template<typename dataT, class verboseT = verbose::d>
class mx::fits::fitsFile< dataT, verboseT >

Class to manage interactions with a FITS file.

This class wraps the functionality of cfitsio.

Template Parameters

dataT is the datatype to use for in-memory storage of the image. This does not have to match the data type stored on disk for reading, but will be the type used for writing.

Definition at line 83 of file fitsFile.hpp.

#include <ioutils/fits/fitsFile.hpp>

Public Member Functions
	fitsFile ()
	Default constructor.
	fitsFile (error_t &errc)
	Default constructor with error code.
	fitsFile (const std::string &fname, error_t &errc)
	Constructor with file name and error code.
	fitsFile (const std::string &fname, bool doopen=true)
	Constructor with file name, and option to open.
	fitsFile (const std::string &fname, bool doopen, error_t &errc)
	Constructor with file name, option to open, and error code.
	~fitsFile ()
	Destructor.
std::string	fileName ()
	Get the current value of m_fileName.
error_t	fileName (const std::string &fname, bool doopen=true)
	Set the file path, and optionally open the file.
int	naxis ()
	Get the current value of m_naxis.
long	naxes (int dim)
	Get the current value of m_naxes for the specified dimension.
error_t	open ()
	Open the file and gets its dimensions.
error_t	open (const std::string &fname)
	Open the file, first setting the file path.
error_t	close ()
	Close the file.
int	getDimensions (error_t &errc)
	Get the number of dimensions (i.e. m_naxis).
long	getSize (error_t &errc)
	Get the total size.
long	getSize (size_t axis, error_t &errc)
	Get the size of a specific dimension.
Reading Eigen Arrays
These methods read FITS data into array types with an Eigen-like interface.
template<typename arrT>
error_t	read (arrT &data)
	Read the contents of the FITS file into an Eigen array type (not a simple pointer).
template<typename arrT>
error_t	read (arrT &data, fitsHeader< verboseT > &head)
	Read the contents of the FITS file into an Eigen array type (not a simple pointer).
template<typename arrT>
error_t	read (arrT &data, const std::string &fname)
	Read the contents of the FITS file into an Eigen array type (not a simple pointer).
template<typename arrT>
error_t	read (arrT &data, fitsHeader< verboseT > &head, const std::string &fname)
	Read the contents of the FITS file into an Eigen array type (not a simple pointer).
template<typename cubeT>
error_t	read (cubeT &cube, const std::vector< std::string > &flist, std::vector< fitsHeader< verboseT > > *heads=0)
	Read data from a vector list of files into an image cube.
template<typename cubeT>
error_t	read (cubeT &cube, std::vector< fitsHeader< verboseT > > &heads, const std::vector< std::string > &flist)
	Read data from a vector of files into an image cube with individual headers.
Reading Headers
error_t	readHeader (fitsHeader< verboseT > &head)
	Read the header from the fits file.
error_t	readHeader (fitsHeader< verboseT > &head, const std::string &fname)
	Read the header from the fits file.
error_t	readHeader (std::vector< fitsHeader< verboseT > > &heads, const std::vector< std::string > &flist)
	Read the headers from a list of FITS files.
Writing Basic Arrays
These methods write basic arrays specified by a pointer to FITS.
error_t	write (const dataT im, int d1, int d2, int d3, fitsHeader< verboseT > head)
	Write the contents of a raw array to the FITS file.
error_t	write (const dataT *im, int d1, int d2, int d3)
	Write the contents of a raw array to the FITS file.
error_t	write (const dataT *im, int d1, int d2, int d3, fitsHeader< verboseT > &head)
	Write the contents of a raw array to the FITS file.
error_t	write (const std::string &fname, const dataT *im, int d1, int d2, int d3)
	Write the contents of a raw array to the FITS file.
error_t	write (const std::string &fname, const dataT *im, int d1, int d2, int d3, fitsHeader< verboseT > &head)
	Write the contents of a raw array to the FITS file.
Writing Eigen Arrays
These methods write array types with an Eigen-like interface.
template<typename arrT>
error_t	write (const std::string &fname, const arrT &im)
	Write the contents of an Eigen-type array to a FITS file.
template<typename arrT>
error_t	write (const std::string &fname, const arrT &im, fitsHeader< verboseT > &head)
	Write the contents of an Eigen-type array to a FITS file.
Reading Subsets
It is often desirable to read only a subset of an image or images into memory. These methods allow you to specify this.
void	setReadSize ()
	Set to read all the pixels in the file.
void	setReadSize (long x0, long y0, long xpix, long ypix)
	Set to read only a subset of the pixels in the file.
void	setCubeReadSize ()
	Set to read all frames from a cube.
void	setCubeReadSize (long z0, long zframes)
	Set the number of frames to read from a cube.

Protected Member Functions
void	construct ()
	One time initialization common to all constructors.

Protected Attributes
std::string	m_fileName
	The path to the file.
fitsfile *	m_fptr { nullptr }
	The cfitsio data structure.
int	m_naxis { 0 }
	The dimensions of the image (1D, 2D, or 3D).
long	m_naxes [3]
	The size of each dimension.
bool	m_isOpen { false }
	Flag indicating whether the file is open or not.
dataT	m_nulval { 0 }
	The value to replace null values with.
int	m_anynul { 0 }
	Records whether any null values were replaced.
int	m_noComment { 0 }
	Flag to control whether the comment string is read.
long	m_x0 { -1 }
	The starting x-pixel to read from.
long	m_y0 { -1 }
	The starting y-pixel to read from.
long	m_xpix { -1 }
	The number of x-pixels to read.
long	m_ypix { -1 }
	The number of y-pixels to read.
long	m_z0 { -1 }
	The starting frame to read from a cube.
long	m_zframes { -1 }
	The number of frames to read from a cube.

Reading Basic Arrays
These methods read FITS data into basic or raw arrays specified by a pointer.
error_t	calcPixarrs (pixarrT &pixarr)
	Fill in the read-size arrays for reading a subset (always used).
error_t	read (dataT *data)
	Read the contents of the FITS file into an array.
error_t	read (dataT *data, fitsHeader< verboseT > &head)
	Read the contents of the FITS file into an array.
error_t	read (dataT *data, const std::string &fname)
	Read the contents of the FITS file into an array.
error_t	read (dataT *data, fitsHeader< verboseT > &head, const std::string &fname)
	Read the contents of the FITS file into an array and read the header.
error_t	read (dataT *im, const std::vector< std::string > &flist)
	Read data from a vector list of files into an image cube.
error_t	read (dataT *im, std::vector< fitsHeader< verboseT > > &heads, const std::vector< std::string > &flist)
	Read data from a vector of files into an image cube with individual headers.

Constructor & Destructor Documentation

◆ fitsFile() [1/5]

template<typename dataT, class verboseT>

mx::fits::fitsFile< dataT, verboseT >::fitsFile ( )

Default constructor.

Definition at line 712 of file fitsFile.hpp.

◆ fitsFile() [2/5]

template<typename dataT, class verboseT>

mx::fits::fitsFile< dataT, verboseT >::fitsFile ( error_t & errc )

Default constructor with error code.

Parameters

[out] errc error_t code indicating success or error

Definition at line 717 of file fitsFile.hpp.

References mx::noerror.

◆ fitsFile() [3/5]

template<typename dataT, class verboseT>

mx::fits::fitsFile< dataT, verboseT >::fitsFile	(	const std::string &	fname,
		error_t &	errc )

Constructor with file name and error code.

The file is not opened.

Parameters

[in]	fname	File name to set on construction
[out]	errc	error_t code indicating success or error

Definition at line 723 of file fitsFile.hpp.

References fileName(), and mx::internal::mxlib_error_report().

◆ fitsFile() [4/5]

template<typename dataT, class verboseT>

mx::fits::fitsFile< dataT, verboseT >::fitsFile	(	const std::string &	fname,
		bool	doopen = true )

Constructor with file name, and option to open.

Parameters

[in]	fname	File name to set on construction
[in]	doopen	[optional] If true, then the file is opened (the default).

Definition at line 730 of file fitsFile.hpp.

References fileName(), and mx::internal::mxlib_error_report().

◆ fitsFile() [5/5]

template<typename dataT, class verboseT>

mx::fits::fitsFile< dataT, verboseT >::fitsFile	(	const std::string &	fname,
		bool	doopen,
		error_t &	errc )

Constructor with file name, option to open, and error code.

Parameters

	fname	File name to set on construction
	doopen	If true, then the file is opened (the default).
[out]	errc	error_t code indicating success or error

Definition at line 738 of file fitsFile.hpp.

References fileName(), and mx::internal::mxlib_error_report().

◆ ~fitsFile()

template<typename dataT, class verboseT>

mx::fits::fitsFile< dataT, verboseT >::~fitsFile ( )

Destructor.

Definition at line 746 of file fitsFile.hpp.

References close(), m_isOpen, and mx::internal::mxlib_error_report().

Member Function Documentation

◆ calcPixarrs()

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::calcPixarrs ( pixarrT & pixarr )

protected

Fill in the read-size arrays for reading a subset (always used).

Parameters

[out] pixarr Populated with the allocated read-size arrays

Definition at line 956 of file fitsFile.hpp.

References m_naxes, m_naxis, m_x0, m_xpix, m_y0, m_ypix, m_z0, m_zframes, mx::internal::mxlib_error_report(), and mx::noerror.

Referenced by read(), read(), read(), and mx::unitTest::fitsTest::fitsFileTest::TEST_CASE().

◆ close()

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::close ( )

Close the file.

Returns: mx::error_t::noerror on success; mx::error_t::fits_* codes from cfitsio functions

Definition at line 851 of file fitsFile.hpp.

References mx::fits_status2error_t(), m_fileName, m_fptr, m_isOpen, mx::internal::mxlib_error_report(), and mx::noerror.

Referenced by ~fitsFile(), fileName(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), and write().

◆ construct()

template<typename dataT, class verboseT = verbose::d>

void mx::fits::fitsFile< dataT, verboseT >::construct ( )

protected

One time initialization common to all constructors.

◆ fileName() [1/2]

template<typename dataT, class verboseT>

std::string mx::fits::fitsFile< dataT, verboseT >::fileName ( )

Get the current value of m_fileName.

Returns: the current value of m_fileName.

Definition at line 755 of file fitsFile.hpp.

References m_fileName.

Referenced by fitsFile(), fitsFile(), fitsFile(), open(), read(), read(), read(), read(), read(), read(), read(), readHeader(), readHeader(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), write(), and write().

◆ fileName() [2/2]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::fileName	(	const std::string &	fname,
		bool	doopen = true )

Set the file path, and optionally open the file.

Returns: mx::error_t::noerror on success; mx::error_t codes from close or open

Parameters

fname	The new file name.
doopen	If true, then the file is opened (the default).

Definition at line 761 of file fitsFile.hpp.

References close(), m_fileName, m_isOpen, mxlib_error_check, mx::noerror, and open().

◆ getDimensions()

template<typename dataT, class verboseT>

int mx::fits::fitsFile< dataT, verboseT >::getDimensions ( error_t & errc )

Get the number of dimensions (i.e. m_naxis).

Definition at line 873 of file fitsFile.hpp.

References mx::invalidconfig, m_isOpen, and m_naxis.

Referenced by mx::unitTest::fitsTest::fitsFileTest::TEST_CASE().

◆ getSize() [1/2]

template<typename dataT, class verboseT>

long mx::fits::fitsFile< dataT, verboseT >::getSize ( error_t & errc )

Get the total size.

Definition at line 885 of file fitsFile.hpp.

References mx::invalidconfig, m_isOpen, m_naxes, m_naxis, m_x0, m_xpix, m_y0, m_ypix, and mx::noerror.

Referenced by read(), read(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), and mx::unitTest::fitsTest::fitsFileTest::TEST_CASE().

◆ getSize() [2/2]

template<typename dataT, class verboseT>

long mx::fits::fitsFile< dataT, verboseT >::getSize	(	size_t	axis,
		error_t &	errc )

Get the size of a specific dimension.

Definition at line 921 of file fitsFile.hpp.

References mx::invalidarg, mx::invalidconfig, m_isOpen, m_naxes, m_naxis, m_x0, m_xpix, m_y0, m_ypix, and mx::noerror.

◆ naxes()

template<typename dataT, class verboseT>

long mx::fits::fitsFile< dataT, verboseT >::naxes ( int dim )

Get the current value of m_naxes for the specified dimension.

Returns: the current value of m_naxes for the specified dimension. -1 if no such dimension

Parameters

[in] dim the dimension

Definition at line 785 of file fitsFile.hpp.

References m_naxes, and m_naxis.

Referenced by mx::unitTest::fitsTest::fitsFileTest::TEST_CASE().

◆ naxis()

template<typename dataT, class verboseT>

int mx::fits::fitsFile< dataT, verboseT >::naxis ( )

Get the current value of m_naxis.

Returns: the current value of m_naxis

Definition at line 779 of file fitsFile.hpp.

References m_naxis.

Referenced by mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), and mx::unitTest::fitsTest::fitsFileTest::TEST_CASE().

◆ open() [1/2]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::open ( )

Open the file and gets its dimensions.

File name needs to already have been set. If the file has already been opened, this returns immediately with no re-open.

Returns: mx::error_t::noerror on success; mx::invalidconfig if m_filename is empty.; mx::error_t::bad_alloc on an allocation error; mx::error_t::std_exception on other errors during allocations; mx::error_t::exception on unexpected errors during allocations; mx::error_t::allocerr if allocation fails without an exception; mx::error_t::fits_* codes from cfitsio functions

Definition at line 796 of file fitsFile.hpp.

References mx::fits_status2error_t(), mx::invalidconfig, m_fileName, m_fptr, m_isOpen, m_naxes, m_naxis, mx::internal::mxlib_error_report(), and mx::noerror.

Referenced by fileName(), read(), read(), readHeader(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), and mx::unitTest::fitsTest::fitsFileTest::TEST_CASE().

◆ open() [2/2]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::open ( const std::string & fname )

Open the file, first setting the file path.

Returns: mx::error_t::noerror on success; mx::invalidconfig if m_filename is empty.; mx::error_t::bad_alloc on an allocation error; mx::error_t::std_exception on other errors during allocations; mx::error_t::exception on unexpected errors during allocations; mx::error_t::allocerr if allocation fails without an exception; mx::error_t::fits_* codes from cfitsio functions

Parameters

fname The name of the file to open.

Definition at line 845 of file fitsFile.hpp.

References fileName(), and mxlib_error_return.

◆ read() [1/12]

template<typename dataT, class verboseT>

template<typename arrT>

error_t mx::fits::fitsFile< dataT, verboseT >::read ( arrT & data )

Read the contents of the FITS file into an Eigen array type (not a simple pointer).

The type arrT can be any type with the following members defined:

resize(int, int) (allocates memory)
data() (returns a pointer to the underlying array)
typedef arrT::Scalar (is the data type, does not have to be dataT)

Template Parameters

arrT	is the type of array, see requirements above.

Returns: 0 on success; -1 on error

Todo: this can probably be made part of one read function (or call read(data *)) with a call to resize with SFINAE

Parameters

[out] data is the array, which will be resized as necessary using its resize(int, int) member

Definition at line 1264 of file fitsFile.hpp.

References calcPixarrs(), mx::fits_status2error_t(), mx::fits::fitsType(), m_anynul, m_fileName, m_fptr, m_isOpen, m_naxis, m_nulval, mxlib_error_check, mx::internal::mxlib_error_report(), mx::noerror, and open().

◆ read() [2/12]

template<typename dataT, class verboseT>

template<typename arrT>

error_t mx::fits::fitsFile< dataT, verboseT >::read	(	arrT &	data,
		const std::string &	fname )

Read the contents of the FITS file into an Eigen array type (not a simple pointer).

The type arrT can be any type with the following members defined:

resize(int, int) (allocates memory)
data() (returns a pointer to the underlying array)
typedef arrT::Scalar (is the data type, does not have to be dataT)

Template Parameters

arrT	is the type of array, see requirements above.

Returns: 0 on success; -1 on error

Parameters

[out]	data	is the array, which will be resized as necessary using its resize(int, int) member
[in]	fname	is the file path, which is passed to fileName

Definition at line 1337 of file fitsFile.hpp.

References fileName(), mx::internal::mxlib_error_report(), mx::noerror, and read().

◆ read() [3/12]

template<typename dataT, class verboseT>

template<typename arrT>

error_t mx::fits::fitsFile< dataT, verboseT >::read	(	arrT &	data,
		fitsHeader< verboseT > &	head )

Read the contents of the FITS file into an Eigen array type (not a simple pointer).

The type arrT can be any type with the following members defined:

resize(int, int) (allocates memory)
data() (returns a pointer to the underlying array)
typedef arrT::Scalar (is the data type, does not have to be dataT)

Template Parameters

arrT	is the type of array, see requirements above.

Returns: 0 on success; -1 on error

Parameters

[out]	data	is the array, which will be resized as necessary using its resize(int, int) member
[out]	head	is a fitsHeader object which is passed to readHeader

Definition at line 1317 of file fitsFile.hpp.

References mx::internal::mxlib_error_report(), mx::noerror, read(), and readHeader().

◆ read() [4/12]

template<typename dataT, class verboseT>

template<typename arrT>

error_t mx::fits::fitsFile< dataT, verboseT >::read	(	arrT &	data,
		fitsHeader< verboseT > &	head,
		const std::string &	fname )

Read the contents of the FITS file into an Eigen array type (not a simple pointer).

The type arrT can be any type with the following members defined:

resize(int, int) (allocates memory)
data() (returns a pointer to the underlying array)
typedef arrT::Scalar (is the data type, does not have to be dataT)

Template Parameters

arrT	is the type of array, see requirements above.

Returns: 0 on success; -1 on error

Parameters

[out]	data	the array, which will be resized as necessary using its resize(int, int) member
[out]	head	a fitsHeader object which is passed to readHeader
[in]	fname	the file path, which is passed to fileName

Definition at line 1356 of file fitsFile.hpp.

References fileName(), mx::internal::mxlib_error_report(), mx::noerror, read(), and readHeader().

◆ read() [5/12]

template<typename dataT, class verboseT>

template<typename cubeT>

error_t mx::fits::fitsFile< dataT, verboseT >::read	(	cubeT &	cube,
		const std::vector< std::string > &	flist,
		std::vector< fitsHeader< verboseT > > *	heads = 0 )

Read data from a vector list of files into an image cube.

The type cubeT can be any type with the following members defined:

resize(int, int, int) (allocates memory)
data() (returns a pointer to the underlying array)
typedef cubeT::Scalar (is the data type, does not have to be dataT)

Note: The images must all be the same size, or all be as large or larger than the subset specified.

Template Parameters

cubeT is the type of array, see requirements above.

Returns: 0 on success; -1 on error

Parameters

[out]	cube	A cube which will be resized using its resize(int, int, int) member.
[in]	flist	The list of files to read.
[out]	heads	[optional] A vector of fits headers, allocated to contain one per image.

Definition at line 1382 of file fitsFile.hpp.

References calcPixarrs(), fileName(), mx::fits_status2error_t(), mx::fits::fitsType(), mx::invalidarg, m_anynul, m_fileName, m_fptr, m_nulval, mx::internal::mxlib_error_report(), mx::noerror, and readHeader().

◆ read() [6/12]

template<typename dataT, class verboseT>

template<typename cubeT>

error_t mx::fits::fitsFile< dataT, verboseT >::read	(	cubeT &	cube,
		std::vector< fitsHeader< verboseT > > &	heads,
		const std::vector< std::string > &	flist )

Read data from a vector of files into an image cube with individual headers.

The type cubeT can be any type with the following members defined:

resize(int, int, int) (allocates memory)
data() (returns a pointer to the underlying array)
typedef cubeT::Scalar (is the data type, does not have to be dataT)

Template Parameters

cubeT is the type of array, see requirements above.

Returns: 0 on success; -1 on error

Parameters

[out]	cube	A cube which will be resized using its resize(int, int, int) member.
[out]	heads	The vector of fits headers, allocated to contain one per image.
[in]	flist	The list of files to read.

Definition at line 1484 of file fitsFile.hpp.

References mxlib_error_return, and read().

◆ read() [7/12]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::read ( dataT * data )

Read the contents of the FITS file into an array.

The array pointed to by data must have been allocated.

Returns: 0 on success; -1 on error

Todo: test if there is a speed difference for full reads for fits_read_pix/subset

Parameters

[out] data an allocated arrray large enough to hold the entire image

Definition at line 1045 of file fitsFile.hpp.

References calcPixarrs(), mx::fits_status2error_t(), mx::fits::fitsType(), m_anynul, m_fileName, m_fptr, m_isOpen, m_nulval, mxlib_error_check, mx::internal::mxlib_error_report(), mx::noerror, and open().

Referenced by mx::AO::applyPupil2Basis(), mx::AO::analysis::calculatedWFS< realT, iosT >::beta_p(), mx::AO::analysis::calculatedWFS< realT, iosT >::beta_r(), mx::AO::sim::pywfsSlopeReconstructor< _floatT >::calcMask(), mx::AO::sim::turbAtmosphere< _aoSystemT, _verboseT >::genLayers(), mx::AO::ifPInv(), mx::AO::sim::simulatedAOSystem< _realT, _wfsT, _reconT, _filterT, _dmT, _turbSeqT, _coronT >::initSystem(), mx::AO::analysis::fourierTemporalPSD< _realT, aosysT >::intensityPSD(), mx::wfp::lyotCoronagraph< _realT, _fpmaskFloatT >::loadApodizer(), mx::wfp::lyotCoronagraph< _realT, _fpmaskFloatT >::loadFocalMask(), mx::wfp::lyotCoronagraph< _realT, _fpmaskFloatT >::loadLyotStop(), mx::wfp::idealCoronagraph< _realT >::loadPupil(), mx::AO::sim::directPhaseReconstructor< realT >::loadRecon(), mx::AO::sim::pywfsSlopeReconstructor< _floatT >::loadRecon(), mx::AO::m2cMatrix(), mx::AO::makeZernikeBasis(), mx::AO::modalDMM2cMatrix(), mx::AO::modesOnDM(), mx::AO::orthogonalizeBasis(), read(), read(), read(), read(), read(), read(), read(), read(), read(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), and mx::unitTest::fitsTest::fitsFileTest::TEST_CASE().

◆ read() [8/12]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::read	(	dataT *	data,
		const std::string &	fname )

Read the contents of the FITS file into an array.

The array pointed to by data must have been allocated.

Returns: 0 on success; -1 on error

Parameters

[out]	data	is an allocated arrray large enough to hold the entire image
[in]	fname	is the file path, which is passed to fileName

Definition at line 1088 of file fitsFile.hpp.

References fileName(), mxlib_error_check, mxlib_error_return, and read().

◆ read() [9/12]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::read	(	dataT *	data,
		fitsHeader< verboseT > &	head )

Read the contents of the FITS file into an array.

The array pointed to by data must have been allocated.

Returns: 0 on success; -1 on error

Parameters

[out]	data	an allocated arrray large enough to hold the entire image
[out]	head	a fitsHeader object which is passed to readHeader

Definition at line 1080 of file fitsFile.hpp.

References mxlib_error_check, mxlib_error_return, read(), and readHeader().

◆ read() [10/12]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::read	(	dataT *	data,
		fitsHeader< verboseT > &	head,
		const std::string &	fname )

Read the contents of the FITS file into an array and read the header.

The array pointed to by data must have been allocated.

Returns: 0 on success; -1 on error

Parameters

[out]	data	an allocated arrray large enough to hold the entire image
[out]	head	a fitsHeader object which is passed to readHeader
[in]	fname	the file path, which is passed to fileName

Definition at line 1096 of file fitsFile.hpp.

References fileName(), mxlib_error_check, mxlib_error_return, read(), and readHeader().

◆ read() [11/12]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::read	(	dataT *	im,
		const std::vector< std::string > &	flist )

Read data from a vector list of files into an image cube.

Parameters

[out]	im	An allocated array large enough to hold all the images
[in]	flist	The list of files to read.

Definition at line 1106 of file fitsFile.hpp.

References fileName(), getSize(), mx::invalidarg, mxlib_error_check, mx::internal::mxlib_error_report(), mx::noerror, and read().

◆ read() [12/12]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::read	(	dataT *	im,
		std::vector< fitsHeader< verboseT > > &	heads,
		const std::vector< std::string > &	flist )

Read data from a vector of files into an image cube with individual headers.

Parameters

[out]	im	An allocated array large enough to hold all the images
	heads	[in/out] The vector of fits headers, allocated to contain one per image.
[in]	flist	The list of files to read.

Definition at line 1133 of file fitsFile.hpp.

References fileName(), getSize(), mx::invalidarg, mxlib_error_check, mx::internal::mxlib_error_report(), mx::noerror, read(), and readHeader().

◆ readHeader() [1/3]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::readHeader ( fitsHeader< verboseT > & head )

Read the header from the fits file.

If head is not empty, then only the keywords already in head are updated. Otherwise the complete header is read.

Returns: 0 on success; -1 on error

Parameters

[out] head a fitsHeader object

Definition at line 1492 of file fitsFile.hpp.

References mx::fits::fitsHeader< verboseT >::append(), mx::fits::fitsHeader< verboseT >::begin(), mx::fits::fitsHeader< verboseT >::end(), mx::fits::fitsHeader< verboseT >::erase(), mx::fits_status2error_t(), m_fileName, m_fptr, m_isOpen, m_noComment, mxlib_error_check, mx::internal::mxlib_error_report(), mx::noerror, open(), and mx::fits::fitsHeader< verboseT >::size().

Referenced by read(), read(), read(), read(), read(), read(), readHeader(), readHeader(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), and mx::unitTest::fitsTest::fitsFileTest::TEST_CASE().

◆ readHeader() [2/3]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::readHeader	(	fitsHeader< verboseT > &	head,
		const std::string &	fname )

Read the header from the fits file.

If head is not empty, then only the keywords already in head are updated. Otherwise the complete header is read.

Returns: 0 on success; -1 on error

Parameters

[out]	head	a fitsHeader object
[in]	fname	the file path, which is passed to fileName

Definition at line 1605 of file fitsFile.hpp.

References fileName(), mxlib_error_check, mx::noerror, and readHeader().

◆ readHeader() [3/3]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::readHeader	(	std::vector< fitsHeader< verboseT > > &	heads,
		const std::vector< std::string > &	flist )

Read the headers from a list of FITS files.

In each case, if the header is not empty then only the keywords already in head are updated. Otherwise the complete header is read.

Returns: 0 on success; -1 on error

Parameters

flist A vector of fitsHeader objects to read into. [in] A list of files, each of which is passed to fileName

Definition at line 1614 of file fitsFile.hpp.

References fileName(), mx::invalidarg, mxlib_error_check, mx::internal::mxlib_error_report(), mx::noerror, and readHeader().

◆ setCubeReadSize() [1/2]

template<typename dataT, class verboseT>

void mx::fits::fitsFile< dataT, verboseT >::setCubeReadSize ( )

Set to read all frames from a cube.

Definition at line 1792 of file fitsFile.hpp.

References m_z0, and m_zframes.

Referenced by mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), and mx::unitTest::fitsTest::fitsFileTest::TEST_CASE().

◆ setCubeReadSize() [2/2]

template<typename dataT, class verboseT>

void mx::fits::fitsFile< dataT, verboseT >::setCubeReadSize	(	long	z0,
		long	zframes )

Set the number of frames to read from a cube.

Parameters

z0	is the starting frame to read
zframes	is the number of frames to read

Definition at line 1799 of file fitsFile.hpp.

References m_z0, and m_zframes.

◆ setReadSize() [1/2]

template<typename dataT, class verboseT>

void mx::fits::fitsFile< dataT, verboseT >::setReadSize ( )

Set to read all the pixels in the file.

Definition at line 1774 of file fitsFile.hpp.

References m_x0, m_xpix, m_y0, and m_ypix.

Referenced by mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), mx::unitTest::fitsTest::fitsFileTest::TEST_CASE(), and mx::unitTest::fitsTest::fitsFileTest::TEST_CASE().

◆ setReadSize() [2/2]

template<typename dataT, class verboseT>

void mx::fits::fitsFile< dataT, verboseT >::setReadSize	(	long	x0,
		long	y0,
		long	xpix,
		long	ypix )

Set to read only a subset of the pixels in the file.

Parameters

x0	is the starting x-pixel to read
y0	is the starting y-pixel to read
xpix	is the number of x-pixels to read
ypix	is the number of y-pixels to read

Definition at line 1783 of file fitsFile.hpp.

References m_x0, m_xpix, m_y0, and m_ypix.

◆ write() [1/7]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::write	(	const dataT *	im,
		int	d1,
		int	d2,
		int	d3 )

Write the contents of a raw array to the FITS file.

Returns: 0 on success; -1 on error

Parameters

[in]	im	is the array
[in]	d1	is the first dimension
[in]	d2	is the second dimension
[in]	d3	is the third dimenesion (minimum value is 1)

Definition at line 1727 of file fitsFile.hpp.

References mxlib_error_return, and write().

◆ write() [2/7]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::write	(	const dataT *	im,
		int	d1,
		int	d2,
		int	d3,
		fitsHeader< verboseT > &	head )

Write the contents of a raw array to the FITS file.

Note: the type of the array must match dataT

Returns: 0 on success; -1 on error

Parameters

[in]	im	is the array
[in]	d1	is the first dimension
[in]	d2	is the second dimension
[in]	d3	is the third dimenesion (minimum value is 1)
[in]	head	is the header

Definition at line 1733 of file fitsFile.hpp.

References mxlib_error_return, and write().

◆ write() [3/7]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::write	(	const dataT *	im,
		int	d1,
		int	d2,
		int	d3,
		fitsHeader< verboseT > *	head )

Write the contents of a raw array to the FITS file.

Returns: 0 on success; -1 on error

Parameters

[in]	im	is the array
[in]	d1	is the first dimension
[in]	d2	is the second dimension
[in]	d3	is the third dimenesion (minimum value is 1)
[in]	head	a pointer to the header. Set to 0 if not used.

Definition at line 1640 of file fitsFile.hpp.

References mx::fits::fitsHeader< verboseT >::begin(), close(), mx::fits::fitsHeader< verboseT >::end(), mx::fits_status2error_t(), mx::fits::fitsBITPIX(), mx::fits::fitsType(), m_fileName, m_fptr, m_isOpen, m_naxes, m_naxis, mxlib_error_check, mx::internal::mxlib_error_report(), mxlib_error_return, and mx::noerror.

◆ write() [4/7]

template<typename dataT, class verboseT>

template<typename arrT>

error_t mx::fits::fitsFile< dataT, verboseT >::write	(	const std::string &	fname,
		const arrT &	im )

Write the contents of an Eigen-type array to a FITS file.

The type arrT can be any type with the following members defined:

data() (returns a pointer to the underlying array)
rows() (returrns the number of rows)
cols() (returns the number of columns)
may have planes() defined

Note: as with all write methods, the Scalar type of the array must match dataT

Template Parameters

arrT	is the type of array, see requirements above.

Returns: 0 on success; -1 on error

Parameters

[in]	fname	is the name of the file.
[in]	im	is the array

Definition at line 1757 of file fitsFile.hpp.

References mxlib_error_return, and write().

◆ write() [5/7]

template<typename dataT, class verboseT>

template<typename arrT>

error_t mx::fits::fitsFile< dataT, verboseT >::write	(	const std::string &	fname,
		const arrT &	im,
		fitsHeader< verboseT > &	head )

Write the contents of an Eigen-type array to a FITS file.

The type arrT can be any type with the following members defined:

data() (returns a pointer to the underlying array)
rows() (returrns the number of rows)
cols() (returns the number of columns)
may have planes() defined.

Note: as with all write methods, the Scalar type of the array must match dataT

Template Parameters

arrT	is the type of array, see requirements above.

Returns: 0 on success; -1 on error

Parameters

[in]	fname	is the file path, which is passed to fileName
[in]	im	is the array
[in]	head	is a fitsHeader object which is passed to readHeader

Definition at line 1766 of file fitsFile.hpp.

References write().

◆ write() [6/7]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::write	(	const std::string &	fname,
		const dataT *	im,
		int	d1,
		int	d2,
		int	d3 )

Write the contents of a raw array to the FITS file.

Returns: 0 on success; -1 on error

Parameters

[in]	fname	is the name of the file.
[in]	im	is the array
[in]	d1	is the first dimension
[in]	d2	is the second dimension
[in]	d3	is the third dimenesion (minimum value is 1)

Definition at line 1739 of file fitsFile.hpp.

References fileName(), mxlib_error_check, mxlib_error_return, and write().

◆ write() [7/7]

template<typename dataT, class verboseT>

error_t mx::fits::fitsFile< dataT, verboseT >::write	(	const std::string &	fname,
		const dataT *	im,
		int	d1,
		int	d2,
		int	d3,
		fitsHeader< verboseT > &	head )

Write the contents of a raw array to the FITS file.

Returns: 0 on success; -1 on error

Parameters

[in]	fname	is the name of the file.
[in]	im	is the array
[in]	d1	is the first dimension
[in]	d2	is the second dimension
[in]	d3	is the third dimenesion (minimum value is 1)
[in]	head	is the header

Definition at line 1747 of file fitsFile.hpp.

References fileName(), mxlib_error_check, mxlib_error_return, and write().

Member Data Documentation

◆ m_anynul

template<typename dataT, class verboseT = verbose::d>

int mx::fits::fitsFile< dataT, verboseT >::m_anynul { 0 }

protected

Records whether any null values were replaced.

Definition at line 111 of file fitsFile.hpp.

Referenced by read(), read(), and read().

◆ m_fileName

template<typename dataT, class verboseT = verbose::d>

std::string mx::fits::fitsFile< dataT, verboseT >::m_fileName

protected

The path to the file.

Definition at line 93 of file fitsFile.hpp.

Referenced by close(), fileName(), fileName(), open(), read(), read(), read(), readHeader(), and write().

◆ m_fptr

template<typename dataT, class verboseT = verbose::d>

fitsfile* mx::fits::fitsFile< dataT, verboseT >::m_fptr { nullptr }

protected

The cfitsio data structure.

Definition at line 96 of file fitsFile.hpp.

Referenced by close(), open(), read(), read(), read(), readHeader(), and write().

◆ m_isOpen

template<typename dataT, class verboseT = verbose::d>

bool mx::fits::fitsFile< dataT, verboseT >::m_isOpen { false }

protected

Flag indicating whether the file is open or not.

Definition at line 105 of file fitsFile.hpp.

Referenced by ~fitsFile(), close(), fileName(), getDimensions(), getSize(), getSize(), open(), read(), read(), readHeader(), and write().

◆ m_naxes

template<typename dataT, class verboseT = verbose::d>

long mx::fits::fitsFile< dataT, verboseT >::m_naxes[3]

protected

The size of each dimension.

Definition at line 102 of file fitsFile.hpp.

Referenced by calcPixarrs(), getSize(), getSize(), naxes(), open(), and write().

◆ m_naxis

template<typename dataT, class verboseT = verbose::d>

int mx::fits::fitsFile< dataT, verboseT >::m_naxis { 0 }

protected

The dimensions of the image (1D, 2D, or 3D).

Definition at line 99 of file fitsFile.hpp.

Referenced by calcPixarrs(), getDimensions(), getSize(), getSize(), naxes(), naxis(), open(), read(), and write().

◆ m_noComment

template<typename dataT, class verboseT = verbose::d>

int mx::fits::fitsFile< dataT, verboseT >::m_noComment { 0 }

protected

Flag to control whether the comment string is read.

Definition at line 114 of file fitsFile.hpp.

Referenced by readHeader().

◆ m_nulval

template<typename dataT, class verboseT = verbose::d>

dataT mx::fits::fitsFile< dataT, verboseT >::m_nulval { 0 }

protected

The value to replace null values with.

Definition at line 108 of file fitsFile.hpp.

Referenced by read(), read(), and read().

◆ m_x0

template<typename dataT, class verboseT = verbose::d>

long mx::fits::fitsFile< dataT, verboseT >::m_x0 { -1 }

protected

The starting x-pixel to read from.

Definition at line 117 of file fitsFile.hpp.

Referenced by calcPixarrs(), getSize(), getSize(), setReadSize(), and setReadSize().

◆ m_xpix

template<typename dataT, class verboseT = verbose::d>

long mx::fits::fitsFile< dataT, verboseT >::m_xpix { -1 }

protected

The number of x-pixels to read.

Definition at line 123 of file fitsFile.hpp.

Referenced by calcPixarrs(), getSize(), getSize(), setReadSize(), and setReadSize().

◆ m_y0

template<typename dataT, class verboseT = verbose::d>

long mx::fits::fitsFile< dataT, verboseT >::m_y0 { -1 }

protected

The starting y-pixel to read from.

Definition at line 120 of file fitsFile.hpp.

Referenced by calcPixarrs(), getSize(), getSize(), setReadSize(), and setReadSize().

◆ m_ypix

template<typename dataT, class verboseT = verbose::d>

long mx::fits::fitsFile< dataT, verboseT >::m_ypix { -1 }

protected

The number of y-pixels to read.

Definition at line 126 of file fitsFile.hpp.

Referenced by calcPixarrs(), getSize(), getSize(), setReadSize(), and setReadSize().

◆ m_z0

template<typename dataT, class verboseT = verbose::d>

long mx::fits::fitsFile< dataT, verboseT >::m_z0 { -1 }

protected

The starting frame to read from a cube.

Definition at line 129 of file fitsFile.hpp.

Referenced by calcPixarrs(), setCubeReadSize(), and setCubeReadSize().

◆ m_zframes

template<typename dataT, class verboseT = verbose::d>

long mx::fits::fitsFile< dataT, verboseT >::m_zframes { -1 }

protected

The number of frames to read from a cube.

Definition at line 132 of file fitsFile.hpp.

Referenced by calcPixarrs(), setCubeReadSize(), and setCubeReadSize().

The documentation for this class was generated from the following file:

ioutils/fits/fitsFile.hpp

Public Member Functions

Protected Member Functions

Protected Attributes

Reading Basic Arrays

Constructor & Destructor Documentation

◆ fitsFile() [1/5]

◆ fitsFile() [2/5]

◆ fitsFile() [3/5]

◆ fitsFile() [4/5]

◆ fitsFile() [5/5]

◆ ~fitsFile()

Member Function Documentation

◆ calcPixarrs()

◆ close()

◆ construct()

◆ fileName() [1/2]

◆ fileName() [2/2]

◆ getDimensions()

◆ getSize() [1/2]

◆ getSize() [2/2]

◆ naxes()

◆ naxis()

◆ open() [1/2]

◆ open() [2/2]

◆ read() [1/12]

◆ read() [2/12]

◆ read() [3/12]

◆ read() [4/12]

◆ read() [5/12]

◆ read() [6/12]

◆ read() [7/12]

◆ read() [8/12]

◆ read() [9/12]

◆ read() [10/12]

◆ read() [11/12]

◆ read() [12/12]

◆ readHeader() [1/3]

◆ readHeader() [2/3]

◆ readHeader() [3/3]

◆ setCubeReadSize() [1/2]

◆ setCubeReadSize() [2/2]

◆ setReadSize() [1/2]

◆ setReadSize() [2/2]

◆ write() [1/7]

◆ write() [2/7]

◆ write() [3/7]

◆ write() [4/7]

◆ write() [5/7]

◆ write() [6/7]

◆ write() [7/7]

Member Data Documentation

◆ m_anynul

◆ m_fileName

◆ m_fptr

◆ m_isOpen

◆ m_naxes

◆ m_naxis

◆ m_noComment

◆ m_nulval

◆ m_x0

◆ m_xpix

◆ m_y0

◆ m_ypix

◆ m_z0

◆ m_zframes