https://github.com/davidmoten/rtree-3d

3D R-Tree in java
https://github.com/davidmoten/rtree-3d

Last synced: 16 days ago
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3D R-Tree in java

• Host: GitHub
• URL: https://github.com/davidmoten/rtree-3d
• Owner: davidmoten
• License: apache-2.0
• Created: 2016-01-31T10:28:45.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2024-09-19T16:21:37.000Z (about 2 months ago)
• Last Synced: 2024-10-14T07:46:37.419Z (30 days ago)
• Language: Java
• Size: 1.02 MB
• Stars: 35
• Watchers: 4
• Forks: 17
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# rtree-3d

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**Note**: this project is NOT under active development. See [rtree-multi](https://github.com/davidmoten/rtree-multi) for an n-dimensional R-Tree.

Three dimensional R-Tree in java.

* motivated by spatio-temporal queries

* nodes can be serialized to disk or network storage.  

* particularly interested in serializing large static datasets into a top tree and many sub-tree files that might be accessed over medium latency and medium bandwidth io (e.g. using AWS S3 from EC2).

Status: *pre-alpha*

Progress is being made on this project. I've copied my [rtree 2D implementation](https://github.com/davidmoten/rtree) and beefed it up for 3D. 

* expanded the R* `Selector` and `Splitter` implementations to handle 3 dimensions

* enhanced Quadratic `Selector` and `Splitter` implementations to handle 3 dimensions

* normalized coordinates so they range from 0..1

* added [R language code](src/main/r/source.r) to produce PNG visualizations of tree structure (below) 

If the coordinates are normalized to the [0..1] range then the data structure doesn't favour one dimension over another. To favour time over position for instance just scale the time value down by a constant (experiment with your data!).

Note also that if your entries are added to the R-tree in say ascending time order then the resultant R-tree may be affected negatively in terms of the efficiency of its structure. A useful strategy to avoid this is to shuffle the entries before adding. For example:

```java

RTree tree = 

  tree.add(

    entries

      .toList()

      .flatMapIterable(list -> {Collections.shuffle(list);return list}));

```

Visualization

-----------------------

Given the 38,377 data points of greek earthquakes (lat, long, time) from 1964 to 2000, the data is scanned to establish the ranges for each coordinate then normalized to a [0,1] range. The points are shuffled then added to an R-tree with `minChildren=2` and `maxChildren=4` using either the R* heuristics or standard R-tree heuristics. Visualization of the bounding boxes at nodes by method and depth is below.

Generated with this [commit](tree/83c760b3ee7f9fb7d64f581554424ee7ab88cac7).

The plots below are generated from the same shuffle of data points.

| Quadratic split | R*-tree split |

| :-------------: | :-----------: |

|  |  |

|  |  |

|  |  |

|  |  |

|  |  |

|  |  |

|  |  |

|  |  |

|  |  |

|  |  |

Commands to generate:

```bash

mvn test

cd src/test/r

./source.r

```

Images are generated in `target` directory (`plot*.png`).