Automatic reduction of spectral data using Pipeline 2a

SpcAudace

 1. Configuration and preliminary tunings in Audela

1. Specify the directory containing the data to be processed :
   In the Configuration menu, select Répertoires.
   

   

   Use "..." to reach the desired directory.

   

   Beware:all the data to be processed ( 2D spectral images (including those associated with the calibration lamps), darks, flats, darks associated with the flats, offsets (if relevant)) must be located in this directory.

2. Use Audela's "Visionneuse bis" to have  an overview of the concerned files:
   
   

   

   By clicking on a file, it will be displayed. You can also use the keyboard Up and Down buttons to navigate from one file to its neighbours.
   
3. Tune the display thresholds:
   The goal is to make visible in the same time the telluric lines within the continuum as well as possible cosmics.

   

   
   It is preferable to uncheck the automatic threshold adjustment. In this end, click on the "..." button, just left to the cursors used for the tuning of the thresholds:

   

4. Check the raw spectral images and eliminate images showing poor quality data:
   

   

 2. Launch the pipeline dedicated to the automatic reduction of spectral data

We process here the spectral data acquired on zeta Tau, a bright Be star in the Taurus constellation.

1. Launch SpcAudace :
   This is achieved through the Analyse menu in Audela..

   

2. Launch pipeline number 2a for an automatic reduction of spectral data:

   From the Pipelines menu, click on "Pipeline 2a". The pipeline number 2a window shows up:

   

 3. Fill the associated form

1. 2D calibration file's name or calibration lines profile's name (name of the 2D spectrum of the calibration images):
   In order to calibrate spectra, you have taken calibration images (images of a calibration lamp, neon in general) before and after the acquisition of the spectral images. By clicking on "....", select the first of the calibration image you have taken, here, in our example, "ne_zet_tau-1.fit". In case only one calibration image is available, select it.
   However, it is highly recommended to take several calibration images, at least one just before capturing the spectrum of an object and one just after, if a long (more than 15 minutes) exposure is required. Indeed the calibration images are used, not only for the calibration, but also for the horizontal registration of the different images.
   

   

2. Unprocessed files' generic name (genenic name for raw spectra):
   Since we are interested in the data associated with zeta Tau, the names of the acquisition images for this target are: zet_tau-1.fit, zet_tau-2.fit and zet_tau-3.fit. Thus the generic name to be specified is: "zet_tau-".
3. Dark's generic name (genenic name for darks):
   In the same way, we specify the generic name, here d2400t-, for the raw dark images. However, if a master dark has already been computed, we just have to give its name, for instance, "d2400t--smd3.fit". 
   
4. Flat's generic name (generic name for flats):
   Specify the generic name for the raw images.
5. Flat's dark generic name (generic name for the darks to be applied to flats):
   Again, we can either specify the generic name for the raw images or the name of the master image: "df2400t--smd3".
6. Offset's generic name (generic name for bias images):
   If bias images are to be used (that is in case of different exposure durations for the images and the corresponding darks), enter the bias generic name. Otherwise, keep "none".
7. Reference star's lines profil (1D spectrum of the instrumental response):
   In order to account for the spectral sensitivity of the instrumentation, we will have to divide the level 1b profile by the instrumental response computed by Pipeline number 1. Unless you do not have this instrumental response at hand (in this case you can leave the box empty), you have to give the name of the FITS file containing this instrumental response: click on "...." to select the file (it must be located in the same directory as the other images):
   

   

 4. Computational options

The remaining of the form concerns different options to be specified for the computation. The default settings are appropriate for most of the cases you will encounter. They rarely have to be changed, especially for high resolution spectroscopy. Thus the information in this section is mainly given for sake of completeness.

• Sélection manuelle d'une raie pour la géométrie (manual selection of a ray for geometrical corrections):
  n(non/no) or o(oui/yes) depending on whether you want or not an automatic detection of the central line in the calibration image. The selected line will be the one used for the estimation of the smilex in the spectra.
• Calibration avec plusieurs spectres de lampe (calibration using several calibration images):
  For an enhanced accuracy, it is highly recommended to take at least one calibration image just before and one just after the acquisition of the spectral data associated with a target. Here, the calibration images ne_zet_tau-1.fit and ne_zet_tau-2.fit have been recorded. In this case keep the default option "o" (oui).
• Calibration supplémentaire avec les raies telluriques (use telluric lines to improve the calibration):
  If you have enough spectral resolution, you may expect telluric lines to be observable. Using these lines is likely to improve the calibration. If you want to catch this opportunity select option "o" (oui/yes).
• Normalisation (normalization of the continuum):
  Different operations can be envisaged to allow an easy comparison between spectra of the same object. These operation are accessible through the options below:
  
  • "o" (oui): the profile is normalized by dividing it by an automatic estimation of the continuum;
  • "e" (emission): this normalization is based on the main emission line;
  • "a" (absorption): this normalization is based on the main absorption line;
  • "r" (rescale continuum) : the profile is divided by a constant which corresponds to its mean value; this is the safest option since it does not bring any distorsion; it is the default option;
  • "n" (non) : no normalization is applied.
• Inversion gauche-droite des profils (left-right inversion):
  The convention is to have the blue side at the left of the spectra. Your data fulfill this convention if your camera is properly mounted on the spectrograph. If not, choose "o" (oui) in order to invert left and right. The default setting corresponds to data that fulfill the convention.
• Retrait des cosmics (cosmics removal):
  If your raw images are contaminated by many cosmics, you can attempt at removing them by choosing option "o". But the drawback is a slight degradation of the signal to noise ratio. Alternatively, you can apply the procedure spc_scar to the profile you will obtain. This procedure modifies the profile only locally.
• Export au format BeSS (Bess format export):
  This option will open a window dedicated to Bess format export at the end of the pipeline.
• Export vers un graphique au format PNG (export an image in PNG format):
  This option will open a window allowing a conversion of the graphics in PNG format. The title will be automatically defined from the information found in the FITS header, but this can be changed by filling the boxes in this new window.

Click on "OK" to lauch spectral data reduction.

The pipeline starts with the determination of the smilex correction that makes the lines in the calibration image as straight as possible.

Next, it preprocesses the raw images and after that, it opens a new window dedicated to the spectal calibration.

 5. Spectral calibration

At this stage, the profile computed from the calibration image is displayed in the SpcAudace window:

To help the user, an annotated image of the neon spectrum is displayed in Audela's Visu 1 window:

It is then straightforward to match the lines in the uncalibrated profile with those of the neon lamp. In our example, three lines, with almost equal separation and with increasing intensities are to be found. You will recognize lines with wavelenghts 6532.93 A, 6598.95 A et 6678.28 A. Matching the main lines in the profile and neon wavelengths is achieved through the calibration window:

By clicking on the downward pointing arrow, rignt to the empty boxes, on the lines "Longueur d'onde associée à la raie n° X" (wavelength associated with line number X), you can span the wavelengths specific of each chemical element. "NeI" corresponds to neon. Using the accurate wavelengths available from the library allows an accurate calibration.

If one of the lines in the profile is not detected, it is possible to enter its location (in pixels) through the keyboard.

It is mandatory to keep the wavelength boxes associated with lines that SpcAudace may have erroneously detected empty. These lines will then be ignored.

In our example, only lines with coordinates 1386.137, 684.057 and 121.0 pixels are to be paired with wavelengths. The pixel coordinates may show slight variations for different runs of the pipeline. This stems from slight variations in the geometrical corrections since the pipeline is adaptative according to the situation it meets.

The pixel coordinate to wavelength map (calibration map) is modeled by a low degree polynomial. Its degree depends on how many lines you have selected:

• with two rays (minimum required), first degree polynomial;
• with three rays, second degree polynomial;
• with four rays or more, third degree polynomial;

The parameters that define the calibration map are stored in the FITS header:

• coefficients describing the polynomial : SPC_A, SPC_B, SPC_C et SPC_D for λ=a+b*x+c*x²+d*x³.
• in case of a profile regularly sampled in wavelength (linear calibration map): CRVAL1 et CDELT1 for λ=CRVAL1+CDELT1*x.

with x defined by: x=pixel number-CRPIX1 (CRPIX1 is the FITS keyword defining the reference pixel).

In the end, the pipeline produces profiles that are regularly sampled in wavelength: an interpolation is then required unless the polynomial was first degree (this interpolation is inproperly called "linéarisation de la loi de calibration"). This allows these profiles to be read by all astromical softwares.

 6. The pipeline run

You can inspect the progress in the pipeline computations through Audela's console. The different steps of these computations are:

1. Preprocess of raw images.
2. Geometrical corrections:
   
   1. Correction for the smilex.
   2. Correction for tilt.
   3. Vertical registration.
   4. Horizontal registration (whenever 2 calibration images are available).
3. Stack (summation) of the so-corrected images.
4. Sky background estimation and subtraction.
5. Binning of columns to produce a spectral profile.
6. Application of the computed calibration map to the profile of the star (here zet Tau)
7. Correction for the instrumental response.
8. Regular resampling (in wavelength) of the profile.
9. Display of the final profile in the SpcAudace window.

Finally, the spectral profile with level 2b of zeta Tau is displayed:

Final products are stored in the working directory. You may find the following files, depending on options selected in the pipeline:

• zet_tau--profil-final-ocal: lines profil of the star with all options applied, in our example, continuum is rescaled and it is calibrated with telluric lines (-ocal suffix);
• zet_tau--profil-2b-ocal: same file as described;
• zet_tau--profil-2b: lines profil with continuum rescaled;
• zet_tau--profil-1c: lines profil corrected from instrumental response;
• zet_tau--profil-1b: lines profil with wavelength calibration made with the spectral lamp;
• zet_tau--profil-1a: uncalibrated lines profil;
• zet_tau--spectre2D: 2D spectrum coming from the 32 bit summation of the 3 preprocessed spectra of zet Tau and corrected from geometrical deformations.

 7. Quality check of the wavelength calibration

You can easily check this quality by superimposing the telluric lines with the computed profile: from the Calibration menu, click on "Superposer le profil de raies de l'eau" :

You then have to specify the name of the file containing the star profile:

The intensity of profile of the telluric lines is automatically adapted so as to match the intensity of the stellar profile:

You can zoom on the lines right to the Halpha line for a more accurate inspection:

To come back to the no zoom display, right click on the SpcAudace window. In the same way, you can inspect the area left to the Halpha line:

There is good match between telluric lines and absorption lines in the stellar profile, an indicator of a correct calibration.

Besides, numeric indicators concerning the quality of the calibration are computed. The results are stored the FITS header through the keywords below:

• SPC_RMSO : estimate of the RMS mismatch between telluric lines and the corresponding lines observed in the stellar spectrum; this estimate depends on several factors such as the signal to noise ratio for instance.
• SPC_MDEC : the average mismatch, indicator of a possible global shift using telluric lines.
• SPC_CALO : name of the method used to improve calibration using telluric lines.
• SPC_RESP : spectral resolution estimated from the calibration image.

 8. Export an image in PNG format

At the end of the pipeline, the window dedicated to export an image in PNG format shows up, if asked by the user when filling the first form. You just have to fill the form unless the information can be found in the FITS header.

Usually, just the name of the spectrograph and the name of the star are to be specified:

The constructed PNG file is displayed in Audela's Visu 1 window, with the title matching the information given above.

Afterwards, another window shows up, if asked by the user when filling the first form.

 9. Export to BeSS format

Once the quality of the calibration has been checked and if no anomaly is revealed, you can submit the profile to the BeSS database and thus participate in a collaboration between professionnals and amateurs focused on the observation of Be stars. You just have to fill the form below:

For that you must :

1. Give the correct name of the star (e.g.: alp Gem, del Sco) : "zet Tau".
2. Specify your instrumentation by scrolling the dedicated menu. However, your instrumentation has first to be registered in your Bess account.
3. Choose the observation site still by scrolling the dedicated menu. Again, this site has first to be registered in your Bess account.
4. Give the observer's name provided that this name is registered in your Bess account.

For a first use of this export window, you must edit the different lines using the button "Editer les configs".

Once the different items have been completed, click on "enregister les modifications". The exported spectrum appears with the prefix "bess_". You can now submit this spectrum to the BeSS web site: click on "Web BeSS". The Bess web page then appears in your web browser:

Just enter your identifier and password and upload your spectrum.

The processing is completed. You can proceed to the data associated with the next object!