[GRASS-user] error in i.sentinel.mask: nan values in xml file

[Markus Metz]

Hi Vero, Roberta,

there is no error output because of ...

On Wed, Jan 29, 2020 at 11:15 PM Veronica Andreo <veroandreo at gmail.com>
wrote:
>
> Hi Robi,
>
> So I found that i.sentinel.import fails for latlong locations. I moved to
UTM as in the original data and all fine. I reached the cloud masking step,
and I find a different problem now.
[...]
>
> --- Start computing the east and north clouds shift at steps of 100m of
> clouds height---
> Traceback (most recent call last):
>   File "/home/veroandreo/.grass7/addons/scripts/i.sentinel.mask", line
638, in <module>
>     main()
>   File "/home/veroandreo/.grass7/addons/scripts/i.sentinel.mask", line
561, in main
>     quiet=True, stderr=subprocess.DEVNULL)

stderr=subprocess.DEVNULL means that stderr output is discarded, thus no
error output.


>   File
"/home/veroandreo/software/grass79-dev/dist.x86_64-pc-linux-gnu/etc/python/grass/script/core.py",
line 499, in run_command
>     return handle_errors(returncode, result=None, args=args,
kwargs=kwargs)
>   File
"/home/veroandreo/software/grass79-dev/dist.x86_64-pc-linux-gnu/etc/python/grass/script/core.py",
line 392, in handle_errors
>     returncode=returncode)
> grass.exceptions.CalledModuleError: Module run v.overlay v.overlay --o
--q ainput=addcat_5922 binput=cl_shift_5922 operator=and
output=overlay_5922 ended with error
> Process ended with non-zero return code 1. See errors in the (error)
output.
>
> Where is this error output to inspect?

disappeared in /dev/null

Markus M
>
> This is the UUID in case you want to test:
541021f8-63f5-4e9d-ba28-425c4c8451df
>
> Thanks much in advance
> Vero
>
> ps: I use grass-dev with python 3.7.4 (because of the ctypes issue)
>
>
>
> El mié., 29 ene. 2020 a las 14:53, Veronica Andreo (<veroandreo at gmail.com>)
escribió:
>>
>> Hi Robi,
>>
>> My bad, region was wrong... anyway, trying to replicate from the
beginning I see that i.sentinel.import with -r is importing empty maps.
However, the jp2 files have data. I can visualize them in QGIS. I'll report
in a different thread. Once I can figure it out and reach this point again,
I'll report back to you. Thanks for the clarification!
>>
>> Cheers
>> Vero
>>
>> El mié., 29 ene. 2020 a las 9:08, roberta fagandini (<
robifagandini at hotmail.it>) escribió:
>>>
>>> Hi Vero,
>>> i.sentinel.mask doesn't retrieve the maximum from the xml file but
computes the value from the image using r.univar. The error could be due to
the computational region..has the region been set correctly?
>>> Can you send the MTD_TL.xml file? I can download the image and make
some tests.
>>>
>>> Roberta
>>>
>>> ________________________________
>>> Da: grass-user <grass-user-bounces at lists.osgeo.org> per conto di
Veronica Andreo <veroandreo at gmail.com>
>>> Inviato: martedì 28 gennaio 2020 19:57
>>> A: grass-user <grass-user at lists.osgeo.org>
>>> Oggetto: [GRASS-user] error in i.sentinel.mask: nan values in xml file
>>>
>>> Hello
>>>
>>> I try to use i.sentinel.mask but I get the following error:
>>>
>>> i.sentinel.mask blue=$blue green=$green red=$red swir11=$swir11
nir=$nir swir12=$swir12 nir8a=$nir8a cloud_mask=cloud shadow_mask=shadow
mtd_file=`find $out_dir -name 'MTD_TL.xml'`
>>>
>>> ADVERTENCIA: All subsequent operations will be limited to the current
>>>              computational region
>>> ADVERTENCIA: Any rescale factor has been applied
>>> --- Start computing maximum values of bands ---
>>> T21JYM_20200126T134201_B02_10m
>>> T21JYM_20200126T134201_B03_10m
>>> T21JYM_20200126T134201_B04_10m
>>> T21JYM_20200126T134201_B08_10m
>>> T21JYM_20200126T134201_B8A_20m
>>> T21JYM_20200126T134201_B11_20m
>>> T21JYM_20200126T134201_B12_20m
>>> --- Computed maximum value: dict_values([nan, nan, nan, nan, nan, nan,
>>> nan]) ---
>>> --- Statistics have been computed! ---
>>> --- Start clouds detection procedure ---
>>> --- Computing cloud mask... ---
>>> Mapa no válido <nan>
>>> Parse error
>>> ERROR: error al parsear
>>> ERROR: An error occurred while running r.mapcalc with expression:
>>>        cloud_def82115 = if((((T21JYM_20200126T134201_B02_10m >
(0.08*nan))
>>>        && (T21JYM_20200126T134201_B03_10m > (0.08*nan)) &&
>>>        (T21JYM_20200126T134201_B04_10m > (0.08*nan))) == 1) &&
>>>        (((T21JYM_20200126T134201_B04_10m < ((0.08*nan)*1.5)) &&
>>>        (T21JYM_20200126T134201_B04_10m >
>>>        T21JYM_20200126T134201_B12_20m*1.3)) == 0) &&
>>>        (((T21JYM_20200126T134201_B11_20m < (0.1*nan)) &&
>>>        (T21JYM_20200126T134201_B12_20m < (0.1*nan))) == 0) &&
>>>        ((if(T21JYM_20200126T134201_B8A_20m ==
>>>        max(T21JYM_20200126T134201_B8A_20m, 2 *
>>>        T21JYM_20200126T134201_B02_10m, 2 *
T21JYM_20200126T134201_B03_10m,
>>>        2 * T21JYM_20200126T134201_B04_10m))) == 0) &&
>>>        ((T21JYM_20200126T134201_B02_10m > 0.2) == 1), 0, null())
>>>
>>> I checked the xml file and there are a lot of nan's yes, but there are
also real values. Why doesn't the max function in this part:
https://github.com/OSGeo/grass-addons/blob/master/grass7/imagery/i.sentinel/i.sentinel.mask/i.sentinel.mask.py#L321
recognize them? Isn't there a way to avoid nan while computing max?
>>>
>>> Thanks much in advance
>>> Vero
>>>
>>> ps: I can provide the xml if needed.
>
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