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BEAMFIT

Fits beam features in a two-dimensional NDF

Description:

This fits generalised Gaussians (cf. PSF) to beam features within the data array of a two-dimensional NDF given approximate initial co-ordinates. It uses an unconstrained least-squares minimisation involving the residuals and a modified Levenberg-Marquardt algorithm. The beam feature is a set of connected pixels which are either above or below the surrounding background region. The errors in the fitted coefficients are also calculated.

You may apply various constraints. These are either fixed, or relative. Fixed values include the FWHM, background level, or the shape exponent that defaults to 2 thus fits a normal distribution. Relative constraints define the properties of secondary beam features with respect to the primary (first given) feature, and can specify amplitude ratios, and beam separations in Cartesian or polar co-ordinates.

Four methods are available for obtaining the initial positions, selected using Parameter MODE:

In the first two modes the application loops, asking for new feature co-ordinates until it is told to quit or encounters an error or the maximum number of features is reached. The last is five, unless Parameters POS2—POS5 define the location of the secondary beams and then only the primary beam’s position is demanded.

BEAMFIT both reports and stores in parameters its results. These are fit coefficients and their errors, the offsets and position angles of the secondary beam features with respect to the primary beam, and the offset of the primary beam from a reference position. Also a listing of the fit results may be written to a log file geared more towards human readers, including details of the input parameters (see Parameter LOGFILE).

Usage:

beamfit ndf [mode] {
incat=? [beams] coin=? [beams] pos pos2-pos5=?

                  mode

Parameters:

AMPRATIO( ) = _REAL (Read)
If number of beam positions given by BEAMS is more than one, this specifies the ratio of the amplitude of the secondary beams to the primary. Thus you should supply one fewer value than the number of beams. If you give fewer than that the last ratio is copied to the missing values. The ratios would normally be negative, usually −1 or −0.5. AMPRATIO is ignored when there is only one beam feature to fit. [!]
BEAMS = _INTEGER (Read)
The number of beam positions to fit. This will normally be 1, unless a chopped observation is supplied, when there may be two or three beam positions. This parameter is ignored for "File" and "Catalogue" modes, where the number comes from the number of beam positions read from the files; and for "Interface" mode when the beam positions POS, POS2, etc. are supplied in full on the command line without BEAMS. In all modes there is a maximum of five positions, which for "File" or "Catalogue" modes will be the first five. [1]
CIRCULAR = _LOGICAL (Read)
If set TRUE only circular beams will be fit. [FALSE]
COIN = FILENAME (Read)
Name of a text file containing the initial guesses at the co-ordinates of beams to be fitted. It is only accessed if Parameter MODE is given the value "File". Each line should contain the formatted axis values for a single position, in the current Frame  of the NDF. Axis values can be separated by spaces, tabs or commas. The file may contain comment lines with the first character # or !.
DESCRIBE = _LOGICAL (Read)
If TRUE, a detailed description of the co-ordinate Frame in which the beam positions will be reported is displayed before the positions themselves. [current value]
DEVICE = DEVICE (Read)
The graphics device which is to be used to give the initial guesses at the beam positions. Only accessed if Parameter MODE is given the value "Cursor". [Current graphics device]
FITAREA() = _INTEGER (Read)
Size in pixels of the fitting area to be used. This should fully encompass the beam and also include some background signal. If only a single value is given, then it will be duplicated to all dimensions so that a square region is fitted. Each value must be at least 9. A null value requests that the full data array is used. [!]
FIXAMP = _DOUBLE (Read)
This specifies the fixed amplitude of the first beam. Secondary sources arising from chopped data use FIXAMP multiplied by the AMPRATIO. A null value indicates that the amplitude should be fitted. [!]
FIXBACK = _DOUBLE (Read)
If a non-null value is supplied then the model fit will use that value as the constant background level otherwise the background is a free parameter of the fit. [!]
FIXFWHM = LITERAL (Read)
If this is set TRUE then the model fit will use the full-width half-maximum values for the beams supplied through Parameter FWHM. FALSE demands that the FWHM values are free parameters of the fit. [FALSE]
FIXPOS = _LOGICAL (Read)
If TRUE, the supplied position of each beam is used and the centre co-ordinates of the beam features are not fit. FALSE causes the initial estimate of the location of each beam to come from the source selected by Parameter MODE, and all these locations are part of the fitting process (however note the exception when FIXSEP=TRUE. It is advisable not to use this option in the inaccurate "Cursor" mode. [FALSE]
FIXSEP = _LOGICAL (Read)
If TRUE, the separations of secondary beams from the primary beam are fixed, and this takes precedence over Parameter FIXPOS. If FALSE, the beam separations are free to be fitted (although it is actually the centres being fit). It is advisable not to use this option in the inaccurate "Cursor" mode. [FALSE]
FWHM = LITERAL (Read)
The initial full-width half-maximum (FWHM) values for each beam. These become fixed values if FIXFWHM is set TRUE.

A number of options are available.

  • A single value gives the same circular FWHM for all beams.

  • When Parameter CIRCULAR is TRUE, supply a list of values one for each of the number of beams. These should be supplied in the same order as the corresponding beam positions.

  • A pair of values sets the major- and minor-axis values for all beams, provided Parameter CIRCULAR is FALSE.

  • Major- and minor-axis pairs, whose order should match that of the corresponding beams. Again CIRCULAR should be FALSE.

Multiple values are separated by commas. An error is issued should none of these options be offered.

If the current co-ordinate Frame of the NDF is a SKY Frame (e.g. right ascension and declination), then the value should be supplied as an increment of celestial latitude (e.g. declination). Thus, "5.7" means 5.7 arcseconds, "20:0" would mean 20 arcminutes, and "1:0:0" would mean 1 degree. If the current co-ordinate Frame is not a SKY Frame, then the widths should be specified as an increment along Axis 1 of the current co-ordinate Frame. Thus, if the Current Frame is PIXEL, the value should be given simply as a number of pixels.

Null requests that BEAMFIT itself estimates the initial FWHM values. [!]

GAUSS = _LOGICAL (Read)
If TRUE, the shape exponent is fixed to be 2; in other words the beams are modelled as two-dimensional normal distributions. If FALSE, the shape exponent is a free parameter in each fit. [TRUE]
INCAT = FILENAME (Read)
A catalogue containing a positions list giving the initial guesses at the beam positions, such as produced by applications CURSOR, LISTMAKE, etc. It is only accessed if Parameter MODE is given the value "Catalogue".
LOGFILE = FILENAME (Read)
Name of the text file to log the results. If null, there will be no logging. Note this is intended for the human reader and is not intended for passing to other applications. [!]
MARK = LITERAL (Read)
Only accessed if Parameter MODE is given the value "Cursor". It indicates which positions are to be marked on the screen using the marker type given by Parameter MARKER. It can take any of the following values.

  • "Initial" — The position of the cursor when the mouse button is pressed is marked.

  • "Fit" — The corresponding fit position is marked.

  • "Ellipse" — As "Fit" but it also plots an ellipse at the HWHM radii and orientation.

  • "None" — No positions are marked.

[current value]

MARKER = INTEGER (Read)
This parameter is only accessed if Parameter MARK is set TRUE. It specifies the type of marker with which each cursor position should be marked, and should be given as an integer PGPLOT marker type. For instance, 0 gives a box, 1 gives a dot, 2 gives a cross, 3 gives an asterisk, 7 gives a triangle. The value must be larger than or equal to −31. [current value]
MODE = LITERAL (Read)
The mode in which the initial co-ordinates are to be obtained. The supplied string can be one of the following values.

  • "Interface" — positions are obtained usingparameters POS, POS2–POS5.

  • "Cursor" — positions are obtained using the graphics cursor of the device specified by Parameter DEVICE.

  • "Catalogue" — positions are obtained from a positions list using Parameter INCAT.

  • "File" — positions are obtained from a text file using Parameter COIN. [current value]

NDF = NDF (Read)
The NDF structure containing the data array to be analysed. In cursor mode (see Parameter MODE), the run-time default is the displayed data, as recorded in the graphics database. In other modes, there is no run-time default and the user must supply a value. []
PLOTSTYLE = GROUP (Read)
A group of attribute settings describing the style to use when drawing the graphics markers specified by Parameter MARK.

A comma-separated list of strings should be given in which each string is either an attribute setting, or the name of a text file preceded by an up-arrow character "^". Such text files should contain further comma-separated lists which will be read and interpreted in the same manner. Attribute settings are applied in the order in which they occur within the list, with later settings overriding any earlier settings given for the same attribute.

Each individual attribute setting should be of the form:

<name>=<value>

where <name> is the name of a plotting attribute, and <value> is the value to assign to the attribute. Default values will be used for any unspecified attributes. All attributes will be defaulted if a null value (!)—the initial default—is supplied. To apply changes of style to only the current invocation, begin these attributes with a plus sign. A mixture of persistent and temporary style changes is achieved by listing all the persistent attributes followed by a plus sign then the list of temporary attributes.

See Section E for a description of the available attributes. Any unrecognised attributes are ignored (no error is reported). [current value]

POLAR = _LOGICAL (Read)
If TRUE, the co-ordinates supplied through POS2–POS5 are interpreted in polar co-ordinates (offset, position angle) about the primary beam. The radial co-ordinate is a distance measured in units of the latitude axis if the current WCS Frame  is a SKY DOMAIN or the first axis for other Frames. For a SKY current WCS Frame, position angle follows the standard convention of North through East. For other Frames the angle is measured from the second axis anticlockwise, e.g. for a PIXEL Frame it would be from y through negative x, not the standard x through y.

If FALSE, the co-ordinates are the regular axis co-ordinates in the current Frame.

POLAR is only accessed when there is more than one beam to fit. [TRUE]

POS = LITERAL (Read)
When MODE = "Interface" POS specifies the co-ordinates of the primary beam position. This is either merely an initial guess for the fit, or if Parameter FIXPOS is TRUE, it defines a fixed location. It is specified in the current co-ordinate Frame of the NDF (supplying a colon ":" will display details of the current co-ordinate Frame). A position should be supplied as a list of formatted WCS axis values separated by spaces or commas, and should lie within the bounds of the NDF.

If the initial co-ordinates are supplied on the command line without BEAMS the number of contiguous POS, POS2,…parameters specifies the number of beams to be fit. If the initial co-ordinates are supplied on the command line without BEAMS specified only one beam will be fit.

POS2-POS5 = LITERAL (Read)
When MODE = "Interface" these parameters specify the co-ordinates of the secondary beam positions. These should lie within the bounds of the NDF. For each parameter the supplied location may be merely an initial guess for the fit, or if Parameter FIXPOS is TRUE, it defines a fixed location, unless Parameter FIXSEP is TRUE, whereupon it defines a fixed separation from the primary beam.

For POLAR = FALSE each distance should be given as a single literal string containing a space- or comma-separated list of formatted axis values measured in the current co-ordinate Frame of the NDF. The allowed formats depends on the class of the current Frame. Supplying a single colon ":" will display details of the current Frame, together with an indication of the format required for each axis value, and a new parameter value is then obtained.

If Parameter POLAR is TRUE, POS2–POS5 may be given as an offset followed by a position angle. See Parameter POLAR for more details of the sense of the angle and the offset co-ordinates.

The parameter name increments by 1 for each subsequent beam feature. Thus POS2 applies to the first secondary beam (second position in all), POS3 is for the second secondary beam, and so on. As the total number of parameters required is one fewer than the value of Parameter BEAMS, POS2–POS5 are only accessed when BEAMS exceeds 1.

REFPOS = LITERAL (Read)
The reference position. This is often the desired position for the beam. The offset of the primary beam with respect to this point is reported and stored in Parameter REFOFF. It is only accessed if the current WCS Frame in the NDF is not a SKY Domain containing a reference position.

The co-ordinates are specified in the current WCS Frame of the NDF (supplying a colon ":" will display details of the current co-ordinate Frame). A position should be supplied either as a list of formatted WCS axis values separated by spaces or commas. A null value (!) requests that the centre of the supplied map is deemed to be the reference position.

RESID = NDF (Write)
The map of the residuals (data minus model) of the fit. It inherits the properties of the input NDF, except that its data type is _DOUBLE or _REAL depending on the precision demanded by the type of IN, and no variance is propagated. A null (!) value requests that no residual map be created. [!]
TITLE = LITERAL (Read)
The title for the NDF to contain the residuals of the fit. If null (!) is entered the NDF will not contain a title. ["KAPPA - BEAMFIT"]
VARIANCE = _LOGICAL (Read)
If TRUE, then any VARIANCE component present within the input NDF will be used to weight the fit; the weight used for each data value is the reciprocal of the variance. If set to FALSE or there is no VARIANCE present, all points will be given equal weight. [FALSE]

Results Parameters

AMP( 2 * BEAMS ) = _DOUBLE (Write)
The amplitude and its error for each beam.
BACK( 2 * BEAMS ) = _DOUBLE (Write)
The background level and its error at each beam position.
CENTRE( 2 * BEAMS ) = LITERAL (Write)
The formatted co-ordinates and their errors of each beam in the current co-ordinate Frame of the NDF.
GAMMA( 2 * BEAMS ) = _DOUBLE (Write)
The shape exponent and its error for each beam.
MAJFWHM( 2 * BEAMS ) = _DOUBLE (Write)
The major-axis FWHM and its error, measured in the current co-ordinate Frame of the NDF, for each beam. Note that the unit for sky co-ordinate Frames is radians.
MINFWHM( 2 * BEAMS ) = _DOUBLE (Write)
The minor-axis FWHM and its error, measured in the current co-ordinate Frame of the NDF, for each beam. Note that the unit for sky co-ordinate Frames is radians.
OFFSET( ) = LITERAL (Write)
The formatted offset and its error of each secondary beam feature with respect to the primary beam. They are measured in the current Frame of the NDF along a latitude axis if that Frame is in the SKY Domain, or the first axis otherwise. The number of values stored is twice the number of beams. The array alternates an offset, then its corresponding error, appearing in beam order starting with the first secondary beam.
ORIENT( 2 * BEAMS ) = _DOUBLE (Write)
The orientation and its error, measured in degrees for each beam. If the current WCS Frame  is a SKY Frame, the angle is measured from North through East. For other Frames the angle is from the x-axis through y.
PA() = _REAL (Write)
The position angle and its errors of each secondary beam feature with respect to the primary beam. They are measured in the current Frame of the NDF from North through East if that is a SKY Domain, or anticlockwise from the y axis otherwise. The number of values stored is twice the number of beams. The array alternates a position angle, then its corresponding error, appearing in beam order starting with the first secondary beam.
REFOFF( 2 ) = LITERAL (Write)
The formatted offset followed by its error of the primary beam’s location with respect to the reference position (see Parameter REFPOS). The offset might be used to assess the optical alignment of an instrument. The ofset and its error are measured in the current Frame of the NDF along a latitude axis if that Frame is in the SKY Domain, or the first axis otherwise. The error is derived entirely from the uncertainities in the fitted position of the primary beam, i.e. the reference position has no error attached to it. By definition the error is zero when FIXPOS is TRUE.
RMS = _REAL (Write)
The primary beam position’s root mean-squared deviation from the fit.
SUM = _DOUBLE (Write)
The total data sum of the multi-Gaussian fit above the background. The fit is evaluated at the centre of every pixel in the input NDF (including bad-valued pixels). The fitted background level is then removed from the fit value, and the sum of these is written to this output parameter.

Examples:

beamfit mars_3pos i 1 "5.0,-3.5"
This finds the Gaussian coefficients of the primary beam feature in the NDF called mars_3pos, using the supplied beam’s centre. The co-ordinates are measured in the NDF’s current co-ordinate Frame. In this case they are offsets in arcseconds.
beamfit ndf=mars_3pos mode=interface beams=1 init1="5.0,-3.5" fixback=0
As above but now the background is fixed to be zero.
beamfit mars_3pos i pos="5.0,-3.5"
As the first example. The presence of POS indicates a single is required.
beamfit ndf=mars_3pos mode=interface beams=1 pos="5.0,-3.5" fixfwhm fwhm=16.5 gauss=f
As above but now the Gaussian is constrained to have a FWHM of 16.5 arcseconds and be circular, but the shape exponent is not constrained to be 2.
beamfit mars_3pos in beams=1 fwhm=16.5 fitarea=51 pos="5.,-3.5"
As above but now the fitted data is restricted to areas 51×51 pixels about the initial guess positions. All the other examples use the full array. Also the FWHM value is now just an initial guess.
beamfit mars_3pos int 3 "5.0,-3.5" ampratio=-0.5 resid=mars_res
As the first example except this finds the Gaussian coefficients of the primary beam feature and two secondary features. The secondary features have fixed amplitudes that are half that of the primary feature and of the opposite polarity. The residuals after subtracting the fit are stored in NDF mars_res. In all the other examples no residual map is created.
beamfit mars_3pos int 2 "5.0,-3.5" pos2="60.0,90" fixpos
This finds the Gaussian coefficients of the primary beam feature and a secondary feature in the NDF called mars_3pos. The supplied co-ordinates (5.0,−3.5) define the centre, i.e. they are not fitted. Also the secondary beam is fixed at 60 arcseconds towards the East (position angle 90 degrees).
beamfit mars_3pos int 2 "5.0,-3.5" pos2="60.0,90" fixsep
As the previous example, except now the separation of the second position is fixed at 60 arcseconds towards the East from the primary beam, instead of being an absolute location.
beamfit mars_3pos int 2 "5.0,-3.5" pos2="-60.5,0.6" polar=f fixpos
As the last-but-one example, but now location of the secondary beam is fixed at (−55.5,−2.9).
beamfit s450 int beams=2 fwhm="7.9,25" ampratio=0.06 circular pos=’"0:0:0,0:0:0"’ nopolar pos2="0:0:0,0:0:0"
This fits two superimposed circular Gaussians in the NDF called s450, whose current WCS is SKY. The beam second being fixed at 6 percent the strength of the first, with initial widths of 7.9 and 25 arcseconds.
beamfit mode=cu beams=1
This finds the Gaussian coefficients of the primary beam feature of an NDF, using the graphics cursor on the current graphics device to indicate the approximate centre of the feature. The NDF being analysed comes from the graphics database.
beamfit uranus cu 2 mark=ce plotstyle=’colour=red’ marker=3
This fits to two beam features in the NDF called uranus via the graphics cursor on the current graphics device. The beam positions are marked using a red asterisk.
beamfit uranus file 4 coin=features.dat logfile=uranus.log
This fits to the beam features in the NDF called uranus. The initial positions are given in the text file features.dat in the current co-ordinate Frame. Only the first four positions will be used. The last three positions are in polar co-ordinates with respect to the primary beam. A log of selected input parameter values, and the fitted coefficients and errors is written to the text file uranus.log.
beamfit uranus mode=cat incat=uranus_beams polar=f
This example reads the initial guess positions from the positions list in file uranus_beams.FIT. The number of beam features fit is the number of positions in the catalogue subject to a maximum of five. The input file may, for instance, have been created using the application CURSOR.

Notes:

Related Applications

KAPPA: PSF, CENTROID, CURSOR, LISTSHOW, LISTMAKE; ESP: GAUFIT; FIGARO: FITGAUSS.

Implementation Status: