Package 'ForestTools'

Grey-Level Co-Occurrence Matrix

Description

Generate textural metrics using Grey-Level Co-Occurrence Matrices (GLCM). Can be applied to an entire or image or, if a coterminous raster of segments is provided, GLCM can be calculated for each segment.

Usage

glcm(image, segs = NULL, n_grey = 32, angle = c(0, 1), discretize_range = NULL)

Arguments

image	SpatRaster. A single-band raster layer from which texture is measured
segs	SpatRaster. A segmented raster. Cell values should be equal to segment numbers. If segs are not provided, GLCM will be calculated for the entire image.
n_grey	integer. Number of grey levels into which the image will be discretized
angle	integer. Angle at which GLCM will be calculated. Ex.: 'c(0,1)'
discretize_range	numeric. Vector of two values indicating the minimum and maximum input values for discretizing the image. This can be useful when processing tiles of a larger image, for which you may want to impose a consistent value range.

Value

data.frame

References

Parmar, C., Velazquez, E.R., Leijenaar, R., Jermoumi, M., Carvalho, S., Mak, R.H., Mitra, S., Shankar, B.U., Kikinis, R., Haibe-Kains, B. and Lambin, P. (2014). Robust radiomics feature quantification using semiautomatic volumetric segmentation. PloS one, 9(7)

See Also

mcws

Examples

## Not run: 
library(terra)
library(ForestTools)

chm <- rast(kootenayCHM)
image <- rast(kootenayOrtho)[[1]]

# Generate raster segments
segs <- mcws(kootenayTrees, chm, minHeight = 0.2, format = "raster")

# Get textural metrics for ortho's red band
tex <- glcm(image, segs)

## End(Not run)

---

Kootenay forest - Cut blocks

Description

Boundaries of cut blocks within a 1.5 hectare section of forest in the Kootenay mountains, in British Columbia, Canada. Each block contains trees of different levels of maturity. Overlaps with kootenayTrees, kootenayCrowns, kootenayOrtho and kootenayCHM.

Usage

kootenayBlocks

Format

Simple polygon feature collection with the following attributes:

BlockID

numerical identifier for each block

Shape_Leng

length of polygon on meters

Shape_Area

area of polygon in square meters

See Also

kootenayTrees kootenayCHM kootenayCrowns kootenayOrtho

---

Kootenay forest - Canopy height model

Description

A canopy height model of a 1.5 hectare section of forest in the Kootenay mountains, in British Columbia, Canada.

Usage

kootenayCHM

Format

PackedSpatRaster object

Cell values are equal to canopy height above ground (in meters)

Source

Data acquired from a photogrammetric drone survey performed by Spire Aerobotics on June 16th, 2016.

See Also

kootenayTrees kootenayBlocks kootenayCrowns kootenayOrtho

---

Kootenay forest - Tree crowns

Description

Outlines of tree crowns corresponding to the kootenayTrees treetops. Generated using mcws.

Usage

kootenayCrowns

Format

Simple polygon feature collection with the following attributes:

height

height of the tree's apex, in meters above ground. Inherited from kootenayTrees.

winRadius

radius of the moving window at the treetop's location. Inherited from kootenayTrees.

crownArea

area of crown outline in square meters

See Also

kootenayTrees kootenayCHM kootenayBlocks kootenayOrtho

---

Kootenay forest - Orthomosaic

Description

An orthomosaic of a 1.5 hectare section of forest in the Kootenay mountains, in British Columbia, Canada.

Usage

kootenayOrtho

Format

PackedSpatRaster object

Cell values are equal to canopy height above ground (in meters)

Source

Data acquired from a photogrammetric drone survey performed by Spire Aerobotics on June 16th, 2016.

See Also

kootenayTrees kootenayBlocks kootenayCrowns kootenayCHM

---

Kootenay forest - Dominant trees over 2 m

Description

Dominant trees from a 1.5 hectare section of forest in the Kootenay mountains, in British Columbia, Canada. Trees were detected by applying the vwf function to the kootenayCHM raster dataset. Only trees over 2 m above ground were detected.

Usage

kootenayTrees

Format

Simple point feature collection with the following attributes:

height

height of the tree's apex, in meters above ground

winRadius

radius of the moving window (see vwf) at the treetop's location

See Also

kootenayCHM kootenayBlocks kootenayCrowns kootenayOrtho

---

Marker-Controlled Watershed Segmentation

Description

This function implements the watershed function to segment (i.e.: outline) crowns from a CHM (canopy height model). Segmentation is guided by the point locations of treetops, typically detected using the vwf function. See Meyer & Beucher (1990) for details on watershed segmentation.

Usage

mcws(
  treetops,
  CHM,
  minHeight = 0,
  format = "raster",
  OSGeoPath = NULL,
  IDfield = "treeID"
)

Arguments

treetops	sf. The point locations of treetops in sf format.
CHM	SpatRaster. Canopy height model in SpatRaster format. This should be the same CHM that was used to the detect the treetops.
minHeight	numeric. The minimum height value for a CHM pixel to be considered as part of a crown segment. All CHM pixels beneath this value will be masked out. Note that this value should be lower than the minimum height of treetops.
format	string. Format of the function's output. Can be set to either 'raster' or 'polygons'.
OSGeoPath	character. Obsolete. Will be removed next version
IDfield	character. Name of the field for storing the unique tree identifier

Details

Crown segments are returned as either a SpatRaster or a sf (Simple Feature) class object, as defined using the format argument. For many analytic purposes, it is preferable to have crown outlines as polygons. However, polygonal crown maps take up significantly more disk space, and take longer to process. It is advisable to run this function using a raster output first to review results and adjust parameters.

NOTE: when setting format to 'polygons', orphaned segments (i.e.: outlines without an associated treetop) will be removed. This will NOT occur using 'raster' format. This issue will be resolved eventually but requires the watershed function to be rewritten.

Value

Depending on the setting for format, this function will return a map of outlined crowns as either a SpatRaster class object, in which distinct crowns are given a unique cell value, or a sf class object, in which each crown is represented by a polygon.

References

Meyer, F., & Beucher, S. (1990). Morphological segmentation. Journal of visual communication and image representation, 1(1), 21-46.

See Also

vwf

Examples

## Not run: 
library(terra)
library(ForestTools)

chm <- rast(kootenayCHM)

# Use variable window filter to detect treetops
ttops <- vwf(chm, winFun = function(x){x * 0.06 + 0.5}, minHeight = 2)

# Segment tree crowns
segs <- mcws(ttops, chm, minHeight = 1)

## End(Not run)

---

Quesnel forest - Cut blocks

Description

Boundaries of cut blocks within a 125 hectare section of forest in the Quesnel Timber Supply Area, in British Columbia, Canada. Each block contains trees of different levels of maturity. Overlaps with quesnelTrees and quesnelCHM.

Usage

quesnelBlocks

Format

Simple polygon feature collection with the following attributes:

BlockID

numerical identifier for each block

Shape_Leng

length of polygon on meters

Shape_Area

area of polygon in square meters

See Also

quesnelTrees quesnelCHM

---

Quesnel forest - Canopy height model

Description

A canopy height model of a 125 hectare section of forest in the Quesnel Timber Supply Area, in British Columbia, Canada.

Usage

quesnelCHM

Format

PackedSpatRaster object

Cell values are equal to canopy height above ground (in meters)

Source

Data acquired from a photogrammetric drone survey performed by Spire Aerobotics on September 15th, 2016.

See Also

quesnelTrees quesnelBlocks

---

Quesnel forest - Dominant trees over 2 m

Description

Dominant trees from a 125 hectare section of forest in the Quesnel Timber Supply Area, in British Columbia, Canada. Trees were detected by applying the vwf function to the quesnelCHM raster dataset. Only trees over 2 m above ground were detected.

Usage

quesnelTrees

Format

Simple point feature collection with the following attributes:

height

height of the tree's apex, in meters above ground

winRadius

radius of the moving window (see vwf) at the treetop's location

See Also

quesnelCHM quesnelBlocks

---

Variable Window Filter

Description

Implements the variable window filter algorithm (Popescu & Wynne, 2004) for detecting treetops from a canopy height model.

Usage

vwf(
  CHM,
  winFun,
  minHeight = NULL,
  warnings = TRUE,
  minWinNeib = "queen",
  IDfield = "treeID",
  resolution_round = 5
)

Arguments

CHM	SpatRaster. Canopy height model in SpatRaster format.
winFun	function. The function that determines the size of the window at any given location on the canopy. It should take the value of a given CHM pixel as its only argument, and return the desired *radius* of the circular search window when centered on that pixel. Size of the window is in map units.
minHeight	numeric. The minimum height value for a CHM pixel to be considered as a potential treetop. All CHM pixels beneath this value will be masked out.
warnings	logical. If set to FALSE, this function will not emit warnings related to inputs.
minWinNeib	character. Define whether the smallest possible search window (3x3) should use a queen or a rook neighborhood.
IDfield	character. Name of field for unique tree identifier
resolution_round	integer. The raster resolution is used to compute the dimensions of the search windows. By default, this resolution is rounded to 5 decimal places. The number of decimal places can be changed using this parameter. Increasing this value is also a work-around for errors relating to non-square cell sizes.

Details

This function uses the resolution of the raster to figure out how many cells the window needs to cover. This means that the raster value (representing height above ground) and the map unit (represented by the raster's resolution), need to be in the _same unit_. This can cause issues if the raster is in lat/lon, whereby its resolution is in decimal degrees.

Value

Simple feature collection of POINT type. The point locations of detected treetops. The object contains two fields in its data table: height is the height of the tree, as extracted from the CHM, and winRadius is the radius of the search window when the treetop was detected. Note that winRadius does not necessarily correspond to the radius of the tree's crown.

References

Popescu, S. C., & Wynne, R. H. (2004). Seeing the trees in the forest. Photogrammetric Engineering & Remote Sensing, 70(5), 589-604.

See Also

mcws

Examples

## Not run: 
library(terra)
library(ForestTools)

chm <- rast(kootenayCHM)

# Set function for determining variable window radius
winFunction <- function(x){x * 0.06 + 0.5}

# Set minimum tree height (treetops below this height will not be detected)
minHgt <- 2

# Detect treetops in demo canopy height model
ttops <- vwf(chm, winFunction, minHgt)

## End(Not run)

---