Imfit

Help on imfit task:

Fit one or more elliptical Gaussian components on an image region(s)
PARAMETER SUMMARY
imagename        Name of the input image
box              One or more box regions to use for fitting,
                 eg "100, 120, 200, 220, 300, 300, 400, 400"
                 to use two boxes. If both box and region
                 parameters are specified, box is used.
region           Region name or region specified using rg tool.
                 A region from another image can be specified using the
                 imagename:regionname syntax, eg "mycontinuumimage:mysourceregion"
chan             Spectral channel on which to perform fit (only one may be specified).
stokes           Stokes parameter to fit.
mask             Mask to be applied to the image. Can be a mask associated with the
                 image or an LEL expression. 
includepix       Range of pixel values to include for fitting. Array of two numeric
                 values assumed to have same units as image pixel values. Only one
                 of includepix or excludepix can be specified.
excludepix       Range of pixel values to exclude for fitting. Array of two numeric
                 values assumed to have same units as image pixel values. Only one
                 of includepix or excludepix can be specified.
residual         Name of the residual image to write.
model            Name of the model image to write.
estimates        Name of file containing initial estimates of component parameters
                 (see below for formatting details).
logfile          Name of file to write fit results.
append           If logfile exists, append to it (True) or overwrite it (False).
newestimates     File to write fit results which can be used as initial estimates
                 for next run.

OVERVIEW

Imfit is used to fit one or more gaussians to sources in an image.
Fitting is limited to a single spectral channel and a single polarization.
If the image has a clean beam, the task will report both the convolved
and the deconvolved fit results.

The task returns a dictionary with two keys, 'converged' and 'results'.
The value of 'converged' is a boolean which indicates if the fit converged.
The value of 'results' is a component list reflecting the fit results. In the
case of a clean image, the results are the convolved results.

The region can either be specified by a box (blc,trc) or a region (if both
are given, the box is used). Ranges of pixel values can be included or
excluded from the fit.
If specified, the task will write the residual and/or model images for
successful fits.

If an estimates file is not specified, the task will attempt to estimate
initial parameters and fit a single Gaussian. If a multiple Gaussian fit
is desired, the user must specify initial estimates via a text file
(see below for details).

The user has the option of writing the result of the fit to a log file,
and has the option of either appending to or overwriting an existing file.

The user has the option of writing the (convolved) parameters of a successful
fit to a file which can be fed back to imfit as the estimates file for a
subsequent run.

MASK SPECIFICATION

Mask specification can be done using an LEL expression. For example

mask = '"myimage">5' will use only pixels with values greater than 5.

INCLUDING AND EXCLUDING PIXELS

Pixels can be included or excluded from the fit based on their values
using these parameters. Note that specifying both is not permitted and
will cause an error. If specified, both take an array of two numeric
values.

ESTIMATES

Initial estimates of fit parameters may be specified via an estimates
text file. Each line of this file should contain a set of parameters for
a single gaussian. Optionally, some of these parameters can be fixed during
the fit. The format of each line is

peak intensity, peak x-pixel value, peak y-pixel value, major axis, minor axis, position angle, fixed

The fixed parameter is optional. The peak intensity is assumed to be in the
same units as the image pixel values (eg Jy/beam). The peak coordinates are specified
by pixel values. The major and minor axes and the position angle are the convolved
parameters if the image has been convolved with a clean beam and are specified as quantities.
The fixed parameter is optional and is a string. It may contain any combination of the
following characters 'f' (peak intensity), 'x' (peak x position), 'y' (peak y position),
'a' (major axis), 'b' (minor axis), 'p' (position angle).

In addition, lines in the file starting with a "#" are considered comments.

An example of such a file is:

# peak intensity must be in map units
120, 150, 110, 23.5arcsec, 18.9arcsec, 120deg  
90, 60, 200, 46arcsec, 23arcsec, 140deg, fxp

This is a file which specifies that two gaussians are to be simultaneously fit,
and for the second gaussian the specified peak intensity, x position, and position angle
are to be held fixed during the fit.

EXAMPLE: 

Here is how one might fit two gaussians to multiple channels of a cube using the fit
from the previous channel as the initial estimate for the next. It also illustrates
how one can specify a region in the associated continuum image as the region to use
as the fit for the channel.

imagename = "co_cube.im"
# specify region using region from continuum
region = "continuum.im:source.rgn"
chan = 2
# only use pixels with positive values in the fit
excludepix = [-1e10,0]
# estimates file contains initial parameters for two Gaussians in channel 2
estimates = "initial_estimates.txt"
logfile = "co_fit.log"
# append results to the log file for all the channels
append = "True"
# write file to use as estimates for next channel
newestimates = "estimates3.txt"
imfit
# now loop through channels
for x in range(3,20):
    chan = x
    # feed initial estimates using results of last fit
    estimates = "estimates" + str(x) + ".txt"
    newestimates = "estimates" + str(x + 1) + ".txt"
    imfit