Store encoded LST in microscope system metadata

openflexure_microscope/api/v2/blueprints/actions/camera.py

@@ -87,13 +87,7 @@ class CaptureAPI(MicroscopeView):
             )
 
             # Inject system metadata
-            system_metadata = {
+            output.system_metadata.update(self.microscope.metadata)
-                "microscope_settings": self.microscope.read_settings(),
-                "microscope_state": self.microscope.state,
-                "microscope_id": self.microscope.id,
-                "microscope_name": self.microscope.name,
-            }
-            output.system_metadata.update(system_metadata)
 
             # Insert custom metadata
             output.put_metadata(metadata)

openflexure_microscope/microscope.py

@@ -10,7 +10,9 @@ from openflexure_microscope.stage.base import BaseStage
 from openflexure_microscope.stage.mock import MockStage
 from openflexure_microscope.camera.base import BaseCamera
 from openflexure_microscope.camera.mock import MockStreamer
+from openflexure_microscope.camera.pi import PiCameraStreamer
 
+from openflexure_microscope.utilities import serialise_array_b64
 from openflexure_microscope.plugins import PluginLoader
 from openflexure_microscope.task import TaskOrchestrator
 from openflexure_microscope.common.lock import CompositeLock
@@ -270,3 +272,30 @@ class Microscope:
             Please use apply_settings method instead."
         )
         self.apply_settings(config)
+
+    @property
+    def metadata(self):
+        """
+        Microscope system metadata, to be applied to basically all captures
+        """
+        system_metadata = {
+            "microscope_settings": self.read_settings(),
+            "microscope_state": self.state,
+            "microscope_id": self.id,
+            "microscope_name": self.name,
+        }
+
+        # Store an encoded copy of the PiCamera lens shading table, if it exists
+        if self.camera and isinstance(self.camera, PiCameraStreamer):
+            # Read LST. Returns None if no LST is active
+            lst_arr = self.camera.read_lens_shading_table()
+
+            b64_string, dtype, shape = serialise_array_b64(lst_arr)
+            
+            system_metadata["lens_shading_table"] = {
+                "b64_string": b64_string,
+                "dtype": dtype,
+                "shape": shape
+            }
+        
+        return system_metadata

openflexure_microscope/plugins/default/scan/plugin.py

@@ -100,13 +100,7 @@ class ScanPlugin(MicroscopePlugin):
             tags.append("scan")
 
         # Inject system metadata
-        system_metadata = {
+        output.system_metadata.update(self.microscope.metadata)
-            "microscope_settings": self.microscope.read_settings(),
-            "microscope_state": self.microscope.state,
-            "microscope_id": self.microscope.id,
-            "microscope_name": self.microscope.name,
-        }
-        output.system_metadata.update(system_metadata)
 
         # Insert custom metadata
         output.put_metadata(metadata)

openflexure_microscope/utilities.py

@@ -1,11 +1,23 @@
 import re
 import copy
 import operator
+import base64
+import numpy as np
 from collections import abc
 from functools import reduce
 from contextlib import contextmanager
 
 
+def deserialise_array_b64(b64_string, dtype, shape):
+    flat_arr = np.fromstring(base64.b64decode(b64_string), dtype)
+    return flat_arr.reshape(shape)
+
+def serialise_array_b64(npy_arr):
+    b64_string = base64.b64encode(npy_arr).decode('ascii')
+    dtype = str(npy_arr.dtype)
+    shape = npy_arr.shape
+    return b64_string, dtype, shape
+
 def get_by_path(root, items):
     """Access a nested object in root by item sequence."""
     return reduce(operator.getitem, items, root)