moore updated with extra question

mendeley.rb

@@ -537,6 +537,7 @@ def render(context)
       category = m.folder_documents(@category, 1, 10000)  # max of 10000 items, should get max from all_categories[]['size']
 #      category = m.folder_documents("56626111",1, 10)
 
+      file = @category + "_library.json" 
 
       if !File.exist?("library.json") 
         doc_ids = JSON.parse(category.body)["document_ids"]
@@ -548,12 +549,12 @@ def render(context)
         end
         ## Sort everything in the library by date added
         library = library.sort_by { |k| k["date_added"] }
-        # Write out 
-        File.open("library.json","w") do |f|
+        # Write out
+        File.open(file, "w") do |f|
             f.write(JSON.pretty_generate(library))
         end
       else 
-        buffer = open('library.json')
+        buffer = open(file)
         library = JSON.load(buffer) 
       end 
 

moore.Rmd

@@ -18,7 +18,7 @@ j <- sample(1:dim(M)[2], 1)  # another random number between 1 and 8
 
 And then grab all the points in the Moore neighborhood 
 
-```
+```{r}
 r <- 1
 neighborhood <- 
 cbind(c(i-r, i,   i+r, i-r, i,  i+r,  i-r, i,   i+r),
@@ -40,9 +40,9 @@ wrapped_neighborhood[,2] <- (neighborhood[,2] - 1) %% dim(M)[2] + 1
 ```
 
 
-Clearly this can be extended to $r > 1$. 
+This can be extended to $r > 1$. 
 
-```
+```{r}
 r_max <- 3
 rows <- numeric(0)
 cols <- numeric(0)
@@ -61,7 +61,35 @@ Once again we have to deal with boundary cases, e.g. wrapping as before:
 wrapped_neighborhood <- neighborhood
 wrapped_neighborhood[,1] <- (neighborhood[,1] - 1) %% dim(M)[1] + 1
 wrapped_neighborhood[,2] <- (neighborhood[,2] - 1) %% dim(M)[2] + 1
+```
+
 
 
+What if we wanted to wrap just the neighborhood if we hit the boundary?
+
+```{r}
+r_max <- 3
+rows <- numeric(0)
+cols <- numeric(0)
+
+wrap <- function(i, r, n){
+ if(i-r < 0)
+   out <- i+r+1
+ if(i+r > n)
+   out <- i-r-1
+ out
+}
+
+for(r in 1:r_max){
+ rows <- c(rows, c(i-r, i,   i+r, i-r, i,  i+r,  i-r, i,   i+r))
+ cols <- c(cols, c(j-r, j-r, j-r, j,   j,  j,    j+r, j+r, j+r))
+ rows <- wrap(rows, i, r, dim(M)[1])
+ cols <- wrap(cols, j, r, dim(M)[2])
+} 
+
+neighborhood <- cbind(rows, cols)
+```
+
 
+Note that this does not handle the case of a neighborhood that is larger than the matrix in some dimension; e.g. we don't guarentee $i+r+1<n$, etc.  
 

moore.md

@@ -21,13 +21,14 @@ j <- sample(1:dim(M)[2], 1)  # another random number between 1 and 8
 
 And then grab all the points in the Moore neighborhood 
 
-```
+
+```r
 r <- 1
-neighborhood <- 
-cbind(c(i-r, i,   i+r, i-r, i,  i+r,  i-r, i,   i+r),
-      c(j-r, j-r, j-r, j,   j,  j,    j+r, j+r, j+r))
+neighborhood <- cbind(c(i - r, i, i + r, i - r, i, i + r, i - r, i, i + r), 
+    c(j - r, j - r, j - r, j, j, j, j + r, j + r, j + r))
 ```
 
+
 We can then access the cells from M in our neighborhood.  We tell R to display these points as a matrix 
 
 
@@ -36,7 +37,10 @@ matrix(M[neighborhood], nrow = 3)
 ```
 
 ```
-## Error: object 'neighborhood' not found
+##         [,1]     [,2]     [,3]
+## [1,] -1.5540  0.69641  0.37012
+## [2,] -0.7645 -0.23802 -1.65624
+## [3,] -0.1179  0.03133  0.03626
 ```
 
 
@@ -45,48 +49,75 @@ matrix(M[neighborhood], nrow = 3)
 
 ```r
 wrapped_neighborhood <- neighborhood
+wrapped_neighborhood[, 1] <- (neighborhood[, 1] - 1)%%dim(M)[1] + 1
+wrapped_neighborhood[, 2] <- (neighborhood[, 2] - 1)%%dim(M)[2] + 1
 ```
 
-```
-## Error: object 'neighborhood' not found
-```
+
+
+This can be extended to $r > 1$. 
+
 
 ```r
-wrapped_neighborhood[, 1] <- (neighborhood[, 1] - 1)%%dim(M)[1] + 1
-```
+r_max <- 3
+rows <- numeric(0)
+cols <- numeric(0)
 
+for (r in 1:r_max) {
+    rows <- c(rows, c(i - r, i, i + r, i - r, i, i + r, i - r, i, i + r))
+    cols <- c(cols, c(j - r, j - r, j - r, j, j, j, j + r, j + r, j + r))
+}
+
+neighborhood <- cbind(rows, cols)
 ```
-## Error: object 'neighborhood' not found
-```
+
+
+Once again we have to deal with boundary cases, e.g. wrapping as before:  
+
 
 ```r
+wrapped_neighborhood <- neighborhood
+wrapped_neighborhood[, 1] <- (neighborhood[, 1] - 1)%%dim(M)[1] + 1
 wrapped_neighborhood[, 2] <- (neighborhood[, 2] - 1)%%dim(M)[2] + 1
 ```
 
-```
-## Error: object 'neighborhood' not found
-```
 
 
 
-Clearly this can be extended to $r > 1$. 
+What if we wanted to wrap just the neighborhood if we hit the boundary?
 
-```
+
+```r
 r_max <- 3
 rows <- numeric(0)
 cols <- numeric(0)
 
-for(r in 1:r_max){
- rows <- c(rows, c(i-r, i,   i+r, i-r, i,  i+r,  i-r, i,   i+r))
- cols <- c(cols, c(j-r, j-r, j-r, j,   j,  j,    j+r, j+r, j+r))
-} 
+wrap <- function(i, r, n) {
+    if (i - r < 0) 
+        out <- i + r + 1
+    if (i + r > n) 
+        out <- i - r - 1
+    out
+}
 
-neighborhood <- cbind(rows, cols)
+for (r in 1:r_max) {
+    rows <- c(rows, c(i - r, i, i + r, i - r, i, i + r, i - r, i, i + r))
+    cols <- c(cols, c(j - r, j - r, j - r, j, j, j, j + r, j + r, j + r))
+    rows <- wrap(rows, i, r, dim(M)[1])
+    cols <- wrap(cols, j, r, dim(M)[2])
+}
 ```
 
+```
+## Error: unused argument (dim(M)[1])
+```
 
+```r
 
+neighborhood <- cbind(rows, cols)
+```
 
 
 
+Note that this does not handle the case of a neighborhood that is larger than the matrix in some dimension; e.g. we don't guarentee $i+r+1<n$, etc.