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PAGE UNDER CONSTRUCTION --- AND WORK IN DEVELOPMENT
Defining graphical output
After a run of CosmoSIS, the postprocessor may be called with an input file, which provides options to the postprocess application and stipulates the plots which should be produced of the CosmoSIS results. This page describes the parameter file.
Overview
Like the other CosmoSIS input files, the parameter file is in the ini format. It consists of sections, marked by [square brackets], and parameters set in the form name = value within each section. The spaces around the "=" are optional.
Comments are marked by semi-colons.
Example
Here's an example parameter file from demo 1, with some of the comments removed, just to show the structure:
#!ini [DEFAULT] inifile = demos/demo1.ini [MCMC] burn = thin = weights = [General] outdir = plots prefix = demo1 more-latex = no-latex = blind-add = blind-mul = pdb = [Inputs] text = derive = [Plotting] legend = legend-loc = swap = only = either = no-plots = no-2d = no-alpha = file-type = no-smooth = n-kde = factor-kde = no-fill = extra = tweaks = no-image = run-max-post =
We now go through each of these sections in turn to see what they contain.
The [DEFAULT] section
This section defines the one piece of information postprocess has to have to run: the location of the output from CosmoSIS.
#!ini [DEFAULT] inifile = demos/demo1.ini
| Parameter | Meaning |
|---|---|
| inifile | This should be the path either to the .ini file which was used to drive cosmosis, a single output file produced by CosmoSIS, or a directory into which CosmoSIS wrote many output files. |
The [MCMC] section
This section provides options for MCMC-type samplers, where some kind of semi-random walk takes place through the parameter space to find the optimal parameter set. It is seldom meaningful to look at every single point sampled; more often we want to get an overall idea of how the method is converging to the solution in the final stages of the search.
#!ini [MCMC] burn = 100 thin = 10 weights =
| Parameter | Meaning |
|---|---|
| burn | If this is a value less than one, it is the fraction of data points to ignore at the start of the parameter search. If greater than one, it gives the number of points to ignore directly. |
| thin | This says to keep only every Nth sample point. |
| weights | This gives the name of a column in the output file which indicates the weight of the sample point.. |
The [General] section
This section provides general, high-level options.
#!ini [General] outdir = plots prefix = demo1 more-latex = no-latex = blind-add = blind-mul = pdb =
| Parameter | Meaning |
|---|---|
| outdir | The directory to which postprocess should output all of its files. |
| prefix | A string which is prepended to all the output files. If this option is used, an extra _ will be placed between the prefix and the rest of the file name. |
| more-latex | Specify an additional latex file to be loaded. |
| no-latex | Take all label specifications to be verbatim text. |
| blind-add | Blind results by adding a secret value to each parameter. |
| blind-mul | Further blind the results by applying a secret muliplier to each parameter. |
| pdb | Run the Python debugger if any failures occur during the running of postprocess. |
The [Inputs] section
This section provides options to inform of the nature of the inputs to the postprocess application.
#!ini [Inputs] text = derive =
| Parameter | Meaning |
|---|---|
| text | Force the input inifile to be read as a text file, regardless of file-name extension. |
| derive | Read a Python script which will generate more columns which can be plotted. |
The [MCMC] section
This section provides options for MCMC-type samplers, where some kind of semi-random walk takes place through the parameter space to find the optimal parameter set. It is seldom meaningful to look at every single point sampled; more often we want to get an overall idea of how the method is converging to the solution in the final stages of the search.
#!ini [Plotting] legend = legend-loc = swap = only = either = no-plots = no-2d = no-alpha = file-type = no-smooth = n-kde = factor-kde = no-fill = extra = tweaks = no-image = run-max-post =
| Parameter | Meaning |
|---|---|
| legend | Add a legend to the plot with the specified titles, separated by the pipe symbol. |
| legend-loc | The location of the legend: best, UR, UL, LL, LR, R, CL, CR, LC, UC, C. |
| swap | Swap the ordering of the parameters in (x,y). |
| only | Only make 2D plots where both parameter names start with this. |
| either | Only make 2D plots where one of the parameter names starts with this. |
| no-plots | Do not make any default plots. |
| no-2d | Do not make any 2D plots. |
| no-alpha | No alpha effect - shaded contours will not be visible through other ones. |
| file-type | Filename suffix for plots. |
| no-smooth | Do not smooth grid plot joint constraints. |
| n-kde | Number of KDE smoothing points per dimension to use for MCMC 2D curves. Reduce to speed up, but can make plots look worse. |
| factor-kde | Smoothing factor for MCMC plots. More makes plots look better but can smooth out too much. |
| no-fill | Do not fill in 2D constraint plots with color. |
| extra | Load extra post-processing steps from this file. |
| tweaks | Load plot tweaks from this file. |
| no-image | Do not plot the image in 2D grids; just show the contours. |
| run-max-post | Run the test sampler on maximum-posterior sample and save to the named directory. |
Updated