Blackened files

openflexure_microscope/stage/base.py

@@ -1,3 +1,4 @@
+import numpy as np
 from abc import ABCMeta, abstractmethod
 from openflexure_microscope.common.lock import StrictLock
 
@@ -110,4 +111,4 @@ class BaseStage(metaclass=ABCMeta):
         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)
+        return self.scan_linear([[0, 0, z] for z in dz], **kwargs)

openflexure_microscope/stage/mock.py

@@ -5,6 +5,7 @@ from collections.abc import Iterable
 import numpy as np
 import time
 
+
 class MockStage(BaseStage):
     def __init__(self, port=None, **kwargs):
         BaseStage.__init__(self)
@@ -68,7 +69,9 @@ class MockStage(BaseStage):
         else:
             self._backlash = np.array([int(blsh)] * self.n_axes, dtype=np.int)
 
-    def move_rel(self, displacement: list, axis=None, backlash=True, simulate_time: bool=True):
+    def move_rel(
+        self, displacement: list, axis=None, backlash=True, simulate_time: bool = True
+    ):
         if simulate_time:
             time.sleep(1)
         if axis is not None:
@@ -81,7 +84,7 @@ class MockStage(BaseStage):
 
             self._position = list(np.array(self._position) + np.array(move))
 
-    def move_abs(self, final, simulate_time: bool=True, **kwargs):
+    def move_abs(self, final, simulate_time: bool = True, **kwargs):
         if simulate_time:
             time.sleep(1)
 

openflexure_microscope/stage/sangaboard/sangaboard.py

@@ -136,7 +136,7 @@ class Sangaboard(ExtensibleSerialInstrument):
             # make sure we close the serial port cleanly (otherwise it hangs open).
             self.close()
             logging.error(e)
-            logging.error(
+            logging.warning(
                 "You may need to update the firmware running on the Sangaboard."
             )
             raise e
@@ -164,12 +164,12 @@ class Sangaboard(ExtensibleSerialInstrument):
                     r"OpenFlexure Motor Board v(([\d]+)(?:\.([\d]+))+)", self.firmware
                 )
             if not match:
-                logging.error(
+                logging.warning(
                     'Version string "{}" not recognised.'.format(self.firmware)
                 )
                 return False
         else:
-            logging.error("No firmware version string was returned.")
+            logging.warning("No firmware version string was returned.")
             return False
 
         # Check for matching/valid version number
@@ -179,7 +179,7 @@ class Sangaboard(ExtensibleSerialInstrument):
         self.firmware_version = match.group(1)
 
         if version_tuple not in Sangaboard.valid_firmwares:
-            logging.error(
+            logging.warning(
                 "This version of the Python module requires firmware v0.5 (with legacy support for v0.4)"
             )
             return False