Edge detection of clusters for point-cloud data using an alpha-hull. Scripts written in R are used for the simulation of test data (see edgeParticleSimulator.R ) and finding the edge clusters from the associated cluster pos file results (see findEdgeClustersConvex.R). The "full" pos file, cluster data or statistics (including the data required to get the cluster bounding box) as well as some settings (atomic density, detection efficiency and sampling fraction). The code is based on the following paper.
library("tidyverse")
library("geometry")
library("alphashape3d")
library("spatstat")
Copy or extract the contents of the repository into a local folder called “ClusterAlphaEdge”. The experiment scripts, detailed below, assume the posgen exe is available in one folder above the R scripts directory:
folder/
├── ClusterAlphaEdge
├── posgen
The findEdgeClustersConvex.R script can use an unmodified version of posgen, however the findEdgeClusters.R script requires the bounding box of each cluster in the cluster statistics file produced by the cluster search step. A source code patch is available to add this functionality to posgen (posgenBoundingBoxPatch.txt). This will require the program to be compiled from scratch after the patch has been applied.
Then you should be able to run any of the edgeParticleSimulator scripts which generate a simulated dataset, cluster search and then find edge clusters. Or you can use the findEdgeClustersConvex function on your own data to identify the edge clusters. See the findEdgeClustersConvex file for usage.
Different simulation experiments are identified by an id, a description of each can be found in the script ending in the id number, also below in the reference table. Composition refers to the tables given below. All clusters had a radius of 2 nm and the core/shell particles had an inner core radius of 1.58 nm.
Summary of details in scripts edgeParticleSimulator_id001.R etc.
| Exp. | Box | Size (nm) | Core/shell? | Cluster edge method | Composition | Simulations |
|---|---|---|---|---|---|---|
| id001 | Cube | 20 | No | Bounding box | A | 1000 |
| id004 | Cube | 20 | No | Bounding box | A | 1000 |
| id005 | Sphere | 40 | No | Bounding box | A | 1000 |
| id006 | Sphere | 40 | Yes | Bounding box | B | 1000 |
| id007 | Sphere | 40 | Yes | Convex hull | B | 2000 |
| id008 | Sphere | 40 | No | Convex hull | A | 2000 |
Particle compositions are either A or B for the clusters with no structure and the core/shell clusters respectively.
| Part | H | C | Fe |
|---|---|---|---|
| Particle | 50 | 50 | 0 |
| Matrix | 0.01 | 0.01 | 99.8 |
| Part | H | C | Fe |
|---|---|---|---|
| Core | 99.9 | 0.01 | 0 |
| Shell | 0.01 | 99.9 | 0 |
| Matrix | 0.01 | 0.01 | 99.8 |
- Andrew London
- Ben Jenkins
Copyright 2019 A. London, B. Jenkins This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.