|
|
|
|
Software | |
|
| ||
|
These notes show what is required to access CDS data, calibrate it and
begin to analyse the data arrays.
Topics covered in these notes:
Details of what CDS has planned for the next few weeks/months can be seen in the
on-line
Request Diary .
The process of designing a CDS observation starts with the instrument setup. For either spectrometer
this involves deciding on:
a) The slit to be used - there are several
options .
Once the data have been loaded, a quick look at it and some analysis can be
done within various packages provided in the CDS software. The QuickLook
package itself (the same as is available from xcat ) is run with the command
3) Cleaning and calibrating the data
(Index)
4) Analysis of the data
(Index)
The Xmin Xmax numbers give the detector start and stop pixels for each
data window. The wavelengths are calculated using an average pixel-wavelength
conversion applicable to the date of observation. The table above also shows
that the data windows are 18 pixels wide.
To obtain a wavelength array applicable to a particular data window (eg HeI) use
the pix2wave function.
where N is the window index (0 to 3 in the example above). The variable
data will then be a data array with from 2 to 4 dimensions. The dimensions
are always in the order (Wavelength , SolarX, SolarY, Time). The fourth dimension (Time)
is only added where the observation sits at the same SolarX location
and takes repeated exposures. In that case the SolarX dimension is retained, but only has
one element.
Typically:
will give an array something like
indicating that the wavelength dimension has 18 pixels, 143 pixels (the maximum)
were selected
along the slit (SolarY) and 120 exposures were taken by stepping in SolarX.
The simplest ways are to average over the spectral dimension:
or, using the QLDS rather than the extracted data array,
choose a specific wavelength range (w1 to w2) over which to integrate
The resultant image can be displayed:
The last command may not give the expected display because of the presence of
missing data
.
You may wish to plot the spectrum obtained in a single exposure
and at a single location along the slit.
or equivalently if the data array has already been extracted from the data structure
where the wave array was defined earlier.
Various gt_xxxx routines may be packaged to define the average spectrum
over a given spatial area, but if the area is simply rectangular then for instance
will do.
5) CDS Frequently Asked Questions
(Index)
Data and software
Instrument performance
Data features
Miscellaneous
We recommend the
SolarSoft
installation This gives access not only to CDS software but software from other
instruments on SOHO and from other solar missions.
CDS maintains a catalogue and atlas of all its observations. Check out our
data rights policy
and see the section
Finding and reading the data on this page
for details of how to search for and retrieve data.
The CDS ATLAS of observations is available from
here
A variety of
on-line help
is available within IDL.
CDS Software Notes
are available, many of which deal with data analysis.
The data from each CDS raster are stored in a
FITS file
as a binary table.
From a comparison with Sumer data a figure of 30-40% is suggested
for the absolute calibration. A summary of the history and current position
of the calibration can be
found here .
The calibration is under continuous development.
Bill Thompson gives an
update
on some calibration topics in the Sept 2001 issue of the CDS Newsletter,
where he suggests a correction factor of
1.45 for post-recovery NIS-1 data, somewhat lower than previously suggested.
This correction factor is still under review
by the CDS team.
The solar irradiance is defined as the total flux density of the radiation from
the entire solar disc at a distance of 1 AU. It is measured in W/m2 or
erg/cm2/s. This is also often called the 'solar constant' and is
approximately 1368 W/m2. When the irradiance is resolved into specific
wavelengths, or wavelength bins, then it is called the spectral irradiance.
Since the wavelength is given,
spectral irradiance can also be expressed in photons rather than ergs.
Radiance is the specific intensity of a resolved feature on the solar
disk and is measured in W/m2/ster or erg/cm2/sec/sterad.
When CDS data are calibrated, the user has a choice of output units.
Using NIS data and the routine NIS_CALIB, for example, the data may be
calibrated into ergs/cm2/sec/arcsec2 by the use of the command
this gives the value of the radiance in each pixel. Multiplying by the
size of each pixel (in arcsec2) gives the contribution of each pixel to
the total irradiance of the Sun. It is also the total flux in a
single pixel received at the position of SOHO.
The difference between radiance and flux is that radiance is independent of
distance while flux is not. To estimate the flux emitted at the solar surface
one needs to model how the radiance varies as a function of direction. It is
usual to assume a Lambertian surface. On that assumption we may obtain the
flux, at the Sun, of a solar feature in a particular emission line in the
following way:
Note that taking the alternate route
gives a completely different result, but with the same units. This is because
the unit area in each case is in a different location. Using step (3a) gives a
flux at the solar surface, while step (3b) gives a flux at the instrument.
Although nominally CDS has a fixed wavelength range, small changes
in the zero point of the pixel-wavelength relation can occur, primarily
from on board temperature changes caused by varying illumination of the structure by the Sun.
The wavelength array returned by the
gt_xxxx functions or the pix2wave
function is only an average determined
from sample spectra. For accurate wavelength analyses, the zero point should
be determined from each spectrum individually.
The calibration appropriate to a particular dataset is loaded when the data file is read.
If you want to know what the currently loaded coefficients are, use the routine
A demonstration of how the wavelength zero-point varied before the optical bench temperature
was stabilised can be seen
here .
Note that small changes in the zero-point still occur (even during a raster) and so without careful
analysis no reliance should be placed upon absolute or relative velocity changes of less than 10-15 km/s.
CDS uses its offset pointing system (OPS) to move to any location within
range. This pointing has an
rms of 5" or better .
When a dataset is read in using
readcdsfits the pointing values in
the QLDS are updated according to current knowledge of the spacecraft pointing -
see Software Note #48 (
PostScript 87 Kb
)
The reliability of the pointing has been checked from the year 2000 synoptic North limb rasters. The distribution of residuals
of the observed limb from the calculated one is
shown here .
In the upper plot some large negative residuals are present, but checking the raw data reveals that these result from corruption of
the OV limb data by filaments.
The lower distribution ignores those values and confirms that there has been no degradation in the pointing
which in one dimension has an rms of less than 3".
The extent of the CDS pointing capability (its Field Of View - FOV) can be seen using
where x and y can be arrays of Solar (X,Y) locations (arcsecs from disk centre)
to plot on the diagram.
produces
this plot
showing that the latter is an invalid
location for CDS.
Note also that there are
pointing offsets
between the two NIS channels and between NIS and GIS.
These should be allowed for if accurate location of a feature is required.
From launch to the loss in June 98, the CDS/NIS line profiles were
very closely approximated by Gaussians. A number of routines allow fitting
of these profiles. See the options in the QL software, the cfit package
described in Software note #47 (
PostScript 6.6 Mb
)
and the low-level routine cds_gauss. After recovery
the NIS line profiles had changed. See Software note #53 (
PostScript 132 Kb
) for details.
33: The CHIANTI Synthetic Spectrum Program
(PostScript 85 Kb)
The Atomic Data and Analysis Structure (
ADAS )
is an interconnected set of computer
codes and data collections
for modelling the radiating properties of ions and atoms in plasmas
and for assisting in the analysis and
interpretation of spectral measurements and has also been used in connection with CDS data, particularly
in the production of the NIS linelist .
As with any instrument/detector system there are a few features of the data
produced that must be corrected for, or taken account of, in the data analysis.
All of the features of NIS data currently known can be corrected for in the software, but users
should be aware of their presence to avoid drawing erroneous conclusions or over-interpeting the data.
The most obvious features of the NIS spectral data are
1) Spectrum
ROTATION and TILT
(Index)
Both of these features are illustrated in
this diagram
If these features are not corrected they will have the following effects upon the results:
Update:
It appears that the spectral line tilt may have changed post-recovery.
diagram
shows a suggestion for updated values for NIS2. If these new values are agreed, they
will be loaded into the databases used by the correction software.
Note, however, that the tilt often
appears not to be a linear function of position along the slit (so the values
displayed are only average values) and furthermore recent work by
Danielle Bewsher and Clare Parnell in St Andrews suggests that, for
some datasets at least, the tilt (cf the wavelength zeropoint) may also
be a function of time.
nis_rotate.
corrects for
these effects. Note also that when data extraction windows are used in
the design of a raster, their Y-pixel location on the CCD is automatically
calculated to take account of the rotation. Consequently each data window array
should have the same Y-pixel/SolarY correspondence. However if the windows are
very wide some correction for rotation may still be necessary.
2) Wavelength change with scan mirror position
(Index)
As the scan mirror rotates to provide the internal East/West spatial coverage it also
introduces a small non-linear change in the wavelength scale zeropoint. The effect can be
corrected for by again using
nis_rotate.
If you want to check what the correction values are as a function of mirror location
say, for example, for NIS2 data taken in early 1996, try:
3) CCD flatfield
(Index)
The sensitivity of the NIS CCD varies from pixel to pixel by a few percent. In order to eliminate
this effect the routine vds_calib divides each exposure by
a flatfield array which was determined in the laboratory before launch. Because of a
slight shift of the alignment during launch, the laboratory flatfield array had to be modified
after launch and while it does a pretty good job, some small residual inaccuracies persist.
In flight it is possible to take data which can approximate a uniform exposure of the detector by moving
the OPS while the camera is exposing with the wide (90"x240") slit. A useful signal is of course only
detected in the spectral position of the brighter lines. An example of this and of how such in-flight
flatfields can be used if necessary for very accurate flatfielding is shown in
this display
.
4) MCP Burn-in
(Index)
The detector for NIS consists of a micro-channel plate (MCP) intensified CCD. The MCP suffers from
degradation when exposed to radiation such that its sensitivity declines exponentially with photons
detected (or, almost equivalently, with time).
Since the CDS spectral format is fixed, the emission lines fall more or less on the same area of the MCP
all the time and the brightest lines affect the MCP the most, resulting in BURN-IN
, which is a region of reduced sensitivity on the detector.
Special observations are taken to try and track the progress of the burn-in and the variation of
sensitivity with MCP/CCD location and time is recorded in a database and a suitable correction applied
in the routine
After the SOHO recovery the location of the NIS spectra on the MCP had changed and so a
new burn-in correction was established and is being monitored. Details are given in
CDS software note 51
This plot
shows a recent (July 2000) 'flat-field' exposure
at the wavelength of HeI 584 Å. On the left is the raw data, showing the pre-loss and the current
(to the right) burn in of that line. The profile of the image is overlayed - notice that the
post-recovery burn in is already larger (at about 50%) than pre-loss. The image on the right shows the
same data after the standard corrections have been applied.
5) Other fixed pattern effects
(Index)
The NIS1 readout electronics create a low-level fixed-pattern effect in the
spectrum. Every fourth pixel appears to have a lower count than expected. The
effect is illustrated in this
diagram.
The effect is also corrected for in the routine
vds_calib.
Note also the first and last two columns of CCD data should not be used in
analysis. This only becomes relevant when the full spectrum is extracted or data
windows cover the extreme columns of the CCD (as possibly in the OV 629A line in post-recovery data).
6) Cosmic rays
(Index)
While the NIS is exposing, particles hit the CCD and release electrons which are then counted as
signal when the CCD is read out.
A recent paper (PostScript 284 Kb) gives
details of the longterm
detection of cosmic rays by the CDS CCDs.
The main
figure
shows that the count had declined by approximately 45%
since launch owing to the increased strength of the heliospheric magnetic field at solar maximum.
During that time 1-2% of pixels on the CCD are affected by cosmic rays in a 100 second exposure.
It is advantageous, before proceeding with any analysis,
to identify which pixels are affected and to either mark them as
missing data . or to replace them with
interpolated values.
Several routines are available to perform this process. They are described in
CDS Software Note 46
Note that the routine cds_new_spike has beed added since
that software note was written.
7) NIS Bias
(Index)
The NIS CCD readout electronics adds a constant value to the readout data to make sure the
data values are well clear of any low-level effects. This is known as the
BIAS level, and this value must be subtracted from the data
value before any further (multiplicative) operations are applied to calibrate the data.
The bias level can change slightly as the characteristics of the electronic components vary. The level
is therefore monitored on each exposure by reading out four small areas (10 x 10 pixels) of the
unilluminated CCD. The subtraction is performed by the routine
vds_debias and
in a raster the bias is subtracted on an exposure-by-exposure basis. Since there is noise on this value, this can
cause apparent variations if very low signal levels are being compared from exposure to exposure or
from raster to raster.
The bias level has been known to
vary slowly with time since launch.
Note, however, that it seems to have been very stable since recovery.
One instance has also been noted when the bias
varied abruptly .
During the year 2000 two
abrupt changes
in the bias occurred. These coincide with proton storms reaching SOHO on
July 14 and November 9. Further interruptions for storms in 2001 do not
appear to have had a similar effect!
If rasters are designed without the inclusion of the bias windows (a user option)
then a suitable bias value must
be supplied manually to the vds_debias routine.
The bias levels recorded within a raster's exposures can be plotted:
8) NIS continuum
(Index)
After de-biasing the spectra, there will usually remain a non-zero
continuum. This is largely scattered light coming from
outside of
the NIS wavebands. The main contributors are probably the Lyman-alpha 1216 Å
line, the Lyman continuum, He II 304 Å and perhaps strong coronal lines such
as Fe IX 171 Å. The scattering arises from the grating in the spectrograph.
Note also that the scattering has a strong spatial variation
along the slit and is dependent upon the solar features under the
slit. One consequence of this is that if the intensity data are
simply averaged or summed over the line window, without any
attempt at background or continuum subtraction, the resulting
image may show faint spatial features which are not at all
related to the line in question.
See also the notes about scattered light under the Instrument Performance
section.
9) NIS data (noise) statistics
(Index)
Since the NIS detector is not a photon-counting system, the data statistics cannot be derived from the
raw data numbers alone. However, it is possible to derive
the correct counting statistics and this is explained
in
CDS Software Note #49 Deriving Statistics from NIS data
(PostScript 174 Kb) .
10) Spatial offset between NIS1 and NIS2 (and GIS)
(Index)
Both NIS1 and NIS2 use the same entrance slit to the spectrograph. However, there appears to be
a N/S offset, sometimes amounting to several arcseconds, between the solar features that NIS1 sees and
those that NIS2 sees.
A more detailed discussion
is available.
If you want to see what the 'official' value of the offset
is for any particular observation
(it's a function of date and CDS (X,Y) location), try:
where x and y are the offset of NIS1 relative to NIS2 in arcseconds.
Note that the routine nis_rotate has been modified to include a call to
gt_nis_alignment if the /ALIGN keyword is set.
See an example
of the effect.
Note: There is also an offset between the imaging of NIS
and GIS. GIS images appear approximately 13" south of their NIS equivalents. Specific
(X,Y) pointings for GIS should therefore be 13" south of the values determined
by the software (image_tool for instance).
11) Changed line profiles after recovery of SOHO
(Index)
The bakeout that CDS suffered during the SOHO loss changed the line profiles produced by the
NIS spectrometer. The
NIS1 profiles
exhibit broader wings and the
NIS2 profiles
show a broadened and asymmetrical
long wavelength wing.
The new profiles were characterised, and the fitting software modified to cater for them, as described in
CDS Software Note #53 (
PostScript 132 Kb
).
The GIS has four SPAN detectors positioned around the Rowland circle of the grating.
Each detector provides a 2048 pixel one-dimensional spectrum with complementary
wavelength ranges . Since the GIS optics are astigmatic
a small slit (2"x2" or 4"4") must be used and rasters are built up by scanning both the internal mirror
(E-W) and the slit (N-S).
The setup of the detector is dependant upon the feature to be observed. Loading a new setup requires
approximately 20 minutes of on board CPU time so it is unwise to plan observations that require
frequent switching between different sources. Contact the GIS
team for advice if you
are planning some GIS observations.
-------------------------------------------------------
Detailed information on handling GIS data can be found on the GIS Home page and in the CDS Software Notes:
54: CDS-GIS Instrument Guide
(PostScript 3 Mb)
-------------------------------------------------------
Note also that there are
pointing offsets
between NIS and GIS.
Since the pointing determined in the planning software (image_tool) is calculated for NIS, the GIS offset
should be allowed for if accurate location of a feature is required.
It is possible to make maps from CDS data which have the pointing information
associated with them and then to compare those with data from other instruments.
The package of programs is described at
Dominic Zarro's web site.
quick example of how to create a map object from CDS data.
Brooks et al. have compiled a quiet Sun line list for NIS and
here .
There is also a
line list
created from the CHIANTI database.
Some spectra from previous solar missions that may be useful for identifying
lines in NIS spectra are:
The internal scan mirror and slit movement of CDS allow CDS rasters to cover a maximum area of
4' square within a single raster. The E-W coverage is created by the scan mirror which can
move in steps of 2.03" (normally assumed to be 2").
Movement can only be in one direction from West to East.
In NIS the N-S coverage is usually provided by the long slit (normal slits are 2"x240" or 4"x240").
For GIS the N-S dimension is scanned by moving one of the small square slits which can move in
steps of 1.01" (normally assumed to be 1"!).
Because of readout problems with the slit movement encoder, there are restrictions on the movement
of the GIS slits when rastering in the North-South direction.
The planning software has been updated so that the corrections to handle this problem are
automatically calculated and the user should not see any effect or need to take any specific action.
GIS rasters can once again be planned as normal.
Planners should continue to take note of the
pointing offsets
between NIS and GIS images if accurate
feature location is required.
The whole CDS instrument can be pointed anywhere on the solar disk by use of the Offset Pointing
System (OPS). The area reachable can extend out to a maximum 1.4 solar radii in
certain directions.
See the procedure cdsfov for details.
The paper
where J is the
first-order Bessel function and the parameter b has a value of 0.31 giving a
slightly elliptical form with FWHM(x) = 6" and FWHM(y) = 8".
Their data were taken with the 4" wide slit and it is possible
that a slightly better spatial resolution (in SolarX) is
achievable in pre-loss data which used the 2" slit.
A discussion of the
post-recovery PSF .
is also available, where it is suggested that the post-recovery PSF is changed considerably.
Information on the spectral coverage and resolution of NIS is given
here.
After the SOHO recovery the NIS line profiles changed, exhibiting extended wings and an
asymmetry in the NIS2 profiles. The software was modified to permit fitting of these
new profiles and is described in CDS Software Note 53:
The PSF of the spectrograph (as opposed to the telescope) optics affects the
line profiles and can, if asymmetric, affect the interpretation of velocity
information. This is discussed in a paper by S. V. H. Haugan
Anomalous Line Shifts from Local Intensity Gradients on the SOHO/CDS NIS Detector
(Solar Physics 185, 275, 1999)
where it is predicted that the NIS spectrograph
PSF must be slightly elliptical and rotated. From NIS observations taken with the small
2"x2" slit, this indeed appears to be the case.
See the routine CDS_CORR_GRADIENT for a possible
correction technique.
Information on the spectral coverage and resolution of GIS is given
here .
The temporary loss of SOHO appears to have had little effect upon the spectral
characteristics of GIS.
Some pre-flight information is available in
Harrison et al (1995), Solar Physics, 162, 233.
which gives results for measures at a wavelength of 68 Å.
For a scientific application and extension of this to CDS observed wavelengths see
David et al (1997), Fifth SOHO Workshop, SP-404, Page 313.
Routines to calculate
the amount of scattered light and an explanation of how to apply them
are available.
Yes and no!
Please read software note #45 for details, but remember the "feature
tracking" option cannot be relied on to give stable
pointing at the 2" level. Remember also the
difference
between feature tracking and rotation compensation.
If you have further questions about CDS data please contact the
project staff.
If you would like to advertise (and be given credit for) any tricks/titbits you've
discovered about dealing with CDS data please
let us know.
As a start, see these points
that have been notified to us.
Watch out for
NIS second order lines
contributed by Enrico Landi.
|
