netcdf_file.rst

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+The SCC netCDF file format
+==========================
+
+Rationale
+---------
+
+The Single Calculus Chain (SCC) is composed by two different modules:
+
+-  pre-processing module ( scc\_preprocessing)
+
+-  optical processing module ( ELDA)
+
+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 the
+present the SCC can handle four different types of input files:
+
+1. Raw Lidar Data
+2. Sounding Data
+3. Overlap
+4. 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 explanation 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.
+Every comments or suggestions regarding this document can be sent to
+Giuseppe D’Amico by e-mail at ``damico@imaa.cnr.it``
+
+This document is available for downloading at ``www.earlinetasos.org``
+
+In table tab:rawdata is reported 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.
+
+In table tab:sounding, tab:overlap and tab:lr are reported 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           | :math:`30^{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:
+
+1. 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      |
+   +------------------------------+-------------------------------+
+
+2. 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        |
+   +-----------------------------+---------------------------------+
+
+3. 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     |
+   +-----------------------------+---------------------------------+
+
+4. 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
+29:math:`^\mathrmth` January 2009.
+
+Dimensions
+~~~~~~~~~~
+
+Looking at table tab:rawdata 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
+30 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 30
+   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, 0,
+         60, 30,
+         120, 60,
+         180, 90,
+         240, 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 =
+         60, 30,
+         120, 60,
+         180, 90,
+         240, 120,
+         300, 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        | :math:`\rightarrow` is the time-series of 1064 nm          |
+   +-------------------------------------+------------------------------------------------------------+
+   | Raw_Lidar_Data(time,1,points        | :math:`\rightarrow` is the time-series of 532 cross        |
+   +-------------------------------------+------------------------------------------------------------+
+   | Raw_Lidar_Data(time,2,points        | :math:`\rightarrow` is the time-series of 532 parallel     |
+   +-------------------------------------+------------------------------------------------------------+
+   | Raw_Lidar_Data(time,3,points        | :math:`\rightarrow` is the time-series of 607 nm           |
+   +-------------------------------------+------------------------------------------------------------+
+
+   from now on the channel index 0 is associated to the 1064 channel, 
+   1 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, 0,
+         60, 30,
+         120, 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 =
+         60, 30,
+         120, 60,
+         180, 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        | :math:`\rightarrow` dark time-series at 1064 nm          |
+   +---------------------------------------------+----------------------------------------------------------+
+   | Background_Profile(time_bck,1,points        | :math:`\rightarrow` dark time-series at 532 cross        |
+   +---------------------------------------------+----------------------------------------------------------+
+   | Background_Profile(time_bck,2,points        | :math:`\rightarrow` dark time-series at 532 parallel     |
+   +---------------------------------------------+----------------------------------------------------------+
+   | Background_Profile(time_bck,3,points        | :math:`\rightarrow` 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        | :math:`\rightarrow` channel ID=7     |
+   +----------------+--------------------------------------+
+   | 532 cross      | :math:`\rightarrow` channel ID=5     |
+   +----------------+--------------------------------------+
+   | 532 parallel   | :math:`\rightarrow` channel ID=6     |
+   +----------------+--------------------------------------+
+   | 607 nm         | :math:`\rightarrow` 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,
+         _, 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 =
+         1500, 3000, 3000, 3000, 
+         1500, 3000, 3000, 3000, 
+         1500, 3000, 3000, 3000, 
+         1500, 3000, 3000, 3000, 
+         1500, 3000, 3000, 3000, 
+         1500, _, _, _, 
+         1500, _, _, _, 
+         1500, _, _, _, 
+         1500, _, _, _, 
+         1500, _, _, _ ;
+
+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 ;
+
+ID_Range(channels)
+   This optional array defines if a particular channel is configured as
+   high, low or ultranear range channel. In particular a value 0
+   indicates a low range channel, a value 1 a high range channel and a
+   value of 2 an ultranear range channel. If for a particular channel
+   you don’t separate between high and low range channel, please set the
+   corresponding value to 1. This information can be also taken from
+   SCC\_DB. In our case we have to set:
+
+   ::
+
+       ID_Range = 1, 1, 1, 1 ;
+
+Scattering_Mechanism(channels)
+   This optional array defines the scattering mechanism involved in
+   each lidar channel. In particular the following values are adopted:
+
+   +------+---------------------------------------------------------------------------------------------+
+   | 0    | :math:`\rightarrow` Total elastic backscatter                                               |
+   +------+---------------------------------------------------------------------------------------------+
+   | 1    | :math:`\rightarrow` :math:`N_2` vibrational Raman backscatter                               |
+   +------+---------------------------------------------------------------------------------------------+
+   | 2    | :math:`\rightarrow` Cross polarization elastic backscatter                                  |
+   +------+---------------------------------------------------------------------------------------------+
+   | 3    | :math:`\rightarrow` Parallel polarization elastic backscatter                               |
+   +------+---------------------------------------------------------------------------------------------+
+   | 4    | :math:`\rightarrow` :math:`H_2O` vibrational Raman backscatter                              |
+   +------+---------------------------------------------------------------------------------------------+
+   | 5    | :math:`\rightarrow` Rotational Raman Stokes line close to elastic line                      |
+   +------+---------------------------------------------------------------------------------------------+
+   | 6    | :math:`\rightarrow` Rotational Raman Stokes line far from elastic line                      |
+   +------+---------------------------------------------------------------------------------------------+
+   | 7    | :math:`\rightarrow` Rotational Raman anti-Stokes line close to elastic line                 |
+   +------+---------------------------------------------------------------------------------------------+
+   | 8    | :math:`\rightarrow` Rotational Raman anti-Stokes line far from elastic line                 |
+   +------+---------------------------------------------------------------------------------------------+
+   | 9    | :math:`\rightarrow` Rotational Raman Stokes and anti-Stokes lines close to elastic line     |
+   +------+---------------------------------------------------------------------------------------------+
+   | 10   | :math:`\rightarrow` Rotational Raman Stokes and anti-Stokes lines far from elastic line     |
+   +------+---------------------------------------------------------------------------------------------+
+
+   This information can be also taken from SCC\_DB. In our example we have:
+
+   ::
+
+        Scattering_Mechanism = 0, 2, 3, 1 ;
+
+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 tab:sounding). 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 ;
+
+Depolarization_Factor(channels)
+   This array is required only for lidar systems that use the two
+   depolarization channels for the backscatter retrieval. It represents
+   the factor :math:`f` to calculate the total backscatter signal
+   :math:`S_t` combining its cross :math:`S_c` and parallel
+   :math:`S_p` components: :math:`S_t=S_p+fS_c`. This factor is
+   mandatory only for systems acquiring :math:`S_c` and :math:`S_p`
+   and not :math:`S_t`. For systems acquiring :math:`S_c`,
+   :math:`S_p` and :math:`S_t` this factor is optional and it will
+   be used only for depolarizaton ratio calculation. Moreover only the
+   values of the array corresponding to cross polarization channels will
+   be considered; all other values will be not taken into account and
+   should be set to undefined value. In our example for the wavelength
+   532nm we have only the cross and the parallel components and not the
+   total one. So we have to give the value of this factor only in
+   correspondence of the 532nm cross polarization channel that
+   corresponds to the channel index 1. Suppose that this factor is 0.88.
+   Moreover, because we don’t have any other depolarization channels we
+   have also to set all other values of the array to undefined value.
+
+   ::
+
+       Depolarization_Factor = _,0.88,_,_ ;
+
+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 tab:lr). 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 ID_Range(channels) ;
+            int Scattering_Mechanism(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 ;
+
+     ID_Range = 1, 1, 1, 1 ;
+
+     Scattering_Mechanism = 0, 2, 3, 1 ;
+
+     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,
+      _, 0,
+      _, 0,
+      _, 0,
+      _, 0,
+      _, 0 ;
+
+
+     Raw_Data_Start_Time =
+      0, 0,
+      60, 30,
+      120, 60,
+      180, 90,
+      240, 120,
+      _, 150,
+      _, 180,
+      _, 210,
+      _, 240,
+      _, 270 ;
+
+     Raw_Data_Stop_Time =
+      60, 30,
+      120, 60,
+      180, 90,
+      240, 120,
+      300, 150,
+      _, 180,
+      _, 210,
+      _, 240,
+      _, 270,
+      _, 300 ;
+
+
+     Raw_Bck_Start_Time =
+      0, 0,
+      60, 30,
+      120, 60,
+      _, 90,
+      _, 120,
+      _, 150;
+
+
+    Raw_Bck_Stop_Time =
+      60, 30,
+      120, 60,
+      180, 90,
+      _, 120,
+      _, 150,
+      _, 180 ;
+
+
+     Laser_Shots =
+      1500, 3000, 3000, 3000, 
+      1500, 3000, 3000, 3000, 
+      1500, 3000, 3000, 3000, 
+      1500, 3000, 3000, 3000, 
+      1500, 3000, 3000, 3000, 
+      1500, _, _, _, 
+      1500, _, _, _, 
+      1500, _, _, _, 
+      1500, _, _, _, 
+      1500, _, _, _ ;
+
+
+     Raw_Lidar_Data = ... 
+
+     Background_Profile = ...
+
+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,
+      _, 0,
+      _, 0,
+      _, 0,
+      _, 0,
+      _, 0 ;
+
+
+     Raw_Data_Start_Time =
+      0, 0,
+      60, 30,
+      120, 60,
+      180, 90,
+      240, 120,
+      _, 150,
+      _, 180,
+      _, 210,
+      _, 240,
+      _, 270 ;
+
+     Raw_Data_Stop_Time =
+      60, 30,
+      120, 60,
+      180, 90,
+      240, 120,
+      300, 150,
+      _, 180,
+      _, 210,
+      _, 240,
+      _, 270,
+      _, 300 ;
+
+
+     Raw_Bck_Start_Time =
+      0, 0,
+      60, 30,
+      120, 60,
+      _, 90,
+      _, 120,
+      _, 150;
+
+
+     Raw_Bck_Stop_Time =
+      60, 30,
+      120, 60,
+      180, 90,
+      _, 120,
+      _, 150,
+      _, 180 ;
+
+
+     Laser_Shots =
+      1500, 3000, 3000, 3000, 
+      1500, 3000, 3000, 3000, 
+      1500, 3000, 3000, 3000, 
+      1500, 3000, 3000, 3000, 
+      1500, 3000, 3000, 3000, 
+      1500, _, _, _, 
+      1500, _, _, _, 
+      1500, _, _, _, 
+      1500, _, _, _, 
+      1500, _, _, _ ;
+
+
+     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 tab:sounding.
+
+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 tab:overlap.
+
+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 tab:lr.
+
+Moreover we need to apply the following changes to the  Raw Lidar Data
+input file:
+
+1. 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.
+
+2. Change the values of the array ``LR_Input`` as follows:
+
+   ::
+
+       LR_Input = 0,_,_,_ ;
+
+3. Add the global attribute ``Sounding_File_Name``
+
+   ::
+
+       Sounding_File_Name = "rs_20090130cc00.nc" ;
+
+5. Add the global attribute ``LR_File_Name``
+
+   ::
+
+       LR_File_Name = "lr_20090130cc00.nc" ;
+
+6. Add the global attribute ``Overlap_File_Name``
+
+   ::
+
+       Overlap_File_Name = "ov_20090130cc00.nc" ;

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