script/devices/LEEM2000.py

@@ -7,7 +7,10 @@ class LEEM2000(TcpDevice):
        self.NUMBER_MNEMONICS = 100
        self._mnemonics = None
        self._names = None
-       self.high_voltage = Channel("X11MA-ES1-PEEM:UMON", alias = "PEEM high voltage", monitored=True)     
+       try:
+            self.high_voltage = Channel("X11MA-ES1-PEEM:UMON", alias = "PEEM high voltage", monitored=True)     
+       except:
+            self.high_voltage = None
        self.debug = False
        self.retries = 1
        self.timeout = 1000
@@ -119,10 +122,10 @@ class LEEM2000(TcpDevice):
     def get_high_voltage(self):
         return  self.high_voltage.get(False)
 
-    def get_child(self, var, name=None):           
+    def get_child(self, var, name=None, scale=None):           
         if name is None:
             name=var
-        ret = LEEM2000Child(name, var, self)
+        ret = LEEM2000Child(name, var, self, scale)
         ret.initialize()
         return ret
 
@@ -203,15 +206,23 @@ class LEEM2000(TcpDevice):
         
 
 class LEEM2000Child(RegisterBase):    
-    def __init__(self,name, var, microscope):
+    def __init__(self,name, var, microscope, scale=None):
         RegisterBase.__init__(self,name)
         self.var = var
+        self.scale = scale
         self.microscope = microscope
         
     def doRead(self):
-        return self.microscope.get_value(self.var)
+        ret = self.microscope.get_value(self.var)
+        if ret is not None:
+            if self.scale is not None: 
+                ret = float(ret)*self.scale
+        return ret
 
     def doWrite(self, val):
+        if val is not None:
+            if self.scale is not None: 
+                val = float(val)/self.scale
         self.microscope.set_value(self.var, val)
 
 class LEEM2000Positioner (PositionerBase):
@@ -283,7 +294,7 @@ add_device (microscope.get_tilt('D','U', "tilt_v"), True)
 add_device (microscope.get_child("MOBJ","objective"), True) 
 add_device (microscope.get_child("OSTIGA","obj_stig_a"), True)
 add_device (microscope.get_child("OSTIGB","obj_stig_b"), True)
-add_device (microscope.get_child("MDRIVE","azimuth_rot"), True)
+add_device (microscope.get_child("MDRIVE","azimuth_rot", 0.01794), True)
 add_device (microscope.get_child("BOMBV","bv"), True)
 add_device (microscope.get_child("FIL","fil"), True)
 add_device (microscope.get_child("STV","start_voltage"), True)
@@ -321,8 +332,11 @@ class Fov(ReadonlyRegisterBase):
         self.position = 0
     
     def doRead(self):
-        return self.mic.get_preset_label()
-
+        ret = self.mic.get_preset_label()
+        if ret is not None:
+            if ":" in ret:
+                ret = ret[0:ret.rindex(":")]
+        return ret
         
 
 def init_tilt():
@@ -337,6 +351,8 @@ tilt_horizontal.polling=500
 manip_x.polling=500
 manip_y.polling=500
 fov.polling=5000
+azimuth_rot.precision=2
+azimuth_rot.polling=5000
 bv.polling=1000
 fil.polling=1000
 

script/imaging/shifts.py

@@ -36,10 +36,15 @@ def load_corr_stack(title="Corr", show=False):
         file_list.append("{images}/TestObjAligner_corr/i210517_0" + str(index) + "#001.tif")
     return load_stack(title, file_list, show)
 
+def instantiate_dynamic_class(name):
+    if get_context().getPluginManager().getDynamicClass(name) is None:
+        get_context().getPluginManager().loadInitializePlugin(name + ".java")
+    return get_context().getClassByName(name).newInstance()
+
+
 def complex_edge_filtering(imp, complex=True, g_sigma=3.0, g_resolution=1e-4, show=False, java_code=False):
     if java_code:
-        get_context().getPluginManager().loadInitializePlugin("Align_ComplexEdgeFiltering.java")
-        complex_edge_filter = get_context().getClassByName("Align_ComplexEdgeFiltering").newInstance()
+        complex_edge_filter = instantiate_dynamic_class("Align_ComplexEdgeFiltering")
         complex_edge_filter.setup(str(g_sigma)+","+str(complex)+","+str(show), imp)   #Gaussian blur radius, Complex (True) or Real (False), show dialog = False
         complex_edge_filter.run(imp.getProcessor())
         return complex_edge_filter.output
@@ -151,8 +156,7 @@ class TranslationFilter(ExtendedPlugInFilter):
 def translate(stack, shifts, show=False, java_code=False):
     WindowManager.setTempCurrentImage(stack)
     if java_code:
-        get_context().getPluginManager().loadInitializePlugin("Align_TranslationFilter.java")
-        translation_filter = get_context().getClassByName("Align_TranslationFilter").newInstance()
+        translation_filter = instantiate_dynamic_class("Align_TranslationFilter")
         translation_filter.imp = imp
         translation_filter.shifts = shifts
         pfr = PlugInFilterRunner(translation_filter, "", "" )
@@ -170,13 +174,11 @@ def translate(stack, shifts, show=False, java_code=False):
 
 
 def load_shifts(filename):
-    get_context().getPluginManager().loadInitializePlugin("ShiftsIO.java")
-    sio = get_context().getClassByName("ShiftsIO").newInstance()
+    sio = instantiate_dynamic_class("ShiftsIO")
     return sio.load(expand_path(filename), "directshifts")
 
 def save_shifts(filename, shifts):
-    get_context().getPluginManager().loadInitializePlugin("ShiftsIO.java")
-    sio = get_context().getClassByName("ShiftsIO").newInstance()
+    sio = instantiate_dynamic_class("ShiftsIO")
     sio.save(expand_path(filename), shifts, "directshifts")
 
 
@@ -588,8 +590,7 @@ def calculate_shifts(imp_r, imp_i, roi, upscale_factor=100, reference_slide=1, j
     if roi is None or roi.bounds.minX <0 or roi.bounds.minY<0 or roi.bounds.maxX>=imp_r.width or roi.bounds.maxY>=imp_r.height:
         raise Exception("Invalid roi: " + str(roi))
     if java_code:
-        get_context().getPluginManager().loadInitializePlugin("Align_ComputeShifts.java")
-        compute_shifts_filter = get_context().getClassByName("Align_ComputeShifts").newInstance()
+        compute_shifts_filter = instantiate_dynamic_class("Align_ComputeShifts")
         compute_shifts_filter.setup(upscale_factor, False, imp_r, imp_i, 1, roi)
         compute_shifts_filter.run(None)
         return compute_shifts_filter.shifts

script/local.py

@@ -834,6 +834,10 @@ def peem_optics_default_15kV():
     obj_align_y.write(0)
     start_voltage.write(0)
 #    fov.write(100)
+    microscope.send_receive("sep 100um")
+    microscope.send_receive("mmp 7 -9044.7", 60000)
+    microscope.send_receive("mmp 2 -5998.6", 60000)
+    microscope.send_receive("mmp 1 0.0", 60000)
 
 def peem_optics_default_10kV():
     objective.write(1220)
@@ -842,12 +846,18 @@ def peem_optics_default_10kV():
     obj_align_x.write(0)
     obj_align_y.write(0)
     start_voltage.write(0)
+    microscope.send_receive("sep 100um")
+    microscope.send_receive("mmp 7 -9044.7", 60000)
+    microscope.send_receive("mmp 2 -5998.6", 60000)
+    microscope.send_receive("mmp 1 0.0", 60000)
+
+
 
 # x-rays default setup
 def xrays_default():
     exit_slit.write(300.0)
     caput ('X11MA-FE-DSAPER', 0)  # close FE-slits
-    set_beamline_setup(id ="ID2", en=800, pol2="Lin_Hor", grat="G3_600", order=1, Cff=2.25)
+    set_beamline_setup(id ="PGM_ID2",en=800, pol2="Lin_Hor", har2 = "1", off2 = "-2.0", grat="G3_600", order="1", Cff=2.25)
 
 def neutralize_position(retries = 3):
     for i in range(retries):

script/templates/FocusScan.py

@@ -102,16 +102,16 @@ def scan_contrast(positioner, pos_range, pos_step, roi = None, average = 1, upda
             positioner.write(mn)  
     else:
         print "Invalid fit for ",  positioner.name, mn, range_scan
-    time.sleep(1.0) # Wait restoring positions
+    time.sleep(SETTLING_TIME) # Wait restoring positions
     return r
 
 
 def update_roi_pos(cur_data, former_data):
-    roi=get_focus_scan_roi()
-    calc_roi = Roi(roi.x,roi.y,roi.width, roi.height)
     try:    
+        roi=get_focus_scan_roi()
+        calc_roi = Roi(roi.x,roi.y,roi.width, roi.height)
         xoff, yoff, error, diffphase, _ = calculate_shift(former_data,cur_data, calc_roi)
-        print "Calculated shift: ", xoff, yoff, error, diffphase
+        print "Calculated shift: ", xoff, yoff, error, diffphase, 
         if (abs(xoff) <= MAX_SHIFT) and (abs(yoff) <= MAX_SHIFT):
             x,y=int(roi.x - xoff), int(roi.y - yoff)
             print "Updating ROI location to ", x, y
@@ -144,10 +144,11 @@ def scan_focus(positioner, pos_range, pos_step, average = 1, update_position = T
 
     def before_read(pos,scan):
         global former_data 
-        if str(eiger.grabMode)=="Single":
-            eiger.start()    
-            image.waitNext(20000)
-            
+        if str(eiger.grabMode)=="Single":            
+            eiger.start()                
+        else:
+            time.sleep(eiger.exposure)
+        image.waitNext(20000)   
         cur_data = image.data
         try:
             print "----- Pos: ", pos                          
@@ -178,7 +179,7 @@ def scan_focus(positioner, pos_range, pos_step, average = 1, update_position = T
                     
         
     r = lscan( positioner, [sensor,], -pos_range, pos_range, pos_step, \
-           latency=eiger.exposure+SETTLING_TIME, relative=True, initial_move=False, restore_position=False, \
+           latency=SETTLING_TIME, relative=True, initial_move=False, restore_position=False, \
            before_read=before_read, after_read=after_read, before_pass=before_pass)       
 
     ydata, xdata = r[sensor], r[positioner]
@@ -206,5 +207,5 @@ def scan_focus(positioner, pos_range, pos_step, average = 1, update_position = T
         print "Invalid fit for ",  positioner.name, mn, range_scan
         apply_focus_scan_pos(initial_state)
         if initial_roi_location: roi.location=initial_roi_location
-    time.sleep(1.0) # Wait restoring positions
+    time.sleep(0.) # Wait restoring positions
     return r