Merge branch 'dev' into 'main'

Dev

See merge request aletrn/gis-prediction!1

.coveragerc

@@ -1,9 +1,9 @@
 [run]
-source = src
+source = samgis
 omit = ./venv/*,*tests*,*apps.py,*manage.py,*__init__.py,*migrations*,*asgi*,*wsgi*,*admin.py,*urls.py,./tests/*
 
 [report]
 omit = ./venv/*,*tests*,*apps.py,*manage.py,*__init__.py,*migrations*,*asgi*,*wsgi*,*admin.py,*urls.py,./tests/*
 
 exclude_lines =
-     if __name__ == .__main__.:
+     if __name__ == .__main__.:

.dockerignore

@@ -7,3 +7,10 @@ tmp/
 __pycache__
 .DS_Store
 .pytest_cache
+node_modules
+dist
+static/node_modules
+static/dist
+static/.env*
+.coverage
+.git

.idea/misc.xml

@@ -3,5 +3,5 @@
   <component name="Black">
     <option name="sdkName" value="Python 3.11 (samgis)" />
   </component>
-  <component name="ProjectRootManager" version="2" project-jdk-name="Pipenv (samgis)" project-jdk-type="Python SDK" />
+  <component name="ProjectRootManager" version="2" project-jdk-name="Poetry (samgis)" project-jdk-type="Python SDK" />
 </project>

Dockerfile

@@ -0,0 +1,41 @@
+FROM localhost/samgis-base-fastapi:latest
+
+# Include global arg in this stage of the build
+ARG LAMBDA_TASK_ROOT="/var/task"
+ARG PYTHONPATH="${LAMBDA_TASK_ROOT}:${PYTHONPATH}:/usr/local/lib/python3/dist-packages"
+ENV VIRTUAL_ENV=${LAMBDA_TASK_ROOT}/.venv \
+    PATH="${LAMBDA_TASK_ROOT}/.venv/bin:$PATH"
+
+# Set working directory to function root directory
+WORKDIR ${LAMBDA_TASK_ROOT}
+
+# don't copy here the "static" folder, is already present because of dist and node_modules folders
+COPY machine_learning_models ${LAMBDA_TASK_ROOT}/machine_learning_models
+COPY samgis ${LAMBDA_TASK_ROOT}/samgis
+COPY wrappers ${LAMBDA_TASK_ROOT}/wrappers
+
+RUN ls -l /usr/bin/which
+RUN /usr/bin/which python
+RUN python -v
+RUN echo "PYTHONPATH: ${PYTHONPATH}."
+RUN echo "PATH: ${PATH}."
+RUN echo "LAMBDA_TASK_ROOT: ${LAMBDA_TASK_ROOT}."
+RUN ls -l ${LAMBDA_TASK_ROOT}
+RUN ls -ld ${LAMBDA_TASK_ROOT}
+RUN ls -l ${LAMBDA_TASK_ROOT}/machine_learning_models
+RUN python -c "import sys; print(sys.path)"
+RUN python -c "import cv2"
+RUN python -c "import fastapi"
+RUN python -c "import geopandas"
+RUN python -c "import loguru"
+RUN python -c "import onnxruntime"
+RUN python -c "import rasterio"
+RUN python -c "import uvicorn"
+RUN df -h
+RUN ls -l ${LAMBDA_TASK_ROOT}/samgis/
+RUN ls -l ${LAMBDA_TASK_ROOT}/wrappers/
+RUN ls -l ${LAMBDA_TASK_ROOT}/static/
+RUN ls -l ${LAMBDA_TASK_ROOT}/static/dist
+RUN ls -l ${LAMBDA_TASK_ROOT}/static/node_modules
+
+CMD ["uvicorn", "wrappers.fastapi_wrapper:app", "--host", "0.0.0.0", "--port", "7860"]

Pipfile

@@ -1,31 +0,0 @@
-[[source]]
-url = "https://pypi.org/simple"
-verify_ssl = true
-name = "pypi"
-
-[packages]
-sphinx = "*"
-sphinx-autodoc-typehints = "*"
-myst-parser = "*"
-
-[dev-packages]
-aws-lambda-powertools = "*"
-awslambdaric = "*"
-bson = "*"
-geopandas = "*"
-jmespath = "*"
-matplotlib = "*"
-numpy = "*"
-onnxruntime = "*"
-opencv-python-headless = "*"
-pillow = "*"
-pydantic = ">=2.0.3"
-python-dotenv = "*"
-rasterio = "*"
-requests = "*"
-pytest = "*"
-pytest-cov = "*"
-
-[requires]
-python_version = "3.11"
-python_full_version = "3.11.6"

README.md

@@ -1,36 +1,64 @@
-# SamGIS
+---
+title: SamGIS
+emoji: 📉
+colorFrom: red
+colorTo: blue
+sdk: docker
+pinned: false
+---
 
-## todo
+## SamGIS - HuggingFace version
 
-1. export output to mask: OK local, OK aws lambda
-2. resolve model paths: OK local
-3. inference: 
-4. from mask to json (rasterio + geopandas, check for re-projection to EPSG_4326)
-5. check mandatory dependencies
-6. check for alternative python interpreters
+Build the docker image this way:
 
-## Build instructions
+```bash
+# clean any old active containers
+docker stop $(docker ps -a -q); docker rm $(docker ps -a -q)
+
+# build the base docker image with the ARG DEPENDENCY_GROUP=fastapi used by poetry
+docker build . -f dockerfiles/dockerfile-samgis-base --build-arg DEPENDENCY_GROUP=fastapi --tag localhost/samgis-base-fastapi --progress=plain
 
-Build the docker image:
+# build the image, use the tag "samgis-huggingface"
+docker build . --tag localhost/samgis-huggingface --progress=plain
+```
+
+Run the container (keep it on background) and show logs
+
+```bash
+docker run  -d --name samgis-huggingface -p 7860:7860 localhost/samgis-huggingface; docker logs -f samgis-huggingface
+```
+
+Test it with curl:
+
+```bash
+curl -X 'POST' \
+  'http://localhost:7860/infer_samgeo' \
+  -H 'accept: application/json' \
+  -d '{}'
+```
+
+or better visiting the swagger page on http://localhost:7860/docs 
+
+
+## SamGIS - lambda AWS version
+
+Build the docker image this way:
 
 ```bash
 # clean any old active containers
 docker stop $(docker ps -a -q); docker rm $(docker ps -a -q)
 
 # build the base docker image with the docker aws repository tag
-docker build . -f dockerfiles/dockerfile-lambda-gdal-runner --tag 686901913580.dkr.ecr.eu-west-1.amazonaws.com/lambda-gdal-runner
-
-# OPTIONAL: to build the lambda-gdal-runner image on a x86 machine use the build arg `RIE="https://github.com/aws/aws-lambda-runtime-interface-emulator/releases/latest/download/aws-lambda-rie"`:
-docker build . -f dockerfiles/dockerfile-lambda-gdal-runner --build-arg RIE="https://github.com/aws/aws-lambda-runtime-interface-emulator/releases/latest/download/aws-lambda-rie" --tag 686901913580.dkr.ecr.eu-west-1.amazonaws.com/lambda-gdal-runner --progress=plain
+docker build . -f dockerfiles/dockerfile-samgis-base --build-arg DEPENDENCY_GROUP=aws_lambda --tag localhost/samgis-base-aws-lambda --progress=plain
 
 # build the final docker image
-docker build . -f dockerfiles/dockerfile-lambda-fastsam-api --tag 686901913580.dkr.ecr.eu-west-1.amazonaws.com/lambda-fastsam-api
+docker build . -f dockerfiles/dockerfile-lambda-fastsam-api --tag localhost/lambda-fastsam-api --progress=plain
 ```
 
 Run the container (keep it on background) and show logs
 
 ```bash
-docker tag 686901913580.dkr.ecr.eu-west-1.amazonaws.com/lambda-fastsam-api:latest lambda-fastsam-api;docker run  -d --name lambda-fastsam-api -p 8080:8080 lambda-fastsam-api; docker logs -f lambda-fastsam-api
+docker run  -d --name lambda-fastsam-api -p 8080:8080 lambda-fastsam-api; docker logs -f lambda-fastsam-api
 ```
 
 Test it with curl:
@@ -43,33 +71,23 @@ curl -X 'POST' \
   -d '{}'
 ```
 
-## Publish the aws lambda
-1. Login on aws ECR with the correct aws profile (details on [ECR page](https://eu-west-1.console.aws.amazon.com/ecr/repositories/private/686901913580/surferdtm-prediction-api?region=eu-west-1))
-    ```
-    aws --profile alessandrotrinca_hotmail_aws_console_ec2_lambda ecr get-login-password --region eu-west-1 | docker login --username AWS --password-stdin 686901913580.dkr.ecr.eu-west-1.amazonaws.com
-    ```
-2. Build and tag the docker images, then push them:
-    ```
-    docker push 686901913580.dkr.ecr.eu-west-1.amazonaws.com/lambda-gdal-runner:latest
-    docker push 686901913580.dkr.ecr.eu-west-1.amazonaws.com/lambda-fastsam-api:latest
-    ```
-3. It's possible to publish a new aws lambda version from cmd or from lambda page
-
-
-## Dependencies installation and local tests
-The docker build process needs only the classic requirements.txt (here renamed to `requirements_dockerfile.txt`), instead for local development and sphinx-docs build 
-there is `Pipfile` (sphinx docs is hosted on Cloudflare Pages).
+### Publish the aws lambda docker image
+Login on aws ECR with the correct aws profile (change the example `localhost/` repository url with the one from
+the [ECR push command instructions page](https://eu-west-1.console.aws.amazon.com/ecr/repositories/)).
 
+### Dependencies installation and local tests
+The docker build process needs only the base dependency group plus the `aws_lambda` or `fastapi` optional one.
+Install also the `test` and/or `docs` groups if needed.
 
-## Tests
+### Tests
 
 Tests are defined in the `tests` folder in this project. Use PIP to install the test dependencies and run tests.
 
 ```bash
-python -m pytest --cov=src --cov-report=term-missing && coverage html
+python -m pytest --cov=samgis --cov-report=term-missing && coverage html
 ```
 
-## Update the static documentation with sphinx
+### How to update the static documentation with sphinx
 
 Run the sphinx-apidoc: it's a tool for automatic generation of Sphinx sources that, using the autodoc
 extension, document a whole package in the style of other automatic API documentation tools. See the 
@@ -78,10 +96,10 @@ Run the command from the project root:
 
 ```bash
 # missing docs folder (run from project root)
-cd docs && sphinx-quickstart -p SamGIS -a "alessandro trinca tornidor" -r 1.0.0 -l python --master index
+cd docs && sphinx-quickstart -p SamGIS -r 1.0.0 -l python --master index
 
 # update docs folder (from project root)
-sphinx-apidoc -f -o docs src
+sphinx-apidoc -f -o docs samgis
 ```
 
 Then it's possible to generate the HTML pages 

dockerfiles/dockerfile-fastapi-fastsam-api

@@ -0,0 +1 @@
+Dockerfile

dockerfiles/dockerfile-fastapi-samgeo

@@ -1,38 +0,0 @@
-FROM ghcr.io/osgeo/gdal:ubuntu-small-3.7.2
-
-WORKDIR /code
-COPY ./requirements_dockerfile.txt /code/requirements_dockerfile.txt
-COPY ./requirements_pip.txt /code/requirements_pip.txt
-
-RUN apt update && apt install -y g++ make cmake unzip libcurl4-openssl-dev python3-pip
-
-# avoid segment-geospatial exception caused by missing libGL.so.1 library
-RUN apt install -y libgl1 curl
-RUN ls -ld /usr/lib/x86_64-linux-gnu/libGL.so* || echo "libGL.so* not found..."
-
-RUN which python
-RUN python --version
-RUN python -m pip install --no-cache-dir --upgrade -r /code/requirements_pip.txt
-RUN python -m pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
-RUN python -m pip install --no-cache-dir -r /code/requirements_dockerfile.txt
-
-RUN useradd -m -u 1000 user
-
-USER user
-
-ENV HOME=/home/user \
-	PATH=/home/user/.local/bin:$PATH
-
-WORKDIR $HOME/app
-
-RUN curl -o ${HOME}/sam_vit_h_4b8939.pth https://dl.fbaipublicfiles.com/segment_anything/sam_vit_h_4b8939.pth
-RUN ls -l ${HOME}/
-COPY --chown=user . $HOME/app
-
-RUN echo $HOME/app
-RUN echo $HOME/
-
-RUN ls -l $HOME/app
-RUN ls -l $HOME/
-
-CMD ["uvicorn", "src.main:app", "--host", "0.0.0.0", "--port", "7860"]

dockerfiles/dockerfile-lambda-fastsam-api

@@ -1,12 +1,15 @@
-FROM 686901913580.dkr.ecr.eu-west-1.amazonaws.com/lambda-gdal-runner:latest
+FROM localhost/samgis-base-aws-lambda:latest
 
 # Include global arg in this stage of the build
 ARG LAMBDA_TASK_ROOT="/var/task"
 ARG PYTHONPATH="${LAMBDA_TASK_ROOT}:${PYTHONPATH}:/usr/local/lib/python3/dist-packages"
+ENV VIRTUAL_ENV=${LAMBDA_TASK_ROOT}/.venv \
+    PATH="${LAMBDA_TASK_ROOT}/.venv/bin:$PATH"
 
 # Set working directory to function root directory
 WORKDIR ${LAMBDA_TASK_ROOT}
-COPY ./src ${LAMBDA_TASK_ROOT}/src
+COPY ./samgis ${LAMBDA_TASK_ROOT}/samgis
+COPY ./wrappers ${LAMBDA_TASK_ROOT}/wrappers
 COPY ./machine_learning_models ${LAMBDA_TASK_ROOT}/machine_learning_models
 
 RUN ls -l /usr/bin/which
@@ -19,16 +22,15 @@ RUN ls -l ${LAMBDA_TASK_ROOT}
 RUN ls -ld ${LAMBDA_TASK_ROOT}
 RUN ls -l ${LAMBDA_TASK_ROOT}/machine_learning_models
 RUN python -c "import sys; print(sys.path)"
+RUN python -c "import awslambdaric"
 RUN python -c "import cv2"
 RUN python -c "import geopandas"
 RUN python -c "import onnxruntime"
 RUN python -c "import rasterio"
-RUN python -c "import awslambdaric"
-RUN python -m pip list
-RUN python -m pip freeze
 RUN df -h
 RUN ls -l /lambda-entrypoint.sh
-RUN ls -l ${LAMBDA_TASK_ROOT}/src/
+RUN ls -l ${LAMBDA_TASK_ROOT}/samgis/
+RUN ls -l ${LAMBDA_TASK_ROOT}/wrappers/
 
-# ENTRYPOINT  ["/lambda-entrypoint.sh"]
-CMD [ "src.app.lambda_handler" ]
+ENTRYPOINT  ["/lambda-entrypoint.sh"]
+CMD [ "wrappers.lambda_wrapper.lambda_handler" ]

dockerfiles/dockerfile-lambda-gdal-runner

@@ -1,32 +0,0 @@
-FROM python:3.11-slim-bookworm
-
-# Include global arg in this stage of the build
-ARG LAMBDA_TASK_ROOT="/var/task"
-ARG PYTHONPATH="${LAMBDA_TASK_ROOT}:${PYTHONPATH}:/usr/local/lib/python3/dist-packages"
-ARG RIE="https://github.com/aws/aws-lambda-runtime-interface-emulator/releases/latest/download/aws-lambda-rie"
-
-RUN echo "ENV RIE: $RIE ..."
-
-# Set working directory to function root directory
-WORKDIR ${LAMBDA_TASK_ROOT}
-COPY requirements_pip.txt ${LAMBDA_TASK_ROOT}/requirements_pip.txt
-COPY requirements_dockerfile.txt ${LAMBDA_TASK_ROOT}/requirements_dockerfile.txt
-
-# avoid segment-geospatial exception caused by missing libGL.so.1 library
-RUN apt update && apt install -y libgl1 curl python3-pip && apt clean
-RUN ls -ld /usr/lib/*linux-gnu/libGL.so* || echo "libGL.so* not found..."
-RUN which python
-RUN python --version
-RUN python -m pip install -r ${LAMBDA_TASK_ROOT}/requirements_pip.txt --upgrade --target ${LAMBDA_TASK_ROOT}
-RUN python -m pip install -r ${LAMBDA_TASK_ROOT}/requirements_dockerfile.txt --target ${LAMBDA_TASK_ROOT}
-RUN python -c "import sys;print(sys.path)"
-# RUN python -m pip install pillow awslambdaric aws-lambda-powertools httpx jmespath --target ${LAMBDA_TASK_ROOT}
-
-RUN curl -Lo /usr/local/bin/aws-lambda-rie ${RIE}
-RUN chmod +x /usr/local/bin/aws-lambda-rie
-
-COPY ./scripts/lambda-entrypoint.sh /lambda-entrypoint.sh
-RUN chmod +x /lambda-entrypoint.sh
-RUN ls -l /lambda-entrypoint.sh
-
-ENTRYPOINT  ["/lambda-entrypoint.sh"]

dockerfiles/dockerfile-samgis-base

@@ -0,0 +1,117 @@
+# Include global ARGs at the dockerfile top
+ARG ARCH="x86_64"
+ARG LAMBDA_TASK_ROOT="/var/task"
+ARG FASTAPI_STATIC="${LAMBDA_TASK_ROOT}/static"
+ARG PYTHONPATH="${LAMBDA_TASK_ROOT}:${PYTHONPATH}:/usr/local/lib/python3/dist-packages"
+ARG POETRY_NO_INTERACTION=1
+ARG POETRY_VIRTUALENVS_IN_PROJECT=1
+ARG POETRY_VIRTUALENVS_CREATE=1
+ARG POETRY_CACHE_DIR=/tmp/poetry_cache
+ARG RIE="https://github.com/aws/aws-lambda-runtime-interface-emulator/releases/latest/download/aws-lambda-rie"
+
+
+FROM python:3.11-bookworm as builder_global
+
+ARG ARCH
+ARG LAMBDA_TASK_ROOT
+ARG PYTHONPATH
+ARG POETRY_NO_INTERACTION
+ARG POETRY_VIRTUALENVS_IN_PROJECT
+ARG POETRY_VIRTUALENVS_CREATE
+ARG POETRY_CACHE_DIR
+ARG RIE
+ARG DEPENDENCY_GROUP
+
+RUN echo "ARCH: $ARCH ..."
+
+RUN echo "ARG RIE: $RIE ..."
+RUN echo "ARG POETRY_CACHE_DIR: ${POETRY_CACHE_DIR} ..."
+RUN echo "ARG PYTHONPATH: $PYTHONPATH ..."
+RUN test -n ${DEPENDENCY_GROUP:?}
+RUN echo "python DEPENDENCY_GROUP: ${DEPENDENCY_GROUP} ..."
+RUN echo "arg dep:"
+
+# Set working directory to function root directory
+WORKDIR ${LAMBDA_TASK_ROOT}
+COPY requirements_poetry.txt pyproject.toml poetry.lock README.md ${LAMBDA_TASK_ROOT}/
+
+# avoid segment-geospatial exception caused by missing libGL.so.1 library
+# RUN apt update && apt install -y libgl1 curl python3-pip && apt clean
+RUN apt update && apt install -y libgl1 curl
+RUN apt update && apt install -y python3-pip && apt clean
+
+# poetry installation path is NOT within ${LAMBDA_TASK_ROOT}: not needed for runtime docker image
+RUN python -m pip install -r ${LAMBDA_TASK_ROOT}/requirements_poetry.txt
+
+RUN which poetry && poetry --version && poetry config --list
+RUN poetry config virtualenvs.path ${LAMBDA_TASK_ROOT}
+RUN echo "# poetry config --list #" && poetry config --list
+RUN poetry install --with ${DEPENDENCY_GROUP} --no-root
+
+RUN curl -Lo /usr/local/bin/aws-lambda-rie ${RIE}
+
+
+FROM python:3.11-slim-bookworm as runtime
+
+ARG ARCH
+ARG LAMBDA_TASK_ROOT
+
+ENV VIRTUAL_ENV=${LAMBDA_TASK_ROOT}/.venv \
+    PATH="${LAMBDA_TASK_ROOT}/.venv/bin:$PATH"
+
+RUN echo "COPY --from=builder_global /usr/lib/${ARCH}-linux-gnu/libGL.so* /usr/lib/${ARCH}-linux-gnu/"
+COPY --from=builder_global /usr/lib/${ARCH}-linux-gnu/libGL.so* /usr/lib/${ARCH}-linux-gnu/
+COPY --from=builder_global ${LAMBDA_TASK_ROOT}/.venv ${LAMBDA_TASK_ROOT}/.venv
+
+RUN echo "new LAMBDA_TASK_ROOT after hidden venv copy => ${LAMBDA_TASK_ROOT}"
+RUN ls -ld ${LAMBDA_TASK_ROOT}/
+RUN ls -lA ${LAMBDA_TASK_ROOT}/
+
+COPY --from=builder_global /usr/local/bin/aws-lambda-rie /usr/local/bin/aws-lambda-rie
+RUN chmod +x /usr/local/bin/aws-lambda-rie
+COPY ./scripts/lambda-entrypoint.sh /lambda-entrypoint.sh
+RUN chmod +x /lambda-entrypoint.sh
+
+
+### conditional section
+FROM node:20-slim AS node_fastapi
+
+ARG DEPENDENCY_GROUP
+ENV PNPM_HOME="/pnpm"
+ENV PATH="$PNPM_HOME:$PATH"
+RUN corepack enable
+
+COPY ./static /appnode
+WORKDIR /appnode
+# RUN if [ "${DEPENDENCY_GROUP}" = "fastapi" ]; then echo "pnpm store path:" && pnpm store path; fi
+
+
+FROM node_fastapi AS node_prod_deps
+
+ARG DEPENDENCY_GROUP
+RUN --mount=type=cache,id=pnpm,target=/pnpm/store if [ "${DEPENDENCY_GROUP}" = "fastapi" ]; then \
+    pnpm install --prod --frozen-lockfile; else \
+    echo "DEPENDENCY_GROUP 1: ${DEPENDENCY_GROUP} ..."; fi
+# here multiple conditions concatenated to avoid failing on check
+RUN if [ "${DEPENDENCY_GROUP}" = "fastapi" ]; then if [ ! -d /appnode/node_modules ]; then echo "no node_modules folder" && exit 1; fi; fi
+
+
+FROM node_fastapi AS node_build
+
+ARG DEPENDENCY_GROUP
+RUN --mount=type=cache,id=pnpm,target=/pnpm/store if [ "${DEPENDENCY_GROUP}" = "fastapi" ]; then \
+    pnpm install --frozen-lockfile; else \
+    echo "DEPENDENCY_GROUP 2: ${DEPENDENCY_GROUP} ..."; fi
+RUN --mount=type=cache,id=pnpm,target=/pnpm/store if [ "${DEPENDENCY_GROUP}" = "fastapi" ]; then \
+    pnpm build; fi
+RUN --mount=type=cache,id=pnpm,target=/pnpm/store if [ "${DEPENDENCY_GROUP}" = "fastapi" ]; then \
+    pnpm tailwindcss -i /appnode/src/input.css -o /appnode/dist/output.css; fi
+RUN if [ "${DEPENDENCY_GROUP}" = "fastapi" ]; then if [ ! -d /appnode/dist ]; then echo "no dist folder" && exit 1; fi; fi
+
+
+FROM runtime
+ARG FASTAPI_STATIC
+RUN mkdir ${FASTAPI_STATIC}
+
+COPY --from=node_prod_deps /appnode/node_modules* ${FASTAPI_STATIC}/node_modules
+COPY --from=node_build /appnode/dist* ${FASTAPI_STATIC}/dist

docs/modules.rst

@@ -1,7 +1,7 @@
-src
-===
+samgis
+======
 
 .. toctree::
    :maxdepth: 4
 
-   src
+   samgis

docs/{src.utilities.rst → samgis.io.rst}

@@ -1,37 +1,45 @@
-src.utilities package
-=====================
+samgis.io package
+=================
 
 Submodules
 ----------
 
-src.utilities.constants module
-------------------------------
+samgis.io.coordinates\_pixel\_conversion module
+-----------------------------------------------
 
-.. automodule:: src.utilities.constants
+.. automodule:: samgis.io.coordinates_pixel_conversion
    :members:
    :undoc-members:
    :show-inheritance:
 
-src.utilities.serialize module
-------------------------------
+samgis.io.geo\_helpers module
+-----------------------------
 
-.. automodule:: src.utilities.serialize
+.. automodule:: samgis.io.geo_helpers
    :members:
    :undoc-members:
    :show-inheritance:
 
-src.utilities.type\_hints module
+samgis.io.lambda\_helpers module
 --------------------------------
 
-.. automodule:: src.utilities.type_hints
+.. automodule:: samgis.io.lambda_helpers
    :members:
    :undoc-members:
    :show-inheritance:
 
-src.utilities.utilities module
-------------------------------
+samgis.io.lambda\_wrapper module
+--------------------------------
+
+.. automodule:: samgis.io.lambda_wrapper
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+samgis.io.tms2geotiff module
+----------------------------
 
-.. automodule:: src.utilities.utilities
+.. automodule:: samgis.io.tms2geotiff
    :members:
    :undoc-members:
    :show-inheritance:
@@ -39,7 +47,7 @@ src.utilities.utilities module
 Module contents
 ---------------
 
-.. automodule:: src.utilities
+.. automodule:: samgis.io
    :members:
    :undoc-members:
    :show-inheritance:

docs/{src.prediction_api.rst → samgis.prediction_api.rst}

@@ -1,21 +1,21 @@
-src.prediction\_api package
-===========================
+samgis.prediction\_api package
+==============================
 
 Submodules
 ----------
 
-src.prediction\_api.predictors module
--------------------------------------
+samgis.prediction\_api.predictors module
+----------------------------------------
 
-.. automodule:: src.prediction_api.predictors
+.. automodule:: samgis.prediction_api.predictors
    :members:
    :undoc-members:
    :show-inheritance:
 
-src.prediction\_api.sam\_onnx module
-------------------------------------
+samgis.prediction\_api.sam\_onnx module
+---------------------------------------
 
-.. automodule:: src.prediction_api.sam_onnx
+.. automodule:: samgis.prediction_api.sam_onnx
    :members:
    :undoc-members:
    :show-inheritance:
@@ -23,7 +23,7 @@ src.prediction\_api.sam\_onnx module
 Module contents
 ---------------
 
-.. automodule:: src.prediction_api
+.. automodule:: samgis.prediction_api
    :members:
    :undoc-members:
    :show-inheritance:

docs/{src.rst → samgis.rst}

@@ -1,5 +1,5 @@
-src package
-===========
+samgis package
+==============
 
 Subpackages
 -----------
@@ -7,25 +7,14 @@ Subpackages
 .. toctree::
    :maxdepth: 4
 
-   src.io
-   src.prediction_api
-   src.utilities
-
-Submodules
-----------
-
-src.app module
---------------
-
-.. automodule:: src.app
-   :members:
-   :undoc-members:
-   :show-inheritance:
+   samgis.io
+   samgis.prediction_api
+   samgis.utilities
 
 Module contents
 ---------------
 
-.. automodule:: src
+.. automodule:: samgis
    :members:
    :undoc-members:
    :show-inheritance:

docs/{src.io.rst → samgis.utilities.rst}

@@ -1,37 +1,37 @@
-src.io package
-==============
+samgis.utilities package
+========================
 
 Submodules
 ----------
 
-src.io.coordinates\_pixel\_conversion module
---------------------------------------------
+samgis.utilities.constants module
+---------------------------------
 
-.. automodule:: src.io.coordinates_pixel_conversion
+.. automodule:: samgis.utilities.constants
    :members:
    :undoc-members:
    :show-inheritance:
 
-src.io.geo\_helpers module
---------------------------
+samgis.utilities.serialize module
+---------------------------------
 
-.. automodule:: src.io.geo_helpers
+.. automodule:: samgis.utilities.serialize
    :members:
    :undoc-members:
    :show-inheritance:
 
-src.io.lambda\_helpers module
------------------------------
+samgis.utilities.type\_hints module
+-----------------------------------
 
-.. automodule:: src.io.lambda_helpers
+.. automodule:: samgis.utilities.type_hints
    :members:
    :undoc-members:
    :show-inheritance:
 
-src.io.tms2geotiff module
--------------------------
+samgis.utilities.utilities module
+---------------------------------
 
-.. automodule:: src.io.tms2geotiff
+.. automodule:: samgis.utilities.utilities
    :members:
    :undoc-members:
    :show-inheritance:
@@ -39,7 +39,7 @@ src.io.tms2geotiff module
 Module contents
 ---------------
 
-.. automodule:: src.io
+.. automodule:: samgis.utilities
    :members:
    :undoc-members:
    :show-inheritance:

events/payload_point.json

@@ -9,6 +9,6 @@
     "label": 0
   }],
   "zoom": 6,
-  "source_type": "Satellite",
+  "source_type": "OpenStreetMap",
   "debug": true
 }

events/payload_point2.json

@@ -9,6 +9,6 @@
     "label": 0
   }],
   "zoom": 10,
-  "source_type": "Satellite",
+  "source_type": "OpenStreetMap",
   "debug": true
 }

events/payload_point_eolie.json

@@ -20,5 +20,5 @@
     }
   ],
   "zoom": 10,
-  "source_type": "Satellite"
+  "source_type": "OpenStreetMap"
 }

pyproject.toml

@@ -0,0 +1,60 @@
+[tool.poetry]
+name = "samgis"
+version = "1.0.0"
+description = "A backend for machine learning instance segmentation on geospatial data even without dedicated graphics cards."
+authors = ["alessandro trinca tornidor <alessandro@trinca.tornidor.com>"]
+license = "MIT license"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+bson = "^0.5.10"
+contextily = "^1.4.0"
+geopandas = "^0.14.1"
+numpy = "^1.26.2"
+onnxruntime = "^1.16.3"
+opencv-python-headless = "^4.8.1.78"
+python = "^3.11"
+python-dotenv = "^1.0.0"
+rasterio = "^1.3.9"
+requests = "^2.31.0"
+pillow = "^10.1.0"
+loguru = "^0.7.2"
+
+[tool.poetry.group.aws_lambda]
+optional = true
+
+[tool.poetry.group.aws_lambda.dependencies]
+aws-lambda-powertools = "^2.30.2"
+awslambdaric = "^2.0.8"
+jmespath = "^1.0.1"
+pydantic = "^2.5.3"
+
+[tool.poetry.group.test]
+optional = true
+
+[tool.poetry.group.test.dependencies]
+pytest = "^7.4.3"
+pytest-cov = "^4.1.0"
+python-dotenv = "^1.0.0"
+
+[tool.poetry.group.docs]
+optional = true
+
+[tool.poetry.group.docs.dependencies]
+sphinx = "^7.2.6"
+sphinx-autodoc-typehints = "^1.25.2"
+sphinxcontrib-openapi = "^0.8.3"
+myst-parser = "^2.0.0"
+
+[tool.poetry.group.fastapi]
+optional = true
+
+[tool.poetry.group.fastapi.dependencies]
+fastapi = "^0.108.0"
+loguru = "^0.7.2"
+pydantic = "^2.5.3"
+uvicorn = "^0.25.0"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

pytest.ini

@@ -3,5 +3,5 @@ env_override_existing_values = 1
 env_files =
     test/.test.env
 [path]
-source = src
-omit = ./venv/*,*tests*,*apps.py,*manage.py,*__init__.py,*migrations*,*asgi*,*wsgi*,*admin.py,*urls.py,./tests/*
+source = samgis
+omit = ./venv/*,*tests*,*apps.py,*manage.py,*__init__.py,*migrations*,*asgi*,*wsgi*,*admin.py,*urls.py,./tests/*

requirements_dev.txt

@@ -1,12 +1,13 @@
 aws-lambda-powertools
 awslambdaric
 bson
+contextily
 geopandas
 jmespath
-matplotlib
+myst-parser
 numpy
 onnxruntime
-opencv-python
+opencv-python-headless
 pillow
 pydantic>=2.0.3
 pytest

requirements_pip.txt

@@ -1,3 +0,0 @@
-pip
-wheel
-setuptools

requirements_poetry.txt

@@ -0,0 +1 @@
+poetry==1.7.1

samgis/__init__.py

@@ -0,0 +1,41 @@
+"""Get machine learning predictions from geodata raster images"""
+# not used here but contextily_tile is imported in samgis.io.tms2geotiff
+from contextily import tile as contextily_tile
+from pathlib import Path
+
+from samgis.utilities.constants import SERVICE_NAME
+
+
+PROJECT_ROOT_FOLDER = Path(globals().get("__file__", "./_")).absolute().parent.parent
+MODEL_FOLDER = Path(PROJECT_ROOT_FOLDER / "machine_learning_models")
+try:
+    from aws_lambda_powertools import Logger
+
+    app_logger = Logger(service=SERVICE_NAME)
+except ModuleNotFoundError:
+    import loguru
+
+    def setup_logging(debug: bool = False, formatter: str = "{time} - {level} - ({extra[request_id]}) {message} "
+                      ) -> loguru.logger:
+        """
+        Create a logging instance with log string formatter.
+
+        Args:
+            debug: logging debug argument
+            formatter: log string formatter
+
+        Returns:
+            Logger
+
+        """
+        import sys
+
+        logger = loguru.logger
+        logger.remove()
+        level_logger = "DEBUG" if debug else "INFO"
+        logger.add(sys.stdout, format=formatter, level=level_logger)
+        logger.info(f"type_logger:{type(logger)}, logger:{logger}.")
+        return logger
+
+
+    app_logger = setup_logging(debug=True)

samgis/__version__.py

@@ -0,0 +1 @@
+__version__ = "1.0.0"

{src → samgis}/io/coordinates_pixel_conversion.py

@@ -1,8 +1,8 @@
 """functions useful to convert to/from latitude-longitude coordinates to pixel image coordinates"""
-from src import app_logger
-from src.utilities.constants import TILE_SIZE, EARTH_EQUATORIAL_RADIUS
-from src.utilities.type_hints import ImagePixelCoordinates, tuple_float, tuple_float_any
-from src.utilities.type_hints import LatLngDict
+from samgis import app_logger
+from samgis.utilities.constants import TILE_SIZE, EARTH_EQUATORIAL_RADIUS
+from samgis.utilities.type_hints import ImagePixelCoordinates, tuple_float, tuple_float_any
+from samgis.utilities.type_hints import LatLngDict
 
 
 def _get_latlng2pixel_projection(latlng: LatLngDict) -> ImagePixelCoordinates:

{src → samgis}/io/geo_helpers.py

@@ -2,8 +2,8 @@
 from affine import Affine
 from numpy import ndarray as np_ndarray
 
-from src import app_logger
-from src.utilities.type_hints import list_float, tuple_float, dict_str_int
+from samgis import app_logger
+from samgis.utilities.type_hints import list_float, tuple_float, dict_str_int
 
 
 def load_affine_transformation_from_matrix(matrix_source_coefficients: list_float) -> Affine:

{src → samgis}/io/lambda_helpers.py

@@ -1,13 +1,12 @@
 """lambda helper functions"""
 from typing import Dict
 from xyzservices import providers
-from aws_lambda_powertools.event_handler import content_types
 
-from src import app_logger
-from src.io.coordinates_pixel_conversion import get_latlng_to_pixel_coordinates
-from src.utilities.constants import CUSTOM_RESPONSE_MESSAGES
-from src.utilities.type_hints import ApiRequestBody
-from src.utilities.utilities import base64_decode
+from samgis import app_logger
+from samgis.io.coordinates_pixel_conversion import get_latlng_to_pixel_coordinates
+from samgis.utilities.constants import CUSTOM_RESPONSE_MESSAGES
+from samgis.utilities.type_hints import ApiRequestBody, ContentTypes
+from samgis.utilities.utilities import base64_decode
 
 
 def get_response(status: int, start_time: float, request_id: str, response_body: Dict = None) -> str:
@@ -34,7 +33,7 @@ def get_response(status: int, start_time: float, request_id: str, response_body:
 
     response = {
         "statusCode": status,
-        "header": {"Content-Type": content_types.APPLICATION_JSON},
+        "header": {"Content-Type": ContentTypes.APPLICATION_JSON},
         "body": dumps(response_body),
         "isBase64Encoded": False
     }
@@ -154,7 +153,7 @@ def get_parsed_request_body(event: Dict or str) -> ApiRequestBody:
 
 
 def get_url_tile(source_type: str):
-    from src.utilities.constants import DEFAULT_TMS_NAME, DEFAULT_TMS_NAME_SHORT
+    from samgis.utilities.constants import DEFAULT_TMS_NAME, DEFAULT_TMS_NAME_SHORT
 
     if source_type.lower() == DEFAULT_TMS_NAME_SHORT:
         return providers.query_name(DEFAULT_TMS_NAME)

{src → samgis}/io/tms2geotiff.py

@@ -2,10 +2,10 @@ import os
 from numpy import ndarray
 from xyzservices import TileProvider
 
-from src import app_logger
-from src.utilities.constants import (OUTPUT_CRS_STRING, DRIVER_RASTERIO_GTIFF, N_MAX_RETRIES, N_CONNECTION, N_WAIT,
-                                     ZOOM_AUTO, BOOL_USE_CACHE)
-from src.utilities.type_hints import tuple_ndarray_transform, tuple_float
+from samgis import app_logger
+from samgis.utilities.constants import (OUTPUT_CRS_STRING, DRIVER_RASTERIO_GTIFF, N_MAX_RETRIES, N_CONNECTION, N_WAIT,
+                                        ZOOM_AUTO, BOOL_USE_CACHE)
+from samgis.utilities.type_hints import tuple_ndarray_transform, tuple_float
 
 bool_use_cache = int(os.getenv("BOOL_USE_CACHE", BOOL_USE_CACHE))
 n_connection = int(os.getenv("N_CONNECTION", N_CONNECTION))
@@ -48,8 +48,8 @@ def download_extent(w: float, s: float, e: float, n: float, zoom: int or str = z
         parsed request input
     """
     try:
-        from src import contextily_tile
-        from src.io.coordinates_pixel_conversion import _from4326_to3857
+        from samgis import contextily_tile
+        from samgis.io.coordinates_pixel_conversion import _from4326_to3857
 
         app_logger.info(f"connection number:{n_connections}, type:{type(n_connections)}.")
         app_logger.info(f"zoom:{zoom}, type:{type(zoom)}.")

{src → samgis}/prediction_api/predictors.py

@@ -1,12 +1,12 @@
 """functions using machine learning instance model(s)"""
 from numpy import array as np_array, uint8, zeros, ndarray
 
-from src import app_logger, MODEL_FOLDER
-from src.io.geo_helpers import get_vectorized_raster_as_geojson
-from src.io.tms2geotiff import download_extent
-from src.prediction_api.sam_onnx import SegmentAnythingONNX
-from src.utilities.constants import MODEL_ENCODER_NAME, MODEL_DECODER_NAME, DEFAULT_TMS
-from src.utilities.type_hints import llist_float, dict_str_int, list_dict, tuple_ndarr_int, PIL_Image
+from samgis import app_logger, MODEL_FOLDER
+from samgis.io.geo_helpers import get_vectorized_raster_as_geojson
+from samgis.io.tms2geotiff import download_extent
+from samgis.prediction_api.sam_onnx import SegmentAnythingONNX
+from samgis.utilities.constants import MODEL_ENCODER_NAME, MODEL_DECODER_NAME, DEFAULT_TMS
+from samgis.utilities.type_hints import llist_float, dict_str_int, list_dict, tuple_ndarr_int, PIL_Image
 
 models_dict = {"fastsam": {"instance": None}}
 

{src → samgis}/prediction_api/sam_onnx.py

@@ -28,7 +28,7 @@ from numpy import array as np_array, concatenate, float32, linalg, matmul, ndarr
 from cv2 import INTER_LINEAR, warpAffine
 from onnxruntime import get_available_providers, InferenceSession
 
-from src import app_logger
+from samgis import app_logger
 
 
 class SegmentAnythingONNX:

{src → samgis}/utilities/serialize.py

@@ -1,8 +1,8 @@
 """Serialize objects"""
 from typing import Mapping
 
-from src import app_logger
-from src.utilities.type_hints import dict_str, dict_str_any
+from samgis import app_logger
+from samgis.utilities.type_hints import dict_str, dict_str_any
 
 
 def serialize(obj: any, include_none: bool = False):

{src → samgis}/utilities/type_hints.py

@@ -7,7 +7,7 @@ from affine import Affine
 from numpy import ndarray
 from pydantic import BaseModel
 
-from src.utilities.constants import DEFAULT_TMS
+from samgis.utilities.constants import DEFAULT_TMS
 
 
 dict_str_int = dict[str, int]
@@ -31,6 +31,13 @@ class LatLngDict(BaseModel):
     lng: float
 
 
+class ContentTypes(str, Enum):
+    """Segment Anything: validation point prompt type"""
+    APPLICATION_JSON = "application/json"
+    TEXT_PLAIN = "text/plain"
+    TEXT_HTML = "text/html"
+
+
 class PromptPointType(str, Enum):
     """Segment Anything: validation point prompt type"""
     point = "point"

{src → samgis}/utilities/utilities.py

@@ -1,6 +1,6 @@
 """Various utilities (logger, time benchmark, args dump, numerical and stats info)"""
-from src import app_logger
-from src.utilities.serialize import serialize
+from samgis import app_logger
+from samgis.utilities.serialize import serialize
 
 
 def _prepare_base64_input(sb):

scripts/lambda-entrypoint.sh

@@ -1,7 +1,17 @@
 #!/bin/sh
 
+# default value for PYTHONBIN=/usr/local/bin/python
+# but it change because of poetry that it uses a virtualenv installed within the LAMBDA_TASK_ROOT=/var/task
+
+echo "python installation path and version:"
+which python
+python --version
+
+echo "lambda-entrypoint.sh: PYTHONPATH ${PYTHONPATH} ..."
+echo "lambda-entrypoint.sh: PATH ${PATH} ..."
+
 if [ -z "${AWS_LAMBDA_RUNTIME_API}" ]; then
-  exec /usr/local/bin/aws-lambda-rie /usr/local/bin/python -m awslambdaric "$@"
+  exec /usr/local/bin/aws-lambda-rie python -m awslambdaric "$@"
 else
-  exec /usr/local/bin/python -m awslambdaric "$@"
+  exec python -m awslambdaric "$@"
 fi

src/__init__.py

@@ -1,12 +0,0 @@
-"""Get machine learning predictions from geodata raster images"""
-from aws_lambda_powertools import Logger
-# not used here but contextily_tile is imported in src.io.tms2geotiff
-from contextily import tile as contextily_tile
-from pathlib import Path
-
-from src.utilities.constants import SERVICE_NAME
-
-
-PROJECT_ROOT_FOLDER = Path(globals().get("__file__", "./_")).absolute().parent.parent
-MODEL_FOLDER = Path(PROJECT_ROOT_FOLDER / "machine_learning_models")
-app_logger = Logger(service=SERVICE_NAME)

static/.gitignore

@@ -0,0 +1,38 @@
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
+lerna-debug.log*
+
+node_modules
+.DS_Store
+dist
+dist-ssr
+coverage
+*.local
+
+tmp*/*
+/cypress/videos/
+/cypress/screenshots/
+vite.config.ts.*
+
+# Editor directories and files
+.vscode/*
+!.vscode/extensions.json
+.idea
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw?
+
+test-results/
+playwright-report/
+
+.env*
+
+# cloudflare workers
+.wrangler

static/.prettierrc.json

@@ -0,0 +1,8 @@
+{
+  "$schema": "https://json.schemastore.org/prettierrc",
+  "semi": false,
+  "tabWidth": 2,
+  "singleQuote": true,
+  "printWidth": 100,
+  "trailingComma": "none"
+}

static/LICENSE

@@ -0,0 +1,176 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
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+      and distribution as defined by Sections 1 through 9 of this document.
+
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+
+      "Legal Entity" shall mean the union of the acting entity and all
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+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
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+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
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+
+      "Work" shall mean the work of authorship, whether in Source or
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+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS

static/README.md

@@ -0,0 +1,36 @@
+# ml-tornidor
+
+## Local development
+
+Since I use Cloudflare pages as hosting for this project there are some required steps to do before it's possible to start a local development environment. This project needs to wrap the node commands with the `npx wrangler [...]` utility to emulate a Cloudflare Worker function. Because this worker function is under auth which use some env variables I to write these env variables inline. Every time I changed or added needed some variables I also needed to update the `npx wrangler` command. To avoid this I prepared a js script, executed by [Deno](https://deno.land/), that read the env variables from the `.env` file composing the command:
+
+1. prepare the .env file copying the template.env file
+2. run the local environment using the command `pnpm dev` or `deno run -A runner.js`
+
+In case of new or updated packages Deno installs the dependencies at the first execution. Do it with a execution  without the `npx wrangler` wrapper:
+
+```bash
+deno run -A --node-modules-dir npm:vite
+```
+
+In case of problem:
+
+1. try executing again the command `deno run -A --node-modules-dir npm:vite`
+
+If this don't solve the problems try to
+
+1. delete the node_modules folder
+2. reinstall the npm packages with `pnpm install`
+3. Run again the local development server, this time with the standard command
+
+Before to commit try also to build using
+
+```bash
+pnpm build
+```
+
+Then run the preview (change the example variables):
+
+```bash
+npx wrangler pages dev --binding VITE_AUTH0_DOMAIN="example-auth0.eu.auth0.com" API_URL="https://example-aws.execute-api.eu-west-1.amazonaws.com/localhost/lambda-ml-fastsam-api" VITE_AUTH0_AUDIENCE="http://localhost-ml-lambda/" API_DOMAIN=example-aws.execute-api.eu-west-1.amazonaws.com CORS_ALLOWED_DOMAIN=http://localhost:8788 VITE_SATELLITE_NAME="tile-provider.image-type" -- pnpm preview
+```

static/env.d.ts

@@ -0,0 +1 @@
+/// <reference types="vite/client" />

static/index.html

@@ -0,0 +1,18 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <link href="output.css" rel="stylesheet" type="text/css">
+    <link href="dist/output.css" rel="stylesheet" type="text/css">
+    <link rel="icon" href="/favicon.ico" sizes="32x32">
+    <link rel="icon" href="/icon.svg" type="image/svg+xml">
+    <link rel="apple-touch-icon" href="/apple-touch-icon.png"><!-- 180×180 -->
+    <link rel="manifest" href="/manifest.webmanifest">
+    <title>ML on GIS</title>
+  </head>
+  <body>
+    <div id="root"></div>
+    <script type="module" src="/src/main.ts"></script>
+  </body>
+</html>