ENH: steps 1,2 completed

step1_compute_radiometric_indices.ipynb

@@ -136,7 +136,7 @@
     "# Compute radiometric indices (NDVI & NDWI2) on a stack of images\n",
     "ndwi_filenames_list = compute_ndwi(utils.list_images(DATA_DIR,\"_RVBPIR.tif\"), OUTPUT_DIR)\n",
     "if ndwi_filenames_list is not None:\n",
-    "    print (ndwi_filenames_list)\n",
+    "    print (ndwi_filenames_list)http://localhost:8888/notebooks/step1_compute_radiometric_indices.ipynb#\n",
     "else:\n",
     "    print (\"TODO: fill the compute_ndwi_function\")"
    ]
@@ -147,14 +147,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "if ndwi_filenames_list is not None:\n",
-    "    # Display on a map\n",
-    "    rasters = list(map(rasterio.open, ndwi_filenames_list))\n",
-    "    overnames = list(map(os.path.basename, ndwi_filenames_list))\n",
-    "    m, dc = display_api.rasters_on_map(rasters, OUTPUT_DIR, overnames)\n",
-    "    m\n",
-    "else:\n",
-    "    print (\"TODO: fill the compute_ndwi_function\")"
+    "# Display on a map\n",
+    "rasters = list(map(rasterio.open, ndwi_filenames_list))\n",
+    "overnames = list(map(os.path.basename, ndwi_filenames_list))\n",
+    "m, dc = display_api.rasters_on_map(rasters, OUTPUT_DIR, overnames)\n",
+    "m"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Go to the [Step 2](./step2_compute_watermask.ipynb)"
    ]
   }
  ],

step2_compute_watermask.ipynb

@@ -14,7 +14,7 @@
     "<b> Press <span style=\"color:black;background:yellow\">SHIFT+ENTER</span> to execute the notebook interactively cell by cell </b></div>\n",
     "\n",
     "\n",
-    "## Step 2 : \n",
+    "## Step 2 : Compute Watermask\n",
     "\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",
@@ -53,7 +53,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "**Compute the NDWI2** \n",
+    "### Compute the NDWI2\n",
     "\n",
     "Do we need to adapt the formula to deal with invalid pixels ? \n",
     "\n",
@@ -66,7 +66,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def app_radiometricindices(images):\n",
+    "def app_radiometricindices(images, out_dir):\n",
     "    index = 0\n",
     "    for im in images:\n",
     "        # Here we create an application\n",
@@ -94,7 +94,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "**Compute watermask from a list of NDWI2 images**\n",
+    "### 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",
@@ -107,25 +107,38 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def compute_watermask(list_app):\n",
+    "        if index==1:\n",
+    "            exp = exp+\"im\"+str(index)+\"b1\"\n",
+    "        else:\n",
+    "            exp = exp+\", \"+\"im\"+str(index)+\"b1\"\n",
+    "        "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def compute_watermask(list_app,outputfilename):\n",
     "    app = otbApplication.Registry.CreateApplication(\"BandMath\")\n",
+    "\n",
     "    index = 1\n",
+    "    input_list = []\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",
+    "            exp = exp # +\", \"+\"im\"+str(index)+\"b1\"def compute_watermask(list_app,outputfilename):\n",
     "        index += 1\n",
     "\n",
-    "\n",
     "    print(exp)\n",
     "\n",
-    "    \n",
-    "    app.SetParameterString(\"out\",NDWI_synthesis)\n",
+    "    app.SetParameterString(\"out\",outputfilename)\n",
     "    app.SetParameterString(\"exp\",exp)\n",
-    "    app.ExecuteAndWriteOutput()\n"
+    "    app.ExecuteAndWriteOutput()"
    ]
   },
   {
@@ -136,7 +149,7 @@
    "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"
+    "compute_watermask(list_app, NDWI_synthesis)"
    ]
   },
   {
@@ -144,14 +157,23 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "import rasterio\n",
+    "import display_api\n",
+    "\n",
+    "raster = rasterio.open(NDWI_synthesis)\n",
+    "m, dc = display_api.rasters_on_map([raster], OUTPUT_DIR, [\"NDWI synthesis\"])\n",
+    "m"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "### Go to the [Step 3](./step3_segment_watermask_threshold_NDWI.ipynb)"
+   ]
   }
  ],
  "metadata": {