[R-sig-Geo] Optimizing spatial query in R

2017-02-20 Thread Ervan Rutishauser 
Dear All,

I am desperately trying to fasten my algorithm to estimate the fraction of
tree crown that overlap a given 10x10 subplot in a forest plot. I have
combined a set of spatial functions (gDistance, extract)  & objects
(SpatialGrid, SpatialPolygons) in a way that is probably not the most
efficient, as it takes dozen of hours to run for a 5 subplots (50 ha
forest plot).

My detailed problem and a reproducible example are posted on Stackoverflow
 and
append below, if you wanna have a look. Apart of Amazon Web Server, is
anyone aware of a sever where to execute (and save results back) R codes
online?
Thanks for any help.
Best regards,


# A. Define objects
require(sp)
require(raster)
require(rgdal)
require(rgeos)
require(dismo)
radius=25   # max search radius around 10 x 10 m cells
res <- vector() # where to store results

# Create a fake set of trees with x,y coordinates and trunk diameter (=dbh)
set.seed(0)
survey <- 
data.frame(x=sample(99,1000,replace=T),y=sample(99,1000,replace=T),dbh=sample(100,1000,replace=T))
coordinates(survey) <- ~x+y

# Define 10 x 10 subplots
grid10 <- SpatialGrid(GridTopology(c(5,5),c(10,10),c(10,10)))
survey$subplot <- over(survey,grid10)
# B. Now find fraction of tree crown overlapping each subplot
for (i in 1:100) {
# Extract centroïd of each the ith cell
centro <- expand.grid(x=seq(5,95,10),y=seq(5,95,10))[i,]
corner <-
data.frame(x=c(centro$x-5,centro$x+5,centro$x+5,centro$x-5),y=c(centro$y-5,centro$y-5,centro$y+5,centro$y+5))


# Find trees in a max radius (define above)
tem <- 
survey[which((centro$x-survey$x)^2+(centro$y-survey$y)^2<=radius^2),]


# Define tree crown based on tree diameter
tem$crownr <- exp(-.438+.658*log(tem$dbh/10)) # crown radius in meter

# Compute the distance from each tree to cell's borders
pDist <- vector()
for (k in 1:nrow(tem))  {
pDist[k] <-
gDistance(tem[k,],SpatialPolygons(list(Polygons(list(Polygon(corner)),1
}

# Keeps only trees whose crown is lower than the above
distance (=overlap)
overlap.trees <- tem[which(pDist<=tem$crownr),]
overlap.trees$crowna <-overlap.trees$crownr^2*pi  # compute crown area

# Creat polygons from overlapping crowns
c1 <- circles(coordinates(overlap.trees),overlap.trees$crownr,
lonlat=F, dissolve=F)
crown <- polygons(c1)
Crown <-
SpatialPolygonsDataFrame(polygons(c1),data=data.frame(dbh=overlap.trees$dbh,crown.area=overlap.trees$crowna))

# Create a fine grid points to retrieve the fraction of
overlapping crowns
max.dist <- ceiling(sqrt(which.max((centro$x -
overlap.trees$x)^2 + (centro$y - overlap.trees$y)^2))) # max distance
to narrow search

finegrid <-
as.data.frame(expand.grid(x=seq(centro$x-max.dist,centro$x+max.dist,1),y=seq(centro$y-max.dist,centro$y+max.dist,1)))
coordinates(finegrid) <- ~ x+y
A <- extract(Crown,finegrid)
Crown@data$ID <- seq(1,length(crown),1)
B <- as.data.frame(table(A$poly.ID))
B <- merge(B,Crown@data,by.x="Var1",by.y="ID",all.x=T)
B$overlap <- B$Freq/B$crown.area
B$overlap[B$overlap>1] <- 1
res[i] <- sum(B$overlap)
}
# C. Check the result
res  # sum of crown fraction overlapping each cell (works fine)

-- 
_
Ervan Rutishauser, PhD
​ STRI post-doctoral fellow
CarboForExpert​
​ 
​Skype: ervan-CH

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Re: [R-sig-Geo] Optimizing spatial query in R

2017-02-20 Thread Chris Reudenbach 

Ervan,

Just on the run, especially if you deal with real data and some 100K 
-1000K of vectors I think the fastest way to do so is to engage GDAL 
GRASS7/SAGA and their ability to deal highly efficient with this kind 
of topological and geometrical queries.


A very good pure R alternative is to use the sf package that is ways 
faster and more satble than sp. It also provides this type of GIS 
functionality like st_overlaps() etc.


cheers Chris



On 20.02.2017 09:45, Ervan Rutishauser wrote:

Dear All,

I am desperately trying to fasten my algorithm to estimate the fraction of
tree crown that overlap a given 10x10 subplot in a forest plot. I have
combined a set of spatial functions (gDistance, extract)  & objects
(SpatialGrid, SpatialPolygons) in a way that is probably not the most
efficient, as it takes dozen of hours to run for a 5 subplots (50 ha
forest plot).

My detailed problem and a reproducible example are posted on Stackoverflow
 and
append below, if you wanna have a look. Apart of Amazon Web Server, is
anyone aware of a sever where to execute (and save results back) R codes
online?
Thanks for any help.
Best regards,


# A. Define objects
 require(sp)
 require(raster)
 require(rgdal)
 require(rgeos)
 require(dismo)
 radius=25   # max search radius around 10 x 10 m cells
 res <- vector() # where to store results

 # Create a fake set of trees with x,y coordinates and trunk diameter (=dbh)
 set.seed(0)
 survey <- 
data.frame(x=sample(99,1000,replace=T),y=sample(99,1000,replace=T),dbh=sample(100,1000,replace=T))
 coordinates(survey) <- ~x+y

 # Define 10 x 10 subplots
 grid10 <- SpatialGrid(GridTopology(c(5,5),c(10,10),c(10,10)))
 survey$subplot <- over(survey,grid10)
# B. Now find fraction of tree crown overlapping each subplot
 for (i in 1:100) {
 # Extract centroïd of each the ith cell
 centro <- expand.grid(x=seq(5,95,10),y=seq(5,95,10))[i,]
 corner <-
data.frame(x=c(centro$x-5,centro$x+5,centro$x+5,centro$x-5),y=c(centro$y-5,centro$y-5,centro$y+5,centro$y+5))


 # Find trees in a max radius (define above)
 tem <- 
survey[which((centro$x-survey$x)^2+(centro$y-survey$y)^2<=radius^2),]


 # Define tree crown based on tree diameter
 tem$crownr <- exp(-.438+.658*log(tem$dbh/10)) # crown radius in meter

 # Compute the distance from each tree to cell's borders
 pDist <- vector()
 for (k in 1:nrow(tem))  {
 pDist[k] <-
gDistance(tem[k,],SpatialPolygons(list(Polygons(list(Polygon(corner)),1
 }

 # Keeps only trees whose crown is lower than the above
distance (=overlap)
 overlap.trees <- tem[which(pDist<=tem$crownr),]
 overlap.trees$crowna <-overlap.trees$crownr^2*pi  # compute crown area

 # Creat polygons from overlapping crowns
 c1 <- circles(coordinates(overlap.trees),overlap.trees$crownr,
lonlat=F, dissolve=F)
 crown <- polygons(c1)
 Crown <-
SpatialPolygonsDataFrame(polygons(c1),data=data.frame(dbh=overlap.trees$dbh,crown.area=overlap.trees$crowna))

 # Create a fine grid points to retrieve the fraction of
overlapping crowns
 max.dist <- ceiling(sqrt(which.max((centro$x -
overlap.trees$x)^2 + (centro$y - overlap.trees$y)^2))) # max distance
to narrow search

 finegrid <-
as.data.frame(expand.grid(x=seq(centro$x-max.dist,centro$x+max.dist,1),y=seq(centro$y-max.dist,centro$y+max.dist,1)))
 coordinates(finegrid) <- ~ x+y
 A <- extract(Crown,finegrid)
 Crown@data$ID <- seq(1,length(crown),1)
 B <- as.data.frame(table(A$poly.ID))
 B <- merge(B,Crown@data,by.x="Var1",by.y="ID",all.x=T)
 B$overlap <- B$Freq/B$crown.area
 B$overlap[B$overlap>1] <- 1
 res[i] <- sum(B$overlap)
 }
# C. Check the result
 res  # sum of crown fraction overlapping each cell (works fine)



--
Dr Christoph Reudenbach, Philipps-University of Marburg, Faculty of 
Geography, GIS and Environmental Modeling, Deutschhausstr. 10, D-35032 
Marburg, fon: ++49.(0)6421.2824296, fax: ++49.(0)6421.2828950, web: 
gis-ma.org, giswerk.org, moc.environmentalinformatics-marburg.de


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Re: [R-sig-Geo] Optimizing spatial query in R

2017-02-20 Thread Ervan Rutishauser 
Dear Chris,

Thanks for your prompt reply and pointing out the "sf" package . I wasn't
aware of it, but I am glad to see it has been released only 2 weeks ago ;)
I'll have a look right now.

Tschüss
Ervan

On 20 February 2017 at 10:56, Chris Reudenbach 
wrote:

> Ervan,
>
> Just on the run, especially if you deal with real data and some 100K
> -1000K of vectors I think the fastest way to do so is to engage GDAL
> GRASS7/SAGA and their ability to deal highly efficient with this kind of
> topological and geometrical queries.
>
> A very good pure R alternative is to use the sf package that is ways
> faster and more satble than sp. It also provides this type of GIS
> functionality like st_overlaps() etc.
>
> cheers Chris
>
>
>
> On 20.02.2017 09:45, Ervan Rutishauser wrote:
>
>> Dear All,
>>
>> I am desperately trying to fasten my algorithm to estimate the fraction of
>> tree crown that overlap a given 10x10 subplot in a forest plot. I have
>> combined a set of spatial functions (gDistance, extract)  & objects
>> (SpatialGrid, SpatialPolygons) in a way that is probably not the most
>> efficient, as it takes dozen of hours to run for a 5 subplots (50 ha
>> forest plot).
>>
>> My detailed problem and a reproducible example are posted on Stackoverflow
>> > ial-query-in-r> and
>>
>> append below, if you wanna have a look. Apart of Amazon Web Server, is
>> anyone aware of a sever where to execute (and save results back) R codes
>> online?
>> Thanks for any help.
>> Best regards,
>>
>>
>> # A. Define objects
>>  require(sp)
>>  require(raster)
>>  require(rgdal)
>>  require(rgeos)
>>  require(dismo)
>>  radius=25   # max search radius around 10 x 10 m cells
>>  res <- vector() # where to store results
>>
>>  # Create a fake set of trees with x,y coordinates and trunk diameter
>> (=dbh)
>>  set.seed(0)
>>  survey <- data.frame(x=sample(99,1000,re
>> place=T),y=sample(99,1000,replace=T),dbh=sample(100,1000,replace=T))
>>  coordinates(survey) <- ~x+y
>>
>>  # Define 10 x 10 subplots
>>  grid10 <- SpatialGrid(GridTopology(c(5,5),c(10,10),c(10,10)))
>>  survey$subplot <- over(survey,grid10)
>> # B. Now find fraction of tree crown overlapping each subplot
>>  for (i in 1:100) {
>>  # Extract centroïd of each the ith cell
>>  centro <- expand.grid(x=seq(5,95,10),y=seq(5,95,10))[i,]
>>  corner <-
>> data.frame(x=c(centro$x-5,centro$x+5,centro$x+5,centro$x-5),
>> y=c(centro$y-5,centro$y-5,centro$y+5,centro$y+5))
>>
>>
>>  # Find trees in a max radius (define above)
>>  tem <- survey[which((centro$x-survey$
>> x)^2+(centro$y-survey$y)^2<=radius^2),]
>>
>>
>>  # Define tree crown based on tree diameter
>>  tem$crownr <- exp(-.438+.658*log(tem$dbh/10)) # crown radius in
>> meter
>>
>>  # Compute the distance from each tree to cell's borders
>>  pDist <- vector()
>>  for (k in 1:nrow(tem))  {
>>  pDist[k] <-
>> gDistance(tem[k,],SpatialPolygons(list(Polygons(list(
>> Polygon(corner)),1
>>  }
>>
>>  # Keeps only trees whose crown is lower than the above
>> distance (=overlap)
>>  overlap.trees <- tem[which(pDist<=tem$crownr),]
>>  overlap.trees$crowna <-overlap.trees$crownr^2*pi  # compute
>> crown area
>>
>>  # Creat polygons from overlapping crowns
>>  c1 <- circles(coordinates(overlap.trees),overlap.trees$crownr,
>> lonlat=F, dissolve=F)
>>  crown <- polygons(c1)
>>  Crown <-
>> SpatialPolygonsDataFrame(polygons(c1),data=data.frame(dbh=
>> overlap.trees$dbh,crown.area=overlap.trees$crowna))
>>
>>  # Create a fine grid points to retrieve the fraction of
>> overlapping crowns
>>  max.dist <- ceiling(sqrt(which.max((centro$x -
>> overlap.trees$x)^2 + (centro$y - overlap.trees$y)^2))) # max distance
>> to narrow search
>>
>>  finegrid <-
>> as.data.frame(expand.grid(x=seq(centro$x-max.dist,centro$x+
>> max.dist,1),y=seq(centro$y-max.dist,centro$y+max.dist,1)))
>>  coordinates(finegrid) <- ~ x+y
>>  A <- extract(Crown,finegrid)
>>  Crown@data$ID <- seq(1,length(crown),1)
>>  B <- as.data.frame(table(A$poly.ID))
>>  B <- merge(B,Crown@data,by.x="Var1",by.y="ID",all.x=T)
>>  B$overlap <- B$Freq/B$crown.area
>>  B$overlap[B$overlap>1] <- 1
>>  res[i] <- sum(B$overlap)
>>  }
>> # C. Check the result
>>  res  # sum of crown fraction overlapping each cell (works fine)
>>
>>
> --
> Dr Christoph Reudenbach, Philipps-University of Marburg, Faculty of
> Geography, GIS and Environmental Modeling, Deutschhausstr. 10, D-35032
> Marburg, fon: ++49.(0)6421.2824296, fax: ++49.(0)6421.2828950, web:
> gis-ma.org, giswerk.org, moc.environmentalinformatics-marburg.de
>
>


-- 
_
Ervan Rutishauser, PhD
​ STRI post-doctoral

Re: [R-sig-Geo] Optimizing spatial query in R

2017-02-20 Thread Roman Luštrik 
The biggest bottleneck was creating a SpatialPolygons object and
calculating gDistance. After computing the SP object outside the for loop,
the run time came down dramatically (see SO post).

Cheers,
Roman

On Mon, Feb 20, 2017 at 10:56 AM, Chris Reudenbach <
reudenb...@uni-marburg.de> wrote:

> Ervan,
>
> Just on the run, especially if you deal with real data and some 100K
> -1000K of vectors I think the fastest way to do so is to engage GDAL
> GRASS7/SAGA and their ability to deal highly efficient with this kind of
> topological and geometrical queries.
>
> A very good pure R alternative is to use the sf package that is ways
> faster and more satble than sp. It also provides this type of GIS
> functionality like st_overlaps() etc.
>
> cheers Chris
>
>
>
>
> On 20.02.2017 09:45, Ervan Rutishauser wrote:
>
>> Dear All,
>>
>> I am desperately trying to fasten my algorithm to estimate the fraction of
>> tree crown that overlap a given 10x10 subplot in a forest plot. I have
>> combined a set of spatial functions (gDistance, extract)  & objects
>> (SpatialGrid, SpatialPolygons) in a way that is probably not the most
>> efficient, as it takes dozen of hours to run for a 5 subplots (50 ha
>> forest plot).
>>
>> My detailed problem and a reproducible example are posted on Stackoverflow
>> > ial-query-in-r> and
>> append below, if you wanna have a look. Apart of Amazon Web Server, is
>> anyone aware of a sever where to execute (and save results back) R codes
>> online?
>> Thanks for any help.
>> Best regards,
>>
>>
>> # A. Define objects
>>  require(sp)
>>  require(raster)
>>  require(rgdal)
>>  require(rgeos)
>>  require(dismo)
>>  radius=25   # max search radius around 10 x 10 m cells
>>  res <- vector() # where to store results
>>
>>  # Create a fake set of trees with x,y coordinates and trunk diameter
>> (=dbh)
>>  set.seed(0)
>>  survey <- data.frame(x=sample(99,1000,re
>> place=T),y=sample(99,1000,replace=T),dbh=sample(100,1000,replace=T))
>>  coordinates(survey) <- ~x+y
>>
>>  # Define 10 x 10 subplots
>>  grid10 <- SpatialGrid(GridTopology(c(5,5),c(10,10),c(10,10)))
>>  survey$subplot <- over(survey,grid10)
>> # B. Now find fraction of tree crown overlapping each subplot
>>  for (i in 1:100) {
>>  # Extract centroïd of each the ith cell
>>  centro <- expand.grid(x=seq(5,95,10),y=seq(5,95,10))[i,]
>>  corner <-
>> data.frame(x=c(centro$x-5,centro$x+5,centro$x+5,centro$x-5),
>> y=c(centro$y-5,centro$y-5,centro$y+5,centro$y+5))
>>
>>
>>  # Find trees in a max radius (define above)
>>  tem <- survey[which((centro$x-survey$
>> x)^2+(centro$y-survey$y)^2<=radius^2),]
>>
>>
>>  # Define tree crown based on tree diameter
>>  tem$crownr <- exp(-.438+.658*log(tem$dbh/10)) # crown radius in
>> meter
>>
>>  # Compute the distance from each tree to cell's borders
>>  pDist <- vector()
>>  for (k in 1:nrow(tem))  {
>>  pDist[k] <-
>> gDistance(tem[k,],SpatialPolygons(list(Polygons(list(
>> Polygon(corner)),1
>>  }
>>
>>  # Keeps only trees whose crown is lower than the above
>> distance (=overlap)
>>  overlap.trees <- tem[which(pDist<=tem$crownr),]
>>  overlap.trees$crowna <-overlap.trees$crownr^2*pi  # compute
>> crown area
>>
>>  # Creat polygons from overlapping crowns
>>  c1 <- circles(coordinates(overlap.trees),overlap.trees$crownr,
>> lonlat=F, dissolve=F)
>>  crown <- polygons(c1)
>>  Crown <-
>> SpatialPolygonsDataFrame(polygons(c1),data=data.frame(dbh=
>> overlap.trees$dbh,crown.area=overlap.trees$crowna))
>>
>>  # Create a fine grid points to retrieve the fraction of
>> overlapping crowns
>>  max.dist <- ceiling(sqrt(which.max((centro$x -
>> overlap.trees$x)^2 + (centro$y - overlap.trees$y)^2))) # max distance
>> to narrow search
>>
>>  finegrid <-
>> as.data.frame(expand.grid(x=seq(centro$x-max.dist,centro$x+
>> max.dist,1),y=seq(centro$y-max.dist,centro$y+max.dist,1)))
>>  coordinates(finegrid) <- ~ x+y
>>  A <- extract(Crown,finegrid)
>>  Crown@data$ID <- seq(1,length(crown),1)
>>  B <- as.data.frame(table(A$poly.ID))
>>  B <- merge(B,Crown@data,by.x="Var1",by.y="ID",all.x=T)
>>  B$overlap <- B$Freq/B$crown.area
>>  B$overlap[B$overlap>1] <- 1
>>  res[i] <- sum(B$overlap)
>>  }
>> # C. Check the result
>>  res  # sum of crown fraction overlapping each cell (works fine)
>>
>>
> --
> Dr Christoph Reudenbach, Philipps-University of Marburg, Faculty of
> Geography, GIS and Environmental Modeling, Deutschhausstr. 10, D-35032
> Marburg, fon: ++49.(0)6421.2824296, fax: ++49.(0)6421.2828950, web:
> gis-ma.org, giswerk.org, moc.environmentalinformatics-marburg.de
>
>
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Re: [R-sig-Geo] Optimizing spatial query in R

2017-02-20 Thread Tim Keitt 
I generally use postgis for this sort of thing.

THK

http://www.keittlab.org/

On Mon, Feb 20, 2017 at 2:45 AM, Ervan Rutishauser  wrote:

> Dear All,
>
> I am desperately trying to fasten my algorithm to estimate the fraction of
> tree crown that overlap a given 10x10 subplot in a forest plot. I have
> combined a set of spatial functions (gDistance, extract)  & objects
> (SpatialGrid, SpatialPolygons) in a way that is probably not the most
> efficient, as it takes dozen of hours to run for a 5 subplots (50 ha
> forest plot).
>
> My detailed problem and a reproducible example are posted on Stackoverflow
> 
> and
> append below, if you wanna have a look. Apart of Amazon Web Server, is
> anyone aware of a sever where to execute (and save results back) R codes
> online?
> Thanks for any help.
> Best regards,
>
>
> # A. Define objects
> require(sp)
> require(raster)
> require(rgdal)
> require(rgeos)
> require(dismo)
> radius=25   # max search radius around 10 x 10 m cells
> res <- vector() # where to store results
>
> # Create a fake set of trees with x,y coordinates and trunk diameter
> (=dbh)
> set.seed(0)
> survey <- data.frame(x=sample(99,1000,replace=T),y=sample(99,1000,
> replace=T),dbh=sample(100,1000,replace=T))
> coordinates(survey) <- ~x+y
>
> # Define 10 x 10 subplots
> grid10 <- SpatialGrid(GridTopology(c(5,5),c(10,10),c(10,10)))
> survey$subplot <- over(survey,grid10)
> # B. Now find fraction of tree crown overlapping each subplot
> for (i in 1:100) {
> # Extract centroïd of each the ith cell
> centro <- expand.grid(x=seq(5,95,10),y=seq(5,95,10))[i,]
> corner <-
> data.frame(x=c(centro$x-5,centro$x+5,centro$x+5,centro$
> x-5),y=c(centro$y-5,centro$y-5,centro$y+5,centro$y+5))
>
>
> # Find trees in a max radius (define above)
> tem <- survey[which((centro$x-survey$x)^2+(centro$y-survey$y)^2<=
> radius^2),]
>
>
> # Define tree crown based on tree diameter
> tem$crownr <- exp(-.438+.658*log(tem$dbh/10)) # crown radius in
> meter
>
> # Compute the distance from each tree to cell's borders
> pDist <- vector()
> for (k in 1:nrow(tem))  {
> pDist[k] <-
> gDistance(tem[k,],SpatialPolygons(list(Polygons(
> list(Polygon(corner)),1
> }
>
> # Keeps only trees whose crown is lower than the above
> distance (=overlap)
> overlap.trees <- tem[which(pDist<=tem$crownr),]
> overlap.trees$crowna <-overlap.trees$crownr^2*pi  # compute crown
> area
>
> # Creat polygons from overlapping crowns
> c1 <- circles(coordinates(overlap.trees),overlap.trees$crownr,
> lonlat=F, dissolve=F)
> crown <- polygons(c1)
> Crown <-
> SpatialPolygonsDataFrame(polygons(c1),data=data.frame(
> dbh=overlap.trees$dbh,crown.area=overlap.trees$crowna))
>
> # Create a fine grid points to retrieve the fraction of
> overlapping crowns
> max.dist <- ceiling(sqrt(which.max((centro$x -
> overlap.trees$x)^2 + (centro$y - overlap.trees$y)^2))) # max distance
> to narrow search
>
> finegrid <-
> as.data.frame(expand.grid(x=seq(centro$x-max.dist,centro$
> x+max.dist,1),y=seq(centro$y-max.dist,centro$y+max.dist,1)))
> coordinates(finegrid) <- ~ x+y
> A <- extract(Crown,finegrid)
> Crown@data$ID <- seq(1,length(crown),1)
> B <- as.data.frame(table(A$poly.ID))
> B <- merge(B,Crown@data,by.x="Var1",by.y="ID",all.x=T)
> B$overlap <- B$Freq/B$crown.area
> B$overlap[B$overlap>1] <- 1
> res[i] <- sum(B$overlap)
> }
> # C. Check the result
> res  # sum of crown fraction overlapping each cell (works fine)
>
> --
> _
> Ervan Rutishauser, PhD
> ​ STRI post-doctoral fellow
> CarboForExpert​
> ​ 
> ​Skype: ervan-CH
>
> [[alternative HTML version deleted]]
>
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> R-sig-Geo mailing list
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