commit last modifications from David and internal info in readme

README.md

@@ -13,7 +13,11 @@
     - Install ipyleaflet : pip install --user ipyleaflet + 
     - OTB : ./OTB-6.6.1-Linux64.run --target /home/otb/OTB
     - Jupyter :
-6. Add dataset
+6. Configure network settings (proxy & certificates) for CNES environment.
+   Instructions from : https://gitlab.cnes.fr/hpc/wikiHPC/wikis/connexion-proxy
+   and https://gitlab.cnes.fr/hpc/wikiHPC/wikis/Acc%C3%A8s-%C3%A0-un-site-https-hors-master-CNES
+7. Add dataset
+
 
 **Note:** Python3 workaround (https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/issues/1540)
 

otb_workshop.ipynb

@@ -30,9 +30,7 @@
     "from rasterio.plot import show\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
-    "\n",
-    "# LUT: color_name (string) <-> band (int)\n",
-    "COLORS_BANDS = {'Red':4, 'Green':3, 'Blue':2, 'Nir':8}\n",
+    "import os\n",
     "\n",
     "# Data directory\n",
     "DATA_DIR = \"data\"\n",
@@ -42,9 +40,11 @@
     "LEVEL = \"L2A\"\n",
     "DATE = \"20180805\"\n",
     "\n",
-    "# Get Band filename\n",
-    "S2DIR = glob(os.path.join(DATA_DIR, \"SENTINEL2?_{0}-*_{1}_T{2}_*\".format(DATE, LEVEL, MGRS)))[0]\n",
-    "BAND_FILENAME = os.path.join(S2DIR, os.path.basename(S2DIR) + \"_FRE_B%d.tif\")\n",
+    "# Color bands\n",
+    "COLORS_BANDS = ['Blue', 'Green', 'Red', 'NIR']\n",
+    "\n",
+    "# Get S2 product\n",
+    "S2_product = glob(os.path.join(DATA_DIR, \"SENTINEL2?_{0}-*_{1}_T{2}_*\".format(DATE, LEVEL, MGRS)))[0]\n",
     "\n",
     "# Normalize bands into 0.0 - 1.0 scale\n",
     "def normalize(array, quantile=2):\n",
@@ -54,19 +54,19 @@
     "    normalized[normalized<0] = 0\n",
     "    return normalized\n",
     "\n",
-    "# Get visible bands from SENTINEL-2 product\n",
-    "s2_prod, rasters, quicklooks = {}, {}, {}\n",
+    "# Plot bands from SENTINEL-2 product\n",
+    "raster = rasterio.open(S2_product)\n",
+    "quicklooks = {}\n",
+    "\n",
     "fig, ax = plt.subplots(1,len(COLORS_BANDS)+1, figsize=(21,7))\n",
     "for nfig, color in enumerate(COLORS_BANDS):\n",
-    "    s2_prod[color] = BAND_FILENAME % COLORS_BANDS[color]\n",
-    "    rasters[color] = rasterio.open(s2_prod[color])\n",
-    "    quicklooks[color] = normalize(rasters[color].read(1, out_shape=(int(rasters[color].height / 8), int(rasters[color].width / 8))))\n",
+    "    quicklooks[color] = normalize(raster.read(nfig+1, out_shape=(int(raster.height / 8), int(raster.width / 8))))\n",
     "    try:\n",
     "        ax[nfig].imshow(quicklooks[color], cmap=color+'s')\n",
     "    except ValueError:\n",
     "        ax[nfig].imshow(quicklooks[color], cmap='Oranges')\n",
     "    ax[nfig].set_title(color+' channel')\n",
-    "        \n",
+    "\n",
     "ax[len(COLORS_BANDS)].imshow(np.dstack((quicklooks['Red'], quicklooks['Green'], quicklooks['Blue'])))\n",
     "ax[len(COLORS_BANDS)].set_title('RGB')\n",
     "\n",
@@ -82,20 +82,27 @@
    "outputs": [],
    "source": [
     "from rasterio.warp import transform_bounds\n",
-    "from ipyleaflet import Map, Rectangle, ImageOverlay, FullScreenControl, DrawControl\n",
+    "from ipyleaflet import Map, Rectangle, ImageOverlay, FullScreenControl, DrawControl, LayersControl\n",
     "\n",
     "# Plot footprint on a map\n",
     "\n",
     "# - get bounding box\n",
     "epsg4326 = {'init': 'EPSG:4326'}\n",
-    "bounds = transform_bounds(rasters['Red'].crs, epsg4326, *rasters['Red'].bounds)\n",
+    "bounds = transform_bounds(raster.crs, epsg4326, *raster.bounds)\n",
     "center = [(bounds[0]+bounds[2])/2, (bounds[1]+bounds[3])/2]\n",
     "\n",
     "# - get centered map\n",
-    "m = Map(center=(center[-1], center[0]), zoom=7)\n",
+    "m = Map(center=(center[-1], center[0]), zoom=10)\n",
+    "\n",
+    "# - create quicklook\n",
+    "import otbApplication\n",
+    "quicklook_url = os.path.splitext(S2_product)[0] + \"_PREVIEW.JPG\"\n",
+    "app = otbApplication.Registry.CreateApplication(\"DynamicConvert\")\n",
+    "app.SetParameterString('in', S2_product)\n",
+    "app.SetParameterString('out', quicklook_url)\n",
+    "app.ExecuteAndWriteOutput()\n",
     "\n",
     "# - plot quicklook\n",
-    "quicklook_url = os.path.join(S2DIR, os.path.basename(S2DIR) + \"_QKL_ALL.jpg\")\n",
     "quicklook = ImageOverlay(\n",
     "    url=quicklook_url,\n",
     "    bounds=((bounds[1], bounds[0]),(bounds[3], bounds[2])),\n",
@@ -127,12 +134,12 @@
     "    lon_min_max = [np.amin(coordinates[:,0]), np.amax(coordinates[:,0])]\n",
     "    lat_min_max = [np.amin(coordinates[:,1]), np.amax(coordinates[:,1])]\n",
     "    lons, lats = np.meshgrid(lon_min_max, lat_min_max)\n",
-    "    xs, ys = warp.transform({'init': 'EPSG:4326'}, rasters['Red'].crs, lons.flatten(), lats.flatten())\n",
+    "    xs, ys = transform({'init': 'EPSG:4326'}, raster.crs, lons.flatten(), lats.flatten())\n",
     "    \n",
     "    # Get the region of interest in the image\n",
     "    rows, cols = [], []\n",
     "    for x, y in zip(xs, ys):\n",
-    "        row, col = ~rasters['Red'].affine * (x, y)\n",
+    "        row, col = ~raster.affine * (x, y)\n",
     "        rows.append(row)\n",
     "        cols.append(col)\n",
     "    row_min, row_max = np.amin(rows), np.amax(rows)\n",
@@ -142,11 +149,7 @@
     "    return startx, starty, endx, endy\n",
     "\n",
     "startx, starty, endx, endy = get_bounding_box_from_draw()\n",
-    "red_ext = normalize(rasters['Red'].read(1, window=((startx, endx), (starty, endy))))\n",
-    "green_ext = normalize(rasters['Green'].read(1, window=((startx, endx), (starty, endy))))\n",
-    "blue_ext = normalize(rasters['Blue'].read(1, window=((startx, endx), (starty, endy))))\n",
-    "\n",
-    "plt.imshow(np.dstack((red_ext, green_ext, blue_ext)))"
+    "print (startx, starty, endx, endy)"
    ]
   },
   {
@@ -159,9 +162,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "tensorflow",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "tf"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -173,7 +176,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.5.6"
   }
  },
  "nbformat": 4,