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- Quick Reduction of HDS data on IRAF
This page is an explanation of the quick reduction of
Subaru HDS (High Dispersion Spectrograph) data
on ANA system at Subaru summit/remote observation system.
Basically, this page describes the quick reduction scheme on
ANA system at summit or remote observing room.
But, if you want, you can make same environment on your
owned IRAF system.
(Please download and install CL-scrpts here.)
Under this reduction scheme,
all data should be reduced to one dimensional spectra.
If you want to keep the spatial information on them,
you have to find another solution to reduce your data.
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|
| [1] |
Login to ANA from its console,
using the user account foryour obs. (u05XXXX).
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| [2] |
Right click on your desktop.
Select the menu item "Subaru Observatory Software System (ANA Only)
login".
"ANA Menu" Window will come up.
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| [3] |
Push "HDS" button in ANA Menu.
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| [4] |
An xgterm for IRAF and a terminal for "hdsdir" come up.
For the first time, "mkiraf" command to create your IRAF environment
is running in the xgterm.
Please type "xgterm" for your teminal selection in mkiraf.
"hdsdir" is a program which keep watching your data directory.
It can be used as a simple auto log system for your observation.
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| [5] |
You can use tasks "overscan" for overscan region crrection
and "hdsql" for HDS quick data reduction on this IRAF
without any settings by yourself.
The environment arguments, stdimage=imt4096, imtype="fits",
have been also registred already.
|
| [6] |
Copy IRAF user parameters (uparm) optimized for HDS data analysis
to your directory.
cp /opt/share/hds/iparm/* ~/uparm/
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| [7] |
In IRAF terminal,
cl> cd /work/o0XXXX
You should work under this directory.
Your data is archived in "/data/o0XXXX/" (read only).
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|
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[Reduction scheme using "hdsql"]
Left side is the inside of the task "hdsql".
Before "hdsql", you should do preparations (1-3) on the right side.
Red circles
in the figure
are necessary processes at least to get one dimensional spectra.
IRAF tasks used in each processes are written
in this color.
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|
After this,
I will explain how to do quick data look of HDS on ANA,
using the task "hdsql" on IRAF.
Upper figure shows these processes.
If you do full processes of this quick analysis,
you can get one-dimensional, flat-fielded, and wavelength
calibrated spectra.
However, each processes in "hdsql" can be skipped,
if not necessary.
Before using "hdsql", preparations 1-3 on the right side of the
figure are required.
If you can skip flat-fielding and/or wavelength calibration,
you should do preparation 1 at least.
After these preparation processes,
you should use "hdsql" for each object frames.
HDS has two CCD chips on its camera.
So, one exposure has two frame IDs.
The red CCD has odd HDSA numbers (=CCD1/Left side CCD),
and the blue one has even HDSA numbers (=CCD2/Right side CCD).
These Red/Blue frames should be analyzed independently.
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|
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Each red/blue CCDs of HDS have two read out points.
And there is over scan region at the ceter of frame
(please see users' manual of HDS).
Instead of subtruction of independent BIAS frames,
an average count in this overscan region
should be subtructed from object frames.
The task "overscan" does this process.
This task also converts ADU to electron numbers (× ∼1.7)
Raw frames of HDS before "overscan"
have FITS extention table in them.
So, in IRAF, you have to designate each raw frames like
"hogehoge.fits[0]",
attached "[0]" to their file names.
At the beginning of "hdsql" analysis,
we will start form this "overscan" process for raw frames.
Before making of a template for order tracing,
a raw frame for a template should be "overscan" processed.
So, I will explain how to do on;y "overscan"
using "hdsql".
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| [1] |
Confirm the data directory, in which raw data frames
(HDSA000XXXXX.fits) archived.
Usually, it should be like /data/o05XXXX/ .
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| [2] |
In IRAF terminal,
cl> eparam hdsql
determin parameters for "hdsql".
The parameter "indirec" is the raw data directory
confirmed in [1] + header of raw data filename ("HDSA000" usually).
And file number without header should be inserted in parameter
"inid".
Overscanned data are automatically created into the current working
direcotry.
So, you don't have to copy any raw data to your working direcotry.
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PACKAGE = echelle
TASK = hdsql
inid = 22045 Input frame ID
indirec = /data/o05129/HDSA000 directory of Input data
overscan= yes Overscan?
cosmicra= no Cosmicray-event rejection?
scatter = no Scattered light subtraction?
flat = no Flat fielding?
apall = no Extract spectra with apall?
wavecal = no Wavelength calibration?
(os_save= yes) Save overscaned data?
......
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|
| [2] |
Execute "hdsql" with these parameters.
An overscanned file "H22045o.fits" should be created.
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↑Before OverScan(Red CCD)
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→
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↑After OverScan(Red CCD)
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[Preparation 1]
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Templates for order trace can be made from
a frame of a bright (standard) star or
flats.
If you are using standard wavelength setting (cf. StdYb),
you can use standard templates like "StdYbLshsl2x2.fits"
in "/opt/sharey/hds/" directory.
This "StdYbLshsl2x2.fits", filename means
Wavelength Setting : StdYb, The Left CCD (Red), 2x2 binning.
Then, you can skip the following process of making a template.
In this case,
you should also copy a aperture information file in
"/opt/share/hds/database/" directory to the "database/"
directory in your working place.
|
| [1] |
Using "hdsql", do only overscan for a frame, which you want to
make a template.
Rename created HXXXXXo.fits to some meaning filename
(Here, we use "apYbL2x2.fits".).
|
| [2] |
Execute task "apall" for this overscanned file
with following parameters.
If the process fails in aparture extraction
due to bad column,
it can be solved by a small change of the parameter "line"
(default "INDEF" means the center of the chip along the dispersion
direction.
For example, in the case of 2x2 binning, this default value is
1000. So, try 1200 or 800 as the value of "line".).
In aperture extraction display (xgterm, the below left image),
"m"-key is for manual detection of a order.
"o"-key on the line which should be the 1st order
→Aperture(1)="1" sort the order of aperture number.
Then, "q"-key for the next fitting.
For the following some questions, basically just say "yes"
(hit return) in usual case.
In fitting display (the below right image),
"s"→"s"-keys is for the elimination
of affected region with bad column.
"t"-key is for the clear of this regional selection.
"f"-key is re-fit of the tracing.
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PACKAGE = echelle
TASK = apall
input = apYbL2x2 List of input images
(output = ) List of output spectra
(apertur= ) Apertures
(format = echelle) Extracted spectra format
(referen= ) List of aperture reference images
(profile= ) List of aperture profile images
(interac= yes) Run task interactively?
(find = yes) Find apertures?
(recente= yes) Recenter apertures?
(resize = yes) Resize apertures?
(edit = yes) Edit apertures?
(trace = yes) Trace apertures?
(fittrac= yes) Fit the traced points interactively?
(extract= yes) Extract spectra?
(extras = yes) Extract sky, sigma, etc.?
(review = yes) Review extractions?
(line = INDEF) Dispersion line
(nsum = 20) Number of dispersion lines to sum or median
# DEFAULT APERTURE PARAMETERS
(lower = -20) Lower aperture limit relative to center
(upper = 20) Upper aperture limit relative to center
(apidtab= ) Aperture ID table (optional)
# DEFAULT BACKGROUND PARAMETERS
(b_funct= chebyshev) Background function
(b_order= 1) Background function order
(b_sampl= -10:-6,6:10) Background sample regions
(b_naver= -3) Background average or median
(b_niter= 0) Background rejection iterations
(b_low_r= 3.) Background lower rejection sigma
(b_high_= 3.) Background upper rejection sigma
(b_grow = 0.) Background rejection growing radius
# APERTURE CENTERING PARAMETERS
(width = 15.) Profile centering width
(radius = 30.) Profile centering radius
(thresho= 0.) Detection threshold for profile centering
# AUTOMATIC FINDING AND ORDERING PARAMETERS
nfind = 22 Number of apertures to be found automatically
(minsep = 40.) Minimum separation between spectra
(maxsep = 1000.) Maximum separation between spectra
(order = increasing) Order of apertures
# RECENTERING PARAMETERS
(aprecen= ) Apertures for recentering calculation
(npeaks = INDEF) Select brightest peaks
(shift = no) Use average shift instead of recentering?
# RESIZING PARAMETERS
(llimit = -17.) Lower aperture limit relative to center
(ulimit = 17.) Upper aperture limit relative to center
(ylevel = 0.05) Fraction of peak or intensity for automatic width
(peak = yes) Is ylevel a fraction of the peak?
(bkg = no) Subtract background in automatic width?
(r_grow = 0.) Grow limits by this factor
(avglimi= yes) Average limits over all apertures?
# TRACING PARAMETERS
(t_nsum = 10) Number of dispersion lines to sum
(t_step = 3) Tracing step
(t_nlost= 10) Number of consecutive times profile is lost befor
(t_funct= legendre) Trace fitting function
(t_order= 3) Trace fitting function order
(t_sampl= *) Trace sample regions
(t_naver= 1) Trace average or median
(t_niter= 2) Trace rejection iterations
(t_low_r= 3.) Trace lower rejection sigma
(t_high_= 3.) Trace upper rejection sigma
(t_grow = 0.) Trace rejection growing radius
# EXTRACTION PARAMETERS
(backgro= none) Background to subtract
(skybox = 1) Box car smoothing length for sky
(weights= none) Extraction weights (none|variance)
(pfit = fit1d) Profile fitting type (fit1d|fit2d)
(clean = no) Detect and replace bad pixels?
(saturat= INDEF) Saturation level
(readnoi= 0.) Read out noise sigma (photons)
(gain = 1.) Photon gain (photons/data number)
(lsigma = 4.) Lower rejection threshold
(usigma = 4.) Upper rejection threshold
(nsubaps= 1) Number of subapertures per aperture
(mode = ql)
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|
| [3] |
An one-dimensional spectrum, "apYbL2x2.ec.fits",
is created now.
The aparture information of this file is saved in
"database/apapYbL2x2" .
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↑Aperture finding in "apall"
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↑Order fitting in "apall"
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[Preparation 2]
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Using above order trace template,
make a normalized flat frame from raw flat frames.
Of course, you can skip this process,
if you don't need flat-fielding in your quick look analysis.
Even for standard settings,
standard flat frames are not saved in "/opt/share/hds" directory.
So, if you want to do flat-fielding,
this process is always required at least at once.
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| [1] |
Overscan each raw flat frames using "hdsql".
In the most case (except in the case of Near-IR),
two sets of flat frames,
whose maximum ADU optimized for red and blue CCD respectively,
are taken.
So, you should select raw flat frames only optimized for your
analyzing color.
|
| [2] |
Make a text list file of your overscanned flat frames (HXXXXXo.fits)
with a text editor ("vi" or "mule" etc).
Using "imcombine" task, make an averaged flat frame.
(combine=average).
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| [3] |
Using the task "apflatten", make a normalized flat frame.
For "refren" field, input the filename of order trace template.
The order of fitting function (the below right image)
should be relatively high (7-13?).
In xgterm window, type like ":order 11" to change the fitting order
number. Then type "f"-key for re-fitting.
The process to exclude effect of bad column and/or chip edges
is similar to the case of "apall".
The output file, "FlatYbL2x2.nm.fits", will be used as
a flat frame in the following "hdsql".
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PACKAGE = echelle
TASK = apflatten
input = FlatYbL2x2 List of images to flatten
output = FlatYbL2x2.nm List of output flatten images
(apertur= ) Apertures
(referen= apYbL2x2) List of reference images
(interac= yes) Run task interactively?
(find = yes) Find apertures?
(recente= yes) Recenter apertures?
(resize = yes) Resize apertures?
(edit = yes) Edit apertures?
(trace = yes) Trace apertures?
(fittrac= yes) Fit traced points interactively?
(flatten= yes) Flatten spectra?
(fitspec= yes) Fit normalization spectra interactively?
(line = INDEF) Dispersion line
(nsum = 100) Number of dispersion lines to sum or median
(thresho= 10.) Threshold for flattening spectra
(pfit = fit1d) Profile fitting type (fit1d|fit2d)
(clean = no) Detect and replace bad pixels?
(saturat= INDEF) Saturation level
(readnoi= 0.) Read out noise sigma (photons)
(gain = 1.) Photon gain (photons/data number)
(lsigma = 4.) Lower rejection threshold
(usigma = 4.) Upper rejection threshold
(functio= spline3) Fitting function for normalization spectra
(order = 3) Fitting function order
(sample = *) Sample regions
(naverag= 1) Average or median
(niterat= 5) Number of rejection iterations
(low_rej= 3.) Lower rejection sigma
(high_re= 3.) High upper rejection sigma
(grow = 0.) Rejection growing radius
(mode = q)
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↑Aperture finding in "apflatten"
(Using order trace template with
resize and recenter)
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↑Order fitting in "apflatten"
(Fitted by spline3 order=9)
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[Preparation 3]
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Using above order trace templates,
making a wavelength information frame from
a Th-Ar (comparison) frame.
If you don't need wavelength calibration in your quick look
analysis, of course you can skip this process.
Wavelength calibrated Th-Ar frames for some standard settings
are stocked also in "/opt/share/hds/" directory.
You can use files like "THARStdYbL2x2.fits"
(Wavelength:StdYb, The left CCD(Red), 2x2 binning)
as a wavelrngth information file,
if it is suitable for your setting.
In such case,
you should also copy an information file in database/ directory
(cf. ecTHARStdYbL2x2) to database/ directory in your working place.
|
| [1] |
Using "hdsql" for a raw frame of Th-Ar,
proceed "overscan" and "apall" at this time.
For the aperture refrence of "apall",
input the source file of order trace template which already
made in other preparation process.
And don't resize, recenter and edit apreture in "apall".
In order to save the file after "apall" set the parameter,
"ap_save=yes".
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PACKAGE = hds
TASK = hdsql
inid = 22073 Input frame ID
indirec = /data/o05129/HDSA000 directory of Input data
overscan= yes Overscan?
cosmicra= no Cosmicray-event rejection?
scatter = no Scattered light subtraction?
flat = no Flat fielding?
apall = yes Extract spectra with apall?
wavecal = no Wavelength calibration?
(os_save= yes) Save overscaned data?
(......)
(ap_save= yes) Save apalled data?
(ap_in = ) Input frame for apall (if necessary)?
(ap_refe= apYbL2x2) Reference frame for apall
(ap_inte= yes) Run apall interactively?
(ap_rece= no) Recenter apertures?
(ap_resi= no) Resize apertures?
(ap_edit= no) Edit apertures?
(ap_trac= no) Trace apertures?
(ap_fitt= no) Fit the traced points interactively?
(ap_llim= INDEF) Lower aperture limit relative to center
(ap_ulim= INDEF) Upper aperture limit relative to center
(ap_ylev= 0.05) Fraction of peak for automatic width determinatio
(ap_peak= yes) Is ylevel a fraction of the peak?
(......)
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|
| [2] |
An one-dimensional spectra, "H22073o_ec.fits", is created.
Rename this file to other filename with
meanings, like "ThArYbL2x2.ec.fits".
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| [3] |
Do "ecidentify" to the renamed one-dimensinal file.
In usual case, you should identify 5 or 6 points per order.
.
After finished inputs along all orders(you can skip 2-3 orders),
"f"-key makes a wavelength fitting.
Then, in xgterm window, change x & y order numbers
with ":xorder 4", ":yorder 4" (In usual case, 4th order is enough
for this fitting.).
Delete out-stand points with "d"-key and re-fit with "f"-key.
If the fitting error becomes small enough
(<0.005Å, It could be changed by the resolution of the
spectrograph),
hit "l"-key to register all lines in the list.
Then, adjust the fitting error again in the same way.
If it becomes small enough, quit with "q"-key.
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PACKAGE = echelle
TASK = ecidentify
images = ThArYbL2x2.ec Images containing features to be identified
(databas= database) Database in which to record feature data
(coordli= linelists$thar.dat) User coordinate list
(units = ) Coordinate units
(match = 1.) Coordinate list matching limit in user units
(maxfeat= 1000) Maximum number of features for automatic identifi
(zwidth = 10.) Zoom graph width in user units
(ftype = emission) Feature type
(fwidth = 4.) Feature width in pixels
(cradius= 5.) Centering radius in pixels
(thresho= 10.) Feature threshold for centering
(minsep = 2.) Minimum pixel separation
(functio= chebyshev) Coordinate function
(xorder = 2) Order of coordinate function along dispersion
(yorder = 2) Order of coordinate function across dispersion
(niterat= 0) Rejection iterations
(lowreje= 3.) Lower rejection sigma
(highrej= 3.) Upper rejection sigma
(autowri= no) Automatically write to database?
(graphic= stdgraph) Graphics output device
(cursor = ) Graphics cursor input
(mode = q)
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↑Th-Ar line identification in "ecidentify"
(about 6 lines in each order)
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↑Fitting error in "ecidentify"
(<0.01Å with 2x2 binning, 0.6 arcsec slit)
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After above "preparations"(1 is indispensable, 2 & 3 are can
be skipped) have been finished,
you can start the quick look of each object spectra with the task
"hdsql".
In "hdsql", you can slect do or skip for
each processes in it (wavelength calib.,
flat-fielding, cosmic ray removement and
scattered light removement).
If you want to skip them,
you should input "no"
in each parameter in "hdsql".
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| [1] |
The order of the reduction processes in "hdsql" can be described as...
(1)overscan, (2)cosmic ray removement, (3)scattered light removement,
(4)flat fielding, (5)aperture trace, (6)wavelength calibration .
At least, (1) & (5) are necessary to get one dimensional
spectra for the quick look.
The following parameter list is showing the setting to get full
reduction of "hdsql".
If you want to skip each process in "hdsql",
just set "no" for the correspond parameter ("overscan",
"cosmicra","scatter", "flat","apall","wavecal").
The insides of each process are described in the following.
| (1) |
overscan
This task calculate the average ADU in overscan regions in
each frame and then subtract this value from the entire
image.
Therefore, this process is very similar to BIAS subtraction.
At the same time, it change counts in the frame from ADU to
electron numbers, multiplying conversion factors (≈1.7)
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| (2) |
cosmic-ray noise removement
This process is done by the task "wacosm11".
This task applies median filter to the object frame at first,
fixes out-stand pixels,
then, replace counts of these pixels with extrapolated values.
The important parameter of this task is the baseline count
"cr_base".
This should be similar to the peak count of the object frame.
(Smaller value is better to find cosmic ray hits.
But it is afraid that smaller value can lead misunderstanding
real count as cosmic ray hits.)
In order to execute this process,
the parameter "cosmicra" should be set to "yes".
And if you want to save the result of this process,
the parameter "cr_save" should be "yes".
The resultant frame becomes like "H22045oc.fits",
added "c" to its file name.
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| (3) |
scattered light removement
This process uses the task "apscatter"
It does the curved surface fitting with
inter order region ,
and subtruct from the object frame.
In order to execute this process,
the parameter "scatter" should be set to "yes".
And if you want to save the result of this process,
the parameter "sc_save" should be "yes".
The resultant frame becomes like "H22045ocs.fits",
added "s" to its file name.
Other parameters (sc_*) are same with ones in the task
"apscatter".
The order trace template (Here, "apYbL2x2")
should be appointed to the parameter "sc_refe".
You can select with the parameter "sc_inte" whether the process
proceeds interactively or not.
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| (4) |
flat fielding
You have to prepare normalized flat with preparation 2
process above, if you want to do flat fielding.
Here, we use "FlatYdL1x1sn.fits" as the resultant normalized
flat.
In order to execute this process,
the parameter "flat" should be set to "yes".
And if you want to save the result of this process,
the parameter "fl_save" should be "yes".
The resultant frame becomes like "H22045ocsf.fits",
added "f" to its file name.
The normalized flat flame should be set in the parameter
"fl_refe".
|
| (5) |
aperture extraction
This process uses the task "apall".
You have to set the order trace template frame,
prepared in the preparation 1 process above,
in "ap_refe" parameter.
You can also select with the parameter "ap_inte" whether this
process proceeds interactively or not.
In order to execute this process,
the parameter "apall" should be set to "yes".
And if you want to save the result of this process,
the parameter "ap_save" should be "yes".
The resultant frame becomes like "H22045ocsf_ec.fits",
added "_ec" to its file name.
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| (6) |
wavelength calibration
This process uses the tasks "refspectra" and "dispcor".
You have to prepare wavelength calibrated comparison frame
with preparation 3 process above, if you want to do wavelength
calibration.
Here, we use "ThArYbL2x2.ec.fits" as the resultant comparison frame.
In order to execute this process,
the parameter "wavecal" should be set to "yes".
And if you want to save the result of this process,
the parameter "wv_save" should be "yes".
The resultant frame becomes like "H22045ocsf_ecw.fits",
added "w" to its file name.
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The following parameter set is an example for the full reduction
on "hdsql".
Here, it appoints an order trace template(apYbL2x2),
a normalized flat (FlatYbL2x2.nm) and
a wavelength calibrated ThAr frame (ThArYbL2x2.ec) as its parameters.
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PACKAGE = hds
TASK = hdsql
inid = 22081 Input frame ID
indirec = /data/o05129/HDSA000 directory of Input data
overscan= yes Overscan?
cosmicra= yes Cosmicray-event rejection?
scatter = yes Scattered light subtraction?
flat = yes Flat fielding?
apall = yes Extract spectra with apall?
wavecal = yes Wavelength calibration?
(os_save= yes) Save overscaned data?
(cr_in = ) Input frame for wacosm1 (if necessary)
(cr_save= yes) Save cosmicray processed data?
(cr_base= 2000.) Baseline for wacosm1
(sc_in = ) Input frame for scattered light subtraction (if
(sc_refe= apYbL2x2) Reference for aperture finding
(sc_save= yes) Save scattered light subtracted data?
(sc_inte= yes) Run apscatter interactively?
(sc_rece= yes) Recenter apertures for apscatter?
(sc_resi= yes) Resize apertures for apscatter?
(sc_edit= yes) Edit apertures for apscatter?
(sc_trac= no) Trace apertures for apscatter?
(sc_fitt= no) Fit the traced points interactively for apscatte
(fl_in = ) Input frame for flat fielding (if necessary)
(fl_refe= FlatYbL2x2.nm) Flat frame
(fl_save= yes) Save flat-fielded data?
(ap_save= yes) Save apalled data?
(ap_in = ) Input frame for apall (if necessary)?
(ap_refe= apYbL2x2) Reference frame for apall
(ap_inte= yes) Run apall interactively?
(ap_rece= yes) Recenter apertures?
(ap_resi= yes) Resize apertures?
(ap_edit= yes) Edit apertures?
(ap_trac= no) Trace apertures?
(ap_fitt= no) Fit the traced points interactively?
(ap_llim= INDEF) Lower aperture limit relative to center
(ap_ulim= INDEF) Upper aperture limit relative to center
(ap_ylev= 0.05) Fraction of peak for automatic width determinati
(ap_peak= yes) Is ylevel a fraction of the peak?
(wv_save= yes) Save wavelength-calibrated data?
(wv_in = ) Input frame for wavelength calibration (if neces
(wv_refe= ThArYbL2x2.ec) Reference frame for refspectra
(mode = q)
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|
| [2] |
If the task works well,
you can get a final resultant spectrum file,
like "H22081ocsf_ecw.fits".
Added "ocsf_ecw" in the filename means
"o"=overscan, "c"=cosmicray removed, "s"=scatterd light removed,
"f"=flat fielded, "_ec"=aparture extracted, "w"=wavelength
caliblated.
If you set parameters to save files after each process,
you should find such processing frames with it.
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↑Scattered light fitting in "apscatter"
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|
| [1] |
HDS creates two frames from Red and blue CCD
with one exposures.
So, you have to create two calibration file sets
in your preparation phase for both color reduction.
If you want to reduce your data simultaneously
(Maybe you want to do it during your observation.),
you can use tasks "hdsql1" and "hdsql2" in ANA,
which has just same function of "hdsql".
So, in ANA, you can use "hdsql" for Red CCD reduction
and "hdsql1" for Blue CCD's for example.
|
| [2] |
This task cannot overwrite resultant frames.
So, before you redo the same process for the same file,
you should rename or delete existing resultant files.
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| [3] |
If the task stopped for some reasons with some errors,
some temporary files with "tmp*" filename could be remained in your
working directory.
You shoould delete such file before your next reduction.
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hdsql.cl,
wacosm11.cl,
overscan.cl
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After downloaded above three cl script files
and added following configuration in your "login.cl",
you can use "hdsql" also in your environment.
"/opt/share/hds/hdsql/" (setting in ANA)
should be replaced with the directory in which you put
these scripts.
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set stdimage = imt4096
task overscan = /opt/share/hds/hdsql/overscan.cl
task hdsql = /opt/share/hds/hdsql/hdsql.cl
task wacosm11 = /opt/share/hds/hdsql/wacosm11.cl
set imtype = "fits"
imred
echelle
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Akito Tajitsu
Last modified: 2007/05/22 14:42:30 HST
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How to login to ANA/How to start IRAF