Refactor depth reference handling and cleanup

- Unified reference depth calculation to use a single implementation in common/depth.py.
- Removed server-side reference depth computation and adjusted depth.json to only include image_size and intrinsics.
- Updated depth texture handling to ignore transparent, invalid, and non-positive pixels when calculating reference depth.
- Changed reference depth calculation to use the 95th percentile of valid depth values.
- Adjusted depth direction fitting to return a flat direction when no samples are available.
- Removed cleanup threshold parameters from Cutout and related nodes, simplifying the interface.
- Updated tests to verify new reference depth logic and ensure compatibility with existing functionality.

tests/anyimage/server/test_geometry_artifacts.py

@@ -43,7 +43,6 @@ class GeometryArtifactsTest(ServerTestCase):
             ((1.0, 1.0, 0.0), (1.0, 1.0, 1.0)),
             dtype=np.float32,
         )
-        calibration = np.asarray(((False, True, True), (False, False, True)))
         frame = GeometryFrame(
             depth=np.asarray(
                 ((1.0, 2.0, 3.0), (4.0, 5.0, 6.0)),
@@ -55,14 +54,14 @@ class GeometryArtifactsTest(ServerTestCase):
         )
 
         depth.write_depth_texture(frame, texture_path, alpha=np.ones_like(validity))
-        depth.write_depth_metadata(frame, calibration, metadata_path)
+        depth.write_depth_metadata(frame, metadata_path)
 
         self.assertTrue(texture_path.is_file())
         self.assertEqual(texture_path.read_bytes()[:4], b"v/1\x01")
         metadata = json.loads(metadata_path.read_text(encoding="utf-8"))
         self.assertEqual(metadata["image_size"], [3, 2])
         self.assertEqual(metadata["intrinsics"], np.eye(3).tolist())
-        self.assertAlmostEqual(metadata["reference_depth"], 4.0)
+        self.assertEqual(set(metadata), {"image_size", "intrinsics"})
 
 
     def test_object_normal_texture_matches_depth_surface_axes(self):
@@ -192,7 +191,9 @@ class GeometryArtifactsTest(ServerTestCase):
 
         np.testing.assert_array_equal(write.call_args.args[0][..., 3], [[1, 0], [1, 1]])
         np.testing.assert_array_equal(frame.validity, np.ones((2, 2)))
-        self.assertEqual(json.loads(result["depth_metadata"].read_text())["reference_depth"], 1)
+        metadata = json.loads(result["depth_metadata"].read_text())
+        self.assertEqual(metadata["image_size"], [2, 2])
+        self.assertNotIn("reference_depth", metadata)
         infer.assert_called_once()
         self.assertEqual(
             set(result),
@@ -251,5 +252,4 @@ class GeometryArtifactsTest(ServerTestCase):
             input_path,
             generate_depth=True,
             normal_mode="OBJECT",
-            alpha_threshold=0.9,
         )