Doc 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/how_to_install_alcd.md

@@ -1,6 +1,26 @@
 # ALCD Installation and Usage Guide
 
-**Note**: ALCD is currently not distributed as a Python package. To use ALCD, you first need to clone the ALCD repository and then create either a Docker or Singularity image.
+**Note**: ALCD is currently not distributed as a Python package. To use ALCD, you first need to clone the ALCD repository and then create either a Docker or Singularity image or use it in a conda environment.
+
+## Solution 1 : Use a conda environment
+
+If you don't have conda installed yet, then follow the [conda install guide](https://www.anaconda.com/docs/getting-started/miniconda/install)
+
+```bash
+git clone https://github.com/CNES/ALCD.git
+cd ALCD
+conda env create -f environment.yml
+conda activate ALCD # then your are ready to use ALCD
+```
+
+## Solution 2 : Use the ALCD docker image
+
+```bash
+docker pull cnes/ALCD:latest
+docker run -it cnes/ALCD:latest
+```
+
+## Solution 3: Build your own ALCD docker image
 
 ### Step 1: Clone the ALCD Repository
 To begin, clone the ALCD repository to your local machine:
@@ -34,7 +54,7 @@ Explanation of the command options:
     -v /path/to/local/DATA:/DATA Mounts your local / /path/to/local/DATA directory to /DATA within the Docker container, allowing data access and output within this directory.
     alcd:latest: Refers to the Docker image tagged as alcd, built in step 2.
 
-### Step 3: Create the Singularity Image
+## Solution 4: Build your own ALCD singularity image
 
 Navigate to the /singularity directory within the ALCD project:
 

docs/source/index.md

@@ -1,4 +1,4 @@
-# ACLD documentation
+# ALCD documentation
 
 This is the current user manual for the Active Learning Cloud Detection (ALCD). This code produces classification ref-
 erence masks from a Sentinel-2 L1C product, and is particularly designed to detect clouds and

docs/source/notebooks/montreux.ipynb

@@ -39,7 +39,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "853e763d423e46e3a03b6dfc4ca39b8e",
+       "model_id": "cbf9a41ff98340d8a5da8f984a938a50",
        "version_major": 2,
        "version_minor": 0
       },
@@ -53,7 +53,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "ed53896a773f465da1f70801290550ac",
+       "model_id": "b1d7c666c63e47f3b7a99b30b99c5b7b",
        "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
       },
@@ -388,55 +379,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 5,
    "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": [],
@@ -563,44 +524,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 8,
    "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,