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/*********************************************************************
NoiseChisel - Detect signal in a noisy dataset.
NoiseChisel is part of GNU Astronomy Utilities (Gnuastro) package.
Original author:
Mohammad Akhlaghi <mohammad@akhlaghi.org>
Contributing author(s):
Copyright (C) 2015-2025 Free Software Foundation, Inc.
Gnuastro is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation, either version 3 of the License, or (at your
option) any later version.
Gnuastro is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with Gnuastro. If not, see <http://www.gnu.org/licenses/>.
**********************************************************************/
#ifndef MAIN_H
#define MAIN_H
/* Include necessary headers */
#include <gnuastro/data.h>
#include <gnuastro-internal/options.h>
/* Progarm names. */
#define PROGRAM_NAME "NoiseChisel" /* Program full name. */
#define PROGRAM_EXEC "astnoisechisel" /* Program executable name. */
#define PROGRAM_STRING PROGRAM_NAME" (" PACKAGE_NAME ") " PACKAGE_VERSION
/* Main program parameters structure */
struct noisechiselparams
{
/* From command-line */
struct gal_options_common_params cp; /* Common parameters. */
struct gal_tile_two_layer_params ltl;/* Large tessellation. */
char *inputname; /* Input filename. */
char *kernelname; /* Input kernel filename. */
char *khdu; /* Kernel HDU. */
char *convolvedname; /* Convolved image (to avoid convolution).*/
char *chdu; /* HDU of convolved image. */
char *widekernelname; /* Name of wider kernel to be used. */
char *whdu; /* Wide kernel HDU. */
uint8_t continueaftercheck; /* Don't abort after the check steps. */
uint8_t ignoreblankintiles; /* Ignore input's blank values. */
uint8_t rawoutput; /* Only detection & 1 elem/tile output. */
uint8_t label; /* Label detections that are connected. */
float meanmedqdiff; /* Difference between mode and median. */
float qthresh; /* Quantile threshold on convolved image. */
size_t outliernumngb; /* Number of neighbors to define outliers.*/
float outliersigma; /* Multiple of sigma to define outlier. */
double outliersclip[2]; /* Outlier Sigma-clipping params. */
size_t smoothwidth; /* Interpolation: flat kernel to smooth. */
uint8_t checkqthresh; /* Save the quantile threhsold steps. */
uint8_t blankasforeground; /* Blank as foreg. in erosion and opening.*/
size_t erode; /* Number of erosions after thresholding. */
size_t erodengb; /* Connectivity for erosion. */
float noerodequant; /* Quantile for no erosion. */
size_t opening; /* Depth of opening after erosion. */
size_t openingngb; /* Connectivity to use for opening. */
uint8_t skyfracnoblank; /* No blanks in estimating non-det frac. */
float minskyfrac; /* Undetected area min. frac. in tile. */
double sigmaclip[2]; /* Sigma-clipping parameters. */
uint8_t checkdetsky; /* Check pseudo-detection sky value. */
float dthresh; /* Sigma threshold for Pseudo-detections. */
size_t dopening; /* Depth of opening after dthresh. */
size_t dopeningngb; /* Connectivity for opening after dthresh.*/
size_t holengb; /* Connectivity for defining a hole. */
size_t pseudoconcomp; /* Connectivity for connected components. */
size_t snminarea; /* Minimum pseudo-detection area for S/N. */
uint8_t checksn; /* Save pseudo-detection S/N values. */
size_t minnumfalse; /* Min No. of det/seg for true quantile. */
float snquant; /* True detection quantile. */
float snthresh; /* Manually input S/N value. */
float detgrowquant; /* Quantile to grow true detections. */
size_t detgrowmaxholesize; /* Max. size of holes to fill in growth. */
uint8_t cleangrowndet; /* Remove grown objects with small S/N. */
uint8_t checkdetection; /* Save all detection steps to a file. */
uint8_t checksky; /* Check the Sky value estimation. */
/* Internal. */
char *qthreshname; /* Name of Quantile threshold check image.*/
char *detskyname; /* Name of Initial det sky check image. */
char *detsn_s_name; /* Sky pseudo-detections S/N name. */
char *detsn_d_name; /* Detection pseudo-detections S/N name. */
char *detsn_D_name; /* Final detection S/N name. */
char *detectionname; /* Name of detection steps file. */
char *skyname; /* Name of Sky estimation steps file. */
gal_data_t *input; /* Input image. */
gal_data_t *kernel; /* Sharper kernel. */
gal_data_t *widekernel; /* Wider kernel. */
gal_data_t *conv; /* Convolved wth sharper kernel. */
gal_data_t *wconv; /* Convolved with wider kernel. */
gal_data_t *binary; /* For binary operations. */
gal_data_t *olabel; /* Labels of objects in the detection. */
gal_data_t *expand_thresh; /* Quantile threshold to expand per tile. */
gal_data_t *exp_thresh_full; /* Full array containing growth thresh. */
gal_data_t *noskytiles; /* Tiles to not use for Sky. */
gal_data_t *sky; /* Mean of undetected pixels, per tile. */
gal_data_t *std; /* STD of undetected pixels, per tile. */
size_t maxtcontig; /* Maximum contiguous space for a tile. */
size_t maxltcontig; /* Maximum contiguous space for a tile. */
size_t *maxtsize; /* Maximum size of a single small tile. */
size_t *maxltsize; /* Maximum size of a single large tile. */
size_t numexpand; /* Initial number of pixels to expand. */
time_t rawtime; /* Starting time of the program. */
float medstd; /* Median STD before interpolation. */
float minstd; /* Minimum STD before interpolation. */
float maxstd; /* Maximum STD before interpolation. */
float cpscorr; /* Counts/second correction. */
size_t numinitialdets; /* Number of initial detections. */
size_t numdetections; /* Number of final detections. */
float detsnthresh; /* Pseudo-detection S/N threshold. */
};
#endif
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