fix(eyevolume.py): enable import of B-scans with varying distances by…

… replacing the raised Error by a warning; support deleteion of annotations

eyepy/core/eyevolume.py

@@ -1,4 +1,5 @@
 import json
+import logging
 import shutil
 import tempfile
 import warnings
@@ -21,6 +22,8 @@
 from eyepy.core.eyemeta import EyeBscanMeta, EyeEnfaceMeta, EyeVolumeMeta
 from eyepy.core.utils import intensity_transforms
 
+logger = logging.getLogger("eyepy.core.eyevolume")
+
 
 class LayerKnot(TypedDict):
     knot_pos: Tuple[float, float]
@@ -593,11 +596,14 @@ def set_intensity_transform(self, func: Union[str, Callable]):
                 self.meta["intensity_transform"] = func
                 self.intensity_transform = intensity_transforms[func]
                 self._data = None
+            elif func == "custom":
+                logger.warning(
+                    "Custom intensity transforms can not be loaded currently"
+                )
             else:
-                raise ValueError(
-                    "Provided intensity transform name is not know. Valid names are 'vol' or 'default'. You can also pass your own function."
+                logger.warning(
+                    f"Provided intensity transform name {func} is not know. Valid names are 'vol' or 'default'. You can also pass your own function."
                 )
-
         else:
             self.meta["intensity_transform"] = "custom"
             self.intensity_transform = func
@@ -663,6 +669,16 @@ def add_voxel_annotation(self, voxel_map=None, meta=None, **kwargs):
         self._volume_maps.append(voxel_annotation)
         return voxel_annotation
 
+    def delete_voxel_annotations(self, name):
+        for i, voxel_map in enumerate(self._volume_maps):
+            if voxel_map.name == name:
+                self._volume_maps.pop(i)
+
+        # Remove references from B-scans
+        for bscan in self:
+            if name in bscan.area_maps:
+                bscan.area_maps.pop(name)
+
     def add_layer_annotation(self, height_map=None, meta=None, **kwargs):
         if meta is None:
             meta = {}
@@ -671,6 +687,16 @@ def add_layer_annotation(self, height_map=None, meta=None, **kwargs):
         self._layers.append(layer_annotation)
         return layer_annotation
 
+    def delete_layer_annotation(self, name):
+        for i, layer in enumerate(self._layers):
+            if layer.name == name:
+                self._layers.pop(i)
+
+        # Remove references from B-scans
+        for bscan in self:
+            if name in bscan.layers:
+                bscan.layers.pop(name)
+
     def plot(
         self,
         ax=None,

eyepy/io/__init__.py

@@ -70,8 +70,8 @@ def import_heyex_vol(path):
     )
 
     ## Check if scan is a volume scan
-    if not l_volume.ScanPattern in [3, 4]:
-        msg = f"Only volumes with ScanPattern 3 or 4 are supported. The ScanPattern is {l_volume.ScanPattern} which might lead to exceptions or unexpected behaviour."
+    if not l_volume.ScanPattern in [1, 3, 4]:
+        msg = f"Only volumes with ScanPattern 1, 3 or 4 are supported. The ScanPattern is {l_volume.ScanPattern} which might lead to exceptions or unexpected behaviour."
         logger.warning(msg)
 
     enface_meta = _get_enface_meta(l_volume)

eyepy/io/utils.py

@@ -161,11 +161,10 @@ def _get_volume_meta(lazy_volume: LazyVolume):
             dist_func(bscan_meta[i]["end_pos"], bscan_meta[i + 1]["end_pos"])
             for i in range(len(bscan_meta) - 1)
         ]
-        if set(start_distances) == set(end_distances):
-            bscan_distance = start_distances[0]
-        else:
-            msg = "B-scans are not equally spaced. Data can not be imported."
-            raise ValueError(msg)
+        if not set(start_distances) == set(end_distances):
+            msg = "B-scans are not equally spaced. Projections into the enface space are distorted."
+            logger.warning(msg)
+        bscan_distance = start_distances[0]
     else:
         bscan_distance = 0
 

tests/test_eyevolume.py

@@ -70,3 +70,39 @@ def test_set_layers_on_eyebscan(eyevolume):
     assert np.all(bscan.layers["test_layer_2"].data == 240)
     assert np.nansum(eyevolume.layers["test_layer_2"].data) == eyevolume.size_x * 240
     assert np.all(eyevolume.layers["test_layer_2"].data[-(5 + 1)] == 240)
+
+
+# Test Bscan iteration
+def test_bscan_iteration(eyevolume):
+    bscans = [b for b in eyevolume]
+    bscans_2 = [eyevolume[i] for i in range(len(eyevolume))]
+    assert bscans == bscans_2
+
+
+# Delete layers
+def test_delete_layers(eyevolume):
+    eyevolume.add_layer_annotation(name="delete_layer")
+    assert "delete_layer" in eyevolume.layers
+
+    eyevolume[2].layers["delete_layer"].data = 20
+    assert "delete_layer" in eyevolume[2].layers
+
+    eyevolume.delete_layer_annotation("delete_layer")
+
+    assert "delete_layer" not in eyevolume.layers
+    # Test for references in the B-scans
+    assert "delete_layer" not in eyevolume[2].layers
+
+
+def test_delete_voxel_annotation(eyevolume):
+    eyevolume.add_voxel_annotation(name="delete_volume")
+    assert "delete_volume" in eyevolume.volume_maps
+
+    eyevolume[2].area_maps["delete_volume"][:5, :5] = 20
+    assert "delete_volume" in eyevolume[2].area_maps
+
+    eyevolume.delete_voxel_annotations("delete_volume")
+
+    assert "delete_volume" not in eyevolume.volume_maps
+    # Test for references in the B-scans
+    assert "delete_volume" not in eyevolume[2].area_maps