|
| 1 | +{ |
| 2 | + "cells": [ |
| 3 | + { |
| 4 | + "attachments": {}, |
| 5 | + "cell_type": "markdown", |
| 6 | + "metadata": { |
| 7 | + "id": "W-IgodFVKrQO" |
| 8 | + }, |
| 9 | + "source": [ |
| 10 | + "# Segment Anything Model for Geospatial Data \n", |
| 11 | + "\n", |
| 12 | + "\n", |
| 13 | + "The source code is adapted from [segment-anything-eo](https://github.com/aliaksandr960/segment-anything-eo) repository. Credit to the author [Aliaksandr Hancharenka](https://github.com/aliaksandr960)." |
| 14 | + ] |
| 15 | + }, |
| 16 | + { |
| 17 | + "cell_type": "markdown", |
| 18 | + "metadata": { |
| 19 | + "id": "OeFjtBlhKxh4" |
| 20 | + }, |
| 21 | + "source": [ |
| 22 | + "This tool is developed to easy process spatial data (GeoTIFF and TMS) with Meta AI Segment Anything models\n", |
| 23 | + "\n", |
| 24 | + "You can:\n", |
| 25 | + "- download TMS data as GeoTIFF files\n", |
| 26 | + "- process GeoTIFF files with Meta AI Segment Anything models\n", |
| 27 | + "- save inference data as GeoTIFF raster data or GPKG vector data" |
| 28 | + ] |
| 29 | + }, |
| 30 | + { |
| 31 | + "cell_type": "markdown", |
| 32 | + "metadata": { |
| 33 | + "id": "KyZq008jL64p" |
| 34 | + }, |
| 35 | + "source": [ |
| 36 | + "## Clone repo and install dependancies" |
| 37 | + ] |
| 38 | + }, |
| 39 | + { |
| 40 | + "cell_type": "code", |
| 41 | + "execution_count": null, |
| 42 | + "metadata": { |
| 43 | + "colab": { |
| 44 | + "base_uri": "https://localhost:8080/" |
| 45 | + }, |
| 46 | + "id": "L42UgbyJ6j8W", |
| 47 | + "outputId": "6924c5c8-39a0-4ac6-f114-9f1f8d102e88" |
| 48 | + }, |
| 49 | + "outputs": [], |
| 50 | + "source": [ |
| 51 | + "# !git clone https://github.com/aliaksandr960/segment-anything-eo.git" |
| 52 | + ] |
| 53 | + }, |
| 54 | + { |
| 55 | + "cell_type": "code", |
| 56 | + "execution_count": null, |
| 57 | + "metadata": { |
| 58 | + "id": "J-Yk9v21G9O2" |
| 59 | + }, |
| 60 | + "outputs": [], |
| 61 | + "source": [ |
| 62 | + "import os\n", |
| 63 | + "os.chdir('/home/qiusheng/Documents/Data/')" |
| 64 | + ] |
| 65 | + }, |
| 66 | + { |
| 67 | + "cell_type": "code", |
| 68 | + "execution_count": null, |
| 69 | + "metadata": { |
| 70 | + "colab": { |
| 71 | + "base_uri": "https://localhost:8080/" |
| 72 | + }, |
| 73 | + "id": "pj5yjhMA6nBV", |
| 74 | + "outputId": "f23e269f-43b6-4fad-8ace-9184077b6916" |
| 75 | + }, |
| 76 | + "outputs": [], |
| 77 | + "source": [ |
| 78 | + "# !pip install rasterio\n", |
| 79 | + "# !pip install geopandas\n", |
| 80 | + "\n", |
| 81 | + "!wget https://dl.fbaipublicfiles.com/segment_anything/sam_vit_h_4b8939.pth\n", |
| 82 | + "!wget https://dl.fbaipublicfiles.com/segment_anything/sam_vit_l_0b3195.pth\n", |
| 83 | + "!wget https://dl.fbaipublicfiles.com/segment_anything/sam_vit_b_01ec64.pth" |
| 84 | + ] |
| 85 | + }, |
| 86 | + { |
| 87 | + "cell_type": "code", |
| 88 | + "execution_count": null, |
| 89 | + "metadata": { |
| 90 | + "id": "w5bDCQOV7gvZ" |
| 91 | + }, |
| 92 | + "outputs": [], |
| 93 | + "source": [ |
| 94 | + "import cv2\n", |
| 95 | + "import matplotlib.pyplot as plt\n", |
| 96 | + "from samgeo import SamGeo" |
| 97 | + ] |
| 98 | + }, |
| 99 | + { |
| 100 | + "cell_type": "markdown", |
| 101 | + "metadata": { |
| 102 | + "id": "F1YUWHeWMDet" |
| 103 | + }, |
| 104 | + "source": [ |
| 105 | + "## Initialize SemEO class" |
| 106 | + ] |
| 107 | + }, |
| 108 | + { |
| 109 | + "cell_type": "code", |
| 110 | + "execution_count": null, |
| 111 | + "metadata": { |
| 112 | + "id": "0XzAeiGW8rNk" |
| 113 | + }, |
| 114 | + "outputs": [], |
| 115 | + "source": [ |
| 116 | + "# Availble SamGeo arguments:\n", |
| 117 | + "# checkpoint=\"sam_vit_h_4b8939.pth\",\n", |
| 118 | + "# model_type='vit_h',\n", |
| 119 | + "# device='cpu',\n", |
| 120 | + "# erosion_kernel=(3, 3),\n", |
| 121 | + "# mask_multiplier=255,\n", |
| 122 | + "# sam_kwargs=None\n", |
| 123 | + "\n", |
| 124 | + "# Availble sam_kwargs:\n", |
| 125 | + "# points_per_side: Optional[int] = 32,\n", |
| 126 | + "# points_per_batch: int = 64,\n", |
| 127 | + "# pred_iou_thresh: float = 0.88,\n", |
| 128 | + "# stability_score_thresh: float = 0.95,\n", |
| 129 | + "# stability_score_offset: float = 1.0,\n", |
| 130 | + "# box_nms_thresh: float = 0.7,\n", |
| 131 | + "# crop_n_layers: int = 0,\n", |
| 132 | + "# crop_nms_thresh: float = 0.7,\n", |
| 133 | + "# crop_overlap_ratio: float = 512 / 1500,\n", |
| 134 | + "# crop_n_points_downscale_factor: int = 1,\n", |
| 135 | + "# point_grids: Optional[List[np.ndarray]] = None,\n", |
| 136 | + "# min_mask_region_area: int = 0,\n", |
| 137 | + "# output_mode: str = \"binary_mask\",\n", |
| 138 | + "\n", |
| 139 | + "device = 'cuda:0'\n", |
| 140 | + "\n", |
| 141 | + "sam_eo = SamGeo(checkpoint=\"sam_vit_h_4b8939.pth\",\n", |
| 142 | + " model_type='vit_h',\n", |
| 143 | + " # device=device,\n", |
| 144 | + " erosion_kernel=(3, 3),\n", |
| 145 | + " mask_multiplier=255,\n", |
| 146 | + " sam_kwargs=None)" |
| 147 | + ] |
| 148 | + }, |
| 149 | + { |
| 150 | + "cell_type": "markdown", |
| 151 | + "metadata": { |
| 152 | + "id": "rBYMot8KMLMk" |
| 153 | + }, |
| 154 | + "source": [ |
| 155 | + "## Download file from Openaerialmap and save it" |
| 156 | + ] |
| 157 | + }, |
| 158 | + { |
| 159 | + "cell_type": "code", |
| 160 | + "execution_count": null, |
| 161 | + "metadata": { |
| 162 | + "colab": { |
| 163 | + "base_uri": "https://localhost:8080/" |
| 164 | + }, |
| 165 | + "id": "ZAggTXOR7yIk", |
| 166 | + "outputId": "78ff041f-e6bd-4389-ec68-c94b1989c9f9" |
| 167 | + }, |
| 168 | + "outputs": [], |
| 169 | + "source": [ |
| 170 | + "tms_source = 'https://tiles.openaerialmap.org/642385491a8878000512126c/0/642385491a8878000512126d/{z}/{x}/{y}'\n", |
| 171 | + "pt1 = (29.676840, -95.369222)\n", |
| 172 | + "pt2 = (29.678559, -95.367314)\n", |
| 173 | + "zoom = 20\n", |
| 174 | + "tms_tiff_path = 'test_tms_image.tif'\n", |
| 175 | + "\n", |
| 176 | + "image = sam_eo.download_tms_as_tiff(tms_source, pt1, pt2, zoom, tms_tiff_path)\n", |
| 177 | + "tiff_image = cv2.cvtColor(cv2.imread(tms_tiff_path), cv2.COLOR_BGR2RGB)" |
| 178 | + ] |
| 179 | + }, |
| 180 | + { |
| 181 | + "cell_type": "code", |
| 182 | + "execution_count": null, |
| 183 | + "metadata": { |
| 184 | + "colab": { |
| 185 | + "base_uri": "https://localhost:8080/", |
| 186 | + "height": 316 |
| 187 | + }, |
| 188 | + "id": "cTff_Z1I9cxi", |
| 189 | + "outputId": "d353ecec-e390-4bab-b6ed-ee48ed0adf86" |
| 190 | + }, |
| 191 | + "outputs": [], |
| 192 | + "source": [ |
| 193 | + "plt.figure()\n", |
| 194 | + "f, axarr = plt.subplots(1,2)\n", |
| 195 | + "axarr[0].imshow(image)\n", |
| 196 | + "axarr[1].imshow(tiff_image)\n", |
| 197 | + "plt.show()" |
| 198 | + ] |
| 199 | + }, |
| 200 | + { |
| 201 | + "cell_type": "markdown", |
| 202 | + "metadata": { |
| 203 | + "id": "x7UvOgzoMSGg" |
| 204 | + }, |
| 205 | + "source": [ |
| 206 | + "## Run inference and save result as tiff file" |
| 207 | + ] |
| 208 | + }, |
| 209 | + { |
| 210 | + "cell_type": "code", |
| 211 | + "execution_count": null, |
| 212 | + "metadata": { |
| 213 | + "colab": { |
| 214 | + "base_uri": "https://localhost:8080/" |
| 215 | + }, |
| 216 | + "id": "mG6OdR6T-tKI", |
| 217 | + "outputId": "7335590d-d3ea-45f6-ba14-9ef75b9af0b6" |
| 218 | + }, |
| 219 | + "outputs": [], |
| 220 | + "source": [ |
| 221 | + "pred_tiff_path = 'pred.tiff'\n", |
| 222 | + "sam_eo.tiff_to_tiff(tms_tiff_path, pred_tiff_path)" |
| 223 | + ] |
| 224 | + }, |
| 225 | + { |
| 226 | + "cell_type": "code", |
| 227 | + "execution_count": null, |
| 228 | + "metadata": { |
| 229 | + "colab": { |
| 230 | + "base_uri": "https://localhost:8080/", |
| 231 | + "height": 316 |
| 232 | + }, |
| 233 | + "id": "h1julewLBcxw", |
| 234 | + "outputId": "f9e0a34d-86fe-4829-8667-20c2d28ea0ab" |
| 235 | + }, |
| 236 | + "outputs": [], |
| 237 | + "source": [ |
| 238 | + "pred_image = cv2.cvtColor(cv2.imread(pred_tiff_path), cv2.COLOR_BGR2RGB)\n", |
| 239 | + "\n", |
| 240 | + "plt.figure()\n", |
| 241 | + "f, axarr = plt.subplots(1,2)\n", |
| 242 | + "axarr[0].imshow(image)\n", |
| 243 | + "axarr[1].imshow(pred_image)\n", |
| 244 | + "plt.show()" |
| 245 | + ] |
| 246 | + }, |
| 247 | + { |
| 248 | + "cell_type": "markdown", |
| 249 | + "metadata": { |
| 250 | + "id": "k6caNqkQMVTz" |
| 251 | + }, |
| 252 | + "source": [ |
| 253 | + "## Polygonize result and save as GPKG file" |
| 254 | + ] |
| 255 | + }, |
| 256 | + { |
| 257 | + "cell_type": "code", |
| 258 | + "execution_count": null, |
| 259 | + "metadata": { |
| 260 | + "id": "UYnth2kzD-o8" |
| 261 | + }, |
| 262 | + "outputs": [], |
| 263 | + "source": [ |
| 264 | + "# Adjust simplification tolerance to reduce size (it could be bigger, than raster)\n", |
| 265 | + "sam_eo.tiff_to_gpkg(pred_tiff_path, 'pred.gpkg', simplify_tolerance=None)" |
| 266 | + ] |
| 267 | + } |
| 268 | + ], |
| 269 | + "metadata": { |
| 270 | + "accelerator": "GPU", |
| 271 | + "colab": { |
| 272 | + "provenance": [] |
| 273 | + }, |
| 274 | + "gpuClass": "standard", |
| 275 | + "kernelspec": { |
| 276 | + "display_name": "Python 3", |
| 277 | + "name": "python3" |
| 278 | + }, |
| 279 | + "language_info": { |
| 280 | + "codemirror_mode": { |
| 281 | + "name": "ipython", |
| 282 | + "version": 3 |
| 283 | + }, |
| 284 | + "file_extension": ".py", |
| 285 | + "mimetype": "text/x-python", |
| 286 | + "name": "python", |
| 287 | + "nbconvert_exporter": "python", |
| 288 | + "pygments_lexer": "ipython3", |
| 289 | + "version": "3.9.16" |
| 290 | + } |
| 291 | + }, |
| 292 | + "nbformat": 4, |
| 293 | + "nbformat_minor": 0 |
| 294 | +} |
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