geebeam 0.1.0__tar.gz

geebeam-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
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+
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+.Python
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+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
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+# Abstra is an AI-powered process automation framework.
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+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
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+#  you could uncomment the following to ignore the entire vscode folder
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+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/

geebeam-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Kylen Solvik
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

geebeam-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: geebeam
+Version: 0.1.0
+Summary: Earth Engine + Apache Beam
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: apache-beam[gcp]>=2.71.0
+Requires-Dist: dill>=0.4.1
+Requires-Dist: earthengine-api>=1.7.10
+Requires-Dist: geopandas>=1.0.1
+Requires-Dist: grpcio>=1.62.3
+Requires-Dist: tensorflow-data-validation>=1.16
+Requires-Dist: tensorflow-metadata>=1.16
+Requires-Dist: tensorflow>=2.16
+Requires-Dist: tfx-bsl>=1.16
+Description-Content-Type: text/markdown
+
+# GeeBeam
+
+[![Testing + Linting](https://github.com/kysolvik/geebeam/actions/workflows/pytest-lint.yml/badge.svg)](https://github.com/kysolvik/geebeam/actions/workflows/pytest-lint.yml)
+
+Google Earth Engine + Apache Beam for building geospatial training datasets
+
+## Purpose:
+
+GeeBeam is a lightweight library for building and executing Apache Beam pipelines that download data "chips" from Google Earth Engine and write them to TensorFlow records for model training.
+
+The user defines the Earth Engine images they want to download chips from using the Python earthengine-api. geebeam then serialized the graph-definition of the images so they can be passed to the Beam workers. 
+
+The pipelines can be run locally or on Google Cloud Dataflow. (Note: currently local jobs are limited to short-running tasks due to grpc "Deadline Exceeded" error).
+
+
+## Install:
+
+```bash
+pip install geebeam
+```
+
+## Examples:
+
+Here we'll create a burned area mask for 2024 using the MCD64A1 product.
+For example, this could be the target variable for a burn risk model.
+
+```python
+import ee
+import geebeam
+import google
+
+# Get default project id from environment (or specify PROJECT_ID manually)
+PROJECT_ID = google.auth.default()[1]
+
+# Initialize ee client, replace with your GCP project ID
+ee.Initalize(project=PROJECT_ID)
+
+# Build image for download
+burned_2024 = (ee.ImageCollection('MODIS/061/MCD64A1')
+            .select('BurnDate')
+            .filter(ee.Filter.calendarRange(2024, 2024, 'year'))
+            .min()
+            .gt(0)
+            .rename(['Burn'])
+            )
+
+# Building and triggering the pipeline is done with a single command:
+geebeam.run(
+    image_list = [burned_2024],
+    project=PROJECT_ID,
+    patch_size=128, # Pixel dimensions in each direction
+    scale=500, # Final export resolution in meters
+    n_sample=10, # Number of tiles to sample
+    validation_ratio=0.2, # Fraction to select as validation data
+    output_path='./test/',
+    sampling_region=ee.Geometry.Rectangle(-63.0, -9.0, -56.0, -4.0),
+    num_workers=2
+)
+```
+
+Now let's add another dataset: MapBiomas Amazonia forest fraction
+```python
+# MB Land-use/land-cover forest fraction
+# Note that LULC codes less than 10 area forest in MapBiomas Amazon Collection 6
+mb_amz_lulc = (
+    ee.Image('projects/mapbiomas-public/assets/amazon/lulc/collection6/mapbiomas_collection60_integration_v1')
+    .lt(10)
+   .reduceResolution('mean', maxPixels=500)
+)
+
+# Exporting both together is as simple as this:
+geebeam.run(
+    image_list = [burned_2024, mb_amz_lulc],
+    project=PROJECT_ID,
+    patch_size=128,
+    scale=500,
+    n_sample=10,
+    validation_ratio=0.2,
+    output_path='./test/',
+    sampling_region=ee.Geometry.Rectangle(-63.0, -9.0, -56.0, -4.0),
+    num_workers=2
+)
+
+```
+
+### Dataflow: 
+
+The export process can be scaled to many workers via Google Cloud DataFlow: 
+
+```bash
+python examples/geebeam_run.py \
+    --region us-east1 \
+    --worker_zone us-east1-b \
+    --runner DataflowRunner \
+    --max_num_workers=8 \
+    --num_workers=1 \
+    --experiments=use_runner_v2 \
+    --machine_type=n2-highmem-2 
+```
+
+Note that in this case the output_path defined in geebeam_run.py should be a Google Cloud Storage path.
+
+#### Artifact registry setup:
+
+To speed up the start-up and running of jobs on DataFlow, you can build a Docker image containing `geebeam` and it's dependencies.
+
+See instructions on Google Cloud
+
+First, you'll need to have Docker installed on your computer, either just [Docker Engine](https://docs.docker.com/engine/) or full [Docker Desktop](https://docs.docker.com/desktop/) will do.
+
+Next, you'll need to create  a Google Artifact Registry respository and configure your Docker to authenticate requests for the Artifact Registry. [Google Cloud DataFlow documentation has step-by-step instructions](https://docs.cloud.google.com/dataflow/docs/guides/build-container-image#before_you_begin).
+
+Now you can pre-build the container at the start of your DataFlow job:
+
+```bash
+python examples/geebeam_run.py \
+    --region us-east1 \
+    --worker_zone us-east1-b \
+    --runner DataflowRunner \
+    --max_num_workers=8 \
+    --num_workers=1 \
+    --experiments=use_runner_v2 \
+    --machine_type=n2-highmem-2 
+    --prebuild_sdk_container_engine=local_docker \
+    --docker_registry_push_url=us-east1-docker.pkg.dev/[PROJECT_ID]/[REPO_NAME]/[IMAGE_NAME] \
+    --setup_file=./setup.py
+```
+
+Next time you can use the existing image with:
+
+```bash
+--sdk_container_image=us-east1-docker.pkg.dev/[PROJECT_ID]/[REPO_NAME]/[IMAGE_NAME]:[IMAGE_TAG]
+```
+
+
+## Alternatives:
+
+- [GeeFlow](https://github.com/google-deepmind/geeflow): Google DeepMind's GeeFlow fulfills a similar purpose. It is more flexible, allowing for more user control of data processing, reprojection, and writing, but slower and no longer actively maintained. With the goal of meeting *most* users' needs, GeeBeam is designed to be easier and quicker to use, but allows from more limited data transformations. 
+- Export training data to Google Cloud Storage then download chips from there: This works, but if you need to get data from many different datasets it's slow to export all that data to Cloud Storage and can be expensive to store it there if you don't delete it quickly. This also uses a lot of Earth Engine compute hours, which are now subject to stricter monthly limits.
+- [Xee](https://github.com/google/Xee): Xee allows for accessing Earth Engine objects as xarray.Datasets. You could use this to define a xarray.Dataset and download "chips" from it, but geebeam interfaces with Beam to automatically parallelize this task.

geebeam-0.1.0/README.md

@@ -0,0 +1,140 @@
+# GeeBeam
+
+[![Testing + Linting](https://github.com/kysolvik/geebeam/actions/workflows/pytest-lint.yml/badge.svg)](https://github.com/kysolvik/geebeam/actions/workflows/pytest-lint.yml)
+
+Google Earth Engine + Apache Beam for building geospatial training datasets
+
+## Purpose:
+
+GeeBeam is a lightweight library for building and executing Apache Beam pipelines that download data "chips" from Google Earth Engine and write them to TensorFlow records for model training.
+
+The user defines the Earth Engine images they want to download chips from using the Python earthengine-api. geebeam then serialized the graph-definition of the images so they can be passed to the Beam workers. 
+
+The pipelines can be run locally or on Google Cloud Dataflow. (Note: currently local jobs are limited to short-running tasks due to grpc "Deadline Exceeded" error).
+
+
+## Install:
+
+```bash
+pip install geebeam
+```
+
+## Examples:
+
+Here we'll create a burned area mask for 2024 using the MCD64A1 product.
+For example, this could be the target variable for a burn risk model.
+
+```python
+import ee
+import geebeam
+import google
+
+# Get default project id from environment (or specify PROJECT_ID manually)
+PROJECT_ID = google.auth.default()[1]
+
+# Initialize ee client, replace with your GCP project ID
+ee.Initalize(project=PROJECT_ID)
+
+# Build image for download
+burned_2024 = (ee.ImageCollection('MODIS/061/MCD64A1')
+            .select('BurnDate')
+            .filter(ee.Filter.calendarRange(2024, 2024, 'year'))
+            .min()
+            .gt(0)
+            .rename(['Burn'])
+            )
+
+# Building and triggering the pipeline is done with a single command:
+geebeam.run(
+    image_list = [burned_2024],
+    project=PROJECT_ID,
+    patch_size=128, # Pixel dimensions in each direction
+    scale=500, # Final export resolution in meters
+    n_sample=10, # Number of tiles to sample
+    validation_ratio=0.2, # Fraction to select as validation data
+    output_path='./test/',
+    sampling_region=ee.Geometry.Rectangle(-63.0, -9.0, -56.0, -4.0),
+    num_workers=2
+)
+```
+
+Now let's add another dataset: MapBiomas Amazonia forest fraction
+```python
+# MB Land-use/land-cover forest fraction
+# Note that LULC codes less than 10 area forest in MapBiomas Amazon Collection 6
+mb_amz_lulc = (
+    ee.Image('projects/mapbiomas-public/assets/amazon/lulc/collection6/mapbiomas_collection60_integration_v1')
+    .lt(10)
+   .reduceResolution('mean', maxPixels=500)
+)
+
+# Exporting both together is as simple as this:
+geebeam.run(
+    image_list = [burned_2024, mb_amz_lulc],
+    project=PROJECT_ID,
+    patch_size=128,
+    scale=500,
+    n_sample=10,
+    validation_ratio=0.2,
+    output_path='./test/',
+    sampling_region=ee.Geometry.Rectangle(-63.0, -9.0, -56.0, -4.0),
+    num_workers=2
+)
+
+```
+
+### Dataflow: 
+
+The export process can be scaled to many workers via Google Cloud DataFlow: 
+
+```bash
+python examples/geebeam_run.py \
+    --region us-east1 \
+    --worker_zone us-east1-b \
+    --runner DataflowRunner \
+    --max_num_workers=8 \
+    --num_workers=1 \
+    --experiments=use_runner_v2 \
+    --machine_type=n2-highmem-2 
+```
+
+Note that in this case the output_path defined in geebeam_run.py should be a Google Cloud Storage path.
+
+#### Artifact registry setup:
+
+To speed up the start-up and running of jobs on DataFlow, you can build a Docker image containing `geebeam` and it's dependencies.
+
+See instructions on Google Cloud
+
+First, you'll need to have Docker installed on your computer, either just [Docker Engine](https://docs.docker.com/engine/) or full [Docker Desktop](https://docs.docker.com/desktop/) will do.
+
+Next, you'll need to create  a Google Artifact Registry respository and configure your Docker to authenticate requests for the Artifact Registry. [Google Cloud DataFlow documentation has step-by-step instructions](https://docs.cloud.google.com/dataflow/docs/guides/build-container-image#before_you_begin).
+
+Now you can pre-build the container at the start of your DataFlow job:
+
+```bash
+python examples/geebeam_run.py \
+    --region us-east1 \
+    --worker_zone us-east1-b \
+    --runner DataflowRunner \
+    --max_num_workers=8 \
+    --num_workers=1 \
+    --experiments=use_runner_v2 \
+    --machine_type=n2-highmem-2 
+    --prebuild_sdk_container_engine=local_docker \
+    --docker_registry_push_url=us-east1-docker.pkg.dev/[PROJECT_ID]/[REPO_NAME]/[IMAGE_NAME] \
+    --setup_file=./setup.py
+```
+
+Next time you can use the existing image with:
+
+```bash
+--sdk_container_image=us-east1-docker.pkg.dev/[PROJECT_ID]/[REPO_NAME]/[IMAGE_NAME]:[IMAGE_TAG]
+```
+
+
+## Alternatives:
+
+- [GeeFlow](https://github.com/google-deepmind/geeflow): Google DeepMind's GeeFlow fulfills a similar purpose. It is more flexible, allowing for more user control of data processing, reprojection, and writing, but slower and no longer actively maintained. With the goal of meeting *most* users' needs, GeeBeam is designed to be easier and quicker to use, but allows from more limited data transformations. 
+- Export training data to Google Cloud Storage then download chips from there: This works, but if you need to get data from many different datasets it's slow to export all that data to Cloud Storage and can be expensive to store it there if you don't delete it quickly. This also uses a lot of Earth Engine compute hours, which are now subject to stricter monthly limits.
+- [Xee](https://github.com/google/Xee): Xee allows for accessing Earth Engine objects as xarray.Datasets. You could use this to define a xarray.Dataset and download "chips" from it, but geebeam interfaces with Beam to automatically parallelize this task.

geebeam-0.1.0/pyproject.toml

@@ -0,0 +1,32 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "geebeam"
+version = "0.1.0"
+license = "MIT"
+description = "Earth Engine + Apache Beam"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "apache-beam[gcp]>=2.71.0",
+    "dill>=0.4.1",
+    "earthengine-api>=1.7.10",
+    "geopandas>=1.0.1",
+    "tensorflow>=2.16",
+    "tensorflow-data-validation>=1.16",
+    "tensorflow-metadata>=1.16",
+    "tfx-bsl>=1.16",
+    "grpcio>=1.62.3",
+]
+
+[tool.hatch.build.targets.sdist]
+include = [
+  "src",
+  "tests",
+  "README.md",
+  "LICENSE",
+  "pyproject.toml",
+  "setup.py"
+]

geebeam-0.1.0/src/geebeam/__init__.py

@@ -0,0 +1,15 @@
+"""Runners
+
+Beam and Earth Engine helpers for running data pipelines
+"""
+
+from . import runner, sampler, transforms, ee_utils, climate_indices
+
+
+__all__ = [
+    "ee_utils",
+    "runner",
+    "sampler",
+    "transforms",
+    "climate_indices",
+]

geebeam-0.1.0/src/geebeam/climate_indices.py

@@ -0,0 +1,37 @@
+"""Helpers to download non-spatial climate indices"""
+
+import pandas as pd
+
+def download_clim_indices(
+        index_name: str,
+        year_start: int,
+        year_end: int
+    ) -> pd.DataFrame:
+    clim_registry = {
+        'amo':'https://www.ncei.noaa.gov/pub/data/cmb/ersst/v5/index/ersst.v5.amo.dat',
+        'soi':'https://psl.noaa.gov/data/timeseries/month/data/soi.long.csv',
+        'oni':'https://psl.noaa.gov/data/correlation/oni.csv',
+        'mei': 'https://psl.noaa.gov/data/correlation/meiv2.csv',
+        'tna': 'https://psl.noaa.gov/data/correlation/tna.csv'
+    }
+
+    try:
+        download_url = clim_registry[index_name]
+    except KeyError:
+        raise ValueError(f'{index_name} not found. Current options are {list(clim_registry.keys())}')
+
+    if index_name == 'amo':
+        df = pd.read_csv(download_url, skiprows=1, sep='\s+')
+        df['Date'] = df['Year'].astype(str) + '-' + df['month'].astype(str) + '-01'
+        df = df.drop(columns=['Year','month'])[['Date','SSTA']]
+    else:
+        df = pd.read_csv(download_url)
+
+    df['Date'] = pd.to_datetime(df['Date'])
+    df.columns = ['Date', 'metric']
+
+    df = df.set_index('Date')
+    indexer = (df.index.year >=year_start) & (df.index.year <= year_end)
+    return df.loc[indexer]
+
+

geebeam-0.1.0/src/geebeam/ee_utils.py

@@ -0,0 +1,40 @@
+"""
+Utilities for cleaning, combining, and serializing/deserializing EE objects.
+"""
+import ee
+
+def deserialize(obj_json):
+    """Deserialize Earth Engine JSON DAG"""
+    return ee.deserializer.fromJSON(obj_json)
+
+def serialize(obj_ee):
+    """Serialize Earth Engine object to JSON for Dataflow workers"""
+    return ee.serializer.toJSON(obj_ee)
+
+def get_band_names(input_list):
+    """Get simplified band_names for output (without prefixed image_id)
+
+    TODO: Add year to distinguish multiple years?
+    """
+    return [
+        image.bandNames()
+        for image in input_list
+    ]
+
+def build_prepped_image(input_list, split_processing=False):
+    """Combine a list of EE images into single image"""
+    band_names = get_band_names(input_list)
+    band_names_flat = ee.List(band_names).flatten()
+
+    if split_processing:
+        band_groups = band_names
+    else:
+        band_groups = [band_names_flat]
+    # Final prepped image
+    prepped_im = ee.ImageCollection(input_list).toBands().rename(band_names_flat)
+    return prepped_im, band_groups
+
+
+def list_to_im(input_list):
+    prepped_im, _ = build_prepped_image(input_list)
+    return prepped_im