irplib_slitpos.c

/*
 * This file is part of the irplib package
 * Copyright (C) 2002,2003,2014 European Southern Observatory
 *
 * This program 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 2 of the License, or
 * (at your option) any later version.
 *
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02111-1307  USA
 */
 
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
 
/* The IRPLIB-based application may have checked for the availability of
   memrchr() in which case the macro HAVE_DECL_MEMRCHR is defined as either
   0 or 1. Without checks it is assumed that the function is not available.
   With a suitable version of autoconf the macro can be defined with this
   entry in configure.ac:
   AC_CHECK_DECLS([memrchr])
*/
 
/*-----------------------------------------------------------------------------
                                Includes
 -----------------------------------------------------------------------------*/
 
#include "irplib_slitpos.h"
#include "irplib_flat.h"
 
#include <cpl.h>
 
#include <string.h>
#include <math.h>
#include <assert.h>
 
/*-----------------------------------------------------------------------------
                                Defines
 -----------------------------------------------------------------------------*/
 
#ifndef IRPLIB_SLITPOS_KERNEL_SIZE_Y
#define IRPLIB_SLITPOS_KERNEL_SIZE_Y 5
#endif
 
#ifndef IRPLIB_SLITPOS_MAX_EROSION
#define IRPLIB_SLITPOS_MAX_EROSION 1024
#endif
 
/*-----------------------------------------------------------------------------
                            Functions prototypes
 -----------------------------------------------------------------------------*/
 
static cpl_error_code
irplib_slitpos_find_edges_one_line(const cpl_image *, int, int *, int *);
static cpl_error_code
irplib_slitpos_find_vert_slit_ends(const cpl_image *, int, int *, int *);
static cpl_error_code
irplib_slitpos_find_vert_pos(const cpl_image *, int, cpl_size *);
static cpl_error_code irplib_image_filter_background_line(cpl_image *,
                                                          const cpl_image *,
                                                          int,
                                                          cpl_boolean);
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/

/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
cpl_table *
irplib_slitpos_analysis(const cpl_image *imslit,
                        int slit_max_width,
                        double *slit_flux)
{
    const int size_x = cpl_image_get_size_x(imslit);
    const int size_y = cpl_image_get_size_y(imslit);
    int slit_length;
    cpl_size slit_pos;
    cpl_image *filtered;
    cpl_mask *mask;
    cpl_image *thin_im;
    int slit_top_y = 0; /* Avoid (false) uninit warning */
    int slit_bot_y = 0; /* Avoid (false) uninit warning */
    cpl_table *self;
    double *slit_y, *slit_x_l, *slit_x_r;
    double *coeff_r;
    double *coeff_l;
    int i;
    cpl_error_code error = CPL_ERROR_NONE;
 
    /* Initialize */
    if (slit_flux != NULL)
        *slit_flux = 0.0;
 
    /* Median vertical filtering 3x3 */
    mask = cpl_mask_new(3, 3);
    cpl_mask_not(mask);
    filtered = cpl_image_new(size_x, size_y, cpl_image_get_type(imslit));
    error = cpl_image_filter_mask(filtered, imslit, mask, CPL_FILTER_MEDIAN,
                                  CPL_BORDER_FILTER);
    cpl_mask_delete(mask);
 
    if (error) {
        cpl_image_delete(filtered);
        (void)cpl_error_set_where(cpl_func);
        return NULL;
    }
 
    /* The background may vary strongly along the vertical line. */
    /* Detect and remove background with a 1+2*Slit_max x 1 median filter */
    error = irplib_image_filter_background_line(filtered, NULL, slit_max_width,
                                                CPL_TRUE);
 
    if (error) {
        cpl_image_delete(filtered);
        (void)cpl_error_set_where(cpl_func);
        return NULL;
    }
 
    /* Find the position of the slit */
    if (irplib_slitpos_find_vert_pos(filtered, slit_max_width / 2, &slit_pos)) {
        cpl_image_delete(filtered);
        cpl_msg_error(cpl_func, "Could not find the slit position");
        (void)cpl_error_set_where(cpl_func);
        return NULL;
    }
 
    /* Extract a thin image containing the slit */
    thin_im = cpl_image_extract(filtered, slit_pos - slit_max_width / 2, 1,
                                slit_pos + slit_max_width / 2, size_y);
    if (thin_im == NULL) {
        cpl_msg_error(cpl_func,
                      "Could not extract the %d pixel thin image "
                      "around position %" CPL_SIZE_FORMAT,
                      slit_max_width, slit_pos);
        cpl_image_delete(filtered);
        (void)cpl_error_set_where(cpl_func);
        return NULL;
    }
 
    /* Find the ends of the slit */
    error = irplib_slitpos_find_vert_slit_ends(thin_im,
                                               IRPLIB_SLITPOS_KERNEL_SIZE_Y,
                                               &slit_bot_y, &slit_top_y);
    cpl_image_delete(thin_im);
    if (error) {
        cpl_image_delete(filtered);
        (void)cpl_error_set_where(cpl_func);
        return NULL;
    }
 
    /* Extract an image with exactly the slit */
    thin_im =
        cpl_image_extract(filtered, slit_pos - slit_max_width / 2, slit_bot_y,
                          slit_pos + slit_max_width / 2, slit_top_y);
    cpl_image_delete(filtered);
 
    cpl_ensure(thin_im != NULL, cpl_error_get_code(), NULL);
 
    slit_length = 1 + slit_top_y - slit_bot_y;
 
    /* Allocate some arrays */
    slit_y = cpl_malloc(slit_length * sizeof(double));
    slit_x_l = cpl_malloc(slit_length * sizeof(double));
    slit_x_r = cpl_malloc(slit_length * sizeof(double));
 
    /* Find the edges of the slit */
    for (i = 0; i < slit_length; i++) {
        int right_pos = 0; /* Avoid (false) uninit warning */
        int left_pos = 0;  /* Avoid (false) uninit warning */
 
        if (irplib_slitpos_find_edges_one_line(thin_im, i, &left_pos,
                                               &right_pos)) {
            cpl_msg_error(cpl_func, "cannot find the edges of the [%d]th line",
                          i + 1);
            cpl_image_delete(thin_im);
            cpl_free(slit_y);
            cpl_free(slit_x_l);
            cpl_free(slit_x_r);
            return NULL;
        }
 
        /* Update the slit_flux */
        if (slit_flux != NULL) {
            *slit_flux +=
                cpl_image_get_flux_window(thin_im, left_pos + 1, i + 1,
                                          right_pos + 1, i + 1);
        }
 
        /* Store the edges for the fit */
        slit_x_l[i] = (double)left_pos;
        slit_x_r[i] = (double)right_pos;
        slit_y[i] = (double)(i + slit_bot_y - 1);
    }
    cpl_image_delete(thin_im);
 
    /* Linear regression to find the edges */
    coeff_l = irplib_flat_fit_slope_robust(slit_y, slit_x_l, slit_length);
    coeff_r = irplib_flat_fit_slope_robust(slit_y, slit_x_r, slit_length);
    cpl_free(slit_y);
    cpl_free(slit_x_l);
    cpl_free(slit_x_r);
 
    /* Allocate the table containing the results */
    self = cpl_table_new(slit_length);
    error |= cpl_table_new_column(self, "SLIT_Y", CPL_TYPE_INT);
    error |= cpl_table_new_column(self, "SLIT_LEFT", CPL_TYPE_DOUBLE);
    error |= cpl_table_new_column(self, "SLIT_CENTER", CPL_TYPE_DOUBLE);
    error |= cpl_table_new_column(self, "SLIT_RIGHT", CPL_TYPE_DOUBLE);
 
    error |= cpl_table_set_column_unit(self, "SLIT_Y", "pixel");
    error |= cpl_table_set_column_unit(self, "SLIT_LEFT", "pixel");
    error |= cpl_table_set_column_unit(self, "SLIT_CENTER", "pixel");
    error |= cpl_table_set_column_unit(self, "SLIT_RIGHT", "pixel");
 
    cpl_ensure(!error, cpl_error_get_code(), NULL);
 
    /* Rewrite the edges in the out table, and write the center */
    for (i = 0; i < slit_length; i++) {
        const int islity = i + slit_bot_y;
        const double dslit = slit_pos - slit_max_width / 2.0;
        const double dleft = coeff_l[0] + coeff_l[1] * (double)islity + dslit;
        const double dright = coeff_r[0] + coeff_r[1] * (double)islity + dslit;
        const double dcent = 0.5 * (dleft + dright);
 
        if (cpl_table_set_int(self, "SLIT_Y", i, islity))
            break;
        if (cpl_table_set_double(self, "SLIT_LEFT", i, dleft))
            break;
        if (cpl_table_set_double(self, "SLIT_RIGHT", i, dright))
            break;
        if (cpl_table_set_double(self, "SLIT_CENTER", i, dcent))
            break;
    }
 
    cpl_free(coeff_r);
    cpl_free(coeff_l);
 
    if (i != slit_length) {
        cpl_table_delete(self);
        cpl_ensure(0, cpl_error_get_code(), NULL);
    }
 
    return self;
}

 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
static cpl_error_code
irplib_slitpos_find_edges_one_line(const cpl_image *self,
                                   int line_pos,
                                   int *left_pos,
                                   int *right_pos)
{
    const int size_x = cpl_image_get_size_x(self);
    const float *pself;
    double threshold;
    int i;
 
    cpl_ensure_code(self != NULL, CPL_ERROR_NULL_INPUT);
    cpl_ensure_code(cpl_image_get_type(self) == CPL_TYPE_FLOAT,
                    CPL_ERROR_INVALID_TYPE);
 
    pself = cpl_image_get_data_float_const(self);
 
    /* Find the threshold */
    threshold =
        cpl_image_get_mean_window(self, 1, line_pos + 1, size_x, line_pos + 1);
 
    /* Detect the left edge */
    i = 0;
    while (i < size_x && pself[line_pos * size_x + i] < threshold)
        i++;
    *left_pos = i;
 
    /* Detect the right edge */
    i = size_x - 1;
    while (i >= 0 && pself[line_pos * size_x + i] < threshold)
        i--;
    *right_pos = i;
 
    return CPL_ERROR_NONE;
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
static cpl_error_code
irplib_slitpos_find_vert_slit_ends(const cpl_image *self,
                                   int kernel_size,
                                   int *bot_slit_y,
                                   int *top_slit_y)
{
    cpl_mask *binary;
    cpl_mask *copy = NULL;
    cpl_mask *kernel;
    cpl_image *label_image;
    int erosions_nb;
    cpl_size nobj;
    const int size_x = cpl_image_get_size_x(self);
    const int size_y = cpl_image_get_size_y(self);
    const int npix = size_x * size_y;
    const cpl_binary *pbinary;
    const cpl_binary *pfind;
    int i, itop, ibot;
 
 
    cpl_ensure_code(size_x > 0, cpl_error_get_code());
    cpl_ensure_code(kernel_size > 0, cpl_error_get_code());
 
    /* Threshold to have a binary image */
    binary = cpl_mask_threshold_image_create(self, cpl_image_get_mean(self),
                                             cpl_image_get_max(self));
    cpl_ensure_code(binary != NULL, cpl_error_get_code());
 
    /* Erode until there is 1 object left in the image */
    label_image = cpl_image_labelise_mask_create(binary, &nobj);
    cpl_image_delete(label_image);
 
    if (label_image == NULL) {
        cpl_mask_delete(binary);
        cpl_ensure_code(0, cpl_error_get_code());
    }
 
    /* Define the kernel for morpho operations */
    kernel = cpl_mask_new(kernel_size, 1);
    cpl_mask_not(kernel);
    copy = cpl_mask_wrap(size_x, size_y,
                         cpl_malloc(size_x * size_y * sizeof(cpl_binary)));
    for (erosions_nb = 0; erosions_nb < IRPLIB_SLITPOS_MAX_EROSION && nobj > 1;
         erosions_nb++) {
        /* Should not be possible to break from this loop */
        cpl_mask_copy(copy, binary, 1, 1);
        if (cpl_mask_filter(binary, copy, kernel, CPL_FILTER_EROSION,
                            CPL_BORDER_ZERO))
            break;
 
        label_image = cpl_image_labelise_mask_create(binary, &nobj);
        if (label_image == NULL)
            break; /* Assuming nobj was not set to 1 */
        cpl_image_delete(label_image);
    }
 
    if (nobj > 1) {
        cpl_mask_delete(binary);
        cpl_mask_delete(copy);
        cpl_mask_delete(kernel);
        if (erosions_nb >= IRPLIB_SLITPOS_MAX_EROSION) {
            cpl_msg_error(cpl_func,
                          "Number of erosions reached a limit of %d "
                          "with %" CPL_SIZE_FORMAT " possible slits left",
                          IRPLIB_SLITPOS_MAX_EROSION, nobj);
            cpl_ensure_code(0, CPL_ERROR_CONTINUE);
        }
        cpl_ensure_code(0, cpl_error_get_code());
    }
    else if (nobj < 1) {
        cpl_mask_delete(binary);
        cpl_mask_delete(copy);
        cpl_mask_delete(kernel);
        if (erosions_nb == 0)
            cpl_msg_error(cpl_func,
                          "No slit could be detected across %d "
                          "pixels",
                          size_x);
        else
            cpl_msg_error(cpl_func,
                          "The last of %d erosions removed all the "
                          "possible slits",
                          erosions_nb);
        cpl_ensure_code(0, CPL_ERROR_DATA_NOT_FOUND);
    }
 
    /* Reconstruct the slit with dilations */
    for (i = 0; i < erosions_nb; i++) {
        cpl_mask_copy(copy, binary, 1, 1);
        if (cpl_mask_filter(binary, copy, kernel, CPL_FILTER_DILATION,
                            CPL_BORDER_ZERO))
            break;
    }
    cpl_mask_delete(copy);
    cpl_mask_delete(kernel);
 
    if (i != erosions_nb) {
        cpl_msg_error(cpl_func, "Dilation number %d out of %d failed", i,
                      erosions_nb);
        cpl_mask_delete(binary);
        cpl_ensure_code(0, cpl_error_get_code());
    }
 
    /* Find the ends of the slit */
    pbinary = cpl_mask_get_data(binary);
    assert(pbinary != NULL);
 
    pfind = memchr(pbinary, CPL_BINARY_1, (size_t)npix);
    assert(pfind != NULL);
 
    ibot = (int)(pfind - pbinary);
 
#if defined HAVE_DECL_MEMRCHR && HAVE_DECL_MEMRCHR == 1
    /* FIXME: Not tested */
    pfind = memrchr(pfind, CPL_BINARY_1, (size_t)(npix - ibot));
    assert(pfind != NULL);
 
    itop = (int)(pfind - pbinary);
#else
 
    itop = npix - 1;
    while (itop > ibot && pbinary[itop] == CPL_BINARY_0)
        itop--;
 
#endif
 
    *bot_slit_y = 1 + ibot / size_x;
    *top_slit_y = 1 + itop / size_x;
 
    cpl_msg_info(cpl_func,
                 "Detected %" CPL_SIZE_FORMAT "-pixel slit from pixel %d to %d "
                 "using %d erosions/dilations",
                 cpl_mask_count(binary), *bot_slit_y, *top_slit_y, erosions_nb);
 
    cpl_mask_delete(binary);
 
    /* Should really be an assert() */
    cpl_ensure_code(ibot <= itop, CPL_ERROR_DATA_NOT_FOUND);
 
    return CPL_ERROR_NONE;
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
static cpl_error_code
irplib_slitpos_find_vert_pos(const cpl_image *self,
                             int xwidth,
                             cpl_size *slit_pos)
{
    const int size_x = cpl_image_get_size_x(self);
    cpl_image *image1D;
    cpl_size yone;
    cpl_error_code error;
 
 
    /* Collapse the image to a horizontal 1D image */
    image1D = cpl_image_collapse_create(self, 0);
 
    cpl_ensure_code(image1D != NULL, cpl_error_get_code());
 
    /* Search the max of the 1D image to identify the slit position */
    error = cpl_image_get_maxpos_window(image1D, 1 + xwidth, 1, size_x - xwidth,
                                        1, slit_pos, &yone);
 
    cpl_image_delete(image1D);
 
    cpl_ensure_code(!error, error);
 
    return CPL_ERROR_NONE;
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
static cpl_error_code
irplib_image_filter_background_line(cpl_image *self,
                                    const cpl_image *other,
                                    int hsize,
                                    cpl_boolean vertical)
{
    const int nx = cpl_image_get_size_x(self);
    const int ny = cpl_image_get_size_y(self);
    const int msize = 1 + 2 * hsize;
    cpl_mask *mask;
    cpl_image *background;
    cpl_error_code error = CPL_ERROR_NONE;
 
    cpl_ensure_code(self != NULL, CPL_ERROR_NULL_INPUT);
    cpl_ensure_code(hsize >= 0, CPL_ERROR_ILLEGAL_INPUT);
 
    if (other == NULL)
        other = self;
 
    mask = vertical ? cpl_mask_new(msize, 1) : cpl_mask_new(1, msize);
 
    error |= cpl_mask_not(mask);
 
    background = cpl_image_new(nx, ny, cpl_image_get_type(other));
 
    error |= cpl_image_filter_mask(background, other, mask, CPL_FILTER_MEDIAN,
                                   CPL_BORDER_FILTER);
    cpl_mask_delete(mask);
 
    if (self != other) {
        error |= cpl_image_copy(self, other, 1, 1);
    }
 
    error |= cpl_image_subtract(self, background);
    cpl_image_delete(background);
 
    return error ? cpl_error_set_where(cpl_func) : CPL_ERROR_NONE;
}