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// cookbook CCfits demonstration program, for release version 2.0 Jan 2008
// Astrophysics Science Division,
// NASA/ Goddard Space Flight Center
// HEASARC
// http://heasarc.gsfc.nasa.gov
// e-mail: ccfits@legacy.gsfc.nasa.gov
//
// Original author: Ben Dorman
// The CCfits headers are expected to be installed in a subdirectory of
// the include path.
// The <CCfits> header file contains all that is necessary to use both the CCfits
// library and the cfitsio library (for example, it includes fitsio.h) thus making
// all of cfitsio's symbolic names available.
#ifdef _MSC_VER
#include "MSconfig.h" // for truncation warning
#endif
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
// this includes 12 of the CCfits headers and will support all CCfits operations.
// the installed location of the library headers is $(ROOT)/include/CCfits
// to use the library either add -I$(ROOT)/include/CCfits or #include <CCfits/CCfits>
// in the compilation target.
#include <CCfits>
#include <cmath>
// The library is enclosed in a namespace.
using namespace CCfits;
using std::valarray;
int main();
int writeImage();
int writeAscii();
int writeBinary();
int copyHDU();
int selectRows();
int readHeader();
int readImage();
int readTable();
int main()
{
FITS::setVerboseMode(true);
try
{
if (!writeImage()) std::cerr << " writeImage() \n";
if (!writeAscii()) std::cerr << " writeAscii() \n";
if (!writeBinary()) std::cerr << " writeBinary() \n";
if (!copyHDU()) std::cerr << " copyHDU() \n";
if (!readHeader()) std::cerr << " readHeader() \n";
if (!readImage()) std::cerr << " readImage() \n";
if (!readTable()) std::cerr << " readTable() \n";
if (!selectRows()) std::cerr << " selectRows() \n";
}
catch (FitsException&)
// will catch all exceptions thrown by CCfits, including errors
// found by cfitsio (status != 0).
{
std::cerr << " Fits Exception Thrown by test function \n";
}
return 0;
}
int writeImage()
{
// Create a FITS primary array containing a 2-D image
// declare axis arrays.
long naxis = 2;
long naxes[2] = { 300, 200 };
// declare auto-pointer to FITS at function scope. Ensures no resources
// leaked if something fails in dynamic allocation.
std::auto_ptr<FITS> pFits(0);
try
{
// overwrite existing file if the file already exists.
const std::string fileName("!atestfil.fit");
// Create a new FITS object, specifying the data type and axes for the primary
// image. Simultaneously create the corresponding file.
// this image is unsigned short data, demonstrating the cfitsio extension
// to the FITS standard.
pFits.reset( new FITS(fileName , USHORT_IMG , naxis , naxes ) );
}
catch (FITS::CantCreate)
{
// ... or not, as the case may be.
return -1;
}
// references for clarity.
long& vectorLength = naxes[0];
long& numberOfRows = naxes[1];
long nelements(1);
// Find the total size of the array.
// this is a little fancier than necessary ( It's only
// calculating naxes[0]*naxes[1]) but it demonstrates use of the
// C++ standard library accumulate algorithm.
nelements = std::accumulate(&naxes[0],&naxes[naxis],1,std::multiplies<long>());
// create a new image extension with a 300x300 array containing float data.
std::vector<long> extAx(2,300);
string newName ("NEW-EXTENSION");
ExtHDU* imageExt = pFits->addImage(newName,FLOAT_IMG,extAx);
// create a dummy row with a ramp. Create an array and copy the row to
// row-sized slices. [also demonstrates the use of valarray slices].
// also demonstrate implicit type conversion when writing to the image:
// input array will be of type float.
std::valarray<int> row(vectorLength);
for (long j = 0; j < vectorLength; ++j) row[j] = j;
std::valarray<int> array(nelements);
for (int i = 0; i < numberOfRows; ++i)
{
array[std::slice(vectorLength*static_cast<int>(i),vectorLength,1)] = row + i;
}
#ifdef VALARRAY_DEFECT
const double PI ( std::atan(1.)*4. );
#else
const double PI (std::atan(1.)*4.);
#endif
// create some data for the image extension.
long extElements = std::accumulate(extAx.begin(),extAx.end(),1,std::multiplies<long>());
std::valarray<float> ranData(extElements);
const float PIBY = static_cast < float > (PI/150.);
for ( int jj = 0 ; jj < extElements ; ++jj)
{
float arg = static_cast < float > ( PIBY*jj );
#ifdef VALARRAY_DEFECT
float val = std::cos( arg );
ranData[jj] = val;
#else
ranData[jj] = static_cast < float > ( std::cos(arg) );
#endif
}
long fpixel(1);
// write the image extension data: also demonstrates switching between
// HDUs.
imageExt->write(fpixel,extElements,ranData);
//add two keys to the primary header, one long, one complex.
long exposure(1500);
#ifdef VALARRAY_DEFECT
double re = std::cos( 2*PI/3.0 );
double im = std::sin( 2*PI/3.0 );
std::complex<float> omega( re, im );
#else
float re = static_cast < float > ( std::cos(2*PI/3.) );
float im = static_cast < float > ( std::sin(2*PI/3.) );
std::complex<float> omega( re, im );
#endif
pFits->pHDU().addKey("EXPOSURE", exposure,"Total Exposure Time");
pFits->pHDU().addKey("OMEGA",omega," Complex cube root of 1 ");
// The function PHDU& FITS::pHDU() returns a reference to the object representing
// the primary HDU; PHDU::write( <args> ) is then used to write the data.
pFits->pHDU().write(fpixel,nelements,array);
// PHDU's friend ostream operator. Doesn't print the entire array, just the
// required & user keywords, and is provided largely for testing purposes [see
// readImage() for an example of how to output the image array to a stream].
std::cout << pFits->pHDU() << std::endl;
return 0;
}
int writeAscii ()
//******************************************************************
// Create an ASCII Table extension containing 3 columns and 6 rows *
//******************************************************************
{
// declare auto-pointer to FITS at function scope. Ensures no resources
// leaked if something fails in dynamic allocation.
std::auto_ptr<FITS> pFits(0);
try
{
const std::string fileName("atestfil.fit");
// append the new extension to file created in previous function call.
// CCfits writing constructor.
// if this had been a new file, then the following code would create
// a dummy primary array with BITPIX=8 and NAXIS=0.
pFits.reset( new FITS(fileName,Write) );
}
catch (CCfits::FITS::CantOpen)
{
// ... or not, as the case may be.
return -1;
}
unsigned long rows(6);
string hduName("PLANETS_ASCII");
std::vector<string> colName(3,"");
std::vector<string> colForm(3,"");
std::vector<string> colUnit(3,"");
/* define the name, datatype, and physical units for the 3 columns */
colName[0] = "Planet";
colName[1] = "Diameter";
colName[2] = "Density";
colForm[0] = "a8";
colForm[1] = "i6";
colForm[2] = "f4.2";
colUnit[0] = "";
colUnit[1] = "km";
colUnit[2] = "g/cm^-3";
std::vector<string> planets(rows);
const char *planet[] = {"Mercury", "Venus", "Earth",
"Mars","Jupiter","Saturn"};
const char *mnemoy[] = {"Many", "Volcanoes", "Erupt",
"Mulberry","Jam","Sandwiches","Under",
"Normal","Pressure"};
long diameter[] = { 4880, 12112, 12742, 6800, 143000, 121000};
float density[] = { 5.1f, 5.3f, 5.52f, 3.94f, 1.33f, 0.69f};
// append a new ASCII table to the fits file. Note that the user
// cannot call the Ascii or Bin Table constructors directly as they
// are protected.
Table* newTable = pFits->addTable(hduName,rows,colName,colForm,colUnit,AsciiTbl);
size_t j = 0;
for ( ; j < rows; ++j) planets[j] = string(planet[j]);
// Table::column(const std::string& name) returns a reference to a Column object
try
{
newTable->column(colName[0]).write(planets,1);
newTable->column(colName[1]).write(diameter,rows,1);
newTable->column(colName[2]).write(density,rows,1);
}
catch (FitsException&)
{
// ExtHDU::column could in principle throw a NoSuchColumn exception,
// or some other fits error may ensue.
std::cerr << " Error in writing to columns - check e.g. that columns of specified name "
<< " exist in the extension \n";
}
// FITSUtil::auto_array_ptr<T> is provided to counter resource leaks that
// may arise from C-arrays. It is a std::auto_ptr<T> analog that calls
// delete[] instead of delete.
FITSUtil::auto_array_ptr<long> pDiameter(new long[rows]);
FITSUtil::auto_array_ptr<float> pDensity(new float[rows]);
long* Cdiameter = pDiameter.get();
float* Cdensity = pDensity.get();
Cdiameter[0] = 4880; Cdiameter[1] = 12112; Cdiameter[2] = 12742; Cdiameter[3] = 6800;
Cdiameter[4] = 143000; Cdiameter[5] = 121000;
Cdensity[0] = 5.1f; Cdensity[1] = 5.3f; Cdensity[2] = 5.52f;
Cdensity[3] = 3.94f; Cdensity[4] = 1.33f; Cdensity[5] = 0.69;
// this << operator outputs everything that has been read.
std::cout << *newTable << std::endl;
pFits->pHDU().addKey("NEWVALUE",42," Test of adding keyword to different extension");
pFits->pHDU().addKey("STRING",std::string(" Rope "),"trailing blank test 1 ");
pFits->pHDU().addKey("STRING2",std::string("Cord"),"trailing blank test 2 ");
// demonstrate increaing number of rows and null values.
long ignoreVal(12112);
long nullNumber(-999);
try
{
// add a TNULLn value to column 2.
newTable->column(colName[1]).addNullValue(nullNumber);
// test that writing new data properly expands the number of rows
// in both the file]).write(planets,rows-3);
newTable->column(colName[2]).write(density,rows,rows-3);
// test the undefined value functionality. Undefineds are replaced on
// disk but not in the memory copy.
newTable->column(colName[1]).write(diameter,rows,rows-3,&ignoreVal);
}
catch (FitsException&)
{
// this time we're going to ignore problems in these operations
}
// output header information to check that everything we did so far
// hasn't corrupted the file.
std::cout << pFits->pHDU() << std::endl;
std::vector<string> mnemon(9);
for ( j = 0; j < 9; ++j) mnemon[j] = string(mnemoy[j]);
// Add a new column of string type to the Table.
// type, columnName, width, units. [optional - decimals, column number]
// decimals is only relevant for floatingpoint data in ascii columns.
newTable->addColumn(Tstring,"Mnemonic",10," words ");
newTable->column("Mnemonic").write(mnemon,1);
// write the data string.
newTable->writeDate();
// and see if it all worked right.
std::cout << *newTable << std::endl;
return 0;
}
int writeBinary ()
//*********************************************************************
// Create a BINARY table extension and write and manipulate vector rows
//*********************************************************************
{
std::auto_ptr<FITS> pFits(0);
try
{
const std::string fileName("atestfil.fit");
pFits.reset( new FITS(fileName,Write) );
}
catch (CCfits::FITS::CantOpen)
{
return -1;
}
unsigned long rows(3);
string hduName("TABLE_BINARY");
std::vector<string> colName(7,"");
std::vector<string> colForm(7,"");
std::vector<string> colUnit(7,"");
colName[0] = "numbers";
colName[1] = "sequences";
colName[2] = "powers";
colName[3] = "big-integers";
colName[4] = "dcomplex-roots";
colName[5] = "fcomplex-roots";
colName[6] = "scalar-complex";
colForm[0] = "8A";
colForm[1] = "20J";
colForm[2] = "20D";
colForm[3] = "20V";
colForm[4] = "20M";
colForm[5] = "20C";
colForm[6] = "1M";
colUnit[0] = "magnets";
colUnit[1] = "bulbs";
colUnit[2] = "batteries";
colUnit[3] = "mulberries";
colUnit[4] = "";
colUnit[5] = "";
colUnit[6] = "pico boo";
std::vector<string> numbers(rows);
const string num("NUMBER-");
for ( size_t j = 0; j < rows; ++j)
{
#ifdef SSTREAM_DEFECT
std::ostrstream pStr;
#else
std::ostringstream pStr;
#endif
pStr << num << j+1;
#ifdef SSTREAM_DEFECT
pStr << std::ends;
#endif
numbers[j] = string(pStr.str());
}
const size_t OFFSET(20);
// write operations take in data as valarray<T>, vector<T> , and
// vector<valarray<T> >, and T* C-arrays. Create arrays to exercise the C++
// containers. Check complex I/O for both float and double complex types.
std::valarray<long> sequence(60);
std::vector<long> sequenceVector(60);
std::vector<std::valarray<long> > sequenceVV(3);
for ( size_t j = 0; j < rows; ++j)
{
sequence[OFFSET*j] = 1 + j;
sequence[OFFSET*j+1] = 1 + j;
sequenceVector[OFFSET*j] = sequence[OFFSET*j];
sequenceVector[OFFSET*j+1] = sequence[OFFSET*j+1];
// generate Fibonacci numbers.
for (size_t i = 2; i < OFFSET; ++i)
{
size_t elt (OFFSET*j +i);
sequence[elt] = sequence[elt-1] + sequence[elt - 2];
sequenceVector[elt] = sequence[elt] ;
}
sequenceVV[j].resize(OFFSET);
sequenceVV[j] = sequence[std::slice(OFFSET*j,OFFSET,1)];
}
std::valarray<unsigned int> unsignedData(60);
unsigned int base (1 << 31);
std::valarray<double> powers(60);
std::vector<double> powerVector(60);
std::vector<std::valarray<double> > powerVV(3);
std::valarray<std::complex<double> > croots(60);
std::valarray<std::complex<float> > fcroots(60);
std::vector<std::complex<float> > fcroots_vector(60);
std::vector<std::valarray<std::complex<float> > > fcrootv(3);
const double PI (std::atan(1.)*4.);
// create complex data as 60th roots of unity.
double PIBY = PI/60.;
for ( size_t j = 0; j < rows; ++j)
{
for (size_t i = 0; i < OFFSET; ++i)
{
size_t elt (OFFSET*j+i);
unsignedData[elt] = sequence[elt];
#ifdef VALARRAY_DEFECT
double re = std::cos(PIBY*elt);
double im = std::sin(PIBY*elt);
croots[elt] = std::complex<double>( re, im );
#else
croots[elt] = std::complex<double>(std::cos(PIBY*elt),std::sin(PIBY*elt));
#endif
fcroots[elt] = std::complex<float>(croots[elt].real(),croots[elt].imag());
double x = i+1;
powers[elt] = pow(x,(int)j+1);
powerVector[elt] = powers[elt];
}
powerVV[j].resize(OFFSET);
powerVV[j] = powers[std::slice(OFFSET*j,OFFSET,1)];
}
#ifdef TEMPLATE_AMBIG7_DEFECT
std::slice s ( 0, 20, 1 );
std::valarray<std::complex<float> > fcroots_sliced ( fcroots[s] );
FITSUtil::fillMSva(fcroots_vector, fcroots_sliced );
#else
FITSUtil::fill(fcroots_vector,fcroots[std::slice(0,20,1)]);
#endif
unsignedData += base;
// syntax identical to Binary Table
Table* newTable = pFits->addTable(hduName,rows,colName,colForm,colUnit);
// numbers is a scalar column
newTable->column(colName[0]).write(numbers,1);
// write valarrays to vector column: note signature change
newTable->column(colName[1]).write(sequence,rows,1);
newTable->column(colName[2]).write(powers,rows,1);
newTable->column(colName[3]).write(unsignedData,rows,1);
newTable->column(colName[4]).write(croots,rows,1);
newTable->column(colName[5]).write(fcroots,rows,3);
newTable->column(colName[6]).write(fcroots_vector,1);
// write vectors to column: note signature change
newTable->column(colName[1]).write(sequenceVector,rows,4);
newTable->column(colName[2]).write(powerVector,rows,4);
std::cout << *newTable << std::endl;
for (size_t j = 0; j < 3 ; ++j)
{
fcrootv[j].resize(20);
fcrootv[j] = fcroots[std::slice(20*j,20,1)];
}
// write vector<valarray> object to column.
newTable->column(colName[1]).writeArrays(sequenceVV,7);
newTable->column(colName[2]).writeArrays(powerVV,7);
// create a new vector column in the Table
newTable->addColumn(Tfloat,"powerSeq",20,"none");
// add data entries to it.
newTable->column("powerSeq").writeArrays(powerVV,1);
newTable->column("powerSeq").write(powerVector,rows,4);
newTable->column("dcomplex-roots").write(croots,rows,4);
newTable->column("powerSeq").write(sequenceVector,rows,7);
std::cout << *newTable << std::endl;
// delete one of the original columns.
newTable->deleteColumn(colName[2]);
// add a new set of rows starting after row 3. So we'll have 14 with
// rows 4,5,6,7,8 blank
newTable->insertRows(3,5);
// now, in the new column, write 3 rows (sequenceVV.size() = 3). This
// will place data in rows 3,4,5 of this column,overwriting them.
newTable->column("powerSeq").writeArrays(sequenceVV,3);
newTable->column("fcomplex-roots").writeArrays(fcrootv,3);
// delete 3 rows starting with row 2. A Table:: method, so the same
// code is called for all Table objects. We should now have 11 rows.
newTable->deleteRows(2,3);
//add a history string. This function call is in HDU:: so is identical
//for all HDUs
string hist("This file was created for testing CCfits write functionality");
hist += " it serves no other useful purpose. This particular part of the file was ";
hist += " constructed to test the writeHistory() and writeComment() functionality" ;
newTable->writeHistory(hist);
// add a comment string. Use std::string method to change the text in the message
// and write the previous junk as a comment.
hist.insert(0, " COMMENT TEST ");
newTable->writeComment(hist);
// ... print the result.
std::cout << *newTable << std::endl;
return 0;
}
int copyHDU()
{
//*******************************************************************/
// copy the 1st and 3rd HDUs from the input file to a new FITS file */
//*******************************************************************/
const string inFileName("atestfil.fit");
const string outFileName("btestfil.fit");
int status(0);
status = 0;
remove(outFileName.c_str()); /* Delete old file if it already exists */
// open the existing FITS file (Read is the default anyway)
FITS inFile(inFileName,Read);
// custom constructor FITS::FITS(const string&, const FITS&) for
// this particular task.
FITS outFile(outFileName,inFile);
// copy extension by number...
outFile.copy(inFile.extension(2));
// copy extension by name...
outFile.copy(inFile.extension("TABLE_BINARY"));
return 0;
}
int readHeader()
{
const string SPECTRUM("SPECTRUM");
// read a particular HDU within the file. This call reads just the header
// information from SPECTRUM
std::auto_ptr<FITS> pInfile(new FITS("file1.pha",Read,SPECTRUM));
// define a reference for clarity.
ExtHDU& table = pInfile->extension(SPECTRUM);
// read all the keywords, excluding those associated with columns.
table.readAllKeys();
// print the result.
std::cout << table << std::endl;
return 0;
}
int readImage()
{
std::auto_ptr<FITS> pInfile(new FITS("atestfil.fit",Read,true));
PHDU& image = pInfile->pHDU();
std::valarray<unsigned long> contents;
// read all user-specifed, coordinate, and checksum keys in the image
image.readAllKeys();
image.read(contents);
// this doesn't print the data, just header info.
std::cout << image << std::endl;
long ax1(image.axis(0));
long ax2(image.axis(1));
for (long j = 0; j < ax2; j+=10)
{
std::ostream_iterator<short> c(std::cout,"\t");
std::copy(&contents[j*ax1],&contents[(j+1)*ax1-1],c);
std::cout << '\n';
}
std::cout << std::endl;
return 0;
}
int readTable()
{
// read a table and explicitly read selected columns. To read all the
// data on construction, set the last argument of the FITS constructor
// call to 'true'. This has been tested.
std::vector<String> hdus(2);
hdus[0] = "PLANETS_ASCII";
hdus[1] = "TABLE_BINARY";
std::auto_ptr<FITS> pInfile(new FITS("atestfil.fit",Read,hdus,false));
ExtHDU& table = pInfile->extension(hdus[1]);
std::vector < valarray <int > > pp;
table.column("powerSeq").readArrays( pp, 1,3 );
std::vector < valarray <std::complex<double> > > cc;
table.column("dcomplex-roots").readArrays( cc, 1,3 );
std::valarray < std::complex<float> > ff;
table.column("fcomplex-roots").read( ff, 4 );
std::cout << pInfile->extension(hdus[0]) << std::endl;
std::cout << pInfile->extension(hdus[1]) << std::endl;
return 0;
}
int selectRows()
{
const string inFile("atestfil.fit");
const string outFile("btestfil.fit");
const string newFile("ctestfil.fit");
remove(newFile.c_str());
// test 1: write to a new file
std::auto_ptr<FITS> pInfile(new FITS(inFile,Write,string("PLANETS_ASCII")));
FITS* infile = pInfile.get();
std::auto_ptr<FITS> pNewfile(new FITS(newFile,Write));
ExtHDU& source = infile->extension("PLANETS_ASCII");
const string expression("DENSITY > 3.0");
Table& sink1 = pNewfile.get()->filter(expression,source,false,true);
std::cout << sink1 << std::endl;
// test 2: write a new HDU to the current file, overwrite false, read true.
// AS OF 7/2/01 does not work because of a bug in cfitsio, but does not
// crash, simply writes a new header to the file without also writing the
// selected data.
Table& sink2 = infile->filter(expression,source,false,true);
std::cout << sink2 << std::endl;
// reset the source file back to the extension in question.
source = infile->extension("PLANETS_ASCII");
// test 3: overwrite the current HDU with filtered data.
Table& sink3 = infile->filter(expression,source,true,true);
std::cout << sink3 << std::endl;
return 0;
}
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