test readme

README.md

 # Water color TriOS package
 
 Package to process TriOS-like radiometer data for various acquisition protocols:
-- above-water radiometry
+
+- **Above-Water Radiometry** (_awr_): R<sub>rs</sub> (sr<sup>-1</sup>)
 
 <p align="center">
     <img src="images/above_water_system.png" width="400">
 </p>
 
-- in-water radiometry
+- **In-Water Radiometry** (_iwr_): R<sub>rs</sub> (sr<sup>-1</sup>), K<sub>d</sub> (m<sup>-1</sup>), K<sub>Lu</sub> (m<sup>-1</sup>)
+
+<p align="center">
+    <img src="images/in_water_system.png" width="400">
+</p>
+
+- **Surface-Water Radiometry** (_swr_): R<sub>rs</sub> (sr<sup>-1</sup>)
 
-![figure](images/inwater_water_system.png) 
+<p align="center">
+    <img src="images/surface_water_radiometry.png" width="400">
+</p>
 
-- surface-water radiometry
 
-![figure](images/surface_water_radiometry.png)
 
 This package also contains tools for interactive visualization of the radiometric data: 
 
 ![animated1](images/visu_trios_data.gif)
 
+
 ## Getting Started
 
 These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
@@ -28,20 +36,35 @@ These instructions will get you a copy of the project up and running on your loc
 What things you need to install the software and how to install them
 
 ```
-Give examples
+python3 -m pip install --user --upgrade setuptools
 ```
 
 ### Installing
 
-A step by step series of examples that tell you how to get a development env running
+First, clone `the repository <https://gitlab.irstea.fr/telquel-obs2co/insitu/trios>`__ and execute the following command in the
+local copy:
 
+::
 
-```
-python setup.py install
-```
+    $ python setup.py install
+
+This will install the package into the system's Python path. If another
+destination directory is preferred, it can be set by
+
+::
+
+    $ python setup.py install --prefix=<where-to-install>
+
+This installation is supposed to download
+and compile all the associated packages as well as prepare the executables `trios_processing` and `trios_visual`.
 
 ## Running the tests
 
+```
+trios_processing ./test/data/ 150 awr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --no_clobber
+trios_processing ./test/data/ 150 awr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --method M99 --name _M99 --plot --figdir ./test/fig
+trios_processing ./test/data/ 150 awr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --method osoaa --name _osoaa --plot
+```
 
 
 ## Authors
@@ -56,6 +79,5 @@ This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md
 
 ## Acknowledgments
 
-* Hat tip to anyone whose code was used
-* Inspiration
-* etc
+This work has been partially supported by the _Programme National de Télédétection Spatiale_ (PNTS,
+http://www.insu.cnrs.fr/pnts ), grant n°PNTS-2019-13
\ No newline at end of file

setup.py

@@ -25,6 +25,6 @@ setup(
     entry_points={
         'console_scripts': [
             'trios_processing = trios.main:main',
-            'visu_trios = visu.data_visu:main'
+            'trios_visual = visu.data_visu:main'
         ]}
 )

trios.egg-info/PKG-INFO

 Metadata-Version: 1.0
 Name: trios
-Version: 1.1.4
+Version: 1.0.0
 Summary: Package to help trios TriOS radiometer data for various above-water or in-water setups
-Home-page: https://gitlab.irstea.fr/ETL-TELQUEL/etl/tree/dev/preprocessing/trios
+Home-page: https://gitlab.irstea.fr/telquel-obs2co/insitu/trios
 Author: T. Harmel
 Author-email: tristan.harmel@gmail.com
 License: MIT

trios.egg-info/SOURCES.txt

@@ -14,10 +14,12 @@ aux/surface_reflectance_factor_rho_fine_aerosol_rg0.06_sig0.46.csv
 aux/water_coef.txt
 exe/__init__.py
 exe/db_martinez.py
+exe/db_petit-saut.py
 simulation/__init__.py
 simulation/rho_snapshot.py
 trios/__init__.py
 trios/config.py
+trios/main.py
 trios/process.py
 trios/process_compar_awr.py
 trios/process_sabine.py

trios.egg-info/entry_points.txt

 [console_scripts]
-trios = main:main
+trios_processing = trios.main:main
 visu_trios = visu.data_visu:main
 

trios/main.py

@@ -2,7 +2,8 @@
 
 Usage:
   trios_processing <input_dir> <IDpr> <measurement_type> --lat <lat> --lon <lon> \
-   [--altitude=alt] [--ofile <ofile>] [--odir <odir>] [--plot] [--figdir <figdir>]
+   [--altitude=alt] [--ofile <ofile>] [--odir <odir>] [--plot] [--figdir <figdir>] \
+   [--name <name>] [--method <method>] [--no_clobber]
   trios_processing -h | --help
   trios_processing -v | --version
 
@@ -22,6 +23,9 @@ Options:
   --ofile ofile       basename of the output file.
   --plot  Plot output data and save figure in <figdir>
   --figdir figdir  Directory where figures are saved [default: ./]
+  --name name  Keyword to append to file name and figures [default: ]
+  --method method  Keyword for the method to apply for data processing.
+                   For awr: M99, M15, osoaa, temp_opt [default: M99]
   --no_clobber     Do not process  <input_dir> <IDpr> files if <output_file> already exists.
 '''
 
@@ -51,14 +55,16 @@ def main():
     idir = os.path.abspath(args['<input_dir>'])
     idpr = args['<IDpr>']
     meas_type = args['<measurement_type>']
+    method = args['--method']
     lat = float(args['--lat'])
     lon = float(args['--lon'])
     alt = float(args['--altitude'])
     odir = os.path.abspath(args['--odir'])
     ofile = args['--ofile']
-    name = ""
+    name = args['--name']
     plot = args['--plot']
     figdir = os.path.abspath(args['--figdir'])
+    noclobber = args['--no_clobber']
 
     try:
         type_ = type_list[meas_type]
@@ -82,6 +88,10 @@ def main():
             else:
                 ofile = os.path.join(odir, 'Rrs_swr_' + date + '_idpr' + idpr + name + '.csv')
 
+            if noclobber and os.path.exists(ofile):
+                print('Skip processing: data already processed with "--no_clobber" set')
+                return
+
             swr = swr_process(df, wl)
             Rrs = swr.call_process(ofile)
 
@@ -93,7 +103,7 @@ def main():
                 ax.set_ylabel(r'$R_{rs}\  (sr^{-1})$')
                 ax.set_xlabel(r'Wavelength (nm)')
                 ax.set_title('ID: ' + idpr + ', ' + date + ', sza=' + str(round(df.sza.mean(), 2)))
-                fig.savefig(os.path.join(figdir, 'trios_swr_' + date + '_idpr' + idpr + '.png'), bbox_inches='tight')
+                fig.savefig(os.path.join(figdir, 'trios_swr_' + date + '_idpr' + idpr + name+'.png'), bbox_inches='tight')
                 plt.close()
 
     elif meas_type == 'awr':
@@ -113,14 +123,18 @@ def main():
             else:
                 ofile = os.path.join(odir, 'Rrs_awr_' + date + '_idpr' + idpr + name + '.csv')
 
+            if noclobber and os.path.exists(ofile):
+                print('Skip processing: data already processed with "--no_clobber" set')
+                return
+
             awr = awr_process(df, wl, name, idpr)
 
             if plot:
-                figfile = os.path.join(figdir, 'trios_awr_' + date + '_idpr' + idpr + '.png')
+                figfile = os.path.join(figdir, 'trios_awr_' + date + '_idpr' + idpr + name +'.png')
             else:
-                figfile=""
+                figfile = ""
 
-            Rrs = awr.call_process(method, ofile, vza=vza, azi=azi,plot_file=figfile)
+            Rrs = awr.call_process(method, ofile, vza=vza, azi=azi, plot_file=figfile)
 
     elif meas_type == 'iwr':
         pass