Completed multi drift correction

Drift-Correction/MultiDriftCorrection.py

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+
+from ij import IJ
+from ij.plugin.frame import RoiManager
+
+print "Testing 123..."
+
+#converts microns (or whatever the physical dist is to pixels)
+'''
+def getPixelPos(x,y, imp):
+	point = [0,0]
+	point[0] = (x / cal.piXelW)
+	point[1] = (imp.height * (y / 100))
+	return point
+'''
+rm = RoiManager.getInstance() #get the open ROI manager instance
+ra = rm.getRoisAsArray()  #get all the ROIs in an array
+#print r1.getPosition()
+imp = IJ.getImage() #get current image
+stack = imp.getStack() #get current 
+rm = RoiManager.getInstance()
+ra = rm.getRoisAsArray()
+nRois = len(ra)
+proc = IJ.getProcessor() #get the image processor
+cal = imp.getCalibration();
+#print cal.pixelWidth
+#print imp.width
+nSlices = int(stack.getSize())
+#print stack.getSize()
+#print r1.getFloatPolygon().xpoints[0]  #get xpoint
+#first convert our ROIs to something more useful, a tuple containing the point (x,y) and the Z position => (x,y,z)
+for i in range(0, nRois-1):
+	roi1 = rm.getRoi(i)
+	roi2 = rm.getRoi(i+1)
+	pt1 = (roi1.getFloatPolygon().xpoints[0],roi1.getFloatPolygon().ypoints[0],roi1.getPosition())
+	pt2 = (roi2.getFloatPolygon().xpoints[0],roi2.getFloatPolygon().ypoints[0],roi2.getPosition())
+	xcorrect = (pt1[0]-pt2[0]);
+   	ycorrect = (pt1[1]-pt2[1]);
+   	print "Point pair: "
+   	print pt1
+   	print pt2
+
+   	IJ.setSlice(pt1[2]) #set starting slice
+	driftx = xcorrect/nSlices; 
+	offsetx = 0;
+	startSlice = pt1[2]
+	endSlice = pt2[2]
+	print "startSlice: %s ;endSlice: %s" % (startSlice, endSlice)
+	for j in range(startSlice,endSlice): 
+		IJ.setSlice(j)
+		offsetx += driftx
+		IJ.run("Translate...", "interpolation=Bicubic slice y=0 x="+str(offsetx)); 
+
+	drifty = ycorrect/nSlices; 
+	offsety = 0; 
+	for k in range(startSlice,endSlice):
+		IJ.setSlice(k)
+		offsety += drifty
+		IJ.run("Translate...", "interpolation=Bicubic slice x=0 y="+str(offsety));
+
+