Add step2

step2_compute_watermask.ipynb

@@ -16,9 +16,48 @@
     "\n",
     "## Step 2 : \n",
     "\n",
-    "The aim of this second exercise is to compute a water mask, from NDWI2 values\n",
+    "The aim of this second exercise is to combine NDWI2 values to create a water mask\n",
     "- what kind of function do we need to implement ?\n",
-    "- are all the pixels valid ?"
+    "- are all the pixels valid ?\n",
+    "- we want to maximize water extent\n",
+    "\n",
+    "We are also going to use OTB pipeline, to avoid writing intermediate file : \n",
+    "- the first step will be plugged as input of the second step\n",
+    "- only the final application will launch the pipeline, with ExecuteAndWriteOutput()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import otbApplication\n",
+    "import rasterio\n",
+    "\n",
+    "import display_api\n",
+    "import utils\n",
+    "\n",
+    "# Data directory\n",
+    "DATA_DIR = \"data\"\n",
+    "\n",
+    "# Output directory\n",
+    "OUTPUT_DIR = \"output\"\n",
+    "\n",
+    "# NDWI synthesis\n",
+    "NDWI_synthesis = os.path.join(OUTPUT_DIR,\"synthesis_NDWI2.tif\")\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Compute the NDWI2** \n",
+    "\n",
+    "Do we need to adapt the formula to deal with invalid pixels ? \n",
+    "\n",
+    "What happens with clouds ?"
    ]
   },
   {
@@ -35,16 +74,84 @@
     "        # BandMath takes a list of images as input,\n",
     "        # so we have to give a Python list [ image ], or [ image1, image2, .., imageN]\n",
     "        app.SetParameterStringList(\"il\",[im])\n",
-    "        app.SetParameterString(\"out\",im.replace(\"RVBPIR.tif\",\"_ndwi2.tif\"))\n",
+    "        out = os.path.join(out_dir, os.path.basename(im.replace(\"_RVBPIR.tif\",\"_NDWI2.tif\")))\n",
+    "        app.SetParameterString(\"out\",out)\n",
     "        app.SetParameterString(\"exp\",\"(im1b2-im1b4)/(im1b2+im1b4)\")\n",
+    "        # Plug the application in the pipeline \n",
+    "        # does NOT launch the pipeline yet !\n",
     "        app.Execute()\n",
+    "        # we save the application in a list\n",
     "        if (index == 0):\n",
     "            tab_App = [app]\n",
     "        else:\n",
     "            tab_App.append(app)\n",
     "        index += 1\n",
+    "    # the list of applications is returned\n",
     "    return tab_App"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Compute watermask from a list of NDWI2 images**\n",
+    "\n",
+    "We are going to use a list of images to compute a watermask (0 for land, 1 for water) : \n",
+    "- the inputs must be set in a list with app.AddImageToParameterInputImageList\n",
+    "- the expression will be use all the images im1b1, im2b1, etc."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def compute_watermask(list_app):\n",
+    "    app = otbApplication.Registry.CreateApplication(\"BandMath\")\n",
+    "    index = 1\n",
+    "    exp = \"?????\"\n",
+    "    for appli in list_app:\n",
+    "        app.AddImageToParameterInputImageList(\"il\",appli.GetParameterOutputImage(\"out\"))\n",
+    "        if index==1:\n",
+    "            exp = exp # + \"some function that involves im1b1\"\n",
+    "        else:\n",
+    "            exp = exp # +\", \"+\"im\"+str(index)+\"b1\"\n",
+    "        index += 1\n",
+    "\n",
+    "\n",
+    "    print(exp)\n",
+    "\n",
+    "    \n",
+    "    app.SetParameterString(\"out\",NDWI_synthesis)\n",
+    "    app.SetParameterString(\"exp\",exp)\n",
+    "    app.ExecuteAndWriteOutput()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Compute radiometric indices (NDVI & NDWI2) on a stack of images\n",
+    "list_app = app_radiometricindices(utils.list_images(DATA_DIR,\"_RVBPIR.tif\"), OUTPUT_DIR)\n",
+    "compute_watermask(os.path.join(OUTPUT_DIR, NDWI_synthesis), list_app)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {