GAUSS-Interactive fit of Gaussians to emission or absorption lines

Description:

The GAUSS command will plot a spectrum on the current soft graphics device and allow interactive Gaussian fitting of upto ten Gaussians on a polynomial continuum.

Parameters:

TOL

The tolerance on the value of the optimised function required by the NAG routine E04JBF.

SPECTRUM

The name of the spectrum to be plotted and analysed. It should be a 1-dimensional array

FILE

Yes if results of the continuum and Gaussian fitting are to be written to a data file

FILNAM

The name for the data file to which results of the continuum and Gaussian fit are written

WHOLE

If set, the whole of the spectrum is plotted. Otherwise, the limits plotted are determined by the values of XSTART and XEND, which you will be prompted for if they were not specified in the command string.

AUTOSCALE

If set, the plot is scaled so that all of the data to be plotted just fits on the display. Otherwise, the scale of the plot is determined by the values of HIGH and LOW, which you will be prompted for if they were not specified in the command string.

XSTART

Specifies the first X value to be plotted, in the units used by the data - angstroms, for example, if the data is wavelength calibrated. XSTART can be set before the start of the data, if necessary. RESET will set XSTART to the first X value in the data.

XEND

Specifies the last X value to be plotted, in the units used by the data - angstroms, for example, if the data is wavelength calibrated. XEND can be set after the end of the data, if necessary. RESET will set XEND to the last X value in the data.

HIGH

The maximum data value to be plotted - i.e. the top Y axis value for the plot.

LOW

The minimum data value to be plotted - i.e. the bottom Y axis value for the plot.

BIAS

A bias value applied to the data, usually to bias up a plot which is to be superimposed upon a previous plot of almost identical data values. This makes the comparison easier. BIAS N is essentially equivalent to setting HIGH and LOW down by an amount N, so can result in unexpected axis values if it is not accompanied by AXES=NO.

LABEL

The label that will appear at the top of the plot and the results data file.

ORD

The order of the least squares polynomial fit to the continuum (maximum = 7).

SIG

The factor * the sigma on the last polynomial continuum fit such that a point with a deviation greater than SIG * sigma from the last fitted continuum will not be included in the next fit.

ERR

The factor * the error on a point such that a point with a deviation greater than ERR * error from the fitted continuum will not be included in the next fit.

ITN

The number of iterations for performing the polynomial fit to the continuum with rejection of points with large deviations from the fit (maximum = 10).

INDEX

The index number ( as listed ) of the Gaussian whose parameters are to be altered.

DELE

The index number ( as listed ) of the Gaussian which is to be deleted.

Pn_Hn_Wn_S

P followed by number -100 to 100 to alter position. ( 1 unit = line extent/100 ) H followed by number -100 to 100 to alter height. ( 1 unit = line height/100 ) W followed by number -100 to 100 to increase width. ( 1 unit = line extent/100 ) S to plot modified line and return to menu.

CONSTR

The fitted Gaussian parameters (peak position, peak height or line width) can be singly constrained or chained to vary together in groups.

SINCON

The fit parameters (peak position, peak height and width) of any of the Gaussian components can be constrained so as not to vary in the optimization process.

NPCON

The Gaussian number n can be constrained to the manually fitted value of peak position (P), height (H) or width (W). A value of -1 indicates the end of the single constraints.

MULTCON

Sets of Gaussians can have their fit parameters constrained so that the values are "chained" to vary together. The line seperations of Gaussians can be set; the ratio of their peak heights can be fixed and the ratio of their line widths can be fixed.

NCHAIN

NCHAIN is the number of Gaussians to chain together so that line seperation, height or width varies together. Must be less than or equal to the number of fitted Gaussians. A value of -1 indicates that there are no more chains to input.

CHAIN

Gaussian parameter to be chained: - P to keep Gaussian line seperations fixed; H to keep peak heights in specific ratio; W to keep Gaussian widths varying in ratio.

ICHAIN

ICHAIN is the index number of the Gaussian which is to be chained.

RCHAIN

RCHAIN is the value of the seperation between two chained Gaussians, the ratio of the heights of two chained Gaussians or the ratio of their line widths.

WGHT

Weighting of the residuals to be used in the optimization.

Options are: N for no weighting V for weighting by Y value E for weighting by 1/error**2

MAN

If set, the results of the manual fit will be written to the terminal and the results file (if open). If not set, then a return to the menu is made so the fit can be altered.

RECNAME

The name of the data file produced by GAUSS from which a fit is to be recalled and plotted for subsequent manipulation.

GAUFIT

The name of the continuum and Gaussian fit spectrum file to be written. It has the same dimension as the input spectrum.

CCMD

Continuum fitting menu entry. Alternatives are:

CUR - indicate continuum regions by cursor. ORD - order of polynomial fit. SIG - factor*sigma on fit for continuum point rejection. ERR - factor*error on point for rejection from continuum fit. ITN - number of iterations for continuum point rejection. FIT - perform the polynomial fitting. GAU - proceed to Gaussian fitting (continuum set).

GCMD

Gaussian fitting menu entry. Alternatives are:

LIM _ delimit edges of line (default is adjacent continuum edges). SIN - fit a single Gaussian to an indicated line. NEW - introduce a Gaussian at the cursor defined position. NEX - introduce a new Gaussian at the peak. INCH - interactively alter peak position, height or width. LIS - list the Gaussians fitted. SEL - select a line to be modified. DEL - delete a selected Gaussian. OPT - optimize the fit. RECAL - read a previous fit data file and plot this fit. HARD - plot results of fit for hardcopy device. SAVE - save the Gaussian fit spectrum as a file (name prompted for on quitting). CON - move to another section of continuum for more fitting. QUIT - quit from program (spectrum analysis complete).

Source comments:

 G A U S S

 Interactively fits Gaussians to an emission or absorption
 feature in a spectrum. A spectrum, whose length is prompted
 for, is plotted on the selected 'SOFT' device together with a
 residual plot above. Regions of continuum are demarcated with
 the cursor. Continuum is fitted by a polynomial with rejection
 of points a selected sigma from this continuum or a fraction
 of the error bar ( if available ). Single or multiple Gaussian
 fits are made to the emission/absorption feature. In the case
 of multiple fits interactive fitting of the profile by Gaussians
 whose parameters are altered from the terminal occurs. The
 residuals on the fit ( observed - fitted ) are plotted in the
 residuals box above the main plot. If error bars are available
 for the spectrum they are plotted in the residuals box. The fit
 may be optimized and any single Gaussian parameter can be
 constrained or its value chained to another. The residuals on
 the fit for the purposes of the optimization can be weighted either
 by value or error. Data on the fit - central wavelength, height and
 sigma - are reported for each Gaussian and r.m.s. and mean
 fractional error ( if errors available ) on fit. The results may be
 recorded on a data file. The final fit spectrum can be saved as a
 file for subsequent analysis.

 Command parameters -

 SPECTRUM    The data to be fitted. This should be a
             1-d .dst file with a .z.data component.  If there
             is a .x.data component this will be used to
             give the x-axis.  If not, the x-axis will just
             have to be the numbers from 1 to n.
 XSTART      The x-value at which plotting is to start.
 XEND        The x-value at which plotting is to end.
             (XSTART and XEND are not required if the
             WHOLE keyword is set.)
 HIGH        The maximum value to be used for the plot.
 LOW         The minimum value to be used for the plot.
 BIAS        Value to be added to zero for the plot.
 LABEL       A label for the plot and the data file.

 Command keywords -

 AUTOSCALE   The program is to work out the values for HIGH
             and LOW, using the maximum and minimum values
             in the data over the specified range.
 WHOLE       The program is to display all of the spectrum.

 User variables -    (">" input, "<" output)

 (>) SOFT    Specifies the device and type to be used for soft
             plots.  See the SOFT command for more details.
 (>) HARD    Specifies the device and type to be used for hard
             plots.  See the HARD command for more details.
 (<) TVXST   is set to the starting x-value for the plot.
 (<) TVXEN   Is set to the final x-value for the plot.
 (<) TVHIGH  Is set to the same value as HIGH.
 (<) TVLOW   Is set to the same value as LOW.
 (<) TVFILE  Is set to the value of SPECTRUM.

 Subroutines called:
   MAPSPEC  -  unmaps the X and Z from virtual memory into arrays
               in the program
   MAPSPECE  -  unmaps the X, Z and error data from virtual memory
                into arrays in the program
   MAPSPECG  - maps the output fitting spectrum Z component into
               virtual memory
   GAUS_XZPLOT  -  handles all the PGPLOT plotting of spectrum,
                   continuum fit, Gaussian fit, residuals and
                   error bars
   CONMENU  -  the continuum fitting menu for polynomial continuum
               fitting
   GAUMENU  -  the Gaussian fitting menu for all Gaussian fitting

                                      JRW / AAO March 1987