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mwalmsley committed Apr 4, 2024
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Expand Up @@ -24,6 +24,7 @@ Zoobot is trained using millions of answers by Galaxy Zoo volunteers. This code
- [Pretrained Weights](https://zoobot.readthedocs.io/en/latest/pretrained_models.html)
- [Datasets](https://www.github.com/mwalmsley/galaxy-datasets)
- [Documentation](https://zoobot.readthedocs.io/) (for understanding/reference)
- [Mailing List](https://groups.google.com/g/zoobot) (for updates)

## Installation

Expand Down Expand Up @@ -59,44 +60,43 @@ The [Colab notebook](https://colab.research.google.com/drive/1A_-M3Sz5maQmyfW2A7

Let's say you want to find ringed galaxies and you have a small labelled dataset of 500 ringed or not-ringed galaxies. You can retrain Zoobot to find rings like so:

```python
```python
import pandas as pd
from galaxy_datasets.pytorch.galaxy_datamodule import GalaxyDataModule
from zoobot.pytorch.training import finetune

import pandas as pd
from galaxy_datasets.pytorch.galaxy_datamodule import GalaxyDataModule
from zoobot.pytorch.training import finetune
# csv with 'ring' column (0 or 1) and 'file_loc' column (path to image)
labelled_df = pd.read_csv('/your/path/some_labelled_galaxies.csv')

# csv with 'ring' column (0 or 1) and 'file_loc' column (path to image)
labelled_df = pd.read_csv('/your/path/some_labelled_galaxies.csv')
datamodule = GalaxyDataModule(
label_cols=['ring'],
catalog=labelled_df,
batch_size=32
)

datamodule = GalaxyDataModule(
label_cols=['ring'],
catalog=labelled_df,
batch_size=32
)
# load trained Zoobot model
model = finetune.FinetuneableZoobotClassifier(checkpoint_loc, num_classes=2)

# load trained Zoobot model
model = finetune.FinetuneableZoobotClassifier(checkpoint_loc, num_classes=2)

# retrain to find rings
trainer = finetune.get_trainer(save_dir)
trainer.fit(model, datamodule)
```
# retrain to find rings
trainer = finetune.get_trainer(save_dir)
trainer.fit(model, datamodule)
```

Then you can make predict if new galaxies have rings:

```python
from zoobot.pytorch.predictions import predict_on_catalog
```python
from zoobot.pytorch.predictions import predict_on_catalog

# csv with 'file_loc' column (path to image). Zoobot will predict the labels.
unlabelled_df = pd.read_csv('/your/path/some_unlabelled_galaxies.csv')
# csv with 'file_loc' column (path to image). Zoobot will predict the labels.
unlabelled_df = pd.read_csv('/your/path/some_unlabelled_galaxies.csv')

predict_on_catalog.predict(
unlabelled_df,
model,
label_cols=['ring'], # only used for
save_loc='/your/path/finetuned_predictions.csv'
)
```
predict_on_catalog.predict(
unlabelled_df,
model,
label_cols=['ring'], # only used for
save_loc='/your/path/finetuned_predictions.csv'
)
```

Zoobot includes many guides and working examples - see the [Getting Started](#getting-started) section below.

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