python-microscopy · David-Baddeley · Jan 12, 2021 · Dec 21, 2020 · Jan 12, 2021
diff --git a/PYME/Acquire/ExecTools.py b/PYME/Acquire/ExecTools.py
@@ -91,20 +91,20 @@ def execBG(codeObj, localVars = defLocals, globalVars = defGlobals):
     t.start()
     return t
 
-def execFile(filename, localVars = defLocals, globalVars = defGlobals):
+def execFile(filename, localVars = defLocals, globalVars = defGlobals, then=None):
     #fid = open(checkFilename(filename))
     #code = fid.read()
     #fid.close()
 
     _execfile(filename, localVars, globalVars)
+    if then is not None:
+        then()
 
-def execFileBG(filename, localVars = defLocals, globalVars = defGlobals):
-    #fid = open(checkFilename(filename))
-    #code = fid.read()
-    #fid.close()
-
-    #execBG(checkFilename(filename), localVars, globalVars)
-    threading.Thread(target=execFile, args = (filename, localVars, globalVars)).start()
+def execFileBG(filename, localVars = defLocals, globalVars = defGlobals, then=None):
+    t = threading.Thread(target=execFile, args = (filename, localVars, globalVars, then))
+    t.start()
+    #return the thread so we can join it ...
+    return t
 
 def _bginit(name, codeObj):
     global defGlobals

diff --git a/PYME/Acquire/acquire_server.py b/PYME/Acquire/acquire_server.py
@@ -126,10 +126,7 @@ def _initialize_hardware(self):
         logger.debug('Init run, waiting on background threads')
 
     def _wait_for_init_complete(self):
-        while not self.scope.initDone:
-            time.sleep(0.1)
-
-        #if self.scope.initDone == True:
+        self.scope.wait_for_init()
         logger.debug('Backround initialization done')
 
     def _on_frame_group(self, *args, **kwargs):

diff --git a/PYME/Acquire/acquiremainframe.py b/PYME/Acquire/acquiremainframe.py
@@ -163,7 +163,7 @@ def _initialize_hardware(self):
 
 
     def _check_init_done(self):
-        if self.scope.initDone == True and self._check_init_done in self.time1.WantNotification:
+        if self.scope.initialized == True and self._check_init_done in self.time1.WantNotification:
             logger.debug('Backround initialization done')
             self.time1.WantNotification.remove(self._check_init_done)
 

diff --git a/PYME/Acquire/microscope.py b/PYME/Acquire/microscope.py
@@ -877,7 +877,43 @@ def initialize(self, init_script_name, locals={}):
 
         locals.update(scope=self)
         ExecTools.setDefaultNamespace(locals, globals())
-        ExecTools.execFileBG(init_script_name, locals, globals())
+        self._init_thread = ExecTools.execFileBG(init_script_name, locals, globals(), then=self._post_init)
+
+        return self._init_thread
+
+    @property
+    def initialized(self):
+        """
+        Checks if the initialisation thread has run (replaces check of initDone flag which needed to be manually set
+        in initialisation script). Semantics are slightly different in that this returns true even if there is an error
+        whist the old way of checking would get forever stuck at the splash screen.
+
+        Returns
+        -------
+
+        True if the initialisation script has run, False otherwise
+
+        """
+        try:
+            return not self._init_thread.is_alive()
+        except AttributeError:
+            # don't have and _init_thread yet
+            return False
+
+    def wait_for_init(self):
+        self._init_thread.join()
+
+    def _post_init(self):
+        """
+        Called after the init script runs to do stuff based on what hardware is present
+        """
+
+        if len(self.positioning) > 0:
+            # we have registered piezos => we can do z-stacks
+            from PYME.Acquire import stackSettings
+
+            # FIXME - this looks like it will create a circular reference
+            self.stackSettings = stackSettings.StackSettings(self)
 
     def register_piezo(self, piezo, axis_name, multiplier=1, needCamRestart=False, channel=0):
         """

diff --git a/PYME/Acquire/ui/HDFSpoolFrame.py b/PYME/Acquire/ui/HDFSpoolFrame.py
@@ -83,6 +83,9 @@ def _protocol_pan(self):
         self.rbZStepped = wx.RadioButton(pan, -1, 'Z stepped')
         self.rbZStepped.Bind(wx.EVT_RADIOBUTTON, self.OnToggleZStepping)
         hsizer.Add(self.rbZStepped, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 2)
+
+        if not hasattr(self.scope, 'stackSettings'):
+            self.rbZStepped.Disable()
 
         if self.spoolController.z_stepped:
             self.rbZStepped.SetValue(True)
@@ -279,11 +282,12 @@ def _spool_pan(self):
     def _init_ctrls(self):
         self.AddNewElement(self._protocol_pan())
 
-        clp = afp.collapsingPane(self, caption='Z stepping ...')
-        self._seq_panel = seqdialog.seqPanel(clp, self.scope, mode='sequence')
-        clp.AddNewElement(self._seq_panel)
-        self.AddNewElement(clp)
-        self.seq_pan = clp
+        if hasattr(self.scope, 'stackSettings'):
+            clp = afp.collapsingPane(self, caption='Z stepping ...')
+            self._seq_panel = seqdialog.seqPanel(clp, self.scope, mode='sequence')
+            clp.AddNewElement(self._seq_panel)
+            self.AddNewElement(clp)
+            self.seq_pan = clp
 
         self.AddNewElement(self._spool_to_pan())
 

diff --git a/PYME/Acquire/ui/seqdialog.py b/PYME/Acquire/ui/seqdialog.py
@@ -205,9 +205,9 @@ def __init__(self, parent, scope, mode='default'):
 
         #if not ('sa' in self.scope.__dict__):
         #    self.stackSettings = simplesequenceaquisator.SimpleSequenceAquisitor(self.scope.chaninfo, self.scope.cam, self.scope.shutters, self.scope.piezos)
-        if not 'stackSettings' in dir(self.scope):
+        #if not 'stackSettings' in dir(self.scope):
             #inject stack settings into the scope object
-            self.scope.stackSettings = stackSettings.StackSettings(scope)
+        #    self.scope.stackSettings = stackSettings.StackSettings(scope)
         #for pz in self.scope.piezos:
         #    self.chPiezo.Append(pz[2])