viewspectra

viewspectra is a graphical tool for viewing 1-d or 2-d spectra, either single spectra or spectral stacks produced with extract or extract-2dspec.

USAGE

viewspectra

INPUT

none

OUTPUT

none

PARAMETERS

smooth	smoothing width, in angstroms
linelist	file with list of object lines, for identification and analysis
halfwdth	halfwidth, in rows, of extraction strip for 2-d spectra
shuffle	subtract shuffled region?
nod	nod distance, in pixels, for nod & shuffle data
lamint	halfwidth, in Angstroms, of line examination window

Details:

The main viewspectra window looks like this:

Menus

The file menu does the usual. Note that, in specifying a file name, you need not include the .fits extension.

The edit menu allows one to change some of the parameters set in the viewspectra.par file, as well as other parameters.

pref

The line list file may contain a list of candidate object lines, to aid in line identification. It's format is as follows:

wavelength type label name

type may be 0, 1, or 2. Lines of type are displayed in blue, type 1 in green, and type 2 in red. The label and name are optional. The label parameter identifies the line in the display. The name is used in connection with the line buttons option. If line buttons is set a another window is opened with one button for each line in the line list file which has a name specified:

lines

Pressing a button inserts the wavelength of that line into the Rest Lambda box (for which see below).

If a log file name is specified, then a record of the session is maintained in a log file. This record includes the name of each object whose spectrum is displayed, and parameters of each line measured in each object. Be sure that this entry is blank if no logfile is desired.

The EW/(1+z) button affects the calculation of equivalent widths in the line examination window. If this button is set, than measured equivalent widths are adjusted to rest frame values, using the current value of the redshift.

The Autoscale button determines whether the grayscale levels of the spectrum image are calculated automatically, or are set the the values specified in the Min, max inten boxes.

Plots

The upper plot is a trace of the spectrum. If a 2-d spectrum, the displayed spectrum is extracted in a strip centered on the expected slit position of the object +- the number of rows specified with the hlfwd parameter. If parameter nod is set to a non-zero value, the trace is the sum of the spectrum in the strip and the negative of the spectrum in a strip offset by nod distance.
The lower plot is a gray-scale image of the spectrum (if 2-d). If shuffle is set to "yes", it is the image of the difference between the two shuffled spectra. Clicking on a row within this image changes the central extraction line for the upper plot. viewspectra usually does a good job of calculating appropriate intensity ranges for the spectrum image. However, if the range needs changing, clicking the right mouse button within the lower window brings up a popup window:

contrast

New values entered take effect when a carriage return is hit, or when Done is pressed.

Buttons

View buttons

Zoom:      zoom in on the plots. Move the mouse to the lower left hand corner of the region desired, click
   and hold while moving to the upper right hand corner, then release.
Unzoom:    go back to full plot
Print:     send current plot to printer.
Examine: Opens the line examination window, centered on the wavelength specified in the Lambda window.

If the opened file is a stack of 1-d or 2-d spectra, then the following buttons allow one to move between spectra:

< > move forward or back one spectrum.
goto: enter a spectrum number and hit return, to move to that spectrum.

Line ID buttons

Lambda:         displays the wavelength of a feature pointed to with a mouse click, or calculated in the line
                           examination window (see below).
Rest Lambda   Used in combination with a value in the Lambda box to calculate the redshift
z        Redshift, calculated from Rest Lambda and Lambda, or entered for use with Try. Entering a
                         value followed by <return> executes Try.
Try:    displays, in the spectrum plot, the expected wavelengths of the lines listed in the linelist file, for the
                        redshift in the z box. The buttons to the right of the Try button set which of the three types of lines are
                         displayed.

Line examination window

The line examination window shows a section of spectrum, centered on the wavelength given in the Lambda window, and of halfwidth set by the lamint parameter. Spectral lines may be fit with a gaussian by clicking on two points to the left and right of the line, at wavelengths which are the minimum and maximum wavelengths over which the fit is to be made, and at flux levels which specify the continuum levels at these two wavelengths. The continuum is set to a straight line between these two points, subtracted off, and a gaussian fit to the remaining flux. The results for line center, standard deviation and equivalent width (corrected, if set in preferences, to rest frame values) , all in Angstroms, are displayed in the Lambda, sigma and EW boxes. The redshift, z, is recalculated on the basis of the Rest Lamba and the new line center. A rest wavelength must be specified for all of this to work correctly.

The Clear button clears the current fit; the Done button closes the window. The Record button writes the Rest lambda, Lambda, z, sigma, and EW values into the log file, if data logging is switched on.

Note: the nod parameter in the viewspectra parameter file is only needed for older COSMOSdata, or data created with other software. Data created with the current version of COSMOS includes this parameter in the FITS header of _2spec.fits files.

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