f_mesh = open(m_in, 'r')
lines = f_mesh.readlines()
nF = len(lines)-1
nX = int(lines[0].split(',')[1])
truestates = np.zeros((nF, nX*4), dtype = np.float32)
predstates = np.zeros((nF, nX*4), dtype = np.float32)
for i in range(1,nF+1):
line = lines[i]
truestates[i-1,:] = [float(x) for x in line.split(',')[1:]]
predstates[0,:] = truestates[0,:]
rms_vel = np.zeros(nF)
rms_pos = np.zeros(nF)
flowstream = FlowStream(flow_in)
ret_flow, flowframe = flowstream.read()
kf = IteratedKalmanFilter(distmesh, frame, flowframe, cuda = cuda, sparse = sparse)
self = kf.state
#Test labels
#with self._fbo4:
# m = gloo.read_pixels()
#np.max(m[:,:,2])
#np.sum(m[:,:,2] == 255)
#np.unique(m[:,:,2])
#kf.state.E[0]
#kf.state.labels
#np.unique(m[:,:,1])
def runIEKF(eps_Z, eps_J, eps_M, eps_F):
print 'Running with:'
print '- eps_Z:', eps_Z
print '- eps_J:', eps_J
print '- eps_M:', eps_M
print '- eps_F:', eps_F
if mask_flow:
notes = 'masked_iekf'
else:
notes = 'iekf'
notes += '_eps_Z_%f'%eps_Z
notes += '_eps_J_%f'%eps_J
notes += '_eps_M_%f'%eps_M
notes += '_eps_F_%f'%eps_F
img_out = './synthetictests/' + name + '/' + ff + '_' + notes + '_pred/'
if not os.path.isdir(img_out):
os.makedirs(img_out)
print 'Loading synthetic data streams'
capture = VideoStream(v_in, threshold)
frame = capture.current_frame()
mask, ctrs, fd = capture.backsub()
distmesh = DistMesh(frame, h0 = gridsize)
distmesh.load(dm_in)
#Load true data
f_mesh = open(m_in, 'r')
lines = f_mesh.readlines()
nF = len(lines)-1
nX = int(lines[0].split(',')[1])
truestates = np.zeros((nF, nX*4), dtype = np.float32)
predstates = np.zeros((nF, nX*4), dtype = np.float32)
for i in range(1,nF+1):
line = lines[i]
truestates[i-1,:] = [float(x) for x in line.split(',')[1:]]
predstates[0,:] = truestates[0,:]
rms_vel = np.zeros(nF)
rms_pos = np.zeros(nF)
flowstream = FlowStream(flow_in)
ret_flow, flowframe = flowstream.read()
kf = IteratedKalmanFilter(distmesh, frame, flowframe, cuda = cuda, sparse = sparse,\
eps_F = eps_F, eps_Z = eps_Z, eps_J = eps_J, eps_M = eps_M, nI = nI)
count = 0
print 'Tracking with Kalman filter'
while(capture.isOpened() and count < max_frames):
#for idx in range(1):
count += 1
ret, frame, grayframe, mask = capture.read()
ret_flow, flowframe = flowstream.read()
if ret is False or ret_flow is False:
break
print 'Frame %d' % count
kf.compute(grayframe, flowframe, mask, maskflow = mask_flow, imageoutput = img_out+'solution_frame_%03d'%count)
#kf.compute(grayframe, flowframe, mask, maskflow = mask_flow)
predstates[count,:] = np.squeeze(kf.state.X)
r_pos = truestates[count,0:(2*nX)]-predstates[count,0:(2*nX)]
r_vel = truestates[count,(2*nX):]-predstates[count,(2*nX):]
rms_pos[count] = np.sqrt(np.mean(np.multiply(r_pos, r_pos)))
rms_vel[count] = np.sqrt(np.mean(np.multiply(r_vel, r_vel)))
print 'RMS_pos:', rms_pos[count], 'RMS_vel:', rms_vel[count]
print 'Saving'
np.savez('./synthetictests/' + name + '/' + ff + '_' + notes + '_pred.npz', predstates, truestates, rms_pos, rms_vel)
print 'Done... how\'d we do?'
#Make plot of tracking error
plt.plot(range(nF), rms_pos, label='RMS position')
plt.plot(range(nF), rms_vel, label='RMS velocity')
plt.legend(loc='upper left')
plt.ylabel('RMS')
plt.xlabel('Frame')
plt.savefig('./synthetictests/' + name + '/' + ff + '_' + notes + '_pred_rms.eps')
def main():
usage = """run_kalmanfilter.py [input_avi_file] [optic_flow_path] [output_avi_file] [threshold]
HydraGL. State space model using an extended Kalman filter to track Hydra in video
Dependencies:
-Vispy*
-Numpy
-PyCuda**
-DistMesh
-HDF
-OpenCV2
-matplotlib
Notes:
* Uses OpenGL rendering. If using remotely, you'll need to set up a VirtualGL server
** If have a CUDA compatible graphics card
Example:
./run_kalmanfilter.py ./video/johntest_brightcontrast_short.avi ...
./video/johntest_brightcontrast_short/flow ./video/output.avi -s 15
For help:
./run_kalmanfilter.py -h
Ben Lansdell
02/16/2016
"""
parser = argparse.ArgumentParser()
parser.add_argument('fn_in', default='./video/johntest_brightcontrast_short.avi',
help='input video file, any format readable by OpenCV', nargs = '?')
parser.add_argument('flow_in', default='./video/johntest_brightcontrast_short/flow',
help='input optic flow path', nargs = '?')
parser.add_argument('fn_out', default='./video/johntest_brightcontrast_short_output.avi',
help='avi output video file', nargs='?')
parser.add_argument('-n', '--name', default='johntest_brightcontrast_short',
help='name for saving run images', nargs='?')
parser.add_argument('-t', '--threshold', default=9,
help='threshold intensity below which is background', type = int)
parser.add_argument('-s', '--gridsize', default=22,
help='edge length for mesh (smaller is finer; unstable much further below 18)', type = int)
parser.add_argument('-c', '--cuda', default=True,
help='whether or not to do analysis on CUDA', type = bool)
args = parser.parse_args()
if len(sys.argv) == 1:
print("No command line arguments provided, using defaults")
capture = VideoStream(args.fn_in, args.threshold)
frame = capture.current_frame()
mask, ctrs, fd = capture.backsub()
distmesh = DistMesh(frame, h0 = args.gridsize)
distmesh.createMesh(ctrs, fd, frame, plot = True)
#Load flow data from directory
flowstream = FlowStream(args.flow_in)
ret_flow, flowframe = flowstream.peek()
if ret_flow:
kf = IteratedMSKalmanFilter(distmesh, frame, flowframe, cuda = args.cuda, sparse = True, multi = True)
else:
print 'Cannot read flow stream'
return
#kf.compute(capture.gray_frame(), flowframe)
nI = 3
count = 0
while(capture.isOpened()):
count += 1
print 'Frame %d' % count
ret, frame, grayframe, mask = capture.read()
ret_flow, flowframe = flowstream.read()
if ret is False or ret_flow is False:
break
#for i in range(nI):
# print 'Iteration %d' % i
# raw_input("Finished. Press Enter to continue")
# kf.compute(grayframe, flowframe)
kf.compute(grayframe, flowframe, mask, imageoutput = 'screenshots/' + args.name + '_frame_' + str(count))
capture.release()
output.release()
cv2.destroyAllWindows()
raw_input("Finished. Press ENTER to exit")
def main(argv):
if len(argv) < 3:
print 'Not enough arguments'
return
ff = argv[1]
name = argv[2]
if len(argv) == 4:
flownotes = argv[3]
elif len(argv) == 3:
flownotes = ''
else:
print 'Too many arguments'
return
#name = 'square5_gradient_texture_rot2'
#name = 'square4_gradient_texture_rot1'
#name = 'square3_gradient_texture'
#name = 'square2_gradient'
#name = 'square1'
#name = 'hydra1'
#ff = 'translate_leftup_stretch'
#ff = 'translate_leftup'
cuda = True
sparse = True
#Brox flow:
#flownotes = ''
#flownotes = '_solver_it_20'
#flownotes = '_solver_it_5'
#flownotes = '_inner_it_20'
#flownotes = '_inner_it_5'
#flownotes = '_alpha_0.4'
#flownotes = '_alpha_0.1'
#flownotes = '_gamma_100'
#flownotes = '_gamma_25'
#DeepFlow
#flownotes = '_deep'
#SimpleFlow
#flownotes = '_simple'
m_in = './synthetictests/' + name + '/' + ff + '_mesh.txt'
#Video and Brox flow in
v_in = './synthetictests/' + name + '/' + ff + '/' + ff + '.avi'
flow_in = './synthetictests/' + name + '/' + ff + '/' + ff + '_flow' + flownotes
#Output
img_out = './synthetictests/' + name + '/' + ff + '_testflow' + flownotes + '/'
if not os.path.isdir(img_out):
os.makedirs(img_out)
threshold = 8
print 'Loading synthetic data streams'
capture = VideoStream(v_in, threshold)
frame = capture.current_frame()
mask, ctrs, fd = capture.backsub()
f_mesh = open(m_in, 'r')
lines = f_mesh.readlines()
nF = len(lines)-1
nX = frame.shape[0]
flowstream = FlowStream(flow_in)
ret_flow, flowframe = flowstream.read()
rms_flow = np.zeros(nF)
true_flow = np.zeros((nX, nX, 2))
rel_abs_res = np.zeros((nF, nX, nX))
abs_res = np.zeros((nF, nX, nX))
video = np.zeros((nF, nX, nX))
samp_frac = 0.1
count = 0
print 'Comparing true flow to computed flow'
abs_flow_sample = []
abs_res_sample = []
video_sample = []
while(capture.isOpened()):
count += 1
ret, frame, grayframe, mask = capture.read()
ret_flow, flowframe = flowstream.read()
if ret is False or ret_flow is False:
break
print 'Frame %d'%count
video[count,:,:] = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
#Compute true flow based on all points in object undergoing flow field
#Find all pts in mask
#.... HORRIBLY horribly slow
for i in range(nX):
for j in range(nX):
m = mask[i,j]
(fx, fy) = flowfields[ff]((i,j),0)
true_flow[i,j,:] = [fx*m, fy*m]
res = m*(true_flow[i,j,:] - flowframe[i,j,:])
abs_res[count,i,j] = np.sqrt(np.sum(res*res))
if m > 0:
rel_abs_res[count,i,j] = np.sqrt(np.sum(res*res))/np.sqrt(fx*fx+fy*fy)
u = np.random.uniform()
if u < samp_frac:
abs_flow_sample += [np.sqrt(fx*fx+fy*fy)]
abs_res_sample += [abs_res[count,i,j]]
video_sample += [video[count,i,j]]
#Load computed flow and compare
r = true_flow - flowframe
s = np.sum(mask)
rms_flow[count] = np.sqrt(np.sum(np.multiply(r, r))/s)
plt.clf()
plt.imshow(abs_res[count,:,:])
plt.colorbar()
plt.savefig(img_out + 'flow_abs_res_%03d.png'%count)
plt.clf()
plt.imshow(rel_abs_res[count,:,:])
plt.colorbar()
plt.savefig(img_out + 'flow_rel_abs_res_%03d.png'%count)
#cv2.imwrite(img_out + 'flow_abs_res_%03d.png'%count, abs_res[count,:,:])
print 'RMS_flow:', rms_flow[count]
print 'Done... how\'d we do?'
df = pd.DataFrame({'abs_flow_sample':pd.Series(abs_flow_sample),\
'abs_res_sample':pd.Series(abs_res_sample),\
'video_sample':pd.Series(video_sample)})
#Save output
df.to_pickle(img_out + "flow_errors.pkl")
np.save(img_out + "rms_flow.npz",rms_flow)
g1 = sns.jointplot("video_sample", "abs_res_sample", data = df, kind="kde", color="b")
g1.savefig(img_out + 'intensity_abs_res.eps')
g2 = sns.jointplot("abs_flow_sample", "abs_res_sample", data = df, kind="kde", color="b")
g2.savefig(img_out + 'flow_abs_res.eps')
#Plot abs error in flow vs abs magnitude of flow
plt.clf()
plt.plot(range(nF), rms_flow, label='RMS flow')
plt.legend(loc='upper left')
plt.ylabel('RMS')
plt.xlabel('Frame')
plt.savefig(img_out + 'flow_rms.eps')
