gelos/tests/fixtures/example_config.yaml at main · ClarkCGA/gelos · GitHub

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experiment_name: "Terramind V1 Base - No Perturbation"
data_version: "v0.50.1"
chip_tracker: "gelos_chip_tracker.geojson"
chip_id_column: "id"

seed_everything: 0
trainer:
  accelerator: auto
  strategy: auto
  devices: auto
  num_nodes: 1
  callbacks: []
  max_epochs: 0

data:
  class_path: gelos.gelosdatamodule.GELOSDataModule
  init_args:
    dataset_class: tests.test_data.ExampleGELOSDataSet
    batch_size: 1
    num_workers: 0
    bands:
      S2L2A:
        - blue
        - green
        - red
        - nir08
        - swir16
        - swir22
      S1RTC:
        - VV
        - VH
      DEM:
        - DEM
    repeat_bands:
      DEM: 4
    transform:
      - class_path: terratorch.datasets.transforms.FlattenTemporalIntoChannels
      - class_path: albumentations.augmentations.geometric.resize.Resize
        init_args:
          height: 96
          width: 96
          interpolation: 0 # Nearest Neighbor
      - class_path: albumentations.pytorch.transforms.ToTensorV2
      - class_path: terratorch.datasets.transforms.UnflattenTemporalFromChannels
        init_args:
          n_timesteps: 4
model:
  class_path: terratorch.tasks.EmbeddingGenerationTask
  title: Terramind V1 Base
  init_args:
    model: terramind_v1_base
    model_args:
      modalities:
        - S2L2A
        - S1RTC
        - DEM
      merge_method: mean
      pretrained: True
    output_format: parquet
    embed_file_key: filename
    layers: [-1] # Model layers to extract embeddings from, -1 means the last layer
    embedding_pooling: null
    has_cls: False
    temporal_cfg:
      temporal_wrapper: True
      temporal_pooling: keep


# each strategy defines extraction args (slice_args) and optional analysis steps (transforms, plots, models)
embedding_extraction_strategies:
  # since terramind embeddings are nested lists, the first args dict gets all time steps, the second gets patch at idx 18 (center)
  all_steps_middle_patch:
    title: "All Steps of Middle Patch"
    slice_args:
      - start: 0
        stop: null
        step: 1
      - start: 18
        stop: 19
        step: 1
    transforms:
      - type: tsne
      - type: pca
        params:
          n_components: 2
      - type: umap
    plots:
      - type: scatter_2d
        transform: tsne
      - type: temporal_cosine_similarity
        transform: raw
        params:
          n_timesteps: 4
          timestep_labels: ["Jan-Mar", "Apr-Jun", "Jul-Sep", "Oct-Dec"]
    models:
      - type: knn
        transform: pca
        params:
          n_neighbors: 5
      - type: linear_probe
        transform: pca
  all_patches_april_to_june:
    title: "All Patches from April to June"
    slice_args:
      - start: 1
        stop: 2
        step: 1
    transforms:
      - type: tsne
    plots:
      - type: scatter_2d
        transform: tsne
  all_embeddings:
    title: "All Embeddings"
    slice_args:
      - start: 0
        stop: null
        step:
    transforms:
      - type: pca
        params:
          n_components: 2
    models:
      - type: random_forest
        transform: pca
        params:
          n_estimators: 50

style:
  category_column: "lulc"
  colors:
    "1": "#419bdf"    # Water
    "2": "#397d49"    # Trees
  labels:
    "1": "Water"
    "2": "Trees"