# HG changeset patch
# User Victor Nicolae <victor.nicolae@inoe.ro>
# Date 1506081773 -10800
# Node ID e59cdc4fd4c0b3aaa49de79628cf8693492df5ce
# Parent  33826498a1257db028160e95622370546230becc
Include all parameters from the NetCDF parameters file in the final output file.

Better inform the user if any mandatory parameter misses from the file.

In case of extra (optional) parameters, allow missing values in the output file.

diff -r 33826498a125 -r e59cdc4fd4c0 atmospheric_lidar/generic.py
--- a/atmospheric_lidar/generic.py	Fri Sep 22 14:33:51 2017 +0300
+++ b/atmospheric_lidar/generic.py	Fri Sep 22 15:02:53 2017 +0300
@@ -334,12 +334,20 @@
         temp_v = f.createVariable(channel_var, variable_type, ('channels',))
         for n, channel in enumerate(channels):
             temp_v[n] = params.channel_parameters[channel][channel_var]
-
-        # Write the values of fixed channel parameters
-        for (var, t) in channel_variables.iteritems():
-            temp_v = f.createVariable(var, t[1], t[0])
+        
+        # Write the values of fixed channel parameters:
+        fill_value = -9999
+        for param in self._get_provided_extra_parameters():
+            if param in channel_variables.keys():
+                temp_v = f.createVariable(param, channel_variables[param][1], channel_variables[param][0])
+            else:
+                temp_v = f.createVariable(param, 'd', ('channels',), fill_value = fill_value)
+                
             for (channel, n) in zip(channels, range(len(channels))):
-                temp_v[n] = params.channel_parameters[channel][var]
+                try:
+                    temp_v[n] = params.channel_parameters[channel][param]
+                except KeyError: # The parameter was not provided for this channel so we mask the value.
+                    temp_v[n] = fill_value
 
         # Write the id_timescale values
         temp_id_timescale = f.createVariable('id_timescale', 'i', ('channels',))
@@ -403,6 +411,34 @@
              'DAQ_Range': (('channels',), 'd'),
              }
         return channel_variables
+        
+    def _get_provided_extra_parameters(self):
+        # When looking for non-mandatory channel parameters, ignore the following parameter names:
+        ignore = ['channel_ID', 'channel string ID', 'Depolarization_Factor', 'Laser_Shots']
+        
+        channels = self.channels.keys()
+        params = self.extra_netcdf_parameters.channel_parameters
+        mandatory = self._get_scc_mandatory_channel_variables()
+        
+        # Get all the provided extra parameters (both mandatory and optional):
+        provided_extra_parameters = []
+        for (channel, n) in zip(channels, range(len(channels))):
+            # Check all the mandatory parameters are provided for each of the channels:
+            for var in mandatory.keys():
+                if var not in params[channel].keys():
+                    raise ValueError ("Mandatory parameter '{0}' not provided for channel {1}!".format(
+                        var,
+                        channel
+                    ))
+                    
+            provided_extra_parameters.extend(params[channel].keys())
+            
+        provided_extra_parameters = set(provided_extra_parameters)
+        # Discard certain parameter names:
+        for param in ignore:
+            provided_extra_parameters.discard(param)
+            
+        return provided_extra_parameters
 
     def add_dark_measurements_to_netcdf(self, f, channels):