Skip to content

Latest commit

 

History

History
324 lines (286 loc) · 11.6 KB

README.md

File metadata and controls

324 lines (286 loc) · 11.6 KB
Raw

Prithvi Finetuning

This repo contains materials for Prithvi Global Finetuning. Here, we will cover geospatial foundation models and Weather Foundation model. We will also be fine-tuning the aforementioned models for specific usecases. For the purposes of this tutorial, we will be utilizing AWS sagemaker environment. The repo will also demonstrate how to get inferences from the fine-tuned prithvi models after the training is complete.

Slides:

Geospatial Foundation Model - Dr. Sujit Roy

Prithvi Weather and Foundation Model - Dr. Rajat Shinde

Prerequisites

  1. Basic understanding of git
  2. Python and jupyter environment knowledge
  3. Basic understanding of docker
  4. Basic understanding of cloud services
  5. Machine Learning knowledge
  6. Some understanding of Geo-spatial datasets.

Getting started

  1. Get your credentials and other information using https://creds-workshop.nasa-impact.net/ Get Credentials Credentials
  2. Navigate to Login URL Login Page
  3. Log in using the credential provided Login with username and password
  4. Once the Studio starts, Click on JupyterLab Sagemaker studio JupyterLab spaces
  5. Click Create JupyterLab Space JupyterLab spaces
  6. Give it a name. Eg: Workshop
  7. Once initialized, change Instance type to ml.t3.2xlarge and storage to 75 Change instance type
  8. Click on Run Space. If it throws an error, you might have to pick an Image. The top setting called Latest works. Run space

Steps to Train (Parts of these steps are also available in the fine-tuning notebook):

  1. Open a new terminal and run the following command to install git lfs

sudo apt update;sudo apt-get install git-lfs; git lfs install

  1. Clone this repository

git clone https://github.com/NASA-IMPACT/prithvi-global-workshop.git

Cloned repository

Note: We will follow through in the Notebook from this step. 3. Change directory into the cloned repository cd prithvi-global-workshop 4. Open the fine-tuning notebook 5. Install required packages

pip install -r requirements.txt
  1. Create required folders
!mkdir datasets
!mkdir models
!mkdir configs
  1. Download HLS Burn scars dataset
! cd datasets; git clone https://huggingface.co/datasets/ibm-nasa-geospatial/hls_burn_scars; tar -xvzf hls_burn_scars/hls_burn_scars.tar.gz
  1. Define constants. Note: Please update the variables as needed
BUCKET_NAME = '<your-bucket-name>' # Replace this with the bucket name available from https://creds-workshop.nasa-impact.net/
CONFIG_PATH = './configs'
DATASET_PATH = './datasets'
MODEL_PATH = './models'
  1. Download model configuration and pre-trained model from huggingface
from huggingface_hub import hf_hub_download

hf_hub_download(repo_id="ibm-nasa-geospatial/Prithvi-100M-burn-scar", filename="burn_scars_Prithvi_100M.py", local_dir='./configs')
hf_hub_download(repo_id="ibm-nasa-geospatial/Prithvi-100M", filename="Prithvi_100M.pt", local_dir='./models')
  1. Update the configuration file
1. Update line number 13 from `data_root = '<path to data root>'` to `data_root = '/opt/ml/data/'`. This is the base of our data inside of sagemaker.
2. Update line number 41 from `pretrained_weights_path = '<path to pretrained weights>'` to `pretrained_weights_path = f"{data_root}/models/prithvi-global-300M.pt"`. This provides the pre-trained model path to the train script.
3. Update line number 52 from `experiment = '<experiment name>'` to `experiment = 'burn_scars'` or your choice of experiment name.
4. Update line number 53 from `project_dir = '<project directory name>'` to `project_dir = 'v1'` or your choice of project directory name.
5. Save the config file.
  1. Upload downloaded data using sagemaker to the desired s3 bucket
import sagemaker

sagemaker_session = sagemaker.Session()
train_images = sagemaker_session.upload_data(path='datasets/training', bucket=BUCKET_NAME, key_prefix='data/training')
val_images = sagemaker_session.upload_data(path='datasets/validation', bucket=BUCKET_NAME, key_prefix='data/validation')
test_images = sagemaker_session.upload_data(path='datasets/validation', bucket=BUCKET_NAME, key_prefix='data/test')
  1. Rename and upload configuration file and pre-trained model
import os

identifier = '<your choice of identifier>' # Please update this with an identifier

config_filename = 'configs/burn_scars_Prithvi_100M.py'
new_config_filename = f"configs/{identifier}-burn_scars_Prithvi_100M.py"
os.rename(config_filename, new_config_filename)

configs = sagemaker_session.upload_data(path=new_config_filename, bucket=BUCKET_NAME, key_prefix='data/configs')
models = sagemaker_session.upload_data(path='models/Prithvi_100M.pt', bucket=BUCKET_NAME, key_prefix='data/models')
  1. Setup variables for training using Sagemaker
from datetime import time
from sagemaker import get_execution_role
from sagemaker.estimator import Estimator


name = f'{identifier}-sagemaker'
role = get_execution_role()
input_s3_uri = f"s3://{BUCKET_NAME}/data"

environment_variables = {
    'CONFIG_FILE': f"/opt/ml/data/{new_config_filename}",
    'MODEL_DIR': "/opt/ml/models/",
    'MODEL_NAME': f"{identifier}-workshop.pth",
    'S3_URL': input_s3_uri,
    'ROLE_ARN': role,
    'ROLE_NAME': role.split('/')[-1],
    'EVENT_TYPE': 'burn_scars',
    'VERSION': 'v1'
}

ecr_container_url = '637423382292.dkr.ecr.us-west-2.amazonaws.com/sagemaker_hls:latest'
sagemaker_role = 'SageMaker-ExecutionRole-20240206T151814'

instance_type = 'ml.p3.2xlarge'

instance_count = 1
memory_volume = 50
  1. Initialize sagemaker estimator and start training
estimator = Estimator(image_uri=ecr_container_url,
                      role=get_execution_role(),
                      base_job_name=name,
                      instance_count=1,
                      environment=environment_variables,
                      instance_type=instance_type)
estimator.fit()

Interacting with the fine-tuned model (Parts of these steps are covered in the fm-usage notebook)

  1. Install required packages
! pip install leafmap numpy --quiet
  1. Import packages
import json
import leafmap
import numpy as np
import xarray as xr
  1. Set existing events
#configure settings for selected events
INFERENCE_URL = 'https://hls-01.workshop.nasa-impact.net'

EVENT_DETAILS = {
    'mongolian_fire': {
        'center_lon': 119.3,
        'center_lat': 47.1,
        'default_zoom': 8,
        'start_date': '2022-04-19T00:00:00Z',
        'end_date': '2022-04-19T23:59:59Z'
    },
    'new_mexico_black_fire': {
        'center_lon': -107.5,
        'center_lat': 33.5,
        'default_zoom': 10,
        'start_date': '2022-05-16T00:00:00Z',
        'end_date': '2022-06-10T23:59:59Z'
    },
    'alberta_fire': {
        'center_lon': -124.2,
        'center_lat': 61.8,
        'default_zoom': 8,
        'start_date': '2023-05-27T00:00:00Z',
        'end_date': '2023-05-28T23:59:59Z'
    },
    'maui_fire': {
        'center_lon': -156.659394,
        'center_lat': 20.886984,
        'default_zoom': 12,
        'start_date': '2023-08-13T00:00:00Z',
        'end_date': '2023-08-13T23:59:59Z'
    }
}

event = 'maui_fire'
event_details = EVENT_DETAILS[event]

#configure settings for selected events
INFERENCE_URL = 'https://hls-01.workshop.nasa-impact.net'

EVENT_DETAILS = {
    'mongolian_fire': {
        'center_lon': 119.3,
        'center_lat': 47.1,
        'default_zoom': 8,
        'start_date': '2022-04-19T00:00:00Z',
        'end_date': '2022-04-19T23:59:59Z'
    },
    'new_mexico_black_fire': {
        'center_lon': -107.5,
        'center_lat': 33.5,
        'default_zoom': 10,
        'start_date': '2022-05-16T00:00:00Z',
        'end_date': '2022-06-10T23:59:59Z'
    },
    'alberta_fire': {
        'center_lon': -124.2,
        'center_lat': 61.8,
        'default_zoom': 8,
        'start_date': '2023-05-27T00:00:00Z',
        'end_date': '2023-05-28T23:59:59Z'
    },
    'maui_fire': {
        'center_lon': -156.659394,
        'center_lat': 20.886984,
        'default_zoom': 12,
        'start_date': '2023-08-13T00:00:00Z',
        'end_date': '2023-08-13T23:59:59Z'
    }
}
  1. Initialize a map for bounding box selection
map = leafmap.Map(
        center=(event_details['center_lat'],
        event_details['center_lon']),
        zoom=event_details['default_zoom'],
        draw_control=True,
        measure_control=False,
        fullscreen_control=False,
        attribution_control=True
    )
map.add_tile_layer(HLSL30_TILE_LAYER, name='HLSL30', attribution='NASA')
map.add_tile_layer(HLSS30_TILE_LAYER, name='HLSS30', attribution='NASA')
map
  1. Draw a bounding box and save it to bbox.geojson
map.save_draw_features("bbox.geojson")
  1. Prepare payload and call API for results using the fine-tuned model

def bbox_from_geojson(geojson):
    """
        Get the coordinates of bounding box from an extended notation to flat coordinate
        notation
    Args:
        geojson: File path of geojson

    Returns:
        list: [left, down, right, top]
    """
    with open(geojson) as geojson_file:
        geojson_detail = json.load(geojson_file)
    coordinates = np.asarray(geojson_detail['features'][0]['geometry']['coordinates'])
    lats = coordinates[:, :, 1]
    lons = coordinates[:, :, 0]
    return [lons.min(), lats.min(), lons.max(), lats.max()]

# Convert geojson to flat bounding box representation.
bbox = bbox_from_geojson('bbox.geojson')

import requests
import json

# prepare payload
payload = json.dumps({
  "config_path": f"s3://{BUCKET_NAME}/data/configs/{new_config_filename}",
  "model_path": f"s3://smd-workshop-01/{MODEL_NAME}",
  "model_type": "burn_scars",
  "date": event_details['start_date'].split('T')[0],
  "bounding_box": bbox
})

headers = {
  'Content-Type': 'application/json'
}

# Use deployed app to get inference on the selected date/location
response = requests.request(
      "POST",
      f"{INFERENCE_URL}/infer",
      headers=headers,
      data=payload
  )

predictions = response.json()
  1. Visualize the result
geojson = predictions['predictions']

detection_map = leafmap.Map(
        center=(event_details['center_lat'],
        event_details['center_lon']),
        zoom=event_details['default_zoom'],
        draw_control=True,
        measure_control=False,
        fullscreen_control=False,
        attribution_control=True
    )
detection_map.add_tile_layer(HLSL30_TILE_LAYER, name='HLSL30', attribution='NASA')
detection_map.add_tile_layer(HLSS30_TILE_LAYER, name='HLSS30', attribution='NASA')
detection_map.add_geojson(geojson, layer_name=f"{event}-detections")

detection_map

Note: BUCKET_NAME, new_config_filename, and MODEL_NAME are variables set in the previous notebook. Please copy paste those variables here for this step to run smoothly.