[GRASS-user] raster boxplots wrong assignment

Mon Jun 3 03:55:23 PDT 2024

Dear Micha

Dear community

Find enclosed the two files necessary to run the code:

*	The raster file to plot boxplots: al_pres_apple_spring_merged.tif
*	The vector/shape file for the different quares (classes, regions…):Untersuchungsquadrate_2020-2024_shp

https://drive.google.com/drive/folders/14UwptmBQTtKYQFGeecRWa0n_lWDhRc9s?usp=sharing

Code based on 

https://ecodiv.earth/post/drawing-boxplots-of-raster-values/

g.region -a vector=Untersuchungsquadrate_2020_2024 

raster= al_pres_apple_spring_merged.tif

r.mask vector=Untersuchungsquadrate_2020_2024

v.to.rast input=Untersuchungsquadrate_2020_2024 at PERMANENT output=Quadrate use=attr attribute_column="ID_Quadrat" label_column="ID_Quadrat"

--> Here is the identified challenge: transformation form “Untersuchungsquadrate” to “Quadrate” (as input for r.boxplot). attribute_column ID_Quadrat or cat provide false assignment. It just takes Number 1 (either cat or ID_Quadrat.

r.boxplot -o input=al_pres_apple_spring_merged.tif zones=Quadrate bx_sort=ascending raster_statistics=median

Kind regards

Sibylle

From: sibylle.stoeckli at gmx.ch <sibylle.stoeckli at gmx.ch> 
Sent: Friday, May 31, 2024 12:10 PM
To: 'Micha Silver' <tsvibar at gmail.com>; 'grass-user at lists.osgeo.org' <grass-user at lists.osgeo.org>
Subject: RE: [GRASS-user] raster boxplots wrong assignment

Yes: see line 3

From: Micha Silver <tsvibar at gmail.com <mailto:tsvibar at gmail.com> > 
Sent: Friday, May 31, 2024 12:06 PM
To: sibylle.stoeckli at gmx.ch <mailto:sibylle.stoeckli at gmx.ch> ; grass-user at lists.osgeo.org <mailto:grass-user at lists.osgeo.org> 
Subject: Re: [GRASS-user] raster boxplots wrong assignment

On 31/05/2024 12:48, sibylle.stoeckli at gmx.ch <mailto:sibylle.stoeckli at gmx.ch>  wrote:

Dear Micha

Thanks a lot interesting idea: Unfortunately I got a parse error. However the error/challenge is bevore selecting a specific region or site. I was able to plot one boxplot using a different code.

The challenge is that I use this code here to make “Quadrate/Squares” out of the vector layer “Untersuchungsquadrate”, because in r.boxplot you have input raster and zonal raster. Exactly in this code you make the assignment by defining attribute_column. I used both cat and ID_Quadrate, but it seems that my rasterized file “Quadrate” is not yet the one I need.

Can you post the output of: v.info -c Untersuchungsquadrate_2020_2024  ? (Just to verify the ID_Quadrate column)

Ecodiv.earth - Boxplots based on raster data in GRASS GIS <https://ecodiv.earth/post/drawing-boxplots-of-raster-values/> 

v.to.rast input=Untersuchungsquadrate_2020_2024 at PERMANENT output=Quadrate use=attr attribute_column=cat label_column="ID_Quadrat"

OK, after this command you should have a new raster "Quadrate" with pixel values taken from the cat values of the vector. (Why cat and not the ID_Quadrate?)

In the r.mapcalc expression:

1- The full expression needs to be in double quotes, 

2- You need to use an existing **raster** map. Not the vector attribute values.

i.e.

r.mapcalc "MASK = if(Quadrate == 803174), 1, NULL())"

But, as you can see below (since you used the Untersuchungsquadrate_2020_2024 cat values (instead of the ID_Quadrate attrib), the raster values vary from 1 to 179. No value 803174...

I'd suggest to go back to using ID_Quadrate as attribute_column in your v.to.rast .  Then try the r.mapcalc expression to get the mask defined. (Don't forget to remove the mask after: r.mask -r)

HTH

From: Micha Silver  <mailto:tsvibar at gmail.com> <tsvibar at gmail.com> 
Sent: Friday, May 31, 2024 11:09 AM
To: sibylle.stoeckli at gmx.ch <mailto:sibylle.stoeckli at gmx.ch> ; grass-user at lists.osgeo.org <mailto:grass-user at lists.osgeo.org> 
Subject: Re: [GRASS-user] raster boxplots wrong assignment

Hi Sibylle:

I'm not sure I fully understand the problem. If the below example is not relevant, just ignore...

I did a simple test using the nc_spm_08 location. The PERMANENT mapset includes an elevation raster 'elev_srtm_30m' and a categorical landcover raster 'landclass96'. I used the landcover raster as zones, and elevation for the values in the boxplots.

g.region -ap rast=elev_srtm_30m

# All landcover zones

r.boxplot input=elev_srtm_30m zones=landclass96 raster_statistics=median output=~/work/tmp/boxplot.png --o

# See attached boxplot image

# Now limit to only one zone, the forests, class 5 in this raster:

r.mapcalc "MASK = if(landclass96 == 5, 1, null())"

r.boxplot input=elev_srtm_30m zones=landclass96 raster_statistics=median output=~/work/tmp/boxplot_forest.png

# See attached boxplot_forest

r.mask -r

Hope this is somehow helpful.

On 31/05/2024 10:35, sibylle via grass-user wrote:

Dear community

I tested the r.boxplot addon and it is definitively possible to run the addon with more than 20 classes/regions/sites/squares.

Furthermore I realised the reason for the wrong assignment of class to raster, but I am not yet able to fix it.

1.	The challenge is, that (at the moment) I have raster data for one class (one square), but in total I have 150 squares. So at the moment it just selects the first square (either by cat oder ID_Quadrat).
2.	It seems however, if I have raster data for all squares, r.boxplot is working fine.
3.	My question: Is it possible to assign raster data for one individual class/squares, of you have missing data for other classes/squares?

Kind regards

Sibylle

First using this code here:

v.to.rast input=Untersuchungsquadrate_2020_2024 at PERMANENT output=Quadrate use=attr attribute_column="ID_Quadrat" label_column="ID_Quadrat"

r.boxplot -o input=U803174_abgeschnitten zones=Quadrate bx_sort=ascending raster_statistics=median

Second using this code here:

v.to.rast input=Untersuchungsquadrate_2020_2024 at PERMANENT output=Quadrate use=attr attribute_column=cat label_column="ID_Quadrat"

r.boxplot -o input=U803174_abgeschnitten zones=Quadrate bx_sort=ascending raster_statistics=median

From: sibylle.stoeckli at gmx.ch <mailto:sibylle.stoeckli at gmx.ch>   <mailto:sibylle.stoeckli at gmx.ch> <sibylle.stoeckli at gmx.ch> 
Sent: Thursday, May 30, 2024 9:27 AM
To: 'grass-user at lists.osgeo.org <mailto:grass-user at lists.osgeo.org> '  <mailto:grass-user at lists.osgeo.org> <grass-user at lists.osgeo.org>
Subject: RE: raster boxplots wrong assignment

Dear community

I am still wondering, if the r.boxplot addon is working with just a limited number of areass/sites/regions?

Kind regards

Sibylle

From: sibylle.stoeckli at gmx.ch <mailto:sibylle.stoeckli at gmx.ch>  <sibylle.stoeckli at gmx.ch <mailto:sibylle.stoeckli at gmx.ch> > 
Sent: Saturday, May 25, 2024 3:48 PM
To: 'grass-user at lists.osgeo.org <mailto:grass-user at lists.osgeo.org> ' <grass-user at lists.osgeo.org <mailto:grass-user at lists.osgeo.org> >
Subject: raster boxplots wrong assignment

Dear community

I would like to plot boxplots from a raster _pres_apple_spring_merged  for different 1 km2 squares (38 squares, Fig. 1, layer “Untersuchungsquadrate”). I was using the same code as used before for 12 regions:

https://ecodiv.earth/post/drawing-boxplots-of-raster-values/ (Author Paulo van Breugel). All layers have the same projection (EPSG:2056, CH1903+/LV95).  However, when loading the layer squares (Untersuchungsquadrate) GRASS GIS was asking for reprojection.

1.	I got now a warning message, that I have a lot of categories, however, the modelling time was fast (Fig 2)
2.	The error is now, that the boxplot is not showing all squares  (e.g. ID_Quadrat 803174) and the boxplots are assigned to the wrong square (ID_Quadrat) (Fig. 3)

Kind regards

Sibylle Stöckli

Fig. 1

Fig. 2

Figure 3

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-- 
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918

-- 
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918
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