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#include "fitsfile.h"
#include <limits>
#include <cmath>
#include <sstream>
#include <iostream>
#include <boost/algorithm/string/trim.hpp>
#include "../util/logger.h"
FitsFile::FitsFile(const std::string &filename) : _filename(filename), _fptr(0), _isOpen(false)
{
}
FitsFile::~FitsFile()
{
if(_isOpen)
Close();
}
void FitsFile::CheckStatus(int status) const {
if(status) {
/* fits_get_errstatus returns at most 30 characters */
char err_text[31];
fits_get_errstatus(status, err_text);
char err_msg[81];
std::stringstream errMsg;
errMsg << "CFITSIO reported error when performing IO on file '" << _filename << "':" << err_text << " (";
while(fits_read_errmsg(err_msg))
errMsg << err_msg;
errMsg << ')';
throw FitsIOException(errMsg.str());
}
}
void FitsFile::CheckOpen() const {
if(!_isOpen)
throw FitsIOException("No open file, call Open() first");
}
void FitsFile::Open(FitsFile::FileMode mode)
{
if(_isOpen) {
throw FitsIOException("File was opened twice");
} else {
int status = 0;
int modeInt = 0;
switch(mode) {
case ReadOnlyMode: modeInt = READONLY; break;
case ReadWriteMode: modeInt = READWRITE; break;
default: throw FitsIOException("Incorrect mode specified"); break;
}
fits_open_diskfile(&_fptr, _filename.c_str(), modeInt, &status);
CheckStatus(status);
_isOpen = true;
}
}
void FitsFile::Create()
{
if(_isOpen) {
throw FitsIOException("File was opened twice");
} else {
int status = 0;
fits_create_file(&_fptr, (std::string("!") + _filename).c_str(), &status);
CheckStatus(status);
_isOpen = true;
}
}
void FitsFile::Close()
{
if(_isOpen) {
int status = 0;
fits_close_file(_fptr, &status);
CheckStatus(status);
_isOpen = false;
_fptr = 0;
} else {
throw FitsIOException("Non-opened file was closed");
}
}
int FitsFile::GetHDUCount()
{
CheckOpen();
int hdunum = 0, status = 0;
fits_get_num_hdus(_fptr, &hdunum, &status);
CheckStatus(status);
return hdunum;
}
int FitsFile::GetCurrentHDU()
{
CheckOpen();
int hdunum = 0;
fits_get_hdu_num(_fptr, &hdunum);
return hdunum;
}
void FitsFile::MoveToHDU(int hduNumber)
{
CheckOpen();
int status = 0;
fits_movabs_hdu(_fptr, hduNumber, NULL, &status);
CheckStatus(status);
}
enum FitsFile::HDUType FitsFile::GetCurrentHDUType()
{
CheckOpen();
int hdutypeInt = 0, status = 0;
fits_get_hdu_type(_fptr, &hdutypeInt, &status);
CheckStatus(status);
enum HDUType hduType;
switch(hdutypeInt) {
case IMAGE_HDU: hduType = ImageHDUType; break;
case ASCII_TBL: hduType = ASCIITableHDUType; break;
case BINARY_TBL: hduType = BinaryTableHDUType; break;
default: throw FitsIOException("Unknown HDUType returned");
}
return hduType;
}
enum FitsFile::ImageType FitsFile::GetCurrentImageType()
{
CheckOpen();
int bitPixInt = 0, status = 0;
fits_get_img_type(_fptr, &bitPixInt, &status);
CheckStatus(status);
enum ImageType imageType;
switch(bitPixInt) {
case BYTE_IMG: imageType = Int8ImageType; break;
case SHORT_IMG: imageType = Int16ImageType; break;
case LONG_IMG: imageType = Int32ImageType; break;
case FLOAT_IMG: imageType = Float32ImageType; break;
case DOUBLE_IMG: imageType = Double64ImageType; break;
default: throw FitsIOException("Unknown image type returned");
}
return imageType;
}
int FitsFile::GetCurrentImageDimensionCount()
{
CheckOpen();
int status = 0, naxis = 0;
fits_get_img_dim(_fptr, &naxis, &status);
CheckStatus(status);
return naxis;
}
long FitsFile::GetCurrentImageSize(int dimension)
{
CheckOpen();
if(dimension > GetCurrentImageDimensionCount())
throw FitsIOException("Parameter outside range");
int status = 0;
long *sizes = new long[dimension];
fits_get_img_size(_fptr, dimension, sizes, &status);
long size = sizes[dimension-1];
delete[] sizes;
CheckStatus(status);
return size;
}
void FitsFile::ReadCurrentImageData(long startPos, num_t *buffer, long bufferSize, long double nullValue)
{
CheckOpen();
int status = 0, dimensions = GetCurrentImageDimensionCount();
long *firstpixel = new long[dimensions];
for(int i=0;i < dimensions;i++) {
firstpixel[i] = 1 + startPos%GetCurrentImageSize(i+1);
startPos = startPos/GetCurrentImageSize(i+1);
}
double *dblbuffer = new double[bufferSize];
double dblNullValue = nullValue;
int anynul = 0;
fits_read_pix(_fptr, TDOUBLE, firstpixel, bufferSize, &dblNullValue, dblbuffer, &anynul, &status);
for(int i=0;i<bufferSize;i++)
buffer[i] = dblbuffer[i];
delete[] dblbuffer;
delete[] firstpixel;
CheckStatus(status);
}
void FitsFile::AppendImageHUD(enum FitsFile::ImageType imageType, long width, long height)
{
int status = 0;
int bitPixInt;
switch(imageType) {
case Int8ImageType: bitPixInt = BYTE_IMG; break;
case Int16ImageType: bitPixInt = SHORT_IMG; break;
case Int32ImageType: bitPixInt = LONG_IMG; break;
case Float32ImageType: bitPixInt = FLOAT_IMG; break;
case Double64ImageType: bitPixInt = DOUBLE_IMG; break;
default: throw FitsIOException();
}
long *naxes = new long[2];
naxes[0] = width;
naxes[1] = height;
fits_create_img(_fptr, bitPixInt, 2, naxes, &status);
delete[] naxes;
CheckStatus(status);
}
void FitsFile::WriteImage(long startPos, double *buffer, long bufferSize, double nullValue)
{
CheckOpen();
int status = 0, dimensions = GetCurrentImageDimensionCount();
long *firstpixel = new long[dimensions];
for(int i=0;i < dimensions;i++) {
firstpixel[i] = 1 + startPos%GetCurrentImageSize(i+1);
startPos = startPos/GetCurrentImageSize(i+1);
}
fits_write_pixnull(_fptr, TDOUBLE, firstpixel, bufferSize, buffer, &nullValue, &status);
delete[] firstpixel;
CheckStatus(status);
}
void FitsFile::WriteImage(long startPos, float *buffer, long bufferSize, float nullValue)
{
CheckOpen();
int status = 0, dimensions = GetCurrentImageDimensionCount();
long *firstpixel = new long[dimensions];
for(int i=0;i < dimensions;i++) {
firstpixel[i] = 1 + startPos%GetCurrentImageSize(i+1);
startPos = startPos/GetCurrentImageSize(i+1);
}
fits_write_pixnull(_fptr, TFLOAT, firstpixel, bufferSize, buffer, &nullValue, &status);
delete[] firstpixel;
CheckStatus(status);
}
int FitsFile::GetRowCount()
{
CheckOpen();
long rowCount;
int status = 0;
fits_get_num_rows(_fptr, &rowCount, &status);
CheckStatus(status);
return rowCount;
}
int FitsFile::GetKeywordCount()
{
int status = 0, keysexist;
fits_get_hdrspace(_fptr, &keysexist, NULL, &status);
CheckStatus(status);
return keysexist;
}
std::string FitsFile::GetKeyword(int keywordNumber)
{
char keyName[FLEN_KEYWORD], keyValue[FLEN_VALUE];
int status = 0;
fits_read_keyn(_fptr, keywordNumber, keyName, keyValue, NULL, &status);
CheckStatus(status);
return std::string(keyName);
}
std::string FitsFile::GetKeywordValue(int keywordNumber)
{
char keyName[FLEN_KEYWORD], keyValue[FLEN_VALUE];
int status = 0;
fits_read_keyn(_fptr, keywordNumber, keyName, keyValue, NULL, &status);
CheckStatus(status);
std::string val(keyValue);
if(val.length() >= 2 && *val.begin()=='\'' && *val.rbegin()=='\'')
{
val = val.substr(1, val.length()-2);
boost::trim(val);
}
return val;
}
bool FitsFile::GetKeywordValue(const std::string &keywordName, std::string &value)
{
char keyValue[FLEN_VALUE];
int status = 0;
fits_read_keyword(_fptr, const_cast<char *>(keywordName.c_str()), keyValue, NULL, &status);
if(status == 0) {
value = std::string(keyValue);
if(value.length() >= 2 && *value.begin()=='\'' && *value.rbegin()=='\'')
{
value = value.substr(1, value.length()-2);
boost::trim(value);
}
return true;
} else {
return false;
}
}
std::string FitsFile::GetKeywordValue(const std::string &keywordName)
{
char keyValue[FLEN_VALUE];
int status = 0;
fits_read_keyword(_fptr, const_cast<char *>(keywordName.c_str()), keyValue, NULL, &status);
CheckStatus(status);
std::string val(keyValue);
if(val.length() >= 2 && *val.begin()=='\'' && *val.rbegin()=='\'')
{
val = val.substr(1, val.length()-2);
boost::trim(val);
}
return val;
}
std::string FitsFile::GetKeywordComment(int keywordNumber)
{
char keyName[FLEN_KEYWORD], keyValue[FLEN_VALUE], keyComment[FLEN_COMMENT];
int status = 0;
fits_read_keyn(_fptr, keywordNumber, keyName, keyValue, keyComment, &status);
CheckStatus(status);
return std::string(keyComment);
}
int FitsFile::GetColumnCount()
{
CheckOpen();
int rowCount, status = 0;
fits_get_num_cols(_fptr, &rowCount, &status);
CheckStatus(status);
return rowCount;
}
int FitsFile::GetColumnType(int colNumber)
{
CheckOpen();
int typecode, status = 0;
long repeat, width;
fits_get_coltype(_fptr, colNumber, &typecode, &repeat, &width, &status);
CheckStatus(status);
return typecode;
}
int FitsFile::GetIntKeywordValue(int keywordNumber)
{
return atoi(GetKeyword(keywordNumber).c_str());
}
int FitsFile::GetIntKeywordValue(const std::string &keywordName)
{
return atoi(GetKeywordValue(keywordName).c_str());
}
double FitsFile::GetDoubleKeywordValue(int keywordNumber)
{
return atof(GetKeyword(keywordNumber).c_str());
}
double FitsFile::GetDoubleKeywordValue(const std::string &keywordName)
{
return atof(GetKeywordValue(keywordName).c_str());
}
bool FitsFile::HasGroups()
{
try {
return GetKeywordValue("GROUPS") == "T";
} catch(FitsIOException &e)
{
return false;
}
}
int FitsFile::GetGroupCount()
{
return GetIntKeywordValue("GCOUNT");
}
int FitsFile::GetParameterCount()
{
return GetIntKeywordValue("PCOUNT");
}
long FitsFile::GetImageSize()
{
long size = 1;
for(int i=2;i<=GetCurrentImageDimensionCount();++i)
{
size *= GetCurrentImageSize(i);
}
return size;
}
long FitsFile::GetGroupSize()
{
if(!HasGroups())
throw FitsIOException("HDU has no groups");
long size = 1;
for(int i=2;i<=GetCurrentImageDimensionCount();++i)
{
size *= GetCurrentImageSize(i);
}
size += GetParameterCount();
return size;
}
void FitsFile::ReadGroupParameters(long groupIndex, long double *parametersData)
{
int status = 0;
long pSize = GetParameterCount();
double *parameters = new double[pSize];
fits_read_grppar_dbl(_fptr, groupIndex+1, 1, pSize, parameters, &status);
CheckStatus(status);
for(long i = 0; i<pSize;++i)
parametersData[i] = parameters[i];
delete[] parameters;
}
void FitsFile::ReadGroup(long groupIndex, long double *groupData)
{
int status = 0;
long size = GetImageSize();
long pSize = GetParameterCount();
double *parameters = new double[pSize];
double nulValue = std::numeric_limits<double>::quiet_NaN();
int anynul = 0;
fits_read_grppar_dbl(_fptr, groupIndex+1, 1, pSize, parameters, &status);
CheckStatus(status);
for(long i = 0; i<pSize;++i)
groupData[i] = parameters[i];
delete[] parameters;
double *data = new double[size];
fits_read_img_dbl(_fptr, groupIndex+1, 1, size, nulValue, data, &anynul, &status);
CheckStatus(status);
for(long i = 0; i<size; ++i)
groupData[pSize + i] = data[i];
delete[] data;
if(anynul != 0)
Logger::Warn << "There were nulls in the group\n";
}
void FitsFile::ReadGroupData(long groupIndex, long double *groupData)
{
int status = 0;
long size = GetImageSize();
double nulValue = std::numeric_limits<double>::quiet_NaN();
int anynul = 0;
double *data = new double[size];
fits_read_img_dbl(_fptr, groupIndex+1, 1, size, nulValue, data, &anynul, &status);
CheckStatus(status);
for(long i = 0; i<size; ++i)
groupData[i] = data[i];
delete[] data;
if(anynul != 0)
Logger::Warn << "There were nulls in the group data\n";
}
int FitsFile::GetGroupParameterIndex(const std::string ¶meterName)
{
if(!HasGroups())
throw FitsIOException("HDU has no groups");
int parameterCount = GetParameterCount();
for(int i=1;i<=parameterCount;++i)
{
std::stringstream s;
s << "PTYPE" << i;
if(GetKeywordValue(s.str()) == parameterName)
return i-1;
}
throw FitsIOException(std::string("Can not find parameter with name ") + parameterName);
}
int FitsFile::GetGroupParameterIndex(const std::string ¶meterName, int number)
{
if(!HasGroups())
throw FitsIOException("HDU has no groups");
int parameterCount = GetParameterCount();
for(int i=1;i<=parameterCount;++i)
{
std::stringstream s;
s << "PTYPE" << i;
if(GetKeywordValue(s.str()) == parameterName)
{
--number;
if(number == 0)
return i-1;
}
}
throw FitsIOException(std::string("Can not find parameter with name ") + parameterName);
}
bool FitsFile::HasGroupParameter(const std::string ¶meterName)
{
if(!HasGroups()) return false;
int parameterCount = GetParameterCount();
for(int i=1;i<=parameterCount;++i)
{
std::stringstream s;
s << "PTYPE" << i;
if(GetKeywordValue(s.str()) == parameterName)
return true;
}
return false;
}
bool FitsFile::HasGroupParameter(const std::string ¶meterName, int number)
{
if(!HasGroups()) return false;
int parameterCount = GetParameterCount();
for(int i=1;i<=parameterCount;++i)
{
std::stringstream s;
s << "PTYPE" << i;
if(GetKeywordValue(s.str()) == parameterName)
{
--number;
if(number == 0) return true;
}
}
return false;
}
bool FitsFile::HasTableColumn(const std::string &columnName, int& columnIndex)
{
int colCount = GetColumnCount();
for(int i=1;i<=colCount;++i)
{
std::stringstream s;
s << "TTYPE" << i;
if(GetKeywordValue(s.str()) == columnName)
{
columnIndex = i;
return true;
}
}
return false;
}
int FitsFile::GetTableColumnIndex(const std::string &columnName)
{
int colCount = GetColumnCount();
for(int i=1;i<=colCount;++i)
{
std::stringstream s;
s << "TTYPE" << i;
if(GetKeywordValue(s.str()) == columnName)
return i;
}
throw FitsIOException(std::string("Can not find column with name ") + columnName);
}
int FitsFile::GetTableColumnArraySize(int columnIndex)
{
CheckOpen();
int typecode = 0, status = 0;
long repeat = 0, width = 0;
fits_get_coltype(_fptr, columnIndex, &typecode, &repeat, &width, &status);
CheckStatus(status);
return repeat;
}
std::vector<long> FitsFile::GetColumnDimensions(int columnIndex)
{
CheckOpen();
int naxis = 0, status = 0;
constexpr int maxdim = 10;
std::vector<long> axes(maxdim, 0);
fits_read_tdim(_fptr, columnIndex, maxdim, &naxis, axes.data(), &status);
CheckStatus(status);
axes.resize(naxis);
return axes;
}
long FitsFile::GetColumnDimensionSize(int columnIndex, int dimension)
{
CheckOpen();
int naxis = 0, status = 0, maxdim = 10;
long naxes[10];
for(size_t i=0;i!=10;++i) naxes[i] = 0;
fits_read_tdim(_fptr, columnIndex, maxdim, &naxis, naxes, &status);
CheckStatus(status);
if(dimension >= naxis)
throw FitsIOException("Requested dimension index not available in fits file");
return naxes[dimension];
}
std::string FitsFile::GetTableDimensionName(int index)
{
CheckOpen();
std::ostringstream name;
name << "CTYPE" << (index+1);
int status = 0;
char valueStr[256], commentStr[256];
fits_read_key(_fptr, TSTRING, name.str().c_str(), valueStr, commentStr, &status);
std::string val;
if(!status) {
val = valueStr;
}
return val;
}
void FitsFile::ReadTableCell(int row, int col, double *output, size_t size)
{
int status = 0;
double nulValue = std::numeric_limits<double>::quiet_NaN();
int anynul = 0;
fits_read_col(_fptr, TDOUBLE, col, row, 1, size, &nulValue, output, &anynul, &status);
}
void FitsFile::ReadTableCell(int row, int col, long double *output, size_t size)
{
std::vector<double> data(size);
int status = 0;
double nulValue = std::numeric_limits<double>::quiet_NaN();
int anynul = 0;
fits_read_col(_fptr, TDOUBLE, col, row, 1, size, &nulValue, data.data(), &anynul, &status);
for(size_t i = 0;i<size;++i)
output[i] = data[i];
}
void FitsFile::ReadTableCell(int row, int col, bool *output, size_t size)
{
std::vector<char> data(size);
int status = 0;
char nulValue = 0;
int anynul = 0;
fits_read_col(_fptr, TBIT, col, row, 1, size, &nulValue, data.data(), &anynul, &status);
for(size_t i = 0;i<size;++i)
output[i] = data[i]!=0;
}
void FitsFile::ReadTableCell(int row, int col, char *output)
{
int status = 0;
double nulValue = std::numeric_limits<double>::quiet_NaN();
int anynul = 0;
fits_read_col(_fptr, TSTRING, col, row, 1, 1, &nulValue, &output, &anynul, &status);
}
void FitsFile::WriteTableCell(int row, int col, double *data, size_t size)
{
int status = 0;
fits_write_col(_fptr, TDOUBLE, col, row, 1, size, data, &status);
CheckStatus(status);
}
void FitsFile::WriteTableCell(int row, int col, const bool *data, size_t size)
{
std::vector<char> dataChar(size);
int status = 0;
for(size_t i = 0;i<size;++i)
{
dataChar[i] = data[i] ? 1 : 0;
}
fits_write_col(_fptr, TBIT, col, row, 1, size, dataChar.data(), &status);
}
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