[GRASS-user] sample a strds at specific locations (areas)
Margherita Di Leo
diregola at gmail.com
Fri Aug 9 07:50:49 PDT 2019
Hi,
excuse me if I return on this. I have again the same problem, of v.strds.stats
skipping lots of polygons. Now I'm using a brand new dataset - strds of
Sentinel 1 and a brand now vector of polygons - and the skipped polygons
are not narrow, I'm sure that there are cells centroids in it. See for
example screenshot attached, depicting a polygon that was skipped. I also
tried to run v.strds.stats on that polygon alone, like:
v.strds.stats in=big_areas2 at PERMANENT where="cat == '1'"
strds=db_cross_pol at scaled out=test method=average
v.info test
+----------------------------------------------------------------------------+
| Name: test
|
| Mapset: stats
|
| Location: S1
|
| Database: /media/madi/TOSHIBA EXT/S1/grassdata
|
| Title: Output from v.patch
|
| Map scale: 1:1
|
| Name of creator: madi
|
| Organization:
|
| Source date: Fri Aug 9 12:12:49 2019
|
| Timestamp (first layer): none
|
|----------------------------------------------------------------------------|
| Map format: native
|
|----------------------------------------------------------------------------|
| Type of map: vector (level: 2)
|
|
|
| Number of points: 0 Number of centroids: 0
|
| Number of lines: 0 Number of boundaries: 0
|
| Number of areas: 0 Number of islands: 0
|
|
|
| Map is 3D: No
|
| Number of dblinks: 0
|
|
|
| Projection: UTM (zone 34)
|
|
|
| N: 0 S: 0
|
| E: 0 W: 0
|
|
|
| Digitization threshold: 0
|
| Comment:
|
|
|
+----------------------------------------------------------------------------+
I confess I hadn't look much further into it because I thought it was a
problem with nodata, but this is not the case and I think it's worth of
further investigation. Thanks for any pointers.
Regards,
On Thu, Feb 7, 2019 at 4:10 PM Margherita Di Leo <diregola at gmail.com> wrote:
> Thanks for testing, Vero. I assume it's due to a local problem then.
>
> Cheers,
>
> On Thu, Feb 7, 2019 at 3:29 PM Veronica Andreo <veroandreo at gmail.com>
> wrote:
>
>> Hi Stefan and Madi,
>>
>> Thanks Stefan for the explanations :) Indeed I agree that a flag to avoid
>> the alignment to input rasters (and just use region settings) sounds good.
>> I tested what Madi said, but cannot reproduce in the climate NC location
>> [0]. This is the command I used:
>>
>> v.strds.stats in=boundary_county where="cat == '261'" strds=tempmean
>> t_where="start_time >= '2012-01-01'" out=test
>>
>> to make it faster (it feels indeed kinda slow for the whole vector and
>> full time series), I selected only one polygon and a range of dates. I get
>> the table as expected while leaving methods by default.
>>
>> best,
>> Vero
>>
>> [0]
>> http://courses.ncsu.edu/mea592/common/media/02/nc_climate_spm_2000_2012.zip
>>
>>
>>
>>
>> El jue., 7 feb. 2019 a las 14:39, Margherita Di Leo (<diregola at gmail.com>)
>> escribió:
>>
>>> Thank you Stefan for your help! I figured what happens. v.strds.stats
>>> with default method produces in my case a corrupted output, topology is
>>> there but there's no table associated to it. If I specify method=average, I
>>> do obtain the table, and the mystery is solved: some of the polygons fall
>>> into a nodata (due to cloud mask). If anyone else can reproduce the
>>> corrupted table issue, I can file a ticket for that.
>>>
>>> Thanks for help!
>>> Regards,
>>>
>>> On Thu, Feb 7, 2019 at 12:33 PM Stefan Blumentrath <
>>> Stefan.Blumentrath at nina.no> wrote:
>>>
>>>> Hi Madi,
>>>>
>>>>
>>>>
>>>> With this combination (polygon size vs. raster resolution), the shape
>>>> of the polygons can be an issue (narrow areas that do not cover the center
>>>> of any pixel).
>>>>
>>>>
>>>>
>>>> Debugging should be simple with v.db.select or v.extract.
>>>>
>>>>
>>>>
>>>> Areas that did not get rasterized should be NULL in the column with
>>>> statistics computed with v.rast.stats.
>>>>
>>>>
>>>>
>>>> In verbose mode v.rast.stats (or probably even v.to.rast) should
>>>> probably give a more informative Warning message (e.g. listing categories
>>>> not rasterized). It also would help if you can rasterize the areas yourself
>>>> and provide a raster with categories as (optional) input to v.rast.stats…
>>>>
>>>>
>>>>
>>>> For high resolution data like yours, the speed improvement of multiple
>>>> raster input might help quite a bit esp. with many maps in the time series.
>>>> Will see if I can come up with a patch rather soon…
>>>>
>>>>
>>>>
>>>> Cheers
>>>>
>>>> Stefan
>>>>
>>>>
>>>>
>>>> *From:* Margherita Di Leo <diregola at gmail.com>
>>>> *Sent:* torsdag 7. februar 2019 10:37
>>>> *To:* Stefan Blumentrath <Stefan.Blumentrath at nina.no>
>>>> *Cc:* Veronica Andreo <veroandreo at gmail.com>; grass-user <
>>>> grass-user at lists.osgeo.org>
>>>> *Subject:* Re: [GRASS-user] sample a strds at specific locations
>>>> (areas)
>>>>
>>>>
>>>>
>>>> Hi,
>>>>
>>>>
>>>>
>>>> thank you for your replies. To give a little more context: I selected
>>>> my polygon areas to be > 0.5 ha each (this would be 50000 mq if I'm not
>>>> mistaken) and I'm sampling NDVI maps at 10m resolution (the region being
>>>> the same as NDVI maps). So I think I need an idea on how to debug the areas
>>>> that were excluded to check them individually to see what could be the
>>>> problem...
>>>>
>>>> Regarding the alignment problem, if I understand it correctly: if the
>>>> polygon doesn't include the *center* of the raster beneath it, can't
>>>> retrieve the value and the polygon is discarded? But a value exists, so it
>>>> would be correct that it returned a value in any case. But I admit I don't
>>>> have a full grasp of the problem.
>>>>
>>>>
>>>>
>>>> On Wed, Feb 6, 2019 at 10:52 PM Stefan Blumentrath <
>>>> Stefan.Blumentrath at nina.no> wrote:
>>>>
>>>> Hi Vero,
>>>>
>>>>
>>>>
>>>> I think there is a little misunderstanding.
>>>>
>>>> v.rast.stats did not change it behaviour with regards to the
>>>> computational region (at least not if only one raster map is used). The
>>>> alignment to the input raster (resolution) has been around since the module
>>>> got ported to Python (like 10 years ago):
>>>>
>>>>
>>>> https://trac.osgeo.org/grass/browser/grass/trunk/scripts/v.rast.stats/v.rast.stats.py?rev=33522#L148
>>>>
>>>>
>>>>
>>>> So, adding a flag for skipping the alignment was more an idea for an
>>>> enhancement that allows the behaviour you seem to prefer (too).
>>>>
>>>>
>>>>
>>>> Cheers
>>>>
>>>> Stefan
>>>>
>>>>
>>>>
>>>> *From:* Veronica Andreo <veroandreo at gmail.com>
>>>> *Sent:* onsdag 6. februar 2019 21:38
>>>> *To:* Stefan Blumentrath <Stefan.Blumentrath at nina.no>
>>>> *Cc:* Margherita Di Leo <diregola at gmail.com>; grass-user <
>>>> grass-user at lists.osgeo.org>
>>>> *Subject:* Re: [GRASS-user] sample a strds at specific locations
>>>> (areas)
>>>>
>>>>
>>>>
>>>> I had a similar problem some time ago, just that it was not raster
>>>> resolution, but region resolution that I changed to solve my problem (see
>>>> this thread and MM's answer:
>>>> http://osgeo-org.1560.x6.nabble.com/v-to-rast-for-polygons-not-overlapping-center-of-raster-cell-td5355686.html#a5355729
>>>> )
>>>>
>>>>
>>>>
>>>> IIUC, MM's proposed solution to my case then does not work anymore
>>>> because v.to.rast call inside v.rast.stats is affected by the region
>>>> alignment to the raster to be queried. So, the solution is indeed now, to
>>>> change raster resolution... ? Then the region would be aligned to it (them)?
>>>>
>>>>
>>>>
>>>> If one has large areas or long time series and has to resample all
>>>> rasters to get smallish polygons rasterized, I do not see the advantage of
>>>> this new behavior... but maybe I'm missing something
>>>>
>>>>
>>>>
>>>> Cheers,
>>>>
>>>> Vero
>>>>
>>>>
>>>>
>>>> El mié., 6 feb. 2019 16:54, Stefan Blumentrath <
>>>> Stefan.Blumentrath at nina.no> escribió:
>>>>
>>>> Ciao Madi, Vero,
>>>>
>>>>
>>>>
>>>> Starting with GRASS 7.6, also centroids are used to get the raster
>>>> representation of your area vector map. That increases the likelihood of
>>>> smaller areas to be rasterized.
>>>>
>>>> Increasing the resolution of the current region alone does not help,
>>>> because v.rast.stats temporarily changes the computational region to align
>>>> with the input raster map(s) (see also:
>>>> https://trac.osgeo.org/grass/ticket/3523 and
>>>> https://trac.osgeo.org/grass/ticket/3598 for discussion) Even if the
>>>> first ticket is closed, comments are welcome.
>>>>
>>>> It might make sense to add a flag to v.rast.stats like in
>>>> r.slope.aspect to not align the computational region.
>>>>
>>>>
>>>>
>>>> Furthermore, with regards to efficiency, v.strds.stats could gain some
>>>> speed if multi-raster support in v.rast.stats - added in G 7.6 - would be
>>>> handed down to the addon. Might almost double the speed for larger STRDS…
>>>>
>>>>
>>>>
>>>> Cheers
>>>>
>>>> Stefan
>>>>
>>>>
>>>>
>>>> *From:* grass-user <grass-user-bounces at lists.osgeo.org> *On Behalf Of *Veronica
>>>> Andreo
>>>> *Sent:* onsdag 6. februar 2019 17:20
>>>> *To:* Margherita Di Leo <diregola at gmail.com>
>>>> *Cc:* GRASS user list <grass-user at lists.osgeo.org>
>>>> *Subject:* Re: [GRASS-user] sample a strds at specific locations
>>>> (areas)
>>>>
>>>>
>>>>
>>>> Hi Madi
>>>>
>>>>
>>>>
>>>> El mié., 6 feb. 2019 a las 16:31, Margherita Di Leo (<
>>>> diregola at gmail.com>) escribió:
>>>>
>>>> I have a question regarding v.strds.stats. I get the following warning
>>>> message:
>>>>
>>>>
>>>>
>>>> WARNING: Not all vector categories converted to raster. Converted 120
>>>> of 265.
>>>>
>>>>
>>>>
>>>> What could be the reason for that?
>>>>
>>>>
>>>>
>>>> Some vector areas might not be converted because they are too small
>>>> with respect to the pixel size that you try to query. Others will tell
>>>> better but I think the polygon must overlap the center of the pixel in
>>>> order to be converted into raster. One solution could be to resample your
>>>> rasters to a higher resolution.
>>>>
>>>> HTH,
>>>>
>>>> Vero
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Margherita Di Leo
>>>>
>>>
>>>
>>> --
>>> Margherita Di Leo
>>>
>>
>
> --
> Margherita Di Leo
>
--
Margherita Di Leo
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