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Added fastsam module (#167)
* Add fastsam module * Add fastsam functions and notebook * Add show_anns function * Update dep
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‎.gitignore‎

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**/*.jpg
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**/*.png
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**/*.csv
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**/*.pt
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docs/examples/*.geojson
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# C extensions

‎docs/examples/fast_sam.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Segmenting remote sensing imagery with FastSAM\n",
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"\n",
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"[![image](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/opengeos/segment-geospatial/blob/main/docs/examples/fast_sam.ipynb)\n",
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"[![image](https://img.shields.io/badge/Open-Planetary%20Computer-black?style=flat&logo=microsoft)](https://pccompute.westeurope.cloudapp.azure.com/compute/hub/user-redirect/git-pull?repo=https://github.com/opengeos/segment-geospatial&urlpath=lab/tree/segment-geospatial/docs/examples/fast_sam.ipynb&branch=main)\n",
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"[![image](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/opengeos/segment-geospatial/blob/main/docs/examples/fast_sam.ipynb)\n",
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"\n",
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"FastSAM: https://github.com/CASIA-IVA-Lab/FastSAM\n",
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"\n",
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"Make sure you use GPU runtime for this notebook. For Google Colab, go to `Runtime` -> `Change runtime type` and select `GPU` as the hardware accelerator. "
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Install dependencies\n",
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"\n",
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"Uncomment and run the following cell to install the required dependencies."
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# %pip install segment-geospatial segment-anything-fast"
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import leafmap\n",
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"from samgeo import tms_to_geotiff\n",
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"from samgeo.fast_sam import SamGeo"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Create an interactive map"
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"m = leafmap.Map(center=[-22.17615, -51.253043], zoom=18, height=\"800px\")\n",
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"m.add_basemap(\"SATELLITE\")\n",
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"m"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Download a sample image\n",
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"\n",
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"Pan and zoom the map to select the area of interest. Use the draw tools to draw a polygon or rectangle on the map"
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"bbox = m.user_roi_bounds()\n",
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"if bbox is None:\n",
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" bbox = [-51.2565, -22.1777, -51.2512, -22.175]"
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"image = \"Image.tif\"\n",
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"tms_to_geotiff(output=image, bbox=bbox, zoom=19, source=\"Satellite\", overwrite=True)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"You can also use your own image. Uncomment and run the following cell to use your own image."
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# image = '/path/to/your/own/image.tif'"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Display the downloaded image on the map."
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"m.layers[-1].visible = False\n",
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"m.add_raster(image, layer_name=\"Image\")\n",
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"m"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Initialize SamGeo class\n",
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"\n",
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"The initialization of the SamGeo class might take a few minutes. The initialization downloads the model weights and sets up the model for inference."
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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": null,
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"metadata": {},
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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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"sam = SamGeo(model=\"FastSAM-x.pt\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Set the image."
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"sam.set_image(\"Image.tif\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Segment the image with `everything_prompt`. You can also try `point_prompt`, `box_prompt`, or `text_prompt`."
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"sam.everything_prompt(output=\"mask.tif\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Show the annotated image."
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"sam.show_anns(\"mask.png\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"![](https://i.imgur.com/af4bj7O.png)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Convert the segmentation results from GeoTIFF to vector."
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"sam.raster_to_vector(\"mask.tif\", \"mask.geojson\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Show the segmentation results on the map."
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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": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"m.add_raster(\"mask.tif\", opacity=0.5, layer_name=\"Mask\")\n",
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"m.add_vector(\"mask.geojson\", layer_name=\"Mask Vector\")\n",
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"m"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"![](https://i.imgur.com/LvEAMSl.png)"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "sam",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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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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"nbformat": 4,
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"nbformat_minor": 2
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}

‎docs/installation.md‎

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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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mamba install -c conda-forge groundingdino-py
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mamba install -c conda-forge groundingdino-py segment-anything-fast
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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

‎mkdocs.yml‎

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- API Reference:
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- common module: common.md
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- samgeo module: samgeo.md
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- fast_sam module: fast_sam.md
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- hq_sam module: hq_sam.md
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- text_sam module: text_sam.md

‎requirements_dev.txt‎

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rio-cogeo
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rio-cogeo
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groundingdino-py
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segment-anything-fast

‎samgeo/common.py‎

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def raster_to_vector(source, output, simplify_tolerance=None, **kwargs):
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def raster_to_vector(source, output, simplify_tolerance=None, dst_crs=None, **kwargs):
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gdf = gpd.GeoDataFrame.from_features(fc)
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gdf.set_crs(crs=src.crs, inplace=True)
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if dst_crs is not None:
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gdf = gdf.to_crs(dst_crs)
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gdf.to_file(output, **kwargs)
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