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/* *
* This file is part of the ESO UVES Pipeline *
* Copyright (C) 2004,2005 European Southern Observatory *
* *
* This library 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, 51 Franklin St, Fifth Floor, Boston, MA 02111-1307 USA *
* */
/*
* $Author: amodigli $
* $Date: 2013-08-08 13:36:46 $
* $Revision: 1.39 $
* $Name: not supported by cvs2svn $
*
*/
/*----------------------------------------------------------------------------*/
/**
* @addtogroup uves_response
*/
/*----------------------------------------------------------------------------*/
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
/*-----------------------------------------------------------------------------
Includes
-----------------------------------------------------------------------------*/
#include <uves_response_efficiency.h>
#include <uves_response_utils.h>
#include <uves_reduce.h>
#include <uves_reduce_utils.h>
#include <uves_dfs.h>
#include <uves_pfits.h>
#include <uves_wavecal_utils.h>
#include <uves_utils_polynomial.h>
#include <uves_utils.h>
#include <uves_utils_wrappers.h>
#include <uves_utils_cpl.h>
#include <uves.h>
#include <uves_error.h>
#include <uves_msg.h>
#include <cpl.h>
#include <stdbool.h>
/*-----------------------------------------------------------------------------
Defines
-----------------------------------------------------------------------------*/
#define H_BAR 6.626068e-34 /* SI-units */
#define PRIMARY_DIA 818 /* Primary diameter (cm) */
#define OBSTR_DIA 140 /* Central obstruction diameter (cm) */
#define TELESCOPE_EFFECTIVE_AREA \
(M_PI * (PRIMARY_DIA * PRIMARY_DIA - OBSTR_DIA * OBSTR_DIA) / 4.0) /* (cm^2) */
/**@{*/
/**
@brief Calculate quantum detection efficiency
@param raw_image The raw image
@param raw_header FITS header of raw image
@param rotated_header Header describing the geometry of the raw image after
rotation and removal of pre- and overscan areas
@param master_bias The master bias image for this chip, or NULL
@param master_dark The master dark image for this chip, or NULL
@param mdark_header FITS header of master dark frame
@param ordertable Order table describing the order locations on the raw image
@param order_locations The polynomial describing the order positions
@param linetable Length 3 array of linetable for sky, object, sky.
@param linetable_header Length 3 array of linetable headers for sky, object, sky.
@param dispersion_relation Length 3 array of dispersion relations for sky, object, sky.
@param flux_table Catalogue standard star fluxes
@param atm_extinction Atmospheric extinction coefficients
@param chip CCD chip
@param debug_mode If set to true, intermediate results are saved to
the current directory
@param parameters The recipe parameter list containing parameters
for background subtraction, flat-fielding, extraction, rebinning
@param PACCURACY Pointing accuracy (in arcseconds) used to identify object
@param efficiency (out) The quantum detection efficiency table
@param blaze_efficiency (out) Efficiency at blaze function maximum, for each order
@return The reduced spectrum
**/
/*----------------------------------------------------------------------------*/
cpl_error_code
uves_response_efficiency(const cpl_image *raw_image,
const uves_propertylist *raw_header,
const uves_propertylist *rotated_header,
const cpl_image *master_bias,
const uves_propertylist *mbias_header,
const cpl_image *master_dark,
const uves_propertylist *mdark_header,
const cpl_table *ordertable,
const polynomial *order_locations,
const cpl_table *linetable[3],
const uves_propertylist *linetable_header[3],
const polynomial *dispersion_relation[3],
const cpl_table *flux_table,
const cpl_table *atm_extinction,
enum uves_chip chip,
bool debug_mode,
const cpl_parameterlist *parameters,
/* Identification */
double PACCURACY,
/* Output */
cpl_table **efficiency,
cpl_table **blaze_efficiency)
{
cpl_image *background = NULL;
cpl_image *rebinned_spectrum = NULL;
cpl_image *rebinned_noise = NULL;
cpl_image *merged_sky = NULL;
cpl_image *merged_spectrum = NULL;
cpl_image *merged_noise = NULL;
cpl_image *reduced_spectrum = NULL;
cpl_image *reduced_noise = NULL;
cpl_image *reduced_rebinned = NULL;
cpl_image *reduced_rebinned_noise = NULL;
uves_propertylist *rebinned_header = NULL;
uves_propertylist *reduced_header = NULL;
polynomial *disprel_1d = NULL;
cpl_image *response_orders = NULL;
cpl_image *efficiency_spectrum = NULL;
cpl_table *central_efficiency = NULL;
cpl_table *info_tbl = NULL; /* Local. The info tbl
should not be calculated twice
in the response recipe. It is
calculated in the first extraction */
char *ref_obj_id = NULL;
double wavestep;
double extraction_slit;
cpl_image* wave_map=NULL;
cpl_image* reduced_rebinned_no_bpm=NULL;
cpl_mask* bpm=NULL;
/* Set parameters
wavestep = 10 * 2/3 * mean(pixelsize)
After execution, revert to current value
*/
{
double smooth_step;
/* wavestep */
check( uves_get_parameter(parameters, NULL,
make_str(UVES_RESPONSE_ID) "", "reduce.rebin.wavestep",
CPL_TYPE_DOUBLE, &wavestep),
"Error getting resampling step size");
check( smooth_step = cpl_table_get_column_mean(linetable[1], LINETAB_PIXELSIZE),
"Error reading mean pixelsize");
smooth_step = 10*2*smooth_step/3;
/* Cast to non-const is okay. The parameter is reset to its previous value
(see below), so there is not net change (unless the reduction fails,
in which case parameter list will change).
*/
check( uves_set_parameter((cpl_parameterlist *) parameters,
make_str(UVES_RESPONSE_ID) "", "reduce.rebin.wavestep",
CPL_TYPE_DOUBLE, &smooth_step),
"Error setting resampling step size");
}
check( uves_reduce(raw_image,
raw_header,
rotated_header,
master_bias,
mbias_header,
master_dark,
mdark_header,
NULL,
NULL, /* No master flat */
ordertable,
order_locations,
linetable,
linetable_header,
dispersion_relation,
chip,
debug_mode,
parameters,
make_str(UVES_RESPONSE_ID),
".efficiency",
/* Output */
NULL,
NULL,
NULL, /* 2d products */
NULL, /* Cosmic ray table */
&wave_map,
&background,
NULL,
NULL, /* Variance of flat-fielded spectrum */
NULL,
NULL, /* Don't need these
intermediate products */
&merged_sky,
&rebinned_spectrum,
&rebinned_noise,
&rebinned_header,
&merged_spectrum,
&merged_noise,
&reduced_header,
&reduced_rebinned,
&reduced_rebinned_noise,
&reduced_spectrum,
&reduced_noise,
&info_tbl,
&extraction_slit, /* not passed on to the caller */
NULL),
"Could not reduce frame");
/* Reset parameter to previous value */
{
uves_msg_debug("Resetting parameter wavestep = %e", wavestep);
/* Cast to non-const is okay. There is no net change in the parameter list (see above). */
check( uves_set_parameter((cpl_parameterlist *) parameters,
make_str(UVES_RESPONSE_ID) "", "reduce.rebin.wavestep",
CPL_TYPE_DOUBLE, &wavestep),
"Error resetting resampling step size");
}
/* Save reduced spectrum */
if (debug_mode)
{
/* Window number doesn't apply. This is middle window minus two other (sky) windows */
check( uves_save_image_local("Reduced spectrum (2d)", "reduced",
reduced_rebinned, chip, -1, -1, rebinned_header, true),
"Error saving reduced spectrum (2d)");
check( uves_save_image_local("Reduced spectrum (2d) noise", "errreduced",
reduced_rebinned_noise, chip, -1, -1, rebinned_header, true),
"Error saving reduced spectrum (2d) noise");
check( uves_save_image_local("Reduced spectrum", "merged",
reduced_spectrum, chip, -1, -1, reduced_header, true),
"Error saving reduced spectrum");
check( uves_save_image_local("Reduced spectrum noise", "errmerged",
reduced_noise, chip, -1, -1, reduced_header, true),
"Error saving reduced spectrum noise");
}
uves_msg("Dividing by catalogue flux");
/*
* Calculate 2d response curve (don't scale to unit exposure time, binning, gain, ... )
*/
/* in some cases are flagged too many bad pixels on sky frames used
to compute reduced object in linear extraction method, this
affecting the number of bad pixels of the reduced_rebinned obj spectrum
to fix this we erase the associated bad pixel map
*/
reduced_rebinned_no_bpm=cpl_image_duplicate(reduced_rebinned);
bpm=cpl_image_unset_bpm(reduced_rebinned_no_bpm);
check( response_orders = uves_calculate_response(reduced_rebinned_no_bpm,
rebinned_header,
flux_table,
raw_header, PACCURACY,
false,
&ref_obj_id),/* flux/std_flux */
"Could not calculate response curve");
uves_free_image(&reduced_rebinned_no_bpm);
uves_free_mask(&bpm);
if (debug_mode)
{
check( uves_save_image_local("2d response curve", "resp",
response_orders, chip, -1, -1, rebinned_header, true),
"Error saving 2d response curve");
}
/*
* Extinction correction, exposure time + gain
*/
{
int n_traces = cpl_image_get_size_y(merged_spectrum); /* Number of spatial traces */
assure( n_traces == 1, CPL_ERROR_ILLEGAL_INPUT,
"2d extraction/reduction not supported");
check( efficiency_spectrum = uves_normalize_spectrum(response_orders, NULL,
/* Spectrum, noise */
rebinned_header,
raw_header,
n_traces,
chip,
atm_extinction,
false, /* Don't divide by binning */
NULL), /* Don't need output noise */
"Could not normalize spectrum");
}
/*
* 7 x 1 median filter
*/
uves_msg("Applying 7x1 median filter");
check( uves_filter_image_median(&efficiency_spectrum, 3, 0, false),
"Error applying median filter");
uves_msg("Calculating quantum detection efficiency");
{
int nx, nbins, norders, order;
int first_abs_order, last_abs_order, abs_order; /* Absolute order numbers */
double dlambda;
double average_noise; /* Median of noise of rebinned spectrum */
int row = 0; /* Next unused table row */
double *efficiency_data; /* For efficiency. cpl_image_get() */
double *reduced_noise_data; /* is slow when there are bad pixels */
efficiency_data = cpl_image_get_data_double(efficiency_spectrum);
reduced_noise_data = cpl_image_get_data_double(reduced_rebinned_noise);
nx = cpl_image_get_size_x(raw_image);
nbins = cpl_image_get_size_x(efficiency_spectrum);
norders = cpl_image_get_size_y(efficiency_spectrum);
*efficiency = cpl_table_new(nbins * norders);
cpl_table_new_column(*efficiency, "Wave", CPL_TYPE_DOUBLE);
cpl_table_new_column(*efficiency, "Eff", CPL_TYPE_DOUBLE);
cpl_table_new_column(*efficiency, "Binsize", CPL_TYPE_DOUBLE);
cpl_table_new_column(*efficiency, "Order", CPL_TYPE_INT);
cpl_table_set_column_unit(*efficiency,"Wave","Angstrom");
cpl_table_set_column_unit(*efficiency,"Eff"," ");
cpl_table_set_column_unit(*efficiency,"Binsize","Angstrom");
cpl_table_set_column_unit(*efficiency,"Order"," ");
row = 0;
check( first_abs_order = uves_pfits_get_firstabsorder(linetable_header[1]),
"Could not read order numbers from line table header");
check( last_abs_order = uves_pfits_get_lastabsorder (linetable_header[1]),
"Could not read order numbers from line table header");
check( dlambda = uves_pfits_get_cdelt1(rebinned_header),
"Error reading bin width from header");
check( average_noise = cpl_image_get_median(reduced_rebinned_noise),
"Error reading median noise level");
for (order = 1; order <= norders; order++)
{
double lambda_start, lambda, lambda_end;
double x;
int bin;
abs_order = uves_absolute_order(first_abs_order, last_abs_order, order);
check( lambda_start = uves_pfits_get_wstart(rebinned_header, order),
"Error reading start wavelength from header");
check( lambda_end = uves_pfits_get_wend(rebinned_header, order),
"Error reading end wavelength from header");
/* Get 1d dispersion relation for this order
f_1d = f(x, m=abs_order)
Collapsing a polynomial is slow, so do it
only once per order
*/
uves_polynomial_delete(&disprel_1d);
check( disprel_1d = uves_polynomial_collapse(dispersion_relation[1],
2, /* Independent variable number */
abs_order),
"Error getting 1d dispersion relation for absolute order #%d", abs_order);
x = 1;
for (lambda = lambda_start, bin = 1;
lambda < lambda_end + 0.5 * dlambda && bin <= nbins;
bin++, lambda += dlambda)
{
double flux;
double dldx;
double noise; /* Only use positions with low noise
(middle of blaze function) */
/* flux = cpl_image_get(efficiency_spectrum,
bin, order, &pis_rejected);
noise = cpl_image_get(reduced_rebinned_noise,
bin, order, &pis_rejected); */
flux = efficiency_data [(bin-1) + (order-1) * nbins];
noise = reduced_noise_data[(bin-1) + (order-1) * nbins];
/*
* Energy per (time * area * wavelength) =
* ((electron counts)/gain) * (hc/lambda) /
* (time * area * |dlambda/dx|)
*
* We already divided by exposure time, gain
* We did not multiply by dlambda/dx during rebinning,
* so now is the time to do it
*/
/* Solve f(x,m) = m*lambda for x.
*
* This is equivalent to solving f_1d(x) = m*lambda
*/
check( x = uves_polynomial_solve_1d(
disprel_1d,
abs_order * lambda, /* right hand side */
x, /* guess */
1), /* multiplicity */
"Could not solve dispersion relation for x "
"at (m, lambda) = (%d, %f)", abs_order, lambda);
/* For constant absolute order number, m:
dl/dx = d (l.m)/dx / m */
check( dldx = fabs(uves_polynomial_derivative_2d(
dispersion_relation[1],
x,
abs_order, 1) / abs_order),
"Could not evaluate dispersion relation");
/* Don't make a linear interpolation
weight = (lambda - lambda_start) / (lambda_end - lambda_start);
check( dldx =
fabs(uves_polynomial_derivative_2d(
dispersion_relation[1],
1 , abs_order,
1) / abs_order) * (1 - weight) +
fabs(uves_polynomial_derivative_2d(
dispersion_relation[1],
nx, abs_order, 1) / abs_order) * weight,
"Could not evaluate dispersion relation");
*/
flux = flux * 1e16 * 1e17 * H_BAR * SPEED_OF_LIGHT /
(dldx * lambda * TELESCOPE_EFFECTIVE_AREA);
/* The factor 1e17 accounts for the conversion Joule<-erg
* (10^7) and Angstrom->meters (10^10)
* The factor 1e16 is to correct for the fact that the
* catalogue flux is in units of (10^-16 <standard units>)
*/
if (noise < 3*average_noise)
{
check(( cpl_table_set_double(*efficiency, "Wave", row, lambda),
cpl_table_set_double(*efficiency, "Eff", row, flux),
cpl_table_set_double(*efficiency, "Binsize", row, dldx),
cpl_table_set_int (*efficiency, "Order", row, order),
row++),
"Error updating efficiency table row %d", row);
}
}
}
/* Remove unused rows of efficiency table */
check( cpl_table_set_size(*efficiency, row),
"Error setting size of efficiency table to %d rows", row);
/* remove negative efficiency points */
cpl_table* tmp=cpl_table_duplicate(*efficiency);
row=cpl_table_and_selected_double(tmp,"Eff",CPL_GREATER_THAN,0.);
uves_free_table(efficiency);
*efficiency=cpl_table_extract_selected(tmp);
uves_free_table(&tmp);
/* Get the "top efficiency" (90% percentile efficiency of middle 20% of each order) */
*blaze_efficiency = cpl_table_new(norders);
cpl_table_new_column(*blaze_efficiency, "Order", CPL_TYPE_INT);
cpl_table_new_column(*blaze_efficiency, "Wave" , CPL_TYPE_DOUBLE);
cpl_table_new_column(*blaze_efficiency, "Eff" , CPL_TYPE_DOUBLE);
row = 0;
for (order = 1; order <= norders; order++)
{
double lambda_min;
double lambda_central_min;
double lambda_central;
double lambda_central_max;
double lambda_max;
double top_efficiency;
abs_order = uves_absolute_order(first_abs_order, last_abs_order, order);
check( lambda_min = uves_pfits_get_wstart(rebinned_header, order),
"Error reading bin width from header");
check( lambda_max = uves_pfits_get_wend(rebinned_header, order),
"Error reading bin width from header");
lambda_central_min = lambda_min + 0.4 * (lambda_max - lambda_min);
lambda_central = lambda_min + 0.5 * (lambda_max - lambda_min);
lambda_central_max = lambda_min + 0.6 * (lambda_max - lambda_min);
/* Select rows in this order in range
]lambda_central_min ; lambda_central_max[ */
cpl_table_select_all(*efficiency);
cpl_table_and_selected_int (*efficiency, "Order",
CPL_EQUAL_TO , order);
cpl_table_and_selected_double(*efficiency, "Wave" ,
CPL_GREATER_THAN, lambda_central_min);
cpl_table_and_selected_double(*efficiency, "Wave" ,
CPL_LESS_THAN , lambda_central_max);
uves_msg_debug("%" CPL_SIZE_FORMAT " bins in central 20 %% range of order #%d",
cpl_table_count_selected(*efficiency), order);
if ( cpl_table_count_selected(*efficiency) > 0)
{
uves_free_table(¢ral_efficiency);
central_efficiency = cpl_table_extract_selected(*efficiency);
/* Get 90% percentile efficiency */
uves_sort_table_1(central_efficiency, "Eff", false); /* Ascending */
top_efficiency = cpl_table_get_double(
central_efficiency, "Eff",
(int) (0.9 * cpl_table_get_nrow(central_efficiency)), NULL);
}
else
{
uves_msg_debug("No wavelength bins in central 20%% range of order #%d",
order);
top_efficiency = 0;
}
uves_msg("Efficiency(lambda = %.2f A) = %.2f%%",
lambda_central, top_efficiency*100);
check(( cpl_table_set_int (*blaze_efficiency, "Order", row, order),
cpl_table_set_double(*blaze_efficiency, "Wave" , row, lambda_central),
cpl_table_set_double(*blaze_efficiency, "Eff" , row, top_efficiency),
row++),
"Error updating blaze efficiency table");
} /* for order */
}
cleanup:
uves_free_image(&background);
uves_free_image(&rebinned_spectrum);
uves_free_image(&rebinned_noise);
uves_free_image(&merged_sky);
uves_free_image(&merged_spectrum);
uves_free_image(&merged_noise);
uves_free_image(&reduced_spectrum);
uves_free_image(&reduced_noise);
uves_free_image(&reduced_rebinned);
uves_free_image(&reduced_rebinned_noise);
uves_free_propertylist(&reduced_header);
uves_free_propertylist(&rebinned_header);
uves_polynomial_delete(&disprel_1d);
uves_free_image(&response_orders);
uves_free_image(&efficiency_spectrum);
uves_free_table(¢ral_efficiency);
uves_free_table(&info_tbl);
cpl_free(ref_obj_id);
if (cpl_error_get_code() != CPL_ERROR_NONE)
{
uves_free_table(efficiency);
uves_free_table(blaze_efficiency);
}
return cpl_error_get_code();
}
/**@}*/
|
