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information_for_astronomers:user_guide:reduction_of_spectroscopic_measurements [2015/12/15 09:11]
akraus
information_for_astronomers:user_guide:reduction_of_spectroscopic_measurements [2018/12/12 16:18] (current)
akraus
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-===== Reducing spectral line data =====+====== Reducing spectral line data ======
  
 The raw data (in MBFITS format) are converted to CLASS format automatically. This is done using the method described in Winkel, Kraus, & Bach, //Unbiased flux calibration methods for spectral-line radio observations//,​ [[http://​adsabs.harvard.edu/​abs/​2012arXiv1203.0741W| A&A 540, A140, 2012]] (Section 3.4 and Section 4.5) - assuming a //constant system temperature//​ (Tsys) and //flat calibration signal// (Tcal). The latter is produced by a noise diode the power of which is in most cases directly fed into the waveguide within the receiver. //​Neglecting the frequency-dependence of Tsys and Tcal introduces a bias, especially for wide-band observations!//​ (For more information see Winkel, Kraus, & Bach 2012 where we also show ways to do it better.) The raw data (in MBFITS format) are converted to CLASS format automatically. This is done using the method described in Winkel, Kraus, & Bach, //Unbiased flux calibration methods for spectral-line radio observations//,​ [[http://​adsabs.harvard.edu/​abs/​2012arXiv1203.0741W| A&A 540, A140, 2012]] (Section 3.4 and Section 4.5) - assuming a //constant system temperature//​ (Tsys) and //flat calibration signal// (Tcal). The latter is produced by a noise diode the power of which is in most cases directly fed into the waveguide within the receiver. //​Neglecting the frequency-dependence of Tsys and Tcal introduces a bias, especially for wide-band observations!//​ (For more information see Winkel, Kraus, & Bach 2012 where we also show ways to do it better.)
  
-The data files can be found on the //​observer4//​ or //observer3// in the directory +The data files can be found on the //​observer4//​ or //observer6// in the directory 
-**/​daten/​Class/​class_YYYY_MM_DD.100m**. There might be a short delay until the data is processed and is visible in the class file after the observation has finished+**/​daten/​Class/​[fw_]class_YYYY_MM_DD.100m**. There might be a short delay until the data is processed and is visible in the class file after the observation has finished
  
 **Spectra in Class are always in units of Tcal!** To obtain Kelvins or Jy/Beam you have to multiply with the temperature of the noise diode (Tcal) and appropriate antenna sensitivities/​efficiencies. Approximate values for this can be found on our receiver website [[http://​www3.mpifr-bonn.mpg.de/​div/​effelsberg/​receivers/​receiver.html|receiver website]]. However, it is highly recommended to do calibration measurements during your observation for better accuracy. Furthermore,​ the automatic Class pipeline does not account for atmospheric opacity, elevation-gain curve, and antenna efficiency. Information about these steps can be found in Kraus 2009 (calibration memo). **Spectra in Class are always in units of Tcal!** To obtain Kelvins or Jy/Beam you have to multiply with the temperature of the noise diode (Tcal) and appropriate antenna sensitivities/​efficiencies. Approximate values for this can be found on our receiver website [[http://​www3.mpifr-bonn.mpg.de/​div/​effelsberg/​receivers/​receiver.html|receiver website]]. However, it is highly recommended to do calibration measurements during your observation for better accuracy. Furthermore,​ the automatic Class pipeline does not account for atmospheric opacity, elevation-gain curve, and antenna efficiency. Information about these steps can be found in Kraus 2009 (calibration memo).
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 ===== Using class ===== ===== Using class =====
-To reduce your (spectroscopic and pointing) data with ''​class''​ one should use the or **observer2** or **observer4** computer. ​The latter is in the MPIfR LDAP environment,​ i.e., everyone with an account in the MPIfR network can login to this computer with his/her account. It is connected to the ''/​homes''​ server. It is also connected to ''/​homes/​astro/​gag'',​ so your gildas package of choice should work. It is also possible to use the Effelsberg version of class that is used to write the spectroscopic and pointing data. To enable this, change to the bash shell by typing bash and source the init file:\\ +To reduce your (spectroscopic and pointing) data with ''​class''​ one should use the **observer4** or **observer6** computer. ​Both are in the MPIfR LDAP environment,​ i.e., everyone with an account in the MPIfR network can login to this computer with his/her account. It is connected to the ''/​homes''​ server. It is also connected to ''/​soft/​astro/​gag'',​ so your gildas package of choice should work. It is also possible to use the Effelsberg version of class that is used to write the spectroscopic and pointing data. To enable this (if you are using a C-Shell like tcsh), change to the bash shell by typing ​ 
-<code bash>​source /opt/specpipeline/init_classwriter.sh</​code>​+<​code>​bash</​code>​  
 +and source the init file:\\ 
 +<code bash>​source /opt/bin/init_rtsoft.sh</​code>​
 afterward you can run afterward you can run
 <code bash>​class</​code>​ <code bash>​class</​code>​
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 <code bash> <code bash>
-source /​opt/​specpipeline/​init_classwriter.sh 
 source /​opt/​bin/​init_rtsoft.sh source /​opt/​bin/​init_rtsoft.sh
 </​code>​ </​code>​
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 |shiftFFTSRefChannel|False|Before February 2011 the reference channel of the FFTS was wrong (in Fits header) and has to be shifted by +0.5 channels if the spectrum was not flipped, otherwise -0.5 channels. See also the [[fix:​frequency_shift_in_ffts_observation_due_to_wrong_reference_channel|News section]].| |shiftFFTSRefChannel|False|Before February 2011 the reference channel of the FFTS was wrong (in Fits header) and has to be shifted by +0.5 channels if the spectrum was not flipped, otherwise -0.5 channels. See also the [[fix:​frequency_shift_in_ffts_observation_due_to_wrong_reference_channel|News section]].|
 |autoLsrCorr|True|Per default the class pipeline attempts to correct the data for LSR Doppler shifts (due observer motion w.r.t. the LSR) if not already accounted for by hardware (LO tuning). If you really wanted a fixed-frequency setup (e.g., for system testing) you can disable automatic correction with this keyword.| |autoLsrCorr|True|Per default the class pipeline attempts to correct the data for LSR Doppler shifts (due observer motion w.r.t. the LSR) if not already accounted for by hardware (LO tuning). If you really wanted a fixed-frequency setup (e.g., for system testing) you can disable automatic correction with this keyword.|
 +|doAatm|False|Apply AATM atmospheric model opacity correction (based on weather data).|
 +|gainCurve|(1.,​ 0., 0.)|Apply gain curve correction (must be a tuple of (a0, a1, a2); see [[information_for_astronomers:​rx_list|receiver details]].|
 +|tcal|1.|Apply tcal factor. Note, this can also be used to scale the data (e.g., to produce Jy/Beam instead of K, or to apply antenna efficiency). If you want to use different tcal factors per Baseband or FeBe you will need to use the baseband/​febe arguments and run the pipeline several times (once for each baseband/​febe).|
 +
  
 ==== Shell processing - CmdLinePipeline ==== ==== Shell processing - CmdLinePipeline ====
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   --febe FEBE           ​Filter by febe   --febe FEBE           ​Filter by febe
   --no-fsw-fold ​        do fswitch fold in pipeline (rather than class)   --no-fsw-fold ​        do fswitch fold in pipeline (rather than class)
 +  --aatm ​               apply AATM opacity correction
 +  --gaincurve a0 a1 a2  apply gain curve correction (default: 1., 0., 0.)
 +                        Note, early versions of python-argparse dont support
 +                        scientific notation
 +  --tcal TCAL           apply tcal factor (default: 1.) Note, this can also be
 +                        used to scale the data (e.g., to produce Jy/Beam
 +                        instead of K, or to apply antenna efficiency).If you
 +                        want to use different tcal factors per baseband or
 +                        FeBe you will need to use the --baseband/​--febe
 +                        arguments and run the pipeline several times (once for
 +                        each baseband/​febe)
   --no-auto-lsr-correction   --no-auto-lsr-correction
                         do not automatically correct for LSR shifts in fixed-                         do not automatically correct for LSR shifts in fixed-
information_for_astronomers/user_guide/reduction_of_spectroscopic_measurements.1450167086.txt.gz · Last modified: 2015/12/15 09:11 by akraus