Merge branch 'joram-fix-test' into 'master'

Joram fixes

See merge request openflexure/openflexure-microscope-server!21

openflexure_microscope/plugins/default/autofocus/plugin.py

@@ -45,7 +45,7 @@ class AutofocusPlugin(MicroscopePlugin):
                 sharpnesses.append(self.measure_sharpness(metric_fn))
 
             newposition = positions[np.argmax(sharpnesses)]
-            stage.focus_rel(newposition - stage.position[2])
+            stage.move_rel([0, 0, newposition - stage.position[2]])
 
         return positions, sharpnesses
 

openflexure_microscope/stage/sanga.py

@@ -1,5 +1,7 @@
 import numpy as np
 import time
+import logging
+from collections.abc import Iterable
 from .sangaboard import Sangaboard
 from openflexure_microscope.stage.base import BaseStage
 
@@ -21,6 +23,7 @@ class SangaStage(BaseStage):
 
         self.board = Sangaboard(port, **kwargs)
         self._backlash = None
+        self.axis_names = ['x', 'y', 'z']
 
     @property
     def state(self):
@@ -61,14 +64,21 @@ class SangaStage(BaseStage):
         back by ``backlash[i]``.  This is computed per-axis, so if some axes are moving
         in the same direction as ``backlash``, they won't do two moves.
         """
-        return self._backlash if self._backlash else np.array([0]*self.n_axes)
+        if self._backlash is not None:
+            return self._backlash
+        else:
+            return np.array([0] * self.n_axes)
 
     @backlash.setter
     def backlash(self, blsh):
+        logging.debug("Setting backlash to {}".format(blsh))
         if blsh is None:
             self._backlash = None
-        assert len(blsh) == self.n_axes
-        self._backlash = np.array([int(blsh)]*self.n_axes, dtype=np.int)
+        elif isinstance(blsh, Iterable):
+            assert len(blsh) == self.n_axes
+            self._backlash = np.array(blsh)
+        else:
+            self._backlash = np.array([int(blsh)]*self.n_axes, dtype=np.int)
 
     def move_rel(self, displacement, axis=None, backlash=True):
         """Make a relative move, optionally correcting for backlash.
@@ -98,7 +108,7 @@ class SangaStage(BaseStage):
             # For each axis where we're moving in the *opposite*
             # direction to self.backlash, we deliberately overshoot:
             initial_move -= np.where(
-                self.backlash*displacement < 0,
+                self.backlash * displacement < 0,
                 self.backlash,
                 np.zeros(self.n_axes, dtype=self.backlash.dtype)
             )
@@ -114,6 +124,42 @@ class SangaStage(BaseStage):
         with self.lock:
             self.board.move_abs(final, **kwargs)
 
+    def scan_linear(self, rel_positions, backlash=True, return_to_start=True):
+        """
+        Scan through a list of (relative) positions (generator fn)
+        rel_positions should be an nx3-element array (or list of 3 element arrays).
+        Positions should be relative to the starting position - not a list of relative moves.
+        backlash argument is passed to move_rel
+        if return_to_start is True (default) we return to the starting position after a
+        successful scan.  NB we always attempt to return to the starting position if an
+        exception occurs during the scan..
+        """
+        starting_position = self.position
+        rel_positions = np.array(rel_positions)
+        assert rel_positions.shape[1] == 3, ValueError("Positions should be 3 elements long.")
+        try:
+            self.move_rel(rel_positions[0], backlash=backlash)
+            yield 0
+
+            for i, step in enumerate(np.diff(rel_positions, axis=0)):
+                self.move_rel(step, backlash=backlash)
+                yield i + 1
+        except Exception as e:
+            return_to_start = True  # always return to start if it went wrong.
+            raise e
+        finally:
+            if return_to_start:
+                self.move_abs(starting_position, backlash=backlash)
+
+    def scan_z(self, dz, **kwargs):
+        """Scan through a list of (relative) z positions (generator fn)
+        This function takes a 1D numpy array of Z positions, relative to
+        the position at the start of the scan, and converts it into an
+        array of 3D positions with x=y=0.  This, along with all the
+        keyword arguments, is then passed to ``scan_linear``.
+        """
+        return self.scan_linear([[0, 0, z] for z in dz], **kwargs)
+
     def close(self):
         """Cleanly close communication with the stage"""
         self.board.close()
@@ -141,8 +187,8 @@ class SangaStage(BaseStage):
         need to worry about that here.
         """
         if type is not None:
-            print("An exception occurred inside a with block, resetting " +
-                  "position to its value at the start of the with block")
+            print("An exception occurred inside a with block, resetting position \
+                to its value at the start of the with block")
             try:
                 time.sleep(0.5)
                 self.move_abs(self._position_on_enter)