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‎.github/workflows/docker-image.yml

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Build the Docker image
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run: docker build . --file Dockerfile --tag ${{ github.repository }}:$(date +%s)

‎.github/workflows/docker-publish.yml

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contents: read
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steps:
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- name: Check out the repo
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Log in to Docker Hub
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uses: docker/login-action@v2

‎.github/workflows/docs-build.yml

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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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python-version: "3.11"
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- name: Install GDAL
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run: |
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python -m pip install --upgrade pip
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pip install --no-cache-dir Cython
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pip install -r requirements.txt -r requirements_dev.txt -r requirements_docs.txt
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pip install .
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- name: Discover typos with codespell
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run: codespell --skip="*.csv,*.geojson,*.json,*.js,*.html,*cff,*.pdf" --ignore-words-list="aci,acount,acounts,fallow,hart,hist,nd,ned,ois,wqs,pres"
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# - name: PKG-TEST
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# run: |
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# python -m unittest discover tests/
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- run: mkdocs build
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- name: Deploy to Netlify
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uses: nwtgck/actions-netlify@v2.0

‎.github/workflows/docs.yml

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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: 3.9
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python-version: "3.11"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip

‎.github/workflows/draft-pdf.yml

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name: Paper Draft
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Build draft PDF
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uses: openjournals/openjournals-draft-action@master
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with:

‎.github/workflows/macos.yml

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fail-fast: false
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matrix:
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config:
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- { os: macOS-latest, py: "3.10" }
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- { os: macOS-latest, py: "3.11" }
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env:
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SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
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steps:
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- name: CHECKOUT CODE
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: SETUP PYTHON
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.config.py }}
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# - name: Install GDAL

‎.github/workflows/pypi.yml

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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- name: Install dependencies

‎.github/workflows/ubuntu.yml

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SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
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steps:
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- name: CHECKOUT CODE
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: SETUP PYTHON
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.config.py }}
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- name: Install GDAL

‎.github/workflows/windows.yml

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test-windows:
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runs-on: windows-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Install miniconda
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uses: conda-incubator/setup-miniconda@v2
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uses: conda-incubator/setup-miniconda@v3
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with:
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auto-activate-base: true
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python-version: "3.10"

‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.6.0
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hooks:
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- id: check-toml
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- id: check-yaml
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- id: end-of-file-fixer
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types: [python]
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- id: trailing-whitespace
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- id: requirements-txt-fixer
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- id: check-added-large-files
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args: ["--maxkb=500"]
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- repo: https://github.com/psf/black
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rev: 24.4.2
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hooks:
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- id: black-jupyter
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language_version: python3.11
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- repo: https://github.com/codespell-project/codespell
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rev: v2.2.6
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hooks:
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- id: codespell
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args: [--toml, pyproject-codespell.precommit-toml]
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- repo: https://github.com/kynan/nbstripout
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rev: 0.7.1
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hooks:
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- id: nbstripout

‎Dockerfile

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RUN mamba install -c conda-forge leafmap localtileserver segment-geospatial -y && \
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pip install -U segment-geospatial jupyter-server-proxy && \
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jupyter serverextension enable --sys-prefix jupyter_server_proxy && \
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jupyter server extension enable --sys-prefix jupyter_server_proxy && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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ENV LOCALTILESERVER_CLIENT_PREFIX=$LOCALTILESERVER_CLIENT_PREFIX
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USER root
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RUN apt update; apt install -y libgl1
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RUN chown -R ${NB_UID} ${HOME}
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USER ${NB_USER}

‎README.md

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## Citations
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- Wu, Q., & Osco, L. (2023). samgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM). _Journal of Open Source Software_, 8(89), 5663, <https://doi.org/10.21105/joss.05663>
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- Wu, Q., & Osco, L. (2023). samgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM). _Journal of Open Source Software_, 8(89), 5663. <https://doi.org/10.21105/joss.05663>
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- Osco, L. P., Wu, Q., de Lemos, E. L., Gonçalves, W. N., Ramos, A. P. M., Li, J., & Junior, J. M. (2023). The Segment Anything Model (SAM) for remote sensing applications: From zero to one shot. _International Journal of Applied Earth Observation and Geoinformation_, 124, 103540. <https://doi.org/10.1016/j.jag.2023.103540>
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## Features
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mamba install -c conda-forge segment-geospatial
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```
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Samgeo-geospatial has some optional dependencies that are not included in the default conda environment. To install these dependencies, run the following command:
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If your system has a GPU, but the above commands do not install the GPU version of pytorch, you can force the installation of the GPU version of pytorch using the following command:
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```bash
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mamba install -c conda-forge groundingdino-py segment-anything-fast
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mamba install -c conda-forge segment-geospatial "pytorch=*=cuda*"
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```
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As of July 9th, 2023 Linux systems have also required that `libgl1` be installed for segment-geospatial to work. The following command will install that dependency
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Samgeo-geospatial has some optional dependencies that are not included in the default conda environment. To install these dependencies, run the following command:
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```bash
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apt update; apt install -y libgl1
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mamba install -c conda-forge groundingdino-py segment-anything-fast
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```
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## Examples

‎docs/examples/arcgis.ipynb

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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"scrolled": false
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"sam.show_anns(axis=\"off\", alpha=1, output=\"ag_annotations.tif\")"
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"metadata": {},
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"outputs": [],
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"source": [
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"sam.generate('agriculture.tif', output=\"ag_masks2.tif\", foreground=True)"
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"sam.generate(\"agriculture.tif\", output=\"ag_masks2.tif\", foreground=True)"
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]
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},
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{

‎docs/examples/automatic_mask_generator_hq.ipynb

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"source": [
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"import os\n",
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"import leafmap\n",
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"from samgeo.hq_sam import SamGeo, show_image, download_file, overlay_images, tms_to_geotiff"
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"from samgeo.hq_sam import (\n",
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" SamGeo,\n",
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" show_image,\n",
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" download_file,\n",
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" overlay_images,\n",
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" tms_to_geotiff,\n",
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")"
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]
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},
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{
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"outputs": [],
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"source": [
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"sam = SamGeo(\n",
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" model_type=\"vit_h\", # can be vit_h, vit_b, vit_l, vit_tiny\n",
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" model_type=\"vit_h\", # can be vit_h, vit_b, vit_l, vit_tiny\n",
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" sam_kwargs=None,\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 17,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [

‎docs/examples/box_prompts.ipynb

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"outputs": [],
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"m.add_raster('mask.tif', cmap='viridis', nodata=0, layer_name='Mask')\n",
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"m.add_raster(\"mask.tif\", cmap=\"viridis\", nodata=0, layer_name=\"Mask\")\n",
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"m"
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]
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"url = 'https://opengeos.github.io/data/sam/tree_boxes.geojson'\n",
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"url = \"https://opengeos.github.io/data/sam/tree_boxes.geojson\"\n",
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"geojson = \"tree_boxes.geojson\"\n",
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"leafmap.download_file(url, geojson)"
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]
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.8"
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},
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"orig_nbformat": 4
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2

‎docs/examples/fast_sam.ipynb

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"outputs": [],
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"source": [
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"from samgeo.fast_sam import SamGeo\n",
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"\n",
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"sam = SamGeo(model=\"FastSAM-x.pt\")"
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]
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},
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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},
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"orig_nbformat": 4
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2

‎docs/examples/input_prompts.ipynb

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"execution_count": 1,
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"execution_count": null,
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"metadata": {},
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"source": [
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.8"
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},
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"orig_nbformat": 4
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}
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"nbformat": 4,
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"nbformat_minor": 2

‎docs/examples/input_prompts_hq.ipynb

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"version": "3.9.16"
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},
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"orig_nbformat": 4
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2

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