Configuration File Format

The imfit, imfit-mcmc, and makeimage programs always require a configuration file (“config file” for short): a text file which describes the model to be fit to or compared with the data (in the case of imfit or imfit-mcmc) or to be generated (in the case of makeimage), plus some optional information about the image itself.

Note that you can use the --sample-config command-line option with imfit or makeimage to have an example of a config file saved to the current directory; this can then be edited to taste and used with the appropriate program.

This page provides a basic description of the configuration file format.

(In what follows, I generally use “imfit” to refer to both imfit and imfit-mcmc, unless otherwise noted.)

Blank lines and Comments

Any blank lines in the file are ignored. Any lines beginning with the hash/pound symbol “#” are also ignored.

Finally, if a hash symbol is found in the middle of a line, then it and the rest of the line are ignored. This allows comments to be added on the same line as a meaningful entry (function declaration, parameter name and value, etc.).

(Optional) Prelude: Describing the Image

The configuration file can start with a prelude which provides information about the data image (for imfit) or the output model image (in the case of makeimage). This is in the form of lines containing single “NAME value” pairs, e.g.

GAIN 4.5

These do not have to be provided, and you can provide as many or as few of these as are needed (the exception being the NCOLS and NROWS entries for a makeimage configuration file – both of those should be provided unless you know you will be supplying makimage with relevant info on the command line, via the --nrows and --ncols or --refimage options).

The allowed entries for an imfit configuration file are:

  • GAIN – the A/D gain value (electrons/count) for the image

  • READNOISE – any Gaussian read noise (electrons)

  • EXPTIME – total integration time if pixel values are counts/sec

  • NCOMBINED – number of images combined if pixel values are mean or median

  • ORIGINAL_SKY – any original constant value (e.g., sky background) which has already been subtracted from the image

The allowed entries for a makeimage configuration file are:

  • NCOLS – integer defining the width (number of columns) of the output image

  • NROWS – integer defining the height (number of rows) of the output image

All of this information can also be provided via command-line options, which if present will override any corresponding values in the configuration file.

Main Section: Defining the Model

The main (and required) section of the configuration file is the part which describes the actual model to be fit (or generated and saved in the case of makeimage). This consists of one or more function blocks.

Function Blocks

A function block is a central-coordinate (x0,y0) specification followed by one or more image-function declarations. This specifies a set of image functions which share the same center.

X0  <initial_value>   [<limits>]
Y0  <initial_value>   [<limits>]
FUNCTION <function_name>
<parameter specifications ...>

The optional limit specifications for X0 and Y0, which are only used by imfit, can have one of two forms:

  1. The word “fixed”, which indicates that the parameter should be held fixed. E.g.

    X0  101.5   fixed
    
  2. A comma-separated pair of numbers specifying lower and upper limits, e.g.

    X0  101.5    98.0,103.5
    

Image-Function Declarations

An image-function declaration consists of the word “FUNCTION” followed by the name of one of Imfit’s image functions. (Recall that you can use --list-functions to get a list of the available image functions and --list-parameters to get that list along with the parameter list for each function.) This is followed by the list of parameter values; these are the values for generating a model image with makeimage, or the initial values for the fitting process in imfit.

FUNCTION <function_name>
<parameter_name1>    <initial_value>   [<limits>]
<parameter_name2>    <initial_value>   [<limits>]
[etc.]

A simple example:

FUNCTION Exponential
PA    90
ell   0.5
I_0   100
h     15

The optional limit specifications for the parameters are exactly like those for the X0 and Y0 values (see above):

  1. The word “fixed”, which indicates that the parameter should be held fixed; or

  2. A comma-separated pair of numbers specifying lower and upper limits.

Note that parameter-limit specifications are actually required by imfit-mcmc. They are also required when using imfit’s Differential Evolution solver; they are optional for the other solvers (including the default Levenberg-Marquardt solver). Limit specifications are ignored by makeimage.

Examples

Single-function image

This is based on configuration file in the examples/ subdirectory, where it is meant to be used to fit a single Sersic function to a 256 by 256-pixel cutout of an SDSS image. If used with makeimage, it generates a 2D Sersic-function image using the specified parameters. This example does not contain gain or read-noise specifications. Lower and upper limits are listed for all parameters for use with imfit.

X0   129.0    125,135
Y0   129.0    125,135
FUNCTION Sersic
PA    18.0    0,90
ell    0.2    0,1
n      1.5    0,5
I_e    15     0,500
r_e    25     0,100

Single function block with two functions

This is a modification of the previous configuration file, using an Exponential function along with the Sersic function. In addition, the Sersic index n is held fixed with a value of 4 (making the Sersic profile a de Vaucouleurs profile). Both functions share the same center, and are thus part of a single function block. This version also includes an image-description prelude.

GAIN          4.725
READNOISE     4.3
ORIGINAL_SKY  130.14

X0   129.0    125,135
Y0   129.0    125,135
FUNCTION Sersic
PA    18.0    0,90
ell    0.2    0,1
n      4      fixed
I_e    15     0,500
r_e    25     0,100
FUNCTION Exponential
PA    18.0    0,90
ell   0.5     0,0.8
I_0   100     1,500
h     50      5,500

Multiple function blocks

Multiple function blocks can be included in a configuration file; these indicate different sets of image functions which share common centers (i.e, x0,y0 locations on the image).

A simple example, modifying the previous example by including a Sersic function representing a neighboring galaxy located approximately 110 pixels away in the X direction and 45 pixels away in Y:

GAIN          4.725
READNOISE     4.3
ORIGINAL_SKY  130.14

X0   129.0    125,135
Y0   129.0    125,135
FUNCTION Sersic
PA    18.0    0,90
ell    0.2    0,1
n      4      fixed
I_e    15     0,500
r_e    25     0,100
FUNCTION Exponential
PA    18.0    0,90
ell   0.5     0,0.8
I_0   100     1,500
h     50      5,500

X0   240.0    235,245
Y0   183.0    180,186
FUNCTION Sersic
PA    -40.0    -10,-60
ell    0.5    0,1
n      1      0.5,2.0
I_e    5     0,520
r_e    10     0,20

Using Imfit Output Files with Makeimage

When imfit successfully fits a model to an image, it saves the best-fitting parameters to an output file (by default this file is called bestfit_parameters_imfit.dat). This file has the same basic format as a config file, and can in fact be used as a config file by makeimage (though it will be missing the NCOLS and NROWS parameters, so you will have to add those to the file or else specify them with command-line options).

An imfit best-fit output file can even be used as input to another invocation of imfit itself, though it will lack any prelude parameters describing the data image (GAIN, etc.) and any parameter limits or “fixed” specifications.

Quick and Dirty Generation of Config Files

As noted above, you can always generate a bare-bones sample config file using the --sample-config command-line option.

Calling imfit or makeimage with the --list-parameters option will print a list of all the functions and their parameters. You can copy and paste the relevant parts of this output into a config file to make function entries (aside from needing to fill in the initial values and possible limits, of course!).