[GRASS-user] i.atcorr with Sentinel2
Stefan Blumentrath
Stefan.Blumentrath at nina.no
Mon Dec 18 15:47:07 PST 2017
Dear Moritz,
Thanks so much for your help with trouble shooting! Very much appreciated!
We now tried all possible combinations of options and I rescaled the input band to 0-1 range. All without success.
Result is always just NULL (or nan without -i flag) for S2A.
However, changing the 6s parameters to some random Landsat band configuration worked with the provided input data and produced (of course incorrect but) result with content.
Now I think I was able to narrow it down to the last line in the 6s parameters, the sensor band configuration. i.atcorr with our input data worked with sensor band defined as e.g. 64 (Landsat 7 band 4) but everything we tested >= 166 for band definition returned empty raster (checking now all systematically).
Seems others had similar problems:
http://permalink.gmane.org/gmane.comp.gis.grass.user/53078
But I was not able to find a solution in existing posts, unfortunately...
Any idea what else we could try?
Cheers
Stefan
-----Original Message-----
From: Moritz Lennert [mailto:mlennert at club.worldonline.be]
Sent: mandag 18. desember 2017 17.06
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
See also discussion here:
http://forum.step.esa.int/t/the-quantification-value-has-a-true-value-dn-to-toa-reflectance/1220/
On 18/12/17 16:57, Moritz Lennert wrote:
> 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/produc
>>> t- 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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>>> https://lists.osgeo.org/mailman/listinfo/grass-user
>>> <https://lists.osgeo.org/mailman/listinfo/grass-user>
>>>
>>>
>>>
>>>
>>
>>
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