Merge branch '157-masques-ajout-des-masques-dans-la-configuration' in…

…to 'release'

Resolve "Masques: ajout des masques dans la configuration"

See merge request 3d/PandoraBox/pandora2d!134

docs/source/userguide/input.rst

@@ -41,16 +41,16 @@ Input section is composed of the following keys:
       - If the estimation step is not present
 
 .. warning::
-    If interpolation is used as refinement method, row_disparity and col_disparity ranges must have a size greater than or equal to 2. 
+    If interpolation is used as refinement method, row_disparity and col_disparity ranges must have a size greater than or equal to 2.
 
 
 Image (left and right) and disparity (col_disparity and row_disparity) properties are composed of the following keys:
 
 .. tabs::
 
-  .. tab:: Image properties
+   .. tab:: Image properties
 
-    .. list-table:: 
+    .. list-table::
         :header-rows: 1
 
         * - Name
@@ -68,10 +68,15 @@ Image (left and right) and disparity (col_disparity and row_disparity) propertie
           - int, "NaN" or "inf"
           - -9999
           - No
+        * - *mask*
+          - Path to the mask
+          - string
+          - none
+          - No
 
   .. tab:: Disparity properties
 
-    .. list-table:: 
+    .. list-table::
         :header-rows: 1
 
         * - Name
@@ -87,12 +92,18 @@ Image (left and right) and disparity (col_disparity and row_disparity) propertie
         * - *range*
           - The search radius (see :ref:`initial_disparity`)
           - int >= 0
-          - 
+          -
           - Yes
 
 .. warning::
     With sad/ssd matching_cost_method in the pipeline (see :ref:`Sequencing`) , `nodata` only accepts `int` type.
 
+.. note::
+    Only one-band masks are accepted by pandora2d. Mask must comply with the following convention :
+     - Value equal to 0 for valid pixel
+     - Value not equal to 0 for invalid pixel
+
+
 **Example**
 
 .. code:: json
@@ -103,7 +114,8 @@ Image (left and right) and disparity (col_disparity and row_disparity) propertie
         {
             "left": {
                 "img": "./data/left.tif",
-                "nodata": -9999
+                "nodata": -9999,
+                "mask": "./data/mask_left.tif"
             },
             "right": {
                 "img": "/data/right.tif",

pandora2d/check_configuration.py

@@ -41,6 +41,7 @@
     update_conf,
 )
 
+from pandora.check_configuration import rasterio_can_open
 from pandora2d.state_machine import Pandora2DMachine
 
 
@@ -304,10 +305,12 @@ def get_roi_config(user_cfg: Dict[str, dict]) -> Dict[str, dict]:
     "left": {
         "img": And(str, rasterio_can_open_mandatory),
         "nodata": Or(int, lambda input: np.isnan(input), lambda input: np.isinf(input)),
+        "mask": And(Or(str, lambda input: input is None), rasterio_can_open),
     },
     "right": {
         "img": And(str, rasterio_can_open_mandatory),
         "nodata": Or(int, lambda input: np.isnan(input), lambda input: np.isinf(input)),
+        "mask": And(Or(str, lambda input: input is None), rasterio_can_open),
     },
     "col_disparity": {"init": int, "range": And(int, lambda x: x >= 0)},
     "row_disparity": {"init": int, "range": And(int, lambda x: x >= 0)},
@@ -317,9 +320,11 @@ def get_roi_config(user_cfg: Dict[str, dict]) -> Dict[str, dict]:
     "input": {
         "left": {
             "nodata": -9999,
+            "mask": None,
         },
         "right": {
             "nodata": -9999,
+            "mask": None,
         },
     }
 }

tests/conftest.py

@@ -26,6 +26,9 @@
 import re
 
 import pytest
+import rasterio
+from pandora.common import write_data_array
+import xarray as xr
 
 
 def pytest_collection_modifyitems(config, items):
@@ -149,3 +152,53 @@ def correct_multiband_input_cfg(left_rgb_path, right_rgb_path):
             "row_disparity": {"init": 1, "range": 2},
         }
     }
+
+
+@pytest.fixture
+def mask_path(left_img_path, tmp_path):
+    """Create a mask and save it in tmp"""
+
+    with rasterio.open(left_img_path) as src:
+        width = src.width
+        height = src.height
+
+    mask = xr.DataArray(data=0, dims=["height", "width"], coords={"height": range(height), "width": range(width)})
+    mask[0 : int(height / 2), 0 : int(width / 2)] = 1
+
+    path = tmp_path / "mask_left.tif"
+
+    write_data_array(
+        data_array=mask,
+        filename=str(path),
+    )
+
+    return path
+
+
+@pytest.fixture
+def correct_input_with_left_mask(left_img_path, right_img_path, mask_path):
+    return {
+        "input": {
+            "left": {"img": left_img_path, "nodata": -9999, "mask": str(mask_path)},
+            "right": {
+                "img": right_img_path,
+            },
+            "col_disparity": {"init": 0, "range": 2},
+            "row_disparity": {"init": 0, "range": 2},
+        }
+    }
+
+
+@pytest.fixture
+def correct_input_with_right_mask(left_img_path, right_img_path, mask_path):
+    return {
+        "input": {
+            "left": {
+                "img": left_img_path,
+                "nodata": -9999,
+            },
+            "right": {"img": right_img_path, "mask": str(mask_path)},
+            "col_disparity": {"init": 0, "range": 2},
+            "row_disparity": {"init": 0, "range": 2},
+        }
+    }

tests/functional_tests/test_pipelines.py

@@ -192,3 +192,29 @@ def test_optical_flow_configuration(run_pipeline, correct_input_cfg, correct_pip
     # Check window_size and step parameters
     assert matching_cost_cfg["window_size"] == refinement_cfg["window_size"]
     assert matching_cost_cfg["step"] == refinement_cfg["step"]
+
+
+@pytest.mark.parametrize("input_cfg", ["correct_input_with_left_mask", "correct_input_with_right_mask"])
+def test_configuration_with_mask(run_pipeline, input_cfg, correct_pipeline_without_refinement, request):
+    """
+    Description : Test mask configuration
+    """
+    input_cfg = request.getfixturevalue(input_cfg)
+
+    configuration = {**input_cfg, **correct_pipeline_without_refinement}
+
+    run_dir = run_pipeline(configuration)
+
+    with open(run_dir / "output" / "cfg" / "config.json", encoding="utf8") as output_file:
+        output_config = json.load(output_file)
+
+    result = remove_extra_keys(output_config, configuration)
+
+    assert result == configuration
+    assert list(result["pipeline"].keys()) == list(configuration["pipeline"].keys()), "Pipeline order not respected"
+
+    # Test for report
+    with open(run_dir / "output" / "report.json", encoding="utf8") as report_file:
+        report = json.load(report_file)
+
+    assert report["statistics"]["disparity"].keys() == {"row", "col"}