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Visualizing butterflies from the Natural History Museum

This repository contains code to process images of butterflies from the data portal of the Natural History Museum in London. From the processed images, a web-based, interactive, hierarchical t-SNE plot is created. The code in this repository can be used to reproduce the visualization or to extract the images and use them for something else. Pre-trained models for all three neural networks are included.

Click here for the interactive visualization.

Click here for my blog post that explains the data preparation procedure.

Usage

(This is currently outdated and will be updated soon to reflect changes in the code)

This section explains how to recreate the visualization on your machine. You need a GPU with at least 8 GB of VRAM and ~650 GB of disk space. The full dataset contains 716,000 images. You can use less disk space if you use a subset of the dataset, as explained below.

  1. On the NHM data portal, search for "lepidoptera". At this point, you can narrow the search if you want to work with a smaller dataset. Click the Download button and request an email with the CSV files. The CSV files will be ~1.3 GB for the full dataset.

  2. Clone this repository and unpack the files metadata.csv and occurence.csv from the data portal in the data directory.

  3. Run create_metadata.py. This will create the file metadata.csv in the data directory. The resulting CSV file contains a line for each image that will be used. You can modify the python script or the resulting CSV file if you want to work with a subset of the dataset.

  4. Run download.py. This script will download the original images into the data/raw directory. For the full dataset, this will take ~2 weeks and require 452 GB. The download speed is limited by the NHM servers, which serve around 1 file per second. You can stop the script and it will resume where you left off.

  5. Optional: Train the classifier U-Net.

  • To train a new model, remove the file trained_models/classifier.to. Otherwise, training will use the existing existing model as a starting point.
  • Unpack the file data/masks.zip to data/masks.zip or supply your own dataset. Mask images should be png files and the file name should be the ID of the corresponding images. They should have the same size as the original image and have white pixels for foreground and black pixels for background.
  • Run train_classifier.py. There is no stopping criterion, stop the script once the loss no longer decreases.
  • Run test_classifier.py to create example images in data/test/
  1. Run create_images.py. This part removes the backgrounds and creates images with an alpha channel using the U-Net that classifies every pixel as background or foreground. This will create square PNG images of varying sizes in the data/images_alpha directory of just the butterfly for each original image. The script takes ~24 hours for the full dataset and will use ~160 GB of disk space. You can stop and resume this script.

  2. Optional: Train the rotation network.

This network predicts for each pixel whether it belongs to a butterfly or the background. Instead of training a new one, you can use the pre-trained model in this repository.

  • The network will use the rotation dataset in data/rotations.csv. Delete this file if you want to start from scratch.
  • Run labels_server.py and go to the displayed URL to manually annotate rotation data. If you serve previously generated tiles locally (step 15), you can click on an image and select "Fix rotation" to go to show that particular specimen in the labelling app.
  • Run scale_rotation_dataset.py to create scaled down versions of the images listed in the CSV file that will be used to train the network.
  • Run train_rotation_network.py to train the network. There is no stopping criterion, stop the script once the loss no longer decreases.
  1. Run scale_images.py. This creates JPG images with a resolution of 128x128 and a white background for each of the PNG images and stores them in the data/images_rotated_128 directory. It also uses the rotation network to bring the butterflies into the default rotation using the rotation network. The rotations are also saved to data/rotations_calculated.csv. You can stop and resume this script.

  2. Optional: Train the autoencoder.

  • If you want to start training a new model, delete the current one at trained_models/autoencoder.to or trained_models/variational_autoencoder.to.
  • Run train_autoencoder.py. This runs indefinetely, until you stop it. The longer it trains, the better the result.
  • You can run test_autoencoder.py to create example pairs of input and reconstructed images in the data/test directory. Stop the test script after some images have been created.
  1. Run create_latent_codes.py. This calculates latent codes for all images in the dataset using the autoencoder.

  2. Run create_tsne.py. This calculates the t-SNE embedding.

  3. Run move_points.py. This moves points away from each other that would otherwise overlap in the visualization.

  4. Run create_tiles.py. This creates the leaflet map tiles for the visualization. This takes ~4 hours and creates ~24 GB of data. If you disable CREATE_HQ_TILES in config.py, the result will only be 6 GB.

  5. Run create_json.py. This creates JSON files for the metadata that will be displayed in the web app.

  6. The files for the web app are in the server directory. You can test the web app by going in to the server directory and running python3 -m http.server. Go to the address of the server (i.e. http://0.0.0.0:8000/) to test the web app.

License

The images of the butterflies are provided by the Trustees of the Natural History Museum under a CC BY 4.0 license. The Natural History Museum cannot warrant the quality or accuracy of the data. This project is not endorsed by, affiliated with, supported by or approved by the Museum.

The code in this repository is provided under the MIT license.

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Using deep learning to process images of butterflies from the NHM data portal

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