Add doc

.github/workflows/build_and_test_app.yml

@@ -0,0 +1,62 @@
+name: ALCD
+
+on:
+  pull_request:
+    branches:
+      - "master"
+
+permissions:
+  contents: read
+env:
+  OTB_RELEASE: 9.1.0
+jobs:
+  quality:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: setup python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+      - name: install quality deps
+        run: |
+          pip install pylint mccabe
+      - name: code quality
+        run: |
+          pylint --disable=all --fail-under=10 --enable=too-many-statements --max-statements=100 .
+          pylint --disable=all --fail-under=10 --enable=too-many-nested-blocks .
+          ./continuous_integration/scripts/check_mccabe_complexity.sh 25 .
+  test:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v4
+    - name: setup python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        sudo apt install -y --no-install-recommends g++ swig cmake make
+        pip install "numpy<2"
+        curl https://www.orfeo-toolbox.org/packages/archives/OTB/OTB-$OTB_RELEASE-Linux.tar.gz -o OTB-$OTB_RELEASE-Linux.tar.gz
+        tar xvf OTB-$OTB_RELEASE-Linux.tar.gz --one-top-level="/opt/otb"
+        source /opt/otb/otbenv.profile
+        sh /opt/otb/recompile_bindings.sh
+        python -m pip install --upgrade pip
+        pip install pytest pytest-cov
+        if [ -f docker/requirements.txt ]; then pip install -r docker/requirements.txt; fi
+    - name: pytest
+      run: |
+        cd tests
+        export CMAKE_PREFIX_PATH=/opt/otb
+        export PYTHONPATH=/opt/otb/lib/python3/dist-packages:/opt/otb/lib/otb/python
+        export GDAL_DRIVER_PATH=disable
+        export GDAL_DATA=/opt/otb/share/gdal
+        export PROJ_LIB=/opt/otb/share/proj
+        export PATH=/opt/otb/bin:$PATH
+        export LD_LIBRARY_PATH=/opt/otb/lib:$LD_LIBRARY_PATH
+        export OTB_APPLICATION_PATH=/opt/otb/lib/otb/applications
+        export OTB_INSTALL_DIR=/opt/otb
+        export LC_NUMERIC=C
+
+        pytest -s --cov-fail-under=65

.gitignore

@@ -0,0 +1,5 @@
+*.pyc
+*.py~
+.gitignore~
+*.sh~
+*.json~

L1C_band_composition.py

@@ -115,7 +115,7 @@ def create_specific_indices(in_bands_dir, out_tif, indice_name, resolution=60):
         print('Please enter a valid indice name')
 
 
-def create_time_difference_band(global_parameters, band_num, out_tif, resolution=60):
+def create_time_difference_band(global_parameters, paths_parameters, band_num, out_tif, resolution=60):
     '''
     Create a TIF being the difference between the cloudy date and the clear date
     The band_num is the number of the band of interest
@@ -125,9 +125,9 @@ def create_time_difference_band(global_parameters, band_num, out_tif, resolution
     clear_date = global_parameters["user_choices"]["clear_date"]
 
     current_dir, current_band_prefix, current_date = find_directory_names.get_L1C_dir(
-        location, current_date, display=False)
+        location, current_date,paths_parameters, display=False)
     clear_dir, clear_band_prefix, clear_date = find_directory_names.get_L1C_dir(
-        location, clear_date, display=False)
+        location, clear_date,paths_parameters, display=False)
 
     band_num_str = '{:02d}'.format(band_num)
 
@@ -260,7 +260,7 @@ def dtm_addition(location, out_band, resolution=60):
     Create the adapted Digital Terrain Model
     From the original one, change its resolution
     '''
-    paths_configuration = json.load(open(op.join('..', 'paths_configuration.json')))
+    paths_configuration = json.load(open(op.join('parameters_files', 'paths_configuration.json')))
     tile = paths_configuration["tile_location"][location]
 
     original_DTM_dir = paths_configuration["global_chains_paths"]["DTM_input"]
@@ -293,7 +293,7 @@ def resize_band(in_band, out_band, pixelresX, pixelresY):
     os.system(build_warp)
 
 
-def create_image_compositions(global_parameters, location, current_date, heavy=False, force=False):
+def create_image_compositions(global_parameters, location, paths_parameters, current_date, heavy=False, force=False):
     #
     potential_final_tif = op.join(global_parameters["user_choices"]["main_dir"],
                                   'In_data', 'Image', global_parameters["user_choices"]["raw_img"])
@@ -304,7 +304,7 @@ def create_image_compositions(global_parameters, location, current_date, heavy=F
 
     # get the directory of the bands
     bands_dir, band_prefix, date = find_directory_names.get_L1C_dir(
-        location, current_date, display=True)
+        location, current_date, paths_parameters, display=True)
     # --------------------------------------------
     # ------ Low resolution TIF with all the bands
     # Preparation
@@ -356,7 +356,7 @@ def create_image_compositions(global_parameters, location, current_date, heavy=F
     out_dir_bands = op.join(global_parameters["user_choices"]["main_dir"], 'Intermediate')
     for band_num in bands_num:
         out_tif = op.join(out_dir_bands, ('time_' + str(band_num) + '.tif'))
-        create_time_difference_band(global_parameters, band_num, out_tif, resolution=resolution)
+        create_time_difference_band(global_parameters, paths_parameters, band_num, out_tif, resolution=resolution)
         additional_bands.append(str(out_tif))
 
     # --- Create the main TIF with low resolution
@@ -429,7 +429,7 @@ def create_image_compositions(global_parameters, location, current_date, heavy=F
     return
 
 
-def create_no_data_tif(global_parameters, out_tif, dilation_radius=10):
+def create_no_data_tif(global_parameters, paths_parameters, out_tif, dilation_radius=10):
     '''
     Create the no_data TIF using both the clear and cloudy date.
     Used in the 'layers_creation.create_no_data_shp'
@@ -439,9 +439,9 @@ def create_no_data_tif(global_parameters, out_tif, dilation_radius=10):
     clear_date = global_parameters["user_choices"]["clear_date"]
 
     current_dir, current_band_prefix, current_date = find_directory_names.get_L1C_dir(
-        location, current_date, display=False)
+        location, current_date, paths_parameters, display=False)
     clear_dir, clear_band_prefix, clear_date = find_directory_names.get_L1C_dir(
-        location, clear_date, display=False)
+        location, clear_date, paths_parameters, display=False)
 
     # Band number, the 1 is 20m resolution, change it if
     # other resolution is wanted
@@ -462,8 +462,9 @@ def create_no_data_tif(global_parameters, out_tif, dilation_radius=10):
     Dilatation.SetParameterInputImage("in", BandMathX.GetParameterOutputImage("out"))
     Dilatation.SetParameterString("out", str(out_tif))
     Dilatation.SetParameterString("filter", "dilate")
-    Dilatation.SetParameterInt("structype.ball.xradius", dilation_radius)
-    Dilatation.SetParameterInt("structype.ball.yradius", dilation_radius)
+    Dilatation.SetParameterString("structype", "ball")
+    Dilatation.SetParameterInt("xradius", dilation_radius)
+    Dilatation.SetParameterInt("yradius", dilation_radius)
     Dilatation.UpdateParameters()
     Dilatation.ExecuteAndWriteOutput()
 

OTB_workflow.py

@@ -73,7 +73,7 @@ def compute_image_stats(global_parameters, proceed=True):
     print("  Compute Images Statistics")
     ComputeImagesStatistics = otbApplication.Registry.CreateApplication("ComputeImagesStatistics")
     ComputeImagesStatistics.SetParameterStringList("il", [str(raw_img)])
-    ComputeImagesStatistics.SetParameterString("out", str(img_stats))
+    ComputeImagesStatistics.SetParameterString("out.xml", str(img_stats))
     ComputeImagesStatistics.ExecuteAndWriteOutput()
 
     print('Done')
@@ -85,7 +85,7 @@ def compute_samples_stats(global_parameters, proceed=True):
     '''
     1. Compute the samples stats
     '''
-    print "  Polygon Classes Statistics"
+    print( "  Polygon Classes Statistics")
 
     main_dir = global_parameters["user_choices"]["main_dir"]
     raw_img = op.join(main_dir, 'In_data', 'Image', global_parameters["user_choices"]["raw_img"])
@@ -98,7 +98,7 @@ def compute_samples_stats(global_parameters, proceed=True):
                           global_parameters["general"]["no_data_mask"])
     no_data_mask = no_data_shp[0:-4] + '.tif'
 
-    PolygonClassStatistics = otbApplication.Registry_CreateApplication("PolygonClassStatistics")
+    PolygonClassStatistics = otbApplication.Registry.CreateApplication("PolygonClassStatistics")
     PolygonClassStatistics.SetParameterString("in", str(raw_img))
     PolygonClassStatistics.SetParameterString("vec", str(training_shp))
     PolygonClassStatistics.SetParameterString("out", str(class_stats))
@@ -167,7 +167,7 @@ def select_samples(global_parameters, strategy="smallest", proceed=True):
     no_data_mask = no_data_shp[0:-4] + '.tif'
 
     print("  Training Samples Selection")
-    SampleSelection = otbApplication.Registry_CreateApplication("SampleSelection")
+    SampleSelection = otbApplication.Registry.CreateApplication("SampleSelection")
     SampleSelection.SetParameterString("in", str(raw_img))
     SampleSelection.SetParameterString("vec", str(training_shp))
     SampleSelection.SetParameterString("mask", str(no_data_mask))
@@ -207,7 +207,7 @@ def extract_samples(global_parameters, proceed=True):
         main_dir, 'Samples', global_parameters["general"]["training_samples_location"])
 
     print("  Training Samples Extraction")
-    SampleExtraction = otbApplication.Registry_CreateApplication("SampleExtraction")
+    SampleExtraction = otbApplication.Registry.CreateApplication("SampleExtraction")
     SampleExtraction.SetParameterString("in", str(raw_img))
     SampleExtraction.SetParameterString("vec", str(training_samples_location))
     SampleExtraction.SetParameterString("outfield", "prefix")
@@ -223,12 +223,11 @@ def extract_samples(global_parameters, proceed=True):
 # -------- 2. MODEL TRAINING ---------------------
 
 
-def train_model(global_parameters, shell=True, proceed=True):
+def train_model(global_parameters, model_parameters, shell=True, proceed=True):
     '''
     5. Train the model
     '''
     main_dir = global_parameters["user_choices"]["main_dir"]
-
     method = global_parameters["classification"]["method"]
     training_samples_extracted = op.join(
         main_dir, 'Samples', global_parameters["general"]["training_samples_extracted"])
@@ -249,16 +248,13 @@ def train_model(global_parameters, shell=True, proceed=True):
 
     if proceed == True:
         print("  Train Vector Classifier")
-        # load the model parameters
-        with open(op.join('parameters_files', 'model_parameters.json'), 'r') as file_model:
-            dico = json.load(file_model)
         if shell == True:
             # can be run through the API or through the shell
             command = 'otbcli_TrainVectorClassifier -io.vd {} -cfield {} -io.out {} -classifier {} -feat {}'.format(
                 training_samples_extracted, "class", model_out, method, str(features))
 
             model_options = ''
-            for key, value in dico[method].iteritems():
+            for key, value in model_parameters[method].items():
                 model_options = model_options + ' -classifier.{}.{} {}'.format(method, key, value)
 
             command = command + model_options
@@ -274,7 +270,7 @@ def train_model(global_parameters, shell=True, proceed=True):
             TrainVectorClassifier.SetParameterStringList("feat", features_API)
             TrainVectorClassifier.SetParameterString("classifier", str(method))
 
-            for key, value in dico[method].iteritems():
+            for key, value in model_parameters[method].items():
                 TrainVectorClassifier.SetParameterString(
                     str("classifier.{}.{}".format(method, key)), str(value))
 
@@ -356,7 +352,7 @@ def fancy_classif_viz(global_parameters, proceed=True):
     main_dir = global_parameters["user_choices"]["main_dir"]
 
     img_labeled = op.join(main_dir, 'Out', global_parameters["general"]["img_labeled_regularized"])
-    color_table = op.join('color_tables', global_parameters["color_tables"]["otb"])
+    color_table = global_parameters["color_tables"]["otb"]
     out_image_colorized = op.join(main_dir, 'Out', 'colorized_classif.png')
 
     ColorMapping = otbApplication.Registry.CreateApplication("ColorMapping")
@@ -396,7 +392,7 @@ def compute_mat_conf(global_parameters, show=True, proceed=True):
 
     print('Done')
 
-    with open(conf_matrix, 'rb') as csvfile:
+    with open(conf_matrix, 'r') as csvfile:
         reader = csv.reader(csvfile, delimiter=',')
         rows = []
         for row in reader: