# HG changeset patch
# User Iannis <ioannis@inoe.ro>
# Date 1394463407 -7200
# Node ID 4e3f530ac84e5dd2fc58c0bced4a31c526aa298e
# Parent  98a251a75e806daba454d344808b3bd5460fc786
Added files for the new doc structure.

diff -r 98a251a75e80 -r 4e3f530ac84e docs/administration.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/administration.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,24 @@
+.. Single Calculus Chain interface documentation master file, created by
+   sphinx-quickstart on Tue Feb  7 13:17:19 2012.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+.. _administration:
+
+Station administration
+======================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+   
+   /administration/introduction
+   /administration/adding_station
+   /administration/adding_system
+   /administration/adding_channels
+   /administration/adding_products
+   /administration/adding_otherequipment
+   /administration/usecases.rst
+
+
diff -r 98a251a75e80 -r 4e3f530ac84e docs/administration/adding_channels.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/administration/adding_channels.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,10 @@
+Adding channels
+===============
+
+
+
+.. _signal-types:
+
+Signal types
+~~~~~~~~~~~~
+(explain here all the signal type abreviations).
diff -r 98a251a75e80 -r 4e3f530ac84e docs/administration/adding_otherequipment.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/administration/adding_otherequipment.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,2 @@
+Adding other equipment
+======================
diff -r 98a251a75e80 -r 4e3f530ac84e docs/administration/adding_products.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/administration/adding_products.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,111 @@
+Adding products
+===============
+
+Depending on the product you need to produce, some of the following  tables need to be filled. 
+
+.. note::
+
+   This section is not up-to-date to the latest interface version. It will be updated shortly.
+
+
+Backscatter products
+--------------------
+The following tables need to be filed for the various backscatter products.
+
+Backscatter calibrations 
+------------------------
+For backscatter (product types: Raman backscatter, Combined Raman backscatter and extinction, Elastic backscatter retrieval
+
+LowestHeight   
+   in meters, lowest height for reference height search
+
+TopHeight
+   in meters, maximum height for reference height search
+
+WindowWidth
+   in meters, width of the reference height interval
+
+calValue
+   backscatter ratio, e.g. 1 or 1.01
+   
+calRangeSearchMethod ID: 
+   always 0
+   
+   
+If done, you have to remember the ID for your backscatter calibration options an go the the specific tables below,
+
+for product type 0 and 2: Raman_backscatter_options
+---------------------------------------------------
+
+Raman calculation method
+   at the moment, only 1
+   
+bsc cal options
+   insert ID from previous step
+   
+error method ID: 
+   at the moment, only 1
+   
+for product type 3: elast_backscatter_options
+-----------------------------------------------
+
+ elast bsc method ID
+   at the moment, only 1 (iterative approach)
+   
+bsc cal options
+   insert ID from previous step
+   
+error method ID: 
+   at the moment, only 1
+      
+lr input id:
+   at the moment, only 1 (fixed LR)
+   
+fixed_lr
+   ... in sr, value of the used lidar ratio
+   
+iter_bsc_options
+   if, iterative approach is used, go to table iter_bsc_options and remember ID and insert here
+
+iter_bsc_options
+----------------
+
+iter conv crit
+   ...e.g. 0.1 (=10%) The iteration is stopped when the RELATIVE difference between the actual and the previous column integrated backscatter coefficients is below this value
+
+ram bsc method id
+   at the moment, only 1
+   
+max iteration count: 
+   maximum number of iteration steps   
+
+for product type 1: Extinction options
+--------------------------------------
+
+Extinction method:
+   Standard: 1, (0 weighted linear fit, 1 non-weighted linear fit, 2 difference quotient, 3 polynomial sec order fit, 4 quadratic function, 5 Savitzky-Golay filter, 6 Russo)
+
+error method ID: 
+   at the moment, only 1
+   
+overlap file ID:
+   if overlap file is available, enter ID here
+   
+angstroem: 
+   used angström value for the extinction calculation, e.g. 0,1, or 1.5
+   
+for product type 2: Ext bsc options
+-----------------------------------
+
+product ID
+   ID of product type 2
+   
+extinction option product ID
+   ID of the extinction product (see table products)
+   
+raman backscatter options product ID
+    ID of the Raman backscatter product (see table products)
+    
+error method ID: 
+   at the moment, only 1
+   
diff -r 98a251a75e80 -r 4e3f530ac84e docs/administration/adding_station.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/administration/adding_station.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,14 @@
+Adding stations
+===============
+
+
+
+You can add the definition of new systems that belong to the station by clicking on the Hoi System blue line that 
+appears bollow the main station fields. For more details on the filed you need to fill in see the :ref:`add_new_system` section.
+You can add more stations by clicking on the "Add another Hoi System" option.
+
+.. note::
+
+   You need to have *Javascript* enebled to add a new station from this page.
+   
+
diff -r 98a251a75e80 -r 4e3f530ac84e docs/administration/adding_system.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/administration/adding_system.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,4 @@
+.. _add_new_system:
+
+Adding systems
+==============
diff -r 98a251a75e80 -r 4e3f530ac84e docs/administration/introduction.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/administration/introduction.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,2 @@
+Overview
+========
diff -r 98a251a75e80 -r 4e3f530ac84e docs/administration/usecases.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/administration/usecases.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,74 @@
+.. _usecases:
+
+Usecases
+========
+
+
+Each usecase corresponds to a way to analyze lidar data.The SCC support the following usecases.
+
+.. image:: /images/usecase-0.png
+
+.. image:: /images/usecase-1.png
+
+.. image:: /images/usecase-2.png
+
+.. image:: /images/usecase-3.png
+
+.. image:: /images/usecase-4.png
+
+.. image:: /images/usecase-5.png
+
+.. image:: /images/usecase-6.png
+
+.. image:: /images/usecase-7.png
+
+.. image:: /images/usecase-8.png
+
+.. image:: /images/usecase-9.png
+
+.. image:: /images/usecase-10.png
+
+.. image:: /images/usecase-11.png
+
+.. image:: /images/usecase-12.png
+
+.. image:: /images/usecase-13.png
+
+.. image:: /images/usecase-14.png
+
+.. image:: /images/usecase-15.png
+
+.. image:: /images/usecase-16.png
+
+.. image:: /images/usecase-17.png
+
+.. image:: /images/usecase-18.png
+
+.. image:: /images/usecase-19.png
+
+.. image:: /images/usecase-20.png
+
+.. image:: /images/usecase-21.png
+
+.. image:: /images/usecase-22.png
+
+.. image:: /images/usecase-23.png
+
+.. image:: /images/usecase-24.png
+
+.. image:: /images/usecase-25.png
+
+.. image:: /images/usecase-26.png
+
+.. image:: /images/usecase-27.png
+
+.. image:: /images/usecase-28.png
+
+.. image:: /images/usecase-29.png
+
+.. image:: /images/usecase-30.png
+
+.. image:: /images/usecase-31.png
+
+.. image:: /images/usecase-32.png
+
diff -r 98a251a75e80 -r 4e3f530ac84e docs/data_processing.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/data_processing.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,21 @@
+.. Single Calculus Chain interface documentation master file, created by
+   sphinx-quickstart on Tue Feb  7 13:17:19 2012.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Data processing
+===============
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+   
+   /data_processing/introduction
+   /data_processing/uploading_measurements
+   /data_processing/uploading_ancillary
+   /data_processing/viewing_measurements
+
+
+
+
diff -r 98a251a75e80 -r 4e3f530ac84e docs/data_processing/introduction.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/data_processing/introduction.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,67 @@
+Overview
+========
+
+The "Data processing" section of the SCC is used to upload measurements 
+and ancillary files, monitor the processing progress, and view the output 
+results of the SCC.
+
+The data processing section consist of three subsections:
+
+* The procedures of submitting new data for processing are described 
+  in the :ref:`uploading_measurements` section.
+
+* The procedures of submitting ancillary files (i.e. sounding, overlap, 
+  and lidar ratio files) that are used in the processing are described 
+  in the :ref:`uploading_ancillary` section.
+  
+* The procedure to find and explore existing measurements and ancillary 
+  files are detailed in the :ref:`viewing_measurements` section.
+
+Quick start
+-----------
+
+.. note::
+
+   The following discussion assumed that you have already set-up the system 
+   settings in the "Admin" section (see :ref:`administration` for details).
+
+In order to start processing lidar data, you will need to upload them 
+on the SCC server. The files should be in netcdf format, following the 
+specific format described in :ref:`netcdf_file`. There is no restriction imposed
+in the filename, but we suggest to use the format <measurement_ID>.nc. You can 
+upload using the "Quick upload" link in the menu.
+
+When you submit the processed measurements in the quick upload form, you will 
+need to specify the system configuration that was used to perform the 
+measurement. The *channels* that are defined in the file should be the
+ones defined in the selected system. The uploading of ancillary files or the
+selection of categories for the measurement are optional.
+
+When the file is uploaded, it is checked if it conforms to the needed
+netcdf format. The check guarantees that the mandatory variables are present
+in the file and that they have the correct format. Note that the check is not 
+exhaustive, in the sense it does not guarantee that the file is able to be 
+correctly processed; the aim of this check is to detect as early as possible
+common problems in the file. If some errors are found, the file will be 
+deleted from the server.
+
+If ancillary files are needed for the processing two things should be done:
+
+#. The ancillary file names should be defined in the submitted netcdf file. In 
+   contrast to the measurement files, the file name of the ancillary files
+   should follow a specified format, described in :ref:`netcdf_file`. In brief,
+   a sounding file should have a name rs_YYYYMMDDccNN.nc, a overlap file a name
+   ov_YYYYMMDDccNN.nc, and a lidar ratio file a name lr_YYYYMMDDccNN.nc, where
+   YYYY is a year, MM is the month, DD is the day, cc is the earlinet station 
+   call sign and NN is a number.
+
+#. The ancillary files should be uploaded on the server. The uploading can be
+   done in the same form as before, or independently in the "Upload ancillary"
+   form. If an ancillary file required by a measurement is not present in the
+   database, this file will appear as "Missing" and the processing of the 
+   measurement will not start and will be marked as "pending". When the missing 
+   file is uploaded, its status will change to "OK" and the measurement will be 
+   processed.
+  
+
+
diff -r 98a251a75e80 -r 4e3f530ac84e docs/data_processing/uploading_ancillary.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/data_processing/uploading_ancillary.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,5 @@
+.. _uploading_ancillary:
+
+Uploading ancillary files
+=========================
+123
diff -r 98a251a75e80 -r 4e3f530ac84e docs/data_processing/uploading_measurements.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/data_processing/uploading_measurements.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,5 @@
+.. _uploading_measurements:
+
+Uploading measurements
+======================
+123
diff -r 98a251a75e80 -r 4e3f530ac84e docs/data_processing/viewing_measurements.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/data_processing/viewing_measurements.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,6 @@
+.. _viewing_measurements:
+
+View existing measurements and files
+====================================
+
+123
diff -r 98a251a75e80 -r 4e3f530ac84e docs/handbook.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/handbook.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,18 @@
+.. Single Calculus Chain interface documentation master file, created by
+   sphinx-quickstart on Tue Feb  7 13:17:19 2012.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Handbook of instruments
+=======================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+   
+   /handbook/handbook_of_instruments
+
+
+
+
diff -r 98a251a75e80 -r 4e3f530ac84e docs/handbook/handbook_of_instruments.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/handbook/handbook_of_instruments.rst	Mon Mar 10 16:56:47 2014 +0200
@@ -0,0 +1,2 @@
+The Handbook of instruments
+===========================