reidentify reference images
reference
Image with previously identified features to be used as features reference for
other images. 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 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 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 fit and the
user may chose to enter the interactive identify 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 identify 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 solution will be added to the reference apertures. All
further identifications of the new aperture will then use this solution.
override = no
Override previous solutions? If there are previous solutions for a
particular image vector being identified, because of a previous
identify or reidentify, this parameter selects whether
to simply skip the reidentification or do a reidentification and
overwrite the solution in the database.
refit = yes
Refit the coordinate function? If yes and there is more than one feature
and a coordinate function was defined in the reference image database then a new
coordinate function of the same type as in the reference is fit
using the new pixel positions. Otherwise only a zero point shift is
determined for the revised coordinates without changing the
form of the coordinate function.
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 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.
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 = linelists$idhenear.dat
User coordinate list consisting of an ordered list of line coordinates.
Some standard line lists are available in the directory "linelists$":
cl> dir linelists cl> page linelists$README.le
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 keep a processing log. If a null file, "",
is given then no log is kept.
plotfile =
Optional file to contain metacode plots of the residuals.
verbose = no
Print reidentification information on the standard output?
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.
Features identified in vectors from a reference image are reidentified in other images and the results recorded in the database. 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.
The centering algorithm is described under the topic center1d and also in identify. If a feature positions 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 a fitting function is defined for the features in the reference image, say a dispersion function in arc lamp spectra, then the function is refit at each reidentified line or column if the parameter refit is yes. If refitting is not selected then a zero point shift in the user coordinates is determined without changing the form of the fitting function. The latter may be desirable for tracking detector shifts through a sequence of observation using low quality calibration spectra. When refitting, the fitting parameters from the reference are used including iterative rejection parameters to eliminate misidentifications.
If the parameter addfeatures is set additional features may be added after the initial reidentification and function fit using a line list. 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 identify 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 function fit relative to the number found, the mean pixel, user coordinate, and fractional user coordinate shifts relative to the reference coordinates, and the RMS relative to the final coordinate system (whether refit or simply shifted) excluding any iteratively rejected features from the calculation.
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 examine and/or refit the features. A response of yes or YES will put the user in the interactive graphical mode of identify. See the description of this task for more information. The idea is that one can monitor the statistics information, particularly the RMS if refitting, and select only those which may be questionable to examine interactively. A response of no or NO will continue on to the next reidentification. 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, and the initial shift.
If an accessible file name is given for the plot file then a residual plot of the reidentified lines is recorded in this file. The plot file can be viewed with gkimosaic, stdgraph or reading the file with ".read" when in cursor mode (for example with "=gcur").
1. Arc lines and a dispersion solution were defined for the middle aperture in the multispec for arc spectrum a042.ms. To reidentify the other apertures in the reference image and then another arc image:
cl> reiden a042.ms a045.ms inter+ step=1 ver+
REIDENTIFY: NOAO/IRAF V2.9 valdes@puppis Fri 29-Jun-90
Reference image = a042.ms.imh, New image = a042.ms, Refit = yes
Image Data Found Fit Pix Shift User Shift RMS
a042.ms - Ap 24 48/48 47/48 -2.38E-4 -3.75E-6 0.699
Fit dispersion function interactively? (no|yes|NO|YES) (yes): y
a042.ms - Ap 24 48/48 47/48 -2.38E-4 -3.75E-6 0.699
a042.ms - Ap 23 48/48 47/48 0.216 1.32 0.754
Fit dispersion function interactively? (no|yes|NO|YES) (yes): n
a042.ms - Ap 22 48/48 47/48 0.0627 0.383 0.749
Fit dispersion function interactively? (no|yes|NO|YES) (yes): n
a042.ms - Ap 21 48/48 47/48 0.337 2.06 0.815
Reference image = a042.ms.imh, New image = a045.ms, Refit = yes
Image Data Found Fit Pix Shift User Shift RMS
a045.ms - Ap 24 48/48 47/48 -2.38E-4 -3.75E-6 0.699
Fit dispersion function interactively? (no|yes|NO|YES) (yes): y
a045.ms - Ap 24 48/48 47/48 -2.38E-4 -3.75E-6 0.699
a045.ms - Ap 23 48/48 47/48 0.216 1.32 0.754
Fit dispersion function interactively? (no|yes|NO|YES) (yes): N
a045.ms - Ap 22 48/48 47/48 0.0627 0.383 0.749
a042.ms - Ap 21 48/48 47/48 0.337 2.06 0.815
a042.ms - Ap 20 48/48 47/48 -0.293 -1.79 0.726
a042.ms - Ap 19 48/48 48/48 0.472 2.88 0.912
This example is verbose and includes interactive review of reidentifications. The statistics lines have been shortened.
2. To trace a stellar profile and arc lines in long slit images for the purpose of making a distortion correction:
cl> reiden rog022[135,*] "" trace+ cl> reiden rog023 "" sec="mid line" trace+
REVISIONS
REIDENTIFY V2.10.3
The section, nsum, step, and shift parameter syntax was extended to apply to 3D
images. The previous values and defaults may still be used.
REIDENTIFY V2.10
This task is a new version with many new features. The new features
include an interactive options for reviewing identifications, iterative
rejection of features during fitting, automatic addition of new features
from a line list, and the choice of tracing or using a single master
reference when reidentifying features in other vectors of a reference
spectrum. Reidentifications from a reference image to another image is
done by matching apertures rather than tracing. New apertures not present
in the reference image may be added.