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klipReduce.cpp
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#include <iostream>
// #include <mx/gnuPlot.hpp>
#include <mx/app/application.hpp>
using namespace mx::app;
#include <mx/improc/ADIDerotator.hpp>
#include <mx/improc/KLIPreduction.hpp>
using namespace mx::improc;
#include <libgen.h>
/// A program to run the mxlib KLIP pipeline
/**
*
*/
template <typename _realT, typename _evCalcT = double>
class klipReduce : public application
{
public:
typedef _realT realT;
typedef _evCalcT evCalcT;
protected:
// Basic Setup [HCIobservation]:
std::string directory;
std::string prefix;
std::string extension;
std::string fileList;
// File Reading [HCIobservation]:
int deleteFront;
int deleteBack;
std::string qualityFile;
realT qualityThreshold;
bool thresholdOnly;
std::string MJDKeyword;
bool MJDisISO8601;
int m_imSize{ 0 };
// RDI setup
std::string m_RDIdirectory;
std::string m_RDIprefix;
std::string m_RDIextension;
std::string m_RDIfileList;
int m_RDIdeleteFront{ 0 };
int m_RDIdeleteBack{ 0 };
std::string m_RDIqualityFile;
realT m_RDIqualityThreshold{ 0 };
// Rotation setup [ADIobservation]
std::string angleKeyword;
float angleScale;
float angleConstant;
// Fake Planet Injection [ADIobservation]
std::string fakeMethod{ "single" };
std::string fakeFileName; ///< FITS file containing the fake planet PSF to inject
std::string fakeScaleFileName; ///< One-column text file containing a scale factor for each point in time.
std::vector<realT> fakeSep; ///< Separation(s) of the fake planet(s)
std::vector<realT> fakePA; ///< Position angles(s) of the fake planet(s)
std::vector<realT> fakeContrast; ///< Contrast(s) of the fake planet(s)
realT m_fakeRDIFluxScale{ 1 };
realT m_fakeRDISepScale{ 1 };
// Co-adding
std::string coaddMethod;
int coaddMaxImno;
realT coaddMaxTime;
std::vector<std::string> coaddKeywords;
// Masking
std::string m_maskFile;
// Pre-processing
std::string m_meanSubMethod;
std::string m_pixelTSNormMethod;
bool preProcess_beforeCoadd {false};
bool preProcess_mask {false};
bool preProcess_subradprof {false};
realT preProcess_azUSM_azW {0};
realT preProcess_azUSM_radW {0};
int preProcess_medianUSM_fwhm {0};
realT preProcess_gaussUSM_fwhm {0};
std::string preProcess_meanSubMethod {"none"};
std::string preProcess_pixelTSNormMethod {"none"};
std::string preProcess_outputPrefix;
bool preProcess_only {false};
bool skipPreProcess {false};
// ADI
bool m_postMedSub{ false };
// KLIP parameters
realT minDPx{ 0 };
realT maxDPx{ 0 };
std::string excludeMethod;
std::string excludeMethodMax;
int includeRefNum;
std::vector<int> Nmodes;
std::vector<realT> minRadius;
std::vector<realT> maxRadius;
std::vector<realT> minAngle;
std::vector<realT> maxAngle;
int nWedges {0};
bool m_rightReason{ false };
realT m_rightReasonRadius{ 2.5 };
// Combination and Output
bool noDerotate;
std::string combineMethod;
std::string weightFile;
_realT sigmaThreshold;
_realT minGoodFract{ 0.0 };
std::string outputFile;
bool exactFName;
std::string outputDir;
// Output the individual PSF subtracted images
bool outputPSFSub;
std::string psfSubPrefix;
//************************************//
// Mode of execution //
std::string mode; // Choices are basic [default] and grid [grid manages a fake planet grid]
// Executes a grid of fake planets.
realT gridCenterSep; ///< The separation of the grid center [pixels].
realT gridCenterPA; ///< The PA of the grid center [deg E of N].
realT gridHalfWidthSep; ///< The grid half-width in radius [pixels]
realT gridDeltaSep; ///< The grid spacing in radius [pixels]
realT gridHalfWidthPA; ///< The grid half-wdith in PA [pixels]
realT gridDeltaPA; ///< The grid spacing in PA [pixels]
std::vector<realT> gridContrasts; ///< The grid contrasts, possibly negative.
int doGrid();
KLIPreduction<realT, ADIDerotator<realT>, evCalcT> *obs;
public:
klipReduce()
{
m_configPathGlobal_env = "KLIPREDUCE_GLOBAL_CONFIG";
m_configPathLocal = "klipReduce.conf";
m_requireConfigPathLocal = false;
obs = 0;
deleteFront = 0;
deleteBack = 0;
qualityThreshold = 0;
thresholdOnly = false;
MJDisISO8601 = true;
angleScale = 1;
angleConstant = 0;
coaddMaxImno = 0;
coaddMaxTime = 0;
includeRefNum = 0;
noDerotate = false;
sigmaThreshold = 0;
exactFName = false;
outputPSFSub = false;
// Grid setup
gridCenterSep = 0;
gridCenterPA = 0;
gridHalfWidthSep = 0;
gridDeltaSep = 0;
gridHalfWidthPA = 0;
gridDeltaPA = 0;
mode = "basic";
config.m_sources = true;
}
~klipReduce()
{
if( obs )
delete obs;
}
// This sets up the configuration
void setupConfig()
{
/*>>>> input */
config.add( "input.directory",
"D",
"input.directory",
argType::Required,
"input",
"directory",
false,
"string",
"Directory to search for files" );
config.add( "input.prefix",
"P",
"input.prefix",
argType::Required,
"input",
"prefix",
false,
"string",
"Prefix of the files" );
config.add( "input.extension",
"E",
"input.extension",
argType::Required,
"input",
"extension",
false,
"string",
"Extension of the files, default is .fits" );
config.add(
"input.fileList", "F", "input.fileList", argType::Required, "input", "fileList", false, "string", "" );
config.add( "input.deleteFront",
"",
"input.deleteFront",
argType::Required,
"input",
"deleteFront",
false,
"int",
"The number of files to delete from the front of the list. Default is 0." );
config.add( "input.deleteBack",
"",
"input.deleteBack",
argType::Required,
"input",
"deleteBack",
false,
"int",
"The number of files to delete from the back of the list. Default is 0." );
config.add( "input.qualityFile",
"",
"input.qualityFile",
argType::Required,
"input",
"qualityFile",
false,
"string",
"The path to the file containing image quality, a list of numbers with an entry for each image." );
config.add( "input.qualityThreshold",
"",
"input.qualityThreshold",
argType::Required,
"input",
"qualityThreshold",
false,
"",
"The quality threshold to apply." );
config.add( "input.thresholdOnly",
"",
"input.thresholdOnly",
argType::True,
"input",
"thresholdOnly",
false,
"bool",
"Perform thresholding only, and report the results." );
config.add( "input.angleKeyword",
"",
"input.angleKeyword",
argType::Required,
"input",
"angleKeyword",
false,
"string",
"The header keyword to use for the rotation angle of each image." );
config.add( "input.angleScale",
"",
"input.angleScale",
argType::Required,
"input",
"angleScale",
false,
"float",
"The scale to apply to the angle, default is 1." );
config.add( "input.angleConstant",
"",
"input.angleConstant",
argType::Required,
"input",
"angleConstant",
false,
"float",
"The offset to apply to each angle (e.g. the North angle), default is 0." );
config.add( "input.MJDKeyword",
"",
"input.MJDKeyword",
argType::Required,
"input",
"MJDKeyword",
false,
"string",
"The header keyword specifying the MJD." );
config.add( "input.MJDisISO8601",
"",
"input.MJDisISO8601",
argType::True,
"input",
"MJDisISO8601",
false,
"bool",
"Whether or not the MJD is in ISO 8601 format." );
config.add( "input.imSize",
"S",
"input.imSize",
argType::Required,
"input",
"imSize",
false,
"int",
"The max size to read in from the images. Default is 0, which means read the whole image." );
config.add( "input.maskFile",
"",
"input.maskFile",
argType::Required,
"input",
"maskFile",
false,
"string",
"Path to a file containing a 1/0 mask. 0 pixels are excluded from the search regions." );
/*<<<< input */
/*>>>> rdi */
// RDI setup
config.add( "rdi.directory",
"",
"rdi.directory",
argType::Required,
"rdi",
"directory",
false,
"string",
"Directory to search for RDI files" );
config.add( "rdi.prefix",
"",
"rdi.prefix",
argType::Required,
"rdi",
"prefix",
false,
"string",
"Prefix of the RDI files" );
config.add( "rdi.extension",
"",
"rdi.extension",
argType::Required,
"rdi",
"extension",
false,
"string",
"Extension of the files, default is .fits" );
config.add( "rdi.fileList",
"",
"rdi.fileList",
argType::Required,
"rdi",
"fileList",
false,
"string",
"Path to file containing a list of RDI files" );
config.add( "rdi.deleteFront",
"",
"rdi.deleteFront",
argType::Required,
"rdi",
"deleteFront",
false,
"int",
"The number of files to delete from the front of the RDI file list. Default is 0." );
config.add( "rdi.deleteBack",
"",
"rdi.deleteBack",
argType::Required,
"rdi",
"deleteBack",
false,
"int",
"The number of files to delete from the back of the RDI file list. Default is 0." );
config.add( "rdi.qualityFile",
"",
"rdi.qualityFile",
argType::Required,
"rdi",
"qualityFile",
false,
"string",
"The path to the file containing image quality for the RDI images, a list of numbers with an entry "
"for each image." );
config.add( "rdi.qualityThreshold",
"",
"rdi.qualityThreshold",
argType::Required,
"rdi",
"qualityThreshold",
false,
"",
"The quality threshold to apply to the RDI images." );
/*<<<< rdi */
/*>>>> coadd */
config.add( "coadd.method", "", "coadd.method", argType::Required, "coadd", "method", false, "string", "" );
config.add( "coadd.maxImno", "", "coadd.maxImno", argType::Required, "coadd", "maxImno", false, "int", "" );
config.add( "coadd.maxTime", "", "coadd.maxTime", argType::Required, "coadd", "maxTime", false, "float", "" );
config.add( "coadd.keywords",
"",
"coadd.keywords",
argType::Required,
"coadd",
"keywords",
false,
"vector<string>",
"" );
/*<<<< coadd */
/*>>>> preProcess */
config.add( "preProcess.beforeCoadd",
"",
"preProcess.beforeCoadd",
argType::True,
"preProcess",
"beforeCoadd",
false,
"bool",
"Controls whether pre-processing takes place before (true) or after (false, default) coadding." );
config.add( "preProcess.mask",
"",
"preProcess.mask",
argType::True,
"preProcess",
"mask",
false,
"string",
"Determines if mask is applied for pre-processing." );
config.add( "preProcess.subradprof",
"",
"preProcess.subradprof",
argType::True,
"preProcess",
"subradprof",
false,
"bool",
"If true, the radial profile is subtracted from each image." );
config.add( "preProcess.azUSM_azW",
"",
"preProcess.azUSM_azW",
argType::Required,
"preProcess",
"azUSM_azW",
false,
"float",
"The azimuth USM boxcar azimuthal width in pixels. Enabled if both azW and radW are non-zero." );
config.add( "preProcess.azUSM_radW",
"",
"preProcess.azUSM_radW",
argType::Required,
"preProcess",
"azUSM_radW",
false,
"float",
"The azimuth USM boxcar radial width in pixels. Enabled if both azW and radW are non-zero." );
config.add( "preProcess.gaussUSM_fwhm",
"",
"preProcess.gaussUSM_fwhm",
argType::Required,
"preProcess",
"gaussUSM_fwhm",
false,
"float",
"The gaussian USM kernel full-width at half max. Enabled if non-zero." );
config.add( "preProcess.medianUSM_fwhm",
"",
"preProcess.medianUSM_fwhm",
argType::Required,
"preProcess",
"medianUSM_fwhm",
false,
"float",
"The median USM kernel full-width at half max. Enabled if non-zero." );
config.add( "preProcess.meanSubMethod",
"",
"preProcess.meanSubMethod",
argType::Required,
"preProcess",
"meanSubMethod",
false,
"string",
"The mean subtraction method during pre-processing." );
config.add( "preProcess.pixelTSNormMethod",
"",
"preProcess.pixelTSNormMethod",
argType::Required,
"preProcess",
"pixelTSNormMethod",
false,
"string",
"The pixel time-series normalization method during pre-processing." );
config.add( "preProcess.outputPrefix",
"",
"preProcess.outputPrefix",
argType::Required,
"preProcess",
"outputPrefix",
false,
"string",
"If not empty, then this prefix (which should be a full path) is added to file names and the pre-processed images are output" );
config.add( "preProcess.only",
"",
"preProcess.only",
argType::True,
"preProcess",
"only",
false,
"bool",
"If true, stop after pre-processing. Default is false." );
config.add( "preProcess.skip",
"",
"preProcess.skip",
argType::True,
"preProcess",
"skip",
false,
"bool",
"If true, then pre-processing is skipped. Default is false." );
/*<<<< preProcess */
/*>>>> adi */
config.add( "adi.minDPx",
"",
"adi.minDPx",
argType::Required,
"adi",
"minDPx",
false,
"float",
"Specify the minimum angle or pixel difference at the inner edge of the search region" );
config.add( "adi.maxDPx",
"",
"adi.maxDPx",
argType::Required,
"adi",
"maxDPx",
false,
"float",
"Specify the maximum angle or pixel difference at the inner edge of the search region" );
config.add( "adi.excludeMethod",
"",
"adi.excludeMethod",
argType::Required,
"adi",
"excludeMethod",
false,
"string",
"Method for minimum exclusion. Values are none (default), pixel, angle, imno." );
config.add( "adi.excludeMethodMax",
"",
"adi.excludeMethodMax",
argType::Required,
"adi",
"excludeMethodMax",
false,
"string",
"Method for maximum exclusion. Values are none (default), pixel, angle, imno." );
config.add( "adi.postMedSub",
"",
"adi.postMedSub",
argType::True,
"adi",
"postMedSub",
false,
"string",
"If true, the median image is subtracted after post-processing, before de-rotation" );
/*<<<< adi */
/*>>>> geom */
config.add( "geom.minRadius",
"",
"geom.minRadius",
argType::Required,
"geom",
"minRadius",
false,
"vector<realT>",
"The minimum radius of the search regions" );
config.add( "geom.maxRadius",
"",
"geom.maxRadius",
argType::Required,
"geom",
"maxRadius",
false,
"vector<realT>",
"The maximum radius of the search regions" );
config.add( "geom.minAngle",
"",
"geom.minAngle",
argType::Required,
"geom",
"minAngle",
false,
"vector<realT>",
"The minimum angle of the search regions" );
config.add( "geom.maxAngle",
"",
"geom.maxAngle",
argType::Required,
"geom",
"maxAngle",
false,
"vector<realT>",
"The maximum angle of the search regions" );
config.add( "geom.nWedges",
"",
"geom.nWedges",
argType::Required,
"geom",
"nWedges",
false,
"",
"The number of angular wedges. Overrides minAngle and maxAngle, and expands minRadius and maxRadius" );
/*<<<< geom */
/*>>>> klip */
config.add( "klip.meanSubMethod",
"",
"klip.meanSubMethod",
argType::Required,
"klip",
"meanSubMethod",
false,
"string",
"The method of mean subtraction for PCA: imageMean, imageMedian, meanImage, or medianImage." );
config.add( "klip.pixelTSNormMethod",
"",
"klip.pixelTSNormMethod",
argType::Required,
"klip",
"pixelTSNormMethod",
false,
"int",
"The method of pixel time-series normalization for PCA: none or rms." );
config.add( "klip.includeRefNum",
"",
"klip.includeRefNum",
argType::Required,
"klip",
"includeRefNum",
false,
"int",
"The number of references to include, based on correlation." );
config.add( "klip.Nmodes",
"",
"klip.Nmodes",
argType::Required,
"klip",
"Nmodes",
false,
"vector<int>",
"The number of modes to included in the PSF estimate." );
config.add( "klip.rightReason",
"",
"klip.rightReason",
argType::Required,
"klip",
"rightReason",
false,
"bool",
"Whether or not the right reason mask is applied" );
config.add( "klip.rrRadius",
"",
"klip.rrRadius",
argType::Required,
"klip",
"rrRadius",
false,
"float",
"The radius of the right reason mask" );
/*<<<< klip */
/*>>>> combine */
config.add( "combine.noDerotate",
"",
"combine.noDerotate",
argType::True,
"combine",
"noDerotate",
false,
"bool",
"Do not derotate before combining." );
config.add( "combine.method",
"",
"combine.method",
argType::Required,
"combine",
"method",
false,
"string",
"Averaging method for final combination: mean, median, weighted, sigma" );
config.add( "combine.weightFile",
"",
"combine.weightFile",
argType::Required,
"combine",
"weightFile",
false,
"string",
"File containing weights for the weighted combo. Two column format: filename weight" );
config.add( "combine.sigmaThreshold",
"",
"combine.sigmaThreshold",
argType::Required,
"combine",
"sigmaThreshold",
false,
"float",
"Clipping threshold for sigma clipped mean combination." );
config.add( "combine.minGoodFract",
"",
"combine.minGoodFract",
argType::Required,
"combine",
"minGoodFract",
false,
"float",
"Minimum fraction of good/un-masked pixels to include in final image, otherwise pixel is NaN-ed." );
/*<<<< combine */
/*>>>> output */
config.add( "output.fileName",
"",
"output.fileName",
argType::Required,
"output",
"fileName",
false,
"string",
"Prefix for output file name. A 4 digit 0-padded number is appended." );
config.add( "output.exactFName",
"",
"output.exactFName",
argType::True,
"output",
"exactFName",
false,
"bool",
"Used outputFile exactly as specified, without appending a number or .fits" );
config.add( "output.directory",
"",
"output.directory",
argType::Required,
"output",
"directory",
false,
"string",
"The directory where to output files." );
config.add( "output.outputPSFSub",
"",
"output.outputPSFSub",
argType::True,
"output",
"outputPSFSub",
false,
"bool",
"Output the PSF subtracted images (default false)" );
config.add( "output.psfSubPrefix",
"",
"output.psfSubPrefix",
argType::Required,
"output",
"psfSubPrefix",
false,
"string",
"Prefix of the PSF subtracted output files." );
/*<<<< output */
/*>>>> fake */
config.add( "fake.method",
"",
"fake.method",
argType::Required,
"fake",
"method",
false,
"string",
"How the fake PSF is specified by fileName: single, if a single PSF is used (default); or list, if "
"1 PSF per miage is used." );
config.add( "fake.fileName",
"",
"fake.fileName",
argType::Required,
"fake",
"fileName",
false,
"string",
"Full path to FITS file containing the fake planet PSF to inject, or a file with a list of FITS "
"file paths." );
config.add( "fake.scaleFileName",
"",
"fake.scaleFileName",
argType::Required,
"fake",
"scaleFileName",
false,
"string",
"Path to one-column text file containing a scale factor for each point in time." );
config.add( "fake.sep",
"",
"fake.sep",
argType::Required,
"fake",
"sep",
false,
"vector<float>",
"Separation(s) of the fake planet(s) in pixels." );
config.add( "fake.PA",
"",
"fake.PA",
argType::Required,
"fake",
"PA",
false,
"vector<float>",
"Position angles(s) of the fake planet(s)" );
config.add( "fake.contrast",
"",
"fake.contrast",
argType::Required,
"fake",
"contrast",
false,
"vector<float>",
"Contrast(s) of the fake planet(s)" );
config.add( "fake.RDIFluxScale",
"",
"fake.RDIFluxScale",
argType::Required,
"fake",
"RDIFluxScale",
false,
"vector<float>",
"Flux scaling for the planets injected into the RDI images" );
config.add( "fake.RDISepScale",
"",
"fake.RDISepScale",
argType::Required,
"fake",
"RDISepScale",
false,
"vector<float>",
"Separation scaling for the planets injected into the RDI images" );
/*<<<< fake */
config.add( "mode",
"",
"mode",
argType::Required,
"",
"mode",
false,
"string",
"The mode of operation: either \"grid\" or \"normal\" (the default)" );
config.add( "grid.centerSep",
"",
"grid.centerSep",
argType::Required,
"grid",
"centerSep",
false,
"float",
"The grid center in separation [pixels]" );
config.add( "grid.centerPA",
"",
"grid.centerPA",
argType::Required,
"grid",
"centerPA",
false,
"float",
"The grid center in position angle [degrees]" );
config.add( "grid.halfWidthSep",
"",
"grid.halfWidthSep",
argType::Required,
"grid",
"halfWidthSep",
false,
"float",
"The half width of the grid in spearation [pixels]" );
config.add( "grid.halfWidthPA",
"",
"grid.halfWidthPA",
argType::Required,
"grid",
"halfWidthPA",
false,
"float",
"The half width of the grid in PA [degrees]" );
config.add( "grid.deltaSep",
"",
"grid.deltaSep",
argType::Required,
"grid",
"deltaSep",
false,
"float",
"The grid step size in separation [pixels]" );
config.add( "grid.deltaPA",
"",
"grid.deltaPA",
argType::Required,
"grid",
"deltaPA",
false,
"float",
"The grid step size in PA [degrees]" );
config.add( "grid.contrasts",
"",
"grid.contrasts",
argType::Required,
"grid",
"contrasts",
false,
"vector<float>",
"The contrast grid [planet:star]." );
// config.add("","", "",argType::Required, "", ""));
}
virtual void setConfigPathCL()
{
config.get<std::string>( m_configPathCL, "config" );
}
void loadConfig()
{
/*>>>> input */
config( directory, "input.directory" );
config( prefix, "input.prefix" );
config( extension, "input.extension" );
config( fileList, "input.fileList" );
config( deleteFront, "input.deleteFront" );
config( deleteBack, "input.deleteBack" );
config( qualityFile, "input.qualityFile" );
config( qualityThreshold, "input.qualityThreshold" );
config( thresholdOnly, "input.thresholdOnly" );
config( angleKeyword, "input.angleKeyword" );
config( angleScale, "input.angleScale" );