Loving ISIS - Confessions of a Former XSPEC User


Functions in My .isisrc Files

Below I printout the brief descriptions found at that top of each of my .isisrc files. The order roughly follows that of the example analysis discussed on these web pages. Once my .isisrc files are loaded, most functions will return a brief usage message if they are called without any arguments. (One of these days I will get around to writing real help files for these.)

No guarantees that any of these are particularly intelligently programmed. (In fact, I can guarantee that some most assuredly are not.) But again, they get the job done well-enough.

Loading Data (.isisrc_data)

% list_all      : List all the data, arfs, and rmfs
% read_radio    : Read radio data from an ascii file, load to struct.
% load_radio    : Take the structure above, and load it into data
% read_optical  : Read (optical) data from file where the units are A_lo,
%                 A_hi, mJy, Delta mJy
% clear_all     : Wipe out all data, arfs, and rmfs
% load_data_integral: load INTEGRAL data
% fits_write_pha: Write out a fits pha file; stolen from Manfred Hanke

Errors Bars & Custom Statistics (.isisrc_conf)

% sep_grid           : Set the eval method to SEPARATE_GRID
% mrg_grid           : Set the eval method to MERGED_GRID
% usr_grid           : Set up logarithmically spaced USER_GRIDs
% fstat_mod          : Set the fit statistic to sigma=model
% fstat_gehr         : Set the fit statistic to sigma=gehrels
% fstat_norm         : Set the fit statistic to sigma=data
% lmdif              : Set the fit method to lmdif
% mpfit              : Set the fit method to mpfit
% minim              : Set the fit method to minim
% subplex            : Set the fit method to subplex
% marq               : Set the fit method to marquardt
% conf_map_fail_hook : Switch between subplex/lmdif when doing
%                      error contours, and the fit fails
% conf_map           : Call conf_map_counts with conf_map_fail_hook
% corback            : Set the data background to have a fittable
%                      normalization, using the back_fun utility
% fcorback_fit       : The fit function used by corback
% corfile            : In addition to the data background, set another
%                      background subtracted file as a background with
%                      fittable normalization
% fcorfile_fit       : The fit function used by corfile
% bayes_nconf        : Bayesian estimate of lower/upper counts bound
%                      given observed counts & significance
% bayes_sconf        : Bayesian estimate of lower/upper significance bound
%                      given observed counts & desired lower/upper bounds

Custom Fit Functions (.isisrc_fitfun)

% simple_gpile_fit : Gratings Pileup correction function
%                    (New, better version than in "ABC Guide to Pileup")

% Manfred Hanke's even better simple_gpile + associated functions

% simple_gpile2_fit
% use_simple_gpile
% get_unpiled_fit_fun
% get_unpiled_data_flux

% The following work presuming data x-axis follows keV (i.e., Hz -> keV
% for PSD):

% mgauss_fit     : Gaussian absorption that's never < 0 (multiplicative)
% qpo_fit        : Lorentzian, normalized to QPO rms (counts/bin)
% zfc_fit        : Zero-frequency centered Lorentzian (counts/bin)
% plaw_fit       : Counts/bin power-law
% bkn_plaw_fit   : Counts/bin broken power-law
% dbkn_plaw_fit  : Counts/bin doubly broken power-law
% rms_gauss_fit  : Counts/bin Guassian, normalized to RMS.
% sinwave_fit    : Counts/bin sine wave
% four_chip_fit  : Renorm for specific ACIS chips
% three_chip_fit : Renorm for specific ACIS chips
% chip()         : Combining the above two

% The following work presuming x-axis follows Angstrom:

% aqpo_fit       : Lorentzian, normalized to QPO rms (counts/bin)
% azfc_fit       : Zero-frequency centered Lorentzian (counts/bin)
% aplaw_fit      : Counts/bin power-law
% abkn_plaw_fit  : Counts/bin broken power-law
% adbkn_plaw_fit : Counts/bin doubly broken power-law
% asinwave_fit   : Counts/bin sine wave
% asqrwave_fit   : Counts/bin square wave
Note: A number of the above fit functions were designed for use in timing analysis with ISIS. Normally, ISIS and XSPEC functions calculate a fit function as a bin integral quantity. For timing analysis, I effectively define the average power spectrum in terms of counts per bin, and want to compute models as bin averaged. Hence the models above. (I also find a number of these models, especially the Lorentzian in qpo_fit();, to be more stable when the integral over the bin is done analytically, rather than numerically.) Note also that ISIS has intrinsic fit functions, bin_width and bin_width_en that can be combined with XSPEC fit functions to similar effect.

Flux Calculation Functions (.isisrc_flux)

% eqw         : Calculate a line equivalent width in mA and eV
% data_flux   : Calculate the flux between two bounds, based upon the
%               observed data (does not extend beyond data grid)
% model_flux  : Calculate the flux between two bounds, based upon the
%               fitted model (does not extend beyond model grid)
% calc_flux   : Calculate the flux based upon the fitted model, using
%               an arbitrary grid (full grid must be input)
% flux_err    : Monte Carlo estimate of model flux errors (probably
%               wrong in practice in most cases)

Plotting Functions (.isisrc_plots)

% pg_info          : Writes out useful info about plotting choices.
% pg_color         : Make a few nice colors for pgplot
% sov              : An abbreviation of set_outer_viewport
% apj_size         : An autoset of resize/set_outer_viewport that works
%                    well for a "typical" ApJ one column plot.
% keynote_size     : An autoset of resize/set_outer_viewport that works
%                    well for a "typical" keynote presentation.
% open_print       : A version of open_plot that invokes pg_color first
% close_print      : A version of close_plot that will then display the
%                    hardcopy via a chosen system utility (e.g., gv)
% set_plot_widths  : Routine to set all the plot line thicknesses
% nice_width       : An autoset of plot widths that works well for
%                    papers and presentations (especially on Macs)
% set_plot_labels  : Resets all plot labels to their defaults, and can
%                    be used to change the default font.
% new_plot_labels  : Change the plot labels for all plot styles.
% add_plot_unit    : Create new X-/Y-unit combinations for the plots
% fancy_plot_unit  : My variation on ISIS's plot_unit.  Same choices as
%                    in ISIS, but this saves variables (x_unit, y_unit)
%                    that will be used below.
% data_list        : List version of all_data
% write_plot       : Write the data from the plot functions to ASCII
%                    files
% plot_counts      : Plot background subtracted data as counts/bin,
%                    with choices of three kinds of residuals, or none
%                    at all. (cstat overides defaults)
% plot_data        : Main plotting routine, to plot background sub-
%                    tracted data in detector counts space.  Counts
%                    per second per x_unit, with choices of three
%                    kinds of residuals, or none at all.
% plot_residuals   : A plot of just the data residuals
% plot_fit_model   : An hplot of just the background subtracted model.
% plot_unfold      : A plot of the unfolded spectra, or powers of
%                    energy/freq./wavelength times unfolded spectra.
% plotxy           : Simple x-y (o)plots with error bars.
% plot_comps       : Plot individual components of a model
% plot_double      : Use two fancy plot functions at once, while also
%                    plotting individual components of a model

To actually download the .isisrc files, look here.

Next up: ISIS Power Tools.

This page was last updated Oct 7, 2013 by Michael Nowak. To comment on it or the material presented here, send email to mnowak@space.mit.edu.
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