Merge branch 'master' into 121-pipeline

get_all_settings just reports the values of problem settings as None rather than creating a new __errors__ entry in the returned dict.

Author: mickp

NEWS

@@ -4,11 +4,18 @@ python-microscope releases.
 Version 0.4.0 (upcoming)
 ------------------------
 
+* Selected most important, backwards incompatible, changes:
+
+  * The `Setting` class is now private.  The only supported method to
+    add settings to a `Device` is via its `add_setting` method.
+
 * New devices supported:
 
-  * Coherent Obis laser.
+  * Coherent Obis laser
+  * Lumencor Spectra III light engine
   * Prior ProScan III controller
   * Prior filter wheels
+  * Toptica iBeam laser
 
 * Changes to device ABCs:
 
@@ -17,6 +24,11 @@ Version 0.4.0 (upcoming)
     * The `Device._logger` attribute has been removed.  It is
       recommended to use a logger for the module.
 
+  * DeformableMirror:
+
+    * Concrete classes must implement the `n_actuators` public
+      property instead of the private _n_actuators`.
+
 * The device server and clients no longer force pickle protocol
   version 2.  If the client and server are running different Python
   versions it may be necessary to specify a version number.  This

doc/supported-devices.rst

@@ -37,11 +37,13 @@ Lasers
 ------
 
 - Cobolt (:class:`microscope.lasers.cobolt`)
-- Coherent Sapphire (:class:`microscope.lasers.sapphire`)
 - Coherent Obis (:class:`microscope.lasers.obis`)
+- Coherent Sapphire (:class:`microscope.lasers.sapphire`)
 - Omicron Deepstar (:class:`microscope.lasers.deepstar`)
+- Toptica iBeam (:class:`microscope.lasers.toptica`)
 
 Controllers
 -----------
 
 - Prior ProScan III (:class:`microscope.controllers.prior`)
+- Lumencor Spectra III light engine (:class:`microscope.controllers.lumencor`)

microscope/cameras/atmcd.py

@@ -31,12 +31,11 @@
 """
 
 import logging
-import re, sys, functools, os, platform
+import sys, functools, os, platform
 import ctypes
 from ctypes import Structure, POINTER
 from ctypes import c_int, c_uint, c_long, c_ulong, c_longlong, c_ulonglong
 from ctypes import c_ubyte, c_short, c_float, c_double, c_char, c_char_p
-from ctypes import c_void_p
 from numpy.ctypeslib import ndpointer
 
 
@@ -1132,9 +1131,8 @@ def __str__(self):
 
 
 from threading import Lock
-import functools
 from microscope import devices
-from microscope.devices import keep_acquiring, Setting, Binning, ROI
+from microscope.devices import keep_acquiring, Binning, ROI
 import time
 
 # A lock on the DLL used to ensure DLL calls act on the correct device.
@@ -1255,21 +1253,21 @@ def initialize(self):
         # Mode
         name = 'readout mode'
         if self._readout_modes:
-            self.settings[name] = Setting(name, 'enum',
-                                          None,
-                                          self._set_readout_mode,
-                                          lambda: [str(mode) for mode in self._readout_modes])
-            self.settings[name].set(0)
+            self.add_setting(name, 'enum',
+                             None,
+                             self._set_readout_mode,
+                             lambda: [str(mode) for mode in self._readout_modes])
+            self.set_setting(name, 0)
         # TriggerMode
         name = 'TriggerMode'
-        self.settings[name] = Setting(name, 'enum',
-                                      None,
-                                      self._bind(SetTriggerMode),
-                                      TriggerMode)
+        self.add_setting(name, 'enum',
+                         None,
+                         self._bind(SetTriggerMode),
+                         TriggerMode)
         if self._caps.ulTriggerModes & AC_TRIGGERMODE_EXTERNAL:
-            self.settings[name].set(TriggerMode.EXTERNAL)
+            self.set_setting(name, TriggerMode.EXTERNAL)
         elif self._caps.ulTriggerModes & AC_TRIGGERMODE_CONTINUOUS:
-            self.settings[name].set(TriggerMode.SOFTWARE)
+            self.set_setting(name, TriggerMode.SOFTWARE)
         # Gain - device will use either EMGain or MCPGain
         name = 'gain'
         getter, setter, vrange = None, None, None
@@ -1284,9 +1282,7 @@ def initialize(self):
             setter = self._bind(SetMCPGain)
             vrange = self._bind(GetMCPGainRange)
         if getter or setter:
-            self.settings[name] = Setting(name, 'int',
-                                          getter, setter, vrange,
-                                          setter is None)
+            self.add_setting(name, 'int', getter, setter, vrange, setter is None)
         # Temperature
         name = 'TemperatureSetPoint'
         getter, setter, vrange = None, None, None
@@ -1295,77 +1291,73 @@ def initialize(self):
         if self._caps.ulGetFunctions & AC_GETFUNCTION_TEMPERATURERANGE:
             vrange = self._bind(GetTemperatureRange)
         if setter:
-            self.settings[name] = Setting(name, 'int',
-                                          None, setter, vrange,
-                                          setter is None)
+            self.add_setting(name, 'int', None, setter, vrange, setter is None)
         # Set a conservative default temperature set-point.
-        self.settings[name].set(-20)
+        self.set_setting(name, -20)
         # Fan control
         name = 'Temperature'
-        self.settings[name] = Setting(name, 'int',
-                                      self.get_sensor_temperature,
-                                      None, (None, None), True)
+        self.add_setting(name, 'int', self.get_sensor_temperature, None, (None, None), True)
         name = 'Fan mode'
-        self.settings[name] = Setting(name, 'enum',
-                                      None, # Can't query fan mode
-                                      self._bind(SetFanMode),
-                                      {0:'full', 1:'low', 2:'off'}
-                                      )
+        self.add_setting(name, 'enum',
+                         None, # Can't query fan mode
+                         self._bind(SetFanMode),
+                         {0:'full', 1:'low', 2:'off'}
+                         )
         # Cooler control
         name = 'Cooler Enabled'
-        self.settings[name] = Setting(name, 'bool',
-                                      None,
-                                      self._set_cooler_state,
-                                      None)
-        self.settings[name].set(True)
+        self.add_setting(name, 'bool',
+                         None,
+                         self._set_cooler_state,
+                         None)
+        self.set_setting(name, True)
         # Binning
         name = 'Binning'
-        self.settings[name] = Setting(name, 'tuple',
-                                      self.get_binning,
-                                      self.set_binning,
-                                      None)
+        self.add_setting(name, 'tuple',
+                         self.get_binning,
+                         self.set_binning,
+                         None)
         # Roi
         name = 'Roi'
-        self.settings[name] = Setting(name, 'tuple',
-                                      self.get_roi,
-                                      lambda roi: self.set_roi(*roi),
-                                      None)
+        self.add_setting(name, 'tuple',
+                         self.get_roi,
+                         lambda roi: self.set_roi(*roi),
+                         None)
         # BaselineClamp
         name = 'BaselineClamp'
         if self._caps.ulSetFunctions & AC_SETFUNCTION_BASELINECLAMP:
-            self.settings[name] = Setting(name, 'bool',
-                                          None,
-                                          self._bind(SetBaselineClamp))
-            self.settings[name].set(False)
+            self.add_setting(name, 'bool',
+                             None,
+                             self._bind(SetBaselineClamp))
+            self.set_setting(name, False)
         # BaselineOffset
-        nam = 'BaselineOffset'
+        name = 'BaselineOffset'
         if self._caps.ulSetFunctions & AC_SETFUNCTION_BASELINEOFFSET:
-            self.settings[name] = Setting(name, 'int',
-                                          None,
-                                          self._bind(SetBaselineOffset),
-                                          (-1000, 1000))
-            self.settings[name].set(0)
+            self.add_setting(name, 'int',
+                             None,
+                             self._bind(SetBaselineOffset),
+                             (-1000, 1000))
+            self.set_setting(name, 0)
         # EMAdvanced
         name = 'EMAdvanced'
         if self._caps.ulSetFunctions & AC_SETFUNCTION_EMADVANCED:
-            self.settings[name] = Setting(name, 'bool',
-                                          None,
-                                          self._bind(SetEMAdvanced))
-            self.settings[name].set(False)
+            self.add_setting(name, 'bool',
+                             None,
+                             self._bind(SetEMAdvanced))
+            self.set_setting(name, False)
         # GateMode
         name = 'GateMode'
         if self._caps.ulSetFunctions & AC_SETFUNCTION_GATEMODE:
             vrange = range(0, [5,6][self._caps.ulCameraType & AC_CAMERATYPE_ISTAR])
-            self.setings[name] = Setting(name, 'int',
-                                         None,
-                                         self._bind(SetGateMode),
-                                         vrange)
+            self.add_setting(name, 'int',
+                             None,
+                             self._bind(SetGateMode),
+                             vrange)
         # HighCapacity
         name = 'HighCapacity'
         if self._caps.ulSetFunctions & AC_SETFUNCTION_HIGHCAPACITY:
-            self.settings[name] = Setting(name, 'bool',
-                                          None,
-                                          self._bind(SetHighCapacity))
+            self.add_setting(name, 'bool',
+                             None,
+                             self._bind(SetHighCapacity))
 
     def _fetch_data(self):
         """Poll for data and return it, with minimal processing.
@@ -1431,7 +1423,7 @@ def _on_enable(self):
             SetReadMode(ReadMode.IMAGE)
             x, y = GetDetector()
             self._set_image()
-            if not IsTriggerModeAvailable(self.settings['TriggerMode'].get()):
+            if not IsTriggerModeAvailable(self.get_setting('TriggerMode')):
                 raise AtmcdException("Trigger mode is not valid.")
             StartAcquisition()
         return True
@@ -1508,7 +1500,7 @@ def get_sensor_temperature(self):
 
     def get_trigger_type(self):
         """Return the microscope.devices trigger type."""
-        trig = self.settings['TriggerMode'].get()
+        trig = self.get_setting('TriggerMode')
         if trig == TriggerMode.BULB:
             return devices.TRIGGER_DURATION
         elif trig == TriggerMode.SOFTWARE:

microscope/cameras/pvcam.py

@@ -1255,7 +1255,7 @@ def _on_enable(self):
             t_exp = int(self.exposure_time * 1e6)
         else:
             self._params[PARAM_EXP_RES].set_value(EXP_RES_ONE_MILLISEC)
-            t_exp = value = int(self.exposure_time * 1e3)
+            t_exp = int(self.exposure_time * 1e3)
         # Configure camera, allocate buffer, and register callback.
         if self._trigger == TRIG_SOFT:
             # Software triggering for single frames.

microscope/cameras/ximea.py

@@ -24,7 +24,7 @@
 import numpy as np
 
 from microscope import devices
-from microscope.devices import keep_acquiring, Binning, ROI
+from microscope.devices import keep_acquiring, ROI
 
 #import ximea python module.
 from ximea import xiapi