def find_params():
FRAMES = np.arange(30)*100
frame_images = organizedata.get_frames(ddir("bukowski_04.W2"), FRAMES)
print "DONE READING DATA"
CLUST_EPS = np.linspace(0, 0.5, 10)
MIN_SAMPLES = [2, 3, 4, 5]
MIN_DISTS = [2, 3, 4, 5, 6]
THOLD = 240
fracs_2 = np.zeros((len(CLUST_EPS), len(MIN_SAMPLES), len(MIN_DISTS)))
for cei, CLUST_EP in enumerate(CLUST_EPS):
for msi, MIN_SAMPLE in enumerate(MIN_SAMPLES):
for mdi, MIN_DIST in enumerate(MIN_DISTS):
print cei, msi, mdi
numclusters = np.zeros(len(FRAMES))
for fi, im in enumerate(frame_images):
centers = frame_clust_points(im, THOLD, MIN_DIST,
CLUST_EP, MIN_SAMPLE)
# cluster centers
numclusters[fi] = len(centers)
fracs_2[cei, msi, mdi] = float(np.sum(numclusters == 2))/len(numclusters)
pylab.figure(figsize=(12, 8))
for mdi, MIN_DIST in enumerate(MIN_DISTS):
pylab.subplot(len(MIN_DISTS), 1, mdi+1)
for msi in range(len(MIN_SAMPLES)):
pylab.plot(CLUST_EPS, fracs_2[:, msi, mdi], label='%d' % MIN_SAMPLES[msi])
pylab.title("min_dist= %3.2f" % MIN_DIST)
pylab.legend()
pylab.savefig('test.png', dpi=300)
def average_diode_sep():
clust_eps = 0.2
min_dist = 2.0
min_samples = 3.0
thold = 240
FRAMES = np.arange(4000)*2
dataset = "bukowski_02.C"
cf = pickle.load(open(os.path.join(ddir(dataset), 'config.pickle')))
region = pickle.load(open(os.path.join(ddir(dataset), 'region.pickle')))
env = util.Environmentz(cf['field_dim_m'], cf['frame_dim_pix'])
x_min, y_min = env.gc.real_to_image(region['x_pos_min'], region['y_pos_min'])
x_max, y_max = env.gc.real_to_image(region['x_pos_max'], region['y_pos_max'])
print x_min, x_max
print y_min, y_max
if y_min < 0:
y_min = 0
frame_images = organizedata.get_frames(ddir(dataset), FRAMES)
num_clusters = np.zeros(len(FRAMES))
dists = []
for fi, im in enumerate(frame_images):
im = im[y_min:y_max+1, x_min:x_max+1]
centers = frame_clust_points(im, 240, min_dist,
clust_eps, min_samples)
num_clusters[fi] = len(centers)
if len(centers) == 2:
dists.append(distance.pdist(centers)[0])
dists = np.array(dists)
pylab.hist(dists[dists < 50], bins=20)
pylab.savefig("average_diode_sep.%s.png" % dataset, dpi=300)
def picloud_score_frame(dataset_name, x_range, y_range, phi_range, theta_range,
state_idx, frame, EO_PARAMS, likelihood_i):
"""
pi-cloud runner, every instance builds up full state, but
we only evaluate the states in [state_idx_to_eval[0], state_idx_to_eval[1])
and return scores
"""
print "DATSET_NAME=", dataset_name
dataset_dir = os.path.join(FL_DATA, dataset_name)
dataset_config_filename = os.path.join(dataset_dir, "config.pickle")
dataset_region_filename = os.path.join(dataset_dir, "region.pickle")
frame_hist_filename = os.path.join(dataset_dir, "framehist.npz")
np.random.seed(0)
cf = pickle.load(open(dataset_config_filename))
region = pickle.load(open(dataset_region_filename))
framehist = np.load(frame_hist_filename)
env = util.Environmentz(cf['field_dim_m'], cf['frame_dim_pix'])
tp = template.TemplateRenderCircleBorder()
tp.set_params(*EO_PARAMS)
ls = LIKELIHOOD_SETTING[likelihood_i]
le = likelihood.LikelihoodEvaluator2(env,
tp,
similarity=ls['similarity'],
sim_params=ls['sim_params'])
frames = organizedata.get_frames(dataset_dir, np.array([frame]))
frame = frames[0]
frame[frame < PIX_THRESHOLD] = 0
# create the state vector
state = create_state_vect(y_range, x_range, phi_range, theta_range)
SCORE_N = state_idx[1] - state_idx[0]
scores = np.zeros(SCORE_N, dtype=np.float32)
for i, state_i in enumerate(state[state_idx[0]:state_idx[1]]):
x = state_i['x']
y = state_i['y']
if region['x_pos_min'] <= x <= region['x_pos_max'] and \
region['y_pos_min'] <= y <= region['y_pos_max']:
score = le.score_state(state_i, frame)
scores[i] = score
else:
scores[i] = -1e100
return scores
def picloud_score_frame(dataset_name, x_range, y_range, phi_range, theta_range,
state_idx, frame, EO_PARAMS, likelihood_i):
"""
pi-cloud runner, every instance builds up full state, but
we only evaluate the states in [state_idx_to_eval[0], state_idx_to_eval[1])
and return scores
"""
print "DATSET_NAME=", dataset_name
dataset_dir = os.path.join(FL_DATA, dataset_name)
dataset_config_filename = os.path.join(dataset_dir, "config.pickle")
dataset_region_filename = os.path.join(dataset_dir, "region.pickle")
frame_hist_filename = os.path.join(dataset_dir, "framehist.npz")
np.random.seed(0)
cf = pickle.load(open(dataset_config_filename))
region = pickle.load(open(dataset_region_filename))
framehist = np.load(frame_hist_filename)
env = util.Environmentz(cf['field_dim_m'],
cf['frame_dim_pix'])
tp = template.TemplateRenderCircleBorder()
tp.set_params(*EO_PARAMS)
ls = LIKELIHOOD_SETTING[likelihood_i]
le = likelihood.LikelihoodEvaluator2(env, tp, similarity=ls['similarity'],
sim_params = ls['sim_params'])
frames = organizedata.get_frames(dataset_dir, np.array([frame]))
frame = frames[0]
frame[frame < PIX_THRESHOLD] = 0
# create the state vector
state = create_state_vect(y_range, x_range, phi_range, theta_range)
SCORE_N = state_idx[1] - state_idx[0]
scores = np.zeros(SCORE_N, dtype=np.float32)
for i, state_i in enumerate(state[state_idx[0]:state_idx[1]]):
x = state_i['x']
y = state_i['y']
if region['x_pos_min'] <= x <= region['x_pos_max'] and \
region['y_pos_min'] <= y <= region['y_pos_max']:
score = le.score_state(state_i, frame)
scores[i] = score
else:
scores[i] = -1e100
return scores
def per_frame(basedir, func, config):
config_file = os.path.join(basedir, "config.pickle")
cf = pickle.load(open(config_file))
env = util.Environmentz(cf['field_dim_m'], cf['frame_dim_pix'])
FRAMEN = cf['end_f'] - cf['start_f'] + 1
d = np.zeros(FRAMES_TO_ANALYZE, dtype=DTYPE_POS_CONF)
FRAMES_AT_A_TIME = 10
frames = np.arange(FRAMES_TO_ANALYZE)
for frame_subset in util.chunk(frames, FRAMES_AT_A_TIME):
fs = organizedata.get_frames(basedir, frame_subset)
for fi, frame_no in enumerate(frame_subset):
real_x, real_y, conf = func(fs[fi], env, **config)
d[frame_no]['x'] = real_x
d[frame_no]['y'] = real_y
d[frame_no]['confidence'] = conf
return d
def per_frame(basedir, func, config):
config_file = os.path.join(basedir, "config.pickle")
cf = pickle.load(open(config_file))
env = util.Environmentz(cf['field_dim_m'], cf['frame_dim_pix'])
FRAMEN = cf['end_f'] - cf['start_f'] + 1
d = np.zeros(FRAMES_TO_ANALYZE, dtype=DTYPE_POS_CONF)
FRAMES_AT_A_TIME = 10
frames = np.arange(FRAMES_TO_ANALYZE)
for frame_subset in util.chunk(frames, FRAMES_AT_A_TIME):
fs = organizedata.get_frames(basedir, frame_subset)
for fi, frame_no in enumerate(frame_subset):
real_x, real_y, conf = func(fs[fi], env, **config)
d[frame_no]['x'] = real_x
d[frame_no]['y'] = real_y
d[frame_no]['confidence'] = conf
return d
def find_params():
FRAMES = np.arange(30) * 100
frame_images = organizedata.get_frames(ddir("bukowski_04.W2"), FRAMES)
print "DONE READING DATA"
CLUST_EPS = np.linspace(0, 0.5, 10)
MIN_SAMPLES = [2, 3, 4, 5]
MIN_DISTS = [2, 3, 4, 5, 6]
THOLD = 240
fracs_2 = np.zeros((len(CLUST_EPS), len(MIN_SAMPLES), len(MIN_DISTS)))
for cei, CLUST_EP in enumerate(CLUST_EPS):
for msi, MIN_SAMPLE in enumerate(MIN_SAMPLES):
for mdi, MIN_DIST in enumerate(MIN_DISTS):
print cei, msi, mdi
numclusters = np.zeros(len(FRAMES))
for fi, im in enumerate(frame_images):
centers = frame_clust_points(im, THOLD, MIN_DIST, CLUST_EP,
MIN_SAMPLE)
# cluster centers
numclusters[fi] = len(centers)
fracs_2[cei, msi, mdi] = float(
np.sum(numclusters == 2)) / len(numclusters)
pylab.figure(figsize=(12, 8))
for mdi, MIN_DIST in enumerate(MIN_DISTS):
pylab.subplot(len(MIN_DISTS), 1, mdi + 1)
for msi in range(len(MIN_SAMPLES)):
pylab.plot(CLUST_EPS,
fracs_2[:, msi, mdi],
label='%d' % MIN_SAMPLES[msi])
pylab.title("min_dist= %3.2f" % MIN_DIST)
pylab.legend()
pylab.savefig('test.png', dpi=300)
def average_diode_sep():
clust_eps = 0.2
min_dist = 2.0
min_samples = 3.0
thold = 240
FRAMES = np.arange(4000) * 2
dataset = "bukowski_02.C"
cf = pickle.load(open(os.path.join(ddir(dataset), 'config.pickle')))
region = pickle.load(open(os.path.join(ddir(dataset), 'region.pickle')))
env = util.Environmentz(cf['field_dim_m'], cf['frame_dim_pix'])
x_min, y_min = env.gc.real_to_image(region['x_pos_min'],
region['y_pos_min'])
x_max, y_max = env.gc.real_to_image(region['x_pos_max'],
region['y_pos_max'])
print x_min, x_max
print y_min, y_max
if y_min < 0:
y_min = 0
frame_images = organizedata.get_frames(ddir(dataset), FRAMES)
num_clusters = np.zeros(len(FRAMES))
dists = []
for fi, im in enumerate(frame_images):
im = im[y_min:y_max + 1, x_min:x_max + 1]
centers = frame_clust_points(im, 240, min_dist, clust_eps, min_samples)
num_clusters[fi] = len(centers)
if len(centers) == 2:
dists.append(distance.pdist(centers)[0])
dists = np.array(dists)
pylab.hist(dists[dists < 50], bins=20)
pylab.savefig("average_diode_sep.%s.png" % dataset, dpi=300)
scores = scores[:len(sv)]
pylab.figure()
scores_flat = np.array(scores.flat)
pylab.hist(scores_flat[np.isfinite(scores_flat)], bins=255)
pylab.savefig(outfile_hist, dpi=300)
scores[np.isinf(scores)] = -1e20
TOP_R, TOP_C = 3, 4
TOP_N = TOP_R * TOP_C
score_idx_sorted = np.argsort(scores)[::-1]
#get the frame
frames = organizedata.get_frames(data_p['dataset_dir'],
np.array([data_p['frame']]))
# config file
cf = pickle.load(open(os.path.join(data_p['dataset_dir'],
'config.pickle')))
env = util.Environmentz(cf['field_dim_m'], cf['frame_dim_pix'])
img = frames[0]
f = pylab.figure()
for r in range(TOP_N):
s_i = score_idx_sorted[r]
score = scores[s_i]
ax = f.add_subplot(TOP_R, TOP_C, r + 1)
ax.imshow(img, interpolation='nearest', cmap=pylab.cm.gray)
x_pix, y_pix = env.gc.real_to_image(sv[s_i]['x'], sv[s_i]['y'])
ax.axhline(y_pix, linewidth=1, c='b', alpha=0.5)
cf['frame_dim_pix'])
led_params = pickle.load(open(led_params_filename, 'r'))
eo_params = measure.led_params_to_EO(cf, led_params)
if frame_end > cf['end_f']:
frame_end = cf['end_f']
truth = np.load(os.path.join(epoch_dir, 'positions.npy'))
truth_interp, missing = measure.interpolate(truth)
derived_truth = measure.compute_derived(truth_interp,
T_DELTA)
frame_pos = np.arange(frame_start, frame_end)
# load frames
frames = organizedata.get_frames(epoch_dir, frame_pos)
FRAMEN = len(frames)
coordinates = []
regions = np.zeros((FRAMEN, frames[0].shape[0], frames[0].shape[1]),
dtype=np.uint8)
point_est_track_data = []
for fi, frame in enumerate(frames):
abs_frame_index = frame_pos[fi]
coordinates.append(skimage.feature.peak_local_max(frame,
min_distance=30,
threshold_abs=220))
front_amount = diode_scale, back_amount = diode_scale)
#print "EO PARAMS ARE", eoparams
tr = TemplateObj(0.8, 0.4)
tr.set_params(*eoparams)
le1 = likelihood.LikelihoodEvaluator2(env, tr, similarity='dist',
likeli_params = config_params)
model_inst = model.CustomModel(env, le1,
POS_NOISE_STD=posnoise,
VELOCITY_NOISE_STD=velnoise)
frame_pos = np.arange(frame_start, frame_end)
# load frames
frames = organizedata.get_frames(epoch_dir, frame_pos)
y = frames
prop2 = proposals.HigherIsotropic()
def img_to_points(img):
return dettrack.point_est_track2(img, env, eoparams)
prop3 = proposals.MultimodalData(env, img_to_points, prop2)
mpk = ssm.proposal.MixtureProposalKernel([prop2, prop3],
[0.5, 0.5])
unnormed_weights, particles, ancestors = pf.arbitrary_prop(y, model_inst,
mpk,
PARTICLEN)
# now the real velocity outliers: For the top N velocity outliers,
# plot the image before, during, and after the peak
env = util.Environmentz(cf['field_dim_m'], cf['frame_dim_pix'])
def rc(x, y):
# convenience real-to-immg
return env.gc.real_to_image(x, y)
top_vel_idx = np.argsort(pos_vel)[-1]
tgt_frame_idx = np.array([
top_vel_idx - 2, top_vel_idx - 1, top_vel_idx, top_vel_idx + 1,
top_vel_idx + 2
])
f = organizedata.get_frames(basedir, tgt_frame_idx)
pylab.figure()
for i, fi in enumerate(tgt_frame_idx):
pylab.subplot(2, len(tgt_frame_idx), i + 1)
pylab.imshow(f[i], interpolation='nearest', cmap=pylab.cm.gray)
for l, c in [('led_front', 'g'), ('led_back', 'r')]:
img_x, img_y = rc(positions_interp[l][fi, 0],
positions_interp[l][fi, 1])
pylab.scatter(img_x, img_y, c=c, s=1, linewidth=0)
for i, fi in enumerate(tgt_frame_idx[:-1]):
pylab.subplot(2, len(tgt_frame_idx), len(tgt_frame_idx) + i + 1)
pylab.imshow(f[i + 1] - f[i], interpolation='nearest')
pylab.savefig(velocity_file, dpi=1000)
@merge("%s/*/positions.npy" % DATA_DIR, ["velocity.pdf", "phidot.pdf"])
# plot the image before, during, and after the peak
env = util.Environmentz(cf['field_dim_m'],
cf['frame_dim_pix'])
def rc(x, y):
# convenience real-to-immg
return env.gc.real_to_image(x, y)
top_vel_idx = np.argsort(pos_vel)[-1]
tgt_frame_idx = np.array([top_vel_idx -2,
top_vel_idx - 1,
top_vel_idx,
top_vel_idx + 1,
top_vel_idx + 2])
f = organizedata.get_frames(basedir, tgt_frame_idx)
pylab.figure()
for i, fi in enumerate(tgt_frame_idx):
pylab.subplot(2, len(tgt_frame_idx),
i+1)
pylab.imshow(f[i], interpolation='nearest', cmap=pylab.cm.gray)
for l, c in [('led_front', 'g'), ('led_back', 'r')]:
img_x, img_y = rc(positions_interp[l][fi, 0],
positions_interp[l][fi, 1])
pylab.scatter(img_x, img_y, c=c, s=1, linewidth=0)
for i, fi in enumerate(tgt_frame_idx[:-1]):
pylab.subplot(2, len(tgt_frame_idx),
len(tgt_frame_idx) + i+1)
pylab.imshow(f[i+1] -f[i], interpolation='nearest')
pylab.savefig(velocity_file, dpi=1000)
#print "EO PARAMS ARE", eoparams
tr = TemplateObj(0.8, 0.4)
tr.set_params(*eoparams)
le1 = likelihood.LikelihoodEvaluator2(env,
tr,
similarity='dist',
likeli_params=config_params)
model_inst = model.CustomModel(env,
le1,
POS_NOISE_STD=posnoise,
VELOCITY_NOISE_STD=velnoise)
frame_pos = np.arange(frame_start, frame_end)
# load frames
frames = organizedata.get_frames(epoch_dir, frame_pos)
y = frames
prop2 = proposals.HigherIsotropic()
def img_to_points(img):
return dettrack.point_est_track2(img, env, eoparams)
prop3 = proposals.MultimodalData(env, img_to_points, prop2)
mpk = ssm.proposal.MixtureProposalKernel([prop2, prop3], [0.5, 0.5])
unnormed_weights, particles, ancestors = pf.arbitrary_prop(
y, model_inst, mpk, PARTICLEN)
scores = scores[:len(sv)]
pylab.figure()
scores_flat = np.array(scores.flat)
pylab.hist(scores_flat[np.isfinite(scores_flat)], bins=255)
pylab.savefig(outfile_hist, dpi=300)
scores[np.isinf(scores)] = -1e20
TOP_R, TOP_C = 3, 4
TOP_N = TOP_R * TOP_C
score_idx_sorted = np.argsort(scores)[::-1]
#get the frame
frames = organizedata.get_frames(data_p['dataset_dir'],
np.array([data_p['frame']]))
# config file
cf = pickle.load(open(os.path.join(data_p['dataset_dir'],
'config.pickle')))
env = util.Environmentz(cf['field_dim_m'],
cf['frame_dim_pix'])
img = frames[0]
f = pylab.figure()
for r in range(TOP_N):
s_i = score_idx_sorted[r]
score = scores[s_i]
ax =f.add_subplot(TOP_R, TOP_C, r+1)
ax.imshow(img, interpolation='nearest', cmap=pylab.cm.gray)
x_pix, y_pix = env.gc.real_to_image(sv[s_i]['x'], sv[s_i]['y'])
region = pickle.load(open(region_filename, 'r'))
env = util.Environmentz(cf['field_dim_m'], cf['frame_dim_pix'])
led_params = pickle.load(open(led_params_filename, 'r'))
eo_params = measure.led_params_to_EO(cf, led_params)
if frame_end > cf['end_f']:
frame_end = cf['end_f']
truth = np.load(os.path.join(epoch_dir, 'positions.npy'))
truth_interp, missing = measure.interpolate(truth)
derived_truth = measure.compute_derived(truth_interp, T_DELTA)
frame_pos = np.arange(frame_start, frame_end)
# load frames
frames = organizedata.get_frames(epoch_dir, frame_pos)
FRAMEN = len(frames)
coordinates = []
regions = np.zeros((FRAMEN, frames[0].shape[0], frames[0].shape[1]),
dtype=np.uint8)
point_est_track_data = []
for fi, frame in enumerate(frames):
abs_frame_index = frame_pos[fi]
coordinates.append(
skimage.feature.peak_local_max(frame,
min_distance=30,