Handle None in axes_to_array

None values should be treated the same as missing ones -
previously it would just crash.

openflexure_microscope/utilities.py

@@ -4,7 +4,7 @@ import logging
 import sys
 import time
 from contextlib import contextmanager
-from typing import Dict, List, Optional, Tuple, Type, Union
+from typing import Dict, List, Optional, Tuple, Type, Union, Sequence
 
 import numpy as np
 
@@ -102,12 +102,29 @@ def set_properties(obj, **kwargs):
 
 
 def axes_to_array(
-    coordinate_dictionary: Dict[str, int],
-    axis_keys=("x", "y", "z"),
+    coordinate_dictionary: Dict[str, Optional[int]],
+    axis_keys: Sequence[str] = ("x", "y", "z"),
     base_array: Optional[List[int]] = None,
     asint: bool = True,
 ) -> List[int]:
-    """Takes key-value pairs of a JSON value, and maps onto an array"""
+    """Takes key-value pairs of a JSON value, and maps onto an array
+    
+    This is designed to take a dictionary like `{"x": 1, "y":2, "z":3}`
+    and return a list like `[1, 2, 3]` to convert between the argument
+    format expected by most of our stages, and the usual argument
+    format in JSON.
+    
+    `axis_keys` is an ordered sequence of key names to extract from
+    the input dictionary.
+
+    `base_array` specifies a default value for each axis.  It must 
+    have the same length as `axis_keys`.
+    
+    `asint` casts values to integers if it is `True` (default).
+    
+    Missing keys, or keys that have a `None` value will be left
+    at the specified default value, or zero if none is specified.
+    """
     # If no base array is given
     if not base_array:
         # Create an array of zeros
@@ -119,8 +136,14 @@ def axes_to_array(
     # Do the mapping
     for axis, key in enumerate(axis_keys):
         if key in coordinate_dictionary:
-            base_array[axis] = (
-                int(coordinate_dictionary[key]) if asint else coordinate_dictionary[key]
-            )
+            value = coordinate_dictionary[key]
+            if value is None:
+                # Values set to None should be treated as if they
+                # are missing
+                # i.e. we leave the default value in place.
+                break
+            if asint:
+                value = int(value)
+            base_array[axis] = value
 
     return base_array