Merge remote-tracking branch 'origin/master' into auto-exposure-gain-awb

This was primarily done to disable the warning about f strings in
logging statements, globally rather than per-file.

openflexure_microscope/api/v2/views/actions/stage.py

@@ -1,50 +1,47 @@
 import logging
-from typing import List, Tuple
 
 from labthings import fields, find_component
 from labthings.views import ActionView
 
-from openflexure_microscope.utilities import axes_to_array
-
 
 class MoveStageAPI(ActionView):
     args = {
         "absolute": fields.Boolean(
             missing=False, example=False, description="Move to an absolute position"
         ),
-        "x": fields.Int(missing=0, example=100),
+        "x": fields.Int(missing=None, example=100),
-        "y": fields.Int(missing=0, example=100),
+        "y": fields.Int(missing=None, example=100),
-        "z": fields.Int(missing=0, example=20),
+        "z": fields.Int(missing=None, example=20),
     }
 
     def post(self, args):
         """
         Move the microscope stage in x, y, z
+
+        Any axes that are not specifed will not move.
         """
         microscope = find_component("org.openflexure.microscope")
 
-        # Handle absolute positioning (calculate a relative move from current position and target)
+        if not microscope.stage:
-        if (args.get("absolute")) and (microscope.stage):  # Only if stage exists
-            target_position: List[int] = axes_to_array(args, ["x", "y", "z"])
-            logging.debug("TARGET: %s", (target_position))
-            position: Tuple[int, int, int] = (
-                target_position[i] - microscope.stage.position[i] for i in range(3)
-            )
-            logging.debug("DELTA: %s", (position))
-
-        else:
-            # Get coordinates from payload
-            position = axes_to_array(args, ["x", "y", "z"], [0, 0, 0])
-
-        logging.debug(position)
-
-        # Move if stage exists
-        if microscope.stage:
-            # Explicitally acquire lock with 1s timeout
-            with microscope.stage.lock(timeout=1):
-                microscope.stage.move_rel(position)
-        else:
             logging.warning("Unable to move. No stage found.")
+            return microscope.state["stage"]["position"]
+
+        absolute_move = args.get("absolute")
+        move = [0, 0, 0]  # Default to no motion
+        for i, axis in enumerate(["x", "y", "z"]):
+            if axis in args and args[axis] is not None:
+                if absolute_move:
+                    # We emulate absolute moves by calculating a relative move that
+                    # will take us to the right position.
+                    move[i] = args[axis] - microscope.stage.position[i]
+                else:
+                    move[i] = args[axis]
+
+        logging.debug(f"Moving stage by {move}, request was {args}")
+
+        # Explicitly acquire lock with 1s timeout
+        with microscope.stage.lock(timeout=1):
+            microscope.stage.move_rel(move)
 
         return microscope.state["stage"]["position"]
 

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, Sequence, Tuple, Type, Union
 
 import numpy as np
 
@@ -102,12 +102,29 @@ def set_properties(obj, **kwargs):
 
 
 def axes_to_array(
-    coordinate_dictionary: Dict[str, int],
+    coordinate_dictionary: Dict[str, Optional[int]],
-    axis_keys=("x", "y", "z"),
+    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] = (
+            value = coordinate_dictionary[key]
-                int(coordinate_dictionary[key]) if asint else 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

pyproject.toml

@@ -25,7 +25,13 @@ ensure_newline_before_comments = true
 line_length = 88
 
 [tool.pylint.'MESSAGES CONTROL']
-disable = "fixme,C,R"
+# W1203 warns about using f strings in logging statements.
+# I'm really not concerned about the performance implications of this,
+# particularly as we often have the log level set quite high.  I think
+# for our current purposes, using f strings in logging statements is
+# more readable and thus a good idea in many places - I've disabled
+# this warning code globally for that reason.
+disable = "fixme,C,R,W1203"
 max-line-length = 88
 
 [tool.poe.executor]