rvreidlines: Reidentify spectral lines and measure radial velocities

Package: rv

Usage

rvreidlines reference images

Parameters

reference: Spectrum with previously identified features to be used as reference for other spectra. If there are multiple apertures, lines, or columns in the image a master reference is defined by the section parameter. The other apertures, lines, or columns selected by step are reidentified if needed.

images: List of dispersion corrected spectral images in which the features in the reference image are to be reidentified. In two and three dimensional images the reidentifications are done by matching apertures, lines, columns, or bands with those in the reference image.

interactive = no: Examine and fit features and velocities interactively? If the task is run interactively a query (which may be turned off during execution) will be given for each vector reidentified after printing the results of the automatic determination and the user may chose to enter the interactive rvidlines task.

section = "middle line"

If the reference image is not one dimensional or given as a one dimensional image section then this parameter selects the master reference image vector. The master reference is used when reidentifying other vectors in the reference image or when other images contain apertures not present in the reference image. This parameter also defines the direction (columns, lines, or z) of the image vectors to be reidentified. The section parameter may be specified directly as an image section or in one of the following forms

line|column|x|y|z first|middle|last|# [first|middle|last|#]]
first|middle|last|# [first|middle|last|#] line|column|x|y|z

where each field can be one of the strings separated by | except for # which is an integer number. The field in [] is a second designator which is used with 3D data. See the example section for rvidlines for examples of this syntax. Abbreviations are allowed though beware that 'l' is not a sufficient abbreviation.

newaps = yes: Reidentify new apertures in the images which are not in the reference image? If no, only apertures found in the reference image will be reidentified in the other images. If yes, the master reference spectrum is used to reidentify features in the new aperture and then the new aperture features will be added to the reference apertures. All further identifications of the new aperture will then use this result.

override = no: Override previous solutions? If there are previous measurements for a particular image vector being identified, because of a previous rvidlines or rvreidlines, this parameter selects whether to simply skip the reidentification or do a reidentification and velocity measurement and overwrite the results in the logfile and database.

The following parameters are used for selecting and reidentifying additional lines, columns, or apertures in two dimensional formats.

trace = no: There are two methods for defining additional reference lines, columns, or bands in two and three dimensional format images as selected by the step parameter. When trace is no the master reference line or column is used for each new reference vector. When this parameter is yes then as the reidentifications step across the image the last reidentified features are used as the reference. This "tracing" is useful if there is a coherent shift in the features such as with long slit spectra. However, any features lost during the tracing will be lost for all subsequent lines or columns while not using tracing always starts with the initial set of reference features.

step = "10": The step from the reference aperture, line, column, or band used for selecting and/or reidentifying additional lines, columns, or bands in a two or three dimensional reference image. For three dimensional images there may be two numbers to allow independent steps along different axes. For multiaperture images the step is typically 1 while for long slit or Fabry-Perot images the step is large enough to map any significant changes in the feature positions. If the step is zero then only the reference line, column, or band is used.

nsum = "10": Number of lines, columns, or bands across the designated vector axis to be summed when the image is a two or three dimensional spatial spectrum. It does not apply to multispec format spectra. If the image is three dimensional an optional second number can be specified for the higher dimensional axis (the first number applies to the lower axis number and the second to the higher axis number). If a second number is not specified the first number is used for both axes.

shift = "0": Shift in user coordinates to be added to the reference features before centering when stepping to other lines, columns, or bands in the reference image. Generally no shift is used by setting the value to zero. The shift is used as a slope with positive values increasing towards larger line or column numbers. This parameter is not used for reidentifications from the reference image to other images. If the image is three dimensional then two numbers may be specified for the two axes.

nlost = 0: When reidentifying features by tracing, if the number of features not found in the new image vector exceeds this number then the reidentification record is not written to the logfile and database and the trace is terminated. A warning is printed in the log and in the verbose output.

The following parameters define the finding and recentering of features. See also center1d and rvidlines.

cradius = 5.: Centering radius in pixels. If a reidentified feature falls further than this distance from the previous line or column when tracing or from the reference feature position when reidentifying a new image then the feature is not reidentified.

threshold = 10.: In order for a feature center to be determined, the range of pixel intensities around the feature must exceed this threshold. This parameter is used to exclude noise peaks and terminate tracing when the signal disappears. However, failure to properly set this parameter, particularly when the data values are very small due to normalization or flux calibration, is a common error leading to failure of the task.

The following parameters select and control the automatic addition of new features during reidentification.

addfeatures = no: Add new features from a line list during each reidentification? If yes then the following parameters are used. This function can be used to compensate for lost features from the reference solution, particularly when tracing. Care should be exercised that misidentified features are not introduced.

coordlist = "": User coordinate list consisting of an ordered list of rest spectral line coordinates.

match = 10.: The maximum difference for a match between the feature coordinate function value and a coordinate in the coordinate list (after correction by the velocity).

maxfeatures = 50: Maximum number of the strongest features to be selected automatically from the coordinate list.

minsep = 2.: The minimum separation, in pixels, allowed between feature positions when defining a new feature.

The following parameters determine the input and output of the task.

database = "database": Database containing the feature data for the reference image and in which the features for the reidentified images are recorded.

logfiles = "logfile": List of file in which to record the velocity results and to keep a processing log. If a null file, "", is given then no log is kept.

verbose = no: Print reidentification and velocity information on the standard output?

keywpars = "": The image header keyword translation table as described in the keywpars named pset. This defines the header keywords used to obtain the observation information needed for computing the heliocentric velocity.

graphics = "stdgraph": Graphics device. The default is the standard graphics device which is generally a graphics terminal.

cursor = "": Cursor input file. If a cursor file is not given then the standard graphics cursor is read.

ADDTIONAL PARAMETERS The measured velocities are corrected to a heliocentric frame of reference if possible. This requires determining various parameters about the observation. The latitude, longitude, and altitude of the observation are determined from the observatory database. The observatory is defined by either the OBSERVAT image header keyword or the "observatory" package parameter in that order. See the help for observatory for additional information.

The date, universal time, right ascension, declination, and coordinate epoch for the observation are obtained from the image header. The keywords for these parameters are defined in the keywpars parameter set.

Description

Rvreidlines takes spectral lines previously identified in a reference image and recorded in a database and identifies them in other spectra and determines a radial velocity. If the images are two or three dimensional or multiaperture format and a step greater than zero is specified then additional vectors (lines/columns/bands/apertures) in the reference image will be reidentified from the initial master reference vector (as defined by an image section or section parameter) provided they have not been reidentified previously or the override flag is set. For multiple aperture spectra images, called multiaperture, the step size is typically 1; i.e. reidentify features in all spectra. For two and three dimensional images, such as long slit and Fabry-Perot spectra, the step(s) should be large enough to minimize execution time and storage requirements but small enough to follow shifts in the features (see the discussion below on tracing). The set of reference identifications is applied to other images in the same lines, columns, bands, or apertures. In multiaperture images the same apertures are matched in the reference image regardless of actual line order; i.e. the apertures need not be in the same order or even have all apertures present.

The reidentification of other features in other reference image vectors may be done in two ways selected by the parameter trace. If not tracing, the initial reference vector is applied to the other selected vectors. If tracing, the reidentifications are made with respect to the last set of identifications as successive steps away from the reference vector are made. The tracing method is appropriate for two and three dimensional spatial images, such as long slit and Fabry-Perot spectra, in which the positions of features traced vary smoothly. This allows following large displacements from the initial reference by using suitably small steps. It has the disadvantage that features lost during the reidentifications will not propagate (unless the addfeatures option is used). By not tracing, the original set of features is used for every other vector in the reference image.

When reidentifying other vectors in the reference image the parameter shift may be used to add a shift(s) to the features positions before recentering. The shift is added to lines, columns, or bands, greater than the current line, column, or band and subtracted if less. If tracing the shifts are the same from step to step while if not tracing the shifts are added to the shifts from the previous step. Thus, in both cases an approximation of a slope is used. This allows large slopes in the features to be followed even when not tracing but the shift value must be predetermined.

When tracing, the parameter nlost is used to terminate the tracing whenever this number of features has been lost. This parameter, in conjunction with the other centering parameters which define when a feature is not found, may be useful for tracing features which disappear before reaching the limits of the image.

When reidentifying features in other images, the reference features are those from the same aperture, line, column, or band of the reference image. However, if the newaps parameter is set apertures in multiaperture spectra which are not in the reference image may be reidentified against the master reference aperture and added to the list of aperture to be reidentified in other images. This is useful when specta with different aperture numbers are stored as one dimensional images.

There are two centering algorithms; a flux bisecting algorithm called center1d and a gaussian fitting algorithm. These algorithms are described in the help for rvidlines. The algorithm used and whether the feature is emission or absorption is the same one used in the reference image. The only caveat is that multiple gaussian fitting provided by the interactive 'b' key in rvidlines is not done by this task and those lines will be fit by gaussians independently.

When recentering, if a feature position shifts by more than the amount set by the parameter cradius from the starting position (possibly after adding a shift) or the feature strength (peak to valley) is less than the detection threshold then the new feature is discarded. The cradius parameter should be set large enough to find the correct peak in the presence of any shifts but small enough to minimize incorrect identifications. The threshold parameter is used to eliminate identifications with noise. Failure to set this parameter properly for the data (say if data values are very small due to a calibration or normalization operation) is the most common source of problems in using this task.

In two and three dimensional images, though not multiaperture images, the number of lines, columns, or bands given by the parameter nsum are summed to form the one dimensional image vector in which the features are identified. This increases the accuracy for reidentifying weak features.

If the parameter addfeatures is set additional features may be added after the initial reidentification and velocity determination using a line list of rest wavelengths. A maximum number of added features, a matching distance in user coordinates, and a minimum separation from other features are additional parameters. This option is similar to that available in rvidlines and is described more fully in the help for that task.

A statistics line is generated for each reidentified vector. The line contains the name of the image being reidentified (which for two dimensional images includes the image section and for multiaperture spectra includes the aperture number), the number of features found relative to the number of features in the reference, the number of features used in the velocity determination (currently there is no rejection of lines) relative to the number found, the mean pixel and user coordinate shfits relative to the reference coordinates, and the measured velocity and RMS in the velocity. The velocity is the heliocentric velocity if the necessary observation information in the image and observatory database are found.

If the task is run with the interactive flag the statistics line is printed to the standard output (the terminal) and a query is made whether to fit the lines and measure the velocity interactively. A response of yes or YES will put the user in the interactive graphical mode of rvidlines. See the description of this task for more information. The idea is that one can monitor the statistics information, particularly the velocity RMS, and select only those which may be questionable to examine interactively. A response of no or NO will continue on to the next spectrum. The capitalized responses turn off the query and act as permanent response for all other reidentifications.

This statistics line, including headers, is written to any specified log files. The log information includes the image being reidentified and the reference image. In addition the set of lines, the observatory information used, and the computed observed and heliocentric velocities and redshifts are recorded. This is the same information as is produced by rvidlines.

Database records

The database specified by the parameter database is a directory of simple text files. The text files have names beginning with 'id' followed by the entry name, usually the name of the image. The database text files consist of a number of records. A record begins with a line starting with the keyword "begin". The rest of the line is the record identifier. Records read and written by rvreidlines have "identify" as the first word of the identifier. Following this is a name which may be specified following the ":read" or ":write" commands. If no name is specified then the image name is used. For 1D spectra the database entry includes the aperture number and so to read a solution from a aperture different than the current image and aperture number must be specified. For 2D/3D images the entry name has the 1D image section which is what is specified to read the entry. The lines following the record identifier contain the feature information and redshift (without heliocentric correction).

The database files have the name "identify" and the prefix "id" because these files may also be read by the identify task for changing the dispersion function based on the rest wavelengths.

Examples

1. To generate a rotation curve for a long slit spectrum of a galaxy first use rvidlines to mark some lines at the center of the galaxy. If the velocities are to be absolute then you give the rest wavelengths and do a fit. However to get velocities relative to the center use the measured wavelengths by simply accepting the prompted measured wavelengths. Then run rvreidlines. The nsum and step parameters allow controlling the summing size and spacing.

rv> rvid lsgal sec="mid col" nsum=5
        Mark lines and then quit.
Write velocity data to the logfile (yes)?
Write feature data to the database (yes)?
rv> rvreid lsgal "" sec="mid col" nsum=5 step=5 trace+ v+

RVREIDLINES: NOAO/IRAF V2.10.3 valdes Sat 14:47:55 21-Aug-93
  Reference image = lsgal, New image = lsgal
 Image Data  Found    Fit  Pix Shift  User Shift Velocity    RMS
lsgal[45,*]    7/7    7/7    -0.0181     -0.0212    -1.37   11.3
lsgal[40,*]    7/7    7/7     0.0147      0.0193     1.34   8.73
lsgal[35,*]    7/7    7/7     0.0931       0.116     8.01   9.16
lsgal[30,*]    7/7    7/7    -0.0224     -0.0265    -1.78   27.6
lsgal[25,*]    7/7    7/7     0.0558        0.07     4.83   33.7
lsgal[20,*]    7/7    7/7    -0.0317     -0.0379    -3.08   33.6
lsgal[15,*]    5/7    5/5      0.015      0.0201    0.799   43.7
lsgal[10,*]    7/7    7/7      0.395       0.489     33.7   54.9
lsgal[5,*]     4/7    4/4      -1.22       -1.51    -106.   84.3
lsgal[55,*]    7/7    7/7      0.014      0.0184     1.41   10.5
lsgal[60,*]    7/7    7/7    -0.0897      -0.109    -7.59   7.21
lsgal[65,*]    7/7    7/7    -0.0109     -0.0122   -0.957   10.9
lsgal[70,*]    7/7    7/7     -0.074     -0.0902    -6.55   14.6
lsgal[75,*]    7/7    7/7   -0.00203    -0.00136    0.227   54.3
lsgal[80,*]    6/7    6/6       0.08      0.0997     6.66   96.7
lsgal[85,*]    6/7    6/6      0.289       0.357     27.2   104.
lsgal[90,*]    6/7    6/6      0.459       0.568     40.5   33.2
lsgal[95,*]    6/7    6/6      0.926        1.14     78.5   65.5
lsgal[100,*    5/7    5/5      0.696        0.86     59.1   44.2
rv> match Vobs logfile | fields "" 2,6,11 | \
>>> graph point- mark=vebar szmark=-1

The last command extracts the Vobs results from the logfile using match, the column number, velocity, and mean error are extract using fields, and graphs the points with error bars. One drawback to this method is that the nubmer of columns summed is constant and so the signal-to-noise decreases with the galaxy light.

Revisions

RVREIDLINES V2.11: This task will now work in the units of the input spectra.

RVREIDLINES V2.10.3: This task in new in the version.