I’m trying to detect Chl-a concentration in small lake. I chose 2 atmospheric correction for my study (C2RCC and C2X). C2RCC was performed perfect. But after doing similar steps with C2RCC in C2X processor, the difference of the min. and max values were too high and min. values were minus. Now I would like to change my processing chain to do it right.
-Atmospheric correction -C2X
1.Salinity, Temp, Ozone, Air pressure, Elevation will be set
2.Output -normalized water leaving reflectances and Output -irradiance attenuation coefficients and Output -uncertainties will be chosen
3. other factors will be remained as default
Do you see there any false step? Or could you suggest some method to process C2X in right way?
Mr.Peters wrote me " consider the flags which are created by C2RCC. Especially the invalid flag.". But I didn’t understand how I consider it. Actually I didn’t understand where I use it. and for which propose, however I searched about it in google.
I missed the important thing. The problem is that the values of B5 is always higher than B4 from the beginning. (I mean before and after ATMOSPHERIC CORRECTION it was always similar, B5 is higher that B4).
what water type is your lake? it is eutrophic or clear / oligotrophic?
C2X can cover more extreme concentrations but has larger noise (due to larger training range).
You should also test the C2X-COMPLEX option, which is a good compromise between C2RCC and C2X and it works quite well in inland waters. You find it in the drop-down menue of the set of Neuralnal Nets.
Your second question concerning the masks/flags and how to apply them. If you go to the mask manager, you see a lot of entries that provide you masks you can overlay to your product. they indicate if a pixel is valid or not. C2RCC comes with a lot of flags/masks that help to assess the validity of your pixels.
Also Idepix (which you applied beforehand) provides you flags/masks that identify clouds, land etc. and that should be masked out when only interested in valid water pixels.
the most revant flags are: IDEPIX_CLOUD, IDEPIX_CLOUD_BUFFER, IDEPIX_CIRRUS_SURE, IDEPIX_VEG_RISK, IDEPIX_CLOUD_SHADOW, Cloud_risk, Rtosa_OOS, Rtosa_OOR, Rhow_OOR.
If you have found a good combination of flags, you can apply those in the properties of each band (right mouse click to the band). Here, you can specify the valid pixel expression which can be a combination from a number of different flags/masks. However, your NDCI should already be a good first assessment. You can try to specify as valid_pixel expression “NDCI < 0”.
Within your processing step I am wondering why your are doeing the reprojection. This should not be done before applying C2RCC and it is not needed (?).
In the Atmospheric correction step, I have applied “B8 > 0 && B8 < 0.1 && pixel_classif_flags.IDEPIX_CLOUD == 0 && pixel_classif_flags.IDEPIX_CLEAR_LAND == 0” this expression as Valid_PE expression. As a result, only remained the clear IDEPIX_CLEAR_WATER.
I have been facing this issue since last week.
Most of the reflectance of B4 is higher than B5 from the beginning. After and before the atmospheric correction, it was same.
Because of this, the final min. values are always negative.
What is the purpose of your B5>B4, calculation? You will generally have lower values in the B5 because you are moving to the infrarred part of the spectrum.Valid_PE is indicating which values have a high confidence to be true, it is a flag in itself, you do not need to add any argument.
But the result was unexpected that the minimum Chl-a concentrations were always negative (-20 microgram/leter) in all 3 atmospheric correction.
Then I applied the following expression, in order to eliminate negative values. Unfortunately the result was same again (the minimum Chl concentration were negative, and maximum value were too high(300-500 micrometer/leter) )
coming back to your inital list of processors you are using - which Resampler did you use (your first step)? You should use Optical->Geometric->S2 Resampling Operator .
might not solve the problems with neg. values, but is needed for correct Idepix and C2RCC calculation.
As the products are already projected, you do not need a reproject step.
My first image was processed this way. There is a very slight difference. The process takes time. I don’t know if it will affect for the final result. Maybe tomorrow we will be able to see the final result.