SCC Documentation: docs/netcdf_file.rst@c599c07ecd44 (annotated)

docs/netcdf_file.rst@c599c07ecd44 (annotated)

docs/netcdf_file.rst

Fri, 16 Dec 2016 12:37:23 +0200

author: Ioannis Binietoglou <binietoglou@noa.gr>
date: Fri, 16 Dec 2016 12:37:23 +0200
changeset 94: c599c07ecd44
parent 89: 8310b682c916
child 96: 2f5d5e1d416d
permissions: -rw-r--r--

New usecases.

 .. _netcdf_file:
 The SCC netCDF file format
 ==========================
 A more detailed version of this document can be found in this :download:`pdf file <files/NetCDF_input_file_v3.pdf>`.
 .. note::
    You can check the format of the files you create using the linked `script <https://bitbucket.org/iannis_b/scc-netcdf-checker>`_ .
 Rationale
 ---------
 The Single Calculus Chain (SCC) is composed by three different modules:
 -  pre-processing module (*ELPP*)
 -  optical processing module (*ELDA*)
 -  depolarization calibrator module (*ELDEC*)
 To perfom aerosol optical retrievals the SCC needs not only the raw
 lidar data but also a certain number of parameters to use in both
 pre-processing and optical processing stages. The SCC gets these
 parameters looking at two different locations:
 -  Single Calculus Chain relational database (SCC\_DB)
 -  Input files
 There are some paramenters that can be found only in the input files
 (those ones changing from measurement to measurement), others that can
 be found only in the SCC\_DB and other ones that can be found in both
 these locations. In the last case, if a particular parameter is needed,
 the SCC will search first in the input files and then in SCC\_DB. If the
 parameter is found in the input files, the SCC will keep it without
 looking into SCC\_DB.
 The input files have to be submitted to the SCC in NetCDF format. At
 present the SCC can handle four different types of input files:
 . Raw Lidar Data
 . Sounding Data
 . Overlap
 . Lidar Ratio
 As already mentioned, the *Raw lidar data* file contains not only the
 raw lidar data but also other parameters to use to perform the
 pre-processing and optical processing. The *Sounding Data* file contains
 the data coming from a correlative radiosounding and it is used by the
 SCC for molecular density calculation. The *Overlap* file contains the
 measured overlap function. The *Lidar Ratio* file contains a lidar ratio
 profile to use in elastic backscatter retrievals. The *Raw Lidar Data*
 file is of course mandatory and the *Sounding Data*, *Overlap* and
 *Lidar Ratio* files are optional. If *Sounding Data* file is not
 submitted by the user, the molecular density will be calculated by the
 SCC using the "US Standard Atmosphere 1976". If the *Overlap* file is
 not submitted by the user, the SCC will get the full overlap height from
 SCC\_DB and it will produce optical results starting from this height.
 If *Lidar Ratio* file is not submitted by the user, the SCC will
 consider a fixed value for lidar ratio got from SCC\_DB.
 The user can decide to submit all these files or any number of them (of
 course the file *Raw Lidar Data* is mandatory). For example the user can
 submit together with the *Raw Lidar Data* file only the *Sounding Data*
 file or only the *Overlap* file.
 This document provides a detailed example about the structure of
 the NetCDF input files to use for SCC data submission. All Earlinet
 groups should read it carefully because they have to produce such kind
 of input files if they want to use the SCC for their standard lidar
 retrievals.
 Additionaly, the linked :download:`pdf file <files/NetCDF_input_file_v3.pdf>` contains
 tables with all mandatory and optional variables for the netcdf files
 accepted by the SCC. Table 1 contains a list of dimensions, variables and
 global attributes that can be used in the NetCDF *Raw Lidar Data*
 input file. For each of them it is indicated:
 -  The name. For the multidimensional variables also the corresponding
    dimensions are reported
 -  A description explaining the meaning
 -  The type
 -  If it is mandatory or optional
 As already mentioned, the SCC can get some parameters looking first in
 the *Raw Lidar Data* input file and then into SCC\_DB. This means that
 to use the parameters stored in SCC\_DB the optional variables or
 optional global attributes must not appear within *Raw Lidar Data* file.
 This is the suggested and recommended way to use the SCC. Please include
 optional parameters in the *Raw Lidar Data* only as an exception.
 Tables 2, 3, and 4 report all the
 information about the structure of *Sounding Data*, *Overlap* and *Lidar
 Ratio* input files respectively.
 Example
 -------
 Let's now consider an example of *Raw Lidar Data* input file. Suppose
 we want to generate NetCDF input file corresponding to a measurement
 with the following properties:
 +----------------------+-------------------------------------------+
 | Start Date           | 30\ :sup:`th` January 2009                |
 +----------------------+-------------------------------------------+
 | Start Time UT        | 00:00:01                                  |
 +----------------------+-------------------------------------------+
 | Stop Time UT         | 00:05:01                                  |
 +----------------------+-------------------------------------------+
 | Station Name         | Dummy station                             |
 +----------------------+-------------------------------------------+
 | Earlinet call-sign   | cc                                        |
 +----------------------+-------------------------------------------+
 | Pointing angle       | 5 degrees with respect to the zenith      |
 +----------------------+-------------------------------------------+
 Moreover suppose that this measurement is composed by the following
 lidar channels:
 #. 1064 lidar channel
    +------------------------------+-------------------------------+
    | Emission wavelength=1064nm   | Detection wavelength=1064nm   |
    +------------------------------+-------------------------------+
    | Time resolution=30s          | Number of laser shots=1500    |
    +------------------------------+-------------------------------+
    | Number of bins=3000          | Detection mode=analog         |
    +------------------------------+-------------------------------+
    | Range resolution=7.5m        | Polarization state=total      |
    +------------------------------+-------------------------------+
 #. 532 cross lidar channel
    +-----------------------------+------------------------------------------+
    | Emission wavelength=532nm   | Detection wavelength=532nm               |
    +-----------------------------+------------------------------------------+
    | Time resolution=60s         | Number of laser shots=3000               |
    +-----------------------------+------------------------------------------+
    | Number of bins=5000         | Detection mode=photoncounting            |
    +-----------------------------+------------------------------------------+
    | Range resolution=15m        | Polarization state=cross (transmitted)   |
    +-----------------------------+------------------------------------------+
 #. 532 parallel lidar channel
    +-----------------------------+-------------------------------------------+
    | Emission wavelength=532nm   | Detection wavelength=532nm                |
    +-----------------------------+-------------------------------------------+
    | Time resolution=60s         | Number of laser shots=3000                |
    +-----------------------------+-------------------------------------------+
    | Number of bins=5000         | Detection mode=photoncounting             |
    +-----------------------------+-------------------------------------------+
    | Range resolution=15m        | Polarization state=parallel (reflected)   |
    +-----------------------------+-------------------------------------------+
 #. | 607 :math:`N_2` vibrational Raman channel
    +-----------------------------+---------------------------------+
    | Emission wavelength=532nm   | Detection wavelength=607nm      |
    +-----------------------------+---------------------------------+
    | Time resolution=60s         | Number of laser shots=3000      |
    +-----------------------------+---------------------------------+
    | Number of bins=5000         | Detection mode=photoncounting   |
    +-----------------------------+---------------------------------+
    | Range resolution=15m        |                                 |
    +-----------------------------+---------------------------------+
 Finally let's assume we have also performed dark measurements before the
 lidar measurements from the 23:50:01 UT up to 23:53:01 UT of
 \ :sup:`th` January 2009.
 Dimensions
 ~~~~~~~~~~
 Looking at table 1 of the pdf file we have to fix the following dimensions:
 ::
     points
     channels
     time
     nb_of_time_scales
     scan_angles
     time_bck
 The dimension ``time`` is unlimited so we don’t have to fix it.
 We have 4 lidar channels so:
 ::
     channels=4
 Regarding the dimension ``points`` we have only one channel with a
 number of vertical bins equal to 3000 (the 1064nm) and all other
 channels with 5000 vertical bins. In cases like this the dimension
 ``points`` has to be fixed to the maximum number of vertical bins so:
 ::
     points=5000
 Moreover only one channel (1064nm) is acquired with a time resolution of
 seconds, all the other channels have a time resolution of 60 seconds.
 This means that we have to define two different time scales. We have to
 set:
 ::
     nb_of_time_scales=2
 The measurement is performed only at one scan angle (5 degrees with
 respect to the zenith) so:
 ::
     scan_angles=1
 We have 3 minutes of dark measurements and two different time scales one
 with 60 seconds time resolution and the other one with 30 seconds time
 resolution. So we will have 3 different dark profiles for the channels
 acquired with the first time scale and 6 for the lidar channels acquired
 with the second time scale. We have to fix the dimension ``time_bck`` as
 the maximum between these values:
 ::
     time_bck=6
 Variables
 ~~~~~~~~~
 In this section it will be explained how to fill all the possible
 variables either mandatory or optional of *Raw Lidar Data* input file.
 -  | ``Raw_Data_Start_Time(time, nb_of_time_scales)``
    | This 2 dimensional mandatory array has to contain the acquisition
      start time (in seconds from the time given by the global attribute
      ``RawData_Start_Time_UT``) of each lidar profile. In this example
      we have two different time scales: one is characterized by steps of
 seconds (the 1064nm is acquired with this time scale) the other
      by steps of 60 seconds (532cross, 532parallel and 607nm). Moreover
      the measurement start time is 00:00:01 UT and the measurement stop
      time is 00:05:01 UT. In this case we have to define:
    ::
        Raw_Data_Start_Time =
 , 0,
 , 30,
 , 60,
 , 90,
 , 120,
          _, 150,
          _, 180,
          _, 210,
          _, 240,
          _, 270 ;
    The order used to fill this array defines the correspondence between
    the different time scales and the time scale index. In this example
    we have a time scale index of 0 for the time scale with steps of 60
    seconds and a time scale index of 1 for the other one.
 -  | ``Raw_Data_Stop_Time(time, nb_of_time_scales)``
    | The same as previous item but for the data acquisition stop time.
      Following a similar procedure we have to define:
    ::
        Raw_Data_Stop_Time =
 , 30,
 , 60,
 , 90,
 , 120,
 , 150,
          _, 180,
          _, 210,
          _, 240,
          _, 270,
          _, 300 ;
 -  | ``Raw_Lidar_Data(time, channels, points)``
    | This 3 dimensional mandatory array has to be filled with the
      time-series of raw lidar data. The photoncounting profiles have to
      submitted in counts (so as integers) while the analog ones in mV.
      The order the user chooses to fill this array defines the
      correspondence between channel index and lidar data.
    | For example if we fill this array in such way that:
    +-------------------------------------+---------------------------------------+
    | ``Raw_Lidar_Data(time,0,points)``   |  is the time-series of 1064 nm        |
    +-------------------------------------+---------------------------------------+
    | ``Raw_Lidar_Data(time,1,points)``   |  is the time-series of 532 cross      |
    +-------------------------------------+---------------------------------------+
    | ``Raw_Lidar_Data(time,2,points)``   |  is the time-series of 532 parallel   |
    +-------------------------------------+---------------------------------------+
    | ``Raw_Lidar_Data(time,3,points)``   |  is the time-series of 607 nm         |
    +-------------------------------------+---------------------------------------+
    |
    | from now on the channel index 0 is associated to the 1064 channel,
 to the 532 cross, 2 to the 532 parallel and 3 to the 607nm.
 -  | ``Raw_Bck_Start_Time(time_bck, nb_of_time_scales)``
    | This 2 dimensional optional array has to contain the acquisition
      start time (in seconds from the time given by the global attribute
      ``RawBck_Start_Time_UT``) of each dark measurements profile.
      Following the same procedure used for the variable
      ``Raw_Data_Start_Time`` we have to define:
    ::
        Raw_Bck_Start_Time =
 , 0,
 , 30,
 , 60,
          _, 90,
          _, 120,
          _, 150;
 -  | ``Raw_Bck_Stop_Time(time_bck, nb_of_time_scales)``
    | The same as previous item but for the dark acquisition stop time.
      Following a similar procedure we have to define:
    ::
        Raw_Bck_Stop_Time =
 , 30,
 , 60,
 , 90,
          _, 120,
          _, 150,
          _, 180 ;
 -  | ``Background_Profile(time_bck, channels, points)``
    | This 3 dimensional optional array has to be filled with the
      time-series of the dark measurements data. The photoncounting
      profiles have to submitted in counts (so as integers) while the
      analog ones in mV. The user has to fill this array following the
      same order used in filling the array ``Raw_Lidar_Data``:
    +---------------------------------------------+-------------------------------------+
    | ``Background_Profile(time_bck,0,points)``   |  dark time-series at 1064 nm        |
    +---------------------------------------------+-------------------------------------+
    | ``Background_Profile(time_bck,1,points)``   |  dark time-series at 532 cross      |
    +---------------------------------------------+-------------------------------------+
    | ``Background_Profile(time_bck,2,points)``   |  dark time-series at 532 parallel   |
    +---------------------------------------------+-------------------------------------+
    | ``Background_Profile(time_bck,3,points)``   |  dark time-series at 607 nm         |
    +---------------------------------------------+-------------------------------------+
    |
 -  | ``channel_ID(channels)``
    | This mandatory array provides the link between the channel index
      within the *Raw Lidar Data* input file and the channel ID in
      SCC\_DB. To fill this variable the user has to know which channel
      IDs in SCC\_DB correspond to his lidar channels. For this purpose
      the SCC, in its final version will provide to the user a special
      tool to get these channel IDs through a Web interface. At the
      moment this interface is not yet available and these channel IDs
      will be communicated directly to the user by the NA5 people.
    | Anyway to continue the example let’s suppose that the four lidar
      channels taken into account are mapped into SCC\_DB with the
      following channel IDs:
    +----------------+-----------------+
    | 1064 nm        |  channel ID=7   |
    +----------------+-----------------+
    | 532 cross      |  channel ID=5   |
    +----------------+-----------------+
    | 532 parallel   |  channel ID=6   |
    +----------------+-----------------+
    | 607 nm         |  channel ID=8   |
    +----------------+-----------------+
    |
    | In this case we have to define:
    ::
        channel_ID = 7, 5, 6, 8 ;
 -  | ``id_timescale(channels)``
    | This mandatory array is introduced to determine which time scale is
      used for the acquisition of each lidar channel. In particular this
      array defines the link between the channel index and the time scale
      index. In our example we have two different time scales. Filling
      the arrays ``Raw_Data_Start_Time`` and ``Raw_Data_Stop_Time`` we
      have defined a time scale index of 0 for the time scale with steps
      of 60 seconds and a time scale index of 1 for the other one with
      steps of 30 seconds. In this way this array has to be set as:
    ::
        id_timescale = 1, 0, 0, 0 ;
 -  | ``Laser_Pointing_Angle(scan_angles)``
    | This mandatory array contains all the scan angles used in the
      measurement. In our example we have only one scan angle of 5
      degrees with respect to the zenith, so we have to define:
    ::
        Laser_Pointing_Angle = 5 ;
 -  | ``Laser_Pointing_Angle_of_Profiles(time, nb_of_time_scales)``
    | This mandatory array is introduced to determine which scan angle is
      used for the acquisition of each lidar profile. In particular this
      array defines the link between the time and time scales indexes and
      the scan angle index. In our example we have a single scan angle
      that has to correspond to the scan angle index 0. So this array has
      to be defined as:
    ::
        Laser_Pointing_Angle_of_Profiles =
 , 0,
 , 0,
 , 0,
 , 0,
 , 0,
          _, 0,
          _, 0,
          _, 0,
          _, 0,
          _, 0 ;
 -  | ``Laser_Shots(time, channels)``
    | This mandatory array stores the laser shots accumulated at each
      time for each channel. In our example the number of laser shots
      accumulated is 1500 for the 1064nm channels and 3000 for all the
      other channels. Moreover the laser shots do not change with the
      time. So we have to define this array as:
    ::
         Laser_Shots =
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , _, _, _,
 , _, _, _,
 , _, _, _,
 , _, _, _,
 , _, _, _ ;
 -  | ``Emitted_Wavelength(channels)``
    | This optional array defines the link between the channel index and
      the emission wavelength for each lidar channel. The wavelength has
      to be expressed in nm. This information can be also taken from
      SCC\_DB. In our example we have:
    ::
        Emitted_Wavelength = 1064, 532, 532, 532 ;
 -  | ``Detected_Wavelength(channels)``
    | This optional array defines the link between the channel index and
      the detected wavelength for each lidar channel. Here detected
      wavelength means the value of center of interferential filter
      expressed in nm. This information can be also taken from SCC\_DB.
      In our example we have:
    ::
        Detected_Wavelength = 1064, 532, 532, 607 ;
 -  | ``Raw_Data_Range_Resolution(channels)``
    | This optional array defines the link between the channel index and
      the raw range resolution for each channel. If the scan angle is
      different from zero this quantity is different from the vertical
      resolution. More precisely if :math:`\alpha` is the scan angle used
      and :math:`\Delta z` is the range resolution the vertical
      resolution is calculated as :math:`\Delta
       z'=\Delta z \cos\alpha`. This array has to be filled with
      :math:`\Delta z` and not with :math:`\Delta z'`. The unit is
      meters. This information can be also taken from SCC\_DB. In our
      example we have:
    ::
        Raw_Data_Range_Resolution = 7.5, 15.0, 15.0, 15.0 ;
 -  | ``Scattering_Mechanism(channels)``
    | This optional array defines the scattering mechanism involved in
      each lidar channel. In particular the following values are adopted:
    +-----+---------------------------------------------------+
    | 0   |  Total elastic backscatter                        |
    +-----+---------------------------------------------------+
    | 1   |  N\ :math:`_2` vibrational Raman backscatter      |
    +-----+---------------------------------------------------+
    | 2   |  Cross polarization elastic backscatter           |
    +-----+---------------------------------------------------+
    | 3   |  Parallel polarization elastic backscatter        |
    +-----+---------------------------------------------------+
    | 4   |  H\ :math:`_2`\ O vibrational Raman backscatter   |
    +-----+---------------------------------------------------+
    | 5   |  Rotational Raman low quantum number              |
    +-----+---------------------------------------------------+
    | 6   |  Rotational Raman high quantum number             |
    +-----+---------------------------------------------------+
    |
    | This information can be also taken from SCC\_DB. In our example we
      have:
    ::
         Scattering_Mechanism = 0, 2, 3, 1 ;
 -  | ``Signal_Type(channels)``
    | This optional array defines the type of signal involved in each
      lidar channel. In particular the following values are adopted:
    +------+--------------------------------------------------------------+
    | 0    |  Total elastic                                               |
    +------+--------------------------------------------------------------+
    | 1    |  Total elastic near range                                    |
    +------+--------------------------------------------------------------+
    | 2    |  Total elastic far range                                     |
    +------+--------------------------------------------------------------+
    | 3    |  N\ :math:`_2` vibrational Raman                             |
    +------+--------------------------------------------------------------+
    | 4    |  N\ :math:`_2` vibrational Raman near range                  |
    +------+--------------------------------------------------------------+
    | 5    |  N\ :math:`_2` vibrational Raman far range                   |
    +------+--------------------------------------------------------------+
    | 6    |  Elastic polarization reflected                              |
    +------+--------------------------------------------------------------+
    | 7    |  Elastic polarization transmitted                            |
    +------+--------------------------------------------------------------+
    | 8    |  Rotational Raman line close to elastic line                 |
    +------+--------------------------------------------------------------+
    | 9    |  Rotational Raman line far from elastic line                 |
    +------+--------------------------------------------------------------+
    | 10   |  Elastic polarization reflected near range                   |
    +------+--------------------------------------------------------------+
    | 11   |  Elastic polarization reflected far range                    |
    +------+--------------------------------------------------------------+
    | 12   |  Elastic polarization transmitted near range                 |
    +------+--------------------------------------------------------------+
    | 13   |  Elastic polarization transmitted far range                  |
    +------+--------------------------------------------------------------+
    | 14   |  H\ :math:`_2`\ O vibrational Raman backscatter              |
    +------+--------------------------------------------------------------+
    | 15   |  Rotational Raman line far from elastic line near range      |
    +------+--------------------------------------------------------------+
    | 16   |  Rotational Raman line far from elastic line far range       |
    +------+--------------------------------------------------------------+
    | 17   |  Rotational Raman line close to elastic line near range      |
    +------+--------------------------------------------------------------+
    | 18   |  Rotational Raman line close to elastic line far range       |
    +------+--------------------------------------------------------------+
    | 19   |  H\ :math:`_2`\ O vibrational Raman backscatter near range   |
    +------+--------------------------------------------------------------+
    | 20   |  H\ :math:`_2`\ O vibrational Raman backscatter far range    |
    +------+--------------------------------------------------------------+
    | 21   |  Total elastic ultra near range                              |
    +------+--------------------------------------------------------------+
    | 22   |  +45 rotated elastic polarization transmitted                |
    +------+--------------------------------------------------------------+
    | 23   |  +45 rotated elastic polarization reflected                  |
    +------+--------------------------------------------------------------+
    | 24   |  -45 rotated elastic polarization transmitted                |
    +------+--------------------------------------------------------------+
    | 25   |  -45 rotated elastic polarization reflected                  |
    +------+--------------------------------------------------------------+
    | 26   |  +45 rotated elastic polarization transmitted near range     |
    +------+--------------------------------------------------------------+
    | 27   |  +45 rotated elastic polarization transmitted far range      |
    +------+--------------------------------------------------------------+
    | 28   |  +45 rotated elastic polarization reflected near range       |
    +------+--------------------------------------------------------------+
    | 29   |  +45 rotated elastic polarization reflected far range        |
    +------+--------------------------------------------------------------+
    | 30   |  -45 rotated elastic polarization transmitted near range     |
    +------+--------------------------------------------------------------+
    | 31   |  -45 rotated elastic polarization transmitted far range      |
    +------+--------------------------------------------------------------+
    | 32   |  -45 rotated elastic polarization reflected near range       |
    +------+--------------------------------------------------------------+
    | 33   |  -45 rotated elastic polarization reflected far range        |
    +------+--------------------------------------------------------------+
    |
    | This information can be also taken from SCC\_DB. In our example we
      have:
    ::
         Signal_Type = 0, 7, 6, 3 ;
 -  | ``Acquisition_Mode(channels)``
    | This optional array defines the acquisition mode (analog or
      photoncounting) involved in each lidar channel. In particular a
      value of 0 means analog mode and 1 photoncounting mode. This
      information can be also taken from SCC\_DB. In our example we have:
    ::
         Acquisition_Mode = 0, 1, 1, 1 ;
 -  | ``Laser_Repetition_Rate(channels)``
    | This optional array defines the repetition rate in Hz used to
      acquire each lidar channel. This information can be also taken from
      SCC\_DB. In our example we are supposing we have only one laser
      with a repetition rate of 50 Hz so we have to set:
    ::
        Laser_Repetition_Rate = 50, 50, 50, 50 ;
 -  | ``Dead_Time(channels)``
    | This optional array defines the dead time in ns associated to each
      lidar channel. The SCC will use the values given by this array to
      correct the photoncounting signals for dead time. Of course for
      analog signals no dead time correction will be applied (for analog
      channels the corresponding dead time values have to be set to
      undefined value). This information can be also taken from SCC\_DB.
      In our example the 1064 nm channel is acquired in analog mode so
      the corresponding dead time value has to be undefined. If we
      suppose a dead time of 10 ns for all other channels we have to set:
    ::
         Dead_Time = _, 10, 10, 10 ;
 -  | ``Dead_Time_Corr_Type(channels)``
    | This optional array defines which kind of dead time correction has
      to be applied on each photoncounting channel. The SCC will correct
      the data supposing a not-paralyzable channel if a value of 0 is
      found while a paralyzable channel is supposed if a value of 1 is
      found. Of course for analog signals no dead time correction will be
      applied and so the corresponding values have to be set to undefined
      value. This information can be also taken from SCC\_DB. In our
      example the 1064 nm channel is acquired in analog mode so the
      corresponding has to be undefined. If we want to consider all the
      photoncounting signals as not-paralyzable ones: we have to set:
    ::
         Dead_Time_Corr_Type = _, 0, 0, 0 ;
 -  | ``Trigger_Delay(channels)``
    | This optional array defines the delay (in ns) of the middle of the
      first rangebin with respect to the output laser pulse for each
      lidar channel. The SCC will use the values given by this array to
      correct for trigger delay. This information can be also taken from
      SCC\_DB. Let’s suppose that in our example all the photoncounting
      channels are not affected by this delay and only the analog channel
      at 1064nm is acquired with a delay of 50ns. In this case we have to
      set:
    ::
        Trigger_Delay = 50, 0, 0, 0 ;
 -  | ``Background_Mode(channels)``
    | This optional array defines how the atmospheric background has to
      be subtracted from the lidar channel. Two options are available for
      the calculation of atmospheric background:
    #. Average in the far field of lidar channel. In this case the value
       of this variable has to be 1
    #. Average within pre-trigger bins. In this case the value of this
       variable has to be 0
    This information can be also taken from SCC\_DB. Let’s suppose in our
    example we use the pre-trigger for the 1064nm channel and the far
    field for all other channels. In this case we have to set:
    ::
        Background_Mode = 0, 1, 1, 1 ;
 -  | ``Background_Low(channels)``
    | This mandatory array defines the minimum altitude (in meters) to
      consider in calculating the atmospheric background for each
      channel. In case pre-trigger mode is used the corresponding value
      has to be set to the rangebin to be used as lower limit (within
      pre-trigger region) for background calculation. In our example, if
      we want to calculate the background between 30000 and 50000 meters
      for all photoncounting channels and we want to use the first 500
      pre-trigger bins for the background calculation for the 1064nm
      channel we have to set:
    ::
         Background_Low= 0, 30000, 30000, 30000 ;
 -  | ``Background_High(channels)``
    | This mandatory array defines the maximum altitude (in meters) to
      consider in calculating the atmospheric background for each
      channel. In case pre-trigger mode is used the corresponding value
      has to be set to the rangebin to be used as upper limit (within
      pre-trigger region) for background calculation. In our example, if
      we want to calculate the background between 30000 and 50000 meters
      for all photoncounting channels and we want to use the first 500
      pre-trigger bins for the background calculation for the 1064nm
      channel we have to set:
    ::
        Background_High = 500, 50000, 50000, 50000 ;
 -  | ``Molecular_Calc``
    | This mandatory variable defines the way used by SCC to calculate
      the molecular density profile. At the moment two options are
      available:
    #. US Standard Atmosphere 1976. In this case the value of this
       variable has to be 0
    #. Radiosounding. In this case the value of this variable has to be 1
    If we decide to use the option 1. we have to provide also the
    measured pressure and temperature at lidar station level. Indeed if
    we decide to use the option 2. a radiosounding file has to be
    submitted separately in NetCDF format (the structure of this file is
    summarized in table 2 of the pdf file). Let’s suppose we want to use the
    option 1. so:
    ::
        Molecular_Calc = 0 ;
 -  | ``Pressure_at_Lidar_Station``
    | Because we have chosen the US Standard Atmosphere for calculation
      of the molecular density profile we have to give the pressure in
      hPa at lidar station level:
    ::
        Pressure_at_Lidar_Station = 1010 ;
 -  | ``Temperature_at_Lidar_Station``
    | Because we have chosen the US Standard Atmosphere for calculation
      of the molecular density profile we have to give the temperature in
      C at lidar station level:
    ::
        Temperature_at_Lidar_Station = 19.8 ;
 -  | ``LR_Input(channels)``
    | This array is required only for lidar channels for which elastic
      backscatter retrieval has to be performed. It defines the lidar
      ratio to be used within this retrieval. Two options are available:
    #. The user can submit a lidar ratio profile. In this case the value
       of this variable has to be 0.
    #. A fixed value of lidar ratio can be used. In this case the value
       of this variable has to be 1.
    If we decide to use the option 1. a lidar ratio file has to be
    submitted separately in NetCDF format (the structure of this file is
    summarized in table ). If we decide to use the option 2. the
    fixed value of lidar ratio will be taken from SCC\_DB. In our example
    we have to give a value of this array only for the 1064nm lidar
    channel because for the 532nm we will be able to retrieve a Raman
    backscatter coefficient. In case we want to use the fixed value
    stored in SCC\_DB we have to set:
    ::
        LR_Input = 1,_,_,_ ;
 -  | ``DAQ_Range(channels)``
    | This array is required only if one or more lidar signals are
      acquired in analog mode. It gives the analog scale in mV used to
      acquire the analog signals. In our example we have only the 1064nm
      channel acquired in analog mode. If we have used a 100mV analog
      scale to acquire this channel we have to set:
    ::
        DAQ_Range = 100,_,_,_ ;
 Global attributes
 ~~~~~~~~~~~~~~~~~
 -  | ``Measurement_ID``
    | This mandatory global attribute defines the measurement ID
      corresponding to the actual lidar measurement. It is a string
      composed by 12 characters. The first 8 characters give the start
      date of measurement in the format YYYYMMDD. The next 2 characters
      give the Earlinet call-sign of the station. The last 2 characters
      are used to distinguish between different time-series within the
      same date. In our example we have to set:
    ::
         Measurement_ID= "20090130cc00" ;
 -  | ``RawData_Start_Date``
    | This mandatory global attribute defines the start date of lidar
      measurements in the format YYYYMMDD. In our case we have:
    ::
         RawData_Start_Date = "20090130" ;
 -  | ``RawData_Start_Time_UT``
    | This mandatory global attribute defines the UT start time of lidar
      measurements in the format HHMMSS. In our case we have:
    ::
         RawData_Start_Time_UT = "000001" ;
 -  | ``RawData_Stop_Time_UT``
    | This mandatory global attribute defines the UT stop time of lidar
      measurements in the format HHMMSS. In our case we have:
    ::
         RawData_Stop_Time_UT = "000501" ;
 -  | ``RawBck_Start_Date``
    | This optional global attribute defines the start date of dark
      measurements in the format YYYYMMDD. In our case we have:
    ::
         RawBck_Start_Date = "20090129" ;
 -  | ``RawBck_Start_Time_UT``
    | This optional global attribute defines the UT start time of dark
      measurements in the format HHMMSS. In our case we have:
    ::
         RawBck_Start_Time_UT = "235001" ;
 -  | ``RawBck_Stop_Time_UT``
    | This optional global attribute defines the UT stop time of dark
      measurements in the format HHMMSS. In our case we have:
    ::
         RawBck_Stop_Time_UT = "235301" ;
 Example of file (CDL format)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 To summarize we have the following NetCDF *Raw Lidar Data* file (in CDL
 format):
 ::
     dimensions:
             points = 5000 ;
             channels = 4 ;
             time = UNLIMITED ; // (10 currently)
             nb_of_time_scales = 2 ;
             scan_angles = 1 ;
             time_bck = 6 ;
     variables:
             int channel_ID(channels) ;
             int Laser_Repetition_Rate(channels) ;
             double Laser_Pointing_Angle(scan_angles) ;
             int Signal_Type(channels);
             double Emitted_Wavelength(channels) ;
             double Detected_Wavelength(channels) ;
             double Raw_Data_Range_Resolution(channels) ;
             int Background_Mode(channels) ;
             double Background_Low(channels) ;
             double Background_High(channels) ;
             int Molecular_Calc ;
             double Pressure_at_Lidar_Station ;
             double Temperature_at_Lidar_Station ;
             int id_timescale(channels) ;
             double Dead_Time(channels) ;
             int Dead_Time_Corr_Type(channels) ;
             int Acquisition_Mode(channels) ;
             double Trigger_Delay(channels) ;
             int LR_Input(channels) ;
             int Laser_Pointing_Angle_of_Profiles(time, nb_of_time_scales) ;
             int Raw_Data_Start_Time(time, nb_of_time_scales) ;
             int Raw_Data_Stop_Time(time, nb_of_time_scales) ;
             int Raw_Bck_Start_Time(time_bck, nb_of_time_scales) ;
             int Raw_Bck_Stop_Time(time_bck, nb_of_time_scales) ;
             int Laser_Shots(time, channels) ;
             double Raw_Lidar_Data(time, channels, points) ;
             double Background_Profile(time_bck, channels, points) ;
             double DAQ_Range(channels) ;
     // global attributes:
                     :Measurement_ID = "20090130cc00" ;
                     :RawData_Start_Date = "20090130" ;
                     :RawData_Start_Time_UT = "000001" ;
                     :RawData_Stop_Time_UT = "000501" ;
                     :RawBck_Start_Date = "20090129" ;
                     :RawBck_Start_Time_UT = "235001" ;
                     :RawBck_Stop_Time_UT = "235301" ;
     data:
      channel_ID = 7, 5, 6, 8 ;
      Laser_Repetition_Rate = 50, 50, 50, 50 ;
      Laser_Pointing_Angle = 5 ;
      Signal_Type = 0, 7, 6, 3 ;
      Emitted_Wavelength = 1064, 532, 532, 532 ;
      Detected_Wavelength = 1064, 532, 532, 607 ;
      Raw_Data_Range_Resolution = 7.5, 15, 15, 15 ;
      Background_Mode = 0, 1, 1, 1 ;
      Background_Low = 0, 30000, 30000, 30000 ;
      Background_High = 500, 50000, 50000, 50000 ;
      Molecular_Calc = 0 ;
      Pressure_at_Lidar_Station = 1010 ;
      Temperature_at_Lidar_Station = 19.8 ;
      id_timescale = 1, 0, 0, 0 ;
      Dead_Time = _, 10, 10, 10 ;
      Dead_Time_Corr_Type = _, 0, 0, 0 ;
      Acquisition_Mode = 0, 1, 1, 1 ;
      Trigger_Delay = 50, 0, 0, 0 ;
      LR_Input = 1,_,_,_ ;
      DAQ_Range = 100,_,_,_ ;
      Laser_Pointing_Angle_of_Profiles =
 , 0,
 , 0,
 , 0,
 , 0,
 , 0,
       _, 0,
       _, 0,
       _, 0,
       _, 0,
       _, 0 ;
      Raw_Data_Start_Time =
 , 0,
 , 30,
 , 60,
 , 90,
 , 120,
       _, 150,
       _, 180,
       _, 210,
       _, 240,
       _, 270 ;
      Raw_Data_Stop_Time =
 , 30,
 , 60,
 , 90,
 , 120,
 , 150,
       _, 180,
       _, 210,
       _, 240,
       _, 270,
       _, 300 ;
      Raw_Bck_Start_Time =
 , 0,
 , 30,
 , 60,
       _, 90,
       _, 120,
       _, 150;
     Raw_Bck_Stop_Time =
 , 30,
 , 60,
 , 90,
       _, 120,
       _, 150,
       _, 180 ;
      Laser_Shots =
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , _, _, _,
 , _, _, _,
 , _, _, _,
 , _, _, _,
 , _, _, _ ;
      Raw_Lidar_Data = ...
      Background_Profile = ...
 The name of the input file should have the following format:
 ::
     Measurement_ID.nc
 | so in the example the filename should be 20090130cc00.nc.
 Please keep in mind that in case you submit a file like the previous
 one all the parameters present in it will be used by the SCC even if
 you have different values for the same parameters within the SCC\_DB.
 If you want to use the values already stored in SCC\_DB (this should
 be the usual way to use SCC) the *Raw Lidar Data* input file has to be
 modified as follows:
 ::
     dimensions:
             points = 5000 ;
             channels = 4 ;
             time = UNLIMITED ; // (10 currently)
             nb_of_time_scales = 2 ;
             scan_angles = 1 ;
             time_bck = 6 ;
     variables:
             int channel_ID(channels) ;
             double Laser_Pointing_Angle(scan_angles) ;
             double Background_Low(channels) ;
             double Background_High(channels) ;
             int Molecular_Calc ;
             double Pressure_at_Lidar_Station ;
             double Temperature_at_Lidar_Station ;
             int id_timescale(channels) ;
             int Laser_Pointing_Angle_of_Profiles(time, nb_of_time_scales) ;
             int Raw_Data_Start_Time(time, nb_of_time_scales) ;
             int Raw_Data_Stop_Time(time, nb_of_time_scales) ;
             int Raw_Bck_Start_Time(time_bck, nb_of_time_scales) ;
             int Raw_Bck_Stop_Time(time_bck, nb_of_time_scales) ;
             int LR_Input(channels) ;
             int Laser_Shots(time, channels) ;
             double Raw_Lidar_Data(time, channels, points) ;
             double Background_Profile(time_bck, channels, points) ;
             double DAQ_Range(channels) ;
     // global attributes:
                     :Measurement_ID = "20090130cc00" ;
                     :RawData_Start_Date = "20090130" ;
                     :RawData_Start_Time_UT = "000001" ;
                     :RawData_Stop_Time_UT = "000501" ;
                     :RawBck_Start_Date = "20090129" ;
                     :RawBck_Start_Time_UT = "235001" ;
                     :RawBck_Stop_Time_UT = "235301" ;
     data:
      channel_ID = 7, 5, 6, 8 ;
      Laser_Pointing_Angle = 5 ;
      Background_Low = 0, 30000, 30000, 30000 ;
      Background_High = 500, 50000, 50000, 50000 ;
      Molecular_Calc = 0 ;
      Pressure_at_Lidar_Station = 1010 ;
      Temperature_at_Lidar_Station = 19.8 ;
      id_timescale = 1, 0, 0, 0 ;
      LR_Input = 1,_,_,_ ;
      DAQ_Range = 100,_,_,_ ;
      Laser_Pointing_Angle_of_Profiles =
 , 0,
 , 0,
 , 0,
 , 0,
 , 0,
       _, 0,
       _, 0,
       _, 0,
       _, 0,
       _, 0 ;
      Raw_Data_Start_Time =
 , 0,
 , 30,
 , 60,
 , 90,
 , 120,
       _, 150,
       _, 180,
       _, 210,
       _, 240,
       _, 270 ;
      Raw_Data_Stop_Time =
 , 30,
 , 60,
 , 90,
 , 120,
 , 150,
       _, 180,
       _, 210,
       _, 240,
       _, 270,
       _, 300 ;
      Raw_Bck_Start_Time =
 , 0,
 , 30,
 , 60,
       _, 90,
       _, 120,
       _, 150;
      Raw_Bck_Stop_Time =
 , 30,
 , 60,
 , 90,
       _, 120,
       _, 150,
       _, 180 ;
      Laser_Shots =
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , 3000, 3000, 3000,
 , _, _, _,
 , _, _, _,
 , _, _, _,
 , _, _, _,
 , _, _, _ ;
      Raw_Lidar_Data = ...
      Background_Profile = ...
 This example file contains the minimum collection of mandatory
 information that has to be found within the *Raw Lidar Data* input file.
 If it is really necessary, the user can decide to add to these mandatory
 parameters any number of additional parameters considered in the
 previous example.
 Finally, suppose we want to make the following changes with respect to
 the previous example:
 #. use a sounding file for molecular density calculation instead of “US
    Standar Atmosphere 1976”
 #. supply a lidar ratio profile to use in elastic backscatter retrieval
    instead of a fixed value
 #. provide a overlap function for overlap correction
 In this case we have to generate the following NetCDF additional files:
 -  | ``rs_20090130cc00.nc``
    | The name of *Sounding Data* file has to be computed as follows:
    | ``"rs_"``\ +\ ``Measurement_ID``
    | The structure of this file is summarized in table 2 of the pdf.
 -  | ``ov_20090130cc00.nc``
    | The name of *Overlap* file has to be computed as follows:
    | ``"ov_"``\ +\ ``Measurement_ID``
    | The structure of this file is summarized in table 3 of the pdf.
 -  | ``lr_20090130cc00.nc``
    | The name of *Lidar Ratio* file has to be computed as follows:
    | ``"lr_"``\ +\ ``Measurement_ID``
    | The structure of this file is summarized in table 4 of the pdf.
 Moreover we need to apply the following changes to the *Raw Lidar Data*
 input file:
 #. Change the value of the variable ``Molecular_Calc`` as follows:
    ::
        Molecular_Calc = 1 ;
    Of course the variables ``Pressure_at_Lidar_Station`` and
    ``Temperature_at_Lidar_Station`` are not necessary anymore.
 #. Change the values of the array ``LR_Input`` as follows:
    ::
        LR_Input = 0,_,_,_ ;
 #. Add the global attribute ``Sounding_File_Name``
    ::
        Sounding_File_Name = "rs_20090130cc00.nc" ;
 #. Add the global attribute ``LR_File_Name``
    ::
        LR_File_Name = "lr_20090130cc00.nc" ;
 #. Add the global attribute ``Overlap_File_Name``
    ::
        Overlap_File_Name = "ov_20090130cc00.nc" ;

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docs/netcdf_file.rst