Tilt homing

script/imaging/FOV_table.py

@@ -0,0 +1,17 @@
+FOV_ARROWS = { \
+    "120um[0.0]": [84.0],   \
+    "100um[0.0]": [82.0],   \
+    "75um[0.0]": [77.0],   \
+    "50um[0.0]": [72.0],   \
+    "40um[0.0]": [66.0],   \
+    "30um[0.0]": [61.0],   \
+    "25um[0.0]": [50.0],   \
+    "20um[0.0]": [45.0],   \
+    "15um[0.0]": [32.0],   \
+    "10um[0.0]": [5.0],   \
+    "7.5um[0.0]": [15.0],   \
+    "5m[0.0]": [10.0],   \
+    "2.5m[0.0]": [5.0],   \
+    "1.25m[0.0]": [0.0],   \
+    "new_entry": [0.0]   \
+}

script/imaging/fov_arrows.py

@@ -0,0 +1,103 @@
+arrows_renderer = arrow_x = arrow_y = arrow_a = label_x = label_y = arrow_y =None
+"""
+FOV_ARROWS = { \
+    "100um[0.0]": [10.0],   \
+    "50um[0.0]": [20.0],   \
+    "new_entry": [0.0]
+}
+"""
+run("imaging/FOV_table")
+
+FOV_ARROWS_SIZE=80
+FOV_LABEL_POS=FOV_ARROWS_SIZE+15
+#FOV_ARROWS_ORIGIN=Point(image.getData().width/4, image.getData().height*3/4)
+#FOV_ARROWS_ORIGIN=Point(image.getData().width*3/4, image.getData().height/4)
+FOV_ARROWS_ORIGIN=Point(image.getData().width-(FOV_LABEL_POS+5), FOV_LABEL_POS+5)
+FOV_FUTURE=None
+FOV_FUTURE=None
+FOV_LABEL_FONT=java.awt.Font("Verdana", java.awt.Font.PLAIN, 12)
+FOV_OFFSET=0.0
+FOV_COLOR_X = Color.GREEN
+FOV_COLOR_Y = Color(173,216,230) # Light Blue
+FOV_COLOR_A = Color.YELLOW
+
+
+AZIMUTH_ROT=0.0
+def get_azimuth():
+    return AZIMUTH_ROT
+
+def set_fov_offset(value):    
+    global FOV_OFFSET
+    FOV_OFFSET = value
+    update_arrows()
+    
+def  update_arrows():
+    global arrows_renderer, arrow_x, arrow_y, arrow_a, label_x, label_y
+    if arrows_renderer is not None:
+        args = FOV_ARROWS.get(fov.take(), None) 
+        if args is not None:
+            azimuth=get_azimuth()
+            angle=args[0] + FOV_OFFSET
+            angle=angle+180
+            x,y = FOV_ARROWS_ORIGIN.x, FOV_ARROWS_ORIGIN.y   
+            a=math.radians(angle)
+            xa,ya=int(x+FOV_ARROWS_SIZE*math.cos(a)),  int(y-FOV_ARROWS_SIZE*math.sin(a))
+            arrow_a.update(FOV_ARROWS_ORIGIN, Point(xa,ya))
+            angle=angle+azimuth         
+            a=math.radians(angle)
+            xa,ya=int(x+FOV_ARROWS_SIZE*math.cos(a)),  int(y-FOV_ARROWS_SIZE*math.sin(a))
+            arrow_x.update(FOV_ARROWS_ORIGIN, Point(xa,ya))
+            xa,ya=int(x+FOV_LABEL_POS*math.cos(a)),  int(y-FOV_LABEL_POS*math.sin(a))
+            label_x.update(Point(xa,ya))   
+            angle=angle-90
+            a=math.radians(angle)
+            xa,ya=int(x+FOV_ARROWS_SIZE*math.cos(a)),  int(y-FOV_ARROWS_SIZE*math.sin(a))
+            arrow_y.update(FOV_ARROWS_ORIGIN, Point(xa,ya))   
+            xa,ya=int(x+FOV_LABEL_POS*math.cos(a)),  int(y-FOV_LABEL_POS*math.sin(a))              
+            label_y.update(Point(xa,ya))               
+        else:
+            log("Cannot draw reference arrows - Invalid microscope preset label: " + fov, False)
+            arrow_x.update(FOV_ARROWS_ORIGIN, FOV_ARROWS_ORIGIN)
+            arrow_y.update(FOV_ARROWS_ORIGIN, FOV_ARROWS_ORIGIN)   
+            arrow_a.update(FOV_ARROWS_ORIGIN, FOV_ARROWS_ORIGIN)   
+            label_x.update(label_x.UNDEFINED_POINT)         
+            label_y.update(label_y.UNDEFINED_POINT)         
+            
+def  task_update_arrows():  
+    global arrows_renderer
+    while arrows_renderer is not None:
+        try:
+            if arrows_renderer.isShowing():
+                update_arrows()
+                time.sleep(5.0)
+            time.sleep(1.0)
+        except:         
+            pass
+            
+
+def start_arrows(renderer=None):
+    global arrows_renderer, arrow_x, arrow_y, arrow_a, label_x, label_y, FOV_FUTURE
+    if arrows_renderer is None:
+        arrows_renderer = renderer if renderer else show_panel(image)
+        arrow_x = Overlays.Arrow(Pen(FOV_COLOR_X))
+        arrow_y = Overlays.Arrow(Pen(FOV_COLOR_Y))
+        arrow_a = Overlays.Arrow(Pen(FOV_COLOR_A))
+        label_x = Overlays.Text(arrow_x.pen, "X",FOV_LABEL_FONT)
+        label_y = Overlays.Text(arrow_y.pen, "Y",FOV_LABEL_FONT)
+        arrows_renderer.addOverlays([arrow_a, arrow_x,arrow_y,label_x, label_y])
+        #update_arrows()
+        FOV_FUTURE = fork(task_update_arrows,)[0]
+    
+
+def stop_arrows(renderer=None):
+    global arrows_renderer, arrow_x, arrow_y, label_x, label_y, FOV_FUTURE
+    if arrows_renderer is not None:
+        arrows_renderer.removeOverlays([arrow_a, arrow_x,arrow_y, label_x, label_y])
+    arrows_renderer=None
+    if FOV_FUTURE is not None:
+        FOV_FUTURE.cancel(True)
+        try:
+            join(FOV_FUTURE)
+        except:
+            pass    
+