Documentation updates

doc/source/resources/macros/ptSpeed.py

+from ij import WindowManager
+from ij.text import TextWindow
+from ij.measure import ResultsTable
+
+
+# ----------------- USER INPUT ------------------
+
+# Name of a tables for input (All Trajectories to Table) and output
+inputTableName = "Results";
+outputTableName = "Velocity";
+
+# prints ready to copy/paste data in CSV format and/or shows another results table (set to False to disable)
+printOutputData = True
+showOutputTable = True
+
+# if both set to 1 then velocity is calculated as a pixels/frame ratio. 
+# if resolution and fram interval known set it correctly for example if resolution is 5um/pixel
+# and frame interval is 20 ms/frame then pixelResolution = 5e-06 and frameInterval = 20e-03
+pixelResolution = 1e0 # in m/pixel
+frameInterval = 1e0 # in s/frame
+
+
+# ----------------- CODE -----------------------
+
+def findResultsTable(nameOfTable):
+	''' Find the window with results '''
+	resultsTable = None
+	nonImgWindows = WindowManager.getNonImageWindows()
+	for win in nonImgWindows:
+		if not isinstance(win, TextWindow): continue
+		if nameOfTable == win.getTitle(): 
+		    resultsTable = win.getTextPanel().getOrCreateResultsTable()
+		    break
+		    
+	return resultsTable
+
+
+def mean(data):
+	''' calculate mean of data '''
+	n = len(data)
+	if n < 1:
+		raise ValueError('mean requires at least one data point')
+	return sum(data)/float(n)
+
+
+def stddev(data):
+	''' calculate standard dev. of data '''
+	n = len(data)
+	if n < 1:
+		raise ValueError('stddev requires at least one data point')
+	m = mean(data)
+	return (sum((x-m)**2 for x in data)/n)**0.5
+
+
+def runScript():
+
+	# find table with trajectories
+	rt = findResultsTable(inputTableName)
+	if rt == None:
+	    print("Results table window titled [" + inputTableName + "] not found!")
+	    return
+	
+	numOfRows = rt.getCounter();	
+	
+	if numOfRows > 1: 
+	
+		#create output tableName
+		if showOutputTable: velocityRT = ResultsTable()
+
+		# if output in csv format requested print header
+		if printOutputData:
+			print("trajectory;pathLen;noOfFrames;velocity;velocity stddev");
+
+		# read first data point
+		trajectoryId = rt.getValue("Trajectory", 0)
+		posX = rt.getValue("x", 0)
+		posY = rt.getValue("y", 0)
+		posZ = rt.getValue("z", 0)
+		startFrame = rt.getValue("Frame", 0);
+		frame = startFrame
+		trajDistances = [] # distances per frame measured in pixels
+		
+		for idx in range(1, numOfRows): 
+			currTrajectoryId = rt.getValue("Trajectory", idx)
+			currPosX = rt.getValue("x", idx)
+			currPosY = rt.getValue("y", idx)
+			currPosZ = rt.getValue("z", idx)
+			currFrame = rt.getValue("Frame", idx)
+
+			# if true we are still reading data from 'current' trajectory
+			if trajectoryId == currTrajectoryId:
+				distance = ((currPosX - posX)**2 + (currPosY - posY)**2 + (currPosZ - posZ)**2)**(0.5)
+				# since trajectory data point can "jump" over some frames (depending on link range setting) calculated distance
+				# is divided to get average per one frame and added multiple time if needed (necessary for calculating correct stddev)
+				noOfFrames = currFrame - frame
+				distancePerFrame = distance / (currFrame - frame)
+				for i in range(int(noOfFrames)):
+					trajDistances.append(distancePerFrame)
+					
+			# if true we have read data point from next trajectory or this is very last point of data
+			# calculate trajectory info
+			if trajectoryId != currTrajectoryId or idx == numOfRows - 1:
+
+				# calculate trajectory lenght
+				trajDistancesTrueLen = [pixelResolution * d for d in trajDistances]
+				pathLen = sum(trajDistancesTrueLen)
+
+				# calculate length of trajectory in frames
+				if idx == numOfRows - 1:
+					stopFrame = currFrame
+				else:
+					stopFrame = frame
+				numOfFrames = stopFrame - startFrame;
+
+				# calculate velocity and std dev
+				velocity = pathLen/(numOfFrames * frameInterval);
+				standardDev = stddev([d/frameInterval for d in trajDistancesTrueLen])
+
+				# if output in csv format requested print it
+				if printOutputData: 
+					print(str(int(trajectoryId)) + ";" + str(pathLen) + ";" + str(numOfFrames) + ";" + str(velocity) + ";" + str(standardDev)); 
+				
+				# if output table requested update it with data
+				if showOutputTable:
+					velocityRT.incrementCounter()
+					velocityRT.addValue("trajectory", int(trajectoryId))
+					velocityRT.addValue("pathLen", pathLen)
+					velocityRT.addValue("noOfFrames", numOfFrames)
+					velocityRT.addValue("velocity", velocity)				
+					velocityRT.addValue("velocity stddev", standardDev)
+				
+				# beginning of new trajectory
+				trajDistances = []
+				startFrame = rt.getValue("Frame", idx)
+	
+				
+			trajectoryId = currTrajectoryId
+			posX = currPosX
+			posY = currPosY
+			posZ = currPosZ
+			frame = currFrame
+			
+		velocityRT.show(outputTableName)
+
+
+if __name__ in ['__builtin__','__main__']:
+    runScript()