| title | output | ||||
|---|---|---|---|---|---|
Reading from Petrel |
|
Convert the sparse matrix representation of coordinates in a GRDECL file to a matrix of n rows and 10 columns in R.
library(dplyr)
# read the Petrel/Eclipse file. Assign it to tbl object
tbl <- read.csv("wellRegion.GRDECL", skip = 1, header = FALSE,
stringsAsFactors = FALSE, strip.white = TRUE)
head(tbl)
#> V1
#> 1 25*0 5*47 83*0 34 34 13*47 69*0 12*34 16*47 65*0 13*34 17*47 63*0 14*34 17*47 63*0 14*34 17*47 63*0 15*34 16*47 63*0 34 34 34 34
#> 2 10*34 17*47 63*0 15*34 16*47 63*0 15*34 15*47 64*0 15*34 14*47 6*37 59*0 15*34 22 22 22 22 6*47 5*23 6*37 59*0 13*34 22 22 22 22
#> 3 5*22 7*23 10*37 55*0 11*34 31 31 9*22 6*23 11*37 55*0 7*34 6*31 8*22 7*23 13*37 54*0 34 34 34 34 8*31 8*22 7*23 13*37 55*0 31 31
#> 4 10*31 7*22 23 23 23 26 23 23 23 13*37 55*0 12*31 6*22 23 23 23 23 26 26 23 23 13*37 55*0 12*31 6*22 23 23 23 23 26 26 26 26 37 37
#> 5 11*37 55*0 12*31 5*22 5*23 26 26 26 13*37 21 21 54*0 13*31 22 22 22 22 8*23 12*37 21 21 21 21 53*0 13*31 22 22 22 27 27 23 23 23
#> 6 23 23 23 23 10*37 6*21 54*0 11*31 45 45 24 24 27 27 27 24 24 24 24 23 23 9*37 8*21 53*0 9*31 5*45 24 27 27 27 6*24 7*41 21 21 21
tail(tbl)
#> V1
#> 1412 13 13 7*6 10*53 14*55 30*0 42 42 42 42 14*43 10*15 13 13 13 10*6 9*53 13*55 31*0 42 42 16*43 5*15 5*28 14*6 8*53 12*55 34*0 43 43
#> 1413 14*43 15 15 8*28 14*6 8*53 11*55 34*0 18*43 9*28 15*6 7*53 10*55 35*0 18*43 8*28 17*6 5*53 12*46 34*0 18*43 28 28 28 28 50 50 50
#> 1414 50 50 50 15*6 0 0 0 0 14*46 34*0 17*43 13*50 12*6 0 0 0 16*46 33*0 17*43 14*50 10*6 0 0 0 0 16*46 33*0 17*43 15*50 9*6 0 0 0 46 46
#> 1415 16*46 33*0 16*43 17*50 6*6 0 0 0 0 18*46 33*0 15*43 20*50 6 6 6 0 0 0 0 20*46 33*0 14*43 0 20*50 6*0 20*46 34*0 11*43 0 0 0 50 50
#> 1416 17*50 7*0 20*46 36*0 8*43 5*0 18*50 7*0 20*46 50*0 16*50 8*0 20*46 51*0 14*50 9*0 20*46 52*0 12*50 11*0 19*46 54*0 8*50 14*0 46 46
#> 1417 15*46 78*0 16*46 78*0 15*46 80*0 13*46 83*0 9*46 87*0 5*46 667*0 /# dimensions of the dataframe
dim(tbl)
#> [1] 1417 1# convert string to character vectors.
alist_vectors <- lapply(tbl$V1, function(x) unlist(strsplit(x, " ")))
alist_vectors[[1]] # show a sample
#> [1] "25*0" "5*47" "83*0" "34" "34" "13*47" "69*0" "12*34"
#> [9] "16*47" "65*0" "13*34" "17*47" "63*0" "14*34" "17*47" "63*0"
#> [17] "14*34" "17*47" "63*0" "15*34" "16*47" "63*0" "34" "34"
#> [25] "34" "34"# number of rows in the list
length(alist_vectors)
#> [1] 1417# show the number of elements in each row
len_str <- unlist(lapply(tbl$V1, function(x)
length(unlist(strsplit(trimws(x), " ")))))
head(len_str)
#> [1] 26 27 28 35 33 35
tail(len_str)
#> [1] 30 28 35 34 26 13
length(len_str) # total number of rows in the file
#> [1] 1417# extract row and values for all the strings in the file
# including numbers without the asterisk
all_df <- data.frame()
invisible(lapply(seq_along(alist_vectors), function(x) {
r <- data.frame(row=x, value=alist_vectors[[x]], stringsAsFactors = FALSE)
all_df <<- rbind(all_df, r)
}))
tibble::as_tibble(all_df)
#> # A tibble: 44,610 x 2
#> row value
#> <int> <chr>
#> 1 1 25*0
#> 2 1 5*47
#> 3 1 83*0
#> 4 1 34
#> 5 1 34
#> 6 1 13*47
#> 7 1 69*0
#> 8 1 12*34
#> 9 1 16*47
#> 10 1 65*0
#> # … with 44,600 more rows# dimensions of the dataframe
dim(all_df)
#> [1] 44610 2# example
# we provide a sample of what will results if we apply grep/grepl
# the asterisk in between numbers is accepted as valied with regex "\\d"
grep("\\d", c("10*5", "34", "7*7", "/", "3*5", "*", "\\", "-", "\\."), value = TRUE)
#> [1] "10*5" "34" "7*7" "3*5"# we proceed to remove extraneous characters from the value variable
all_df %>%
filter(grepl("\\d", value)) %>%
as_tibble() %>%
print() -> all_df
#> # A tibble: 44,609 x 2
#> row value
#> <int> <chr>
#> 1 1 25*0
#> 2 1 5*47
#> 3 1 83*0
#> 4 1 34
#> 5 1 34
#> 6 1 13*47
#> 7 1 69*0
#> 8 1 12*34
#> 9 1 16*47
#> 10 1 65*0
#> # … with 44,599 more rows# dimensions of the dataframe
dim(all_df)
#> [1] 44609 2Notice that a row has been removed from the GRDECL file. If you go to the raw data file you will see that the end character in the files is "\". That characters has been removed.
all_df1 <-
all_df %>%
mutate(A = as.integer(gsub("\\*.*", "", value))) %>% # extract the part on the left
mutate(B = as.integer(gsub("(^[0-9]{1,2}|.*\\*)", "", value))) %>% # part on the right
rowwise() %>% # operate on the row
mutate(C = ifelse(!is.na(B), list(rep(B, A)), A)) %>% # when B is not NA
as_tibble() %>%
print()
#> # A tibble: 44,609 x 5
#> row value A B C
#> <int> <chr> <int> <int> <list>
#> 1 1 25*0 25 0 <int [25]>
#> 2 1 5*47 5 47 <int [5]>
#> 3 1 83*0 83 0 <int [83]>
#> 4 1 34 34 NA <int [1]>
#> 5 1 34 34 NA <int [1]>
#> 6 1 13*47 13 47 <int [13]>
#> 7 1 69*0 69 0 <int [69]>
#> 8 1 12*34 12 34 <int [12]>
#> 9 1 16*47 16 47 <int [16]>
#> 10 1 65*0 65 0 <int [65]>
#> # … with 44,599 more rowsVariable C has vectors for each of the parsed strings in value.
Verifying from the file for the first 9 rows:
1 25*0
2 5*47
3 83*0
4 34
5 34
6 13*47
7 69*0
8 12*34
9 16*47
Corresponds to the follwoing matrix:
matrix(c(
all_df1$C[[1]], # 1 25*0
all_df1$C[[2]], # 2 5*47
all_df1$C[[3]], # 3 83*0
all_df1$C[[4]], # 4 34
all_df1$C[[5]], # 5 34
all_df1$C[[6]], # 6 13*47
all_df1$C[[7]], # 7 69*0
all_df1$C[[8]], # 8 12*34
all_df1$C[[9]] # 9 16*47
), ncol=10, byrow = TRUE)
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 47 47 47 47 47
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [5,] 0 0 0 0 0 0 0 0 0 0
#> [6,] 0 0 0 0 0 0 0 0 0 0
#> [7,] 0 0 0 0 0 0 0 0 0 0
#> [8,] 0 0 0 0 0 0 0 0 0 0
#> [9,] 0 0 0 0 0 0 0 0 0 0
#> [10,] 0 0 0 0 0 0 0 0 0 0
#> [11,] 0 0 0 0 0 0 0 0 0 0
#> [12,] 0 0 0 34 34 47 47 47 47 47
#> [13,] 47 47 47 47 47 47 47 47 0 0
#> [14,] 0 0 0 0 0 0 0 0 0 0
#> [15,] 0 0 0 0 0 0 0 0 0 0
#> [16,] 0 0 0 0 0 0 0 0 0 0
#> [17,] 0 0 0 0 0 0 0 0 0 0
#> [18,] 0 0 0 0 0 0 0 0 0 0
#> [19,] 0 0 0 0 0 0 0 0 0 0
#> [20,] 0 0 0 0 0 0 0 34 34 34
#> [21,] 34 34 34 34 34 34 34 34 34 47
#> [22,] 47 47 47 47 47 47 47 47 47 47
#> [23,] 47 47 47 47 47 0 0 0 0 0sa <- sapply(all_df1$C, c) # dataframe var to list of vectors
m <- matrix(unlist(sa), ncol=10, byrow=TRUE) # list of vectors to matrix. 10 cols
dim(m) # dimensions of the matrix
#> [1] 45675 10m[1, ]
#> [1] 0 0 0 0 0 0 0 0 0 0m[3, ]
#> [1] 0 0 0 0 0 47 47 47 47 47m[21, ]
#> [1] 34 34 34 34 34 34 34 34 34 47m[nrow(m),]
#> [1] 0 0 0 0 0 0 0 0 0 0m[nrow(m):(nrow(m)-100),]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [5,] 0 0 0 0 0 0 0 0 0 0
#> [6,] 0 0 0 0 0 0 0 0 0 0
#> [7,] 0 0 0 0 0 0 0 0 0 0
#> [8,] 0 0 0 0 0 0 0 0 0 0
#> [9,] 0 0 0 0 0 0 0 0 0 0
#> [10,] 0 0 0 0 0 0 0 0 0 0
#> [11,] 0 0 0 0 0 0 0 0 0 0
#> [12,] 0 0 0 0 0 0 0 0 0 0
#> [13,] 0 0 0 0 0 0 0 0 0 0
#> [14,] 0 0 0 0 0 0 0 0 0 0
#> [15,] 0 0 0 0 0 0 0 0 0 0
#> [16,] 0 0 0 0 0 0 0 0 0 0
#> [17,] 0 0 0 0 0 0 0 0 0 0
#> [18,] 0 0 0 0 0 0 0 0 0 0
#> [19,] 0 0 0 0 0 0 0 0 0 0
#> [20,] 0 0 0 0 0 0 0 0 0 0
#> [21,] 0 0 0 0 0 0 0 0 0 0
#> [22,] 0 0 0 0 0 0 0 0 0 0
#> [23,] 0 0 0 0 0 0 0 0 0 0
#> [24,] 0 0 0 0 0 0 0 0 0 0
#> [25,] 0 0 0 0 0 0 0 0 0 0
#> [26,] 0 0 0 0 0 0 0 0 0 0
#> [27,] 0 0 0 0 0 0 0 0 0 0
#> [28,] 0 0 0 0 0 0 0 0 0 0
#> [29,] 0 0 0 0 0 0 0 0 0 0
#> [30,] 0 0 0 0 0 0 0 0 0 0
#> [31,] 0 0 0 0 0 0 0 0 0 0
#> [32,] 0 0 0 0 0 0 0 0 0 0
#> [33,] 0 0 0 0 0 0 0 0 0 0
#> [34,] 0 0 0 0 0 0 0 0 0 0
#> [35,] 0 0 0 0 0 0 0 0 0 0
#> [36,] 0 0 0 0 0 0 0 0 0 0
#> [37,] 0 0 0 0 0 0 0 0 0 0
#> [38,] 0 0 0 0 0 0 0 0 0 0
#> [39,] 0 0 0 0 0 0 0 0 0 0
#> [40,] 0 0 0 0 0 0 0 0 0 0
#> [41,] 0 0 0 0 0 0 0 0 0 0
#> [42,] 0 0 0 0 0 0 0 0 0 0
#> [43,] 0 0 0 0 0 0 0 0 0 0
#> [44,] 0 0 0 0 0 0 0 0 0 0
#> [45,] 0 0 0 0 0 0 0 0 0 0
#> [46,] 0 0 0 0 0 0 0 0 0 0
#> [47,] 0 0 0 0 0 0 0 0 0 0
#> [48,] 0 0 0 0 0 0 0 0 0 0
#> [49,] 0 0 0 0 0 0 0 0 0 0
#> [50,] 0 0 0 0 0 0 0 0 0 0
#> [51,] 0 0 0 0 0 0 0 0 0 0
#> [52,] 0 0 0 0 0 0 0 0 0 0
#> [53,] 0 0 0 0 0 0 0 0 0 0
#> [54,] 0 0 0 0 0 0 0 0 0 0
#> [55,] 0 0 0 0 0 0 0 0 0 0
#> [56,] 0 0 0 0 0 0 0 0 0 0
#> [57,] 0 0 0 0 0 0 0 0 0 0
#> [58,] 0 0 0 0 0 0 0 0 0 0
#> [59,] 0 0 0 0 0 0 0 0 0 0
#> [60,] 0 0 0 0 0 0 0 0 0 0
#> [61,] 0 0 0 0 0 0 0 0 0 0
#> [62,] 0 0 0 0 0 0 0 0 0 0
#> [63,] 0 0 0 0 0 0 0 0 0 0
#> [64,] 0 0 0 0 0 0 0 0 0 0
#> [65,] 0 0 0 0 0 0 0 0 0 0
#> [66,] 0 0 0 0 0 0 0 0 0 0
#> [67,] 0 0 0 0 0 0 0 0 0 0
#> [68,] 0 0 0 0 46 46 46 46 46 0
#> [69,] 0 0 0 0 0 0 0 0 0 0
#> [70,] 0 0 0 0 0 0 0 0 0 0
#> [71,] 0 0 0 0 0 0 0 0 0 0
#> [72,] 0 0 0 0 0 0 0 0 0 0
#> [73,] 0 0 0 0 0 0 0 0 0 0
#> [74,] 0 0 0 0 0 0 0 0 0 0
#> [75,] 0 0 0 0 0 0 0 0 0 0
#> [76,] 0 0 0 0 0 0 0 0 0 0
#> [77,] 46 46 46 46 46 46 46 0 0 0
#> [78,] 0 0 0 0 0 0 0 0 46 46
#> [79,] 0 0 0 0 0 0 0 0 0 0
#> [80,] 0 0 0 0 0 0 0 0 0 0
#> [81,] 0 0 0 0 0 0 0 0 0 0
#> [82,] 0 0 0 0 0 0 0 0 0 0
#> [83,] 0 0 0 0 0 0 0 0 0 0
#> [84,] 0 0 0 0 0 0 0 0 0 0
#> [85,] 0 0 0 0 0 0 0 0 0 0
#> [86,] 46 46 46 46 46 0 0 0 0 0
#> [87,] 0 0 46 46 46 46 46 46 46 46
#> [88,] 0 0 0 0 0 0 0 0 0 0
#> [89,] 0 0 0 0 0 0 0 0 0 0
#> [90,] 0 0 0 0 0 0 0 0 0 0
#> [91,] 0 0 0 0 0 0 0 0 0 0
#> [92,] 0 0 0 0 0 0 0 0 0 0
#> [93,] 0 0 0 0 0 0 0 0 0 0
#> [94,] 0 0 0 0 0 0 0 0 0 0
#> [95,] 46 46 0 0 0 0 0 0 0 0
#> [96,] 46 46 46 46 46 46 46 46 46 46
#> [97,] 0 0 0 0 0 0 0 46 46 46
#> [98,] 0 0 0 0 0 0 0 0 0 0
#> [99,] 0 0 0 0 0 0 0 0 0 0
#> [100,] 0 0 0 0 0 0 0 0 0 0
#> [101,] 0 0 0 0 0 0 0 0 0 0Finally we convert the dense matrix to a sparse matrix.
library(Matrix)
ms <- Matrix(m, sparse = TRUE)
ms[1:50,]
#> 50 x 10 sparse Matrix of class "dgCMatrix"
#>
#> [1,] . . . . . . . . . .
#> [2,] . . . . . . . . . .
#> [3,] . . . . . 47 47 47 47 47
#> [4,] . . . . . . . . . .
#> [5,] . . . . . . . . . .
#> [6,] . . . . . . . . . .
#> [7,] . . . . . . . . . .
#> [8,] . . . . . . . . . .
#> [9,] . . . . . . . . . .
#> [10,] . . . . . . . . . .
#> [11,] . . . . . . . . . .
#> [12,] . . . 34 34 47 47 47 47 47
#> [13,] 47 47 47 47 47 47 47 47 . .
#> [14,] . . . . . . . . . .
#> [15,] . . . . . . . . . .
#> [16,] . . . . . . . . . .
#> [17,] . . . . . . . . . .
#> [18,] . . . . . . . . . .
#> [19,] . . . . . . . . . .
#> [20,] . . . . . . . 34 34 34
#> [21,] 34 34 34 34 34 34 34 34 34 47
#> [22,] 47 47 47 47 47 47 47 47 47 47
#> [23,] 47 47 47 47 47 . . . . .
#> [24,] . . . . . . . . . .
#> [25,] . . . . . . . . . .
#> [26,] . . . . . . . . . .
#> [27,] . . . . . . . . . .
#> [28,] . . . . . . . . . .
#> [29,] . . . . . . . . . .
#> [30,] 34 34 34 34 34 34 34 34 34 34
#> [31,] 34 34 34 47 47 47 47 47 47 47
#> [32,] 47 47 47 47 47 47 47 47 47 47
#> [33,] . . . . . . . . . .
#> [34,] . . . . . . . . . .
#> [35,] . . . . . . . . . .
#> [36,] . . . . . . . . . .
#> [37,] . . . . . . . . . .
#> [38,] . . . . . . . . . .
#> [39,] . . . 34 34 34 34 34 34 34
#> [40,] 34 34 34 34 34 34 34 47 47 47
#> [41,] 47 47 47 47 47 47 47 47 47 47
#> [42,] 47 47 47 47 . . . . . .
#> [43,] . . . . . . . . . .
#> [44,] . . . . . . . . . .
#> [45,] . . . . . . . . . .
#> [46,] . . . . . . . . . .
#> [47,] . . . . . . . . . .
#> [48,] . . . . . . . 34 34 34
#> [49,] 34 34 34 34 34 34 34 34 34 34
#> [50,] 34 47 47 47 47 47 47 47 47 47dim(ms)
#> [1] 45675 10