Fixed overlap failure in tiles construction

src/microglia_analyzer/_tests/workflow.py

@@ -21,24 +21,5 @@ def microglia_to_tiles():
             tile_name = im_name.replace(".tif", f"_{str(i).zfill(2)}.tif")
             tifffile.imwrite(os.path.join(output_folder, tile_name), tile)
 
-def classic_workflow_test():
-    def logging(message):
-        print("[MA] " + message)
-
-    img_target = "/home/benedetti/Documents/projects/2060-microglia/data/_testing_images/adulte 4.tif"
-
-    mam = MicrogliaAnalyzer(logging)
-    mam.load_image(img_target)
-    mam.set_calibration(0.325, "µm")
-    mam.export_patches()
-    mam.set_segmentation_model("/home/benedetti/Documents/projects/2060-microglia/µnet/µnet-V004")
-    mam.segment_microglia()
-    return
-    mam.set_classification_model("µyolo-V005")
-    mam.classify_microglia()
-    mam.make_skeletons()
-    mam.extract_metrics()
-
-
 if __name__ == "__main__":
-    classic_workflow_test()
+    microglia_to_tiles()

src/microglia_analyzer/tiles/patch.py

@@ -41,6 +41,9 @@ def __init__(self, patch_size, overlap, indices, shape, grid):
         self._check_neighbours()
         self._process_overlap()
 
+    def __str__(self):
+        return f"Patch2D({self.patch_size} > {self.ul_corner}, {self.lr_corner}, {self.overlaps})"
+
     def _process_patch(self):
         """
         From the indices on the grid, determines the upper-left and lower-right corners of the patch.
@@ -86,9 +89,9 @@ def _process_overlap(self):
         if self.has_neighbour[0]:
             self.overlaps[0] = max(self.overlap, x - self.ul_corner[1])
         if self.has_neighbour[1]:
-            self.overlaps[1] = self.overlap if self.lr_corner[0] + self.patch_size <= self.shape[0] else self.shape[0] - self.lr_corner[0]
+            self.overlaps[1] = self.overlap if (self.lr_corner[0] + self.patch_size - self.overlap <= self.shape[0]) else (self.shape[0] - self.lr_corner[0])
         if self.has_neighbour[2]:
-            self.overlaps[2] = self.overlap if self.lr_corner[1] + self.patch_size <= self.shape[1] else self.shape[1] - self.lr_corner[1]
+            self.overlaps[2] = self.overlap if (self.lr_corner[1] + self.patch_size - self.overlap <= self.shape[1]) else (self.shape[1] - self.lr_corner[1])
         if self.has_neighbour[3]:
             self.overlaps[3] = max(self.overlap, y - self.ul_corner[0])
 

src/microglia_analyzer/tiles/tiler.py

@@ -228,4 +228,30 @@ def tiles_to_image(self, patches):
             coef = np.stack([self.blending_coefs[i]] * n_channels, axis=-1) if n_channels > 1 else self.blending_coefs[i]
             copies[i] *= coef
             canvas[p.ul_corner[0]:p.lr_corner[0], p.ul_corner[1]:p.lr_corner[1]] += copies[i]
-        return canvas.astype(patches[0].dtype)
+        return canvas.astype(patches[0].dtype)
+
+
+if __name__ == "__main__":
+    import tifffile
+    from microglia_analyzer.experimental.tiles import generate_checkerboard
+
+    # checkerboard_img = np.squeeze(np.array(generate_checkerboard(2048, 2048, 16, 16)))
+    checkerboard_img = np.ones((2048, 2048), np.float32)
+    tifffile.imwrite("/tmp/exp/01-original.tif", checkerboard_img)
+
+    tiles_manager = ImageTiler2D(512, 128, checkerboard_img.shape)
+    tiles = tiles_manager.image_to_tiles(checkerboard_img)
+    tifffile.imwrite("/tmp/exp/02-tiles.tif", tiles)
+
+    merged = tiles_manager.tiles_to_image(tiles)
+    tifffile.imwrite("/tmp/exp/03-merged.tif", merged)
+
+    tifffile.imwrite("/tmp/exp/04-coefs.tif", tiles_manager.blending_coefs)
+
+    tifffile.imwrite(
+        "/tmp/exp/05-gradient.tif", 
+        tiles_manager.tiles_to_image(tiles_manager.blending_coefs)
+    )
+
+    for p in tiles_manager.layout:
+        print(p)