The ICEBERG Penguin colony usecase package
Project description
Quality Metrics
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:
$ 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:
$ 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
[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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