Merge branch 'master' into fix-onebox-adc

Author: zm711

neo/io/kwikio.py

@@ -20,8 +20,12 @@
 from neo.io.baseio import BaseIO
 
 # to import from core
-from neo.core import Segment, SpikeTrain, AnalogSignal, Block, Group
+from neo.core import Segment, SpikeTrain, AnalogSignal, Block, Group, NeoReadWriteError
 
+import importlib.metadata
+from packaging.version import Version, parse
+
+numpy_version = parse(importlib.metadata.version('numpy'))
 
 class KwikIO(BaseIO):
     """
@@ -58,6 +62,12 @@ def __init__(self, filename):
         Arguments:
             filename : the filename
         """
+
+        if numpy_version >= Version("2.3.0"):
+            deprecation_msg = ("As the kwik package is no longer actively maintained it only works with NumPy < 2.3.0 and your environment "
+            f"has {numpy_version}. Downgrade your NumPy version to use this IO")
+            raise NeoReadWriteError(deprecation_msg)
+        
         from klusta import kwik
 
         BaseIO.__init__(self)

neo/rawio/biocamrawio.py

@@ -460,4 +460,10 @@ def generate_synthetic_noise(rf, data, well_ID, start_frame, num_frames):
         else:
             data[ch_idx] = np.array(np.random.normal(median_mean, median_std, num_frames), dtype=np.uint16)
 
+    # Assuming a 12-bit unsigned to signed conversion downstream, the baseline should read at 2048 raw
+    # However, synthetic noise is generated with a baseline of 0, which requires an offset of + 2048
+    # See issue #1743
+
+    data = data + 2048
+
     return data