Script execution

script/sim/utils.py

@@ -8,7 +8,33 @@ import java.awt.Rectangle as Rectangle
 import ch.psi.pshell.imaging.Data as Data
 
 
-def integrate(ips, as_float=True):    
+###############################################################################
+# ROI Integration
+###############################################################################
+
+def integrate_roi(source, x,y, w, h):
+    if source.data is None:
+        source.update()
+    roi = source.data.getRoi(Rectangle(x,y, w, h))
+    return sum(roi.integrateHorizontally(False))
+
+
+
+class RoiIntensity(ReadonlyRegisterBase):
+    def __init__(self, name, source, x,y, w, h):
+        ReadonlyRegisterBase.__init__(self, name)
+        self.source=source
+        self.roi = x,y, w, h
+        
+    def doRead(self):
+        x,y, w, h = self.roi
+        return integrate_roi(self.source, x,y, w, h)
+
+###############################################################################
+# Frame integration
+###############################################################################
+
+def integrate_ips(ips, as_float=True):    
     aux = None
     for i in range(len(ips)):
         if i==0:        
@@ -17,7 +43,7 @@ def integrate(ips, as_float=True):
         op_image(aux, ips[i], "add", float_result=as_float, in_place=True)    
     return aux
 
-def average (ips, roi=None, as_float=True):   
+def average_ips (ips, roi=None, as_float=True):   
     aux = integrate(ips, as_float)     
     op_const(aux, "divide", float(len(ips)), in_place=True)    
     return aux
@@ -38,12 +64,16 @@ def grab_frames(source, samples, roi=None, wait_next=False, sleep=0):
     return frames
     
 def average_frames(source, samples=1, roi=None, wait_next=False, sleep=0, as_float=True):
-    return average(grab_frames(source, samples, roi, wait_next, sleep), as_float)
+    return average_ips(grab_frames(source, samples, roi, wait_next, sleep), as_float)
 
 def integrate_frames(source, samples=1, roi=None, wait_next=False, sleep=0, as_float=True):
-    return integrate(grab_frames(source, samples, roi, wait_next, sleep), as_float)
+    return integrate_ips(grab_frames(source, samples, roi, wait_next, sleep), as_float)
     
 
+###############################################################################
+# Image manipulation 
+###############################################################################
+
 def get_image_array(ip):
     if type(ip.getProcessor()) == ij.process.FloatProcessor:
         return ip.getProcessor().getFloatArray()
@@ -52,16 +82,9 @@ def get_image_array(ip):
 
 def open_image(file_name):
     file_name = get_context().setup.expandPath(file_name)
-    return Opener().openTiff(file_name, 1)
+    #return Opener().openTiff(file_name, 1)
+    return Opener().openImage(file_name)
 
+#Save TIFF from 
+#save_image(av, "{images}/float.tif","tiff")
         
-ret = grab_frames(image, 10, sleep=0.1)
-av = average(ret, None, True)
-print type(av.getProcessor())
-#db=av.getBufferedImage().getData().getDataBuffer()
-data = get_image_array(av)
-plot(data)
-
-save_image(av, "{images}/float.tif","tiff")
-av = average(ret, None, False)
-save_image(av, "{images}/int.tif","tiff")