Re: [R] Asking Favor For the Script of Median Filter
Here is one I wrote for the raster package. It searches a raster layer for
NA's and takes the median of the number of non NA adjacent cells determined
by neighbor count. You could turn your matrix into a raster to make it work
or change the code.
Hope you find it useful, Robert
neighbor.filter - function(raster.layer,neighbor.count = 3) {
require(raster)
base.rast - raster.layer
count - 1
NA.ind - which(is.na(base.rast[]))
median.vals - matrix(NA,length(NA.ind),3)
for (j in 1:length(NA.ind)) {
row.ind.NA - rowFromCell(base.rast, NA.ind[j])
col.ind.NA - colFromCell(base.rast, NA.ind[j])
row.ind - c(row.ind.NA-1,row.ind.NA,row.ind.NA+1)
col.ind - c(col.ind.NA-1,col.ind.NA,col.ind.NA+1)
row.ind.check - expand.grid(row.ind,col.ind)[,1]
col.ind.check - expand.grid(row.ind,col.ind)[,2]
ind.del.1 - c(which(row.ind.check dim(base.rast)[1]),which(row.ind.check
1))
if (length(ind.del.1) 0) {
row.ind.check - row.ind.check[-ind.del.1]
col.ind.check - col.ind.check[-ind.del.1] }
ind.del.2 - c(which(col.ind.check 1),which(col.ind.check
dim(base.rast)[2]))
if (length(ind.del.2) 0) {
row.ind.check - row.ind.check[-ind.del.2]
col.ind.check - col.ind.check[-ind.del.2] }
if (length(which(base.rast[cellFromRowCol(base.rast, row.ind.check,
col.ind.check)] 0)) = neighbor.count) {
median.vals[count,c(1:3)] - c(NA.ind[j],
median(base.rast[cellFromRowCol(base.rast,
row.ind.check, col.ind.check)], na.rm = T),
length(which(base.rast[cellFromRowCol(base.rast,
row.ind.check, col.ind.check)] 0)))
count - count + 1
}
}
median.vals - median.vals[which(median.vals[,1] 0),]
base.rast[median.vals[,1]] - median.vals[,2]
return(base.rast) }
Robert Leaf, PhD
NOAA Narragansett Laboratory
--
View this message in context:
http://r.789695.n4.nabble.com/Asking-Favor-For-the-Script-of-Median-Filter-tp3409462p3517365.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Asking Favor For the Script of Median Filter
Hello,everybody. My name is Chuan Zun Liang. I come from Malaysia. I am just
a beginner for R. Kindly to ask favor about median filter. The problem I
facing as below:
x-matrix(sample(1:30,25),5,5)
x
[,1] [,2] [,3] [,4] [,5]
[1,]78 30 29 13
[2,]46 1259
[3,] 253 22 14 24
[4,]2 15 26 23 19
[5,] 28 18 10 11 20
This is example original matrices of an image. I want apply with median
filter with window size 3X# to remove salt and pepper noise in my matric.
Here are the script I attend to writing.The script and output shown as
below:
MedFilter-function(mat,sz)
+ {out-matrix(0,nrow(mat),ncol(mat))
+ for(p in 1:(nrow(mat)-(sz-1)))
+ {for(q in 1:(ncol(mat)-(sz-1)))
+ {outrow-median(as.vector(mat[p:(p+(sz-1)),q:(q+(sz-1))]))
+ out[(p+p+(sz-1))/2,(q+q+(sz-1))/2]-outrow}}
+ out}
MedFilter(x,3)
[,1] [,2] [,3] [,4] [,5]
[1,]00000
[2,]08 12 140
[3,]0 12 14 190
[4,]0 18 15 200
[5,]00000
Example to getting value 8 and 12 as below:
7 8 30 8 30 29
4 6 12 (median=8) 6 12 5 (median=12)
25 3 22 3 22 14
Even the script can give output. However, it is too slow. My image size is
364*364. It is time consumption. Is it get other ways to improving it?
Best Wishes
Chuan
--
View this message in context:
http://r.789695.n4.nabble.com/Asking-Favor-For-the-Script-of-Median-Filter-tp3409462p3409462.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Asking Favor For the Script of Median Filter
( sorry if this is a duplicate, I am not sure if hotmail is
dropping some of my posts. Thanks )
You obviously want to delegate inner loops to R packages that
execute as native, hopefully optimized, code.
Generally a google search that starts with R CRAN will help.
In this case it looks like a few packages available,
http://www.google.com/search?sclient=psyhl=enq=R+cran+median+filter
Date: Sun, 27 Mar 2011 07:56:11 -0700
From: chuan...@hotmail.com
To: r-help@r-project.org
Subject: [R] Asking Favor For the Script of Median Filter
Hello,everybody. My name is Chuan Zun Liang. I come from Malaysia. I am just
a beginner for R. Kindly to ask favor about median filter. The problem I
facing as below:
x-matrix(sample(1:30,25),5,5)
x
[,1] [,2] [,3] [,4] [,5]
[1,] 7 8 30 29 13
[2,] 4 6 12 5 9
[3,] 25 3 22 14 24
[4,] 2 15 26 23 19
[5,] 28 18 10 11 20
This is example original matrices of an image. I want apply with median
filter with window size 3X# to remove salt and pepper noise in my matric.
Here are the script I attend to writing.The script and output shown as
below:
MedFilter-function(mat,sz)
+ {out-matrix(0,nrow(mat),ncol(mat))
+ for(p in 1:(nrow(mat)-(sz-1)))
+ {for(q in 1:(ncol(mat)-(sz-1)))
+ {outrow-median(as.vector(mat[p:(p+(sz-1)),q:(q+(sz-1))]))
+ out[(p+p+(sz-1))/2,(q+q+(sz-1))/2]-outrow}}
+ out}
MedFilter(x,3)
[,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 8 12 14 0
[3,] 0 12 14 19 0
[4,] 0 18 15 20 0
[5,] 0 0 0 0 0
Example to getting value 8 and 12 as below:
7 8 30 8 30 29
4 6 12 (median=8) 6 12 5 (median=12)
25 3 22 3 22 14
Even the script can give output. However, it is too slow. My image size is
364*364. It is time consumption. Is it get other ways to improving it?
Best Wishes
Chuan
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Asking Favor For the Script of Median Filter
On Mar 27, 2011, at 10:56 AM, chuan_zl wrote:
Hello,everybody. My name is Chuan Zun Liang. I come from Malaysia. I
am just
a beginner for R. Kindly to ask favor about median filter. The
problem I
facing as below:
x-matrix(sample(1:30,25),5,5)
x
[,1] [,2] [,3] [,4] [,5]
[1,]78 30 29 13
[2,]46 1259
[3,] 253 22 14 24
[4,]2 15 26 23 19
[5,] 28 18 10 11 20
This is example original matrices of an image. I want apply with
median
filter with window size 3X# to remove salt and pepper noise in my
matric.
Here are the script I attend to writing.The script and output shown as
below:
MedFilter-function(mat,sz)
+ {out-matrix(0,nrow(mat),ncol(mat))
+ for(p in 1:(nrow(mat)-(sz-1)))
+ {for(q in 1:(ncol(mat)-(sz-1)))
+ {outrow-median(as.vector(mat[p:(p+(sz-1)),q:(q+(sz-1))]))
+ out[(p+p+(sz-1))/2,(q+q+(sz-1))/2]-outrow}}
+ out}
Noting that median is probably the rate-limiting factor, I looked
for another way to get the middle of 9 items. Using order seem faster:
system.time( replicate(10, x2s - sort(x2)))
user system elapsed
9.829 0.212 10.029
system.time( replicate(10, x2m - median(x2)))
user system elapsed
7.169 0.126 7.272
system.time( replicate(10, x2s -x2[order(x2)[5] ]))
user system elapsed
1.907 0.051 1.960
So see if this is any faster. On my system it's about three times
faster:
x - matrix(sample(364*364), 364,364)
out - matrix(0, 364,364)
for(xi in 1:(nrow(x)-2)) {
for(yi in 1:(ncol(x)-2) ) {
xm - x[xi+0:2, yi+0:2]
d[xi+1, yi+1] -xm[order(xm)[5] ]}}
#-tests --
system.time(for(xi in 1:(nrow(x)-2)) {
+ for(yi in 1:(ncol(x)-2) ) {
+ xm - x[xi+0:2, yi+0:2]
+ d[xi+1, yi+1] -xm[order(xm)[5] ]}} )
user system elapsed
3.806 0.083 3.887
system.time(MedFilter(x,3) )
user system elapsed
11.242 0.202 11.427
MedFilter(x,3)
[,1] [,2] [,3] [,4] [,5]
[1,]00000
[2,]08 12 140
[3,]0 12 14 190
[4,]0 18 15 200
[5,]00000
Example to getting value 8 and 12 as below:
7 8 30 8 30 29
4 6 12 (median=8) 6 12 5 (median=12)
25 3 22 3 22 14
Even the script can give output. However, it is too slow. My image
size is
364*364. It is time consumption. Is it get other ways to improving it?
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Asking Favor For the Script of Median Filter
On Mar 27, 2011, at 1:07 PM, Mike Marchywka wrote:
You obviously want to delegate inner loops to R packages that
execute as native, hopefully optimized, code.
Generally a google search that starts with R CRAN will help.
In this case it looks like a few packages available,
http://www.google.com/search?sclient=psyhl=enq=R+cran+median+filter
Did you find any that include a 2D median filter? All the ones I
looked at were for univariate data.
--
David.
Date: Sun, 27 Mar 2011 07:56:11 -0700
From: chuan...@hotmail.com
To: r-help@r-project.org
Subject: [R] Asking Favor For the Script of Median Filter
Hello,everybody. My name is Chuan Zun Liang. I come from Malaysia.
I am just
a beginner for R. Kindly to ask favor about median filter. The
problem I
facing as below:
x-matrix(sample(1:30,25),5,5)
x
[,1] [,2] [,3] [,4] [,5]
[1,] 7 8 30 29 13
[2,] 4 6 12 5 9
[3,] 25 3 22 14 24
[4,] 2 15 26 23 19
[5,] 28 18 10 11 20
This is example original matrices of an image. I want apply with
median
filter with window size 3X# to remove salt and pepper noise in my
matric.
Here are the script I attend to writing.The script and output
shown as
below:
MedFilter-function(mat,sz)
+ {out-matrix(0,nrow(mat),ncol(mat))
+ for(p in 1:(nrow(mat)-(sz-1)))
+ {for(q in 1:(ncol(mat)-(sz-1)))
+ {outrow-median(as.vector(mat[p:(p+(sz-1)),q:(q+(sz-1))]))
+ out[(p+p+(sz-1))/2,(q+q+(sz-1))/2]-outrow}}
+ out}
MedFilter(x,3)
[,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 8 12 14 0
[3,] 0 12 14 19 0
[4,] 0 18 15 20 0
[5,] 0 0 0 0 0
Example to getting value 8 and 12 as below:
7 8 30 8 30 29
4 6 12 (median=8) 6 12 5 (median=12)
25 3 22 3 22 14
Even the script can give output. However, it is too slow. My image
size is
364*364. It is time consumption. Is it get other ways to improving
it?
Best Wishes
Chuan
--
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Asking Favor For the Script of Median Filter
?runmed
-- Bert
On Sun, Mar 27, 2011 at 2:44 PM, David Winsemius dwinsem...@comcast.net wrote:
On Mar 27, 2011, at 10:56 AM, chuan_zl wrote:
Hello,everybody. My name is Chuan Zun Liang. I come from Malaysia. I am
just
a beginner for R. Kindly to ask favor about median filter. The problem I
facing as below:
x-matrix(sample(1:30,25),5,5)
x
[,1] [,2] [,3] [,4] [,5]
[1,] 7 8 30 29 13
[2,] 4 6 12 5 9
[3,] 25 3 22 14 24
[4,] 2 15 26 23 19
[5,] 28 18 10 11 20
This is example original matrices of an image. I want apply with median
filter with window size 3X# to remove salt and pepper noise in my matric.
Here are the script I attend to writing.The script and output shown as
below:
MedFilter-function(mat,sz)
+ {out-matrix(0,nrow(mat),ncol(mat))
+ for(p in 1:(nrow(mat)-(sz-1)))
+ {for(q in 1:(ncol(mat)-(sz-1)))
+ {outrow-median(as.vector(mat[p:(p+(sz-1)),q:(q+(sz-1))]))
+ out[(p+p+(sz-1))/2,(q+q+(sz-1))/2]-outrow}}
+ out}
Noting that median is probably the rate-limiting factor, I looked for
another way to get the middle of 9 items. Using order seem faster:
system.time( replicate(10, x2s - sort(x2)))
user system elapsed
9.829 0.212 10.029
system.time( replicate(10, x2m - median(x2)))
user system elapsed
7.169 0.126 7.272
system.time( replicate(10, x2s -x2[order(x2)[5] ]))
user system elapsed
1.907 0.051 1.960
So see if this is any faster. On my system it's about three times faster:
x - matrix(sample(364*364), 364,364)
out - matrix(0, 364,364)
for(xi in 1:(nrow(x)-2)) {
for(yi in 1:(ncol(x)-2) ) {
xm - x[xi+0:2, yi+0:2]
d[xi+1, yi+1] -xm[order(xm)[5] ]}}
#-tests --
system.time(for(xi in 1:(nrow(x)-2)) {
+ for(yi in 1:(ncol(x)-2) ) {
+ xm - x[xi+0:2, yi+0:2]
+ d[xi+1, yi+1] -xm[order(xm)[5] ]}} )
user system elapsed
3.806 0.083 3.887
system.time(MedFilter(x,3) )
user system elapsed
11.242 0.202 11.427
MedFilter(x,3)
[,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 8 12 14 0
[3,] 0 12 14 19 0
[4,] 0 18 15 20 0
[5,] 0 0 0 0 0
Example to getting value 8 and 12 as below:
7 8 30 8 30 29
4 6 12 (median=8) 6 12 5 (median=12)
25 3 22 3 22 14
Even the script can give output. However, it is too slow. My image size is
364*364. It is time consumption. Is it get other ways to improving it?
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Asking Favor For the Script of Median Filter
Oops. My error! You wanted a 2D filter.
I suspect a search will find some implementation, but you may wish to consider
?loess instead (there are numerous others, no doubt).
-- Bert
On Sun, Mar 27, 2011 at 3:30 PM, David Winsemius dwinsem...@comcast.net wrote:
On Mar 27, 2011, at 1:07 PM, Mike Marchywka wrote:
You obviously want to delegate inner loops to R packages that
execute as native, hopefully optimized, code.
Generally a google search that starts with R CRAN will help.
In this case it looks like a few packages available,
http://www.google.com/search?sclient=psyhl=enq=R+cran+median+filter
Did you find any that include a 2D median filter? All the ones I looked at
were for univariate data.
--
David.
Date: Sun, 27 Mar 2011 07:56:11 -0700
From: chuan...@hotmail.com
To: r-help@r-project.org
Subject: [R] Asking Favor For the Script of Median Filter
Hello,everybody. My name is Chuan Zun Liang. I come from Malaysia. I am
just
a beginner for R. Kindly to ask favor about median filter. The problem I
facing as below:
x-matrix(sample(1:30,25),5,5)
x
[,1] [,2] [,3] [,4] [,5]
[1,] 7 8 30 29 13
[2,] 4 6 12 5 9
[3,] 25 3 22 14 24
[4,] 2 15 26 23 19
[5,] 28 18 10 11 20
This is example original matrices of an image. I want apply with median
filter with window size 3X# to remove salt and pepper noise in my
matric.
Here are the script I attend to writing.The script and output shown as
below:
MedFilter-function(mat,sz)
+ {out-matrix(0,nrow(mat),ncol(mat))
+ for(p in 1:(nrow(mat)-(sz-1)))
+ {for(q in 1:(ncol(mat)-(sz-1)))
+ {outrow-median(as.vector(mat[p:(p+(sz-1)),q:(q+(sz-1))]))
+ out[(p+p+(sz-1))/2,(q+q+(sz-1))/2]-outrow}}
+ out}
MedFilter(x,3)
[,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 8 12 14 0
[3,] 0 12 14 19 0
[4,] 0 18 15 20 0
[5,] 0 0 0 0 0
Example to getting value 8 and 12 as below:
7 8 30 8 30 29
4 6 12 (median=8) 6 12 5 (median=12)
25 3 22 3 22 14
Even the script can give output. However, it is too slow. My image size
is
364*364. It is time consumption. Is it get other ways to improving it?
Best Wishes
Chuan
--
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Asking Favor For the Script of Median Filter
CC: chuan...@hotmail.com; r-help@r-project.org From: dwinsem...@comcast.net To: marchy...@hotmail.com Subject: Re: [R] Asking Favor For the Script of Median Filter Date: Sun, 27 Mar 2011 18:30:48 -0400 On Mar 27, 2011, at 1:07 PM, Mike Marchywka wrote: You obviously want to delegate inner loops to R packages that execute as native, hopefully optimized, code. Generally a google search that starts with R CRAN will help. In this case it looks like a few packages available, http://www.google.com/search?sclient=psyhl=enq=R+cran+median+filter Did you find any that include a 2D median filter? All the ones I looked at were for univariate data. I put almost zero thought or effort into that but an interested party could modify the words a bit and and, for example image and one of the first interesting hits is this, http://cran.r-project.org/web/packages/biOps/biOps.pdf x - readJpeg(system.file(samples, violet.jpg, package=biOps)) y - imgBlockMedianFilter(x, 5) -- David. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
