Should have as input:

• The OSOAA object
• The wavelengths for which we want to run the simulation as an iterable
• The view angle for which to run the simulation
• The expected output from the vsVZA file
  the output are the wavelengths for which the values are calculated, the angles and the output value.

It must include all the variables accepted by the OSOAA.

You know, we need a range of solar zenith angles and sensor zenith angles to generate a lookup table. When i change solar zenith angle, problem arise.

1 No Output file

When i run the following code, it works normally.

import numpy as np
import pyOSOAA
from pyOSOAA.osoaahelpers import RunWavelengths

s = pyOSOAA.OSOAA()
view = 0
wavelengths = np.array([412, 443, 490, 510, 555, 670, 765, 865])/1000

s.view.phi = 90
s.ang.thetas = 60

# Sea bottom configuration
s.sea.depth = 0.05
s.sea.bottype = 1
s.sea.botalb = 0

# Sea particles configuration
s.phyto.chl = 0
s.sed.csed = 0
s.det.abs440 = 0
s.ys.abs440 = 0

# Sea surface configuration
s.sea.wind = 10

# Small optical thickness
s.aer.aotref = 0.00001

s.ap.SetPressure(1013.25)

# Set view level at TOA
s.view.level = 1
rhor = RunWavelengths(s, wavelengths, view)/np.cos(np.pi*view/180.0)

I change the s.ang.thetas = 40. The output is ⬇️

==> Angles calculation
 ==> Aerosols radiative properties computation
 Aerosols --> Mie files repertory : /usr/local/OSOAA/DATABASE/MIE_AER
 Aerosols --> Mie files repertory : /usr/local/OSOAA/DATABASE/MIE_AER
 ==> Hydrosols radiative properties computation
 ==> Atmospheric and sea profiles computation
 ==> Sea / atmosphere interface matrices computation
 Surface matrices repertory : /usr/local/OSOAA/DATABASE/SURF_MATR
 Matrix RAA : RAA-1.340-10.0-RadMU48-NB80
 -- RAA Matrix file is being calculated
   OSOAA_MISE_FORMAT : ERROR_991 on a file opening
   OSOAA_SURFACE_CASE : ERROR_998  
       on subroutine OSOAA_MISE_FORMAT
       for case : RAA
   OSOAA_SURFACE : ERROR_3000  
       on subroutine OSOAA_SURFACE_RAA
   OSOAA_MAIN : ERROR_8000 on subroutine OSOAA_SURFACE
Traceback (most recent call last):
  File "/home/qiaofeng/.vscode/extensions/ms-python.python-2019.6.24221/pythonFiles/ptvsd_launcher.py", line 43, in <module>
    main(ptvsdArgs)
  File "/home/qiaofeng/.vscode/extensions/ms-python.python-2019.6.24221/pythonFiles/lib/python/ptvsd/__main__.py", line 434, in main
    run()
  File "/home/qiaofeng/.vscode/extensions/ms-python.python-2019.6.24221/pythonFiles/lib/python/ptvsd/__main__.py", line 312, in run_file
    runpy.run_path(target, run_name='__main__')
  File "/usr/lib/python3.6/runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "/usr/lib/python3.6/runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "/usr/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/qiaofeng/Documents/Atmospheric-correction-for-GOCI/test.py", line 81, in <module>
    results = RunWavelengths(s, wavelengths, view)/np.cos(np.pi*view/180.0)
  File "/usr/local/lib/python3.6/dist-packages/pyOSOAA-1.1-py3.6.egg/pyOSOAA/osoaahelpers.py", line 75, in RunWavelengths
  File "/usr/local/lib/python3.6/dist-packages/pyOSOAA-1.1-py3.6.egg/pyOSOAA/osoaa.py", line 1311, in run
  File "/usr/local/lib/python3.6/dist-packages/pyOSOAA-1.1-py3.6.egg/pyOSOAA/outputs.py", line 429, in __init__
  File "/usr/local/lib/python3.6/dist-packages/pyOSOAA-1.1-py3.6.egg/pyOSOAA/outputs.py", line 68, in __init__
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/OSOAA/results/M39N3x3dFo0ULQV4/Standard_outputs/LUM_vsVZA.txt'

When i change s.ang.thetas = 40 to s.ang.thetas = 80, the problem still exists. I don't know why and how to do.

2 RunWavelengths(s, wavelengths, view) not support numpy

I use this sensor_zenith_angles = np.arange(60,90,2) to create a range of sensor zenith angles.
Then in the for loop run RunWavelengths(s, wavelengths, view)

for solar_zenith_angle in solar_zenith_angles:
    s.ang.thetas = solar_zenith_angle
    results = RunWavelengths(s, wavelengths, view)

Errors are reported as follows ⬇️:

 ==> Angles calculation
 ==> Aerosols radiative properties computation
 Aerosols --> Mie files repertory : /usr/local/OSOAA/DATABASE/MIE_AER
 Aerosols --> Mie files repertory : /usr/local/OSOAA/DATABASE/MIE_AER
 ==> Hydrosols radiative properties computation
 ==> Atmospheric and sea profiles computation
 ==> Sea / atmosphere interface matrices computation
 Surface matrices repertory : /usr/local/OSOAA/DATABASE/SURF_MATR
 ==> Radiative transfer computation
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_DENORMAL
Traceback (most recent call last):
  File "/home/qiaofeng/.vscode/extensions/ms-python.python-2019.6.24221/pythonFiles/ptvsd_launcher.py", line 43, in <module>
    main(ptvsdArgs)
  File "/home/qiaofeng/.vscode/extensions/ms-python.python-2019.6.24221/pythonFiles/lib/python/ptvsd/__main__.py", line 434, in main
    run()
  File "/home/qiaofeng/.vscode/extensions/ms-python.python-2019.6.24221/pythonFiles/lib/python/ptvsd/__main__.py", line 312, in run_file
    runpy.run_path(target, run_name='__main__')
  File "/usr/lib/python3.6/runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "/usr/lib/python3.6/runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "/usr/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/qiaofeng/Documents/Atmospheric-correction-for-GOCI/test.py", line 83, in <module>
    results = RunWavelengths(s, wavelengths, view)/np.cos(np.pi*view/180.0)
  File "/usr/local/lib/python3.6/dist-packages/pyOSOAA-1.1-py3.6.egg/pyOSOAA/osoaahelpers.py", line 80, in RunWavelengths
**IndexError: invalid index to scalar variable.**

3 Can your boss let you share the code that generates the lookup table?

Follow

Gordon, Howard R., and Menghua Wang. "Retrieval of water-leaving radiance and aerosol optical thickness over the oceans with SeaWiFS: a preliminary algorithm." Applied optics 33.3 (1994): 443-452.

I made a comparison between the results from OSOAA and HydroLight and found that there was a big gap between them.

• The spectral shapes of the two are similar, but the order of magnitude is quite different.
• When the concentration difference is large, the simulation results of OSOAA are relatively concentrated.
  This shows that the sensitivity of remote sensing reflectance simulated by OSOAA is not as high as that of HydroLight.
• The simulated value of HydroLight is closer to the measured value.

Here are some detailed comparisons:

1. Remote sensing reflectance curves of different chlorophyll concentrations

2. The absorption coefficient of yellow matter = 0.3m-1, the concentration of inorganic suspended particles = 30mg / L, and the effect of chlorophyll concentration on water spectrum

3. Remote sensing reflectance curve of inorganic suspended sediment with different concentrations
   
   

4. The concentration of chlorophyll is 20mg / m3, the absorption coefficient of the yellow matter is 0.3m-1, and the influence of the concentration of inorganic suspended particles on the spectrum of the water body

5. Remote sensing reflectance curves of CDOM with different concentrations
   
   

6. The concentration of chlorophyll is 20mg / m3, the concentration of inorganic suspended particles is 20mg / L, and the influence of the absorption coefficient of yellow matter on water spectrum
   
   

The figure above of each example is simulated by HydroLight, and the figure below is simulated by OSOAA.

I believe in the results of HydroLight more because it is closer to the measured results. What do you think is the problem with OSOAA?

Hello,

From the previous comments from OSOAA and pyOSOAA repositories, I understand that you were able to generate Rayleigh and Aerosol LUTs for Atmospheric Correction in SeaDAS. Can you please tell about the steps involved in generating those LUTs using OSOAA..?

Regards,
Suhail

Hello developers, I have some questions that I need your help with.
I want to generate lookup tables, so when I am using the runwavelengths function in pyosoaa, I set the solar zenith angle to 0-80° at 10° intervals and the relative azimuth to 0-180° at 5° intervals, resulting in an advanced and standard output file for each band and each angle under the OSOAA_ROOT results, so it takes up up all my ubuntu space.
What should I do? It seems that in order to use the pyOSOAA code you must have OSOAA simulate the results file, can you share the code for the lookup table?

Should include library description, required python libraries and OSOAA installation details.

Hi @fnemina, I am a new user to pyOSOAA and I think it is a really useful software. Thanks for sharing it!

I'd like to ask if a list of the various possibilities to update parameters is documented somewhere.
For example, I am not sure if the aerosol height scale ap.ha

Thank you

Hi,

I recently wanted to use the result advphi in my use of pyOSOAA, and I noticed a WARNING in the outputs.py file, which requires a modified OSOAA code form. I downloaded the latest version of OSOAA in the https://github.com/fnemina/RadiativeTransferCode-OSOAA and unfortunately still no advphi, pls how can I get the modified version of OSOAA?

Bset regards,
Qiang

Hi, Have you ever tried to check the results of OSOAA MIE scattering calculation? I found in the log_aer.txt (/Advanced_outputs/log_aer.txt) that there is a difference between the calculated aerosol phase function and the calculated result of the Giss's FORTRAN code (https://www.giss.nasa.gov/staff/mmishchenko/ftpcode/spher.pbrf.f). For details, you can check the results of the Scattering cross-section and Asymmetry factor. Do you have any idea?

This error often occurs.

Exception has occurred: FileNotFoundError
[Errno 2] No such file or directory: '/home/lwk/RadiativeTransferCode-OSOAA/results/91f656cc11413214c60126e44f8389c2/Standard_outputs/LUM_vsVZA.txt'

import pyOSOAA
pyOSOAA.test()
Traceback (most recent call last):
File "", line 1, in
File "/Users/bjiang/Documents/pyOSOAA/pyOSOAA/osoaa.py", line 1386, in test
s = OSOAA()
File "/Users/bjiang/Documents/pyOSOAA/pyOSOAA/osoaa.py", line 1020, in init
self.dirmie = DIRMIE(osoaaroot=self.root)
File "/Users/bjiang/Documents/pyOSOAA/pyOSOAA/osoaa.py", line 198, in init
self.hyd = os.path.join(osoaaroot, hid)
File "/Users/bjiang/opt/anaconda3/envs/osoaa/lib/python3.7/posixpath.py", line 80, in join
a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType

We know that the polarization component is becoming more and more important in the study of atmospheric radiative transport, so why not add the function of the output polarization component Q and U respectively?
(There seem to be "OSOAA.ResFile.Adv.Up" in the OSOAA code that output Q and U.)

When writing values to the albedo variables (s.sea.botalb y s.sea.surfalb) the values are written in scientific notation by the script if they are small enough. If this happens but the number of number in the mantissa is to big OSOAA code doesn't read the value of the exponent and only the mantissa.

A general solution for this should be implemented by changing the precision of the written number in OSOAA.

Here a minimal example is shown

import pyOSOAA
import numpy as np
s = pyOSOAA.OSOAA()
s.sea.surfalb = np.pi/1e5
s.view.level = 1
s.run()
print(s.outputs.vsvza.I.max())

give us 5.68087 which is greater than 1 the maximum expected value. If we do

import pyOSOAA
import numpy as np
s = pyOSOAA.OSOAA()
s.sea.surfalb = np.round(np.pi/1e5,8)
s.view.level = 1
s.run()
print(s.outputs.vsvza.I.max())

we have 0.342374, the real value we were looking for.

dear author:
I want to use pyOSOAA package on windows platform to calculate IOPS of inland water，and coupled with other model. The manual of pyOSOAA guide for Ubuntu, if something wrong with my computer environment variable path or gfortran?(error display just when i runing pyOSOAA.test()); in addition, may i get your email for further question.

Hi fnemina~
I would like to ask whether it is possible to use OSOAA to simulate the underwater reflection process. For example, I put a known object 1 meter underwater and want to know the radiation field in 3 meters of water. Can OSOAA do this? If the model can do this, how should I set the parameters? Looking forward to your reply.

When i set sediment concentration s.sed.csed = 0.2.
Error:

OSOAA_MAIN : ERROR_2640 on parameters
   -->  Junge model for Mineral-Like Particles
        is required (-Keyword Value)  : 
           -SED.JD.slope (Float): Slope.
           -SED.JD.MRwa (Float): 
                real part of refractive index.
           -SED.JD.MIwa (Float): 
                imaginary part of refractive index.
           -SED.JD.rate (Float): Ratio of this mode
                for Mineral-Like Particles.

There is no default value for this value in your source code, can you add it?

I use the method you mentioned to compare NASA Seawifs Rayleigh lookup table with OSOAA Rayleigh scattering.
But there are some differences between my results and yours.
My results:

Relative error is as high as 10%.
My code is here
So, i have some question:

1. The tau which in NASA Seawifs Rayleigh lookup table cannot be used to calculate transmittance because OSOAA has its own Tau.

2. What is the step size of the parameters in the Rayleigh scattering lookup table you generated? Can you share your code?

Originally posted by @QiaoFeng0419 in https://github.com/fnemina/AtmosphericCorrection/issues/1#issuecomment-512065537

I see your case study. Simple radiative transfer equation: 𝜌𝑡 = 𝜌𝑟 + 𝜌𝑎 + 𝜌𝑟𝑎 + 𝜌𝑔 + 𝑡𝜌𝑤. But no whitecaps reflectance included. How to compute whitecaps reflectance?

Add the option to have different report levels with warnings and errors.

I'm a Cyber Security researcher and developer of PackjGuard [1] to address open-source software supply chain attacks.

Issue

During my research, I detected a deleted package in this repository.

Details

Specifically, the package pyOSOAA mentioned in file README at line 27 does not exist on the public PyPI registry. A bad actor can hijack this package to propagate malicious code.

Impact

Not only your apps/services using https://github.com/fnemina/pyOSOAA repo code are vulnerable to this attack, but the users of your open-source Github repo could also fall victim.

You could read more about such attacks here: https://medium.com/@alex.birsan/dependency-confusion-4a5d60fec610

Remediation

Please highlight this in file README and register a placeholder package for pyOSOAA on public PyPI soon to remediate.

To automatically fix such issues in future, please install PackjGuard Github app [1].

Thanks!

1. PackjGuard is a Github app that monitors your repos 24x7, detects vulnerable/malicious/risky open-source dependencies, and creates pull requests for auto remediation: https://github.com/marketplace/packjguard

When i run rho_toa, tau = RunWavelengths(s, wl/1e3, angle=view, tau=True),
i get a exception TypeError: RunWavelengths() got an unexpected keyword argument 'tau'.
I find function RunWavelengths in your source code, but not see tau parameters.
If you update your local code, but not update to github?