Plotting strokelitude wing tracking data on fmf frames

I have been working on a Python script to save movies in which strokelitude wingstroke tracking data are plotted on original frames from an .fmf movie. My current version is below.

	import argparse # need to install argparse: sudo apt-get install python-argparse
	import os, ast
	import numpy as np
	import motmot.FlyMovieFormat.FlyMovieFormat as FMF
	import pylab
	pylab.ion()
	import roslib
	roslib.load_manifest('rosbag')
	import rosbag
	#================================ function to load .bag files ======================================
	def loadBag(inFileName):
	"""
	Script to import strokelitude bag file
	usage: outDict = loadBag(inFileName)
	PTW 02/04/12
	"""
	if inFileName[-4:] != '.bag':
	inFileName = inFileName + '.bag'
	bag = rosbag.Bag(inFileName)
	timeSec = list()
	leftWingRad = list()
	rightWingRad = list()
	for topic, msg, t in bag.read_messages():
	if topic == '/strokelitude' or topic == 'strokelitude':
	timeSec.append(msg.header.stamp.secs + msg.header.stamp.nsecs*float(1e-9))
	leftWingRad.append(msg.left_wing_angle_radians)
	rightWingRad.append(msg.right_wing_angle_radians)
	timeSec = np.array(timeSec)
	leftWingRad=np.array(leftWingRad)
	rightWingRad = np.array(rightWingRad)
	outDict = {'timeSec':timeSec, 'leftWingRad':leftWingRad, 'rightWingRad':rightWingRad}
	return outDict
	def main():
	""" it can be a bit tricky to enter the mask data in at the command line. Try copying this line and changing the values to what you need:
	python makeFmfStrokelitudeMovie.py "{'x':310.0, 'y':202.0, 'view_from_below':False, 'wingsplit':54.0, 'gamma':90.0}"
	"""
	#================================ Parse arguments ======================================
	parser = argparse.ArgumentParser(description='Save a movie with strokelitude wingstroke amplitude tracking superimposed on original frames from .fmf file', epilog='PTW 2012')
	parser.add_argument('strokelitudeMaskData', type=str, help="dict of strokelitude mask for the .bag data file, e.g. {'x':310.0, 'y':202.0, 'view_from_below':False, 'wingsplit':54.0, 'gamma':90.0}")
	parser.add_argument('inFmfFileName', nargs='?', type=str, default=None, help='the .fmf file containing original movie frames')
	parser.add_argument('inBagFileName', nargs='?', type=str, default=None, help='the .bag file containing strokelitude tracking data')
	parser.add_argument('outFileName', nargs='?', type=str, default=None, help='the out file name')
	parser.add_argument('-s','--startTime', type=float, default=0, help='time in seconds from start of .fmf to start saved movie')
	parser.add_argument('-e','--endTime', type=float, default=0, help='time in seconds from start of .fmf to end saved movie')
	parser.add_argument('-r','--frameRateMultiplicationFactor', type=float, default=1, help='multiplicative factor to change frame rate from input to output movie')
	args = parser.parse_args()
	fileNames = os.listdir(os.getcwd())
	fileNames.sort()
	if args.inFmfFileName is None:
	fmfFileNames = [f for f in fileNames if f[-3:].lower()=='fmf']
	if len(fmfFileNames) > 0:
	print 'since no input .fmf file specified, using', fmfFileNames[0]
	args.inFmfFileName = fmfFileNames[0]
	else:
	parser.print_help()
	parser.error('need to specify .fmf file name')
	if args.inBagFileName is None:
	bagFileNames = [f for f in fileNames if f[-3:].lower()=='bag']
	if len(bagFileNames) > 0:
	print 'since no input .bag file specified, using', bagFileNames[0]
	args.inBagFileName = bagFileNames[0]
	else:
	parser.print_help()
	parser.error('need to specify .bag file name')
	if args.inFmfFileName[-4:].lower() != '.fmf':
	args.inFmfFileName = args.inFmfFileName+'.fmf'
	if args.inBagFileName[-4:].lower() != '.bag':
	args.inBagFileName = args.inBagFileName+'.bag'
	if args.outFileName is None:
	args.outFileName = 'out'+args.inFmfFileName[:-4]+args.inBagFileName[:-4]+'.mpeg'
	print 'no output name specified, using', args.outFileName
	if args.outFileName[-5:].lower() != '.mpeg':
	args.outFileName = args.outFileName+'.mpeg'
	print 'in fmf file name is', args.inFmfFileName
	print 'in bag file name is', args.inBagFileName
	print 'out file name is', args.outFileName
	#================================ strokelitude conversion stuff ======================================
	strokelitudeMaskData = ast.literal_eval(args.strokelitudeMaskData)
	D2R = np.pi/180.0
	mult_sign={True:{'left':1,
	'right':-1},
	False:{'left':-1,
	'right':1}}
	gammaRad = strokelitudeMaskData['gamma']*D2R
	rotation = np.array([[ np.cos( gammaRad ), -np.sin(gammaRad)],[ np.sin( gammaRad ), np.cos(gammaRad)]])
	translation = np.array([[strokelitudeMaskData['x']],[strokelitudeMaskData['y']]])
	def get_wingsplit_translation(side):
	sign = mult_sign[strokelitudeMaskData['view_from_below']][side]
	return np.array([[0.0],[sign*strokelitudeMaskData['wingsplit']]])
	def get_span_lineseg(side,theta_user):
	"""draw line on side at angle theta_user (in radians)"""
	linesegs = []
	sign = mult_sign[strokelitudeMaskData['view_from_below']][side]
	theta = 90*D2R - theta_user
	theta *= sign
	verts = np.array( [[ 0, 1000.0*np.cos(theta)],
	[ 0, 1000.0*np.sin(theta)]] )
	verts = verts + get_wingsplit_translation(side)
	verts = np.dot(rotation, verts) + translation
	linesegs.append( verts.T.ravel() )
	return linesegs
	# ======= read bag strokelitude data ==============
	allBagData = loadBag(args.inBagFileName)
	bagTime = allBagData['timeSec'].copy()
	leftWingRad = allBagData['leftWingRad'].copy()
	rightWingRad = allBagData['rightWingRad'].copy()
	os.system('mkdir TEMPDIRFORMOVIEFRAMES')
	outDirName = os.path.join(os.getcwd(),'TEMPDIRFORMOVIEFRAMES')
	# ======= open fmf file===========================
	infmffile = FMF.FlyMovie(args.inFmfFileName)
	numFlyFrames = infmffile.get_n_frames()
	flyTime = infmffile.get_all_timestamps()
	flyFrameRate = 1.0/np.mean(np.diff(flyTime))
	if flyFrameRate*args.frameRateMultiplicationFactor < 15:
	print 'ERROR: cannot have output frame rate below 15 fps, your frameRateMultiplicationFactor of', args.frameRateMultiplicationFactor, 'combined with the input frame rate of', flyFrameRate, 'results in a desired frame rate of', flyFrameRate*args.frameRateMultiplicationFactor
	return
	inFMFHeight = infmffile.get_height()
	inFMFWidth = infmffile.get_width()
	flyFrameStartTime = flyTime[0] + args.startTime
	flyFrameStopTime = flyTime[0] + args.endTime
	flyStartInd = np.argmin(abs(flyTime - flyFrameStartTime))
	flyStopInd = np.argmin(abs(flyTime - flyFrameStopTime))
	bagStopInd = np.argmin(abs(bagTime - flyFrameStopTime))
	fig = pylab.figure(figsize=(8,6))
	fig.set_facecolor('w')
	LEFTCOLOR = 'b'
	RIGHTCOLOR = [0,1,0]
	#fig.text(.05,.96,'10x normal speed, diffuser above polarizer')
	flyAxes = fig.add_axes([0.15, 0.28, 0.7, 0.7])
	flyAxes.axis('image')
	wingsTimePlotAxes = fig.add_axes([0.15, 0.1, 0.7, 0.15])
	wingsTimePlotAxes.plot(bagTime-flyFrameStartTime,leftWingRad*180/np.pi,color=LEFTCOLOR,linewidth=.5,zorder=10)
	wingsTimePlotAxes.plot(bagTime-flyFrameStartTime,rightWingRad*180/np.pi,color=RIGHTCOLOR,linewidth=.5,zorder=10)
	wingsTimePlotAxes.set_ylim((0,90))
	wingsTimePlotAxes.spines['bottom'].set_position(('outward',8))
	wingsTimePlotAxes.spines['bottom'].set_position(('outward',8))
	wingsTimePlotAxes.xaxis.set_ticks_position('bottom')
	wingsTimePlotAxes.set_xlim((0,flyFrameStopTime-flyFrameStartTime))
	wingsTimePlotAxes.spines['left'].set_position(('outward',8))
	wingsTimePlotAxes.spines['top'].set_visible(False)
	wingsTimePlotAxes.spines['right'].set_visible(False)
	wingsTimePlotAxes.yaxis.set_ticks_position('left')
	wingsTimePlotAxes.set_yticks([0,45,90])
	wingsTimePlotAxes.set_yticklabels(['0$^\circ$','45$^\circ$','90$^\circ$'])
	wingsTimePlotAxes.set_ylabel('Wingstroke \namplitude')
	wingsTimePlotAxes.set_xlabel('Time from start (s)')
	wingsTimePlotAxes.text(wingsTimePlotAxes.get_xlim()[1],leftWingRad[bagStopInd]*180/np.pi,'Left',color=LEFTCOLOR)
	wingsTimePlotAxes.text(wingsTimePlotAxes.get_xlim()[1],rightWingRad[bagStopInd]*180/np.pi,'Right',color=RIGHTCOLOR)
	flyAxes.cla()
	for flyIndThisFrameInd, flyIndThisFrame in enumerate(range(flyStartInd, flyStopInd)):
	print 'processing frame ', flyIndThisFrameInd, ' of ', flyStopInd - flyStartInd
	flyTimeThisFrame = flyTime[flyIndThisFrame]
	bagIndThisFrame = np.argmin(abs(bagTime - flyTimeThisFrame))
	bagTimeThisFrame = bagTime[bagIndThisFrame]
	flyFrame,flyTimeThisFrameFromFMF = infmffile.get_frame(flyIndThisFrame)
	if flyTimeThisFrameFromFMF != flyTimeThisFrame:
	print 'different fly times this frame??'
	flyAxes.imshow(flyFrame,cmap='gray',origin='lower')
	leftLineSegs = get_span_lineseg('left',leftWingRad[bagIndThisFrame])
	rightLineSegs = get_span_lineseg('right',rightWingRad[bagIndThisFrame])
	flyAxes.plot([leftLineSegs[0][0],leftLineSegs[0][2]],[leftLineSegs[0][1],leftLineSegs[0][3]],color=LEFTCOLOR,linewidth=2)
	flyAxes.plot([rightLineSegs[0][0],rightLineSegs[0][2]],[rightLineSegs[0][1],rightLineSegs[0][3]],color=RIGHTCOLOR,linewidth=2)
	flyAxes.axis('off')
	flyAxes.set_xlim((0,flyFrame.shape[1]))
	flyAxes.set_ylim((0,flyFrame.shape[0]))
	movingWingsLine = wingsTimePlotAxes.axvline(bagTimeThisFrame-flyFrameStartTime,color='k')
	wingsTimePlotAxes.set_xlim((0,flyFrameStopTime-flyFrameStartTime))
	fig.savefig(os.path.join(outDirName,'frame')+("%05d" %(flyIndThisFrameInd+1))+'.png')
	if flyIndThisFrame < flyStopInd - 1:
	flyAxes.cla()
	movingWingsLine.remove()
	ffmpegCommandString = 'ffmpeg -b 8000000 -r '+str(flyFrameRate*args.frameRateMultiplicationFactor)+' -i '+os.path.join(outDirName,'frame%05d.png ')+args.outFileName
	#print ffmpegCommandString
	os.system(ffmpegCommandString)
	#=================== clean up temp folders and directory ==========================
	os.system('rm '+os.path.join(outDirName,'frame*.png '))
	os.system('rmdir '+outDirName)
	return
	if __name__ == "__main__":
	main()

view raw makeFmfStrokelitudeMovie.py hosted with ❤ by GitHub

Load strokelitude data from .bag file into Python

Here is a script I've been using to load the strokelitude data contained in a .bag file. It should be easy to convert it to load data from other ros topics.

	import sys, os
	import numpy as np
	import roslib
	roslib.load_manifest('rosbag')
	import rosbag
	def loadBag(inFileName):
	"""
	Script to import strokelitude bag file
	usage: outDict = loadBag(inFileName)
	PTW 02/04/12
	"""
	if inFileName[-4:] != '.bag':
	inFileName = inFileName + '.bag'
	bag = rosbag.Bag(inFileName)
	timeSec = list()
	leftWingRad = list()
	rightWingRad = list()
	for topic, msg, t in bag.read_messages():
	if topic == '/strokelitude' or topic == 'strokelitude':
	timeSec.append(msg.header.stamp.secs + msg.header.stamp.nsecs*float(1e-9))
	leftWingRad.append(msg.left_wing_angle_radians)
	rightWingRad.append(msg.right_wing_angle_radians)
	timeSec = np.array(timeSec)
	leftWingRad=np.array(leftWingRad)
	rightWingRad = np.array(rightWingRad)
	outDict = {'timeSec':timeSec, 'leftWingRad':leftWingRad, 'rightWingRad':rightWingRad}
	return outDict

view raw loadBag.py hosted with ❤ by GitHub

Using Github for Windows

I have started using the Github Windows GUI for using git on Windows, and so far I am very impressed. Github has made it very easy to download (clone) an entire directory tree of code files to a new computer, something I have to do more often that I would like. Git is an incredibly powerful tool for version control, and I really do not scratch the surface of its functionality. An important thing to remember for a novice user is that it is best to make sure you are working with the newest version of the repository before you start making edits on any given computer. Otherwise merging the edits from different computers (or users) can be hard. This can be accomplished by opening the github GUI before editing any files and clicking 'sync.'

Note: If, when setting up your repository, you accidentally included files that you did not want to have git follow, you can use this command:

git rm --cached <filename> 

by going to tools>open a shell here in the github GUI. You may also have to include a new line in your .gitignore file...

When you inevitably (in my experience) get an error message along the lines of "failed to sync this branch" with options to "open shell to debug" or "cancel," choose the former, and typing

git push

or

git pull 

depending on if you are trying to upload (push) or download (pull) changes from github.com will sometimes work.