Convert raw images to Parquet to optimize dataset loading (#10)

- Rebuild dataset from metadata.csv with Image feature (058574ea48109a2d8b167dd6a1626b0da0be36d2)
- Remove raw dataset folder; Parquet data lives under data/ (fe5f0d757be2532d0c3d45dbf0d652494486b392)
- Update dataset structure and provide legacy format export instructions (ef566ad95b1e8547d334774f9965184b464a6020)
- Fix typo (0377eca7ab247461f8d0f425228230100d7f049e)
- Add clarifying statement of previous dataset organization (f4a1ca168781a261b7c52a8f02de8dac8dd61b32)

README.md

@@ -25,8 +25,42 @@ size_categories: 10K<n<100K
 configs:
 - config_name: default
   data_files:
-  - "metadata.csv"
-  - "dataset/*/*.jpg"
+  - split: train
+    path: data/train-*
+dataset_info:
+  features:
+  - name: file_name
+    dtype: image
+  - name: rarespecies_id
+    dtype: string
+  - name: eol_content_id
+    dtype: string
+  - name: eol_page_id
+    dtype: string
+  - name: kingdom
+    dtype: string
+  - name: phylum
+    dtype: string
+  - name: class
+    dtype: string
+  - name: order
+    dtype: string
+  - name: family
+    dtype: string
+  - name: genus
+    dtype: string
+  - name: species
+    dtype: string
+  - name: sciName
+    dtype: string
+  - name: common
+    dtype: string
+  splits:
+  - name: train
+    num_bytes: 4109920786.974
+    num_examples: 11983
+  download_size: 4322391527
+  dataset_size: 4109920786.974
 ---
 
 # Dataset Card for Rare Species Dataset
@@ -74,9 +108,76 @@ Baseline for Random guessing is 0.3.
 English, Latin
 
 ## Dataset Structure
+The repository consists of the following:
 
 ```
-/dataset/
+├── data
+│   ├── train-00000-of-00009.parquet
+│   ├── ...
+│   └── train-00008-of-00009.parquet
+├── metadata
+│   ├── licenses.csv
+│   └── rarespecies-catalog.csv
+├── metadata.csv
+├── README.md
+└── visuals
+    ├── phyla_ToL_tree.html
+    ├── phyla_ToL_tree.pdf
+    └── phyla_ToL_tree.png
+```
+To load the dataset, use the `datasets` library.
+```python
+from datasets import load_dataset
+
+ds = load_dataset("imageomics/rare-species", split="train")
+```
+
+You will have:
+```python
+ds
+Dataset({
+    features: ['file_name', 'rarespecies_id', 'eol_content_id', 'eol_page_id', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species', 'sciName', 'common'],
+    num_rows: 11983
+})
+```
+Where, for example, an entry `ds[0]` contains:
+```python
+{ 'file_name': <PIL.JpegImagePlugin.JpegImageFile image mode=RGB size=400x400 at 0x14F5F54C9940>,
+  'rarespecies_id': '75fd91cb-2881-41cd-88e6-de451e8b60e2',
+  'eol_content_id': '12853737',
+  'eol_page_id': '449393',
+  'kingdom': 'Animalia',
+  'phylum': 'Mollusca',
+  'class': 'Bivalvia',
+  'order': 'Unionida',
+  'family': 'Unionidae',
+  'genus': 'Cyclonaias',
+  'species': 'tuberculata',
+  'sciName': 'Cyclonaias tuberculata',
+  'common': 'purple wartyback'
+}
+```
+For more information about Hugging Face datasets, see the [documentation](https://huggingface.co/docs/datasets/loading#hugging-face-hub).
+
+Previously, data were organized as JPGs in folders named with taxonomic labels.
+To export the data into a format matching the previously used dataset structure, you may do the following without cloning the repository:
+
+1) Create and activate a virtual environment.
+2) Install dependencies.
+```bash
+pip install -r \
+  https://huggingface.co/datasets/imageomics/rare-species/resolve/main/scripts/requirements.txt
+```
+3) Run the export script. You may customize the output directory by specifying the `--dataset-path` argument.
+```bash
+curl -s https://huggingface.co/datasets/imageomics/rare-species/raw/main/scripts/export_rare_species.py \
+  | python3 - --dataset-path ./exported_dataset
+```
+
+
+This will create a directory structure like the following:
+```
+/exported_dataset/dataset/
     <kingdom-phylum-class-order-family-genus-species-1>/
         <eol_content_id_1>_<eol_page_id>_eol_full-size-copy.jpg
         <eol_content_id_2>_<eol_page_id>_eol_full-size-copy.jpg

dataset/Animalia-Arthropoda-Arachnida-Araneae-Pisauridae-Dolomedes-plantarius/10797020_1198625_eol-full-size-copy.jpg → data/train-00000-of-00009.parquet

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dataset/Animalia-Chordata-Mammalia-Artiodactyla-Bovidae-Addax-nasomaculatus/29355174_331074_eol-full-size-copy.jpg → data/train-00001-of-00009.parquet

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dataset/Animalia-Arthropoda-Arachnida-Araneae-Pisauridae-Dolomedes-plantarius/10797022_1198625_eol-full-size-copy.jpg → data/train-00002-of-00009.parquet

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dataset/Animalia-Chordata-Aves-Sphenisciformes-Spheniscidae-Eudyptes-chrysolophus/29428351_45512086_eol-full-size-copy.jpg → data/train-00003-of-00009.parquet

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dataset/Animalia-Chordata-Aves-Charadriiformes-Laridae-Larosterna-inca/22109854_45509337_eol-full-size-copy.jpg → data/train-00004-of-00009.parquet

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dataset/Animalia-Arthropoda-Arachnida-Araneae-Pisauridae-Dolomedes-plantarius/10797023_1198625_eol-full-size-copy.jpg → data/train-00005-of-00009.parquet

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dataset/Animalia-Arthropoda-Arachnida-Araneae-Pisauridae-Dolomedes-plantarius/10797025_1198625_eol-full-size-copy.jpg → data/train-00006-of-00009.parquet

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dataset/Animalia-Cnidaria-Anthozoa-Scleractinia-Euphylliidae-Fimbriaphyllia-ancora/20385765_51259222_eol-full-size-copy.jpg → data/train-00007-of-00009.parquet

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