Mercurial > public > atmospheric_lidar / changeset

--- a/generic.py	Wed Apr 01 13:06:08 2015 +0300
+++ b/generic.py	Mon Feb 22 16:39:23 2016 +0200
@@ -26,7 +26,7 @@
     
     """
     
-    def __init__(self, filelist= None):
+    def __init__(self, filelist = None):
         self.info = {}
         self.dimensions = {}
         self.variables =  {}
@@ -34,10 +34,11 @@
         self.attributes = {}
         self.files = []
         self.dark_measurement = None
+        
         if filelist:
             self.import_files(filelist)
         
-    def import_files(self,filelist):
+    def import_files(self, filelist):
         for f in filelist:
             self.import_file(f)
         self.update()
@@ -114,7 +115,7 @@
         self.variables['id_timescale'] = dict(channel_timescales)
     
     def _get_duration(self, raw_start_in_seconds):
-        ''' Return the duration for a given time scale. In some files (ex. Licel) this
+        ''' Return the duration for a given time scale. In some files (e.g. Licel) this
         can be specified from the files themselves. In others this must be guessed.
          
         '''
@@ -414,7 +415,7 @@
         self.binwidth = float(channel_parameters['binwidth'])  # in microseconds
         self.data = {}
         self.resolution = self.binwidth * c / 2
-        self.z = np.arange(len(channel_parameters['data'])) * self.resolution + self.resolution/2.0 # Change: add half bin in the z 
+        self.z = np.arange(len(channel_parameters['data'])) * self.resolution + self.resolution / 2.0 # Change: add half bin in the z 
         self.points = len(channel_parameters['data'])
         self.rc = []
         self.duration  = 60

--- a/licel.py	Wed Apr 01 13:06:08 2015 +0300
+++ b/licel.py	Mon Feb 22 16:39:23 2016 +0200
@@ -5,7 +5,7 @@
 import musa_2009_netcdf_parameters
 
 licel_file_header_format = ['Filename',
-                            'Site StartDate StartTime EndDate EndTime Altitude Longtitude Latitude ZenithAngle',
+                            'StartDate StartTime EndDate EndTime Altitude Longtitude Latitude ZenithAngle',  # Appart from Site that is read manually
                             'LS1 Rate1 LS2 Rate2 DataSets', ]
 licel_file_channel_format = 'Active AnalogPhoton LaserUsed DataPoints 1 HV BinW Wavelength d1 d2 d3 d4 ADCbits NShots Discriminator ID'
 
@@ -28,53 +28,83 @@
         Input: filename
         Output: object """
 
-        raw_info = {}
         channels = {}
-        channel_info = []
+
+        with open(filename, 'rb') as f:
+
+            self.read_header(f)
+            
+            # Check the complete header is read
+            a = f.readline()
 
-        f = open(filename, 'rb')
-
+            # Import the data
+            for current_channel_info in self.channel_info:
+                raw_data = np.fromfile(f, 'i4', int(current_channel_info['DataPoints']))
+                a = np.fromfile(f, 'b', 1)
+                b = np.fromfile(f, 'b', 1)
+                
+                if (a[0] != 13) | (b[0] != 10):
+                    print "Warning: No end of line found after record. File could be corrupt"
+                channel = LicelFileChannel(current_channel_info, raw_data, self.duration())
+                
+                channel_name = channel.channel_name
+                
+                if channel_name in channels.keys():
+                    # If the analog/photon naming scheme is not enough, find a new one!
+                    raise IOError('Trying to import two channels with the same name')
+                
+                channels[channel_name] = channel
+                
+        self.channels = channels
+    
+    
+    def read_header(self, f):
+        """ Read the header of a open file f. 
+        
+        Returns raw_info and channel_info. Updates some object properties. """
+        
         #Read the first 3 lines of the header
         raw_info = {}
-        for c1 in range(3):
-            raw_info.update(match_lines(f.readline(), licel_file_header_format[c1]))
-
+        channel_info = []
+        
+        # Read first line
+        raw_info['Filename'] = f.readline().strip()
+        
+        # Read second line
+        second_line = f.readline()
+        
+        # Many licel files don't follow the licel standard. Specifically, the
+        # measurement site is not always 8 characters, and can include white
+        # spaces. For this, the site name is detect everything before the first 
+        # date. For efficiency, the first date is found by the first '/'.
+        # e.g. assuming a string like 'Site name 01/01/2010 ...' 
+        
+        site_name = second_line.split('/')[0][:-2]
+        clean_site_name = site_name.strip()
+        raw_info['Site'] = clean_site_name
+        raw_info.update(match_lines(second_line[len(clean_site_name) + 1:], licel_file_header_format[1]))
+        
+        # Read third line
+        third_line = f.readline()
+        raw_info.update(match_lines(third_line, licel_file_header_format[2]))
+        
+        # Update the object properties based on the raw info
         start_string = '%s %s' % (raw_info['StartDate'], raw_info['StartTime'])
         stop_string = '%s %s' % (raw_info['EndDate'], raw_info['EndTime'])
         date_format = '%d/%m/%Y %H:%M:%S'
+        
         self.start_time = datetime.datetime.strptime(start_string, date_format)
         self.stop_time = datetime.datetime.strptime(stop_string, date_format)
         self.latitude = float(raw_info['Latitude'])
         self.longitude = float(raw_info['Longtitude'])
-        
+            
         # Read the rest of the header.
         for c1 in range(int(raw_info['DataSets'])):
             channel_info.append(match_lines(f.readline(), licel_file_channel_format))
-
-        # Check the complete header is read
-        a = f.readline()
-
-        # Import the data
-        for current_channel_info in channel_info:
-            raw_data = np.fromfile(f, 'i4', int(current_channel_info['DataPoints']))
-            a = np.fromfile(f, 'b', 1)
-            b = np.fromfile(f, 'b', 1)
+        
+        self.raw_info = raw_info
+        self.channel_info = channel_info
             
-            if (a[0] != 13) | (b[0] != 10):
-                print "Warning: No end of line found after record. File could be corrupt"
-            channel = LicelFileChannel(current_channel_info, raw_data, self.duration())
-            
-            channel_name = channel.channel_name
-            if channel_name in channels.keys():
-                # If the analog/photon naming scheme is not enough, find a new one!
-                raise IOError('Trying to import two channels with the same name')
-            
-            channels[channel_name] = channel
-        f.close()
-
-        self.raw_info = raw_info
-        self.channels = channels
-    
     def duration(self):
         """ Return the duration of the file. """
         dt = self.stop_time - self.start_time
@@ -194,7 +224,7 @@
 class LicelChannel(LidarChannel):
     
     def __init__(self, channel_file):
-        c = 299792458.0 # Speed of light
+        c = 299792458.0  # Speed of light
         self.wavelength = channel_file.wavelength
         self.name = channel_file.channel_name
         self.binwidth = channel_file.dz * 2 / c  # in seconds