From 94a10078d7f01eaade91c09d9a678970a0370253 Mon Sep 17 00:00:00 2001 From: Kevin Booth Date: Wed, 12 Jul 2023 21:19:32 +0000 Subject: [PATCH 1/2] WIP Prototype --- .devcontainer.json | 31 +++++++ .gitmodules | 3 + .vscode/settings.json | 5 ++ Dockerfile | 1 + examples/landcovernet/__init__.py | 0 examples/landcovernet/input/landcovernet.json | 89 +++++++++++++++++++ examples/landcovernet/main.py | 77 ++++++++++++++++ stac-task | 1 + 8 files changed, 207 insertions(+) create mode 100644 .devcontainer.json create mode 100644 .gitmodules create mode 100644 .vscode/settings.json create mode 100644 Dockerfile create mode 100644 examples/landcovernet/__init__.py create mode 100644 examples/landcovernet/input/landcovernet.json create mode 100644 examples/landcovernet/main.py create mode 160000 stac-task diff --git a/.devcontainer.json b/.devcontainer.json new file mode 100644 index 0000000..f01186c --- /dev/null +++ b/.devcontainer.json @@ -0,0 +1,31 @@ +{ + "name": "Python 3.8", + "build": { + "dockerfile": "Dockerfile", + "context": ".." + }, + "customizations": { + "vscode": { + "settings": { + "python.defaultInterpreterPath": "/usr/local/bin/python", + "python.linting.enabled": true, + "python.linting.pylintEnabled": false, + "python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8", + "python.formatting.blackPath": "/usr/local/py-utils/bin/black", + "python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf", + "python.linting.banditPath": "/usr/local/py-utils/bin/bandit", + "python.linting.flake8Path": "/usr/local/py-utils/bin/flake8", + "python.linting.mypyPath": "/usr/local/py-utils/bin/mypy", + "python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle", + "python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle", + "python.linting.pylintPath": "/usr/local/py-utils/bin/pylint" + }, + "extensions": [ + "ms-python.python", + "ms-python.vscode-pylance" + ] + } + }, + "postCreateCommand": "pip install -e stac-task/" +} + \ No newline at end of file diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..d596efb --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "stac-task"] + path = stac-task + url = git@github.com:stac-utils/stac-task.git diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..4651cc7 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,5 @@ +{ + "python.analysis.extraPaths": [ + "./stac-task" + ] +} \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..d469c57 --- /dev/null +++ b/Dockerfile @@ -0,0 +1 @@ +FROM mcr.microsoft.com/devcontainers/python:3.8 \ No newline at end of file diff --git a/examples/landcovernet/__init__.py b/examples/landcovernet/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/examples/landcovernet/input/landcovernet.json b/examples/landcovernet/input/landcovernet.json new file mode 100644 index 0000000..032c536 --- /dev/null +++ b/examples/landcovernet/input/landcovernet.json @@ -0,0 +1,89 @@ +{ + "type": "FeatureCollection", + "process": { + "input_collections": [ + "sentinel-2-l2a" + ], + "workflow": "cog-archive", + "upload_options": { + "path_template": "s3://sentinel-cogs/${collection}/${grid:utm_zone}/${grid:latitude_band}/${grid:grid_square}/${year}/${month}/${id}", + "public_assets": "ALL", + "collections": { + "sentinel-2-l2a": "$[?(@.id =~ 'S2[AB].*')]" + }, + "headers": { + "CacheControl": "public, max-age=31536000, immutable" + } + }, + "tasks": [ + { + "name": "inference", + "parameters": { + "test": "foobar" + } + } + ] + }, + "features": [ + { + "id": "ref_landcovernet_sa_v1_labels_17NRB_00", + "datetime": "2018-07-01T00:00:00Z", + "geometry": { + "type": "Polygon", + "coordinates": [ + [ + [ + -77.81057792539683, + 0.9392721120508254 + ], + [ + -77.81055668144066, + 0.962397053731636 + ], + [ + -77.83353035617907, + 0.9624186203295519 + ], + [ + -77.83355144774016, + 0.9392931603458728 + ], + [ + -77.81057792539683, + 0.9392721120508254 + ] + ] + ] + }, + "assets": { + "labels": { + "href": "https://radiantearth.blob.core.windows.net/mlhub/landcovernet_sa/data/v1.0/2018/17NRB/00/17NRB_00_2018_LC_10m.tif", + "title": "Land Cover" + }, + "source_dates": { + "href": "https://radiantearth.blob.core.windows.net/mlhub/landcovernet_sa/data/v1.0/2018/17NRB/00/17NRB_00_labeling_dates.csv", + "type": "text/csv", + "title": "Source Imagery Dates" + }, + "documentation": { + "href": "https://radiantearth.blob.core.windows.net/mlhub/landcovernet_sa/Documentation.pdf", + "type": "application/pdf" + } + }, + "collection": "ref_landcovernet_sa_v1_labels", + "properties": { + "datetime": "2018-07-01T00:00:00Z" + }, + "bbox": [ + -77.83355144774016, + 0.9392721120508254, + -77.81055668144066, + 0.9624186203295519 + ], + "type": "Feature", + "stac_version": "1.0.0", + "links": [ + ] + } + ] +} \ No newline at end of file diff --git a/examples/landcovernet/main.py b/examples/landcovernet/main.py new file mode 100644 index 0000000..80a463a --- /dev/null +++ b/examples/landcovernet/main.py @@ -0,0 +1,77 @@ +import json +import torch +from stactask import Task +from typing import List, Dict, Any + + +class LandCoverClassificationModel(torch.nn.Module): + def __init__(self, checkpoint=None): + self.checkpoint = checkpoint + pass + + +class TrainTask(Task): + name = "train" + description = "This task trains the model" + + def batches(self, batch_size: int): + l = len(self.items_as_dicts) + for i in range(0, l, batch_size): + yield self.items_as_dicts[i:min(i+batch_size, l)] + + def process(self, batch_size=100, checkpoint=None) -> List[Dict[str, Any]]: + model = LandCoverClassificationModel() + + for i, batch in enumerate(self.batches(batch_size=batch_size)): + print(f"Working on Batch {i+1}") + + return [] + + +class InferenceTask(Task): + name = "inference" + description = "This task creates inferences for the model" + + def process(self, **kwargs) -> List[Dict[str, Any]]: + print(kwargs) + input_item = self.items_as_dicts[0] + + """ + TODO: + - Take the geometry and datetime from the given input STAC item + - Load the imagery required for this model using something like stackstac + - Transform the imagery as needed + - Run the model inferencing code using the transformed imagery + - Transform the inference output as needed + - Upload the transformed inference output to some cloud object storage + - Return the output STAC item with the inference item as an asset + """ + + output_item = { + "type": "Feature", + "id": input_item["id"], + "stac_version": input_item["stac_version"], + "geometry": input_item["geometry"], + "properties": { + "datetime": input_item["properties"]["datetime"] + }, + "links": [], + "assets": { + "inference": { + "href": "s3://foobar/inferences/id.tif", + "type": "image/tiff; application=geotiff; profile=cloud-optimized" + } + } + } + return [ + output_item + ] + + +if __name__ == "__main__": + with open("examples/landcovernet/input/landcovernet.json", "r") as f: + item_collection = json.load(f) + + t = TrainTask(item_collection) + items = t.process(batch_size=100) + print(items) \ No newline at end of file diff --git a/stac-task b/stac-task new file mode 160000 index 0000000..8cd7cb0 --- /dev/null +++ b/stac-task @@ -0,0 +1 @@ +Subproject commit 8cd7cb0f4545f3fe18b477d811edb9af6e17d4b1 From d618c2ccfc2b5c41c7f6ed91b1e3fe5513006767 Mon Sep 17 00:00:00 2001 From: doug-newman-nasa Date: Thu, 30 Nov 2023 11:04:35 -0500 Subject: [PATCH 2/2] Create module env with poetry --- .gitignore | 5 + client/README.md | 48 ++++ client/client/__init__.py | 0 client/client/myFunction.py | 24 ++ client/poetry.lock | 422 ++++++++++++++++++++++++++++++++ client/pyproject.toml | 15 ++ client/tests/__init__.py | 0 client/tests/test_myFunction.py | 9 + 8 files changed, 523 insertions(+) create mode 100644 .gitignore create mode 100644 client/README.md create mode 100644 client/client/__init__.py create mode 100644 client/client/myFunction.py create mode 100644 client/poetry.lock create mode 100644 client/pyproject.toml create mode 100644 client/tests/__init__.py create mode 100644 client/tests/test_myFunction.py diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..198cb88 --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +.DS_store +.pytest_cache +**.pytest_cache** +**__pycache__** +data/** \ No newline at end of file diff --git a/client/README.md b/client/README.md new file mode 100644 index 0000000..c778452 --- /dev/null +++ b/client/README.md @@ -0,0 +1,48 @@ +# MLRD client +Python client which can read a MLRD training dataset catalog and provide an iterator which for each iteration loads a label chip and its source imagery and returns a numpy array for use in training + +## Install Dependencies + +With dev dependencies: +```shell +poetry install +``` + +Without dev dependencies: +```shell +poetry install --no-dev +``` + +## Update Dependencies + +```shell +poetry update +``` + +## Add new Dependency + +```shell +poetry add requests +``` +Development-only dependency: +```shell +poetry add --dev pytest +``` + +## Build project + +```shell +poetry build +``` + +## Lint project + +```shell +poetry run flake8 +``` + +## Run Tests + +```shell +poetry run pytest tests +``` \ No newline at end of file diff --git a/client/client/__init__.py b/client/client/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/client/client/myFunction.py b/client/client/myFunction.py new file mode 100644 index 0000000..12aee06 --- /dev/null +++ b/client/client/myFunction.py @@ -0,0 +1,24 @@ +from math import radians, cos, sin, asin, sqrt + +def haversine(lon1: float, lat1: float, lon2: float, lat2: float) -> float: + """ + Calculate the great circle distance between two points on the + earth (specified in decimal degrees), returns the distance in + kilometers. + All arguments must be of equal length. + :param lon1: longitude of first place + :param lat1: latitude of first place + :param lon2: longitude of second place + :param lat2: latitude of second place + :return: distance in kilometers between the two sets of coordinates + """ + # Convert decimal degrees to radians + lon1, lat1, lon2, lat2 = map(radians, [lon1, lat1, lon2, lat2]) + + # Haversine formula + dlon = lon2 - lon1 + dlat = lat2 - lat1 + a = sin(dlat/2)**2 + cos(lat1) * cos(lat2) * sin(dlon/2)**2 + c = 2 * asin(sqrt(a)) + r = 6371 # Radius of earth in kilometers + return c * r \ No newline at end of file diff --git a/client/poetry.lock b/client/poetry.lock new file mode 100644 index 0000000..a883668 --- /dev/null +++ b/client/poetry.lock @@ -0,0 +1,422 @@ +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. + +[[package]] +name = "filelock" +version = "3.13.1" +description = "A platform independent file lock." +optional = false +python-versions = ">=3.8" +files = [ + {file = "filelock-3.13.1-py3-none-any.whl", hash = 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(>=1)"] +dask = ["dask", "distributed"] +devel = ["pytest", "pytest-cov"] +dropbox = ["dropbox", "dropboxdrivefs", "requests"] +full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"] +fuse = ["fusepy"] +gcs = ["gcsfs"] +git = ["pygit2"] +github = ["requests"] +gs = ["gcsfs"] +gui = ["panel"] +hdfs = ["pyarrow (>=1)"] +http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "requests"] +libarchive = ["libarchive-c"] +oci = ["ocifs"] +s3 = ["s3fs"] +sftp = ["paramiko"] +smb = ["smbprotocol"] +ssh = ["paramiko"] +tqdm = ["tqdm"] + +[[package]] +name = "jinja2" +version = "3.1.2" +description = "A very fast and expressive template engine." +optional = false +python-versions = ">=3.7" +files = [ + {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"}, + {file 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