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ForestTools

ForestTools 1.0.2 (2024-04-27)

Since version 0.2.4, the glcm function has used Rcpp code that was inherited from the now-defunct radiomics package. My intention was for ForestTool to adapt GCLM metrics for segmented tree crowns, not provide the foundational code to compute those metrics. Now that the GLCMTextures library is carrying the GLCM computation torch, I have added it as a dependency for ForestTools.

The glcm function still works the same way, although it is now 1) a bit faster and 2) calculates fewer metrics. See table below for changes in metrics output by glcm.

Metric	v1.0.1	v1.0.2	Notes
glcm_mean	✔	✔
glcm_variance	✔	✔
glcm_autoCorrelation	✔
glcm_cProminence	✔
glcm_cShade	✔
glcm_cTendency	✔
glcm_contrast	✔	✔
glcm_correlation	✔	✔
glcm_differenceEntropy	✔
glcm_dissimilarity	✔	✔
glcm_energy	✔
glcm_entropy	✔	✔
glcm_homogeneity1	✔	✔	Renamed to ‘glcm_honogeneity’
glcm_homogeneity2	✔
glcm_IDMN	✔
glcm_IDN	✔
glcm_inverseVariance	✔
glcm_maxProb	✔
glcm_sumAverage	✔	✔	Renamed to ‘glcm_SA’
glcm_sumEntropy	✔
glcm_sumVariance	✔
glcm_ASM		✔

ForestTools 1.0.1 (2023-09-27)

Add additional tests and fixed a few bugs.

ForestTools 1.0.0 (2023-04-10)

Replaced raster, sf, and rgeos dependencies with terra and sf.

Performance improvements for glcm. Tests indicate it’s now running 2.7x faster than before.

Removed glcm_img. If you would like to generate GLCM statistics for a single, unsegmented image, simply use glcm without a segs argument.

Removed sp_summarise. Other packages offered better, more flexible options for summarizing tree-level information by geographical units. If you thought this tool was useful and would like me to restore it, please let me know.

ForestTools 0.2.6 (2021-09-21)

Behaviour change for gclm: images are now discretized BEFORE segmentation. Note that this will impact the results returned by the function.

ForestTools 0.2.5 (2021-09-09)

Added glcm_img to allow GLCM statistics to be computed for an entire unsegmented image.

ForestTools 0.2.4 (2021-04-13)

The radiomics package is no longer maintained, so with permission from the author, Joel Carlson, I’ve integrated the code for computing GLCM statistics into this library

ForestTools 0.2.1

Added:

kootenayOrtho, an orthographic image of the area covered by kootenayCHM, kootenayTrees and kootenayCrowns

New function:

glcm, for computing textural metrics of a segmented canopy. Thanks to Jean-Romain Roussel for providing code for this function.

ForestTools 0.2.0

BACKWARD INCOMPATIBILITY WARNING

Although this can cause backward compatibility issues, I felt it was necessary to rename the following functions:

TreetopFinder -> vwf (stands for Variable Window Filter)
SegmentCrowns -> mcws (stands for Marker-Controlled Watershed Segmentation)
SpatialStatistics -> sp_summarise

Reasons for the changes are:

To follow the convention of avoiding capitalized function names.
To bring more specificity to the underlying algorithms involved.
To credit the developers of said algorithms by using the names assigned to them.
To acknowledge the fact that alternative algorithms are available for both finding trees and segmenting crowns.

In addition, I’ve made the following changes to vwf (formerly TreetopFinder):

Extended the default value of the maxWinDiameter argument to 99. Note that this value sets the maximum width in cells of the widest allowable window diameter. As explained in the documentation, this argument is to prevent the function from gobbling up too much memory, and can be disabled by setting to NULL.
In addition to controlling the maximum window diameter, the user can now tweak the behavior of the minimum diameter as well. Essentially, the smallest window will always be a 3x3 cell window, regardless of the computed window radius. The neighborhood of this smallest window can be set to either a rook or a queen case contiguity using the minWinNeib argument.
I’ve removed the function’s compatibility with the TileManager package. Although I had put considerable effort into adding this feature initially, I’ve realized that A) no one was using it, B) it is preferable for the user to manage tiles him or herself instead of having them managed “under the hood” by the vwf function. Let me know if you thought this feature was useful and perhaps I can write a vignette suggesting preferable ways to manage a tiled CHM.

ForestTools 0.1.5

Fixed a persistent bug in ‘TreeTopFinder’ whereby CHMs with imprecise cell sizes (i.e.: cell dimensions that aren’t accurate after a certain number of decimals), would cause issues with the shape of the focal windows. Internally, CHM cell dimensions are now rounded to the fifth decimal.

ForestTools 0.1.4

Add a new option for generating polygonal tree crowns with ‘SegmentCrowns’ using GDAL utilities from OSGeo4W. See documentation for ‘SegmentCrowns’ as well as new vignette: “Options for creating polygonal crown maps”.

ForestTools 0.1.2

Added the ‘Quesnel’ dataset. Added a new vignette: “Calculating inventory attributes using Forest Tools”.

ForestTools 0.1.1

Modified ‘SegmentCrowns’ function so that it can produce tree crowns in polygon format. The function will also calculate crown area, and filter out crowns that are not associated with a treetop point location.
Changed name of ‘TreeTopSummary’ function to ‘SpatialStatistics’. This reflects its new functionality, which allows crown maps to be inputted as well as treetop locations.

ForestTools 0.1.0

Initial release of ForestTools

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.