[GRASS-dev] compile 6S library in GRASS
Roberta Fagandini
robifagandini at gmail.com
Thu Jun 28 09:14:35 PDT 2018
Moritz, I don't know why but today I have some trouble with your email, I
receive them after some hours...anyway I read the last from the dev digest.
Regarding AERONET data, it's not possible to completely automate the
procedure (search for the proper file, download, unzip, read and so on..),
I had already verified and the AERONET website does not provide any API or
something that allows connecting from GRASS.
However, I think I can add the interpolation suggested by Markus (thank
you, Markus, for the link) so regarding the AOT value, users can choose to:
- provide their own value
- read the "nearest" value (timestamp) from an AERONET file (this part
of the script is almost ready) and apply the interpolation (using the
closest available wavelength)
Roberta
2018-06-28 15:26 GMT+02:00 Roberta Fagandini <robifagandini at gmail.com>:
>
>
> 2018-06-28 14:46 GMT+02:00 Markus Metz <markus.metz.giswork at gmail.com>:
>
>>
>>
>> On Thu, Jun 28, 2018 at 12:17 PM, Roberta Fagandini <
>> robifagandini at gmail.com> wrote:
>> >
>> >
>> >
>> > 2018-06-28 10:26 GMT+02:00 Moritz Lennert <mlennert at club.worldonline.be
>> >:
>> >>
>> >> On 27/06/18 15:40, Roberto Marzocchi wrote:
>> >>>
>> >>>
>> >>>
>> >>> Il giorno mer 27 giu 2018 alle ore 15:25 Markus Metz <
>> markus.metz.giswork at gmail.com <mailto:markus.metz.giswork at gmail.com>> ha
>> scritto:
>> >>>
>> >>>
>> >>>
>> >>> On Wed, Jun 27, 2018 at 3:06 PM, Roberta Fagandini
>> >>> <robifagandini at gmail.com <mailto:robifagandini at gmail.com>> wrote:
>> >>> >
>> >>> >
>> >>> >
>> >>> > 2018-06-27 14:24 GMT+02:00 Markus Metz
>> >>> <markus.metz.giswork at gmail.com <mailto:markus.metz.giswork at gm
>> ail.com>>:
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >> On Wed, Jun 27, 2018 at 2:16 PM, Roberta Fagandini
>> >>> <robifagandini at gmail.com <mailto:robifagandini at gmail.com>> wrote:
>> >>> >> >
>> >>> >> > I'm trying to create an automatic procedure to retrieve all
>> >>> the input parameters for the control file of i.atcorr.
>> >>> >> > I need py6S because I want to automatically read and compute
>> >>> AOT at 550nm from an AERONET file.
>> >>> >>
>> >>> >> With AOT you mean aerosol optical thickness right? This is
>> user
>> >>> input to i.atcorr. There are various sources for AOT at 550nm,
>> e.g.
>> >>> MODIS.
>> >>> >
>> >>> >
>> >>> > Right!
>> >>> >
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >> Anyway, it is probably much easier to to write your own
>> routine
>> >>> to read the AERONET file and get the corresponding formula for AOT
>> >>> than to fight with 51821 lines of Fortran source code that is
>> >>> numerically unstable. Maybe I can help with getting AOT at 550nm
>> >>> from an AERONET file avoiding the Fortran version of 6S.
>> >>> >
>> >>> >
>> >>> > Ok but I'm not able to create this kind of routine on my own.
>> If
>> >>> someone, more expert than me, can help me in translating the
>> 6S/Py6S
>> >>> functions I can go on in this way otherwise for me it's easier to
>> >>> use the fortran source code.
>> >>>
>> >>> Apparently the AERONET data are simple CSV files. You can import
>> >>> them with r.in.xyz <http://r.in.xyz> or v.in.ascii.
>> >>>
>> >>> Still, I think it is up to the user to decide on the source of AOT
>> >>> values. AERONET is one of many possible sources.
>> >>>
>> >>>
>> >>> Ok but I know that Roberta want try to simplify the procedure for
>> atmospheric correction. In particular she would like to add an option (not
>> the only one) to read automatically the AOT at the wave length of 550 nm
>> from the AERONET file.
>> >>>
>> >>> The steps to do this IMHO are:
>> >>>
>> >>> 1) read the file (using GRASS or maybe better Python)
>> >>>
>> >>> 2) a formula to calculate the AOT550
>> >>>
>> >>> Unfortunately I have no idea about the 2nd point :-(
>> >>
>> >>
>> >> I'm not sure either, what exactly the necessary calculations are.
>> >>
>> >> Superficially reading through the relevant class in Py6S [1], I
>> understasnd that it does two things:
>> >>
>> >> 1) Get the value of AOT550
>> >> 2) Create a continuous profile by interpolating values
>> >>
>> >> If all you need is 1), then all they do (see _get_aot() method at the
>> end) is to read all the AOT_* columns and chose the value of the line with
>> the timestamp closest to the one asked for and the wavelength closest to
>> 550.
>> >>
>> >>
>> >> As the code is GPL you could probably just extract the necessary parts
>> and integrate them into your code. The only thing I'm not to sure about is
>> their use of pandas which creates yet again another dependency which I
>> don't really think necessary and desirable.
>> >
>> >
>> > Yesterday I studied the library better and I understood that it only
>> extracts the available AOT values closest to the wavelength 550 for the
>> specified timestamp. No calculation is made so I'm trying to write my own
>> routine avoiding any dependency.
>> >
>> >>
>> >>
>> >>
>> >> It should be enough to extract from the file the date and time (or
>> maybe easier to work with: year and the Julian day) and all AOT_* columns,
>> parse the AOT_* columns for their wavelength value and then identify the
>> value which has closes time and wavelength to the time requested and 550nm.
>> >
>> >
>> > That's exactly what I want to do and I'm working on it!
>>
>> open the file with your preferred spreadsheet program and copy the
>> corresponding value;-)
>> >
>> >>
>> >>
>> >> Moritz
>> >
>> >
>> > I know that AERONET is not the only source and obviously in my module
>> there will be both an option for providing manually the value, as Markus
>> and Stefan suggested, and an option to extract the AOT from an AERONET
>> file. I'm not an expert in MODIS data so if someone wants to give
>> suggestions about how to retrieve the AOT from these data, I will
>> definitely add this option too.
>>
>
> ok..now I'm a bit confused..
>
>
>>
>> about your module: it is concerned with Sentinel-2 cloud and shadow
>> detection. As a general rule, a module should do one thing, and should do
>> it right. In this sense, importing AERONET data should be a separate
>> module, and your module should do Sentinel-2 cloud and shadow detection,
>> nothing else, this is already complex enough.
>>
>
> the module i.sentinel.mask does only the cloud and shadow detection.
>
>
>>
>> Regarding a new module e.g. v.in.aeronet:
>> It should interpolate AOT at 550nm considering the closest wavelengths
>> with valid data. Unfortunately most of the AERONET data are nodata.
>> Interpolation can be a simple linear interpolation, see
>> https://aeronet.gsfc.nasa.gov/new_web/V2/climo_new/explain/e
>> xplain_new.html
>>
>> It should perform spatial interpolation because the stations are
>> scattered with large distances in between. Spatial interpolation can be
>> done with any of the v.surf.* modules.
>>
>> It should offer temporal interpolation in case there are no data for the
>> required date. This can be done with the temporal GIS framework or with
>> r.series.lwr.
>>
>
> Regarding AERONET, this is only a small part of another possible
> module/script. My intention is to create an iterative procedure that
> executes i.atcorr for all bands of the input image changing accordingly the
> requested input parameters, this module/script should do:
>
> - read input bands from metadata file,
> - write the control file retrieving as many parameters as possible
> from the metadata
> - add other parameters provided by users to the control file
> - change the control file according to the input band
> - run i.atcorr
>
> Reading the AOT from an AERONET file, it is only one possible option to
> further automate the module/script. Obviously users can specify manually
> the AOT value and they can retrieve it from their favourite source.
>
>
>> Regarding MODIS data, r.in.gdal can import MODIS data, and there is
>> r.modis
>>
>> Putting it all together:
>> that would be a wrapper script that helps to
>> 1) import visibility as a map or estimate a fixed visibility value
>> 2) perform atmospheric correction with i.atcorr
>> 3) detect clouds and shadows
>>
>
> My idea was to create a module (e.g. i.sentinel.preproc) that wraps the
> dowload and import phase (i.sentinel.download and i.sentinel.import), the
> atmosperic correction using i.atcorr (and the iterative procedure that I'm
> trying to implement) and the cloud and shadow detection procedure.
>
>
>> Markus M
>>
>>
>> Roberta
>
>
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