[GRASS-user] i.atcorr with Sentinel2
Stefan Blumentrath
Stefan.Blumentrath at nina.no
Mon Dec 18 23:44:47 PST 2017
Hi again,
A little update on the problem:
Now I ran i.atcorr with all possible band values for Sentinel-2 in the 6s parameters (166-178) with input maps ranges scaled to 0-1, 0-255, 0-10000
All runs resulted in completely empty maps!
Any ideas?
Thanks for helping in advance!
Kind regards,
Stefan
-----Original Message-----
From: Moritz Lennert [mailto:mlennert at club.worldonline.be]
Sent: mandag 18. desember 2017 16.58
To: Stefan Blumentrath <Stefan.Blumentrath at nina.no>; Žofie Cimburová <zoficimburova at gmail.com>
Cc: GRASS user list <grass-user at lists.osgeo.org>
Subject: Re: [GRASS-user] i.atcorr with Sentinel2
On 18/12/17 16:35, Stefan Blumentrath wrote:
> Hi Moritz,
>
> Thanks for helping with troubleshooting!
> QUANTIFICATION_VALUE is 10000, Thus dividing with it gives a maximum value of 2.8...
> Any idea how to figure out if it is 12 or 16 bit image. It is directly downloaded from ESA...
Check which proportion of the image is > 1. AFAIR (which is a bit limited), you might have reflectances above 1 in saturated pixels. I just checked on a random image and I also have some pixels above 1, but only 0.25% of the pixels:
GRASS 7.5.svn (UTM32N):/data/home/mlennert > r.mapcalc "test = if(b04_refl>1,1,0)"
100%
GRASS 7.5.svn (UTM32N):/data/home/mlennert > r.stats -cp test
100%
0 120259106 99.75%
1 301294 0.25%
And all the pixels with value 1 are in clouded areas.
Moritz
>
> Cheers
> Stefan
>
> -----Original Message-----
> From: grass-user [mailto:grass-user-bounces at lists.osgeo.org] On Behalf
> Of Moritz Lennert
> Sent: mandag 18. desember 2017 16.26
> To: Žofie Cimburová <zoficimburova at gmail.com>
> Cc: GRASS user list <grass-user at lists.osgeo.org>
> Subject: Re: [GRASS-user] i.atcorr with Sentinel2
>
> On 18/12/17 16:13, Žofie Cimburová wrote:
>> Dear Moritz,
>>
>> According to
>> https://earth.esa.int/web/sentinel/user-guides/sentinel-2-msi/product
>> - types , the L1C product I am using already is in top of atmosphere
>> reflectance, so this should not be the problem (?).
>> I tried running i.atcorr both with and without the -r flag.
>
> Reflectance is the percentage of light that is reflected either from
> the top of the atmosphere or from the surface. Reflectance values
> should thus be real values between 0 and 1. Your data have
>
> Range of data: min = 1 max = 28000
>
> This means that they are expressed in digital (integer) numbers. Try transforming these DN into real numbers. IIRC, in the metadata, you have a variable QUANTIFICATION_VALUE. Divide your pixel values by that value to get real TOA reflectance values.
>
> AFAIK, it also depends on whether you directly imported the original 12-bit file, or possibly a modified, e.g. 16-bit, version.
>
> Moritz
>
>> On Mon, Dec 18, 2017 at 3:35 PM, Moritz Lennert
>> <mlennert at club.worldonline.be <mailto:mlennert at club.worldonline.be>> wrote:
>>
>> On 18/12/17 13:14, Žofie Cimburová wrote:
>>
>> Hi all,
>> Now the 6S parameters are complete, but the output map contains
>> only NULLs, no matter what combinations of input parameters and
>> flags I use. Have anyone encountered the same issue? (Info
>> below.)
>>
>>
>> In the i.atcorr man page it says:
>>
>> "If flag -r is used, the input raster data are treated as
>> reflectance. Otherwise, the input raster data are treated as
>> radiance values"
>>
>> IIUC, your data is still in DN. You might want to try to transform
>> this into radiance values before sending it into i.atcorr.
>>
>> Moritz
>>
>>
>> Thanks again.
>> Zofie
>>
>> ----------------------------------------
>> Version:
>> g.version -g
>> version=7.4.0RC1
>> date=2017
>> revision=exported
>> build_date=2017-11-18
>> build_platform=x86_64-pc-linux-gnu
>> build_off_t_size=8
>>
>> ----------------------------------------
>> Region:
>> g.region -p
>> projection: 1 (UTM)
>> zone: 33
>> datum: etrs89
>> ellipsoid: grs80
>> north: 6653695
>> south: 6643685
>> west: 256495
>> east: 266505
>> nsres: 10
>> ewres: 10
>> rows: 1001
>> cols: 1001
>> cells: 1002001
>>
>> ----------------------------------------
>> Input data: Sentinel2 L1C product B02 (tried with B01 too)
>> r.info <http://r.info> <http://r.info>
>> map=test_B02 at p_Sentinel4Nature_S2_Oslo
>> +----------------------------------------------------------------------------+
>> | Map: test_B02 at p_Sentinel4Nat Date: Wed Dec 6
>> 12:06:39 2017
>> | Mapset: p_Sentinel4Nature_S2_Oslo Login of Creator:
>> stefan.blumentr
>> | Location: ETRS_33N
>> | DataBase: /data/grass
>> | Title:
>> S2A_OPER_PRD_MSIL1C_PDMC_20160907T044118_R008_V20160905T104022_2
>> | Timestamp: none
>> |----------------------------------------------------------------------------|
>> |
>> | Type of Map: raster Number of Categories: 0
>> | Data Type: CELL
>> | Rows: 1001
>> | Columns: 1001
>> | Total Cells: 1002001
>> | Projection: UTM (zone 33)
>> | N: 6653695 S: 6643685 Res: 10
>> | E: 266505 W: 256495 Res: 10
>> | Range of data: min = 1 max = 28000
>> |
>> | Data Description:
>> | generated by r.in.gdal
>>
>> +--------------------------------------------------------------------
>> +-
>> -------+
>>
>> ----------------------------------------
>> 6s file:
>> 25- geometrical conditions=Sentinel-2A
>> 9 5 10.6728 10.73413 59.90647- month day hh.ddd longitude latitude
>> 4 - atmospheric model=subarctic summer
>> 3- aerosol model=urban
>> 50- visibility [km] (aerosol model concentration) (this is
>> estimated, I also tried with AOD specified)
>> -0.055- mean target elevation above sea level [km]
>> -1000- sensor height
>> 166- Sentinel2A Blue band B2 (440nm - 535nm)
>>
>> ----------------------------------------
>> Command:
>> i.atcorr input=test_B02 at p_Sentinel4Nature_S2_Oslo range=1,28000
>> elevation=dem_10m_25833 at p_Sentinel4Nature_S2_Oslo
>> parameters=/home/NINA.NO/zofie.cimburova/Sentinel4Nature/DATA/6s.txt
>> <http://NINA.NO/zofie.cimburova/Sentinel4Nature/DATA/6s.txt>
>> <http://NINA.NO/zofie.cimburova/Sentinel4Nature/DATA/6s.txt
>> <http://NINA.NO/zofie.cimburova/Sentinel4Nature/DATA/6s.txt>>
>> output=test_B02_atcorr
>> >Atmospheric correction...
>> >Atmospheric correction complete.
>>
>> (I am not sure about the range parameter, tried with 0,255 too.
>> The DEM contains no NULLs. Also tried running with -r and -a
>> flags.)
>>
>> ----------------------------------------
>> Output:
>> r.info <http://r.info> <http://r.info>
>> map=test_B02_atcorr at p_Sentinel4Nature_S2_Oslo
>> +----------------------------------------------------------------------------+
>> | Map: test_B02_atcorr at p_Sentinel4N Date: Mon Dec 18
>> 13:10:14 2017
>> | Mapset: p_Sentinel4Nature_S2_Oslo Login of Creator:
>> zofie.cimburova
>> | Location: ETRS_33N
>> | DataBase: /data/grass
>> | Title: test_B02_atcorr2
>> | Timestamp: none
>> |----------------------------------------------------------------------------|
>> |
>> | Type of Map: raster Number of Categories: 0
>> | Data Type: FCELL
>> | Rows: 1001
>> | Columns: 1001
>> | Total Cells: 1002001
>> | Projection: UTM (zone 33)
>> | N: 6653695 S: 6643685 Res: 10
>> | E: 266505 W: 256495 Res: 10
>> | Range of data: min = -nan max = -nan
>> |
>> | Data Description:
>> | generated by i.atcorr
>> |
>> | Comments:
>> | i.atcorr input="test_B02 at p_Sentinel4Nature_S2_Oslo"
>> range=1,28\
>> | 000 elevation="dem_10m_25833 at p_Sentinel4Nature_S2_Oslo"
>> para\
>> |
>> meters="/home/NINA.NO/zofie.cimburova/Sentinel4Nature/DATA/6s.txt <http://NINA.NO/zofie.cimburova/Sentinel4Nature/DATA/6s.txt>
>> <http://NINA.NO/zofie.cimburova/Sentinel4Nature/DATA/6s.txt
>> <http://NINA.NO/zofie.cimburova/Sentinel4Nature/DATA/6s.txt>>" o\
>> | utput="test_B02_atcorr2" rescale=0,255
>> |
>>
>> +--------------------------------------------------------------------
>> +-
>> -------+
>>
>>
>>
>> On Fri, Dec 15, 2017 at 5:12 PM, Žofie Cimburová
>> <zoficimburova at gmail.com <mailto:zoficimburova at gmail.com>
>> <mailto:zoficimburova at gmail.com
>> <mailto:zoficimburova at gmail.com>>> wrote:
>>
>> Dear Markus,
>> thanks for your reply, this is exactly what I need to know!
>>
>> Best, Zofie
>>
>> On Fri, Dec 15, 2017 at 5:09 PM, Markus Neteler
>> <neteler at osgeo.org <mailto:neteler at osgeo.org>
>> <mailto:neteler at osgeo.org <mailto:neteler at osgeo.org>>> wrote:
>>
>>
>> On Dec 15, 2017 3:54 PM, "Žofie Cimburová"
>> <zoficimburova at gmail.com
>> <mailto:zoficimburova at gmail.com> <mailto:zoficimburova at gmail.com
>> <mailto:zoficimburova at gmail.com>>> wrote:
>> >
>> > Dear all,
>> > I am trying to use i.atcorr (GRASS 7.4) to apply
>> atmospheric corrections for Sentinel 2 data. The documentation
>> provides a great help, but there are two points I am not sure
>> about - >
>> > - I don't need the atmospheric correction to be
>> applied to the whole scene, so I only imported a small clip of
>> the scene to GRASS. What longitude and latitude shall I then
>> specify in the 6S parameters?
>>
>> I'd use the center coordinates of the clipped area.
>>
>> > Or is it necessary to apply the corrections to the
>> entire scene?
>>
>> No since it is a pixel based algorithm.
>>
>> > - How can I estimate the value of visibility (aerosol
>> model concentration)?
>> There are AERONET data online somewhere which might be
>> the best
>> choice.
>>
>> Markus
>>
>>
>>
>>
>>
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>
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