Merge branch '164-mise-a-jour-des-pixels-size-en-sortie-en-fonction-d…

…u-pas' into 'release'

Resolve "Mise à jour des pixels size en sortie en fonction du pas"

See merge request 3d/PandoraBox/pandora2d!148

pandora2d/common.py

@@ -34,7 +34,7 @@
     from xarray import Coordinate as Coordinates
 
 import os
-from typing import Dict, Union
+from typing import Dict, Union, Tuple
 import xarray as xr
 import numpy as np
 from numpy.typing import NDArray
@@ -65,8 +65,8 @@ def save_dataset(dataset: xr.Dataset, cfg: Dict, output: str) -> None:
     # remove ROI margins to save only user ROI in tif files
     if "ROI" in cfg:
         dataset = remove_roi_margins(dataset, cfg)
-        # Translate georeferencement origin to ROI origin:
-        dataset.attrs["transform"] *= Affine.translation(cfg["ROI"]["col"]["first"], cfg["ROI"]["row"]["first"])
+    if dataset.attrs["transform"] is not None:
+        adjust_georeferencement(dataset, cfg)
     # create output dir
     mkdir_p(output)
 
@@ -95,6 +95,52 @@ def save_dataset(dataset: xr.Dataset, cfg: Dict, output: str) -> None:
     )
 
 
+def adjust_georeferencement(dataset: xr.Dataset, cfg: Dict) -> None:
+    """
+    Change origin in case a ROI is present and set pixel size to the matching cost step.
+
+    :param dataset: dataset to configure.
+    :type dataset: xr.Dataset
+    :param cfg: configuration
+    :type cfg: Dict
+    """
+    if "ROI" in cfg:
+        # Translate georeferencement origin to ROI origin:
+        dataset.attrs["transform"] *= Affine.translation(cfg["ROI"]["col"]["first"], cfg["ROI"]["row"]["first"])
+    row_step, col_step = get_step(cfg)
+    set_pixel_size(dataset, row_step, col_step)
+
+
+def get_step(cfg: Dict) -> Tuple[int, int]:
+    """
+    Get step from matching cost or retun default value.
+    :param cfg: configuration
+    :type cfg: Dict
+    :return: row_step, col_step
+    :rtype: Tuple[int, int]
+    """
+    try:
+        return cfg["pipeline"]["matching_cost"]["step"]
+    except KeyError:
+        return 1, 1
+
+
+def set_pixel_size(dataset: xr.Dataset, row_step: int = 1, col_step: int = 1) -> None:
+    """
+    Set the pixel size according to the step used in calculating the matching cost.
+
+    This ensures that all pixels are well geo-referenced in case a step is applied.
+
+    :param dataset: Data to save
+    :type dataset: xr.Dataset
+    :param row_step: step used in row
+    :type row_step: int
+    :param col_step: step used in column
+    :type col_step: int
+    """
+    dataset.attrs["transform"] *= Affine.scale(col_step, row_step)
+
+
 def dataset_disp_maps(
     delta_row: np.ndarray,
     delta_col: np.ndarray,