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X-shooter Pipeline Reference Manual 3.8.15
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#include <string.h>#include <math.h>#include <cpl.h>#include "mf_wrap.h"#include "mf_wrap_config.h"#include "mf_spectrum.h"#include "xsh_molecfit_utils.h"Go to the source code of this file.
Macros | |
| #define | XSHOOTER_INPUT_DATA_FLUX_COLUMN "Flux" |
| #define | XSH_MOLECFIT_PARAMETER_LIST_DESC "List of molecules to include in the fit (comma separated). If set to 'NULL', the values provided in MOLECULES_XXX will be used, where XXX is UVB, VIS or NIR. If not, the provided list overrides what is specified in the MOLECULES_XXX input. Note: in order to override MOLECULES_XXX, the recipe parameters REL_COL, FIT_MOLEC, and LIST_MOLEC must be all specified and different from 'NULL'." |
| #define | XSH_MOLECFIT_PARAMETER_FIT_DESC "List of flags (1 and 0), comma separated, that specifies if a molecule has to be fitted (flag=1) or computed (flag=0). If set to 'NULL', the values provided in MOLECULES_XXX will be used, where XXX is UVB, VIS or NIR. If not, the provided list overrides what is specified in the MOLECULES_XXX input. Note: in order to override MOLECULES_XXX, the following recipe parameters rel_col, fit_molec, and list_molec must be all specified and different from 'NULL'." |
| #define | XSH_MOLECFIT_PARAMETER_RELATIVE_VALUE_DESC "List of relative column densities of the molecules used (comma separated). If set to 'NULL', the values provided in MOLECULES_XXX will be used, where XXX is UVB, VIS or NIR. If not, the provided list overrides what is specified in the MOLECULES_XXX input. Note: in order to override MOLECULES_XXX, the following recipe parameters rel_col, fit_molec, and list_molec must be all specified and different from 'NULL'." |
| #define | XSH_MOLECFIT_PARAMETER_WAVE_RANGE_INCLUDE_DESC "Comma separated list of values that define the boundaries of the wavelength regions to fit (low_1, upper_1, low_2, upper_2,...,low_n, upper_n), in microns. If set to 'NULL' the values specified in the fits table given by the tag WAVE_INCLUDE_XXX will be used, where XXX is UVB, VIS or NIR. If not, these values override those specified in WAVE_INCLUDE_XXX." |
| #define | XSH_MOLECFIT_PARAMETER_WAVE_RANGE_EXCLUDE_DESC "Comma separated list of values that define the boundaries of the wavelength regions to exclude in the fit (low_1, upper_1, low_2, upper_2,...,low_n, upper_n), in microns. If set to 'NULL' the values specified in the fits table given by the tag WAVE_EXCLUDE_XXX will be used, where XXX is UVB, VIS or NIR. If not, these values override those specified in WAVE_EXCLUDE_XXX." |
| #define | XSH_MOLECFIT_PARAMETER_PIXEL_RANGE_EXCLUDE_DESC "Comma separated list of values that define the boundaries of the pixel regions to exclude in the fit (low_1, upper_1, low_2, upper_2,...,low_n, upper_n), in pixel units. If set to 'NULL' the values specified in the fits table given by the tag PIXEL_EXCLUDE_XXX will be used, where XXX is UVB, VIS or NIR. If not, these values override those specified in PIXEL_EXCLUDE_XXX." |
| #define | XSH_MF_PARAMETERS_COLUMN_LAMBDA_DESC "Name of the column in the input that identifies the wavelength. Note: this parameter is relevant only for inputs in binary table format." |
| #define | XSH_MF_PARAMETERS_COLUMN_FLUX_DESC "Name of the column in the input that identifies the flux. Note: this parameter is relevant only for inputs in binary table format." |
| #define | XSH_MF_PARAMETERS_COLUMN_DFLUX_DESC "Name of the column in the input that identifies the flux error. Note: this parameter is relevant only for inputs in binary table format." |
| #define | XSH_MF_PARAMETERS_DEFAULT_ERROR_DESC "Default error relative to mean for the case that the error column is not provided." |
| #define | XSH_MF_PARAMETERS_FTOL_DESC "Relative chi2 convergence criterion." |
| #define | XSH_MF_PARAMETERS_XTOL_DESC "Relative parameter convergence criterion." |
| #define | XSH_MF_PARAMETERS_FIT_CONTINUUM_DESC "Comma delimited string of flags (1=true, 0=false) for fitting the continuum in specific regions. The number of values must match the number of wavelength ranges to fit. If one single value is given, then it is assumed to be valid for all the wavelength ranges. If set to 'NULL', then the values are taken from the column CONT_POLY_ORDER of the input table WAVE_INCLUDE. If this file is not given, then the default is used." |
| #define | XSH_MF_PARAMETERS_CONTINUUM_N_DESC "Polynomial order for the continuum model fit to each wavelength region, presented as a comma delimited string. If a single value is given, then it is assumed to be valid for all the wavelength ranges. If set to 'NULL', then the values are taken from the column CONT_POLY_ORDER of the input table WAVE_INCLUDE. If this file is not given, then the default is used." |
| #define | XSH_MF_PARAMETERS_FIT_WLC_DESC "A list of flags (1 or 0) that specifies which ranges are to be included as a part of the wavelength correction fitting if wavelength fitting has been selected. If a single value is given, then it is assumed to be valid for all the wavelength ranges." |
| #define | XSH_MF_PARAMETERS_WLC_N_DESC "Degree of the polynomial used to refine the wavelength solution." |
| #define | XSH_MF_PARAMETERS_WLC_CONST_DESC "Initial term for refinement of the wavelength solution." |
| #define | XSH_MF_PARAMETERS_FIT_RES_BOX_DESC "Flag that specifies if the instrumental line spread function is fitted by a Boxcar function." |
| #define | XSH_MF_PARAMETERS_RES_BOX_DESC "Initial value in pixels of the Boxcar function width that fits the instrumental line spread function (only used if --FIT_RES_BOX=TRUE)." |
| #define | XSH_MF_PARAMETERS_FIT_GAUSS_DESC "Flag that specifies if the instrumental line spread function is fitted by a Gaussian function." |
| #define | XSH_MF_PARAMETERS_RES_GAUSS_DESC "Inital value in pixels of the FWHM of the Gaussian function that fits the instrumental line spread function (only used if --FIT_RES_GAUSS=TRUE)." |
| #define | XSH_MF_PARAMETERS_FIT_LORENTZ_DESC "Flag that specifies if the instrumental line spread function is fitted by a Lorentzian function." |
| #define | XSH_MF_PARAMETERS_RES_LORENTZ_DESC "Initial value in pixels of the FWHM of the Lorentz function that fits the instrumental line spread function (only used if --FIT_RES_LORENTZ=TRUE)." |
| #define | XSH_MF_PARAMETERS_KERN_MODE_DESC "Flag that indicates whether to use a Voigt approximation instead of the Lorentz or Gauss functions to fit the instrumental line spread function." |
| #define | XSH_MF_PARAMETERS_KERN_FAC_DESC "Size of the Gaussian/Lorentzian/Voigtian kernel, expressed in units of FWHM." |
| #define | XSH_MF_PARAMETERS_VAR_KERN_DESC "Flag indicating if the kernel is constant or varies linearly with wavelength (i.e. resolving power is constant)." |
| #define | XSH_MOLECFIT_PARAMETER_USE_INPUT_KERNEL_DESC "If TRUE, use the kernel library if it is provided." |
| #define | XSH_MF_PARAMETERS_FIT_TELESCOPE_BACK_DESC "Flag that indicates whether the telescope background should be fitted." |
| #define | XSH_MF_PARAMETERS_TELESCOPE_BACK_CONST_DESC "Initial value for the telescope background fit." |
| #define | XSH_MF_PARAMETERS_PWV_DESC "Value in mm of the precipitable water vapour for the input water vapor profile. If set to a positive value, then the merged profile composed of ref_atm, GDAS, and local meteorological data will scaled to this value. If negative, then no scaling is done." |
| #define | XSH_MF_PARAMETERS_SLIT_WIDTH_DESC "Slit width in arcsec (taken from FITS header if present)." |
| #define | XSH_MF_LNFL_LINE_DB_DESC "AER version in format aer_v_X.X. For example aer_v_3.8 or aer_v_3.6." |
Functions | |
| cpl_error_code | xsh_molecfit_model_config (cpl_frameset *frameset, const cpl_parameterlist *parlist, cpl_parameterlist *ilist, cpl_parameterlist *iframelist) |
| cpl_error_code | xsh_molecfit_model_spec_header_calcs (const char *fname, const char *arm, cpl_parameterlist *ilist) |
| cpl_error_code | xsh_molecfit_model_spec_data_calcs (mf_wrap_fits *data, const char *is_idp, cpl_parameterlist *ilist, mf_wrap_model_parameter *parameters) |
| cpl_error_code | xsh_molecfit_setup_frameset (cpl_frameset *frameset, cpl_parameterlist *list, const char *arm, const char *input_name) |
| void | xsh_molecfit_model_qc (cpl_propertylist *pl, cpl_table *tab) |
| #define XSH_MF_LNFL_LINE_DB_DESC "AER version in format aer_v_X.X. For example aer_v_3.8 or aer_v_3.6." |
Definition at line 157 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_COLUMN_DFLUX_DESC "Name of the column in the input that identifies the flux error. Note: this parameter is relevant only for inputs in binary table format." |
Definition at line 86 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_COLUMN_FLUX_DESC "Name of the column in the input that identifies the flux. Note: this parameter is relevant only for inputs in binary table format." |
Definition at line 83 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_COLUMN_LAMBDA_DESC "Name of the column in the input that identifies the wavelength. Note: this parameter is relevant only for inputs in binary table format." |
Definition at line 80 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_CONTINUUM_N_DESC "Polynomial order for the continuum model fit to each wavelength region, presented as a comma delimited string. If a single value is given, then it is assumed to be valid for all the wavelength ranges. If set to 'NULL', then the values are taken from the column CONT_POLY_ORDER of the input table WAVE_INCLUDE. If this file is not given, then the default is used." |
Definition at line 101 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_DEFAULT_ERROR_DESC "Default error relative to mean for the case that the error column is not provided." |
Definition at line 89 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_FIT_CONTINUUM_DESC "Comma delimited string of flags (1=true, 0=false) for fitting the continuum in specific regions. The number of values must match the number of wavelength ranges to fit. If one single value is given, then it is assumed to be valid for all the wavelength ranges. If set to 'NULL', then the values are taken from the column CONT_POLY_ORDER of the input table WAVE_INCLUDE. If this file is not given, then the default is used." |
Definition at line 98 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_FIT_GAUSS_DESC "Flag that specifies if the instrumental line spread function is fitted by a Gaussian function." |
Definition at line 119 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_FIT_LORENTZ_DESC "Flag that specifies if the instrumental line spread function is fitted by a Lorentzian function." |
Definition at line 125 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_FIT_RES_BOX_DESC "Flag that specifies if the instrumental line spread function is fitted by a Boxcar function." |
Definition at line 113 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_FIT_TELESCOPE_BACK_DESC "Flag that indicates whether the telescope background should be fitted." |
Definition at line 143 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_FIT_WLC_DESC "A list of flags (1 or 0) that specifies which ranges are to be included as a part of the wavelength correction fitting if wavelength fitting has been selected. If a single value is given, then it is assumed to be valid for all the wavelength ranges." |
Definition at line 104 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_FTOL_DESC "Relative chi2 convergence criterion." |
Definition at line 92 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_KERN_FAC_DESC "Size of the Gaussian/Lorentzian/Voigtian kernel, expressed in units of FWHM." |
Definition at line 134 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_KERN_MODE_DESC "Flag that indicates whether to use a Voigt approximation instead of the Lorentz or Gauss functions to fit the instrumental line spread function." |
Definition at line 131 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_PWV_DESC "Value in mm of the precipitable water vapour for the input water vapor profile. If set to a positive value, then the merged profile composed of ref_atm, GDAS, and local meteorological data will scaled to this value. If negative, then no scaling is done." |
Definition at line 149 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_RES_BOX_DESC "Initial value in pixels of the Boxcar function width that fits the instrumental line spread function (only used if --FIT_RES_BOX=TRUE)." |
Definition at line 116 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_RES_GAUSS_DESC "Inital value in pixels of the FWHM of the Gaussian function that fits the instrumental line spread function (only used if --FIT_RES_GAUSS=TRUE)." |
Definition at line 122 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_RES_LORENTZ_DESC "Initial value in pixels of the FWHM of the Lorentz function that fits the instrumental line spread function (only used if --FIT_RES_LORENTZ=TRUE)." |
Definition at line 128 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_SLIT_WIDTH_DESC "Slit width in arcsec (taken from FITS header if present)." |
Definition at line 152 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_TELESCOPE_BACK_CONST_DESC "Initial value for the telescope background fit." |
Definition at line 146 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_VAR_KERN_DESC "Flag indicating if the kernel is constant or varies linearly with wavelength (i.e. resolving power is constant)." |
Definition at line 137 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_WLC_CONST_DESC "Initial term for refinement of the wavelength solution." |
Definition at line 110 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_WLC_N_DESC "Degree of the polynomial used to refine the wavelength solution." |
Definition at line 107 of file xsh_molecfit_model.h.
| #define XSH_MF_PARAMETERS_XTOL_DESC "Relative parameter convergence criterion." |
Definition at line 95 of file xsh_molecfit_model.h.
| #define XSH_MOLECFIT_PARAMETER_FIT_DESC "List of flags (1 and 0), comma separated, that specifies if a molecule has to be fitted (flag=1) or computed (flag=0). If set to 'NULL', the values provided in MOLECULES_XXX will be used, where XXX is UVB, VIS or NIR. If not, the provided list overrides what is specified in the MOLECULES_XXX input. Note: in order to override MOLECULES_XXX, the following recipe parameters rel_col, fit_molec, and list_molec must be all specified and different from 'NULL'." |
Definition at line 65 of file xsh_molecfit_model.h.
| #define XSH_MOLECFIT_PARAMETER_LIST_DESC "List of molecules to include in the fit (comma separated). If set to 'NULL', the values provided in MOLECULES_XXX will be used, where XXX is UVB, VIS or NIR. If not, the provided list overrides what is specified in the MOLECULES_XXX input. Note: in order to override MOLECULES_XXX, the recipe parameters REL_COL, FIT_MOLEC, and LIST_MOLEC must be all specified and different from 'NULL'." |
Definition at line 62 of file xsh_molecfit_model.h.
| #define XSH_MOLECFIT_PARAMETER_PIXEL_RANGE_EXCLUDE_DESC "Comma separated list of values that define the boundaries of the pixel regions to exclude in the fit (low_1, upper_1, low_2, upper_2,...,low_n, upper_n), in pixel units. If set to 'NULL' the values specified in the fits table given by the tag PIXEL_EXCLUDE_XXX will be used, where XXX is UVB, VIS or NIR. If not, these values override those specified in PIXEL_EXCLUDE_XXX." |
Definition at line 77 of file xsh_molecfit_model.h.
| #define XSH_MOLECFIT_PARAMETER_RELATIVE_VALUE_DESC "List of relative column densities of the molecules used (comma separated). If set to 'NULL', the values provided in MOLECULES_XXX will be used, where XXX is UVB, VIS or NIR. If not, the provided list overrides what is specified in the MOLECULES_XXX input. Note: in order to override MOLECULES_XXX, the following recipe parameters rel_col, fit_molec, and list_molec must be all specified and different from 'NULL'." |
Definition at line 68 of file xsh_molecfit_model.h.
| #define XSH_MOLECFIT_PARAMETER_USE_INPUT_KERNEL_DESC "If TRUE, use the kernel library if it is provided." |
Definition at line 140 of file xsh_molecfit_model.h.
| #define XSH_MOLECFIT_PARAMETER_WAVE_RANGE_EXCLUDE_DESC "Comma separated list of values that define the boundaries of the wavelength regions to exclude in the fit (low_1, upper_1, low_2, upper_2,...,low_n, upper_n), in microns. If set to 'NULL' the values specified in the fits table given by the tag WAVE_EXCLUDE_XXX will be used, where XXX is UVB, VIS or NIR. If not, these values override those specified in WAVE_EXCLUDE_XXX." |
Definition at line 74 of file xsh_molecfit_model.h.
| #define XSH_MOLECFIT_PARAMETER_WAVE_RANGE_INCLUDE_DESC "Comma separated list of values that define the boundaries of the wavelength regions to fit (low_1, upper_1, low_2, upper_2,...,low_n, upper_n), in microns. If set to 'NULL' the values specified in the fits table given by the tag WAVE_INCLUDE_XXX will be used, where XXX is UVB, VIS or NIR. If not, these values override those specified in WAVE_INCLUDE_XXX." |
Definition at line 71 of file xsh_molecfit_model.h.
| #define XSHOOTER_INPUT_DATA_FLUX_COLUMN "Flux" |
Includes Typedefs: Enumeration types Defines
Definition at line 57 of file xsh_molecfit_model.h.
1.9.6