NAME specidentify -- identify features in grating spectrum USAGE specidentify [features_file] [line_list] [output_file] [doppler_shift_unit=] [source_doppler_shift=] [tolerance=] [source_temp_unit=] [source_temp=] [source_density=] [filter_string=] [clobber=] [debug=] DESCRIPTION This program uses the information from the fitted peaks file created by line_measure_features to try to correlate the list of observed lines with the database line list to produce the greatest number of matches within the allowed wavelength error tolerance. It compiles a list of the matched lines and ions; the matched list is also filtered using the user defined source temperature and the user defined source redshift. PARAMETERS features_file [filename] Input data file name; this file is the output of the line_measure_features tool. The file typically ends in .fit#; where .fit1 is the with on the data with continuum and the .fit2 is the fit on the data which has had the continuum subtracted. These ascii .fit# files contain the following columns: # # data file: marx_zoo2.dat # minimum amplitude: continuum level # peaks: 13 # model: gauss # fit region: +/- 2.0 * fwhm # amplitude range: +/- 100.0 % of initial guess # position range: +/- 100.0 % of initial guess # max fwhm: E * 1.0e-02 # # | BEST FIT RESULTS w/ CONTINUUM peak | ampl ampl_min ampl_max cont_ampl cont_slope cont_pos fwhm fwhm_min fwhm_max pos pos_min pos_max Comment lines begin with '#' and are ignored by the program. line_list = [filename] Ascii file containing the database of emission line wavelengths. The current format of this file is: id number in master list. element id = Fe, Si, S, etc. ion id = by roman numeral transition type = defined in e.g. Mewe and Gronenschild, 1981, A&A Supp., 45, 11. wavelength = Angstrom energy = keV list of line strength values at 40 temperatures. (log Kelvin) Example 2 lines, from the current list: Nr ion Transit. E\(eV\) Lambda\(A\) 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 4.9 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 6.8 6.9 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 7.9 8.0 1658 Fe IX A8B 6.327 1959.600 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 8.97 7.42 6.41 5.83 5.54 5.43 5.49 5.80 6.50 7.63 9.21 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 output_file = "." [filename] (root.out) Output file name. "." creates an output file name based on the input data file name, e.g., if features_file = "file.fit", then output_file = "file.out". (doppler_shift_unit = "redshift") [redshift|km/s] The units of source_doppler_shift. (source_doppler_shift = 0) The Doppler shift of the source. The value should be set according to the units set in the 'doppler_shift_unit' parameter. The Doppler shift is used to shift the wavelengths of the observed spectral peaks to the 'rest' wavelength; the rest wavelength is used to match the lines in the data base. The relativistic Doppler shift formula is used: delta_lam = lam_observed - lam_rest z = delta_lam/lam_rest = (sqrt((1+v/c)/(1-v/c))) - 1) C = 2.99792458E5 km/s (tolerance = 0) Maximum allowed fractional error in line position. For example, suppose the measured confidence limits on the line are (c1,c2) with the best position at "c" and suppose the line database lists confidence limits (d1,d2) on the line position with the tabulated position at "d". A line is accepted as a candidate identification if 1) (d1,d2) overlaps (c1,c2) OR 2) if abs(c-d) < tolerance * (c+d)/2 (temp_unit = "Kelvin") [Kelvin|keV] The units of source_temp. (source_temp = 1E4) [1E4 -> 1E8 Kelvins] [1E11 -> 1E15 keV] Estimated source temperature in units of temp_units. The temperature is used to filter the list of candidate identifications for spectral features. Only lines present in collisional ionization equilibrium at this temperature are retained in the identification list. (source_density = 0) [cm^-3] The ion number density. (Currently not being used as a filter parameter). (filter_string = "") [comma separated list] This is a list of elements and/or ions to include or exclude from the line identification search. Elements are specified by their 2 letter chemical symbol ("Fe", "Si"), ions are specified by the chemical symbol and ion charge ("Fe 0" is neutral iron, "Fe 25" is hydrogenic, "Fe 24" is He-like, etc.). If the filter string is empty or blank, all elements and ions in the database are included in the search. If specific elements and ions are listed, only those listed are included in the search. Specific elements or ions can be excluded from the search by prefixing the name with a tilde character ("~Fe" would excluded all iron ions from the search, "~Fe 17" would exclude only Fe XVIII). If inclusive and exclusive filtering is combined, all excluded elements/ions must appear before the inclusive names: if including all iron ions except Fe +15, the string should read "~Fe 15, Fe") EXAMPLE 1: include Mg 7 include Mg 14 exclude Fe 23 include all the rest of the ions of Fe filter_string = "Mg 7, Mg 14, ~Fe 23, Fe" EXAMPLE 2: exclude Mg exclude Si exclude Fe 23 filter_string = "~Mg, ~Si, ~Fe 23" includes all elements and ions in the line list, except Magnesium, Silicon and Fe +23. (clobber = no) [boolean = yes or no] Overwrite output_file if they exist. (display = 1) [0 = no debugging info, 5 = max debugging info] Controls the amount of output on your screen while specidentify is running. 0 means work silently. (mode = "ql") [string] Parameter interface mode. "ql" stands for "query and learn" which prompts you for input and updates "specidentify.par" with your responses. EXAMPLE Find all the matched lines and ions to the fitted peaks found in "marx_zoo.fit1". This file was generated by line_measure_features which fit gaussian peaks to the output from the line_detect_features program. >) pset specidentify Input data file with line features & stats (): marx_zoo.fit1 Database line list for identifications (): Spex_Lines.txt Output identified peaks file (): marx_zoo.out1 Source Doppler shift units (for below) (redshift|km/s) (redshift): Source redshift (0): Allowable tolerance in line position error (0): Source temperature units (for below) (Kelvin|keV) (Kelvin): Source temperature (Kelvins) (10000) (): 10000000 Source density (0): OK to overwrite existing output file? (no): yes Display level (0 = no display) (0:5) (0): mode (ql): > specidentify Input data file with line features & stats (marx_zoo.fit1): Database line list for identifications (Spex_Lines.txt): Output identified peaks file (marx_zoo.out1): > cat marx_zoo.out1 ---------------------------------------------------------------------- VALUE VALUE_MIN VALUE_MAX ----- --------- --------- Peak #1: CONT 53.922 : AMPL 160.454 153.703 167.100 : FWHM 2.862e-02 2.708e-02 3.016e-02 : POS_OBSERVED 6.180 6.180 6.181 : POS_REST 6.180 6.180 6.181 -------------------------------------------------------------- Matched lam_rest strength ID elem ion label ------- -------- -------- -- ---- --- ----- 6.180 3.631e-21 956 si xiv h1a 6.180 7.943e-19 943 si xiii hes4 6.180 1.122e-18 942 si xiii hes3 ---------------------------------------------------------------------- VALUE VALUE_MIN VALUE_MAX ----- --------- --------- Peak #2: CONT 82.996 : AMPL 241.998 67.515 242.000 : FWHM 4.778e-07 1.000e-09 1.042e-04 : POS_OBSERVED 7.099 7.099 7.199 : POS_REST 7.099 7.099 7.199 -------------------------------------------------------------- Matched lam_rest strength ID elem ion label ------- -------- -------- -- ---- --- ----- 7.176 1.023e-19 742 al xiii h1b 7.171 6.310e-20 741 al xiii h1a 7.171 2.042e-17 735 al xii hes4 7.171 2.951e-17 734 al xii hes3 7.169 1.820e-19 4891 fe xxiv li01017 7.169 6.918e-18 4636 fe xxiii li01017* 7.165 9.333e-20 4890 fe xxiv li01018 7.165 3.631e-18 4635 fe xxiii li01018* 7.110 4.365e-19 5385 ni xxvi li4 7.110 3.890e-18 5362 ni xxv li4* 7.100 3.631e-20 700 mg xii h2 7.100 1.479e-17 683 mg xi h2* ---------------------------------------------------------------------- VALUE VALUE_MIN VALUE_MAX ----- --------- --------- Peak #3: CONT 61.440 : AMPL 81.070 75.388 86.590 : FWHM 3.466e-02 3.194e-02 3.890e-02 : POS_OBSERVED 7.987 7.986 7.989 : POS_REST 7.987 7.986 7.989 -------------------------------------------------------------- Matched lam_rest strength ID elem ion label ------- -------- -------- -- ---- --- ----- 7.986 4.677e-20 4897 fe xxiv li01011 7.986 1.622e-18 4649 fe xxiii li01011* ---------------------------------------------------------------------- VALUE VALUE_MIN VALUE_MAX ----- --------- --------- Peak #5: CONT 65.878 : AMPL 134.038 126.552 141.553 : FWHM 2.486e-02 2.319e-02 2.658e-02 : POS_OBSERVED 8.420 8.419 8.421 : POS_REST 8.420 8.419 8.421 -------------------------------------------------------------- Matched lam_rest strength ID elem ion label ------- -------- -------- -- ---- --- ----- 8.420 3.631e-18 688 mg xi hes4 8.420 5.495e-18 687 mg xi hes3 ---------------------------------------------------------------------- VALUE VALUE_MIN VALUE_MAX ----- --------- --------- Peak #7: CONT 31.934 : AMPL 152.000 16.920 152.000 : FWHM 1.000e-09 1.000e-09 1.958e-03 : POS_OBSERVED 10.727 10.659 10.727 : POS_REST 10.727 10.659 10.727 -------------------------------------------------------------- Matched lam_rest strength ID elem ion label ------- -------- -------- -- ---- --- ----- 10.710 7.586e-17 4706 fe xxiii be59241 10.682 1.349e-16 4705 fe xxiii be15184 10.679 1.047e-16 4704 fe xxiii be59254 10.676 4.786e-17 4703 fe xxiii be01022 10.674 8.710e-17 4702 fe xxiii be55244 10.663 2.455e-20 4908 fe xxiv li01005 10.663 1.096e-18 4701 fe xxiii li01005* ---------------------------------------------------------------------- VALUE VALUE_MIN VALUE_MAX ----- --------- --------- Peak #10: CONT 14.233 : AMPL 85.114 80.921 89.316 : FWHM 2.667e-02 2.513e-02 2.826e-02 : POS_OBSERVED 11.178 11.177 11.178 : POS_REST 11.178 11.177 11.178 -------------------------------------------------------------- Matched lam_rest strength ID elem ion label ------- -------- -------- -- ---- --- ----- 11.178 1.023e-20 4910 fe xxiv li03008 11.177 4.677e-17 4739 fe xxiii be25184 ---------------------------------------------------------------------- VALUE VALUE_MIN VALUE_MAX ----- --------- --------- Peak #12: CONT 12.779 : AMPL 87.784 83.543 92.014 : FWHM 2.479e-02 2.323e-02 2.642e-02 : POS_OBSERVED 11.760 11.760 11.761 : POS_REST 11.760 11.760 11.761 -------------------------------------------------------------- Matched lam_rest strength ID elem ion label ------- -------- -------- -- ---- --- ----- 11.761 1.202e-19 4793 fe xxiii be05020 ---------------------------------------------------------------------- VALUE VALUE_MIN VALUE_MAX ----- --------- --------- Peak #13: CONT 14.550 : AMPL 41.474 36.364 46.607 : FWHM 1.000e-09 1.000e-09 1.632e-02 : POS_OBSERVED 12.138 12.138 12.138 : POS_REST 12.138 12.138 12.138 -------------------------------------------------------------- Matched lam_rest strength ID elem ion label ------- -------- -------- -- ---- --- ----- 12.138 9.120e-21 420 ne x h1b DATE 11/18/97