HELP · SEE_ALSO
zwavecal -- Calibrate GHRS wavelength observations.
zwavecal input output
zwavecal locates lines in GHRS wavelength observations and fits the GHRS wavelength solution equation, producing a table of coefficients for the solution. This table is suitable as input back into calhrs for recalibration of GHRS observations that may depend on a particular wavelength range.
- IF YOU REQUESTED A SPECTRUM OF THE CAL LAMP AND YOUR OBSERVATION
IS NOT AN FP-SPLIT:
In this case the cal lamp spectrum and the object spectrum should have been obtained at the same carrousel position. These cal lamp spectra can be identified by examining the header keyword "TARGNAME" of the C1H files for the value "WAVE" and/or the keyword "APERTURE" for the value of "SC1" or "SC2". Confirm that the observations are at the same carrousel position using the hedit task to examine the header keyword, "CARPOS".
For echelle observations, one should examine the cal lamp observation. Due to the high dispersion, echelle cal lamp observations may have only a couple features, typically grouped at one end of the spectrum. If so, the solution derived by zwavecal may actually be worse than the one produced by calhrs. If this is the case, use the method below to improve the science observation's wavelengths.
If all the above conditions are satisfied, run zwavecal on the C1H file of the cal lamp observation. The default values for all the parameters have been set appropriately for the GHRS. The resulting output table will be in a suitable format to be used with calhrs. Edit the header of the science observation(s) to be recalibrated with the new solution using hedit or chcalpar. Modify the value of the keyword "CCR6" to the pathname of the newly created output file, and re-run calhrs on the science observation(s).
The simplest way to improve the wavelengths of a particular science observation is to find a calibration lamp observation near to the time the science observation was taken. Such observations can be identified by examining the header keyword "TARGNAME" of the C1H files for the value "WAVE". These can either be GO-requested wavelength calibration observations (described above), or automatically generated SPYBAL observations. (NOTE: the SPYBAL observations are used to center the spectrum on the diode array. These observation are automatically made about once an orbit and immediately before the first use of a particular grating.) Use this observation and its corresponding wavelength solution as input to the waveoff task. Waveoff will calculate the offset between the wavelength solution provided by calhrs and the actual cal lamp observation. This offset can then be applied to the science calibration wavelength solutions. To apply the offset, add the value of the "woffset" column from the output of waveoff to the contents of the C0H images for the science observations, using the imcalc task.
FPSPLIT observations are made at a series of carrousel positions. It is recommended that one apply the wavelength offset as described above to this type of observation.
- zwavecal requires as input observations of one of the spectral
calibration lamps and the wavelength solution for the observations.
In general, this will be the C1H and C0H files as output by the
calhrs task. These files are specified by, respectively, the
input and wave parameters.
Additionally, wavecal requires two tables. One is a list of wavelengths of emission lines of the Platinum-Neon (PtNe) hollow cathode lamps. The second is a table containing the conversion coefficients to convert the dispersion solution determined by wavecal to be relative to the Small Science Aperture (SSA) as opposed to either of the calibration apertures, SC1 or SC2. These tables are distributed with STSDAS; see below for more information.
Using the input wavelength solution and the line list table, approximate positions are determined for emission features in the observation spectrum. The positions are determined using the IRAF center1d algorithm. The parameters for controlling the algorithm are found in the fitpars pset. See the help for the task zwaveid for a more detailed description.
To determine a new dispersion solution, the following iterative process occurs. A least squares fit of the function
s = a0 + a1mw + a2(mw)**2 + a3m + a4w + a5wm**2 + a6mw**2 + a7(mw)**3 where m - order (for non-echelle data, this is 1) w - wavelength
is applied to the data. The sigma of each line is then determined, and, if it is greater than the value specified in the parameter nsigma, the line is flagged as bad and will not be included in the next iteration. This process is repeated until either no lines are flagged as bad, or the maximum number of iterations specified in the parameter maxtry is reached. If the maximum number of iterations is reached, and there are still lines flagged as bad, a warning message is issued. The warning is just that; the dispersion solution is still written out to the output table.
- INPUT IMAGES AND WAVELENGTH SOLUTIONS
- The input should be the calibrated C1H images of GHRS observations of
the internal calibration lamps. The observations can be identified
when the keyword TARGNAME has a value of "WAVE" and/or the keyword
APERTURE has the value "SC1" or "SC2".
The input wavelength solutions will the C0H images of the observations.
- A table, in the form of the GHRS CCR6 reference table, will be
generated. The columns of the table are as follows:
- The grating used.
- The carrousel position that the dispersion is calculated for.
- A0, A1, A2, A3, A4, A5, A6, A7
- The dispersion coefficients.
- There are twenty-two columns which specify the temperatures of various parts of the instrument at the time the observation was taken which was used to determine the dispersion coefficients. This is used by calhrs to correct for thermal motion.
- For each unique carrousel position, an optional table is created which
contains the evaluation of the fit coefficients with the data used to find
the fit coefficients. The header parameters found in these
- The carrousel position used by the input observations.
- The dispersing element, or grating, used by the input observations.
- The aperture used by the input observations.
The columns of the fit tables are as follows:
- The spectral order of the observations used to produce the line positions. For single order gratings, the value is "1".
- The known wavelength of the identified feature.
- The sample position of the identified feature.
- The sample position of the feature's wavelength as calculated by the equation using the determined set of coefficients.
- The difference between the observed sample position and the calculated sample position.
- LINE WAVELENGTH TABLE
- This input table specifies the known wavelengths of features that may
appear in the input calibration observation images. This table may
have one or two columns. The column names are specified by the
parameters "lines_col" and "strength_col". The columns are defined as
- This column should contain the known wavelengths of features that may be found in the input calibration observations. This column must be present.
- strength_col [optional]
- This column contains the "strengths" of the features. If blank, no line strength information will be read. This information is used by zwavecal only to decide which line identification should be assigned to an observed feature, where stronger lines take precedence over weaker lines. If no strength information is provided, zwavecal will not delete duplicate line identifications.
- INTERACTIVE MODE
- In graphics interaction mode, zwavecal provides graphs showing the
observational spectrum, an artificial spectrum created with the
located lines, and optionally, an artificial spectrum of the line list
before the lines have been located in the observation. Below are the
keystrokes and "colon" commands available to the user while in
- Shows the available cursor commands.
- Hitting the <space> key will return the location of the cursor in both
wavelength and pixel space. The form of the output is:
- Start a colon command. See below for list of colon commands.
- Plot all the spectra. The observational spectrum, the predicted artificial spectrum, and the located artificial spectrum are all plotted. A key on the right of the graph indicate what type of line corresponds to each spectrum.
- Plot both artificial spectra. Both the predicted and located artificial spectra are plotted, omitting the observational spectrum. A key on the right of the graph indicates what type of line corresponds to each spectrum.
- Get information on the line whose located position is nearest the
graphics cursor. The following message is returned:
line xxxx located at pixel xxx wavelength xxxx where 'line xxxx' is the line's known wavelength 'pixel xxx' is the pixel position of the line 'wavelength xxx' is the wavelength of that pixel as determined by the provided wavelength solution
- Identify a line. The use of the i key is a three step process. It
is best to use the i key when the observed spectrum and predicted
line spectrum are plotting simultaneously, (see the p key).
The first time the i key is hit, instructions on the use of the i key are printed:
Select observed feature to identify
Place the graphics cursor on a feature in the observed spectrum that will be identified, then hit the i key again. The following instruction is printed:
Select line associated with feature
Place the graphics cursor on the feature in the predicted spectrum and hit the i key again. The selected feature will be associated with the selected line, determining a new zero-point offset. The locating phase will then re-execute, determining new locations for lines. The zero-point offset calculated can be queried using the "offset" colon command.
- Plot the observational spectrum and the located artificial spectrum. A key to the right of the plot indicates which plot refers to which spectrum.
- Next spectrum. The accept the line locations found for the current spectrum and start processing the next. This is the same functionality as the q and EOF keys.
- Plot predicted and observed spectra. A key to the right of the graph indicates which line type corresponds to which spectrum.
- Next spectrum. The accept the line locations found for the current spectrum and start processing the next. This is the same functionality as the n and EOF keys.
- Redraw. Simply redraw the graphs.
- Silent. Accept the line locations of the current spectrum and end interactive mode. If there are more spectra to be processed, they will be done without graphics interaction.
- Execute the gtools windowing options. Refer to the help for gtools
for more information. The next key may be one of the following:
- Autoscale x and y axes.
- Set bottom edge of window.
- Center window at cursor position.
- Shift window down.
- Expand window (mark lower left and upper right of new window)
- Flip x axis.
- Flip y axis.
- Set left edge of window.
- Set right edge of window.
- Shift window left.
- Autoscale x axis.
- Autoscale y axis.
- Pan x and y axis about cursor.
- Shift window right.
- Set top edge of window.
- Shift window up.
- Zoom x axis about cursor.
- Zoom y axis about cursor.
- Zoom x and y axes about cursor.
- Recalculate zero-point offset with cross correlation.
- Next spectrum. The accept the line locations found for the current spectrum and start processing the next. This is the same functionality as the n and q keys.
Below is the list of colon commands available.
- no_dups [yes/no]
- Show/change state of no_dups. If "yes", only the "brightest" lines, as determined by the line list table, will be allowed at the same pixel location. If "no", all lines located are allowed, despite the fact that some may be assigned to the same observed feature. With no argument, the current state is reported.
- offset [value]
- Show/set value of the zero-point offset. The units of the offset should first be set using the "units" colon command (see below). With no argument, the current offset is displayed.
- radius [value]
- Show/set number of pixels to search around the predicted pixel position for a feature. With no argument, the current value is displayed.
- sigma [value]
- Show/set value of sigma for artificially generated spectra. If an argument is provided, it is taken as the sigma of the gaussian used to create the artificial spectra based on the predicted/located positions of lines. With no argument, the current value is displayed.
- thresh [value]
- Show/set threshold for true observed features. If an observed emission has peak flux less than this value, it will not be used. With no argument, the current value is displayed.
- units [wavelength,pixel,sample]
- Show/set the units of the zero-point offset. The units should be set before the offset is specified with the "offset" colon command. With no argument, the current units are displayed.
- width [value]
- Show/set feature width size. With argument, reset feature width size. With no argument, report on current size.
- xcor [yes/no]
- Show/set whether cross-correlation should be used to find the initial zero-point offset. "yes" will recalculate the zero-point offset before the lines are located. "no" will use the offset specified by the "offset" command or the value specified initially in the "offset" task parameter. This command has no effect on the current spectrum; it will only effect subsequent spectra. With no argument, the current state will be displayed.
- input [file name template]
- The input list of image header file names. A single file, a wildcard-specified template, or an "@" followed by a file name containing the list of observations to process may be specified.
- output [table name]
- Name of the table containing the fitted coefficients.
- (wave = "") [file name template]
- The input list of image header file names which contain the wavelength solutions for the input list of observation images. A single file, a wildcard-specified template, or an "@" followed by a file name containing the list of wavelength solution images may be specified. If an image name does not have an extension, the extension specified in the defwavext parameter will be used. If blank, the rootnames of the input observations and the extension in defwavext will be appended to determine the name of the wavelength solution images.
- (defwavext = "c0h") [string]
- Extension appended to the wavelength image header file names if no extensions are specified. Or, if no wavelength images are specified, the extension appended to the input image header file names to find wavelength solution image names.
- (fittab = "") [table name]
- Rootname of the tables containing the evaluation of the equation using the final coefficients. If blank, no tables are produced. The form of the tables names is the value of fittab appended with the string "_XXXXX" where XXXXX is the carrousel position at which the fit was produced.
- (interactive = no) [yes,no]
- Enter graphics interaction mode.
- (dvpar = "") [pset]
- The pset containing the graphics device parameters. If blank, the pset dvpar is used. The only pertinent parameter in this pset is the device parameter specifying which graphics device should be used.
- (findpars = "") [pset]
- Name of the parameter set specifying the initial parameters for the
line finding algorithm. If blank, the pset findpars will be used.
The parameters in this pset are as follows:
- (lines = "scidata$czptnelinec") [table name]
- Name of the table containing the line list to search for in the input observations.
- (lines_col = "wavelength") [column name]
- The name of the column in the "lines" table which contains the known wavelengths of features that may appear in the input observations. This column is required to exist and be properly populated.
- (strength_col = "intensity") [column name]
- The name of the column in the "lines" table which contains the intensities of the features listed. This column is optional; if blank, this information will not be accessed/used by zwaveid. The effect is that zwaveid will not be able to delete multiple identifications for a feature in an observation.
- (cross_corr = yes) [yes/no]
- When reading each input observation/wavelength solution, perform cross correlation with an artificially generated spectrum based on the provided wavelength solution an information in the "lines" table. The result of the cross correlation is used to determine an initial zero point offset in the wavelength scale. If "no", the initial cross correlation is not done and the initial zero-point offset is that specified by the parameter "offset".
- (max_shift = 20) [integer]
- If doing cross correlation, this is the maximum shift the correlation process will examine for shifts between an observation and its corresponding wavelength solution.
- (offset = 0.) [real]
- If cross correlation is not used, this is the zero-point offset that
should be applied to the provided wavelength solution before lines are
located in the observation. The offset is calculated as follows,
depending on what units are of interest:
pixel(obs) = pixel(predicted) + offset wavelength(known) = wavelength(predicted) + offset sample(obs) = sample(predicted) + offset
where all the "predicted" quantities are determine using the wavelength solution, while the "obs" and "known" quantities are determined from the observation and input line list.
- (units = "pixel") [pixel,sample,wavelength]
- The units of the specified offset.
- (width = 5.) [real]
- Width of the observed features in pixels. This corresponds directly to the width argument for the center1d algorithm (see SEE ALSO).
- (radius = 5.) [real]
- Number of pixels on each side an initial guess of the feature location to search for an observed feature. This corresponds directly to the radius argument for the center1d algorithm (see SEE ALSO).
- (threshold = 20.) [real]
- The minimum flux required for an observed feature to be considered a valid feature. The units need only be the same as the flux units of the input observations.
- (no_dups = yes) [yes,no]
- If "yes" and line strengths were specified in the input line list table, zwaveid will look for observed features assigned to two or more lines. The feature will be identified with the line having the numerically larger strength while the other identifications will be deleted.
- (fitpars = "") [pset]
- Parameter set containing the fitting parameters. The parameters are
- (offlib = "scidata$czscoffc") [table name]
- Name of the table containing the SC1/SC2 to SSA offset coefficients to convert the calculated equation solution to the SSA aperture. If not specified, the conversion will not occur. If the wavelength solution is not converted, and one will use the results in calhrs, the calibration flag, "IAC_CORR" must be set to "OMIT".
- (maxtry = 3) [integer, minimum=0]
- The number of regression tries to improve the fit to the equation by throwing out lines. If the number of tries exceeds this value, a warning message will be posted, and the coefficients for the last attempt will be written to the output table.
- (nsigma = 2.5) [real, minimum=0.]
- The number of sigma away from the fit a point needs to be in order to be removed from the list of valid points to fit in the next attempt.
- (defcoef = yes) [yes/no]
- Find the "default" coefficients in the equation. For the GHRS, each
grating mode need only solve for some of the coefficients in the
equation; the other coefficients are set to zero. If "yes", zwavefit
will find these coefficients (see table below). If "no", zwavefit will
determine which coefficients to solve for from the parameters "a0"
through "a7" (see below).
The default coefficients for the GHRS gratings are as follows:
GRATING COEFFICIENTS G140M a0, a1, a2 G160M a0, a1, a2 G200M a0, a1, a2 G270M a0, a1, a2 G140L a0, a1, a2 ECH-A a1, a1, a2, a4 ECH-B a0, a1, a2, a4
- (a0, a1, a2, a3, a4, a5, a6, a7) [real]
- If defcoef is "no", these parameters will determine whether zwavefit will fit for the coefficient or not. If the value of a parameter is INDEF, zwavefit will fit for its value. If the parameter has any other value, zwavefit will set the coefficient to that value and hold it constant during the fitting process.
- (verbose = no) [yes/no]
- Print detailed messages about the progress of zwavecal. If "no", only the current carrousel position being analyzed is shown, along with the fit information. If "yes", each step in zwavecal prints a message.
- (aper_list = "", cpos_list = "")
- These are non-user parameters used internally by zwavecal.
1. An observer has received two observations. One, z0x10101, is a SPYBAL automatically taken just before the science observation, z0x10102. Since the science and the cal lamp observations are at different carrousel positions, waveoff will be used to determine a linear offset, which will then be applied to the science observation.
cl> waveoff z0x10101 # file woffset poffset soffset correlation z0x10101.c1h[1/1] -0.0188 -0.8046 -0.2015 0.4463 cl> imcalc z0x10102.c0h z0x10102_fixed.c0h "im1-0.0188"
2. A GO has two observations. The first, z0x10101t, is a cal-lamp observation requested by the GO at the same carrousel position as the science observation, z0x10102t. The science observation is not an FP-SPLIT, so a new dispersion can be used in calhrs to improve the wavelength solution. The new calibrated files will have the rootname "new_102_calibrated".
cl> zwavecal z0x10101t new_disp cl> hedit z0x10102t.d0h ccr6 new_disp.tab cl> calhrs z0x10102t new_102_calibrated
Refer to the references in the package level help. Type "help hrs option=sys".
For assistance using this or any other tasks, please contact firstname.lastname@example.org or call the help desk at 410-338-1082.