Re: [GRASS-user] v.kernel - Points weighted with attribute ?
On 28/10/2019 14:08, Taïs wrote:
Hi Micha, Moritz,
I successfully create the kernel density raster. Thanks a lot
for your support ;)
I tried with ~62.000 points on a computational region of +-
1000 cols by 1000 rows, with 10 m. spatial resolution.
How long was the processing?
FYI, I had to change the type of the weights column from
"double precision" to "integer" because I had this error message
when it was on double precision:
I'll have to think about how to handle that...
Error in matrix(rep(w, n[1]), nrow = n[1],
ncol = nx, byrow
= TRUE) * :
non-numeric argument to binary operator
Calls: sp.kde -> fhat
Taïs
Le 25/10/19 à 13:36, Micha Silver a
écrit :
Hi Taïs
Thanks for testing.
As Moritz mentioned, the important parameter in spatial
kernel density is the bandwidth.
Here attached is an improved script that uses the spatialEco
R package (instead of density.ppp from spatstat). To run this,
you'll need to install spatialEco in your R environment.
This package allows to specify both the bandwidth and the
target raster extents and resolution. In this script I take
the extents and resolution from the GRASS region. Bandwidth is
specified on the command line.
So to try this, in your running GRASS session:
Rscript kernel_density.R
I also attached two images in a test I did, with bandwidths
of 10,000 and 20,000.
Hope this helps,
Micha
On 10/25/19 12:17 PM, Taïs wrote:
Hi Micha,
I successfully run your R script. However to output is
weird and I don't know how to fix it.
In v.kernel, you can setup the "raduis" parameter to
control what I assume to be the size of the kernel (of the
moving window). I made one test with radius=300 and another
with value 3000. The result of the first is more what I
would expect in terms of spatial variability.
When I try your script, the output raster has a size of
128x128 which did not correspond at all to my computational
region, and thus the resolution is not the same as the one
defined in the computational region.
The other thing is that I'm wondering if it is possible to
control the size of the moving window with the "density"
function in R. I already tried the 'n' parameter but it
doesn't change anything..
I also tried with real weights (the number of inhabitants)
and a unity weighting (value 1 for all points) to see it
there is a change and there is which proof the weights
affect the output :)
Le 22/10/19 à 13:41, Micha Silver
a écrit :
Here is the script.
Let me know how it goes. (I might try to take time to
make it into a GRASS addon)
On 10/22/19 2:33 PM, Taïs
wrote:
Hi Micha, thanks for your repply.
For my own need, I think your solution is enough and I
would like to try if you agree to send the R script.
Le 22/10/19 à 12:53, Micha
Silver a écrit :
On 10/21/19 1:33 PM, Tais
wrote:
Hi
all,
I would like to compute a raster density map ("heat
map") from vector points using v.kernel. The points
represent house addresses. However, I would need to
weight the points with a value stored in the attribute
table (number of inhabitants). I saw on the module
manual page that this functionality is a "known
issue".
I imagined a solution to by-passe the limitation:
duplicate each point as
Re: [GRASS-user] v.kernel - Points weighted with attribute ?
Hi Micha, Moritz,
I successfully create the kernel density raster. Thanks a lot for your
support ;)
I tried with ~62.000 points on a computational region of +- 1000 cols by
1000 rows, with 10 m. spatial resolution.
FYI, I had to change the type of the weights column from "double
precision" to "integer" because I had this error message when it was on
double precision:
/Error in matrix(rep(w, n[1]), nrow = n[1], ncol = nx, byrow
= TRUE) * :
non-numeric argument to binary operator
Calls: sp.kde -> fhat
/
Taïs
Le 25/10/19 à 13:36, Micha Silver a écrit :
Hi Taïs
Thanks for testing.
As Moritz mentioned, the important parameter in spatial kernel density
is the bandwidth.
Here attached is an improved script that uses the spatialEco R package
(instead of density.ppp from spatstat). To run this, you'll need to
install spatialEco in your R environment.
This package allows to specify both the bandwidth and the target
raster extents and resolution. In this script I take the extents and
resolution from the GRASS region. Bandwidth is specified on the
command line.
So to try this, in your running GRASS session:
Rscript kernel_density.R
I also attached two images in a test I did, with bandwidths of 10,000
and 20,000.
Hope this helps,
Micha
On 10/25/19 12:17 PM, Taïs wrote:
Hi Micha,
I successfully run your R script. However to output is weird and I
don't know how to fix it.
In v.kernel, you can setup the "raduis" parameter to control what I
assume to be the size of the kernel (of the moving window). I made
one test with radius=300 and another with value 3000. The result of
the first is more what I would expect in terms of spatial variability.
When I try your script, the output raster has a size of 128x128 which
did not correspond at all to my computational region, and thus the
resolution is not the same as the one defined in the computational
region.
The other thing is that I'm wondering if it is possible to control
the size of the moving window with the "density" function in R. I
already tried the 'n' parameter but it doesn't change anything..
I also tried with real weights (the number of inhabitants) and a
unity weighting (value 1 for all points) to see it there is a change
and there is which proof the weights affect the output :)
Le 22/10/19 à 13:41, Micha Silver a écrit :
Here is the script.
Let me know how it goes. (I might try to take time to make it into a
GRASS addon)
On 10/22/19 2:33 PM, Taïs wrote:
Hi Micha, thanks for your repply.
For my own need, I think your solution is enough and I would like
to try if you agree to send the R script.
Le 22/10/19 à 12:53, Micha Silver a écrit :
On 10/21/19 1:33 PM, Tais wrote:
Hi all,
I would like to compute a raster density map ("heat map") from
vector points using v.kernel. The points represent house
addresses. However, I would need to weight the points with a
value stored in the attribute table (number of inhabitants). I
saw on the module manual page that this functionality is a "known
issue".
I imagined a solution to by-passe the limitation: duplicate each
point as many time as needed (according to the value stored in
the attribute table) and use this new layer directly in v.kernel.
However, I think it will definitely not be the most efficient way
to do the trick. Do you have an alternative in mind ?
Of course the best solution would be that someone in the
development community would have the time and the kindness to
implement this function directly in the module (I'm not skilled
in C and thus cannot try myself).
Maybe not the answer you are looking for, but you can create a
weighted kernel density in R. I can send an R script that is
intended to be run from within a GRASS session. It accepts a point
vector and attrib column, and creates a kernel density raster,
weighted by the attribute values (using the R defaults for
bandwidth and Gaussian kernel)
Requires, of course, that R is installed, with the packages:
spatstat, raster, rgrass7.
NB: Sorry if I should have posted this on the developer mailing
list. I hesitated but decided to post here finally.
Best,
--
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
--
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918
<>___
grass-user mailing list
grass-user@lists.osgeo.org
https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] v.kernel - Points weighted with attribute ?
Hi Taïs
Thanks for testing.
As Moritz mentioned, the important parameter in spatial kernel
density is the bandwidth.
Here attached is an improved script that uses the spatialEco R
package (instead of density.ppp from spatstat). To run this,
you'll need to install spatialEco in your R environment.
This package allows to specify both the bandwidth and the target
raster extents and resolution. In this script I take the extents
and resolution from the GRASS region. Bandwidth is specified on
the command line.
So to try this, in your running GRASS session:
Rscript kernel_density.R
I also attached two images in a test I did, with bandwidths of
10,000 and 20,000.
Hope this helps,
Micha
On 10/25/19 12:17 PM, Taïs wrote:
Hi Micha,
I successfully run your R script. However to output is weird
and I don't know how to fix it.
In v.kernel, you can setup the "raduis" parameter to control
what I assume to be the size of the kernel (of the moving
window). I made one test with radius=300 and another with value
3000. The result of the first is more what I would expect in
terms of spatial variability.
When I try your script, the output raster has a size of 128x128
which did not correspond at all to my computational region, and
thus the resolution is not the same as the one defined in the
computational region.
The other thing is that I'm wondering if it is possible to
control the size of the moving window with the "density"
function in R. I already tried the 'n' parameter but it doesn't
change anything..
I also tried with real weights (the number of inhabitants) and
a unity weighting (value 1 for all points) to see it there is a
change and there is which proof the weights affect the output :)
Le 22/10/19 à 13:41, Micha Silver a
écrit :
Here is the script.
Let me know how it goes. (I might try to take time to make it
into a GRASS addon)
On 10/22/19 2:33 PM, Taïs wrote:
Hi Micha, thanks for your repply.
For my own need, I think your solution is enough and I
would like to try if you agree to send the R script.
Le 22/10/19 à 12:53, Micha Silver
a écrit :
On 10/21/19 1:33 PM, Tais
wrote:
Hi
all,
I would like to compute a raster density map ("heat map")
from vector points using v.kernel. The points represent
house addresses. However, I would need to weight the
points with a value stored in the attribute table (number
of inhabitants). I saw on the module manual page that this
functionality is a "known issue".
I imagined a solution to by-passe the limitation:
duplicate each point as many time as needed (according to
the value stored in the attribute table) and use this new
layer directly in v.kernel. However, I think it will
definitely not be the most efficient way to do the trick.
Do you have an alternative in mind ?
Of course the best solution would be that someone in the
development community would have the time and the kindness
to implement this function directly in the module (I'm not
skilled in C and thus cannot try myself).
Maybe not the answer you are looking for, but you can
create a weighted kernel density in R. I can send an R
script that is intended to be run from within a GRASS
session. It accepts a point vector and attrib column, and
creates a kernel density raster, weighted by the attribute
values (using the R defaults for bandwidth and Gaussian
kernel)
Requires, of course, that R is installed, with the
packages: spatstat, raster, rgrass7.
NB:
Sorry if I should have posted this on the developer
mailing list. I hesitated but decided to post here
finally.
Best,
--
Micha Silver
Ben Gurion Univ.
Sde Boker,
Re: [GRASS-user] v.kernel - Points weighted with attribute ?
On 25/10/19 11:17, Taïs wrote: Hi Micha, I successfully run your R script. However to output is weird and I don't know how to fix it. In v.kernel, you can setup the "raduis" parameter to control what I assume to be the size of the kernel (of the moving window). AFAIU, radius is not the size of a moving window, it is the bandwidth of the kernel function. If you use a gaussian kernel, for example, it will be the standard deviation of the normal function to be used. If you use a uniform kernel it is the radius of the circular search window. Moritz ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] v.kernel - Points weighted with attribute ?
Here is the script.
Let me know how it goes. (I might try to take time to make it
into a GRASS addon)
On 10/22/19 2:33 PM, Taïs wrote:
Hi Micha, thanks for your repply.
For my own need, I think your solution is enough and I would
like to try if you agree to send the R script.
Le 22/10/19 à 12:53, Micha Silver a
écrit :
On 10/21/19 1:33 PM, Tais wrote:
Hi
all,
I would like to compute a raster density map ("heat map") from
vector points using v.kernel. The points represent house
addresses. However, I would need to weight the points with a
value stored in the attribute table (number of inhabitants). I
saw on the module manual page that this functionality is a
"known issue".
I imagined a solution to by-passe the limitation: duplicate
each point as many time as needed (according to the value
stored in the attribute table) and use this new layer directly
in v.kernel. However, I think it will definitely not be the
most efficient way to do the trick. Do you have an alternative
in mind ?
Of course the best solution would be that someone in the
development community would have the time and the kindness to
implement this function directly in the module (I'm not
skilled in C and thus cannot try myself).
Maybe not the answer you are looking for, but you can create
a weighted kernel density in R. I can send an R script that is
intended to be run from within a GRASS session. It accepts a
point vector and attrib column, and creates a kernel density
raster, weighted by the attribute values (using the R defaults
for bandwidth and Gaussian kernel)
Requires, of course, that R is installed, with the packages:
spatstat, raster, rgrass7.
NB:
Sorry if I should have posted this on the developer mailing
list. I hesitated but decided to post here finally.
Best,
--
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
# Weighted Kernel Density in R
# execute from a GRASS session
# Command line arguments: GRASS point vector, column of weights
#
suppressPackageStartupMessages(c(library(rgrass7),
library(spatstat),
library(sp),
library(raster)))
# Test case, in GRASS location nc_basic_spm, using the schools vector
# This vector has attribut CORECAPACI, used as weight in this case
args = commandArgs(trailingOnly=TRUE)
if (length(args) < 2) {
print("Enter GRASS point vector and weight attribute column as command line arguments")
print("Exiting...")
quit(save="no")
} else {
input_vect = args[1]
output_rast = paste0(input_vect, "_density")
weights_col = args[2]
}
use_sp()
points = readVECT(input_vect)
# Check geometry type and weight attribute column
if (class(points)!= "SpatialPointsDataFrame") {
print("Wrong geometry type. Must be POINT")
quit(save="no")
}
weights_idx = which(names(points) == weights_col)
if (is.empty(weights_idx)) {
print(paste("No attribute column:", weights_col))
quit(save="no")
}
# Remove NA
points = points[!is.na(points[[weights_idx]]),]
wts = points[[weights_idx]]
print(paste("Using:", length(wts), "points"))
# Prepare ppp object
pts_coords = coordinates(points)
pts_ext = c(min(pts_coords[,1]), max(pts_coords[,1]), min(pts_coords[,2]), max(pts_coords[,2]))
pts_ppp = as.ppp(pts_coords, pts_ext)
# Density (default Gaussian kernel)
pts_dens = density(pts_ppp, weights = wts)
# Convert to SGDF to save back to GRASS
pts_sgdf = as(raster(pts_dens), "SpatialGridDataFrame")
writeRAST(x = pts_sgdf, vname = output_rast)
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Re: [GRASS-user] v.kernel - Points weighted with attribute ?
Hi Micha, thanks for your repply.
For my own need, I think your solution is enough and I would like to try
if you agree to send the R script.
Le 22/10/19 à 12:53, Micha Silver a écrit :
On 10/21/19 1:33 PM, Tais wrote:
Hi all,
I would like to compute a raster density map ("heat map") from vector
points using v.kernel. The points represent house addresses. However,
I would need to weight the points with a value stored in the
attribute table (number of inhabitants). I saw on the module manual
page that this functionality is a "known issue".
I imagined a solution to by-passe the limitation: duplicate each
point as many time as needed (according to the value stored in the
attribute table) and use this new layer directly in v.kernel.
However, I think it will definitely not be the most efficient way to
do the trick. Do you have an alternative in mind ?
Of course the best solution would be that someone in the development
community would have the time and the kindness to implement this
function directly in the module (I'm not skilled in C and thus cannot
try myself).
Maybe not the answer you are looking for, but you can create a
weighted kernel density in R. I can send an R script that is intended
to be run from within a GRASS session. It accepts a point vector and
attrib column, and creates a kernel density raster, weighted by the
attribute values (using the R defaults for bandwidth and Gaussian kernel)
Requires, of course, that R is installed, with the packages: spatstat,
raster, rgrass7.
NB: Sorry if I should have posted this on the developer mailing list.
I hesitated but decided to post here finally.
Best,
--
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918
<>___
grass-user mailing list
grass-user@lists.osgeo.org
https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] v.kernel - Points weighted with attribute ?
On 10/21/19 1:33 PM, Tais wrote:
Hi all,
I would like to compute a raster density map ("heat map") from
vector points using v.kernel. The points represent house
addresses. However, I would need to weight the points with a value
stored in the attribute table (number of inhabitants). I saw on
the module manual page that this functionality is a "known issue".
I imagined a solution to by-passe the limitation: duplicate each
point as many time as needed (according to the value stored in the
attribute table) and use this new layer directly in v.kernel.
However, I think it will definitely not be the most efficient way
to do the trick. Do you have an alternative in mind ?
Of course the best solution would be that someone in the
development community would have the time and the kindness to
implement this function directly in the module (I'm not skilled in
C and thus cannot try myself).
Maybe not the answer you are looking for, but you can create a
weighted kernel density in R. I can send an R script that is
intended to be run from within a GRASS session. It accepts a point
vector and attrib column, and creates a kernel density raster,
weighted by the attribute values (using the R defaults for
bandwidth and Gaussian kernel)
Requires, of course, that R is installed, with the packages:
spatstat, raster, rgrass7.
NB:
Sorry if I should have posted this on the developer mailing list.
I hesitated but decided to post here finally.
Best,
--
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918
___
grass-user mailing list
grass-user@lists.osgeo.org
https://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] v.kernel - Points weighted with attribute ?
Hi all,
I would like to compute a raster density map ("heat map") from vector
points using v.kernel. The points represent house addresses. However, I
would need to weight the points with a value stored in the attribute
table (number of inhabitants). I saw on the module manual page that this
functionality is a "known issue".
I imagined a solution to by-passe the limitation: duplicate each point
as many time as needed (according to the value stored in the attribute
table) and use this new layer directly in v.kernel. However, I think it
will definitely not be the most efficient way to do the trick. Do you
have an alternative in mind ?
Of course the best solution would be that someone in the development
community would have the time and the kindness to implement this
function directly in the module (I'm not skilled in C and thus cannot
try myself).
NB: Sorry if I should have posted this on the developer mailing list. I
hesitated but decided to post here finally.
Best,
--
Tais
___
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