Merge branch '110-add-georef-to-disparity-map' into 'release'

Resolve "Formater: mise en place du géoréférencement"

See merge request 3d/PandoraBox/pandora2d!96

pandora2d/common.py

@@ -67,13 +67,28 @@ def save_dataset(dataset: xr.Dataset, cfg: Dict, output: str) -> None:
     mkdir_p(output)
 
     # save disp map for row
-    write_data_array(dataset["row_map"], os.path.join(output, "row_disparity.tif"))
+    write_data_array(
+        dataset["row_map"],
+        os.path.join(output, "row_disparity.tif"),
+        crs=dataset.attrs["crs"],
+        transform=dataset.attrs["transform"],
+    )
 
     # save disp map for columns
-    write_data_array(dataset["col_map"], os.path.join(output, "columns_disparity.tif"))
+    write_data_array(
+        dataset["col_map"],
+        os.path.join(output, "columns_disparity.tif"),
+        crs=dataset.attrs["crs"],
+        transform=dataset.attrs["transform"],
+    )
 
     # save correlation score
-    write_data_array(dataset["correlation_score"], os.path.join(output, "correlation_score.tif"))
+    write_data_array(
+        dataset["correlation_score"],
+        os.path.join(output, "correlation_score.tif"),
+        crs=dataset.attrs["crs"],
+        transform=dataset.attrs["transform"],
+    )
 
 
 def dataset_disp_maps(

pandora2d/state_machine.py

@@ -390,7 +390,11 @@ def disp_maps_run(self, cfg: Dict[str, dict], input_step: str) -> None:
             map_col,
             self.cost_volumes.coords,
             correlation_score,
-            {"invalid_disp": cfg["pipeline"]["disparity"]["invalid_disparity"]},
+            {
+                "invalid_disp": cfg["pipeline"]["disparity"]["invalid_disparity"],
+                "crs": self.left_img.crs,
+                "transform": self.left_img.transform,
+            },
         )
 
     def refinement_run(self, cfg: Dict[str, dict], input_step: str) -> None:

tests/functional_tests/matching_cost/test_subpix.py

@@ -55,6 +55,7 @@ def create_datasets(self, data_left, data_right):
             "crs": None,
             "col_disparity_source": [-2, 2],
             "row_disparity_source": [-2, 2],
+            "transform": None,
         }
 
         right = xr.Dataset(
@@ -66,6 +67,7 @@ def create_datasets(self, data_left, data_right):
             "valid_pixels": 0,
             "no_data_mask": 1,
             "crs": None,
+            "transform": None,
         }
 
         return left, right

tests/unit_tests/conftest.py

@@ -72,11 +72,9 @@ def correct_input_cfg(left_img_path, right_img_path):
         "input": {
             "left": {
                 "img": left_img_path,
-                "nodata": "NaN",
-            },
-            "right": {
-                "img": right_img_path,
+                "nodata": -9999,
             },
+            "right": {"img": right_img_path, "nodata": -9999},
             "col_disparity": [-2, 2],
             "row_disparity": [-2, 2],
         }

tests/unit_tests/test_common.py

@@ -31,18 +31,21 @@
 import numpy as np
 import pytest
 import xarray as xr
+import rasterio
 from skimage.io import imsave
-
-from pandora2d import common
+from rasterio import Affine
+from pandora2d import common, run
+from pandora2d.check_configuration import check_conf
 from pandora2d.img_tools import create_datasets_from_inputs
 from pandora2d import matching_cost, disparity, refinement
+from pandora2d.state_machine import Pandora2DMachine
 
 
 class TestSaveDataset:
     """Test save_dataset method"""
 
     @pytest.fixture
-    def create_test_dataset(self):
+    def create_test_dataset(self, attributes):
         """
         Create a test dataset
         """
@@ -59,21 +62,45 @@ def create_test_dataset(self):
         dataarray_col = xr.DataArray(col, dims=dims, coords=coords)
         dataarray_score = xr.DataArray(score, dims=dims, coords=coords)
 
-        dataset = xr.Dataset({"row_map": dataarray_row, "col_map": dataarray_col, "correlation_score": dataarray_score})
+        dataset = xr.Dataset(
+            {"row_map": dataarray_row, "col_map": dataarray_col, "correlation_score": dataarray_score},
+            attrs=attributes,
+        )
 
         return dataset
 
-    def test_save_dataset(self, create_test_dataset, correct_input_cfg):
+    @pytest.mark.parametrize(
+        "attributes",
+        [
+            {"crs": "EPSG:32632", "transform": Affine(25.94, 0.00, -5278429.43, 0.00, -25.94, 14278941.03)},
+            {"crs": None, "transform": Affine(1.0, 0.0, 0.0, 0.0, 1.0, 0.0)},
+        ],
+    )
+    def test_save_dataset(self, create_test_dataset, correct_input_cfg, attributes):
         """
         Function for testing the dataset_save function
         """
 
         common.save_dataset(create_test_dataset, correct_input_cfg, "./tests/res_test/")
         assert os.path.exists("./tests/res_test/")
 
+        # Test columns disparity map
         assert os.path.exists("./tests/res_test/columns_disparity.tif")
+        columns_disparity = rasterio.open("./tests/res_test/columns_disparity.tif")
+        assert columns_disparity.crs == attributes["crs"]
+        assert columns_disparity.transform == attributes["transform"]
+
+        # Test row disparity map
         assert os.path.exists("./tests/res_test/row_disparity.tif")
+        row_disparity = rasterio.open("./tests/res_test/row_disparity.tif")
+        assert row_disparity.crs == attributes["crs"]
+        assert row_disparity.transform == attributes["transform"]
+
+        # Test correlation score map
         assert os.path.exists("./tests/res_test/correlation_score.tif")
+        correlation_score = rasterio.open("./tests/res_test/correlation_score.tif")
+        assert correlation_score.crs == attributes["crs"]
+        assert correlation_score.transform == attributes["transform"]
 
         os.remove("./tests/res_test/columns_disparity.tif")
         os.remove("./tests/res_test/row_disparity.tif")
@@ -107,7 +134,7 @@ def left_image(self, tmp_path):
         """
         Create a fake image to test dataset_disp_maps method
         """
-        image_path = tmp_path / "left_img.png"
+        image_path = tmp_path / "left_img.tif"
         data = np.full((10, 10), 1, dtype=np.uint8)
         imsave(image_path, data)
 
@@ -118,7 +145,7 @@ def right_image(self, tmp_path):
         """
         Create a fake image to test dataset_disp_maps method
         """
-        image_path = tmp_path / "right_img.png"
+        image_path = tmp_path / "right_img.tif"
         data = np.full((10, 10), 1, dtype=np.uint8)
         imsave(image_path, data)
 
@@ -314,3 +341,28 @@ def test_dataset_disp_maps_with_pipeline_computation(self, roi, step, left_image
         )
 
         assert disparity_maps.equals(dataset_ground_truth)
+
+
+def test_disparity_map_output_georef(correct_pipeline, correct_input_cfg):
+    """
+    Test outputs georef with crs and transform
+    """
+
+    img_left, img_right = create_datasets_from_inputs(input_config=correct_input_cfg["input"])
+
+    # Stock crs and transform information from input
+    img_left.attrs["crs"] = "EPSG:32632"
+    img_left.attrs["transform"] = Affine(25.94, 0.00, -5278429.43, 0.00, -25.94, 14278941.03)
+
+    pandora2d_machine = Pandora2DMachine()
+    # Delete refinement to fastest result
+    del correct_pipeline["pipeline"]["refinement"]
+
+    correct_input_cfg.update(correct_pipeline)
+
+    checked_cfg = check_conf(correct_input_cfg, pandora2d_machine)
+
+    dataset, _ = run(pandora2d_machine, img_left, img_right, checked_cfg)
+
+    assert "EPSG:32632" == dataset.attrs["crs"]
+    assert Affine(25.94, 0.00, -5278429.43, 0.00, -25.94, 14278941.03) == dataset.attrs["transform"]

tests/unit_tests/test_img_tools/test_create_datasets_from_input.py

@@ -62,7 +62,7 @@ def result(self, left_img_path, right_img_path):
         return img_tools.create_datasets_from_inputs(_make_input_section(left_img_path, right_img_path))
 
     def test_use_function_from_pandora(self, mocker, input_section):
-        """Test we use `create_datset_from_inputs` from pandora.
+        """Test we use `create_dataset_from_inputs` from pandora.
 
         We assume this function is well tested in Pandora and that we just need to test that we use it.
         """

tests/unit_tests/test_matching_cost/conftest.py

@@ -37,7 +37,7 @@
 
 @pytest.fixture()
 def squared_image_size():
-    return (10, 10)
+    return 10, 10
 
 
 @pytest.fixture()