Updated Tutorials

.github/workflows/build_and_test_app.yml

@@ -3,7 +3,7 @@ name: ALCD
 on:
   pull_request:
     branches:
-      - "new_add_doc"
+      - "master"
 
 permissions:
   contents: read
@@ -58,4 +58,4 @@ jobs:
         export OTB_INSTALL_DIR=/opt/otb
         export LC_NUMERIC=C
 
-        pytest -s --cov-fail-under=65
+        pytest -s --cov-fail-under=65

docs/source/index.md

@@ -14,7 +14,7 @@ For a quick start, you can directly go to the {doc}`tutorial <tutorial>` parts.
 
 How to install ALCD <how_to_install_alcd>
 configure ALCD <configure_alcd>
-ACLD workflow <workflow>
+ALCD workflow <workflow>
 Tutorials <tutorials>
 Tips and advice <tips>
 Complementary information <complementary_information>

docs/source/notebooks/montreux.ipynb

@@ -17,8 +17,8 @@
     "\n",
     "ALCD requires several types of data for its execution\n",
     "\n",
-    " - raster data on which the classification iterations will be performed.\n",
-    " - json files to parameterise the chain.\n",
+    " - raster data on which the classification iterations will be performed. This data can be directly downloaded on [Geodes](https://geodes-portal.cnes.fr/) by selecting the date, collection, type of product and cloud cover desired.\n",
+    " - json files to parameterise the chain. These files can be filled by the user (see [Contents of the configuration files section](montreux.ipynb#contents-of-the-configuration-files))\n",
     "\n",
     "The following sections will focus on the presentation of this data.\n",
     "\n",
@@ -32,14 +32,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "id": "99bb6b3e-3baf-4652-8924-c1c8ac47556c",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "853e763d423e46e3a03b6dfc4ca39b8e",
+       "model_id": "b7f9d564b3b042779c1c861cf9911626",
        "version_major": 2,
        "version_minor": 0
       },
@@ -53,7 +53,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "ed53896a773f465da1f70801290550ac",
+       "model_id": "adf612381751475b8a94533cb4f8eaac",
        "version_major": 2,
        "version_minor": 0
       },
@@ -264,21 +264,12 @@
    "execution_count": 3,
    "id": "ec8d0240-f49b-43ba-9b48-507b41a66ec7",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/ecadaux/miniconda3/envs/env_otb2/lib/python3.11/site-packages/osgeo/gdal.py:287: FutureWarning: Neither gdal.UseExceptions() nor gdal.DontUseExceptions() has been explicitly called. In GDAL 4.0, exceptions will be enabled by default.\n",
-      "  warnings.warn(\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%%bash\n",
     "# considering PATH_ALCD is the path to the script 'all_run_alcd.py'\n",
     "export PATH_ALCD=\"../../..\"\n",
-    "python $PATH_ALCD/all_run_alcd.py -force True -s 0 -f True -l Montreux -d 20240213 -c 20240213 -dates False -kfold False -global_parameters global_parameters.json -paths_parameters paths_configuration.json -model_parameters model_parameters.json > tuto_log.txt"
+    "python $PATH_ALCD/all_run_alcd.py -force True -s 0 -f True -l Montreux -d 20240213 -c 20240213 -dates False -kfold False -global_parameters global_parameters.json -paths_parameters paths_configuration.json -model_parameters model_parameters.json > tuto_log.txt 2>/dev/null"
    ]
   },
   {
@@ -300,7 +291,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "54378f883c6e421d9a5a201a6dd60063",
+       "model_id": "6b9d43ae4fcb46a19055034f75988224",
        "version_major": 2,
        "version_minor": 0
       },
@@ -314,7 +305,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "0ca57bce63b946c3af59d67828bbeeec",
+       "model_id": "d51dee540def4bfa9ab6d6ac9124011e",
        "version_major": 2,
        "version_minor": 0
       },
@@ -383,60 +374,21 @@
     "\n",
     "### Launching command \n",
     "\n",
-    "The command to run is almost identical to the previous one, except that the ``s`` option changes from 0 to 1."
+    "The command to run is almost identical to the previous one, except that the ``s`` option changes from 0 to 1. This cell may take several seconds to run."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 3,
    "id": "3d43025d-bde6-426c-bd59-7a49dc485e2e",
    "metadata": {
     "scrolled": true
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/ecadaux/miniconda3/envs/env_otb2/lib/python3.11/site-packages/osgeo/ogr.py:560: FutureWarning: Neither ogr.UseExceptions() nor ogr.DontUseExceptions() has been explicitly called. In GDAL 4.0, exceptions will be enabled by default.\n",
-      "  warnings.warn(\n",
-      "WARNING: In /work/THEIA/CES/oso/CD/conda_env/iota2_build_env/conda-bld/otb_1736246894519/work/OTB/Modules/Filtering/Statistics/src/otbSamplerBase.cxx, line 42\n",
-      "RandomSampler (0x5908d47b4570): Needed elements (8000) will be clamped to total elements (165)\n",
-      "\n",
-      "\n",
-      "WARNING: In /work/THEIA/CES/oso/CD/conda_env/iota2_build_env/conda-bld/otb_1736246894519/work/OTB/Modules/Filtering/Statistics/src/otbSamplerBase.cxx, line 42\n",
-      "RandomSampler (0x5908d4bb7fc0): Needed elements (8000) will be clamped to total elements (164)\n",
-      "\n",
-      "\n",
-      "WARNING: In /work/THEIA/CES/oso/CD/conda_env/iota2_build_env/conda-bld/otb_1736246894519/work/OTB/Modules/Filtering/Statistics/src/otbSamplerBase.cxx, line 42\n",
-      "RandomSampler (0x5908d4c61110): Needed elements (8000) will be clamped to total elements (177)\n",
-      "\n",
-      "\n",
-      "WARNING: In /work/THEIA/CES/oso/CD/conda_env/iota2_build_env/conda-bld/otb_1736246894519/work/OTB/Modules/Filtering/Statistics/src/otbSamplerBase.cxx, line 42\n",
-      "RandomSampler (0x5908d47b2eb0): Needed elements (8000) will be clamped to total elements (147)\n",
-      "\n",
-      "\n",
-      "WARNING: In /work/THEIA/CES/oso/CD/conda_env/iota2_build_env/conda-bld/otb_1736246894519/work/OTB/Modules/Filtering/Statistics/src/otbSamplerBase.cxx, line 42\n",
-      "RandomSampler (0x5908d47b2070): Needed elements (8000) will be clamped to total elements (172)\n",
-      "\n",
-      "\n",
-      "/home/ecadaux/miniconda3/envs/env_otb2/lib/python3.11/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.\n",
-      "  return _methods._mean(a, axis=axis, dtype=dtype,\n",
-      "/home/ecadaux/miniconda3/envs/env_otb2/lib/python3.11/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in divide\n",
-      "  ret = ret.dtype.type(ret / rcount)\n",
-      "/home/ecadaux/miniconda3/envs/env_otb2/lib/python3.11/site-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice\n",
-      "  ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,\n",
-      "/home/ecadaux/miniconda3/envs/env_otb2/lib/python3.11/site-packages/numpy/core/_methods.py:163: RuntimeWarning: invalid value encountered in divide\n",
-      "  arrmean = um.true_divide(arrmean, div, out=arrmean,\n",
-      "/home/ecadaux/miniconda3/envs/env_otb2/lib/python3.11/site-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in divide\n",
-      "  ret = ret.dtype.type(ret / rcount)\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%%bash\n",
     "export PATH_ALCD=\"../../..\"\n",
-    "python $PATH_ALCD/all_run_alcd.py -force True -s 1 -f True -l Montreux -d 20240213 -c 20240213 -dates False -kfold False -global_parameters global_parameters.json -paths_parameters paths_configuration.json -model_parameters model_parameters.json > tuto_log.txt"
+    "python $PATH_ALCD/all_run_alcd.py -force True -s 1 -f True -l Montreux -d 20240213 -c 20240213 -dates False -kfold False -global_parameters global_parameters.json -paths_parameters paths_configuration.json -model_parameters model_parameters.json > tuto_log.txt 2>/dev/null"
    ]
   },
   {
@@ -451,14 +403,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 6,
    "id": "bdbb6818-5d4c-4461-8e73-09166ad8580f",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "0f34354a34b24fc59d1972d87aa9e8a2",
+       "model_id": "17f9e12f76bb41528fb02822b874890c",
        "version_major": 2,
        "version_minor": 0
       },
@@ -472,7 +424,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "487bfc0b6f8c49569262ff52c71d139d",
+       "model_id": "51455cfbf17f43ad9559e90d0188d563",
        "version_major": 2,
        "version_minor": 0
       },
@@ -510,19 +462,28 @@
     "\n",
     "Here are the results after the first classification by ALCD.\n",
     "\n",
-    "<div style=\"display: flex; justify-content: space-around;\">\n",
-    "    <figure style=\"text-align: center;\">\n",
-    "        <img src=\"montreux_outputs/Montreux_32TLS_20240213/Out/quicklook.png\" alt=\"Image 2\" style=\"width: 400px;\">\n",
-    "        <figcaption>Sentinel-2 acquisition</figcaption>\n",
-    "    </figure>\n",
-    "    <figure style=\"text-align: center;\">\n",
-    "        <img src=\"montreux_outputs/Montreux_32TLS_20240213/Out/colorized_classif.png\" alt=\"Image 1\" style=\"width: 400px;\">\n",
-    "        <figcaption>Sentinel-2 classified</figcaption>\n",
-    "    </figure>\n",
-    "    <figure style=\"text-align: center;\">\n",
-    "        <img src=\"../images/table.png\" alt=\"Image 2\" style=\"width: 400px;\">\n",
-    "        <figcaption>legend</figcaption>\n",
-    "    </figure>\n",
+    "<div style=\"text-align: center;\">\n",
+    "\n",
+    "  <img src=\"../images/quicklook_1.png\" alt=\"Image 2\" width=\"500\">\n",
+    "  \n",
+    "  <p>Sentinel-2 acquisition</p>\n",
+    "\n",
+    "</div>\n",
+    "\n",
+    "<div style=\"text-align: center;\">\n",
+    "    \n",
+    "  <img src=\"../images/colorized_classif_1.png\" alt=\"Image 2\" width=\"500\">\n",
+    "  \n",
+    "  <p>Sentinel-2 classified</p>\n",
+    "\n",
+    "</div>\n",
+    "\n",
+    "<div style=\"text-align: center;\">\n",
+    "    \n",
+    "  <img src=\"../images/table.png\" alt=\"Image 2\" width=\"500\">\n",
+    "  \n",
+    "  <p>Classification legend</p>\n",
+    "\n",
     "</div>"
    ]
   },
@@ -538,7 +499,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 7,
    "id": "bb41460f-0c58-4629-80ba-70c2b9b7f940",
    "metadata": {},
    "outputs": [],
@@ -558,49 +519,20 @@
     "\n",
     "After this command has been run, it is possible to modify the initial training database. In our case, the results for water were disappointing. We will add water samples.\n",
     "\n",
-    "Then run ALCD again with the command"
+    "Then run ALCD again with the following command. This cell may take several seconds to run."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 4,
    "id": "50c5869e-6851-43ea-aae4-6ff7c0b5f624",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/ecadaux/miniconda3/envs/env_otb2/lib/python3.11/site-packages/osgeo/ogr.py:560: FutureWarning: Neither ogr.UseExceptions() nor ogr.DontUseExceptions() has been explicitly called. In GDAL 4.0, exceptions will be enabled by default.\n",
-      "  warnings.warn(\n",
-      "WARNING: In /work/THEIA/CES/oso/CD/conda_env/iota2_build_env/conda-bld/otb_1736246894519/work/OTB/Modules/Filtering/Statistics/src/otbSamplerBase.cxx, line 42\n",
-      "RandomSampler (0x6007486be5f0): Needed elements (8000) will be clamped to total elements (161)\n",
-      "\n",
-      "\n",
-      "WARNING: In /work/THEIA/CES/oso/CD/conda_env/iota2_build_env/conda-bld/otb_1736246894519/work/OTB/Modules/Filtering/Statistics/src/otbSamplerBase.cxx, line 42\n",
-      "RandomSampler (0x600748c28930): Needed elements (8000) will be clamped to total elements (161)\n",
-      "\n",
-      "\n",
-      "WARNING: In /work/THEIA/CES/oso/CD/conda_env/iota2_build_env/conda-bld/otb_1736246894519/work/OTB/Modules/Filtering/Statistics/src/otbSamplerBase.cxx, line 42\n",
-      "RandomSampler (0x6007485d6b50): Needed elements (8000) will be clamped to total elements (174)\n",
-      "\n",
-      "\n",
-      "WARNING: In /work/THEIA/CES/oso/CD/conda_env/iota2_build_env/conda-bld/otb_1736246894519/work/OTB/Modules/Filtering/Statistics/src/otbSamplerBase.cxx, line 42\n",
-      "RandomSampler (0x6007485d80a0): Needed elements (8000) will be clamped to total elements (150)\n",
-      "\n",
-      "\n",
-      "WARNING: In /work/THEIA/CES/oso/CD/conda_env/iota2_build_env/conda-bld/otb_1736246894519/work/OTB/Modules/Filtering/Statistics/src/otbSamplerBase.cxx, line 42\n",
-      "RandomSampler (0x6007485d6800): Needed elements (8000) will be clamped to total elements (175)\n",
-      "\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%%bash\n",
     "# considering PATH_ALCD is the path to the script 'all_run_alcd.py'\n",
     "export PATH_ALCD=\"../../..\"\n",
-    "python $PATH_ALCD/all_run_alcd.py -force False -s 1 -f False -l Montreux -d 20240213 -c 20240213 -dates False -kfold False -global_parameters global_parameters.json -paths_parameters paths_configuration.json -model_parameters model_parameters.json > log_tuto.txt"
+    "python $PATH_ALCD/all_run_alcd.py -force False -s 1 -f False -l Montreux -d 20240213 -c 20240213 -dates False -kfold False -global_parameters global_parameters.json -paths_parameters paths_configuration.json -model_parameters model_parameters.json > log_tuto.txt  2>/dev/null"
    ]
   },
   {
@@ -612,19 +544,28 @@
    "source": [
     "The results generated during this iteration overwrite the previous ones. With the addition of samples, we can see an evolution in the classification\n",
     "\n",
-    "<div style=\"display: flex; justify-content: space-around;\">\n",
-    "    <figure style=\"text-align: center;\">\n",
-    "        <img src=\"montreux_outputs/Montreux_32TLS_20240213/Out/quicklook.png\" alt=\"Image 2\" style=\"width: 400px;\">\n",
-    "        <figcaption>Sentinel-2 acquisition</figcaption>\n",
-    "    </figure>\n",
-    "    <figure style=\"text-align: center;\">\n",
-    "        <img src=\"montreux_outputs/Montreux_32TLS_20240213/Out/colorized_classif.png\" alt=\"Image 1\" style=\"width: 400px;\">\n",
-    "        <figcaption>Sentinel-2 classified</figcaption>\n",
-    "    </figure>\n",
-    "    <figure style=\"text-align: center;\">\n",
-    "        <img src=\"../images/table.png\" alt=\"Image 2\" style=\"width: 400px;\">\n",
-    "        <figcaption>legend</figcaption>\n",
-    "    </figure>\n",
+    "<div style=\"text-align: center;\">\n",
+    "\n",
+    "  <img src=\"../images/quicklook_2.png\" alt=\"Image 2\" width=\"500\">\n",
+    "  \n",
+    "  <p>Sentinel-2 acquisition</p>\n",
+    "\n",
+    "</div>\n",
+    "\n",
+    "<div style=\"text-align: center;\">\n",
+    "    \n",
+    "  <img src=\"../images/colorized_classif_2.png\" alt=\"Image 2\" width=\"500\">\n",
+    "  \n",
+    "  <p>Sentinel-2 classified</p>\n",
+    "\n",
+    "</div>\n",
+    "\n",
+    "<div style=\"text-align: center;\">\n",
+    "    \n",
+    "  <img src=\"../images/table.png\" alt=\"Image 2\" width=\"500\">\n",
+    "  \n",
+    "  <p>Classification legend</p>\n",
+    "\n",
     "</div>\n",
     "\n",
     "## Advance usages\n",
@@ -720,7 +661,7 @@
     "\t},\n",
     "```\n",
     "\n",
-    "### User features\n",
+    "### User features \n",
     "\n",
     "Users can integrate custom processes to modify the input data before classification by adding *\"user_function\"* and *\"user_module\"* fields in the \"user_choices\" section of the *global_parameters.json* file:\n",
     "\n",
@@ -787,7 +728,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.11.11"
   }
  },
  "nbformat": 4,