Resolve "improve README"

This MR is mostly to propose changes to the edits performed by @mschleiss in #63 (closed).

As most edits were done in the main branch. The Merge Request serves only to add comments and make small edits

README.md

 # Disdrometer data logging software - version 2
 
+[[_TOC_]]
+
 disdroDLv2 is a Python software for acquiring and storing data from the OTT Parsivel2 optical disdrometer, developed by TU Delft, within the framework of the Ruisdael observatory for atmospheric science. 
 
-The software features a main script for setting up a serial connection with the Parsivel, requesting data at regular time intervals, and storing the output in a NetCDF file.
+The software features a main script ([main.py](./main.py)) for setting up a serial connection with the Parsivel, requesting data at regular time intervals, and storing the output in a NetCDF file.
 
 By default, all fields listed on page 29 of the [OTT Parsivel2 official documentation](https://www.ott.com/download/operating-instructions-present-weather-sensor-ott-parsivel2-with-screen-heating-1/) are requested, except for field 61 (List of all particles detected). The NetCDF files are self-descriptive, and include metadata information about dimensions, variables names and units. 
 
-The structure of the NetCDF file depends on two configuration files (general/specific). The general configuration file is applicable to all sites and sensors, while the specific configuration files (1 file per sensor) describe the variable components such as site names, coordinates etc..  
+The structure of the NetCDF file depends on two configuration files, a general and site-specific one. The general configuration ([configs_netcdf/config_general.yml](.configs_netcdf/config_general.yml)) file is applicable to all sites and sensors, while the specific configuration files (1 file per sensor (in [configs_netcdf/](configs_netcdf/)) describe the variable components such as site names, coordinates, etc.  
 
-![](docs/20211011_17_crop.JPG)
+![_Parsivel2 disdrometer in the Cabauw tower, Netherlands. The signal attenuation caused by raindrops falling through the laser beam between the two plates can be used to estimate the size and velocity of hydrometeors._](docs/20211011_17_crop.JPG)
 
 _Parsivel2 disdrometer in the Cabauw tower, Netherlands. The signal attenuation caused by raindrops falling through the laser beam between the two plates can be used to estimate the size and velocity of hydrometeors._
 
+
 ![](docs/DSD_PAR001_Cabauw_20231021_1300_20231021_1730.png)
 
 _The Parsivel2 measures the drop number concentrations for different diameter/velocity bins, with a temporal resolution of 1 minute. These raw spectra can be used to calculate many different state and flux variables, such as liquid water content, rainfall rate, mean drop diameter, radar reflectivity and kinetic energy._
@@ -23,39 +26,44 @@ _The Parsivel2 measures the drop number concentrations for different diameter/ve
     * general: [configs_netcdf/config_general.yml](configs_netcdf/config_general.yml) - *should not need editing*
     * specific: e.g., [configs_netcdf/config_008_GV.yml](configs_netcdf/config_008_GV.yml) - *create 1 per Parsivel*
 * Parsivel reset script: [reset_parsivel.py](reset_parsivel.py)
-* Auxiliary functions: defined in [modules/util_functions.py](modules/util_functions.py)
+* Functions and classes: [modules/classes.py](modules/classes.py), [modules/util_functions.py](modules/util_functions.py)
+
 
 **[main.py](main.py)**
+
 * reads configurations from [configs_netcdf/config_general.yml](configs_netcdf/config_general.yml) and target-device config
 * creates the data and log directories 
 * sets up the serial communication with the Parsivel 
 * in a while loop (every minute):
-    * requests user defined telegram from OTT Parsivel2
-    * stores the received telegram, does some processing and writes the output to a NetCDF file, though `class Telegram` defined in [modules/classes.py](modules/classes.py)
+    * requests the telegram from OTT Parsivel2, outputting all measurement values : `CS/PA<CR>` 
+    * appends the received telegram data into a daily NetCDF file, though `class Telegram` 
 
 
+**[disdrodlv2.service](disdrodlv2.service)**  - Linux's systemd service file responsible for running [main.py](main.py) as a service
+
 ## Conventions
 * Time is set to UTC 
 * The software produces daily NetCDF files
-* the parent data directory is defined in [configs_netcdf/config.yml](configs_netcdf/config.yml) `data_dir` 
-* monthly data directories `yyyymm`are used inside parent data directory 
+* the data destination parent directory is defined in [configs_netcdf/](configs_netcdf/) site specific config files, under the `data_dir` variable 
+* monthly data directories `yyyymm` are created inside parent data directory 
 * every day, a new NetCDF file is created, with the following naming convention:
-`yyyymmdd_{site_name}_{station_code}_{sensor_name}_{fields}`
-* Telegram field names and units can be found in the [OTT Parsivel2 official documentation](https://www.ott.com/download/operating-instructions-present-weather-sensor-ott-parsivel2-with-screen-heating-1/) and defined in [configs_netcdf/config.yml](configs_netcdf/config.yml) `telegram_fields` 
+`yyyymmdd_{site_name}_{station_code}_{sensor_name}.nc`
 
 
 ## Requirements
 
-create and activate a python virtual environment and:
-* install python dependencies: `pip -r requirements.txt`
-* create log directory with read and write permissions to all users: `sudo mkdir /var/log/disdroDL/; sudo chmod a+rw /var/log/disdroDL` 
-* create data directory with read and write permissions to all users: `sudo mkdir /data/disdroDL/; sudo chmod a+rw /data/disdroDL` 
-* run Parsivel [reset script](./reset_parsivel.py): `python reset_parsivel.py`
+* create a python virtual environment:
+* installed python dependencies: `pip -r requirements.txt`
+* create a log directory with read and write permissions to all users: `sudo mkdir /var/log/disdroDL/; sudo chmod a+rw /var/log/disdroDL` 
+* create a data directory with read and write permissions to all users: `sudo mkdir /data/disdroDL/; sudo chmod a+rw /data/disdroDL` 
+* run [reset_parsivel](./reset_parsivel.py): `python reset_parsivel.py` to reset the parsivel time and accumulated rain amount **(TODO:confirm)** 
 * create a station-specific file and commit it to this repo (see [configs_netcdf/config_008_GV.yml](./configs_netcdf/config_008_GV.yml) as an example) 
-
-Install netcdf-bin: `sudo apt install netcdf-bin`, to be able to compress netCDFs with `nccopy -d6` in `Telegram.compress_netcdf()` method.
+* install netcdf-bin: `sudo apt install netcdf-bin`, to be able to compress netCDFs with `nccopy -d6` in `Telegram.compress_netcdf()` method.
 
 ## Run script
+**Manually**: 
+* [main.py](./main.py) manually: `python main.py -c configs_netcdf/config_NNN_*.yml`
+
 
 **As Linux Systemd Service**: 
 * edit the config file name in [disdrodlv2.service](disdrodlv2.service) to match that of the station
@@ -64,12 +72,9 @@ Install netcdf-bin: `sudo apt install netcdf-bin`, to be able to compress netCDF
 * run: `systemctl start disdrodlv2.service`
 * check status: `systemctl status disdrodlv2.service`
 
-**manually**: 
-* [main.py](./main.py) manually: `python main.py -c configs_netcdf/config_NNN_*.yml`
-
 
 ## Outputs
-**[main.py](main.py) netCDF output**
+**netCDF output**
 * [sample_data/20231029_Lutjewad_Atmospheric_Station-LUTJEWAD_PAR009.nc](sample_data/20231029_Lutjewad_Atmospheric_Station-LUTJEWAD_PAR009.nc)
 
 Note that some of the fields sent by the Parsivel are discarded during the creation of the NetCDF file. For example, all the 16bit fields are discarded and only the 32bit values are stored. Rainfall accumulation (field 24) is discarded because it is relative to an unknown starting time and can be re-calculated from the rain rate. Sensor time/date (fields 20-21) are replaced by the actual time (in UTC) of the computer running the logging software. This is more reliable than to use the internal clock of the Parsivel which can drift over time. Sample interval (field 9) is ignored, because it can be inferred from the time difference between successive measurements.
@@ -92,3 +97,14 @@ with 2 different screens (use tmux multiplexer or 2 different shells)
 terminal one: listen to serial port `tail -f /dev/ttyUSB0`
 
 terminal two: send commands to serial port `echo -en "CS/L\r" > /dev/ttyUSB0`
+
+# Authors
+DisdroDLv2 is developed in the context of the [Ruisdael Observatory](https://ruisdael-observatory.nl/) by
+
+* Marc Schleiss (Principal Investigator)
+* Andre Castro
+* Mahaut Sourzac 
+* Rob MacKenzie
+
+# License
+GPLv3. See [LICENSE](LICENSE)
\ No newline at end of file