script/test/CameraCalibration.py

@@ -0,0 +1,71 @@
+import ch.psi.pshell.device.Camera as Camera
+import ch.psi.pshell.imaging.RendererMode as RendererMode
+from ch.psi.pshell.imaging.Overlays import *
+
+"""
+img.camera.setColorMode(Camera.ColorMode.Mono)
+img.camera.setDataType(Camera.DataType.UInt8)
+img.camera.setGrabMode(Camera.GrabMode.Continuous)
+img.camera.setTriggerMode(Camera.TriggerMode.Fixed_Rate)
+img.camera.setExposure(50.00)
+img.camera.setAcquirePeriod(200.00)
+img.camera.setGain(0.0)
+img.config.rotationCrop=True
+
+
+"""
+#img.camera.setROI(200, 0,1200,1200)
+
+img.camera.setROI(0, 0,1600,1200)
+img.config.rotation=0
+img.config.roiX,img.config.roiY, img.config.roiWidth,img.config.roiHeight =0,0,-1,-1
+img.config.setCalibration(None)
+img.camera.stop()
+img.camera.start()
+
+#img.camera.setROI(300, 200,1000,1000)
+#img.config.rotation=17
+#img.config.roiX,img.config.roiY, img.config.roiWidth,img.config.roiHeight = 50,50,900,900
+
+p = show_panel(img)
+p.setMode(RendererMode.Fit)
+ov_text = Text(Pen(java.awt.Color.GREEN.darker()), "", java.awt.Font("Verdana", java.awt.Font.PLAIN, 24), java.awt.Point(20,20))
+ov_text.setFixed(True)
+
+
+
+p.addOverlay(ov_text)
+try:
+    ov_text.update("Click on upper reference...")
+    p1 = p.waitClick(60000)
+    print p1
+    ov_text.update("Click on left reference...")
+    p2 = p.waitClick(60000)
+    print p2
+    ov_text.update("Click on right reference...")
+    p3 = p.waitClick(60000)
+    print p3        
+
+    x, y, z = p1.x+p1.y*1j, p2.x+p2.y*1j, p3.x+p3.y*1j
+    w = z-x
+    w /= y-x
+    c = (x-y)*(w-abs(w)**2)/2j/w.imag-x
+    cx, cy, r =  -c.real, -c.imag, abs(c+x)
+    a = math.degrees(math.atan((cx-p1.x)/(p1.y-cy)))
+
+    print cx, cy, r, a
+    
+    #img.camera.setROI(int((1600-cx)/2),int((1200-cy)/2),1000,1000)
+    img.camera.setROI(int(cx-r),int(cy-r),int(2*r),int(2*r))
+    img.config.rotation=-a
+    #remove rotation border
+    d=int(r/11)
+    img.config.roiX,img.config.roiY, img.config.roiWidth,img.config.roiHeight =d,d, int(2*r-2*d),  int(2*r-2*d)
+    #img.config.setCalibration(None)
+    img.camera.stop()
+    img.camera.start()  
+    
+finally: 
+    p.removeOverlay(ov_text)
+
+  

script/test/CoverDetection.py

@@ -0,0 +1,116 @@
+################################################################################################### 
+# Procedure to detect the cover orientation
+################################################################################################### 
+import ch.psi.pshell.imaging.Utils.integrateVertically as integrateVertically
+img.backgroundEnabled=False
+
+REF = (0,96,125)
+
+line = load_image("{images}/line.png", title="Line")
+#line = load_image("{images}/line360.png", title="Line")
+
+line.getProcessor().setBackgroundValue(0.0)
+
+
+#ip = get_image()
+ip = integrate_frames(10)
+ip = grayscale(ip, True)
+
+
+smooth(ip)
+#bandpass_filter(ip, 30, 1000)
+edges(ip)
+
+#invert(ip)
+#auto_threshold(ip, method = "Default")
+
+
+#auto_threshold(ip, method = "Li")
+auto_threshold(ip, method = "MaxEntropy")
+
+"""
+for m in AutoThresholder.getMethods():   
+    print m
+    aux = ip.duplicate()
+    auto_threshold(aux, method = m)
+    binary_fill_holes(aux, dark_background=False)
+    renderer = show_panel(aux.bufferedImage)
+    time.sleep(1.0)
+"""
+#binary_dilate(ip, dark_background=False)
+#binary_fill_holes(ip, dark_background=False)
+#binary_open(ip, dark_background=Tr)
+
+renderer = show_panel(ip.bufferedImage)
+
+
+
+
+
+
+
+
+#line = sub_image(line, 325, 325, 512, 512)
+#ip = sub_image(ip, 325, 325, 512, 512)
+line = sub_image(line, 453, 453, 256, 256)
+ip = sub_image(ip, 453, 453, 256, 256)
+#op = op_fft(ip, line, "correlate") 
+
+
+renderer = show_panel(ip.bufferedImage)
+
+#renderer = show_panel(op.bufferedImage)
+#line.show()
+ydata = []
+xdata = range (0,180,1)
+for i in xdata:
+    l = line.duplicate()
+    l.getProcessor().setBackgroundValue(0.0)
+    l.getProcessor().rotate(float(i))
+    op = op_fft(ip, l, "correlate") 
+    bi = op.getBufferedImage()
+    p = integrateVertically(bi)
+    ydata.append(sum(p))
+    
+    #renderer = show_panel(op.bufferedImage)
+    #time.sleep(0.001)
+
+def moving_average(arr, n) :
+    ret = []
+    for i in range(len(arr)):
+        ret.append(mean(arr[max(i-n,0):min(i+n,len(arr)-1)]))
+    return ret    
+av = moving_average(ydata, 1)
+    
+p = plot(ydata, xdata=xdata)[0]
+
+p.addSeries(LinePlotSeries("Moving Average"))
+p.getSeries(1).setData(xdata, av)      
+
+peaks = estimate_peak_indexes(ydata, xdata,  (min(ydata) + max(ydata))/2,  25.0)
+left, right = min(peaks), max(peaks)
+if xdata[left]<5 and xdata[right]>(xdata[-1]-5):
+    #del peaks[0 if ydata[right] >  ydata[left]  else -1]
+    peaks.remove(right if ydata[right] >  ydata[left]  else left)
+
+peaks = sorted(peaks[:3])
+peaks_x = map(lambda x:xdata[x], peaks)
+peaks_y = map(lambda x:ydata[x], peaks)
+
+print "Peaks", peaks        
+print "Peak indexes: " + str(peaks_x)
+print "Peak values:  " + str(peaks_y)
+
+
+for i in range(len(peaks)):
+    peak = xdata[peaks[i]]
+    p.addMarker(peak, None, "N="+str(round(peak,2)), Color(80,0,80))
+    if ((peaks[i]>160) and (REF[i]<20)):
+        peaks[i] = peaks[i] - 180.0
+
+print "Peaks x: " + str(peaks_x)
+
+
+d = mean(arrabs(arrsub(REF, peaks_x)))
+
+print "Angle = ", d

script/test/PuckDetection.py

@@ -0,0 +1,24 @@
+################################################################################################### 
+# Example of using ImageJ functionalities through ijutils.
+################################################################################################### 
+
+from ijutils import *
+import java.awt.Color as Color
+
+
+#Image Loading
+ip = load_image("{images}/test2.png", title="Image")
+
+
+#Puck Detection
+aux = grayscale(ip, in_place=False)
+aux.show() 
+plot(get_histogram(aux))
+
+subtract_background(aux)
+threshold(aux,0,50); aux.repaintWindow()
+binary_fill_holes(aux); aux.repaintWindow()
+(results,output_img)=analyse_particles(aux, 10000,50000, 
+            fill_holes = False, exclude_edges = True,print_table=True,
+            output_image = "outlines", minCirc = 0.0, maxCirc = 1.0)
+output_img.show()

script/test/SampleDetection.py

@@ -0,0 +1,23 @@
+################################################################################################### 
+# Example of using ImageJ functionalities through ijutils.
+################################################################################################### 
+
+from ijutils import *
+import java.awt.Color as Color
+
+#Image Loading
+ip = load_image("{images}/test2.png", title="Image")
+
+aux = grayscale(ip, in_place=False)
+aux.show() 
+
+invert(aux); aux.repaintWindow()
+#gaussian_blur(aux); aux.repaintWindow()
+subtract_background(aux); aux.repaintWindow()
+auto_threshold(aux); aux.repaintWindow()
+binary_open(aux); aux.repaintWindow()
+#binary_fill_holes(aux); aux.repaintWindow()
+(results,output_img)=analyse_particles(aux, 250,1000, 
+            fill_holes = False, exclude_edges = True,print_table=True,
+            output_image = "outlines", minCirc = 0.7, maxCirc = 1.0)
+output_img.show()

script/test/TestCoverDetection.py

@@ -7,7 +7,7 @@ pa = []
  #index = i+1
 for i in ['A', 'B', 'C', 'D', 'E', 'F']: 
      hexiposi.move(i)
-     [position, angle, confidence] = run("imgproc/CoverDetection2") 
+     [position, angle, confidence] = run("imgproc/CoverDetection") 
      print [position, angle, confidence]
      pa.append(position)
      aa.append(angle)