSet().get("AntennaName", antName);
    384     Instrument inst = SDAttr::convertInstrument (antName, True);
    385     SDAttr sdAtt;
    386     if (sdAtt.feedPolType(inst) != LINEAR) {
    387       throw(AipsError("Only linear polarizations are supported"));
    388     }
    389   }
    390 
    391   Array<Float> arr;
    392   stokesCol_.get(whichRow, arr);
    393 
    394   if (doPol && (polSel_==1 || polSel_==2)) {       //   Q,U --> P, P.A.
    395 
    396     // Set current cursor location
    397 
    398     const IPosition& shape = arr.shape();
    399     IPosition start, end;
    400     getCursorSlice(start, end, shape);
    401 
    402     // Get Q and U slices
    403 
    404     Array<Float> Q = SDPolUtil::getStokesSlice(arr,start,end,"Q");
    405     Array<Float> U = SDPolUtil::getStokesSlice(arr,start,end,"U");
    406 
    407     // Compute output
    408 
    409     Array<Float> out;
    410     if (polSel_==1) {                                        // P
    411       out = SDPolUtil::polarizedIntensity(Q,U);
    412     } else if (polSel_==2) {                                 // P.A.
    413       out = SDPolUtil::positionAngle(Q,U);
    414     }
    415 
    416     // Copy to output
    417 
    418     IPosition vecShape(1,shape(asap::ChanAxis));
    419     Vector<Float> outV = out.reform(vecShape);
    420     std::vector<float> stlout;
    421     outV.tovector(stlout);
    422     return stlout;
    423 
    424   } else {
    425     // Selects at the cursor location
    426     return getFloatSpectrum(arr);
    427   }
    428 }
    429 
    430 std::string SDMemTable::getPolarizationLabel(Bool linear, Bool stokes,
    431                                               Bool linPol, Int polIdx) const
    432 {
    433    uInt idx = polSel_;
    434    if (polIdx >=0) idx = polIdx;
    435    return SDPolUtil::polarizationLabel(idx, linear, stokes, linPol);
    436 }
    437 
    438 
    439 
    440 std::vector<float> SDMemTable::stokesToPolSpectrum(Int whichRow,
    441                                                    Bool toLinear,
    442                                                    Int polIdx) const
    443 //
    444 // polIdx
    445 //   0:3 -> RR,LL,Real(RL),Imag(RL)
    446 //          XX,YY,Real(XY),Image(XY)
    447 //
    448 // Gets only
    449 //  RR = I + V
    450 //  LL = I - V
    451 // at the moment
    452 //
    453 {
    454   AlwaysAssert(asap::nAxes==4,AipsError);
    455   if (nStokes()!=4) {
    456      throw (AipsError("You must have 4 Stokes to convert to linear or circular"));
    457   }
    458 //
    459   Array<Float> arr, out;
    460   stokesCol_.get(whichRow, arr);
    461 
    462 // Set current cursor location
    463 
    464   const IPosition& shape = arr.shape();
    465   IPosition start, end;
    466   getCursorSlice(start, end, shape);
    467 
    468 // Get the slice
    469 
    470   if (toLinear) {
    471      throw(AipsError("Conversion to linears not yet supported"));
    472   } else {
    473     uInt selection = polSel_;
    474     if (polIdx > -1) selection = polIdx;
    475     Bool doRR = (selection==0);
    476     if (selection>1) {
    477       throw(AipsError("Only conversion to RR & LL is currently supported"));
    478     }
    479 
    480     // Get I and V slices
    481     Array<Float> I = SDPolUtil::getStokesSlice(arr,start,end,"I");
    482     Array<Float> V = SDPolUtil::getStokesSlice(arr,start,end,"V");
    483 
    484     // Compute output
    485     out = SDPolUtil::circularPolarizationFromStokes(I, V, doRR);
    486   }
    487 
    488   // Copy to output
    489    IPosition vecShape(1,shape(asap::ChanAxis));
    490    Vector<Float> outV = out.reform(vecShape);
    491    std::vector<float> stlout;
    492    outV.tovector(stlout);
    493 //
    494    return stlout;
    495 }
    496 
    497 
    498 
    499 
    500 Array<Float> SDMemTable::getStokesSpectrum(Int whichRow, Int iBeam, Int iIF) const
    501 {
    502 
    503 // Get data
    504 
    505   Array<Float> arr;
    506   stokesCol_.get(whichRow, arr);
    507 
    508 // Set current cursor location and overwrite polarization axis
    509 
    510   const IPosition& shape = arr.shape();
    511   IPosition start(shape.nelements(),0);
    512   IPosition end(shape-1);
    513   if (iBeam!=-1) {
    514      start(asap::BeamAxis) = iBeam;
    515      end(asap::BeamAxis) = iBeam;
    516   }
    517   if (iIF!=-1) {
    518      start(asap::IFAxis) = iIF;
    519      end(asap::IFAxis) = iIF;
    520   }
    521 
    522 // Get slice
    523 
    524   return arr(start,end);
    525 }
    526 
    527 
    528 std::vector<string> SDMemTable::getCoordInfo() const
    529 {
    530   String un;
    531   Table t = table_.keywordSet().asTable("FREQUENCIES");
    532   String sunit;
    533   t.keywordSet().get("UNIT",sunit);
    534   String dpl;
    535   t.keywordSet().get("DOPPLER",dpl);
    536   if (dpl == "") dpl = "RADIO";
    537   String rfrm;
    538   t.keywordSet().get("REFFRAME",rfrm);
    539   std::vector<string> inf;
    540   inf.push_back(sunit);
    541   inf.push_back(rfrm);
    542   inf.push_back(dpl);
    543   t.keywordSet().get("BASEREFFRAME",rfrm);
    544   inf.push_back(rfrm);
    545   return inf;
    546 }
    547 
    548 void SDMemTable::setCoordInfo(std::vector<string> theinfo)
    549 {
    550   std::vector<string>::iterator it;
    551   String un,rfrm, brfrm,dpl;
    552   un = theinfo[0];              // Abcissa unit
    553   rfrm = theinfo[1];            // Active (or conversion) frame
    554   dpl = theinfo[2];             // Doppler
    555   brfrm = theinfo[3];           // Base frame
    556   Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
    557 
    558   Vector<Double> rstf;
    559   t.keywordSet().get("RESTFREQS",rstf);
    560 
    561   Bool canDo = True;
    562   Unit u1("km/s");Unit u2("Hz");
    563   if (Unit(un) == u1) {
    564     Vector<Double> rstf;
    565     t.keywordSet().get("RESTFREQS",rstf);
    566     if (rstf.nelements() == 0) {
    567         throw(AipsError("Can't set unit to km/s if no restfrequencies are specified"));
    568     }
    569   } else if (Unit(un) != u2 && un != "") {
    570         throw(AipsError("Unit not conformant with Spectral Coordinates"));
    571   }
    572   t.rwKeywordSet().define("UNIT", un);
    573 
    574   MFrequency::Types mdr;
    575   if (!MFrequency::getType(mdr, rfrm)) {
    576 
    577     Int a,b;const uInt* c;
    578     const String* valid = MFrequency::allMyTypes(a, b, c);
    579     String pfix = "Please specify a legal frame type. Types are\n";
    580     throw(AipsError(pfix+(*valid)));
    581   } else {
    582     t.rwKeywordSet().define("REFFRAME",rfrm);
    583   }
    584 
    585   MDoppler::Types dtype;
    586   dpl.upcase();
    587   if (!MDoppler::getType(dtype, dpl)) {
    588     throw(AipsError("Doppler type unknown"));
    589   } else {
    590     t.rwKeywordSet().define("DOPPLER",dpl);
    591   }
    592 
    593   if (!MFrequency::getType(mdr, brfrm)) {
    594      Int a,b;const uInt* c;
    595      const String* valid = MFrequency::allMyTypes(a, b, c);
    596      String pfix = "Please specify a legal frame type. Types are\n";
    597      throw(AipsError(pfix+(*valid)));
    598    } else {
    599     t.rwKeywordSet().define("BASEREFFRAME",brfrm);
    600    }
    601 }
    602 
    603 
    604 std::vector<double> SDMemTable::getAbcissa(Int whichRow) const
    605 {
    606   std::vector<double> abc(nChan());
    607 
    608   // Get header units keyword
    609   Table t = table_.keywordSet().asTable("FREQUENCIES");
    610   String sunit;
    611   t.keywordSet().get("UNIT",sunit);
    612   if (sunit == "") sunit = "pixel";
    613   Unit u(sunit);
    614 
    615   // Easy if just wanting pixels
    616   if (sunit==String("pixel")) {
    617     // assume channels/pixels
    618     std::vector<double>::iterator it;
    619     uInt i=0;
    620     for (it = abc.begin(); it != abc.end(); ++it) {
    621       (*it) = Double(i++);
    622     }
    623     return abc;
    624   }
    625 
    626   // Continue with km/s or Hz.  Get FreqIDs
    627   Vector<uInt> freqIDs;
    628   freqidCol_.get(whichRow, freqIDs);
    629   uInt freqID = freqIDs(IFSel_);
    630   restfreqidCol_.get(whichRow, freqIDs);
    631   uInt restFreqID = freqIDs(IFSel_);
    632 
    633   // Get SpectralCoordinate, set reference frame conversion,
    634   // velocity conversion, and rest freq state
    635 
    636   SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
    637   Vector<Double> pixel(nChan());
    638   indgen(pixel);
    639 
    640   if (u == Unit("km/s")) {
    641      Vector<Double> world;
    642      spc.pixelToVelocity(world,pixel);
    643      std::vector<double>::iterator it;
    644      uInt i = 0;
    645      for (it = abc.begin(); it != abc.end(); ++it) {
    646        (*it) = world[i];
    647        i++;
    648      }
    649   } else if (u == Unit("Hz")) {
    650 
    651     // Set world axis units
    652     Vector<String> wau(1); wau = u.getName();
    653     spc.setWorldAxisUnits(wau);
    654 
    655     std::vector<double>::iterator it;
    656     Double tmp;
    657     uInt i = 0;
    658     for (it = abc.begin(); it != abc.end(); ++it) {
    659       spc.toWorld(tmp,pixel[i]);
    660       (*it) = tmp;
    661       i++;
    662     }
    663   }
    664   return abc;
    665 }
    666 
    667 std::string SDMemTable::getAbcissaString(Int whichRow) const
    668 {
    669   Table t = table_.keywordSet().asTable("FREQUENCIES");
    670 
    671   String sunit;
    672   t.keywordSet().get("UNIT",sunit);
    673   if (sunit == "") sunit = "pixel";
    674   Unit u(sunit);
    675 
    676   Vector<uInt> freqIDs;
    677   freqidCol_.get(whichRow, freqIDs);
    678   uInt freqID = freqIDs(IFSel_);
    679   restfreqidCol_.get(whichRow, freqIDs);
    680   uInt restFreqID = freqIDs(IFSel_);
    681 
    682   // Get SpectralCoordinate, with frame, velocity, rest freq state set
    683   SpectralCoordinate spc = getSpectralCoordinate(freqID, restFreqID, whichRow);
    684 
    685   String s = "Channel";
    686   if (u == Unit("km/s")) {
    687     s = CoordinateUtil::axisLabel(spc,0,True,True,True);
    688   } else if (u == Unit("Hz")) {
    689     Vector<String> wau(1);wau = u.getName();
    690     spc.setWorldAxisUnits(wau);
    691 
    692     s = CoordinateUtil::axisLabel(spc,0,True,True,False);
    693   }
    694   return s;
    695 }
    696 
    697 void SDMemTable::setSpectrum(std::vector<float> spectrum, int whichRow)
    698 {
    699   Array<Float> arr;
    700   specCol_.get(whichRow, arr);
    701   if (spectrum.size() != arr.shape()(asap::ChanAxis)) {
    702     throw(AipsError("Attempting to set spectrum with incorrect length."));
    703   }
    704 
    705   // Setup accessors
    706   ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
    707   aa0.reset(aa0.begin(uInt(beamSel_)));                   // Beam selection
    708   ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
    709   aa1.reset(aa1.begin(uInt(IFSel_)));                     // IF selection
    710   ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
    711   aa2.reset(aa2.begin(uInt(polSel_)));                    // Pol selection
    712 
    713   // Iterate
    714   std::vector<float>::iterator it = spectrum.begin();
    715   for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
    716     (*i) = Float(*it);
    717     it++;
    718   }
    719   specCol_.put(whichRow, arr);
    720 }
    721 
    722 void SDMemTable::getSpectrum(Vector<Float>& spectrum, Int whichRow) const
    723 {
    724   Array<Float> arr;
    725   specCol_.get(whichRow, arr);
    726 
    727   // Iterate and extract
    728   spectrum.resize(arr.shape()(3));
    729   ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
    730   aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
    731   ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
    732   aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
    733   ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
    734   aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
    735 
    736   ArrayAccessor<Float, Axis<asap::BeamAxis> > va(spectrum);
    737   for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
    738     (*va) = (*i);
    739     va++;
    740   }
    741 }
    742 
    743 
    744 /*
    745 void SDMemTable::getMask(Vector<Bool>& mask, Int whichRow) const {
    746   Array<uChar> arr;
    747   flagsCol_.get(whichRow, arr);
    748   mask.resize(arr.shape()(3));
    749 
    750   ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
    751   aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
    752   ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
    753   aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
    754   ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
    755   aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
    756 
    757   Bool useUserMask = ( chanMask_.size() == arr.shape()(3) );
    758 
    759   ArrayAccessor<Bool, Axis<asap::BeamAxis> > va(mask);
    760   std::vector<bool> tmp;
    761   tmp = chanMask_; // WHY the fxxx do I have to make a copy here. The
    762                    // iterator should work on chanMask_??
    763   std::vector<bool>::iterator miter;
    764   miter = tmp.begin();
    765 
    766   for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
    767     bool out =!static_cast<bool>(*i);
    768     if (useUserMask) {
    769       out = out && (*miter);
    770       miter++;
    771     }
    772     (*va) = out;
    773     va++;
    774   }
    775 }
    776 */
    777 
    778 MaskedArray<Float> SDMemTable::rowAsMaskedArray(uInt whichRow,
    779                                                 Bool toStokes) const
    780 {
    781   // Get flags
    782   Array<uChar> farr;
    783   flagsCol_.get(whichRow, farr);
    784 
    785   // Get data and convert mask to Bool
    786   Array<Float> arr;
    787   Array<Bool> mask;
    788   if (toStokes) {
    789      stokesCol_.get(whichRow, arr);
    790 
    791      Array<Bool> tMask(farr.shape());
    792      convertArray(tMask, farr);
    793      mask = SDPolUtil::stokesData (tMask, True);
    794   } else {
    795      specCol_.get(whichRow, arr);
    796      mask.resize(farr.shape());
    797      convertArray(mask, farr);
    798   }
    799 
    800   return MaskedArray<Float>(arr,!mask);
    801 }
    802 
    803 Float SDMemTable::getTsys(Int whichRow) const
    804 {
    805   Array<Float> arr;
    806   tsCol_.get(whichRow, arr);
    807   Float out;
    808 
    809   IPosition ip(arr.shape());
    810   ip(asap::BeamAxis) = beamSel_;
    811   ip(asap::IFAxis) = IFSel_;
    812   ip(asap::PolAxis) = polSel_;
    813   ip(asap::ChanAxis)=0;               // First channel only
    814 
    815   out = arr(ip);
    816   return out;
    817 }
    818 
    819 MDirection SDMemTable::getDirection(Int whichRow, Bool refBeam) const
    820 {
    821   MDirection::Types mdr = getDirectionReference();
    822   Array<Double> posit;
    823   dirCol_.get(whichRow,posit);
    824   Vector<Double> wpos(2);
    825   Int rb;
    826   rbeamCol_.get(whichRow,rb);
    827   wpos[0] = posit(IPosition(2,beamSel_,0));
    828   wpos[1] = posit(IPosition(2,beamSel_,1));
    829   if (refBeam && rb > -1) {  // use refBeam instead if it exists
    830     wpos[0] = posit(IPosition(2,rb,0));
    831     wpos[1] = posit(IPosition(2,rb,1));
    832   }
    833 
    834   Quantum<Double> lon(wpos[0],Unit(String("rad")));
    835   Quantum<Double> lat(wpos[1],Unit(String("rad")));
    836   return MDirection(lon, lat, mdr);
    837 }
    838 
    839 MEpoch SDMemTable::getEpoch(Int whichRow) const
    840 {
    841   MEpoch::Types met = getTimeReference();
    842 
    843   Double obstime;
    844   timeCol_.get(whichRow,obstime);
    845   MVEpoch tm2(Quantum<Double>(obstime, Unit(String("d"))));
    846   return MEpoch(tm2, met);
    847 }
    848 
    849 MPosition SDMemTable::getAntennaPosition () const
    850 {
    851   Vector<Double> antpos;
    852   table_.keywordSet().get("AntennaPosition", antpos);
    853   MVPosition mvpos(antpos(0),antpos(1),antpos(2));
    854   return MPosition(mvpos);
    855 }
    856 
    857 
    858 SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID) const
    859 {
    860 
    861   Table t = table_.keywordSet().asTable("FREQUENCIES");
    862   if (freqID> t.nrow() ) {
    863     throw(AipsError("SDMemTable::getSpectralCoordinate - freqID out of range"));
    864   }
    865 
    866   Double rp,rv,inc;
    867   String rf;
    868   ROScalarColumn<Double> rpc(t, "REFPIX");
    869   ROScalarColumn<Double> rvc(t, "REFVAL");
    870   ROScalarColumn<Double> incc(t, "INCREMENT");
    871   t.keywordSet().get("BASEREFFRAME",rf);
    872 
    873   // Create SpectralCoordinate (units Hz)
    874   MFrequency::Types mft;
    875   if (!MFrequency::getType(mft, rf)) {
    876     ostringstream oss;
    877     pushLog("WARNING: Frequency type unknown assuming TOPO");
    878     mft = MFrequency::TOPO;
    879   }
    880   rpc.get(freqID, rp);
    881   rvc.get(freqID, rv);
    882   incc.get(freqID, inc);
    883 
    884   SpectralCoordinate spec(mft,rv,inc,rp);
    885   return spec;
    886 }
    887 
    888 
    889 SpectralCoordinate SDMemTable::getSpectralCoordinate(uInt freqID,
    890                                                      uInt restFreqID,
    891                                                      uInt whichRow) const
    892 {
    893 
    894   // Create basic SC
    895   SpectralCoordinate spec = getSpectralCoordinate (freqID);
    896 
    897   Table t = table_.keywordSet().asTable("FREQUENCIES");
    898 
    899   // Set rest frequency
    900   Vector<Double> restFreqIDs;
    901   t.keywordSet().get("RESTFREQS",restFreqIDs);
    902   if (restFreqID < restFreqIDs.nelements()) {    // Should always be true
    903     spec.setRestFrequency(restFreqIDs(restFreqID),True);
    904   }
    905 
    906   // Set up frame conversion layer
    907   String frm;
    908   t.keywordSet().get("REFFRAME",frm);
    909   if (frm == "") frm = "TOPO";
    910   MFrequency::Types mtype;
    911   if (!MFrequency::getType(mtype, frm)) {
    912     // Should never happen
    913     pushLog("WARNING: Frequency type unknown assuming TOPO");
    914     mtype = MFrequency::TOPO;
    915   }
    916 
    917   // Set reference frame conversion  (requires row)
    918   MDirection dir = getDirection(whichRow);
    919   MEpoch epoch = getEpoch(whichRow);
    920   MPosition pos = getAntennaPosition();
    921 
    922   if (!spec.setReferenceConversion(mtype,epoch,pos,dir)) {
    923     throw(AipsError("Couldn't convert frequency frame."));
    924   }
    925 
    926   // Now velocity conversion if appropriate
    927   String unitStr;
    928   t.keywordSet().get("UNIT",unitStr);
    929 
    930   String dpl;
    931   t.keywordSet().get("DOPPLER",dpl);
    932   MDoppler::Types dtype;
    933   MDoppler::getType(dtype, dpl);
    934 
    935   // Only set velocity unit if non-blank and non-Hz
    936   if (!unitStr.empty()) {
    937      Unit unitU(unitStr);
    938      if (unitU==Unit("Hz")) {
    939      } else {
    940         spec.setVelocity(unitStr, dtype);
    941      }
    942   }
    943 
    944   return spec;
    945 }
    946 
    947 
    948 Bool SDMemTable::setCoordinate(const SpectralCoordinate& speccord,
    949                                uInt freqID) {
    950   Table t = table_.rwKeywordSet().asTable("FREQUENCIES");
    951   if (freqID > t.nrow() ) {
    952     throw(AipsError("SDMemTable::setCoordinate - coord no out of range"));
    953   }
    954   ScalarColumn<Double> rpc(t, "REFPIX");
    955   ScalarColumn<Double> rvc(t, "REFVAL");
    956   ScalarColumn<Double> incc(t, "INCREMENT");
    957 
    958   rpc.put(freqID, speccord.referencePixel()[0]);
    959   rvc.put(freqID, speccord.referenceValue()[0]);
    960   incc.put(freqID, speccord.increment()[0]);
    961 
    962   return True;
    963 }
    964 
    965 Int SDMemTable::nCoordinates() const
    966 {
    967   return table_.keywordSet().asTable("FREQUENCIES").nrow();
    968 }
    969 
    970 
    971 std::vector<double> SDMemTable::getRestFreqs() const
    972 {
    973   Table t = table_.keywordSet().asTable("FREQUENCIES");
    974   Vector<Double> tvec;
    975   t.keywordSet().get("RESTFREQS",tvec);
    976   std::vector<double> stlout;
    977   tvec.tovector(stlout);
    978   return stlout;
    979 }
    980 
    981 bool SDMemTable::putSDFreqTable(const SDFrequencyTable& sdft)
     199void Scantable::setupFitTable()
    982200{
    983201  TableDesc td("", "1", TableDesc::Scratch);
    984   td.addColumn(ScalarColumnDesc<Double>("REFPIX"));
    985   td.addColumn(ScalarColumnDesc<Double>("REFVAL"));
    986   td.addColumn(ScalarColumnDesc<Double>("INCREMENT"));
    987   SetupNewTable aNewTab("freqs", td, Table::New);
    988   Table aTable (aNewTab, Table::Memory, sdft.length());
    989   ScalarColumn<Double> sc0(aTable, "REFPIX");
    990   ScalarColumn<Double> sc1(aTable, "REFVAL");
    991   ScalarColumn<Double> sc2(aTable, "INCREMENT");
    992   for (uInt i=0; i < sdft.length(); ++i) {
    993     sc0.put(i,sdft.referencePixel(i));
    994     sc1.put(i,sdft.referenceValue(i));
    995     sc2.put(i,sdft.increment(i));
    996   }
    997   String rf = sdft.refFrame();
    998   if (rf.contains("TOPO")) rf = "TOPO";
    999   String brf = sdft.baseRefFrame();
    1000   if (brf.contains("TOPO")) brf = "TOPO";
    1001 
    1002   aTable.rwKeywordSet().define("BASEREFFRAME", brf);
    1003   aTable.rwKeywordSet().define("REFFRAME", rf);
    1004   aTable.rwKeywordSet().define("EQUINOX", sdft.equinox());
    1005   aTable.rwKeywordSet().define("UNIT", sdft.unit());
    1006   aTable.rwKeywordSet().define("DOPPLER", String("RADIO"));
    1007   Vector<Double> rfvec;
    1008   String rfunit;
    1009   sdft.restFrequencies(rfvec,rfunit);
    1010   Quantum<Vector<Double> > q(rfvec, rfunit);
    1011   rfvec.resize();
    1012   rfvec = q.getValue("Hz");
    1013   aTable.rwKeywordSet().define("RESTFREQS", rfvec);
    1014   table_.rwKeywordSet().defineTable("FREQUENCIES", aTable);
    1015   return true;
    1016 }
    1017 
    1018 bool SDMemTable::putSDFitTable(const SDFitTable& sdft)
    1019 {
    1020   TableDesc td("", "1", TableDesc::Scratch);
     202  td.addColumn(ScalarColumnDesc<uInt>("FIT_ID"));
    1021203  td.addColumn(ArrayColumnDesc<String>("FUNCTIONS"));
    1022204  td.addColumn(ArrayColumnDesc<Int>("COMPONENTS"));
    … …  
    1026208  SetupNewTable aNewTab("fits", td, Table::New);
    1027209  Table aTable(aNewTab, Table::Memory);
    1028   ArrayColumn<String> sc0(aTable, "FUNCTIONS");
    1029   ArrayColumn<Int> sc1(aTable, "COMPONENTS");
    1030   ArrayColumn<Double> sc2(aTable, "PARAMETERS");
    1031   ArrayColumn<Bool> sc3(aTable, "PARMASK");
    1032   ArrayColumn<String> sc4(aTable, "FRAMEINFO");
    1033   for (uInt i; i<sdft.length(); ++i) {
    1034     const Vector<Double>& parms = sdft.getParameters(i);
    1035     const Vector<Bool>& parmask = sdft.getParameterMask(i);
    1036     const Vector<String>& funcs = sdft.getFunctions(i);
    1037     const Vector<Int>& comps = sdft.getComponents(i);
    1038     const Vector<String>& finfo = sdft.getFrameInfo(i);
    1039     sc0.put(i,funcs);
    1040     sc1.put(i,comps);
    1041     sc3.put(i,parmask);
    1042     sc2.put(i,parms);
    1043     sc4.put(i,finfo);
    1044   }
    1045210  table_.rwKeywordSet().defineTable("FITS", aTable);
    1046   return true;
    1047 }
    1048 
    1049 SDFitTable SDMemTable::getSDFitTable() const
    1050 {
    1051   const Table& t = table_.keywordSet().asTable("FITS");
    1052   Vector<Double> parms;
    1053   Vector<Bool> parmask;
    1054   Vector<String> funcs;
    1055   Vector<String> finfo;
    1056   Vector<Int> comps;
    1057   ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
    1058   ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
    1059   ROArrayColumn<Int> compsCol(t, "COMPONENTS");
    1060   ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
    1061   ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
    1062   uInt n = t.nrow();
    1063   SDFitTable sdft;
    1064   for (uInt i=0; i<n; ++i) {
    1065     parmaskCol.get(i, parmask);
    1066     parmsCol.get(i, parms);
    1067     funcsCol.get(i, funcs);
    1068     compsCol.get(i, comps);
    1069     finfoCol.get(i, finfo);
    1070     sdft.addFit(parms, parmask, funcs, comps, finfo);
    1071   }
    1072   return sdft;
    1073 }
    1074 
    1075 SDFitTable SDMemTable::getSDFitTable(uInt whichRow) const {
    1076   const Table& t = table_.keywordSet().asTable("FITS");
    1077   if (t.nrow() == 0 || whichRow >= t.nrow()) return SDFitTable();
    1078   Array<Int> fitid;
    1079   fitCol_.get(whichRow, fitid);
    1080   if (fitid.nelements() == 0) return SDFitTable();
    1081 
    1082   IPosition shp = fitid.shape();
    1083   IPosition start(4, beamSel_, IFSel_, polSel_,0);
    1084   IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
    1085 
    1086   // reform the output array slice to be of dim=1
    1087   Vector<Int> tmp = (fitid(start, end)).reform(IPosition(1,shp[3]));
    1088 
    1089   Vector<Double> parms;
    1090   Vector<Bool> parmask;
    1091   Vector<String> funcs;
    1092   Vector<String> finfo;
    1093   Vector<Int> comps;
    1094   ROArrayColumn<Double> parmsCol(t, "PARAMETERS");
    1095   ROArrayColumn<Bool> parmaskCol(t, "PARMASK");
    1096   ROArrayColumn<Int> compsCol(t, "COMPONENTS");
    1097   ROArrayColumn<String> funcsCol(t, "FUNCTIONS");
    1098   ROArrayColumn<String> finfoCol(t, "FRAMEINFO");
    1099   SDFitTable sdft;
    1100   Int k=-1;
    1101   for (uInt i=0; i< tmp.nelements(); ++i) {
    1102     k = tmp[i];
    1103     if ( k > -1 && k < t.nrow() ) {
    1104       parms.resize();
    1105       parmsCol.get(k, parms);
    1106       parmask.resize();
    1107       parmaskCol.get(k, parmask);
    1108       funcs.resize();
    1109       funcsCol.get(k, funcs);
    1110       comps.resize();
    1111       compsCol.get(k, comps);
    1112       finfo.resize();
    1113       finfoCol.get(k, finfo);
    1114       sdft.addFit(parms, parmask, funcs, comps, finfo);
    1115     }
    1116   }
    1117   return sdft;
    1118 }
    1119 
    1120 void SDMemTable::addFit(uInt whichRow,
    1121                         const Vector<Double>& p, const Vector<Bool>& m,
    1122                         const Vector<String>& f, const Vector<Int>& c)
    1123 {
    1124   if (whichRow >= nRow()) {
    1125     throw(AipsError("Specified row out of range"));
    1126   }
    1127   Table t = table_.keywordSet().asTable("FITS");
    1128   uInt nrow = t.nrow();
    1129   t.addRow();
    1130   ArrayColumn<Double> parmsCol(t, "PARAMETERS");
    1131   ArrayColumn<Bool> parmaskCol(t, "PARMASK");
    1132   ArrayColumn<Int> compsCol(t, "COMPONENTS");
    1133   ArrayColumn<String> funcsCol(t, "FUNCTIONS");
    1134   ArrayColumn<String> finfoCol(t, "FRAMEINFO");
    1135   parmsCol.put(nrow, p);
    1136   parmaskCol.put(nrow, m);
    1137   compsCol.put(nrow, c);
    1138   funcsCol.put(nrow, f);
    1139   Vector<String> fi = mathutil::toVectorString(getCoordInfo());
    1140   finfoCol.put(nrow, fi);
    1141 
    1142   Array<Int> fitarr;
    1143   fitCol_.get(whichRow, fitarr);
    1144 
    1145   Array<Int> newarr;               // The new Array containing the fitid
    1146   Int pos =-1;                     // The fitid position in the array
    1147   if ( fitarr.nelements() == 0 ) { // no fits at all in this row
    1148     Array<Int> arr(IPosition(4,nBeam(),nIF(),nPol(),1));
    1149     arr = -1;
    1150     newarr.reference(arr);
    1151     pos = 0;
    1152   } else {
    1153     IPosition shp = fitarr.shape();
    1154     IPosition start(4, beamSel_, IFSel_, polSel_,0);
    1155     IPosition end(4, beamSel_, IFSel_, polSel_, shp[3]-1);
    1156     // reform the output array slice to be of dim=1
    1157     Array<Int> tmp = (fitarr(start, end)).reform(IPosition(1,shp[3]));
    1158     const Vector<Int>& fits = tmp;
    1159     VectorSTLIterator<Int> it(fits);
    1160     Int i = 0;
    1161     while (it != fits.end()) {
    1162       if (*it == -1) {
    1163         pos = i;
    1164         break;
    1165       }
    1166       ++i;
    1167       ++it;
    1168     };
    1169   }
    1170   if (pos == -1) {
    1171       mathutil::extendLastArrayAxis(newarr,fitarr, -1);
    1172       pos = fitarr.shape()[3];     // the new element position
    1173   } else {
    1174     if (fitarr.nelements() > 0)
    1175       newarr = fitarr;
    1176   }
    1177   newarr(IPosition(4, beamSel_, IFSel_, polSel_, pos)) = Int(nrow);
    1178   fitCol_.put(whichRow, newarr);
    1179 
    1180 }
    1181 
    1182 SDFrequencyTable SDMemTable::getSDFreqTable() const
    1183 {
    1184   const Table& t = table_.keywordSet().asTable("FREQUENCIES");
    1185   SDFrequencyTable sdft;
    1186 
    1187   // Add refpix/refval/incr.  What are the units ? Hz I suppose
    1188   // but it's nowhere described...
    1189   Vector<Double> refPix, refVal, incr;
    1190   ScalarColumn<Double> refPixCol(t, "REFPIX");
    1191   ScalarColumn<Double> refValCol(t, "REFVAL");
    1192   ScalarColumn<Double> incrCol(t, "INCREMENT");
    1193   refPix = refPixCol.getColumn();
    1194   refVal = refValCol.getColumn();
    1195   incr = incrCol.getColumn();
    1196 
    1197   uInt n = refPix.nelements();
    1198   for (uInt i=0; i<n; i++) {
    1199      sdft.addFrequency(refPix[i], refVal[i], incr[i]);
    1200   }
    1201 
    1202   // Frequency reference frame.  I don't know if this
    1203   // is the correct frame.  It might be 'REFFRAME'
    1204   // rather than 'BASEREFFRAME' ?
    1205   String frame;
    1206   t.keywordSet().get("REFFRAME",frame);
    1207   sdft.setRefFrame(frame);
    1208   t.keywordSet().get("BASEREFFRAME",frame);
    1209   sdft.setBaseRefFrame(frame);
    1210 
    1211   // Equinox
    1212   Float equinox;
    1213   t.keywordSet().get("EQUINOX", equinox);
    1214   sdft.setEquinox(equinox);
    1215 
    1216   String unit;
    1217   t.keywordSet().get("UNIT", unit);
    1218   sdft.setUnit(unit);
    1219 
    1220   // Rest Frequency
    1221   Vector<Double> restFreqs;
    1222   t.keywordSet().get("RESTFREQS", restFreqs);
    1223   for (uInt i=0; i<restFreqs.nelements(); i++) {
    1224      sdft.addRestFrequency(restFreqs[i]);
    1225   }
    1226   sdft.setRestFrequencyUnit(String("Hz"));
    1227 
    1228   return sdft;
    1229 }
    1230 
    1231 bool SDMemTable::putSDContainer(const SDContainer& sdc)
    1232 {
    1233   uInt rno = table_.nrow();
    1234   table_.addRow();
    1235 
    1236   timeCol_.put(rno, sdc.timestamp);
    1237   srcnCol_.put(rno, sdc.sourcename);
    1238   fldnCol_.put(rno, sdc.fieldname);
    1239   specCol_.put(rno, sdc.getSpectrum());
    1240   flagsCol_.put(rno, sdc.getFlags());
    1241   tsCol_.put(rno, sdc.getTsys());
    1242   scanCol_.put(rno, sdc.scanid);
    1243   integrCol_.put(rno, sdc.interval);
    1244   freqidCol_.put(rno, sdc.getFreqMap());
    1245   restfreqidCol_.put(rno, sdc.getRestFreqMap());
    1246   dirCol_.put(rno, sdc.getDirection());
    1247   rbeamCol_.put(rno, sdc.refbeam);
    1248   tcalCol_.put(rno, sdc.tcal);
    1249   tcaltCol_.put(rno, sdc.tcaltime);
    1250   azCol_.put(rno, sdc.azimuth);
    1251   elCol_.put(rno, sdc.elevation);
    1252   paraCol_.put(rno, sdc.parangle);
    1253   fitCol_.put(rno, sdc.getFitMap());
    1254   return true;
    1255 }
    1256 
    1257 SDContainer SDMemTable::getSDContainer(uInt whichRow) const
    1258 {
    1259   SDContainer sdc(nBeam(),nIF(),nPol(),nChan());
    1260   timeCol_.get(whichRow, sdc.timestamp);
    1261   srcnCol_.get(whichRow, sdc.sourcename);
    1262   integrCol_.get(whichRow, sdc.interval);
    1263   scanCol_.get(whichRow, sdc.scanid);
    1264   fldnCol_.get(whichRow, sdc.fieldname);
    1265   rbeamCol_.get(whichRow, sdc.refbeam);
    1266   azCol_.get(whichRow, sdc.azimuth);
    1267   elCol_.get(whichRow, sdc.elevation);
    1268   paraCol_.get(whichRow, sdc.parangle);
    1269   Vector<Float> tc;
    1270   tcalCol_.get(whichRow, tc);
    1271   sdc.tcal[0] = tc[0];sdc.tcal[1] = tc[1];
    1272   tcaltCol_.get(whichRow, sdc.tcaltime);
    1273 
    1274   Array<Float> spectrum;
    1275   Array<Float> tsys;
    1276   Array<uChar> flagtrum;
    1277   Vector<uInt> fmap;
    1278   Array<Double> direction;
    1279   Array<Int> fits;
    1280 
    1281   specCol_.get(whichRow, spectrum);
    1282   sdc.putSpectrum(spectrum);
    1283   flagsCol_.get(whichRow, flagtrum);
    1284   sdc.putFlags(flagtrum);
    1285   tsCol_.get(whichRow, tsys);
    1286   sdc.putTsys(tsys);
    1287   freqidCol_.get(whichRow, fmap);
    1288   sdc.putFreqMap(fmap);
    1289   restfreqidCol_.get(whichRow, fmap);
    1290   sdc.putRestFreqMap(fmap);
    1291   dirCol_.get(whichRow, direction);
    1292   sdc.putDirection(direction);
    1293   fitCol_.get(whichRow, fits);
    1294   sdc.putFitMap(fits);
    1295   return sdc;
    1296 }
    1297 
    1298 bool SDMemTable::putSDHeader(const SDHeader& sdh)
     211}
     212
     213void Scantable::attach()
     214{
     215  historyTable_ = table_.keywordSet().asTable("HISTORY");
     216  fitTable_ = table_.keywordSet().asTable("FITS");
     217
     218  timeCol_.attach(table_, "TIME");
     219  srcnCol_.attach(table_, "SRCNAME");
     220  specCol_.attach(table_, "SPECTRA");
     221  flagsCol_.attach(table_, "FLAGTRA");
     222  tsCol_.attach(table_, "TSYS");
     223  cycleCol_.attach(table_,"CYCLENO");
     224  scanCol_.attach(table_, "SCANNO");
     225  beamCol_.attach(table_, "BEAMNO");
     226  integrCol_.attach(table_, "INTERVAL");
     227  azCol_.attach(table_, "AZIMUTH");
     228  elCol_.attach(table_, "ELEVATION");
     229  dirCol_.attach(table_, "DIRECTION");
     230  paraCol_.attach(table_, "PARANGLE");
     231  fldnCol_.attach(table_, "FIELDNAME");
     232  rbeamCol_.attach(table_, "REFBEAMNO");
     233
     234  mfitidCol_.attach(table_,"FIT_ID");
     235  fitidCol_.attach(fitTable_,"FIT_ID");
     236
     237  mfreqidCol_.attach(table_, "FREQ_ID");
     238
     239  mtcalidCol_.attach(table_, "TCAL_ID");
     240
     241  mfocusidCol_.attach(table_, "FOCUS_ID");
     242
     243  mmolidCol_.attach(table_, "MOLECULE_ID");
     244}
     245
     246void Scantable::putSDHeader(const SDHeader& sdh)
    1299247{
    1300248  table_.rwKeywordSet().define("nIF", sdh.nif);
    … …  
    1314262  table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit);
    1315263  table_.rwKeywordSet().define("Epoch", sdh.epoch);
    1316   return true;
    1317 }
    1318 
    1319 SDHeader SDMemTable::getSDHeader() const
     264}
     265
     266SDHeader Scantable::getSDHeader() const
    1320267{
    1321268  SDHeader sdh;
    … …  
    1338285  return sdh;
    1339286}
    1340 void SDMemTable::makePersistent(const std::string& filename)
    1341 {
    1342   table_.deepCopy(filename,Table::New);
    1343 
    1344 }
    1345 
    1346 Int SDMemTable::nScan() const {
    1347   Int n = 0;
    1348   Int previous = -1;Int current=0;
     287
     288int Scantable::rowToScanIndex( int therow )
     289{
     290  int therealrow = -1;
     291
     292  return therealrow;
     293}
     294
     295int Scantable::nScan() const {
     296  int n = 0;
     297  int previous = -1; int current = 0;
    1349298  for (uInt i=0; i< scanCol_.nrow();i++) {
    1350299    scanCol_.getScalar(i,current);
    … …  
    1357306}
    1358307
    1359 String SDMemTable::formatSec(Double x) const
     308std::string Scantable::formatSec(Double x) const
    1360309{
    1361310  Double xcop = x;
    … …  
    1374323};
    1375324
    1376 String SDMemTable::formatDirection(const MDirection& md) const
     325std::string Scantable::formatDirection(const MDirection& md) const
    1377326{
    1378327  Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue();
    … …  
    1387336
    1388337
    1389 std::string SDMemTable::getFluxUnit() const
     338std::string Scantable::getFluxUnit() const
    1390339{
    1391340  String tmp;
    … …  
    1394343}
    1395344
    1396 void SDMemTable::setFluxUnit(const std::string& unit)
     345void Scantable::setFluxUnit(const std::string& unit)
    1397346{
    1398347  String tmp(unit);
    … …  
    1405354}
    1406355
    1407 
    1408 void SDMemTable::setInstrument(const std::string& name)
    1409 {
    1410   Bool throwIt = True;
     356void Scantable::setInstrument(const std::string& name)
     357{
     358  bool throwIt = true;
    1411359  Instrument ins = SDAttr::convertInstrument(name, throwIt);
    1412360  String nameU(name);
    … …  
    1415363}
    1416364
    1417 std::string SDMemTable::summary(bool verbose) const  {
    1418 
    1419   // Format header info
    1420   ostringstream oss;
    1421   oss << endl;
    1422   oss << "--------------------------------------------------------------------------------" << endl;
    1423   oss << " Scan Table Summary" << endl;
    1424   oss << "--------------------------------------------------------------------------------" << endl;
    1425   oss.flags(std::ios_base::left);
    1426   oss << setw(15) << "Beams:" << setw(4) << nBeam() << endl
    1427       << setw(15) << "IFs:" << setw(4) << nIF() << endl
    1428       << setw(15) << "Polarisations:" << setw(4) << nPol() << endl
    1429       << setw(15) << "Channels:"  << setw(4) << nChan() << endl;
    1430   oss << endl;
    1431   String tmp;
    1432   table_.keywordSet().get("Observer", tmp);
    1433   oss << setw(15) << "Observer:" << tmp << endl;
    1434   oss << setw(15) << "Obs Date:" << getTime(-1,True) << endl;
    1435   table_.keywordSet().get("Project", tmp);
    1436   oss << setw(15) << "Project:" << tmp << endl;
    1437   table_.keywordSet().get("Obstype", tmp);
    1438   oss << setw(15) << "Obs. Type:" << tmp << endl;
    1439   table_.keywordSet().get("AntennaName", tmp);
    1440   oss << setw(15) << "Antenna Name:" << tmp << endl;
    1441   table_.keywordSet().get("FluxUnit", tmp);
    1442   oss << setw(15) << "Flux Unit:" << tmp << endl;
    1443   Table t = table_.keywordSet().asTable("FREQUENCIES");
    1444   Vector<Double> vec;
    1445   t.keywordSet().get("RESTFREQS",vec);
    1446   oss << setw(15) << "Rest Freqs:";
    1447   if (vec.nelements() > 0) {
    1448       oss << setprecision(10) << vec << " [Hz]" << endl;
    1449   } else {
    1450       oss << "None set" << endl;
    1451   }
    1452   oss << setw(15) << "Abcissa:" << getAbcissaString() << endl;
    1453   oss << setw(15) << "Cursor:" << "Beam[" << getBeam() << "] "
    1454       << "IF[" << getIF() << "] " << "Pol[" << getPol() << "]" << endl;
    1455   oss << endl;
    1456 
    1457   String dirtype ="Position ("+ MDirection::showType(getDirectionReference()) + ")";
    1458   oss << setw(5) << "Scan"
    1459       << setw(15) << "Source"
    1460       << setw(24) << dirtype
    1461       << setw(10) << "Time"
    1462       << setw(18) << "Integration"
    1463       << setw(7) << "FreqIDs" << endl;
    1464   oss << "--------------------------------------------------------------------------------" << endl;
    1465 
    1466   // Generate list of scan start and end integrations
    1467   Vector<Int> scanIDs = scanCol_.getColumn();
    1468   Vector<uInt> startInt, endInt;
    1469   mathutil::scanBoundaries(startInt, endInt, scanIDs);
    1470 
    1471   const uInt nScans = startInt.nelements();
    1472   String name;
    1473   Vector<uInt> freqIDs, listFQ;
    1474   Vector<uInt> restFreqIDs, listRestFQ;
    1475   uInt nInt;
    1476 
    1477   for (uInt i=0; i<nScans; i++) {
    1478     // Get things from first integration of scan
    1479     String time = getTime(startInt(i),False);
    1480     String tInt = formatSec(Double(getInterval(startInt(i))));
    1481     String posit = formatDirection(getDirection(startInt(i),True));
    1482     srcnCol_.getScalar(startInt(i),name);
    1483 
    1484     // Find all the FreqIDs in this scan
    1485     listFQ.resize(0);
    1486     listRestFQ.resize(0);
    1487     for (uInt j=startInt(i); j<endInt(i)+1; j++) {
    1488       freqidCol_.get(j, freqIDs);
    1489       for (uInt k=0; k<freqIDs.nelements(); k++) {
    1490         mathutil::addEntry(listFQ, freqIDs(k));
    1491       }
    1492 //
    1493       restfreqidCol_.get(j, restFreqIDs);
    1494       for (uInt k=0; k<restFreqIDs.nelements(); k++) {
    1495         mathutil::addEntry(listRestFQ, restFreqIDs(k));
    1496       }
    1497     }
    1498 
    1499     nInt = endInt(i) - startInt(i) + 1;
    1500     oss << setw(3) << std::right << i << std::left << setw(2) << "  "
    1501         << setw(15) << name
    1502         << setw(24) << posit
    1503         << setw(10) << time
    1504         << setw(3) << std::right << nInt  << setw(3) << " x " << std::left
    1505         << setw(6) <<  tInt
    1506         << " " << listFQ << " " << listRestFQ << endl;
    1507   }
    1508   oss << endl;
    1509   oss << "Table contains " << table_.nrow() << " integration(s) in "
    1510       << nScans << " scan(s)." << endl;
    1511 
    1512   // Frequency Table
    1513   if (verbose) {
    1514     std::vector<string> info = getCoordInfo();
    1515     SDFrequencyTable sdft = getSDFreqTable();
    1516     oss << endl << endl;
    1517     oss << "FreqID  Frame   RefFreq(Hz)     RefPix   Increment(Hz)" << endl;
    1518     oss << "--------------------------------------------------------------------------------" << endl;
    1519     for (uInt i=0; i<sdft.length(); i++) {
    1520       oss << setw(8) << i << setw(8)
    1521           << info[3] << setw(16) << setprecision(8)
    1522           << sdft.referenceValue(i) << setw(10)
    1523           << sdft.referencePixel(i) << setw(12)
    1524           << sdft.increment(i) << endl;
    1525     }
    1526     oss << "--------------------------------------------------------------------------------" << endl;
    1527   }
    1528   return String(oss);
    1529 }
    1530 /*
    1531 std::string SDMemTable::scanSummary(const std::vector<int>& whichScans) {
    1532   ostringstream oss;
    1533   Vector<Int> scanIDs = scanCol_.getColumn();
    1534   Vector<uInt> startInt, endInt;
    1535   mathutil::scanBoundaries(startInt, endInt, scanIDs);
    1536   const uInt nScans = startInt.nelements();
    1537   std::vector<int>::const_iterator it(whichScans);
    1538   return String(oss);
    1539 }
    1540 */
    1541 Int SDMemTable::nBeam() const
    1542 {
    1543   Int n;
    1544   table_.keywordSet().get("nBeam",n);
    1545   return n;
    1546 }
    1547 
    1548 Int SDMemTable::nIF() const {
    1549   Int n;
    1550   table_.keywordSet().get("nIF",n);
    1551   return n;
    1552 }
    1553 
    1554 Int SDMemTable::nPol() const {
    1555   Int n;
    1556   table_.keywordSet().get("nPol",n);
    1557   return n;
    1558 }
    1559 
    1560 Int SDMemTable::nChan() const {
    1561   Int n;
    1562   table_.keywordSet().get("nChan",n);
    1563   return n;
    1564 }
    1565 
    1566 Table SDMemTable::getHistoryTable() const
     365MPosition Scantable::getAntennaPosition () const
     366{
     367  Vector<Double> antpos;
     368  table_.keywordSet().get("AntennaPosition", antpos);
     369  MVPosition mvpos(antpos(0),antpos(1),antpos(2));
     370  return MPosition(mvpos);
     371}
     372
     373void Scantable::makePersistent(const std::string& filename)
     374{
     375  String inname(filename);
     376  Path path(inname);
     377  inname = path.expandedName();
     378  table_.deepCopy(inname, Table::New);
     379}
     380
     381int asap::Scantable::nbeam( int scanno ) const
     382{
     383  if ( scanno < 0 ) {
     384    Int n;
     385    table_.keywordSet().get("nBeam",n);
     386    return int(n);
     387  } else {
     388    // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
     389    Table tab = table_(table_.col("SCANNO") == scanno
     390                       && table_.col("POLNO") == 0
     391                       && table_.col("IFNO") == 0
     392                       && table_.col("CYCLENO") == 0 );
     393    ROTableVector<uInt> v(tab, "BEAMNO");
     394    return int(v.nelements());
     395  }
     396  return 0;
     397}
     398
     399int asap::Scantable::nif( int scanno ) const
     400{
     401  if ( scanno < 0 ) {
     402    Int n;
     403    table_.keywordSet().get("nIF",n);
     404    return int(n);
     405  } else {
     406    // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these
     407    Table tab = table_(table_.col("SCANNO") == scanno
     408                       && table_.col("POLNO") == 0
     409                       && table_.col("BEAMNO") == 0
     410                       && table_.col("CYCLENO") == 0 );
     411    ROTableVector<uInt> v(tab, "IFNO");
     412    return int(v.nelements());
     413  }
     414  return 0;
     415}
     416
     417int asap::Scantable::npol( int scanno ) const
     418{
     419  if ( scanno < 0 ) {
     420    Int n;
     421    table_.keywordSet().get("nPol",n);
     422    return n;
     423  } else {
     424    // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
     425    Table tab = table_(table_.col("SCANNO") == scanno
     426                       && table_.col("IFNO") == 0
     427                       && table_.col("BEAMNO") == 0
     428                       && table_.col("CYCLENO") == 0 );
     429    ROTableVector<uInt> v(tab, "POLNO");
     430    return int(v.nelements());
     431  }
     432  return 0;
     433}
     434
     435int asap::Scantable::nrow( int scanno ) const
     436{
     437  if ( scanno < 0 ) {
     438    return int(table_.nrow());
     439  } else {
     440    // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
     441    Table tab = table_(table_.col("SCANNO") == scanno
     442                       && table_.col("BEAMNO") == 0
     443                       && table_.col("IFNO") == 0
     444                       && table_.col("POLNO") == 0 );
     445    return int(tab.nrow());
     446  }
     447  return 0;
     448}
     449
     450
     451int asap::Scantable::nchan( int scanno, int ifno ) const
     452{
     453  if ( scanno < 0 && ifno < 0 ) {
     454    Int n;
     455    table_.keywordSet().get("nChan",n);
     456    return int(n);
     457  } else {
     458    // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these
     459    Table tab = table_(table_.col("SCANNO") == scanno
     460                       && table_.col("IFNO") == ifno
     461                       && table_.col("BEAMNO") == 0
     462                       && table_.col("POLNO") == 0
     463                       && table_.col("CYCLENO") == 0 );
     464    ROArrayColumn<Float> v(tab, "SPECTRA");
     465    cout << v.shape(0) << endl;
     466    return 0;
     467  }
     468  return 0;
     469}
     470
     471Table Scantable::getHistoryTable() const
    1567472{
    1568473  return table_.keywordSet().asTable("HISTORY");
    1569474}
    1570475
    1571 void SDMemTable::appendToHistoryTable(const Table& otherHist)
     476void Scantable::appendToHistoryTable(const Table& otherHist)
    1572477{
    1573478  Table t = table_.rwKeywordSet().asTable("HISTORY");
    1574   const String sep = "--------------------------------------------------------------------------------";
    1575   addHistory(sep);
     479
     480  addHistory(asap::SEPERATOR);
    1576481  TableCopy::copyRows(t, otherHist, t.nrow(), 0, otherHist.nrow());
    1577   addHistory(sep);
    1578 }
    1579 
    1580 void SDMemTable::addHistory(const std::string& hist)
     482  addHistory(asap::SEPERATOR);
     483}
     484
     485void Scantable::addHistory(const std::string& hist)
    1581486{
    1582487  Table t = table_.rwKeywordSet().asTable("HISTORY");
    … …  
    1587492}
    1588493
    1589 std::vector<std::string> SDMemTable::getHistory() const
     494std::vector<std::string> Scantable::getHistory() const
    1590495{
    1591496  Vector<String> history;
    … …  
    1602507}
    1603508
    1604 
    1605 /*
    1606   void SDMemTable::maskChannels(const std::vector<Int>& whichChans ) {
    1607 
    1608   std::vector<int>::iterator it;
    1609   ArrayAccessor<uChar, Axis<asap::PolAxis> > j(flags_);
    1610   for (it = whichChans.begin(); it != whichChans.end(); it++) {
    1611     j.reset(j.begin(uInt(*it)));
    1612     for (ArrayAccessor<uChar, Axis<asap::BeamAxis> > i(j); i != i.end(); ++i) {
    1613       for (ArrayAccessor<uChar, Axis<asap::IFAxis> > ii(i); ii != ii.end(); ++ii) {
    1614         for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > iii(ii);
    1615              iii != iii.end(); ++iii) {
    1616           (*iii) =
    1617         }
    1618       }
    1619     }
    1620   }
    1621 
    1622 }
    1623 */
    1624 void SDMemTable::flag(int whichRow)
    1625   {
    1626   Array<uChar> arr;
    1627   flagsCol_.get(whichRow, arr);
    1628 
    1629   ArrayAccessor<uChar, Axis<asap::BeamAxis> > aa0(arr);
    1630   aa0.reset(aa0.begin(uInt(beamSel_)));//go to beam
    1631   ArrayAccessor<uChar, Axis<asap::IFAxis> > aa1(aa0);
    1632   aa1.reset(aa1.begin(uInt(IFSel_)));// go to IF
    1633   ArrayAccessor<uChar, Axis<asap::PolAxis> > aa2(aa1);
    1634   aa2.reset(aa2.begin(uInt(polSel_)));// go to pol
    1635 
    1636   for (ArrayAccessor<uChar, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
    1637     (*i) = uChar(True);
    1638   }
    1639 
    1640   flagsCol_.put(whichRow, arr);
    1641 }
    1642 
    1643 MDirection::Types SDMemTable::getDirectionReference() const
    1644 {
    1645   Float eq;
    1646   table_.keywordSet().get("Equinox",eq);
    1647   std::map<float,string> mp;
    1648   mp[2000.0] = "J2000";
    1649   mp[1950.0] = "B1950";
    1650   MDirection::Types mdr;
    1651   if (!MDirection::getType(mdr, mp[eq])) {
    1652     mdr = MDirection::J2000;
    1653     pushLog("WARNING: Unknown equinox using J2000");
    1654   }
    1655 
    1656   return mdr;
    1657 }
    1658 
    1659 MEpoch::Types SDMemTable::getTimeReference() const
    1660 {
    1661   MEpoch::Types met;
    1662   String ep;
    1663   table_.keywordSet().get("Epoch",ep);
    1664   if (!MEpoch::getType(met, ep)) {
    1665      pushLog("WARNING: Epoch type unknown - using UTC");
    1666     met = MEpoch::UTC;
    1667   }
    1668 
    1669   return met;
    1670 }
    1671 
    1672 
    1673 Bool SDMemTable::setRestFreqs(const Vector<Double>& restFreqsIn,
    1674                               const String& sUnit,
    1675                               const vector<string>& lines,
    1676                               const String& source,
    1677                               Int whichIF)
    1678 {
    1679    const Int nIFs = nIF();
    1680    if (whichIF>=nIFs) {
    1681       throw(AipsError("Illegal IF index"));
    1682    }
    1683 
    1684    // Find vector of restfrequencies
    1685    // Double takes precedence over String
    1686    Unit unit;
    1687    Vector<Double> restFreqs;
    1688    if (restFreqsIn.nelements()>0) {
    1689       restFreqs.resize(restFreqsIn.nelements());
    1690       restFreqs = restFreqsIn;
    1691       unit = Unit(sUnit);
    1692    } else if (lines.size()>0) {
    1693       const uInt nLines = lines.size();
    1694       unit = Unit("Hz");
    1695       restFreqs.resize(nLines);
    1696       MFrequency lineFreq;
    1697       for (uInt i=0; i<nLines; i++) {
    1698          String tS(lines[i]);
    1699          tS.upcase();
    1700          if (MeasTable::Line(lineFreq, tS)) {
    1701             restFreqs[i] = lineFreq.getValue().getValue();          // Hz
    1702          } else {
    1703             String s = String(lines[i]) +
    1704               String(" is an unrecognized spectral line");
    1705             throw(AipsError(s));
    1706          }
    1707       }
    1708    } else {
    1709       throw(AipsError("You have not specified any rest frequencies or lines"));
    1710    }
    1711 
    1712    // If multiple restfreqs, must be length nIF. In this
    1713    // case we will just replace the rest frequencies
    1714    // We can't disinguish scalar and vector of length 1
    1715    const uInt nRestFreqs = restFreqs.nelements();
    1716    Int idx = -1;
    1717    SDFrequencyTable sdft = getSDFreqTable();
    1718 
    1719    ostringstream oss;
    1720    if (nRestFreqs>1) {
    1721      // Replace restFreqs, one per IF
    1722      if (nRestFreqs != nIFs) {
    1723        throw (AipsError("Number of rest frequencies must be equal to the number of IFs"));
    1724      }
    1725      ostringstream oss;
    1726      oss << "Replaced rest frequencies, one per IF, with given list : " << restFreqs;
    1727      sdft.deleteRestFrequencies();
    1728      for (uInt i=0; i<nRestFreqs; i++) {
    1729        Quantum<Double> rf(restFreqs[i], unit);
    1730        sdft.addRestFrequency(rf.getValue("Hz"));
    1731      }
    1732    } else {
    1733 
    1734      // Add new rest freq
    1735       Quantum<Double> rf(restFreqs[0], unit);
    1736       idx = sdft.addRestFrequency(rf.getValue("Hz"));
    1737       if (whichIF>=0) {
    1738          oss << "Selected given rest frequency (" << restFreqs[0] << ") for IF " << whichIF << endl;
    1739       } else {
    1740          oss << "Selected given rest frequency (" << restFreqs[0] << ") for all IFs" << endl;
    1741       }
    1742    }
    1743    pushLog(String(oss));
    1744    // Replace
    1745    Bool empty = source.empty();
    1746    Bool ok = False;
    1747    if (putSDFreqTable(sdft)) {
    1748       const uInt nRow = table_.nrow();
    1749       String srcName;
    1750       Vector<uInt> restFreqIDs;
    1751       for (uInt i=0; i<nRow; i++) {
    1752          srcnCol_.get(i, srcName);
    1753          restfreqidCol_.get(i,restFreqIDs);
    1754          if (idx==-1) {
    1755            // Replace vector of restFreqs; one per IF.
    1756            // No selection possible
    1757             for (uInt i=0; i<nIFs; i++) restFreqIDs[i] = i;
    1758          } else {
    1759            // Set RestFreqID for selected data
    1760             if (empty || source==srcName) {
    1761                if (whichIF<0) {
    1762                   restFreqIDs = idx;
    1763                } else {
    1764                   restFreqIDs[whichIF] = idx;
    1765                }
    1766             }
    1767          }
    1768          restfreqidCol_.put(i,restFreqIDs);
    1769       }
    1770       ok = True;
    1771    } else {
    1772      ok = False;
    1773    }
    1774 
    1775    return ok;
    1776 }
    1777 
    1778 std::string SDMemTable::spectralLines() const
    1779 {
    1780    Vector<String> lines = MeasTable::Lines();
    1781    MFrequency lineFreq;
    1782    Double freq;
    1783    ostringstream oss;
    1784 
    1785    oss.flags(std::ios_base::left);
    1786    oss << "Line      Frequency (Hz)" << endl;
    1787    oss << "-----------------------" << endl;
    1788    for (uInt i=0; i<lines.nelements(); i++) {
    1789      MeasTable::Line(lineFreq, lines[i]);
    1790      freq = lineFreq.getValue().getValue();          // Hz
    1791      oss << setw(11) << lines[i] << setprecision(10) << freq << endl;
    1792    }
    1793    return String(oss);
    1794 }
    1795 
    1796 void SDMemTable::renumber()
    1797 {
    1798   uInt nRow = scanCol_.nrow();
    1799   Int newscanid = 0;
    1800   Int cIdx;// the current scanid
    1801   // get the first scanid
    1802   scanCol_.getScalar(0,cIdx);
    1803   Int pIdx = cIdx;// the scanid of the previous row
    1804   for (uInt i=0; i<nRow;++i) {
    1805     scanCol_.getScalar(i,cIdx);
    1806     if (pIdx == cIdx) {
    1807       // renumber
    1808       scanCol_.put(i,newscanid);
    1809     } else {
    1810       ++newscanid;
    1811       pIdx = cIdx;   // store scanid
    1812       --i;           // don't increment next loop
    1813     }
    1814   }
    1815 }
    1816 
    1817 
    1818 void SDMemTable::getCursorSlice(IPosition& start, IPosition& end,
    1819                                 const IPosition& shape) const
    1820 {
    1821   const uInt nDim = shape.nelements();
    1822   start.resize(nDim);
    1823   end.resize(nDim);
    1824 
    1825   start(asap::BeamAxis) = beamSel_;
    1826   end(asap::BeamAxis) = beamSel_;
    1827   start(asap::IFAxis) = IFSel_;
    1828   end(asap::IFAxis) = IFSel_;
    1829 
    1830   start(asap::PolAxis) = polSel_;
    1831   end(asap::PolAxis) = polSel_;
    1832 
    1833   start(asap::ChanAxis) = 0;
    1834   end(asap::ChanAxis) = shape(asap::ChanAxis) - 1;
    1835 }
    1836 
    1837 
    1838 std::vector<float> SDMemTable::getFloatSpectrum(const Array<Float>& arr) const
    1839   // Get spectrum at cursor location
    1840 {
    1841 
    1842   // Setup accessors
    1843   ArrayAccessor<Float, Axis<asap::BeamAxis> > aa0(arr);
    1844   aa0.reset(aa0.begin(uInt(beamSel_)));                    // Beam selection
    1845 
    1846   ArrayAccessor<Float, Axis<asap::IFAxis> > aa1(aa0);
    1847   aa1.reset(aa1.begin(uInt(IFSel_)));                      // IF selection
    1848 
    1849   ArrayAccessor<Float, Axis<asap::PolAxis> > aa2(aa1);
    1850   aa2.reset(aa2.begin(uInt(polSel_)));                     // Pol selection
    1851 
    1852   std::vector<float> spectrum;
    1853   for (ArrayAccessor<Float, Axis<asap::ChanAxis> > i(aa2); i != i.end(); ++i) {
    1854     spectrum.push_back(*i);
    1855   }
    1856   return spectrum;
    1857 }
    1858 
    1859 void SDMemTable::calculateAZEL()
     509std::string Scantable::formatTime(const MEpoch& me, bool showdate) const
     510{
     511  MVTime mvt(me.getValue());
     512  if (showdate)
     513    mvt.setFormat(MVTime::YMD);
     514  else
     515    mvt.setFormat(MVTime::TIME);
     516  ostringstream oss;
     517  oss << mvt;
     518  return String(oss);
     519}
     520
     521void Scantable::calculateAZEL()
    1860522{
    1861523  MPosition mp = getAntennaPosition();
     524  MEpoch::ROScalarColumn timeCol(table_, "TIME");
    1862525  ostringstream oss;
    1863526  oss << "Computed azimuth/elevation using " << endl
    1864527      << mp << endl;
    1865   for (uInt i=0; i<nRow();++i) {
    1866     MEpoch me = getEpoch(i);
    1867     MDirection md = getDirection(i,False);
    1868     oss  << " Time: " << getTime(i,False) << " Direction: " << formatDirection(md)
     528  for (uInt i=0; i<nrow(); ++i) {
     529    MEpoch me = timeCol(i);
     530    MDirection md = dirCol_(i);
     531    dirCol_.get(i,md);
     532    oss  << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md)
    1869533         << endl << "     => ";
    1870534    MeasFrame frame(mp, me);
    … …  
    1880544  pushLog(String(oss));
    1881545}
     546
     547double Scantable::getInterval(int whichrow) const
     548{
     549  if (whichrow < 0) return 0.0;
     550  Double intval;
     551  integrCol_.get(Int(whichrow), intval);
     552  return intval;
     553}
     554
     555std::vector<bool> Scantable::getMask(int whichrow) const
     556{
     557  Vector<uChar> flags;
     558  flagsCol_.get(uInt(whichrow), flags);
     559  Vector<Bool> bflag(flags.shape());
     560  convertArray(bflag, flags);
     561  bflag = !bflag;
     562  std::vector<bool> mask;
     563  bflag.tovector(mask);
     564  return mask;
     565}
     566
     567std::vector<float> Scantable::getSpectrum(int whichrow) const
     568{
     569  Vector<Float> arr;
     570  specCol_.get(whichrow, arr);
     571  std::vector<float> out;
     572  arr.tovector(out);
     573  return out;
     574}
     575
     576String Scantable::generateName()
     577{
     578  return (File::newUniqueName("./","temp")).baseName();
     579}
     580
     581const casa::Table& Scantable::table( ) const
     582{
     583  return table_;
     584}
     585
     586casa::Table& Scantable::table( )
     587{
     588  return table_;
     589}
     590
     591std::string Scantable::getPolarizationLabel(bool linear, bool stokes,
     592                                            bool linpol, int polidx) const
     593{
     594  uInt idx = 0;
     595  if (polidx >=0) idx = polidx;
     596  return "";
     597  //return SDPolUtil::polarizationLabel(idx, linear, stokes, linpol);
     598}
     599
     600void Scantable::unsetSelection()
     601{
     602  table_ = originalTable_;
     603  selector_.reset();
     604}
     605
     606void Scantable::setSelection( const STSelector& selection )
     607{
     608  Table tab = const_cast<STSelector&>(selection).apply(originalTable_);
     609  if ( tab.nrow() == 0 ) {
     610    throw(AipsError("Selection contains no data. Not applying it."));
     611  }
     612  table_ = tab;
     613  selector_ = selection;
     614}
     615
     616std::string asap::Scantable::summary( bool verbose )
     617{
     618  // Format header info
     619  ostringstream oss;
     620  oss << endl;
     621  oss << asap::SEPERATOR << endl;
     622  oss << " Scan Table Summary" << endl;
     623  oss << asap::SEPERATOR << endl;
     624  oss.flags(std::ios_base::left);
     625  oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl
     626      << setw(15) << "IFs:" << setw(4) << nif() << endl
     627      << setw(15) << "Polarisations:" << setw(4) << npol() << endl
     628      << setw(15) << "Channels:"  << setw(4) << nchan() << endl;
     629  oss << endl;
     630  String tmp;
     631  //table_.keywordSet().get("Observer", tmp);
     632  oss << setw(15) << "Observer:" << table_.keywordSet().asString("Observer") << endl;
     633  oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl;
     634  table_.keywordSet().get("Project", tmp);
     635  oss << setw(15) << "Project:" << tmp << endl;
     636  table_.keywordSet().get("Obstype", tmp);
     637  oss << setw(15) << "Obs. Type:" << tmp << endl;
     638  table_.keywordSet().get("AntennaName", tmp);
     639  oss << setw(15) << "Antenna Name:" << tmp << endl;
     640  table_.keywordSet().get("FluxUnit", tmp);
     641  oss << setw(15) << "Flux Unit:" << tmp << endl;
     642  Vector<Float> vec;
     643  oss << setw(15) << "Rest Freqs:";
     644  if (vec.nelements() > 0) {
     645      oss << setprecision(10) << vec << " [Hz]" << endl;
     646  } else {
     647      oss << "none" << endl;
     648  }
     649  oss << setw(15) << "Abcissa:" << "channel" << endl;
     650  oss << selector_.print() << endl;
     651  oss << endl;
     652  // main table
     653  String dirtype = "Position ("
     654                  + MDirection::showType(dirCol_.getMeasRef().getType())
     655                  + ")";
     656  oss << setw(5) << "Scan"
     657      << setw(15) << "Source"
     658//      << setw(24) << dirtype
     659      << setw(10) << "Time"
     660      << setw(18) << "Integration" << endl
     661      << setw(5) << "" << setw(10) << "Beam" << dirtype << endl
     662      << setw(15) << "" << setw(5) << "IF"
     663      << setw(8) << "Frame" << setw(16)
     664      << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment" <<endl;
     665  oss << asap::SEPERATOR << endl;
     666  TableIterator iter(table_, "SCANNO");
     667  while (!iter.pastEnd()) {
     668    Table subt = iter.table();
     669    ROTableRow row(subt);
     670    MEpoch::ROScalarColumn timeCol(subt,"TIME");
     671    const TableRecord& rec = row.get(0);
     672    oss << setw(4) << std::right << rec.asuInt("SCANNO")
     673        << std::left << setw(1) << ""
     674        << setw(15) << rec.asString("SRCNAME")
     675        << setw(10) << formatTime(timeCol(0), false);
     676    // count the cycles in the scan
     677    TableIterator cyciter(subt, "CYCLENO");
     678    int nint = 0;
     679    while (!cyciter.pastEnd()) {
     680      ++nint;
     681      ++cyciter;
     682    }
     683    oss << setw(3) << std::right << nint  << setw(3) << " x " << std::left
     684        << setw(6) <<  formatSec(rec.asFloat("INTERVAL")) << endl;
     685
     686    TableIterator biter(subt, "BEAMNO");
     687    while (!biter.pastEnd()) {
     688      Table bsubt = biter.table();
     689      ROTableRow brow(bsubt);
     690      MDirection::ROScalarColumn bdirCol(bsubt,"DIRECTION");
     691      const TableRecord& brec = brow.get(0);
     692      oss << setw(6) << "" <<  setw(10) << brec.asuInt("BEAMNO");
     693      oss  << setw(24) << formatDirection(bdirCol(0)) << endl;
     694      TableIterator iiter(bsubt, "IFNO");
     695      while (!iiter.pastEnd()) {
     696        Table isubt = iiter.table();
     697        ROTableRow irow(isubt);
     698        const TableRecord& irec = irow.get(0);
     699        oss << std::right <<setw(8) << "" << std::left << irec.asuInt("IFNO");
     700        oss << frequencies().print(irec.asuInt("FREQ_ID"));
     701
     702        ++iiter;
     703      }
     704      ++biter;
     705    }
     706    ++iter;
     707  }
     708  /// @todo implement verbose mode
     709  return String(oss);
     710}
     711
     712std::string Scantable::getTime(int whichrow, bool showdate) const
     713{
     714  MEpoch::ROScalarColumn timeCol(table_, "TIME");
     715  MEpoch me;
     716  if (whichrow > -1) {
     717    me = timeCol(uInt(whichrow));
     718  } else {
     719    Double tm;
     720    table_.keywordSet().get("UTC",tm);
     721    me = MEpoch(MVEpoch(tm));
     722  }
     723  return formatTime(me, showdate);
     724}
     725
     726}//namespace asap
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