---
title: "Point cloud analysis"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Point cloud analysis}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---
<style>
body {
text-align: justify}
</style>
```{r, echo = FALSE, eval=TRUE, include=FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
options(knitr.table.format = "html", rmarkdown.html_vignette.check_title = FALSE)

library(eRTG3D)
library(raster)
library(ggplot2)
set.seed(123)
```

## Example trajectories
First some example trajectories are created in form of Correlated Random Walks (CRWs):

```{r eval=TRUE, echo=TRUE, fig.align="center"}
crws <- lapply(X=seq(1:100), FUN = function(X) {
  sim.crw.3d(nStep = 100, rTurn = 0.99, rLift = 0.99, meanStep = 0.1)
  })
plot2d(crws)
```

## Utilization distribution
Count points per voxel and plot counts as raster stack:

```{r eval=TRUE, echo=TRUE, fig.align="center"}
points <- do.call("rbind", crws)
extent <- extent(c(-10, 10, -10, 10))
ud <- voxelCount(points, extent, xyRes=5, zMin=-10, zMax=10)
plotRaster(ud)
```

## Chi square maps
By calculating Chi maps, the over- and underrepresentation of points in the voxel space can be interpreted statistically:

```{r eval=TRUE, echo=TRUE, fig.align="center"}
chi <- chiMaps(ud)
plotRaster(chi, centerColorBar=TRUE)
```

## Export voxel data
The voxel dataCube of type rasterStack can be exported as Tiff image sequence. Image sequences are a common structure to represent voxel data and most of the specific software to visualize voxel data is able to read it (e.g. blender)
```{r eval = FALSE}
saveImageSlices(ud, filename = "utilization-distribution", dir="folder/path")
saveImageSlices(chi, filename = "chi-map-cube", dir="folder/path")
```