| Type: | Package |
| Title: | Density Profiles of Wood from CT Scan Images |
| Version: | 0.1.0 |
| Maintainer: | Robert Schneider <robert_schneider@uqar.ca> |
| Description: | Computerized tomography (CT) can be used to assess certain wood properties when wood disks or logs are scanned. Wood density profiles (i.e. variations of wood density from pith to bark) can yield important information used for studies in forest resource assessment, wood quality and dendrochronology studies. The first step consists in transforming grey values from the scan images to density values. The packages then proposes a unique method to automatically locate the pith by combining an adapted Hough Transform method and a one-dimensional edge detector. Tree ring profiles (average ring density, earlywood and latewood density, ring width and percent latewood for each ring) are then obtained. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| Depends: | xRing, functional, oro.dicom |
| NeedsCompilation: | no |
| Packaged: | 2024-09-05 14:23:04 UTC; schnro01 |
| Author: | Dipak Mahatara [aut], Robert Schneider [cre, aut] |
| Repository: | CRAN |
| Date/Publication: | 2024-09-10 09:40:07 UTC |
Add ring to pith to bark profile from CT scan image
Description
Add ring to pith to bark profile from CT scan image
Usage
addRingFromImage(n = 1, densProfile, im)
Arguments
n |
Number of rings to add |
densProfile |
Density profile |
im |
Density matrix |
Value
Corrected density profile with new ring(s) added and blue bar in plot of added ring
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
image_info <- getImageInfo(hdr = hdr_df)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens,
n_segments = 12,
pixel = TRUE,
toPlot = FALSE)
endPath <- c(472, 284)
densPath <- extractProfile(im_dens,
image_info,
pith_coord,
endPath,
k = 2, r = 5,
threshold = 0.002)
newPath2 <- addRingFromImage(n = 1, densPath, im_dens)
Add ring to pith to bark profile from profile plot
Description
Add ring to pith to bark profile from profile plot
Usage
addRingFromProfile(n = 1, densProfile)
Arguments
n |
Number of rings to add |
densProfile |
Density profile |
Value
Corrected density profile with new ring(s) added and blue bar in plot of added ring
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
# not run - endPath <- locatePathEnd(im_dens, pith_coord) # using the image
path <- extractProfile(im_dens, image_info, pith_coord, endPath, k = 2, r = 5, threshold = 0.002)
plotProfile(path)
newPath <- addRingFromProfile(n = 1, path)
Add years to series
Description
Add years to series
Usage
addYears(lastYear, densProfile)
Arguments
lastYear |
Last year of series |
densProfile |
Density profile |
Value
Density profile with years
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
# not run - endPath <- locatePathEnd(im_dens, pith_coord) # using the image
path <- extractProfile(im_dens, image_info, pith_coord, endPath, k = 2, r = 5, threshold = 0.002)
path <- addYears(2021, path)
Calculate average wood, earlywood and latewood density for every ring
Description
Calculate average wood, earlywood and latewood density for every ring
Usage
calcAvgDens(densProfile)
Arguments
densProfile |
Density profile |
Value
List with several vectors
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
# not run - endPath <- locatePathEnd(im_dens, pith_coord) # using the image
path <- extractProfile(im_dens, image_info, pith_coord, endPath, k = 2, r = 5, threshold = 0.002)
pathEwLw <- getEwLw(path)
plotProfile(pathEwLw)
path_avgDens <- calcAvgDens(pathEwLw)
names(path_avgDens)
Verify position of ring transitions of a density profile
Description
Verify position of ring transitions of a density profile
Usage
checkProfile(profile_with_borders, totRings)
Arguments
profile_with_borders |
xRing profile with transitions between rings located |
totRings |
Total number of rings of the disk |
Value
xRing profile with corrected ring location
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
image_info <- getImageInfo(hdr = hdr_df)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens,
n_segments = 12,
pixel = TRUE,
toPlot = FALSE)
endPath <- c(472, 284)
densPath <- extractProfile(im_dens,
image_info,
pith_coord,
endPath,
k = 2, r = 5,
threshold = 0.002)
newPath <- checkProfile(densPath, 26)
Add ring to pith to bark profile from CT scan image
Description
Add ring to pith to bark profile from CT scan image
Usage
deleteRingFromImage(n = 1, densProfile, im)
Arguments
n |
Number of rings to remove |
densProfile |
Density profile |
im |
Density matrix |
Value
Corrected density profile with ring(s) removed and red bar in plot of deleted ring
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
densPath <- extractProfile(im_dens,
image_info,
pith_coord,
endPath,
k = 2, r = 5,
threshold = 0.002)
newPath2 <- addRingFromImage(n = 1, densPath, im_dens)
oldPath2 <- deleteRingFromImage(n = 1, densPath, im_dens)
Delete ring from a pith to bark profile
Description
Delete ring from a pith to bark profile
Usage
deleteRingFromProfile(n = 1, densProfile)
Arguments
n |
Number of rings to remove |
densProfile |
Density profile |
Value
Corrected density profile with ring(s) removed and red bar in plot of deleted ring
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
# not run - endPath <- locatePathEnd(im_dens, pith_coord) # using the image
densPath <- extractProfile(im_dens,
image_info,
pith_coord,
endPath,
k = 2, r = 5,
threshold = 0.002)
plotProfile(densPath)
newPath <- addRingFromProfile(n = 1, densPath)
oldPath <- deleteRingFromProfile(n = 1, newPath)
Convert to dataframe
Description
Convert to dataframe
Usage
densityDataFrame(densProfile, sampleID = "NoID", addTransitionType = FALSE)
Arguments
densProfile |
Density profile |
sampleID |
Sample ID |
addTransitionType |
add transition type to dataframe |
Value
Dataframe with cambial age, density, years, transition type
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
# not run - endPath <- locatePathEnd(im_dens, pith_coord) # using the image
path <- extractProfile(im_dens, image_info, pith_coord, endPath, k = 2, r = 5, threshold = 0.002)
pathEwLw <- getEwLw(path)
plotProfile(pathEwLw)
path_avgDens <- calcAvgDens(pathEwLw)
densityDf <- densityDataFrame(pathEwLw)
Automatically detect pith in a CT scan image
Description
Automatically detect pith in a CT scan image
Usage
detect_pith(
im,
toPlot = TRUE,
n_segments = 25,
flag = TRUE,
x_0 = 0.5,
y_0 = 0.5,
n_run_max = 15,
threshold = 0.1,
pixel = TRUE
)
Arguments
im |
Matrix of the CT scan image |
toPlot |
Boolean to plot the location of the pith on the image |
n_segments |
Number of segements used to locate pith |
flag |
FALSE if pith location is known |
x_0 |
Estimate of pith location in x |
y_0 |
Estimate of pith location in y |
n_run_max |
Maximum number of iterations |
threshold |
Thershold value for identifying ring transition points |
pixel |
If TRUE, returns x,y coordinates in pixel numbers, else FALSE returns x,y coordinates in relative values of x and y |
Value
x,y pith coordinates
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
Get profile between two points of the CTScan image matrix
Description
Get profile between two points of the CTScan image matrix
Usage
extractProfile(
im,
imHeader,
beginPath,
endPath,
r = 10,
k = 2,
threshold = 0.01
)
Arguments
im |
Density matrix |
imHeader |
image header |
beginPath |
X,Y coordinates of the start point of the path |
endPath |
X,Y coordinates of the start point of the path |
r |
Profile width |
k |
Rolling window width, integer |
threshold |
Threshold value between maximum and minimum density to establish change of ring |
Value
Density profile
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
# not run - endPath <- locatePathEnd(im_dens, pith_coord) # using the image
path <- extractProfile(im_dens, image_info, pith_coord, endPath, k = 2, r = 5, threshold = 0.002)
Establish the transition point from earlywood to latewood for a series of rings
Description
Establish the transition point from earlywood to latewood for a series of rings
Usage
getEwLw(densProfile)
Arguments
densProfile |
Density profile |
Value
xRingList with EW to LW transition points with transition type added (1: low number of points in ring; 2: inflexion point estimated by polynomial; 3: min or max are out of range; 4: inflexion point close to min or max; 5: convex-concave)
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
# not run - endPath <- locatePathEnd(im_dens, pith_coord) # using the image
path <- extractProfile(im_dens, image_info, pith_coord, endPath, k = 2, r = 5, threshold = 0.002)
pathEwLw <- getEwLw(path)
densityDf <- densityDataFrame(path)
Extract from header of CT scan image grayscale number of bits and pixel size
Description
Extract from header of CT scan image grayscale number of bits and pixel size
Usage
getImageInfo(hdr)
Arguments
hdr |
Header dataframe |
Value
List with grayscale values, and pixel size
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
getImageInfo(hdr = hdr_df)
Convert from 8bit gray scale to density
Description
Convert from 8bit gray scale to density
Usage
grayToDensity(im, a = -0.1321, b = 0.01834)
Arguments
im |
Matrix of CT scan image in 8bit gray scale |
a |
Intercept of the calibration curve |
b |
Slope of the calibration curve |
Value
Matrix of density values
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
range(im_8bit)
im_dens <- grayToDensity(im_8bit)
range(im_dens)
Convert dicom image to matrix
Description
Convert dicom image to matrix
Usage
imageToMatrix(img)
Arguments
img |
Dicom image |
Value
Matrix of image
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
dim(im)
image(im)
Get coordinates of the end of the path on a CT scan image
Description
Get coordinates of the end of the path on a CT scan image
Usage
locatePathEnd(im, pithCoord)
Arguments
im |
CT scan image |
pithCoord |
X,Y coordinates of the pith |
Value
Coordinates of the end of the path
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
# not run - endPath <- locatePathEnd(im_dens, pith_coord) # using the image
convert pith coordinates from pixels to length units
Description
convert pith coordinates from pixels to length units
Usage
pithCoordinates(pith_coord, pixel_size_x, pixel_size_y)
Arguments
pith_coord |
Pith coordinates in pixels |
pixel_size_x |
Pixel size in x |
pixel_size_y |
Pixel size in y |
Value
Pixel coordinates in length units
Plot scan image, profile path and ring limits
Description
Plot scan image, profile path and ring limits
Usage
plotImageProfile(densProfile, im)
Arguments
densProfile |
Density profile |
im |
Density matrix |
Value
Plot
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
path <- extractProfile(im_dens, image_info, pith_coord, endPath, k = 2, r = 5, threshold = 0.002)
plotProfile(path)
plotImageProfile(path, im_dens)
Plot density profile
Description
Plot density profile
Usage
plotProfile(densProfile)
Arguments
densProfile |
Density profile |
Value
Figure
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
# not run - endPath <- locatePathEnd(im_dens, pith_coord) # using the image
path <- extractProfile(im_dens, image_info, pith_coord, endPath, k = 2, r = 5, threshold = 0.002)
plotProfile(path)
Change from relative to fixed pixel coordinate system
Description
Change from relative to fixed pixel coordinate system
Usage
relToPixel(pith_coord, im)
Arguments
pith_coord |
Pith coordinates in relative space (x, y) |
im |
Density matrix |
Value
Pixel coordinates in number of pixels (x, y)
Remove the last year of a profile
Description
Remove the last year of a profile
Usage
removeLastYear(densProfile)
Arguments
densProfile |
Density profile |
Value
Density profile with the last year removed
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
endPath <- c(472, 284) # manual
# not run - endPath <- locatePathEnd(im_dens, pith_coord) # using the image
path <- extractProfile(im_dens, image_info, pith_coord, endPath, k = 2, r = 5, threshold = 0.002)
path_last_year_2021 <- addYears(2021, path)
path_last_year_2020 <- removeLastYear(path_last_year_2021)
Check if pith location is correct
Description
Check if pith location is correct
Usage
verifyPith(im, pith_coord)
Arguments
im |
Density matrix of image |
pith_coord |
Pith coordinates |
Value
Corrected pith coordinates
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
im_dens <- grayToDensity(im_8bit)
pith_coord <- detect_pith(im_dens, n_segments = 12, pixel = TRUE, toPlot = FALSE)
pith_coord_checked <- verifyPith(im_dens, pith_coord)
Convert gray scale from measured bits to 8bit
Description
Convert gray scale from measured bits to 8bit
Usage
xBitTo8Bit(im, bits)
Arguments
im |
Matrix of values in x bits |
bits |
Number of bits of the original gray scale |
Value
Matrix of gray scale values in 8bits
Examples
library(oro.dicom)
file_path <- system.file("extdata", "disk.dcm", package = "CTRing")
dcm <- readDICOM(file_path)
hdr_df <- dcm$hdr[[1]]
image_info <- getImageInfo(hdr = hdr_df)
im <- imageToMatrix(dcm$img)
range(im)
im_8bit <- xBitTo8Bit(im, image_info$grayScale)
range(im_8bit)