[GRASS-user] Extracting vegetation phenology from Landsat-based time series

[Blumentrath, Stefan]

Very cool! Thanks Markus.
This sounds very useful.

I hope I find the time soon to test it!

From: grass-user [mailto:grass-user-bounces at lists.osgeo.org] On Behalf Of Markus Metz
Sent: 28. november 2016 09:04
To: Nikos Alexandris <nik at nikosalexandris.net>; Sajid Pareeth <spareeth at gmail.com>
Cc: GRASS user list <grass-user at lists.osgeo.org>; Abel Gelman <abel.gelman at gmail.com>
Subject: Re: [GRASS-user] Extracting vegetation phenology from Landsat-based time series

There is a new addon r.seasons which determines the number of seasons per pixel and extracts start and end dates for the given number of seasons from a time series.
The module is designed for noisy input, e.g.
time|value
0|0
1|0
2|1
3|0
4|1
5|1
6|1
7|0
8|1
9|1
10|1
11|1
12|0
13|0
with threshold 0.5 and minimum season length set to 3 would detect one season. Core season start is at 4, end at 10. Full season start is at 2, end at 10.

Markus M

On Wed, Nov 9, 2016 at 4:17 PM, Nikos Alexandris <nik at nikosalexandris.net<mailto:nik at nikosalexandris.net>> wrote:
Nikos Alexandris:
Is the number of cycles per year in the Wiki as well?  Going through,
last time, I think I didn't grasp that.  Can you pin-point?  It's
exactly what we need at the moment.

Veronica Andreo:
Yes, maybe it is not well explained, but it is here:
https://grasswiki.osgeo.org/wiki/Temporal_data_processing#Filling_and_reconstructing_time_series_data_with_gaps_-_HANTS

and also in the manual under "NOTES"
https://grass.osgeo.org/grass70/manuals/addons/r.hants.html

The idea is, once you are happy with the result of hants, you ask for
amplitude outputs and with those amplitude maps (you'll have one map per
frequency) you run r.series method=max_raster. This will give you the most
important frequency (according to amplitude value of that frequency) in
each pixel. If the result is that the most important frequency is 0, then
you have one cycle per year (that, if you use a base period of one year of
course).

Hope it is clearer now :)

Nikos:
Yes. It was even before -- just me read through quickly.

r.hants is awesome!

We have 24 Landsat 8 derived EVI2 maps (2 for each month) for one year.
Clouds and Water surfaces removed. Another set of "relatively normalised
images, using `i.histo.match` is also ready.  We really need to "fix"
`i.histo.match` to crunch floats directly.  The resulting ranges worry
me a bit -- I just followed the "old" way as discussed some years ago in
a relevant thread (floats > integers > histo-matching > floats).

Anyhow, I am testing the following:

for NF in 4 5 6 7 8 ;do r.hants file=evi2_maps nf=$NF fet=0.05 dod=3 base_period=24 suffix=_hants_nf_$NF amplitude=amplitude_hants_nf_$NF phase=phase_hants_nf_$NF ;done

(thinking loudly... it would be super-nice to have `t.rast.hants`)

Not sure about `dod`. Perhaps it should also follow a patten like 3 4 5
6 and 7 for the above?

for NF in 5 6 7 8 ; do t.rast.series evi2_hants_nf_$NF method=max_raster output=dominant_frequencies_hants_nf_$NF --o

Just in case, the above *should* read:

for NF in 4 5 6 7 8 ;do r.series input=`g.list rast pattern=amplitude*nf_${NF}* separator=comma` method=max_raster output=dominant_frequencies_hants_nf_${NF} --o ;done

"Dominant" frequencies 0, 1, 2 and 3 appear to be within the areas
of our interest (agricultural surfaces).  Very good.  And convincing.
Yet I am learning to interpret this correctly. And the "phase" as well.
Reminds math studies, years ago.

It is a "good" thing to actually have similar dominant frequency "maps"
for all of the experimented Number of Frequencies.

A confirmation would be reassuring.

Thanks, Nikos

[rest deleted]

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