From c013e0eae541b856990b9124edd360b1fbcc205c Mon Sep 17 00:00:00 2001
From: "tristan.harmel" <tristan.harmel@get.omp.eu>
Date: Fri, 13 Sep 2019 14:51:30 +0200
Subject: [PATCH] test readme
---
README.md | 48 ++++++++++++++++++++++++---------
setup.py | 2 +-
trios.egg-info/PKG-INFO | 4 +--
trios.egg-info/SOURCES.txt | 2 ++
trios.egg-info/entry_points.txt | 2 +-
trios/main.py | 26 +++++++++++++-----
6 files changed, 61 insertions(+), 23 deletions(-)
diff --git a/README.md b/README.md
index bbbf081..7a71dce 100644
--- a/README.md
+++ b/README.md
@@ -1,24 +1,32 @@
# 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>)
-
+<p align="center">
+ <img src="images/surface_water_radiometry.png" width="400">
+</p>
-- surface-water radiometry
-
This package also contains tools for interactive visualization of the radiometric data:
+
## 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
diff --git a/setup.py b/setup.py
index 2089c1b..c4fc37b 100644
--- a/setup.py
+++ b/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'
]}
)
diff --git a/trios.egg-info/PKG-INFO b/trios.egg-info/PKG-INFO
index 1202c7b..de18d92 100644
--- a/trios.egg-info/PKG-INFO
+++ b/trios.egg-info/PKG-INFO
@@ -1,8 +1,8 @@
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
diff --git a/trios.egg-info/SOURCES.txt b/trios.egg-info/SOURCES.txt
index 900b5ee..1435d2a 100644
--- a/trios.egg-info/SOURCES.txt
+++ b/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
diff --git a/trios.egg-info/entry_points.txt b/trios.egg-info/entry_points.txt
index 16a4ca1..9462ce9 100644
--- a/trios.egg-info/entry_points.txt
+++ b/trios.egg-info/entry_points.txt
@@ -1,4 +1,4 @@
[console_scripts]
-trios = main:main
+trios_processing = trios.main:main
visu_trios = visu.data_visu:main
diff --git a/trios/main.py b/trios/main.py
index d542eac..13e8b20 100644
--- a/trios/main.py
+++ b/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
--
GitLab