The ICEBERG Penguin colony usecase package
Project description
## Quality Metrics
[![Build Status](https://travis-ci.com/iceberg-project/Penguins.svg?branch=devel)](https://travis-ci.com/iceberg-project/Penguins)
## Software Dependencies
boost==1.66.0
gdal==2.1.4
geotiff==1.4.2
matplotlib==2.1.0
opencv==2.4.13
openjpeg==2.1.2
pillow==4.2.1
python==2.7.15
pytorch==0.3.1
rasterio==0.36.0
scikit-learn==0.19.1
scipy==1.2.1
scipy==0.19.0
torchvision==0.2.0
visdom==0.1.8.9
## Installation
### PSC Bridges >From source: `bash $ git clone https://github.com/iceberg-project/Penguins.git $ module load cuda $ module load python3 $ virtualenv iceberg_penguins $ source iceberg_penguins/bin/activate [iceberg_penguins] $ export PYTHONPATH=<path>/iceberg_penguins/lib/python3.5/site-packages [iceberg_penguins] $ pip install . --upgrade `
>From PyPi: `bash $ module load cuda $ module load python3 $ virtualenv iceberg_penguins $ source iceberg_penguins/bin/activate [iceberg_penguins] $ export PYTHONPATH=<path>/iceberg_penguins/lib/python3.5/site-packages [iceberg_penguins] $ pip install iceberg_penguins.search `
To test `bash [iceberg_penguins] $ iceberg_penguins.detect `
### Prediction - Download a pre-trained model at:
https://drive.google.com/file/d/149j5rlynkO1jQTLOMpL5lextHY0ozw6N/view?usp=sharing
Please put the model file to: <checkpoints_dir>/<model_name>/
The one provided here is at the epoch 300 of the model named “v3weakly_unetr_bs96_main_model_ignore_bad”
The script to run the testing for a single PNG image:
iceberg_penguins.detect [–params …]
## params: - –name: name of the model used for testing - –gpu_ids: the gpu used for testing - –checkpoints_dir: path to the folder containing the trained models - –epoch: which epoch we use to test the model - –input_im: path to the input image - –output: directory to save the outputs
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