ARCLOCAT-Locate line features in a set of spectra.

Usage:

arclocat in fwhm thresh

Description:

This routine locates narrow features in a set of spectra. Features can be located from scratch automatically. In a different mode, feature locations can be added or deleted in a graphical dialogue. The feature location and peak are determined by a Gauss or triangle line fit.

Parameters:

INFO

INFO = _LOGICAL (Read) If true, messages about the progress of auto-locating features are issued. [YES]

DIALOG

DIALOG = _CHAR (Read) If this is 'Y', 'T' or 'G', then no auto-locating takes place and the graphics dialogue is entered. If this is 'N' or 'F' then the dialogue is not entered and auto-locating is done instead. The string is case-insensitive. ['G']

MODE

MODE = _CHAR (Read) This can be 'Gauss' or 'triangle' and chooses the line profile to be fitted. This string is case-insensitive and can be abbreviated to one character. ['Gauss']

IN

IN = NDF (Read) The spectrum or set of spectra in which emission features are to be located. This must be a base NDF, the spectroscopic axis must be the first axis. No spectroscopic values or widths must exist in the Specdre Extension. The pixel centres along the first axis must be NDF pixel coordinates. Update access is necessary, the results structure in the Specdre Extension will be modified, possibly re-created.

FWHM

FWHM = _REAL (Read) The guessed full width at half maximum of the features to be located. This is used to estimate the maximum number of features that might be located, to locate baseline ranges next to suspected features, and as a guess for the line fit.

THRESH

THRESH = _REAL (Read) The threshold. While scanning a pixel must exceed this threshold to initiate a line fit. The fitted peak also must exceed the threshold in order that the feature location be accepted. This parameter is significant only for automatic location of features.

DEVICE

DEVICE = GRAPHICS (Read) The graphics device to be used. This is unused if DIALOG is false.

ROWNUM

ROWNUM = _INTEGER (Read) In graphics dialogue this parameter is used to switch to a different row (spectrum).

Source comments:

   A R C L O C A T

   The input data must be a base NDF. They can be a single spectrum
   or a set of spectra. Examples for the latter are a long slit
   spectrum, a set of extracted fibre spectra, or a collapsed
   echellogram (a set of extracted orders from an echelle
   spectrograph). It is necessary that the spectroscopic axis be the
   first axis in the data set. It does not matter how many further
   axes there are, the data will be treated as a set of rows with
   each row a spectrum.

   The coverage in spectroscopic values of all spectra (rows) should
   either be similar (long slit or fibres) or roughly adjacent
   (echellogram). There must not yet be any spectroscopic value
   information: There must be no array of spectroscopic values or
   widths in the Specdre Extension. The pixel centre array for the
   spectroscopic axis (i.e. the first axis) must be NDF pixel
   coordinates (usually 0.5, 1.5, ...). The data must be arranged
   such that spectroscopic values increase left to right. In the case
   of rows with adjacent coverage spectroscopic values must also
   increase with row number. In a collapsed echellogram this usually
   means that for wavelength calibration the order number must
   decrease with increasing row number.

   In automatic mode this routine works on each row (spectrum) in
   turn. It scans through the spectrum and looks for pixels that
   exceed the local background level by at least the given threshold
   value. When such a pixel is spotted, a single-component line fit
   is tried no the local profile. The local profile is centred on the
   pixel suspected to be part of an emission feature. It includes 1.5
   times the guessed FWHM on either side and a further 5 baseline
   pixels on either side. A local linear baseline is subtracted prior
   to the line fit. In order for the feature to be entered into the
   list of located features, the fit must succeed, the fitted peak
   must exceed the threshold, and the fitted peak must exceed the
   absolute difference of background levels between the left and
   right.

   When run with graphics dialogue this routine works on any choice
   of rows. It uses a pre-existing list of located features to which
   can be added or from which features can be deleted. Graphics
   dialogue can also be used to just check the locations. The graph
   displays the spectrum currently worked on in bin-style. The current
   list of located features is indicated by dashed vertical lines.
   The options in the graphical dialogue are:
      R - Choose different row to work on
      X - X-zoom 2x on cursor
      Y - Y-zoom 2x on cursor
      W - Unzoom to show whole row
      N - Pan left/right by 75% of current x range
      A - Add the feature under cursor to list (subject to line fit)
      S - Add the cursor position as feature to list
      D - Delete the feature nearest cursor from list
      Q - Quit, preserving the updated list of located features
      ? - Help

   The difference between the A and S options is that A tries a line
   fit to the local profile around the cursor, while S accepts the
   cursor x position as exact centre and the cursor y position as
   exact peak of a new feature; (the variance of the centre is set
   to 0.25, the variance of the peak to the bad value).

   The result of this routine is a list of Gauss or triangle
   features. Their locations in NDF pixel coordinates and their peak
   values are stored in the results structure of the Specdre
   Extension of the input data. If run in automatic mode, this
   routine will replace any previously existing results structure. If
   run with graphics dialogue, this routine will try to work with a
   pre-existing list of located features. But if the pre-existing
   results structure does not conform to the required format, then a
   new results structure is created.

   The list of located features (for each row) is always sorted such
   that the locations are strictly monotonically increasing.

   The results structure provides for a certain number of components.
   These have component type 'Gauss feature' or 'triangle feature'.
   Each component has two parameters 'centre' and 'peak'. The number
   of components is determined when the results structure is created,
   it is derived from the approximate width of features and the
   number of pixels in each spectrum.

Examples:

arclocat in 4. 20. mode=triangle dialog=f
   This will scan through (all rows of) the NDF called "in". It
   looks out for features of 4 pixels full width at half maximum
   and with a peak value of at least 20 above the local
   background. The features are fitted as triangles. The search is
   automatic. Thus a new results structure in the input NDF's
   Specdre Extension is created with the locations (centres) and
   peaks of located features.

arclocat in 4. mode=Gauss dialog=g rownum=5
   This will use the graphic dialogue. Starting with the fifth row
   the user can use the mouse cursor to choose features that are
   to be deleted from or added to the list of located features.
   This can be used to improve on an automatic run, or when no
   features have been located so far. If you try to add a feature
   to the list, a Gauss fit is tried in the vicinity of the
   cursor-selected position.

Notes:

This routine recognises the Specdre Extension v. 0.7.

This routine works in situ and modifies the input file.