template<typename _realT, class _derotFunctObj>
struct mx::improc::ADIobservation< _realT, _derotFunctObj >

Process an angular differential imaging (ADI) observation.

Angular differential imaging (ADI) uses sky rotation to differentiate real objects from speckles.

Template Parameters

realT is the floating point type in which to do calculations

_derotFunctObj

is the derotation object with the following minimum interface:

template<typename _realT>
struct derotF
{
   typedef  _realT realT;
 
   //Vector of keywords to extract from the fits headers
   std::vector<std::string> keywords;
   
   //Vector(s) to hold the keyword values
   std::vector<realT> keyValue1;
   
   ///To allow ADIobservation to check for errors.
   bool isSetup()
   {
     if( <any condition indicating not set up>) return false;
     return true;
   }
 
   //Method called by HCIobservation to get keyword-values
   void extractKeywords(vector<fitsHeader> & heads)
   {
      keyValue1 = headersToValues<float>(heads, "KEYWORD1");
   }
   
   //Calculate the derotation angle for a given image number
   realT derotAngle(size_t imno) const
   {
      return some_function_of(keyValue1[imno]); //This function uses keyValue1[imno] to produce the derotation angle in radians.
   }
};

Definition at line 93 of file ADIobservation.hpp.

#include <improc/ADIobservation.hpp>

Inheritance diagram for mx::improc::ADIobservation< _realT, _derotFunctObj >:

Public Member Functions
	ADIobservation (const std::string &dir, const std::string &prefix, const std::string &ext)

	ADIobservation (const std::string &fileListFile)

	ADIobservation (const std::string &dir, const std::string &prefix, const std::string &ext, const std::string &RDIdir, const std::string &RDIprefix, const std::string &RDIext="")

	ADIobservation (const std::string &fileListFile, const std::string &RDIfileListFile)

int	readFiles ()
	Read in the target files. More...

virtual int	postReadFiles ()
	Post target read actions, including fake injection. More...

virtual int	postCoadd ()
	Post target coadd actions. More...

int	readRDIFiles ()
	Read in the RDI files. More...

virtual int	postRDIReadFiles ()
	Post reference read actions, including fake injection. More...

virtual int	postRDICoadd ()
	Post reference coadd actions. More...

int	readPSFSub (const std::string &dir, const std::string &prefix, const std::string &ext, size_t nReductions)
	Read in already PSF-subtracted files. More...

virtual void	makeMaskCube ()
	Populate the mask cube which is used for post-processing. Derived classes can do this as appropriate, e.g. by rotating the mask. More...

void	derotate ()
	De-rotate the PSF subtracted images. More...

Public Member Functions inherited from mx::improc::HCIobservation< _realT >
int	readPSFSub (const std::string &dir, const std::string &prefix, const std::string &ext, size_t nReductions)
	Read in already PSF-subtracted files. More...

	HCIobservation ()
	Default c'tor. More...

	HCIobservation (const std::string &dir, const std::string &prefix, const std::string &ext)
	Construct and load the target file list. More...

	HCIobservation (const std::string &fileListFile)
	Construct using a file containing the target file list. More...

	HCIobservation (const std::string &dir, const std::string &prefix, const std::string &ext, const std::string &RDIdir, const std::string &RDIprefix, const std::string &RDIext="")
	Construct and load the target file list and the RDI file list. More...

	HCIobservation (const std::string &fileListFile, const std::string &RDIfileListFile)
	Construct using a file containing the target file list and a file containing the RDI target file list. More...

void	load_fileList (const std::string &dir, const std::string &prefix, const std::string &ext)
	Load the file list. More...

void	load_fileList (const std::string &fileListFile)
	Load the file list from a file. More...

void	load_RDIfileList (const std::string &dir, const std::string &prefix, const std::string &ext)
	Load the RDI basis file list. More...

void	load_RDIfileList (const std::string &fileListFile)
	Load the RDI basis file list from a file. More...

int	threshold (std::vector< std::string > &fileList, const std::string &qualityFile, realT qualityThreshold)
	Read the image qualities from a qualityFile and apply the threshold to a fileList. More...

int	readFiles ()
	Read the list of files, cut to size, and preprocess. More...

int	readRDIFiles ()
	Read the list of reference files, cut to size, and preprocess. More...

void	coaddImages (int coaddCombineMethod, int coaddMaxImno, int coaddMaxTime, std::vector< std::string > &coaddKeywords, std::vector< double > &imageMJD, std::vector< fits::fitsHeader > &heads, eigenCube< realT > &ims)
	Coadd the images. More...

void	readMask ()
	Read the mask file, resizing to imSize if needed. More...

void	preProcess (eigenCube< realT > &ims)
	Do the pre-processing. More...

int	readWeights ()
	Read the image weights from m_weightFile. More...

void	combineFinim ()
	Combine the images into a single final image. More...

void	outputPreProcessed ()
	Output the pre-processed target images. More...

void	outputRDIPreProcessed ()
	Output the pre-processed reference images. More...

void	stdFitsHeader (fits::fitsHeader &head)
	Fill in the HCIobservation standard FITS header. More...

void	writeFinim (fits::fitsHeader *addHead=0)
	Write the final combined image to disk. More...

void	outputPSFSub (fits::fitsHeader *addHead=0)
	Write the PSF subtracted images to disk. More...

Fake Planets
int	m_fakeMethod {HCI::single}
	Method for reading fake files, either HCI::single or HCI::list. More...

std::string	m_fakeFileName
	FITS file containing the fake planet PSF to inject or a list of fake images. More...

std::string	m_fakeScaleFileName
	One-column text file containing a scale factor for each point in time. More...

std::vector< realT >	m_fakeSep
	Separation(s) of the fake planet(s) More...

std::vector< realT >	m_fakePA
	Position angles(s) of the fake planet(s) More...

std::vector< realT >	m_fakeContrast
	Contrast(s) of the fake planet(s) More...

realT	m_RDIFluxScale {1}
	Flux scaling to apply to fake planets injected in RDI. Would depend on the assumed spectrum in SDI. More...

realT	m_RDISepScale {1}
	Scaling to apply to fake planet separation in RDI. Would be ratio of wavelengths for SDI. More...

int	injectFake (eigenCube< realT > &ims, std::vector< std::string > &fileList, derotFunctObj &derotF, realT RDIfluxScale, realT RDISepScale)
	Inect the fake plants. More...

int	injectFake (eigenImageT &fakePSF, eigenCube< realT > &ims, int image_i, realT derotAngle, realT PA, realT sep, realT contrast, realT scale, realT RDIfluxScale, realT RDISepScale)

Additional Inherited Members
Public Types inherited from mx::improc::HCIobservation< _realT >
typedef _realT	realT
	The arithmetic type used for calculations. Does not have to match the type in images on disk. More...

typedef Eigen::Array< realT, Eigen::Dynamic, Eigen::Dynamic >	eigenImageT
	The Eigen image array type basted on realT. More...

Public Attributes inherited from mx::improc::HCIobservation< _realT >
eigenCube< realT >	m_tgtIms
	The target image cube. More...

int	m_Nims {0}
	Number of images in m_tgtIms. More...

int	m_Nrows {0}
	Number of rows of the images in m_tgtIms. More...

int	m_Ncols {0}
	Number of columns of the images in m_tgtIms. More...

int	m_Npix {0}
	Pixels per image, that is Nrows*Ncols. More...

std::vector< double >	m_imageMJD
	Vector of target image times, in MJD. More...

std::vector< fits::fitsHeader >	m_heads
	Vector of FITS headers, one per file, populated with the values for the keywords. More...

bool	m_filesRead {false}
	Whether or not the m_fileList has been read. More...

bool	m_filesDeleted {false}
	Whether or not the specified files have been deleted from m_fileList. More...

std::vector< realT >	m_comboWeights
	Vector to hold the image weights read from the m_weightFile. More...

eigenCube< realT >	m_refIms
	The optional reference image cube. More...

std::vector< double >	m_RDIimageMJD
	Vector of reference image times, in MJD. More...

std::vector< fits::fitsHeader >	m_RDIheads
	Vector of FITS headers, one per reference file, populated with the values for the keywords. More...

bool	m_RDIfilesRead {false}
	Whether or not the reference files have been read. More...

bool	m_RDIfilesDeleted {false}
	Whether or not the specified files have been deleted from m_RDIfileList. More...

std::vector< eigenCube< realT > >	m_psfsub
	The PSF subtracted images. More...

eigenCube< realT >	m_finim
	The final combined images, one for each cube in psfsub. More...

std::vector< std::string >	m_fileList
	The list of files to read in. More...

int	m_deleteFront {0}
	Specify how many files from m_fileList to delete from the front of the list. More...

int	m_deleteBack {0}
	Specify how many files from m_fileList to delete from the back of the list. More...

std::string	m_qualityFile
	File containing 2 space-delimited columns of fileVame qualityValue pairs. More...

realT	m_qualityThreshold {0}
	Threshold to apply to qualityValues read from qualityFile. More...

bool	m_thresholdOnly {false}
	Just prints the names and qualities of the files which pass threshold, and stop. More...

std::string	m_MJDKeyword {"DATE-OBS"}
	Name of the keyword to use for the image date. More...

bool	m_MJDisISO8601 {true}
	Whether or not the date is in ISO 8601 format. More...

realT	m_MJDUnits {1.0}
	If the date is not ISO 8601, this specifies the conversion to Julian Days (i.e. seconds to days) More...

std::vector< std::string >	m_keywords
	Vector of FITS header keywords to read from the files in m_fileList. More...

int	m_imSize {0}
	Set the image size. Images are cut down to this size after reading. More...

std::vector< std::string >	m_RDIfileList
	The list of files to read in for the RDI basis. More...

int	m_RDIdeleteFront {0}
	Specify how many files from m_RDIfileList to delete from the front of the list. More...

int	m_RDIdeleteBack {0}
	Specify how many files from m_RDIfileList to delete from the back of the list. More...

std::string	m_RDIqualityFile
	File containing 2 space-delimited columns of fileMame qualityValue pairs for the reference images. More...

realT	m_RDIqualityThreshold {0}
	Threshold to apply to qualityValues read from qualityFile. More...

std::vector< std::string >	m_RDIkeywords
	Vector of FITS header keywords to read from the files in m_fileList. More...

int	m_coaddCombineMethod {HCI::noCombine}
	Determine how to coadd the raw images. More...

int	m_coaddMaxImno {0}
	Maximum number of images to coadd. More...

realT	m_coaddMaxTime {0}
	Maximum elapsed time over which to coadd the images. More...

std::vector< std::string >	m_coaddKeywords
	The values of these keywords will be averaged and replaced. More...

std::string	m_maskFile
	Specify a mask file to apply. More...

eigenImageT	m_mask
	The mask. More...

eigenCube< realT >	m_maskCube
	A cube of masks, one for each input image, which may be modified versions (e.g. rotated) of mask. More...

bool	m_skipPreProcess {false}
	Don't do any of the pre-processing steps (including coadding). More...

bool	m_preProcess_beforeCoadd {false}
	controls whether pre-processing takes place before or after coadding More...

bool	m_preProcess_mask {true}
	If true, the mask is applied during each pre-processing step. More...

bool	m_preProcess_subradprof {false}
	If true, a radial profile is subtracted from each image. More...

realT	m_preProcess_azUSM_azW {0}
	Azimuthal boxcar width for azimuthal unsharp mask [pixels]. More...

realT	m_preProcess_azUSM_maxAz {45}
	Mazimum azimuthal boxcar width for azimuthal unsharp mask [degrees]. More...

realT	m_preProcess_azUSM_radW {0}
	Radial boxcar width for azimuthal unsharp mask [pixels]. More...

int	m_preProcess_medianUSM_fwhm {0}
	Kernel FWHM for symmetric box median unsharp mask (USM) More...

realT	m_preProcess_gaussUSM_fwhm {0}
	Kernel FWHM for symmetric Gaussian unsharp mask (USM) More...

std::string	m_preProcess_outputPrefix
	Set path and file prefix to output the pre-processed images. More...

bool	m_preProcess_only {false}
	If true, then we stop after pre-processing. More...

int	m_combineMethod {HCI::meanCombine}
	Determine how to combine the PSF subtracted images. More...

std::string	m_weightFile
	Specifies a file containing the image weights, for combining with weighted mean. More...

realT	m_sigmaThreshold {0}
	The standard deviation threshold used if combineMethod == HCI::sigmaMeanCombine. More...

realT	m_minGoodFract {0.0}
	The minimum fraction of good (un-masked) pixels to include in the final combination (0.0 to 1.0). If not met, then the pixel will be NaN-ed. More...

int	m_doWriteFinim {1}
	Set whether the final combined image is written to disk. More...

std::string	m_outputDir
	The directory where to write output files. More...

std::string	m_finimName {"finim_"}
	The base file name of the output final image. More...

bool	m_exactFinimName {false}
	Use m_finimName exactly as specified, without appending a number or an extension. More...

bool	m_doOutputPSFSub {false}
	Controls whether or not the individual PSF subtracted images are written to disk. More...

std::string	m_PSFSubPrefix
	Prefix of the FITS file names used to write individual PSF subtracted images to disk if m_doOutputPSFSub is true. More...

Constructor & Destructor Documentation

◆ ADIobservation() [1/4]

template<typename _realT , class _derotFunctObj >

mx::improc::ADIobservation< _realT, _derotFunctObj >::ADIobservation	(	const std::string &	dir,
		const std::string &	prefix,
		const std::string &	ext
	)

Parameters

[in]	dir	the directory to search.
[in]	prefix	the initial part of the file name. Can be empty "".
[in]	ext	the extension to append to the file name, must include the '.'.

Definition at line 225 of file ADIobservation.hpp.

◆ ADIobservation() [2/4]

template<typename _realT , class _derotFunctObj >

mx::improc::ADIobservation< _realT, _derotFunctObj >::ADIobservation ( const std::string & fileListFile )

explicit

Parameters

[in] fileListFile a file name path to read.

Definition at line 233 of file ADIobservation.hpp.

◆ ADIobservation() [3/4]

template<typename _realT , class _derotFunctObj >

mx::improc::ADIobservation< _realT, _derotFunctObj >::ADIobservation	(	const std::string &	dir,
		const std::string &	prefix,
		const std::string &	ext,
		const std::string &	RDIdir,
		const std::string &	RDIprefix,
		const std::string &	RDIext = `""`
	)

Parameters

[in]	dir	the directory to search.
[in]	prefix	the initial part of the file name. Can be empty "".
[in]	ext	the extension to append to the file name, must include the '.'.
[in]	RDIdir	the directory to search for the reference files.
[in]	RDIprefix	the initial part of the file name for the reference files. Can be empty "".
[in]	RDIext	[optional] the extension to append to the RDI file name, must include the '.'. If empty "" then same extension as target files is used.

Definition at line 238 of file ADIobservation.hpp.

◆ ADIobservation() [4/4]

template<typename _realT , class _derotFunctObj >

mx::improc::ADIobservation< _realT, _derotFunctObj >::ADIobservation	(	const std::string &	fileListFile,
		const std::string &	RDIfileListFile
	)

Parameters

[in]	fileListFile	a file name path to read for the target file names.
[in]	RDIfileListFile	a file name path to read for the reference file names.

Definition at line 249 of file ADIobservation.hpp.

Member Function Documentation

◆ derotate()

template<typename _realT , class _derotFunctObj >

void mx::improc::ADIobservation< _realT, _derotFunctObj >::derotate

De-rotate the PSF subtracted images.

Definition at line 608 of file ADIobservation.hpp.

References mx::sys::get_curr_time(), and mx::improc::imageRotate().

◆ injectFake()

template<typename _realT , class _derotFunctObj >

int mx::improc::ADIobservation< _realT, _derotFunctObj >::injectFake	(	eigenCube< realT > &	ims,
		std::vector< std::string > &	fileList,
		derotFunctObj &	derotF,
		realT	RDIfluxScale,
		realT	RDISepScale
	)

Inect the fake plants.

Parameters

	ims	[in.out] the image cube in which to inject the fakes.
[in]	fileList	a list of file paths used for per-image fake PSFs. If empty, then m_fakeFileName is used.
[in]	RDIfluxScale	the flux scaling for RDI. In SDI, this is from the planet spectrum.
[in]	RDISepScale	the separation scale for RDI. In SDI, this is the ratio of wavlengths after lambda/D scaling.

Definition at line 438 of file ADIobservation.hpp.

References mx::sys::get_curr_time(), mx::improc::HCI::list, mx::ioutils::pathFilename(), mx::fits::fitsFile< dataT >::read(), mx::ioutils::readColumns(), and mx::improc::HCI::single.

◆ makeMaskCube()

template<typename _realT , class _derotFunctObj >

void mx::improc::ADIobservation< _realT, _derotFunctObj >::makeMaskCube

virtual

Populate the mask cube which is used for post-processing. Derived classes can do this as appropriate, e.g. by rotating the mask.

Reimplemented from mx::improc::HCIobservation< _realT >.

Definition at line 581 of file ADIobservation.hpp.

References mx::improc::rotateMask(), and mx::fits::fitsFile< dataT >::write().

◆ postCoadd()

template<typename _realT , class _derotFunctObj >

int mx::improc::ADIobservation< _realT, _derotFunctObj >::postCoadd

virtual

Post target coadd actions.

Here updates derotation for new average values.

Reimplemented from mx::improc::HCIobservation< _realT >.

Definition at line 293 of file ADIobservation.hpp.

◆ postRDICoadd()

template<typename _realT , class _derotFunctObj >

int mx::improc::ADIobservation< _realT, _derotFunctObj >::postRDICoadd

virtual

Post reference coadd actions.

Here updates derotation for new average values.

Reimplemented from mx::improc::HCIobservation< _realT >.

Definition at line 336 of file ADIobservation.hpp.

◆ postRDIReadFiles()

template<typename _realT , class _derotFunctObj >

int mx::improc::ADIobservation< _realT, _derotFunctObj >::postRDIReadFiles

virtual

Post reference read actions, including fake injection.

Reimplemented from mx::improc::HCIobservation< _realT >.

Definition at line 323 of file ADIobservation.hpp.

◆ postReadFiles()

template<typename _realT , class _derotFunctObj >

int mx::improc::ADIobservation< _realT, _derotFunctObj >::postReadFiles

virtual

Post target read actions, including fake injection.

Reimplemented from mx::improc::HCIobservation< _realT >.

Definition at line 279 of file ADIobservation.hpp.

◆ readFiles()

template<typename _realT , class _derotFunctObj >

int mx::improc::ADIobservation< _realT, _derotFunctObj >::readFiles

Read in the target files.

First sets up the keywords, then calls HCIobservation readFiles

Definition at line 256 of file ADIobservation.hpp.

◆ readPSFSub()

template<typename _realT , class _derotFunctObj >

int mx::improc::ADIobservation< _realT, _derotFunctObj >::readPSFSub	(	const std::string &	dir,
		const std::string &	prefix,
		const std::string &	ext,
		size_t	nReductions
	)

Read in already PSF-subtracted files.

Used to take up final processing after applying some non-klipReduce processing steps to PSF-subtracted images.

Definition at line 346 of file ADIobservation.hpp.

References mx::fits::fitsHeader::count(), mx::ioutils::getFileNames(), mx::ioutils::parseStringVector(), and mx::fits::fitsFile< dataT >::read().

◆ readRDIFiles()

template<typename _realT , class _derotFunctObj >

int mx::improc::ADIobservation< _realT, _derotFunctObj >::readRDIFiles

Read in the RDI files.

First sets up the keywords, then calls HCIobservation readRDIFiles

Definition at line 300 of file ADIobservation.hpp.

Member Data Documentation

◆ m_fakeContrast

template<typename _realT , class _derotFunctObj >

std::vector<realT> mx::improc::ADIobservation< _realT, _derotFunctObj >::m_fakeContrast

Contrast(s) of the fake planet(s)

Definition at line 176 of file ADIobservation.hpp.

◆ m_fakeFileName

template<typename _realT , class _derotFunctObj >

std::string mx::improc::ADIobservation< _realT, _derotFunctObj >::m_fakeFileName

FITS file containing the fake planet PSF to inject or a list of fake images.

Definition at line 170 of file ADIobservation.hpp.

◆ m_fakeMethod

template<typename _realT , class _derotFunctObj >

int mx::improc::ADIobservation< _realT, _derotFunctObj >::m_fakeMethod {HCI::single}

Method for reading fake files, either HCI::single or HCI::list.

Definition at line 168 of file ADIobservation.hpp.

◆ m_fakePA

template<typename _realT , class _derotFunctObj >

std::vector<realT> mx::improc::ADIobservation< _realT, _derotFunctObj >::m_fakePA

Position angles(s) of the fake planet(s)

Definition at line 175 of file ADIobservation.hpp.

◆ m_fakeScaleFileName

template<typename _realT , class _derotFunctObj >

std::string mx::improc::ADIobservation< _realT, _derotFunctObj >::m_fakeScaleFileName

One-column text file containing a scale factor for each point in time.

Definition at line 172 of file ADIobservation.hpp.

◆ m_fakeSep

template<typename _realT , class _derotFunctObj >

std::vector<realT> mx::improc::ADIobservation< _realT, _derotFunctObj >::m_fakeSep

Separation(s) of the fake planet(s)

Definition at line 174 of file ADIobservation.hpp.

◆ m_RDIFluxScale

template<typename _realT , class _derotFunctObj >

realT mx::improc::ADIobservation< _realT, _derotFunctObj >::m_RDIFluxScale {1}

Flux scaling to apply to fake planets injected in RDI. Would depend on the assumed spectrum in SDI.

Definition at line 178 of file ADIobservation.hpp.

◆ m_RDISepScale

template<typename _realT , class _derotFunctObj >

realT mx::improc::ADIobservation< _realT, _derotFunctObj >::m_RDISepScale {1}

Scaling to apply to fake planet separation in RDI. Would be ratio of wavelengths for SDI.

Definition at line 179 of file ADIobservation.hpp.

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

improc/ADIobservation.hpp

template<typename _realT, class _derotFunctObj> struct mx::improc::ADIobservation< _realT, _derotFunctObj >

Public Member Functions

Fake Planets

Additional Inherited Members

Constructor & Destructor Documentation

◆ ADIobservation() [1/4]

◆ ADIobservation() [2/4]

◆ ADIobservation() [3/4]

◆ ADIobservation() [4/4]

Member Function Documentation

◆ derotate()

◆ injectFake()

◆ makeMaskCube()

◆ postCoadd()

◆ postRDICoadd()

◆ postRDIReadFiles()

◆ postReadFiles()

◆ readFiles()

◆ readPSFSub()

◆ readRDIFiles()

Member Data Documentation

◆ m_fakeContrast

◆ m_fakeFileName

◆ m_fakeMethod

◆ m_fakePA

◆ m_fakeScaleFileName

◆ m_fakeSep

◆ m_RDIFluxScale

◆ m_RDISepScale

template<typename _realT, class _derotFunctObj>
struct mx::improc::ADIobservation< _realT, _derotFunctObj >