SUMER at MSSL : Software


What should you do when you want to process SUMER data ?

Take a look at the SUMER instrument home page at MPAe, Lindau, Germany.

Read the chapters
- Reduction and Analysis of SUMER data
- SUMER Data Availability
- Data Cookbook

(There is a lot of SUMER data processing software around. I do not claim that mine is better. Nevertheless, I was asked for it.)

Find the study that you are looking for in the SUMER File Catalogue.

Example: The equatorial CH scan on 30 Aug 1996, 01:01 UTC.

You can get either FITS files from the SOHO data base, or IDL restore files from the Lindau data base. Here, we assume the latter.

Go to the SUMER Image Data Base and enter 30 August 1996 in the "Select images of a day" window. Among other data, you will find a list of 1700 images, the first one taken at 01:01:12.81 UTC, the last one taken at 08:06:17.75 UTC.

If you want to download these images to your directory, you have to register as a user. For this purpose, write an eMail to wilhelm@linmpi.mpg.de. You will be assigned a user-id number.


Preparations

To prepare the download, enter your user-id, the date 30 August 1996, the start time 01:01 and the end time 08:06 in the "DownLoad Image Data" window. After a while, you will be notified automatically by eMail that a tar'ed and zip'ed file is ready for you, e.g. SUMDWN_20031113183526.TAR_GZ;1.

Create a working directory, e.g. with
mkdir /disk/solar0/ied/example/ and go there. This directory pathname is used as a default in all following IDL programs. Please change the default according to your situation.

To download the data, enter:
ftp vms1.mpae.gwdg.de
Name: anonymous
Password: (your eMail address)
cd $TMP3:[ANONYMOUS.SUMER.OUTGOING]
binary
mget SUMDWN_20031113183526.TAR_GZ;1
quit

In your working directory, un-tar and un-zip the data:
tar xvzf 'SUMDWN_20031113183526.TAR_GZ;1' (Don't forget the 'quotes'.)

You will see 1700 files, e.g.
sum_r_19960830_08061775.12420_08
The notation means: SUMER restore file, taken on 30 Aug 1996, at 08:06:17.75 UTC, in a spectral window around 1242.0 Å, in the data format 8, which means 50 spectral x 360 spatial pixels.

In the example, there are four different file extensions, namely 06249 (incl. Mg X), 06297 (incl. O V), 12388 (incl. N V), and 12420 (incl. Fe XII), resulting in four possible scanlists. For the following data processing programs, you need a name for the study, e.g. take the archive identification number s027301 (cf. Chronological List of all SUMER Studies), and a name for each substudy scanlist, e.g. take the extension number 06249.

Create ASCII files for the scanlists:
ls -1 sum_r_19960830_*.06249_08 > direct_s027301_06249.lst
The following IDL programs will take the restore files from these lists as input.

Look at the substudy scanlist, e.g. with
jed direct_s027301_06249.lst to find that the list has 425 entries.


Header Information

Go back to the directory that contains your IDL programs, start
sswidl5.3 and enter:
.run sumer_headinfo
(for the purpose of this program please read the documentation in its source code)
study? s027301
substudy? 06249
list length? 425

The program prints a file
/disk/solar0/ied/example/headinfo_s027301_06249.txt
on your default printer, containing information about the data in the scanlist, and it creates a file
/disk/solar0/ied/example/studyinfo_s027301_06249.dat
containing information used by the following IDL programs.


Quicklook and Parameter Selection

Again in IDL, enter
.run sumer_fast05
(for the purpose of this program please read the documentation in its source code)
study? s027301
substudy? 06249

The program subsequently reads the 425 files from the scanlist and displays several images on the screen:
- a quicklook 2D image (still upside down, like SUMER on SOHO), produced by integrating the whole spectral window for each pixel;
- a 2D detector image intergrated over the whole scanlist;
- several subsets of the scan, integrated across the slit, to detect data faults: files with exceptionally high or low count rates (visible as white or black vertical stripes in the first image) should be removed from the scanlist
/disk/solar0/ied/example/direct_s027301_06249.lst
(please note that IDL starts counting with file 0);
- an average profile, to select "line" and "continuum" pixels: in this case, e.g., pixels 19 to 30 represent the Mg X line, while pixels 0, 7, 8, 17, 18, 31, 32, 47, 48 represent continuum;
- an integrated slit, to detect its borders on the detector, and two subsets at the south and north edge, spreaded to identify the lower and the upper significant slit pixel: in this case number 27 and 316;
- again the average profile, to allow the creation of further substudies by selecting subsets of the spectral window: this can be used to extract ~50-px subsets from a full detector (1024-px) or a half detector (512-px) spectral window, or to duplicate and rename the existing scanlist to extract another line;
e.g., in order to process the C I 1249.4 Å line within the Mg X window, enter
select interval? 0 49
substudy? 12494

To terminate, enter
select interval? 0 0


Image Construction from Gauss-Fits

Change the studyinfo files for Mg X and C I according to the information gained in the last steps; they should now look as follows:
/disk/solar0/ied/example/studyinfo_s027301_06249.dat
and
/disk/solar0/ied/example/studyinfo_s027301_12494.dat
Note to change the wavelength from commanded to theoretical wavelength (the following IDL programs expect it to be given in first order), to insert number and list of continuum pixels, number and list of line pixels, and upper and lower significant detector pixel.

Again in IDL, enter
.run sumer_read05 or .run sumer_read05_cube
(for the purpose of these programs please read the documentation in their resp. source codes)
study? s027301
substudy? 06249 for Mg X, or 12494 for C I
spatial smoothing? 0 (no), or 1 (yes), if you want to smooth each pixel with 50% of both its neighbours to increase the signal-to-noise ratio
position? 25 (the maximum pixel and assumed rest wavelength of the selected Mg X line)
write GIF? 0 (no), or 1 (yes), if you want to produce an image /disk/solar0/ied/example/s027301_06249_spec.gif containing info on the spectral window, the selected line, etc.

The program again reads the 425 files from the scanlist and displays several images on the screen:
- graphics of count rate, deadtime correction factor, and gain correction factor;
- 2D images of continuum and line radiance;
- 2D images of line shift and width;
- an intergrated detector image, and seperately the selected line and the residual continuum and neighbouring lines;
- average line profile and estimated continuum level;
- the GIF image with the spectral info.

Subsequently, arrays and vectors (and possibly the whole data cube, already corrected for north-south orientation and reduced to its significant part on the detector) are stored in an IDL restore file named /disk/solar0/ied/example/s027301_06249.rst


Image Corrections

Again in IDL, enter
.run sumer_correct
(for the purpose of this program please read the documentation in its source code)
study? s027301
substudy? 06249
The program displays several images on the screen:
- delta exposure times, to detect data gaps that are automatically filled by averaging neighbours
- scan interval, incl. upper and lower limits in solar X coordinates
- 2D image, spatial orientation corrected, before "flatfield" correction
- resulting "flatfield" correction factors for periods 2, 7, 15, 29
- 2D image, "flatfield" corrected, borders of significant detector pixels marked with white lines
This sequence is repeated four times, always concluding with
save image? 0 (no), or 1 (yes), if you want to create a restore file for the image just shown on the screen. Thus, the files
/disk/solar0/ied/example/s027301_06249_ba.rst (COMPL=continuum radiance)
/disk/solar0/ied/example/s027301_06249_li.rst (COMPL=line radiance)
/disk/solar0/ied/example/s027301_06249_my.rst (COMPL=line shift)
/disk/solar0/ied/example/s027301_06249_si.rst (COMPL=line width)
can be created. Finally, the program asks
create *****_dia.rst? 0 (no), or 1 (yes), if you want to create the restore file
/disk/solar0/ied/example/s027301_06249_dia.rst
for the initial data used in the dialogue part of the following IDL program.


Image Display

Again in IDL, enter
.run sumer_displaypre
(for the purpose of this program please read the documentation in its source code)
study? s027301
listname? 06249
At this point, the image display parameters can be changed manually, if necessary, before running sumer_display.pro.
Then enter .run sumer_display
(for the purpose of this program please read the documentation in its source code)
full dialog? 0 (no), if existing parameters are used, or 1 (yes) to start dialog, which (in parts) proceeds as follows:

ba, li, my, si? ba (continuum radiance)
#pixels east-west? 638
#pixels north-south? 300
scaling factor? 2
lower limit, upper limit? 25 800
create GIF? 0
(no), or 1 (yes), if you want to create the image file /disk/solar0/ied/example/s027301_06249_ba.gif
save parameters? 0 (no), or 1 (yes), if you want to keep the chosen parameters in the dialog file.

ba, li, my, si? li (line radiance) ...
lower limit, upper limit? 3 750
level of significance? 10
create GIF? 0
(no), or 1 (yes), if you want to create the image file /disk/solar0/ied/example/s027301_06249_li.gif
...

ba, li, my, si? my (line shift) ...
subtract average (1) or cogsn (2)? 1
subtract av. (1), smooth av. (2), or cogew (3)? 2
net shift in px? 0

Correction vectors cogsn or cogew must already be in the file /disk/solar0/ied/example/s027301_06249_cog.rst. Using cogsn or cogew means using a rest wavelength different from the average that is realized during the scan or time series of the (sub)study. This can be useful when the (sub)study is biased by extreme features. - The net shift value allows to correct for a constant pixel offset.
create GIF? 0 (no), or 1 (yes), if you want to create the image file /disk/solar0/ied/example/s027301_06249_my.gif
save compl1raw? 0 (no), or 1 (yes), if you want to create the file /disk/solar0/ied/example/s027301_06249_my1.rst
containing the line shift array after conversion to Doppler shift in km/s, but before scaling.
save cogsn, cogew? 0 (no), or 1 (yes), if you want to create the file /disk/solar0/ied/example/s027301_06249_cog.rst
containing the line shift correction vectors cogsn and cogew.
...

ba, li, my, si? si (line width) ...
lower limit, upper limit? 0.20 0.35
create GIF? 0
(no), or 1 (yes), if you want to create the image file /disk/solar0/ied/example/s027301_06249_si.gif
save compl1raw? 0 (no), or 1 (yes), if you want to create the file /disk/solar0/ied/example/s027301_06249_si1.rst
containing the line width array after conversion to FWHM in Angstrom, but before scaling.
...

The dialog file should now look as follows:
/disk/solar0/ied/example/s027301_06249_dia.dat


Summary

Program Name           | Input Files                      | Output Files
=======================|==================================|============================
sumer_headinfo.pro     | sum_r_19960830_********.06249_08 | headinfo_s027301_06249.txt
                       | direct_s027301_06249.lst         | studyinfo_s027301_06249.dat
-----------------------|----------------------------------|----------------------------
sumer_fast05.pro       | sum_r_19960830_********.06249_08 | s027301_06249.rst
                       | direct_s027301_06249.lst         |
		       | studyinfo_s027301_06249.dat      |
-----------------------|----------------------------------|----------------------------
sumer_read05.pro       | sum_r_19960830_********.06249_08 | s027301_06249.rst
                       | direct_s027301_06249.lst         | s027301_06249_spec.gif
		       | studyinfo_s027301_06249.dat      |
-----------------------|----------------------------------|----------------------------
sumer_correct.pro      | s027301_06249.rst                | s027301_06249_ba.rst
                       |                                  | s027301_06249_li.rst
		       |                                  | s027301_06249_my.rst
		       |                                  | s027301_06249_si.rst
		       |                                  | s027301_06249_dia.rst
-----------------------|----------------------------------|----------------------------
sumer_display(pre).pro | s027301_06249_dia.rst            | s027301_06249_dia.rst
                       | s027301_06249_ba.rst             | s027301_06249_ba.gif
                       | s027301_06249_li.rst             | s027301_06249_li.gif
		       | s027301_06249_my.rst             | s027301_06249_my.gif
		       |                                  | s027301_06249_my1.rst
		       |                                  | s027301_06249_cog.rst
		       | s027301_06249_si.rst             | s027301_06249_si.gif
                       |                                  | s027301_06249_si1.rst
=======================|==================================|============================


IED, 01 Jun 2006