Re: i.atcorr with Sentinel2

Dear Stefan

I have applied i.atcorr to many S2A scenes last year and it worked. Today I
rechecked them again, and it worked on a older svn version (7.3) and also
on the latest trunk version.

All the steps I have taken is similar to what you have done, so I dont
really know whats going wrong with you.

Here is the command I used:

i.atcorr -r input="S2A_OPER_MSI_L1C_TL_MTI_20151012T101024457Z_T32TPR_B02"
> range=0,10000 elevation="eudem_euregio_utm32_10m"
> parameters="S2_B02_T32TPR.txt"
> output="S2A_OPER_MSI_L1C_TL_MTI_20151012T101024457Z_T32TPR_02_6S"
> rescale=0,10000
>


S2_B02_T32TPR.txt:
[image: Inline image 1]


The AOD value is coming from the output of Sen2cor (It was a trial approach
!). I tried with a visibility value of 15 and it works.

And the ouput of r.univar is:

[image: Inline image 2]


I also tried it on a smaller clip (1000 X 1000), and it is giving some
output.

Let me know if you need any more info.

Regards

Sajid


On Tue, Dec 19, 2017 at 11:33 AM, Stefan Blumentrath <
[email protected]> wrote:

> Hi again,
>
> Even with constant spectral conditions and values for filter function from
> Sentinel-2, all combinations of input band ranges result in empty maps.
> Constant spectral conditions and values for filter function from  Landsat7
> however, give results in the expected scale (0-255) regardless input image
> and value ranges...
>
> Shall I open a ticket?
>
> Any idea/chance to get this new feature in G7.4 to work...?
>
> Any pointer/help would be very much appreciated!
>
> Cheers
> Stefan
>
> -----Original Message-----
> From: Stefan Blumentrath
> Sent: tirsdag 19. desember 2017 10.56
> To: Stefan Blumentrath <[email protected]>; Moritz Lennert <
> [email protected]>; Žofie Cimburová <[email protected]>
> Cc: GRASS user list <[email protected]>
> Subject: RE: [GRASS-user] i.atcorr with Sentinel2
>
> Hi again,
>
> Still trying to track down the issue...
> I now ran i.atcorr with constant spectral condition and manually defined
> "wl inf" and "wl sup".
>
> First I got those values for Sentinel-2 band 2:
> *                        spectral condition
>      *
> *                        ------------------
>      *
> *            sentinel2a blue b2
>      *
> *                value of filter function :
>      *
> *                 wl inf=    0.300 mic   wl sup=    2.600 mic
>     *
>
> Then for Landsat 7 band 4 (that was known to give results):
> *                        spectral condition
>      *
> *                        ------------------
>      *
> *            etm+ 4
>      *
> *                value of filter function :
>      *
> *                 wl inf=    0.740 mic   wl sup=    0.913 mic
>     *
>
>
> If I then feed those values into a filter function for constant spectral
> conditions, and again the Sentinel-2 values:
> *                        spectral condition
>      *
> *                        ------------------
>      *
> *            constant
>      *
> *                value of filter function :
>      *
> *                 wl inf=    0.300 mic   wl sup=    2.600 mic
>     *
> lead to empty maps, while Landsat7 values:
> *                        spectral condition
>      *
> *                        ------------------
>      *
> *            constant
>      *
> *                value of filter function :
>      *
> *                 wl inf=    0.740 mic   wl sup=    0.913 mic
>     *
> work fine (with all other settings being equal).
>
> That makes me suspect that the values of the Sentinel-2 filter function
> are actually causing the issue here...
> I am currently testing all thinkable combinations of input band ranges to
> see if any of them works with wl inf=0.300 mic and wl sup=2.600 mic and
> will report back from that exercise.
>
> Meanwhile, can anyone confirm that i.atcorr in GRASS 7.4.0RC1 actually
> works with Sentinel-2 data?
>
> Cheers
> Stefan
>
>
>
> -----Original Message-----
> From: grass-user [mailto:[email protected]] On Behalf Of
> Stefan Blumentrath
> Sent: tirsdag 19. desember 2017 08.45
> To: Moritz Lennert <[email protected]>; Žofie Cimburová <
> [email protected]>
> Cc: GRASS user list <[email protected]>
> Subject: Re: [GRASS-user] i.atcorr with Sentinel2
>
> 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:[email protected]]
> Sent: mandag 18. desember 2017 16.58
> To: Stefan Blumentrath <[email protected]>; Žofie Cimburová <
> [email protected]>
> Cc: GRASS user list <[email protected]>
> 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:[email protected]] On Behalf
> > Of Moritz Lennert
> > Sent: mandag 18. desember 2017 16.26
> > To: Žofie Cimburová <[email protected]>
> > Cc: GRASS user list <[email protected]>
> > 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
> >> <[email protected] <mailto:[email protected]>>
> 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@p_Sentinel4Nature_S2_Oslo
> >>             +---------------------------------------------------------
> -------------------+
> >>             | Map:      test_B02@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@p_Sentinel4Nature_S2_Oslo
> range=1,28000
> >>          elevation=dem_10m_25833@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@p_Sentinel4Nature_S2_Oslo
> >>             +---------------------------------------------------------
> -------------------+
> >>             | Map:      test_B02_atcorr@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@p_Sentinel4Nature_S2_Oslo"
> >>          range=1,28\
> >>             |    000 elevation="dem_10m_25833@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
> >>          <[email protected] <mailto:[email protected]>
> >>          <mailto:[email protected]
> >>          <mailto:[email protected]>>> 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
> >>          <[email protected] <mailto:[email protected]>
> >>               <mailto:[email protected] <mailto:[email protected]>>>
> wrote:
> >>
> >>
> >>                   On Dec 15, 2017 3:54 PM, "Žofie Cimburová"
> >>                   <[email protected]
> >>          <mailto:[email protected]> <mailto:zoficimburova@gmail.
> com
> >>          <mailto:[email protected]>>> 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
> >>
> >>
> >>
> >>
> >>
> >>          _______________________________________________
> >>          grass-user mailing list
> >>          [email protected] <mailto:[email protected]>
> >>          https://lists.osgeo.org/mailman/listinfo/grass-user
> >>          <https://lists.osgeo.org/mailman/listinfo/grass-user>
> >>
> >>
> >>
> >>
> >
> >
> > _______________________________________________
> > grass-user mailing list
> > [email protected]
> > https://lists.osgeo.org/mailman/listinfo/grass-user
> >
>
>
> _______________________________________________
> grass-user mailing list
> [email protected]
> https://lists.osgeo.org/mailman/listinfo/grass-user
> _______________________________________________
> grass-user mailing list
> [email protected]
> https://lists.osgeo.org/mailman/listinfo/grass-user
>

_______________________________________________
grass-user mailing list
[email protected]
https://lists.osgeo.org/mailman/listinfo/grass-user