Angstrom exp and simplifications (#29)

* option mol_modify2 not in libradtran 2.0.4, modify to mol_modify * adaptation to rubin-libradtran library * adaptation to rubin-libradtran library * no input nor output files are written on disk: directly gives the parameters and read the outputs from shell * no input nor output files are written on disk: directly gives the parameters and read the outputs from shell * faster solver * add aerosols and angstrom exponent * simplification of libradtranpy * correct notebooks * update doc --------- Co-authored-by: Jérémy Neveu <jeremy.neveu@universite-paris-saclay.fr> Co-authored-by: sylvielsstfr <dagoret@lal.in2p3.fr>
LSSTDESC · Feb 20, 2024 · 4376fbc · 4376fbc
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diff --git a/README.md b/README.md
@@ -10,16 +10,22 @@ The use of this interface is quite straight forwared provided the
 
 ### 1) Installation of libradtran
 
-The atmospheric simulation LibRadTran for multiple site (different altitudes) must be installed according the instruction given in 
-http://www.libradtran.org/doku.php
+The atmospheric simulation [libradtran](http://www.libradtran.org/doku.php) for multiple site (different altitudes) 
+There are two ways to install this software:
+- use the [Rubin observatory conda package](https://anaconda.org/conda-forge/rubin-libradtran)
+```
+conda install -c conda-forge rubin-libradtran
+```
+- from sources, with instructions given in http://www.libradtran.org/doku.php
 
-This documentation assumes libradtran version 2.0.5 is installed on your computer (version July 2023)
+This documentation assumes libradtran version `>=2.0.4` is installed on your computer.
 
 
 #### To use libradtran inside librandtranpy wrapper
 
-
-Environnement variable **LIBRADTRANDIR** must be set to ``libRadtran`` installation path under which one have each of these directories:
+If `libradtran` is installed from `conda-forge`, there is nothing to do.
+If it is installed from sources, then an environnement variable **LIBRADTRANDIR** must be set to ``libRadtran`` 
+installation path under which one have each of these directories:
 
 - /bin 
 - /share/libRadtran/data
@@ -172,26 +178,18 @@ from libradtranpy import libsimulateVisible
 A call without aerosols:
 
 ```python
-path,thefile=libsimulateVisible.ProcessSimulation(am[index],pwv,ozone,pressure,
-                                                      prof_str='us',proc_str='sa',cloudext=cloudext,altitude_str="LSST")
+wl,transm=libsimulateVisible.ProcessSimulation(am[index],pwv,ozone,pressure,aer_num=0,
+                                                      prof_str='us',proc_str='sa',cloudext=cloudext,altitude="LSST")
 ```
 
 A call with aerosols:
 
 ```python
-path,thefile = libsimulateVisible.ProcessSimulation(am[index],pwv,ozone,aer,pressure,
-                                                      prof_str='us',proc_str='sa',cloudext=cloudext,altitude_str="LSST")
+wl,transm = libsimulateVisible.ProcessSimulation(am[index],pwv,ozone,aer,pressure,aer_num=aer,angstrom_exponent_num=exponent,
+                                                      prof_str='us',proc_str='sa',cloudext=cloudext,altitude="LSST")
 ```
 
-**path,thefilename** are the path and filename of the output ascii file.
-
-The result of the simulation can be obtained in a python environnement by:
-
-```python
-data = np.loadtxt(os.path.join(path,thefile))
-wl = data[:,0]
-atm = data[:,1]
-```                                                                 
+                                                  
 
 The library ``libsimulateThermal`` can be used similarly. Please refers
 to the ``libradtranpy`` package documentation.

diff --git a/docs/introduction.rst b/docs/introduction.rst
@@ -22,15 +22,11 @@ The library ``libradtranpy`` generate the libradtran configuration file which is
 It return the path of the output file generated by ``libRadtran`` in the format expected: two column
 table, one for the wavelength, the second with the air transmission.
 
-This library ``libradtranpy`` consists mainly in two functions with a number of input parameters which definition
+This library ``libradtranpy`` consists mainly in one function with a number of input parameters which definition
 are given in this documentation.
 
-* ``libsimulateVisible.ProcessSimulation()`` without aerosols
-* ``libsimulateVisible.ProcessSimulationaer()`` with aerosols calculated by ``libRadtran``.
+* ``libsimulateVisible.ProcessSimulation()`` 
 
-The two interfaces are very similar. It is recommended for the user to use mostly 
-``libsimulateVisible.ProcessSimulation()`` and to implements himself a simple parameterized
-aerosol scattering fuunction similar to the one provided in ``libsimulateVisible.ApplyAerosols()``.
 
 The ``libsimulateVisible`` module refers to the ``libRadtran visible running mode`` which applies
 in the light visible range by contrast to the ``libRadtran thermal running mode`` which applies in the
@@ -113,6 +109,11 @@ Pressure
 Ground pressure at the observation site. If not null, this value override the standard
 pressure expected for the altitude of the selected observation site.
 
+
+Aerosols
+~~~~~~~~~~
+aer_num,angstrom_exponent_num are respectively the VAOD and the Angtrom parameter,where the VAOD is at wavelength 500 nm.
+
 atmospheric profile
 ~~~~~~~~~~~~~~~~~~~
 

diff --git a/docs/notebooks/libradtranpy/visible/SimuRT_AbsPattern.ipynb b/docs/notebooks/libradtranpy/visible/SimuRT_AbsPattern.ipynb
diff --git a/docs/notebooks/libradtranpy/visible/SimuRT_MultiSitesAbsO2Pattern.ipynb b/docs/notebooks/libradtranpy/visible/SimuRT_MultiSitesAbsO2Pattern.ipynb
diff --git a/docs/notebooks/libradtranpy/visible/SimuRT_MultiSitesScattPattern.ipynb b/docs/notebooks/libradtranpy/visible/SimuRT_MultiSitesScattPattern.ipynb
@@ -10,7 +10,7 @@
     "- Sylvie Dagoret-Campagne\n",
     "- affliliation : IJCLAB/IN2P3/CNRS\n",
     "- creation date :  23 October 2023\n",
-    "- Last verification : October 23th 2023\n",
+    "- Last verification : October 20th 2024\n",
     "\n",
     "==================================================================================="
    ]
@@ -104,15 +104,7 @@
    "cell_type": "code",
    "execution_count": 6,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "libradtranpath= /Users/dagoret/MacOSX/External/libRadtran/\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from libradtranpy import libsimulateVisible"
    ]
@@ -191,7 +183,7 @@
     {
      "data": {
       "text/plain": [
-       "['/Users/dagoret/MacOSX/GitHub/LSST/AtmosphericSimulation/libradtranpy/docs/notebooks/libradtranpy',\n",
+       "['/Users/dagoret/MacOSX/GitHub/LSST/AtmosphericSimulation/libradtranpy/docs/notebooks/libradtranpy/visible',\n",
        " '/Users/dagoret/anaconda3/envs/conda_py310/lib/python310.zip',\n",
        " '/Users/dagoret/anaconda3/envs/conda_py310/lib/python3.10',\n",
        " '/Users/dagoret/anaconda3/envs/conda_py310/lib/python3.10/lib-dynload',\n",
@@ -200,7 +192,7 @@
        " '/Users/dagoret/MacOSX/GitHub/LSST/AtmosphericSimulation/AtmEmulator/src',\n",
        " '/Users/dagoret/MacOSX/GitHub/LSST/AtmosphericSimulation/FitDiffAtmo/src',\n",
        " '/Users/dagoret/MacOSX/GitHub/LSST/AtmosphericSimulation/libradtranpy/src',\n",
-       " '/Users/dagoret/anaconda3/envs/conda_py310/lib/python3.10/site-packages/getObsAtmo-0.1.0-py3.10.egg']"
+       " '/Users/dagoret/MacOSX/GitHub/LSST/AtmosphericSimulation/rubinsimphot/src']"
       ]
      },
      "execution_count": 11,
@@ -251,11 +243,8 @@
     "all_obs = []\n",
     "for index, site in enumerate(List_Of_All_sites):\n",
     "    all_obs.append(site)\n",
-    "    path,thefile=libsimulateVisible.ProcessSimulation(am,pwv,ozone,pressure,\n",
-    "                                                      prof_str='us',proc_str='sc',cloudext=cloudext,altitude_str=site)\n",
-    "    data = np.loadtxt(os.path.join(path,thefile))\n",
-    "    wl = data[:,0]\n",
-    "    atm = data[:,1] \n",
+    "    wl,atm=libsimulateVisible.ProcessSimulation(am,pwv,ozone,pressure,aer_num=aer,\n",
+    "                                                      prof_str='us',proc_str='sc',cloudext=cloudext,altitude=site)\n",
     "    all_trans.append(atm)"
    ]
   },
@@ -342,21 +331,15 @@
    },
    "outputs": [],
    "source": [
-    "path,thefile=libsimulateVisible.ProcessSimulation(am,pwv,ozone,pressure,\n",
-    "                                                      prof_str='us',proc_str='sc',cloudext=cloudext,altitude_str='LSST')\n",
-    "data = np.loadtxt(os.path.join(path,thefile))\n",
-    "wl1 = data[:,0]\n",
-    "atm1 = data[:,1]\n",
+    "wl1,atm1=libsimulateVisible.ProcessSimulation(am,pwv,ozone,pressure,aer_num=aer,\n",
+    "                                                      prof_str='us',proc_str='sc',cloudext=cloudext,altitude='LSST')\n",
     "Pstand = Dict_Of_sitesPressures['LSST']\n",
     "label1 = f\"LSST site with P = {Pstand:.2f} hPa\"\n",
     "\n",
     "\n",
     "Ptest = 743.0\n",
-    "path,thefile=libsimulateVisible.ProcessSimulation(am,pwv,ozone,Ptest,\n",
-    "                                                      prof_str='us',proc_str='sc',cloudext=cloudext,altitude_str='LSST')\n",
-    "data = np.loadtxt(os.path.join(path,thefile))\n",
-    "wl2 = data[:,0]\n",
-    "atm2 = data[:,1]\n",
+    "wl2,atm2=libsimulateVisible.ProcessSimulation(am,pwv,ozone,Ptest,aer_num=aer,\n",
+    "                                                      prof_str='us',proc_str='sc',cloudext=cloudext,altitude='LSST')\n",
     "label2 = f\"LSST site with P = {Ptest:.2f} hPa\"\n",
     "\n"
    ]

diff --git a/docs/notebooks/libradtranpy/visible/SimuRT_MultiSitesTotalTransmission.ipynb b/docs/notebooks/libradtranpy/visible/SimuRT_MultiSitesTotalTransmission.ipynb
diff --git a/docs/notebooks/libradtranpy/visible/SimuRT_One.ipynb b/docs/notebooks/libradtranpy/visible/SimuRT_One.ipynb