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Penguin colony georegistration using camera pose estimation and phototourism

Env Steup

Tested with CUDA 11.3, Ubuntu 20.04

conda env create -f environment.yml
conda activate eg3d

Data

The data are in ./ATA folder, with its structure below.

The licenses of the data are in wu_et_al_appendix_S1.docx.

./ATA
├── Devil_Island
│   |── data.ply (mesh derived from DEM and satellite image)
│   |── image1.json (segmentation - polygons)
│   |── image2.json 
│   |── ... 
│   |── image1.png (image)
│   |── image2.png
│   |── ... 
│   |── image1.xml (camera pose)
│   |── image2.xml
│   |── ... 
│   |── ref.json (bird-eye view segmentation - polygons)
│   |── ref_mask.png (bird-eye view segmentation - mask)
│   |── ref.xml (bird-eye view camera pose)

└──  Devil_Island-GT (manual segmentation - polygons)
│   |── image1.json
│   |── image2.json 
│   └── ...

├── Brown_Bluff
│   └── ...

└── Brown_Bluff-GT
    └── ...

Method

Segmentation

We use AnyLabeling ("Segment Anything (ViT-H Quant)") to create segmentation masks.

If you want to recreate some masks by yourself, you can download AnyLabeling here (windows exe file).

Registration

# set colony_name = Devil_Island/Brown_Bluff
CUDA_VISIBLE_DEVICES=0 python render.py

What does render.py do?

  1. use the segmentation mask (json) to segment, save result -> ./ATA/{colony_name}/results
  2. render top bird-eye view with everything together -> ./ATA/{colony_name}/results/pred_mask.png

Compute Metrics

# set colony_name = Devil_Island/Brown_Bluff
# set test_gt=True for fully manual method
python metrics.py

# metrics with confidence interval or sensitivity analysis
# set eval_mode = confidence_interval/prompts3/promps9/prompts12/prompts15
CUDA_VISIBLE_DEVICES=0 python metrics2.py

Contact