# HG changeset patch
# User Iannis <i.binietoglou@impworks.gr>
# Date 1513075830 -7200
# Node ID e954eecc217f32c10a29fad54a85729891d73e9b
# Parent  b71252bb7f87231236cc69de3e347e97d66ddca5
When subsetting measurements (either by channel, time, or bins) the dark measurements were not tranfered to the new object.

Fixed this (I hope)

diff -r b71252bb7f87 -r e954eecc217f atmospheric_lidar/__init__.py
--- a/atmospheric_lidar/__init__.py	Tue Dec 12 12:02:39 2017 +0200
+++ b/atmospheric_lidar/__init__.py	Tue Dec 12 12:50:30 2017 +0200
@@ -1,1 +1,1 @@
-__version__ = '0.2.11'
\ No newline at end of file
+__version__ = '0.2.12'
\ No newline at end of file
diff -r b71252bb7f87 -r e954eecc217f atmospheric_lidar/generic.py
--- a/atmospheric_lidar/generic.py	Tue Dec 12 12:02:39 2017 +0200
+++ b/atmospheric_lidar/generic.py	Tue Dec 12 12:50:30 2017 +0200
@@ -25,6 +25,8 @@
     
     The class assumes that the input files are consecutive, i.e. there are no measurements gaps.
     """
+    extra_netcdf_parameters = None
+
     def __init__(self, file_list=None):
         """
         This is run when creating a new object.
@@ -41,7 +43,6 @@
         self.attributes = {}
         self.files = []
         self.dark_measurement = None
-        self.extra_netcdf_parameters = None
 
         if file_list:
             self._import_files(file_list)
@@ -177,10 +178,13 @@
         m = self.__class__()  # Create an object of the same type as this one.
         m.channels = dict([(channel, self.channels[channel]) for channel
                            in channel_subset])
+        m.files = self.files
+        m.update()
 
-        m.files = self.files
-
-        m.update()
+        # Dark measurements should also be subseted.
+        if self.dark_measurement is not None:
+            dark_subset = self.dark_measurement.subset_by_channels(channel_subset)
+            m.dark_measurement = dark_subset
 
         return m
 
@@ -235,6 +239,9 @@
             m.channels[channel_name] = channel.subset_by_time(start_time, stop_time)
 
         m.update()
+
+        # Transfer dark measurement to the new object. They don't need time subsetting.
+        m.dark_measurement = self.dark_measurement
         return m
 
     def subset_by_bins(self, b_min=0, b_max=None):
@@ -263,6 +270,11 @@
 
         m.update()
 
+        # Dark measurements should also be subseted.
+        if self.dark_measurement is not None:
+            dark_subset = self.dark_measurement.subset_by_bins(b_min, b_max)
+            m.dark_measurement = dark_subset
+
         return m
 
     def rename_channels(self, prefix="", suffix=""):
@@ -296,7 +308,7 @@
     def subtract_dark(self):
         """
         Subtract dark measurements from the raw lidar signals. 
-         
+
         This method is here just for testing.
         
         Note
diff -r b71252bb7f87 -r e954eecc217f atmospheric_lidar/licel_depol.py
--- a/atmospheric_lidar/licel_depol.py	Tue Dec 12 12:02:39 2017 +0200
+++ b/atmospheric_lidar/licel_depol.py	Tue Dec 12 12:50:30 2017 +0200
@@ -1,7 +1,11 @@
+import logging
+
 import numpy as np
 
 from licel import LicelLidarMeasurement
 
+logger = logging.getLogger(__name__)
+
 
 class LicelCalibrationMeasurement(LicelLidarMeasurement):
 
diff -r b71252bb7f87 -r e954eecc217f atmospheric_lidar/scripts/licel2scc.py
--- a/atmospheric_lidar/scripts/licel2scc.py	Tue Dec 12 12:02:39 2017 +0200
+++ b/atmospheric_lidar/scripts/licel2scc.py	Tue Dec 12 12:50:30 2017 +0200
@@ -7,10 +7,11 @@
 import os
 import sys
 
-
 from ..licel import LicelLidarMeasurement
 from ..__init__ import __version__
 
+logger = logging.getLogger(__name__)
+
 
 def create_custom_class(custom_netcdf_parameter_path, use_id_as_name=False, temperature=25., pressure=1020.,
                         licel_timezone='UTC'):
@@ -35,7 +36,7 @@
     CustomLidarMeasurement:
        A custom sub-class of LicelLidarMeasurement
     """
-
+    logger.debug('Reading parameter files: %s' % custom_netcdf_parameter_path)
     custom_netcdf_parameters = read_settings_file(custom_netcdf_parameter_path)
 
     class CustomLidarMeasurement(LicelLidarMeasurement):
diff -r b71252bb7f87 -r e954eecc217f atmospheric_lidar/scripts/licel2scc_depol.py
--- a/atmospheric_lidar/scripts/licel2scc_depol.py	Tue Dec 12 12:02:39 2017 +0200
+++ b/atmospheric_lidar/scripts/licel2scc_depol.py	Tue Dec 12 12:50:30 2017 +0200
@@ -7,10 +7,11 @@
 import os
 import sys
 
-
 from ..licel_depol import LicelCalibrationMeasurement
 from ..__init__ import __version__
 
+logger = logging.getLogger(__name__)
+
 
 def create_custom_class(custom_netcdf_parameter_path, use_id_as_name=False, temperature=25., pressure=1020.,
                         licel_timezone='UTC'):
@@ -19,13 +20,13 @@
 
     Parameters
     ----------
-    custom_netcdf_parameter_path: str
+    custom_netcdf_parameter_path : str
        The path to the custom channels parameters.
-    use_id_as_name: bool
+    use_id_as_name : bool
        Defines if channels names are descriptive or transient digitizer IDs.
-    temperature: float
+    temperature : float
        The ground temperature in degrees C (default 25.0).
-    pressure: float
+    pressure : float
        The ground pressure in hPa (default: 1020.0).
     licel_timezone : str
        String describing the timezone according to the tz database.