def main(model_path, exp_config):
# Make and restore vagan model
segvae_model = segvae(exp_config=exp_config)
segvae_model.load_weights(model_path, type='latest')
data_loader = data_switch(exp_config.data_identifier)
data = data_loader(exp_config)
ncc_list = []
for ii, batch in enumerate(data.test.iterate_batches(1)):
if ii % 10 == 0:
print('Progress: %d' % ii)
x_b, s_b = batch
s_m, s_v, s_e = segvae_model.predict_mean_variance_and_error_maps(
s_b, x_b, num_samples=100)
ncc_list.append(utils.ncc(s_v, s_e))
ncc_arr = np.asarray(ncc_list)
ncc_mean = np.mean(ncc_arr, axis=0)
ncc_std = np.std(ncc_arr, axis=0)
print('NCC mean: %.4f', ncc_mean)
print('NCC std: %.4f', ncc_std)
def main(model_path, exp_config, do_plots=False):
n_samples = 50
model_selection = 'best_ged'
# Get Data
segvae_model = segvae(exp_config=exp_config)
segvae_model.load_weights(model_path, type=model_selection)
data_loader = data_switch(exp_config.data_identifier)
data = data_loader(exp_config)
N = data.test.images.shape[0]
ged_list = []
ncc_list = []
for ii in range(N):
if ii % 10 == 0:
logging.info("Progress: %d" % ii)
x_b = data.test.images[ii, ...].reshape([1] + list(exp_config.image_size))
s_b = data.test.labels[ii, ...]
x_b_stacked = np.tile(x_b, [n_samples, 1, 1, 1])
feed_dict = {}
feed_dict[segvae_model.training_pl] = False
feed_dict[segvae_model.x_inp] = x_b_stacked
s_arr_sm = segvae_model.sess.run(segvae_model.s_out_eval_sm, feed_dict=feed_dict)
s_arr = np.argmax(s_arr_sm, axis=-1)
# s_arr = np.squeeze(np.asarray(s_list)) # num samples x X x Y
s_b_r = s_b.transpose((2,0,1)) # num gts x X x Y
s_b_r_sm = utils.convert_batch_to_onehot(s_b_r, exp_config.nlabels) # num gts x X x Y x nlabels
ged = utils.generalised_energy_distance(s_arr, s_b_r, nlabels=exp_config.nlabels-1, label_range=range(1,exp_config.nlabels))
ged_list.append(ged)
ncc = utils.variance_ncc_dist(s_arr_sm, s_b_r_sm)
ncc_list.append(ncc)
ged_arr = np.asarray(ged_list)
ncc_arr = np.asarray(ncc_list)
logging.info('-- GED: --')
logging.info(np.mean(ged_arr))
logging.info(np.std(ged_arr))
logging.info('-- NCC: --')
logging.info(np.mean(ncc_arr))
logging.info(np.std(ncc_arr))
np.savez(os.path.join(model_path, 'ged%s_%s.npz' % (str(n_samples), model_selection)), ged_arr)
np.savez(os.path.join(model_path, 'ncc%s_%s.npz' % (str(n_samples), model_selection)), ncc_arr)
def main(exp_config):
logging.info(
'**************************************************************')
logging.info(' *** Running Experiment: %s', exp_config.experiment_name)
logging.info(
'**************************************************************')
# Get Data
data_loader = data_switch(exp_config.data_identifier)
data = data_loader(exp_config)
# Create Model
segvae = phiseg_model.segvae(exp_config)
# Fit model to data
segvae.train(data)
def main(model_path, exp_config):
# Make and restore vagan model
segvae_model = segvae(exp_config=exp_config)
segvae_model.load_weights(model_path, type='best_dice')
data_loader = data_switch(exp_config.data_identifier)
data = data_loader(exp_config)
outfolder = '/home/baumgach/Reports/ETH/MICCAI2019_segvae/raw_figures'
ims = exp_config.image_size
# x_b, s_b = data.test.next_batch(1)
# heart 100
# prostate 165
index = 165 # 100 is a normal image, 15 is a very good slice
x_b = data.test.images[index,
...].reshape([1] + list(exp_config.image_size))
if exp_config.data_identifier == 'lidc':
s_b = data.test.labels[index, ...]
if np.sum(s_b[..., 0]) > 0:
s_b = s_b[..., 0]
elif np.sum(s_b[..., 1]) > 0:
s_b = s_b[..., 1]
elif np.sum(s_b[..., 2]) > 0:
s_b = s_b[..., 2]
else:
s_b = s_b[..., 3]
s_b = s_b.reshape([1] + list(exp_config.image_size[0:2]))
elif exp_config.data_identifier == 'uzh_prostate':
s_b = data.test.labels[index, ...]
s_b = s_b[..., 0]
s_b = s_b.reshape([1] + list(exp_config.image_size[0:2]))
else:
s_b = data.test.labels[index,
...].reshape([1] +
list(exp_config.image_size[0:2]))
x_b_for_cnt = utils.convert_to_uint8(np.squeeze(x_b.copy()))
x_b_for_cnt = cv2.cvtColor(x_b_for_cnt, cv2.COLOR_GRAY2BGR)
x_b_for_cnt = utils.resize_image(x_b_for_cnt, (2 * ims[0], 2 * ims[1]),
interp=cv2.INTER_NEAREST)
x_b_for_cnt = utils.histogram_equalization(x_b_for_cnt)
for ss in range(3):
print(ss)
s_p_list = segvae_model.predict_segmentation_sample_levels(
x_b, return_softmax=False)
accum_list = [None] * exp_config.latent_levels
accum_list[exp_config.latent_levels - 1] = s_p_list[-1]
for lvl in reversed(range(exp_config.latent_levels - 1)):
accum_list[lvl] = accum_list[lvl + 1] + s_p_list[lvl]
print('Plotting accum_list')
for ii, img in enumerate(accum_list):
plt.figure()
img = utils.resize_image(np.squeeze(np.argmax(img, axis=-1)),
(2 * ims[0], 2 * ims[1]),
interp=cv2.INTER_NEAREST)
plt.imshow(img[2 * 30:2 * 192 - 2 * 30, 2 * 30:2 * 192 - 2 * 30],
cmap='gray')
plt.axis('off')
plt.savefig(os.path.join(outfolder,
'segm_lvl_%d_samp_%d.png' % (ii, ss)),
bbox_inches='tight')
print('Plotting s_p_list')
for ii, img in enumerate(s_p_list):
img = utils.softmax(img)
plt.figure()
img = utils.resize_image(np.squeeze(img[..., 1]),
(2 * ims[0], 2 * ims[1]),
interp=cv2.INTER_NEAREST)
plt.imshow(img[2 * 30:2 * 192 - 2 * 30, 2 * 30:2 * 192 - 2 * 30],
cmap='gray')
plt.axis('off')
plt.savefig(os.path.join(outfolder,
'residual_lvl_%d_samp_%d.png' % (ii, ss)),
bbox_inches='tight')
s_p_d = np.uint8((np.squeeze(np.argmax(accum_list[0], axis=-1)) /
(exp_config.nlabels - 1)) * 255)
s_p_d = utils.resize_image(s_p_d, (2 * ims[0], 2 * ims[1]),
interp=cv2.INTER_NEAREST)
print('Calculating contours')
print(np.unique(s_p_d))
rv = cv2.inRange(s_p_d, 84, 86)
my = cv2.inRange(s_p_d, 169, 171)
rv_cnt, hierarchy = cv2.findContours(rv, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
my_cnt, hierarchy = cv2.findContours(my, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
x_b_for_cnt = cv2.drawContours(x_b_for_cnt, rv_cnt, -1, (0, 255, 0), 1)
x_b_for_cnt = cv2.drawContours(x_b_for_cnt, my_cnt, -1, (0, 0, 255), 1)
x_b_for_cnt = cv2.cvtColor(x_b_for_cnt, cv2.COLOR_BGR2RGB)
print('Plotting final images...')
plt.figure()
plt.imshow(x_b_for_cnt[2 * 30:2 * 192 - 2 * 30,
2 * 30:2 * 192 - 2 * 30, :],
cmap='gray')
plt.axis('off')
plt.savefig(os.path.join(outfolder, 'input_img_cnts.png'),
bbox_inches='tight')
plt.figure()
x_b = utils.convert_to_uint8(x_b)
x_b = cv2.cvtColor(np.squeeze(x_b), cv2.COLOR_GRAY2BGR)
x_b = utils.histogram_equalization(x_b)
x_b = utils.resize_image(x_b, (2 * ims[0], 2 * ims[1]),
interp=cv2.INTER_NEAREST)
plt.imshow(x_b[2 * 30:2 * 192 - 2 * 30, 2 * 30:2 * 192 - 2 * 30],
cmap='gray')
plt.axis('off')
plt.savefig(os.path.join(outfolder, 'input_img.png'), bbox_inches='tight')
plt.figure()
s_b = utils.resize_image(np.squeeze(s_b), (2 * ims[0], 2 * ims[1]),
interp=cv2.INTER_NEAREST)
plt.imshow(s_b[2 * 30:2 * 192 - 2 * 30, 2 * 30:2 * 192 - 2 * 30],
cmap='gray')
plt.axis('off')
plt.savefig(os.path.join(outfolder, 'gt_seg.png'), bbox_inches='tight')
def main(model_path, exp_config):
# Make and restore vagan model
segvae_model = segvae(exp_config=exp_config)
segvae_model.load_weights(model_path, type='best_ged')
data_loader = data_switch(exp_config.data_identifier)
data = data_loader(exp_config)
lat_lvls = exp_config.latent_levels
# RANDOM IMAGE
# x_b, s_b = data.test.next_batch(1)
# FIXED IMAGE
# Cardiac: 100 normal image
# LIDC: 200 large lesion, 203, 1757 complicated lesion
# Prostate: 165 nice slice
index = 165 #
x_b = data.test.images[index,
...].reshape([1] + list(exp_config.image_size))
x_b_d = utils.convert_to_uint8(np.squeeze(x_b))
x_b_d = utils.resize_image(x_b_d, video_target_size)
if SAVE_VIDEO:
fourcc = cv2.VideoWriter_fourcc(*'XVID')
outfile = os.path.join(model_path, 'model_samples_id%d.avi' % index)
out = cv2.VideoWriter(outfile, fourcc, 5.0,
(2 * video_target_size[1], video_target_size[0]))
samps = 50
for _ in range(samps):
# fix all below current level (the correct implementation)
feed_dict = {}
feed_dict[segvae_model.training_pl] = False
feed_dict[segvae_model.x_inp] = x_b
s_p, s_p_list = segvae_model.sess.run(
[segvae_model.s_out_eval, segvae_model.s_out_eval_list],
feed_dict=feed_dict)
s_p = np.argmax(s_p, axis=-1)
# s_p_d = utils.convert_to_uint8(np.squeeze(s_p))
s_p_d = np.squeeze(np.uint8((s_p / exp_config.nlabels) * 255))
s_p_d = utils.resize_image(s_p_d,
video_target_size,
interp=cv2.INTER_NEAREST)
img = np.concatenate([x_b_d, s_p_d], axis=1)
img = cv2.cvtColor(img, cv2.COLOR_GRAY2BGR)
img = histogram_equalization(img)
if exp_config.data_identifier == 'acdc':
# labels (0 85 170 255)
rv = cv2.inRange(s_p_d, 84, 86)
my = cv2.inRange(s_p_d, 169, 171)
rv_cnt, hierarchy = cv2.findContours(rv, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
my_cnt, hierarchy = cv2.findContours(my, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
cv2.drawContours(img, rv_cnt, -1, (0, 255, 0), 1)
cv2.drawContours(img, my_cnt, -1, (0, 0, 255), 1)
if exp_config.data_identifier == 'uzh_prostate':
# labels (0 85 170 255)
print(np.unique(s_p_d))
s1 = cv2.inRange(s_p_d, 84, 86)
s2 = cv2.inRange(s_p_d, 169, 171)
# s3 = cv2.inRange(s_p_d, 190, 192)
s1_cnt, hierarchy = cv2.findContours(s1, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
s2_cnt, hierarchy = cv2.findContours(s2, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
# s3_cnt, hierarchy = cv2.findContours(s3, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
cv2.drawContours(img, s1_cnt, -1, (0, 255, 0), 1)
cv2.drawContours(img, s2_cnt, -1, (0, 0, 255), 1)
# cv2.drawContours(img, s3_cnt, -1, (255, 0, 255), 1)
elif exp_config.data_identifier == 'lidc':
thresh = cv2.inRange(s_p_d, 127, 255)
lesion, hierarchy = cv2.findContours(thresh, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
cv2.drawContours(img, lesion, -1, (0, 255, 0), 1)
if SAVE_VIDEO:
out.write(img)
cv2.imshow('frame', img)
if cv2.waitKey(1) & 0xFF == ord('q'):
break
if SAVE_VIDEO:
out.release()
cv2.destroyAllWindows()
def main(model_path, exp_config):
# Make and restore vagan model
segvae_model = segvae(exp_config=exp_config)
segvae_model.load_weights(model_path, type=model_selection)
data_loader = data_switch(exp_config.data_identifier)
data = data_loader(exp_config)
N = data.test.images.shape[0]
n_images = 16
n_samples = 16
# indices = np.arange(N)
# sample_inds = np.random.choice(indices, n_images)
sample_inds = [165, 280, 213] # <-- prostate
# sample_inds = [1551] #[907, 1296, 1551] # <-- LIDC
for ii in sample_inds:
print('------- Processing image %d -------' % ii)
outfolder = os.path.join(model_path, 'samples_%s' % model_selection,
str(ii))
utils.makefolder(outfolder)
x_b = data.test.images[ii,
...].reshape([1] + list(exp_config.image_size))
s_b = data.test.labels[ii, ...]
if np.sum(s_b) < 10:
print('WARNING: skipping cases with no structures')
continue
s_b_r = utils.convert_batch_to_onehot(s_b.transpose((2, 0, 1)),
exp_config.nlabels)
print('Plotting input image')
plt.figure()
x_b_d = preproc_image(x_b)
plt.imshow(x_b_d, cmap='gray')
plt.axis('off')
plt.savefig(os.path.join(outfolder, 'input_img_%d.png' % ii),
bbox_inches='tight')
print('Generating 100 samples')
s_p_list = []
for kk in range(100):
s_p_list.append(
segvae_model.predict_segmentation_sample(x_b,
return_softmax=True))
s_p_arr = np.squeeze(np.asarray(s_p_list))
print('Plotting %d of those samples' % n_samples)
for jj in range(n_samples):
s_p_sm = s_p_arr[jj, ...]
s_p_am = np.argmax(s_p_sm, axis=-1)
plt.figure()
s_p_d = preproc_image(s_p_am, nlabels=exp_config.nlabels)
plt.imshow(s_p_d, cmap='gray')
plt.axis('off')
plt.savefig(os.path.join(outfolder,
'sample_img_%d_samp_%d.png' % (ii, jj)),
bbox_inches='tight')
print('Plotting ground-truths masks')
for jj in range(s_b_r.shape[0]):
s_b_sm = s_b_r[jj, ...]
s_b_am = np.argmax(s_b_sm, axis=-1)
plt.figure()
s_p_d = preproc_image(s_b_am, nlabels=exp_config.nlabels)
plt.imshow(s_p_d, cmap='gray')
plt.axis('off')
plt.savefig(os.path.join(outfolder,
'gt_img_%d_samp_%d.png' % (ii, jj)),
bbox_inches='tight')
print('Generating error masks')
E_ss, E_sy_avg, E_yy_avg = generate_error_maps(s_p_arr, s_b_r)
print('Plotting them')
plt.figure()
plt.imshow(preproc_image(E_ss))
plt.axis('off')
plt.savefig(os.path.join(outfolder, 'E_ss_%d.png' % ii),
bbox_inches='tight')
print('Plotting them')
plt.figure()
plt.imshow(preproc_image(np.log(E_ss)))
plt.axis('off')
plt.savefig(os.path.join(outfolder, 'log_E_ss_%d.png' % ii),
bbox_inches='tight')
plt.figure()
plt.imshow(preproc_image(E_sy_avg))
plt.axis('off')
plt.savefig(os.path.join(outfolder, 'E_sy_avg_%d_.png' % ii),
bbox_inches='tight')
plt.figure()
plt.imshow(preproc_image(E_yy_avg))
plt.axis('off')
plt.savefig(os.path.join(outfolder, 'E_yy_avg_%d_.png' % ii),
bbox_inches='tight')
plt.close('all')
def main(model_path, exp_config, do_plots=False):
# Get Data
segvae_model = segvae(exp_config=exp_config)
segvae_model.load_weights(model_path, type=model_selection)
data_loader = data_switch(exp_config.data_identifier)
data = data_loader(exp_config)
# Run predictions in an endless loop
dice_list = []
num_samples = 1 if exp_config.likelihood is likelihoods.det_unet2D else 100
for ii, batch in enumerate(data.test.iterate_batches(1)):
if ii % 10 == 0:
logging.info("Progress: %d" % ii)
# print(ii)
x, y = batch
# Adding motion corrpution
# x = utils.add_motion_artefacts(np.squeeze(x), 15)
# x = x.reshape([1] + list(exp_config.image_size))
# Add box corruption
# x[:, 192 // 2 - 20:192 // 2 + 20, 192 // 2 - 5:192 // 2 + 5, :] = 0
y_ = np.squeeze(segvae_model.predict(x, num_samples=num_samples))
per_lbl_dice = []
per_pixel_preds = []
per_pixel_gts = []
if do_plots and not sys_config.running_on_gpu_host:
fig = plt.figure()
fig.add_subplot(131)
plt.imshow(np.squeeze(x), cmap='gray')
fig.add_subplot(132)
plt.imshow(np.squeeze(y_))
fig.add_subplot(133)
plt.imshow(np.squeeze(y))
plt.show()
for lbl in range(exp_config.nlabels):
binary_pred = (y_ == lbl) * 1
binary_gt = (y == lbl) * 1
if np.sum(binary_gt) == 0 and np.sum(binary_pred) == 0:
per_lbl_dice.append(1)
elif np.sum(binary_pred) > 0 and np.sum(binary_gt) == 0 or np.sum(
binary_pred) == 0 and np.sum(binary_gt) > 0:
logging.warning(
'Structure missing in either GT (x)or prediction. ASSD and HD will not be accurate.'
)
per_lbl_dice.append(0)
else:
per_lbl_dice.append(dc(binary_pred, binary_gt))
dice_list.append(per_lbl_dice)
per_pixel_preds.append(y_.flatten())
per_pixel_gts.append(y.flatten())
dice_arr = np.asarray(dice_list)
mean_per_lbl_dice = dice_arr.mean(axis=0)
logging.info('Dice')
logging.info(mean_per_lbl_dice)
logging.info(np.mean(mean_per_lbl_dice))
logging.info('foreground mean: %f' % (np.mean(mean_per_lbl_dice[1:])))
np.savez(os.path.join(model_path, 'dice_%s.npz' % model_selection),
dice_arr)
def main(model_path, exp_config):
# Make and restore vagan model
segvae_model = segvae(exp_config=exp_config)
segvae_model.load_weights(model_path, type='best_ged')
data_loader = data_switch(exp_config.data_identifier)
data = data_loader(exp_config)
lat_lvls = exp_config.latent_levels
# RANDOM IMAGE
# x_b, s_b = data.test.next_batch(1)
# FIXED IMAGE
# Cardiac: 100 normal image
# LIDC: 200 large lesion, 203, 1757 complicated lesion
# Prostate: 165 nice slice
index = 165 #
x_b = data.test.images[index,
...].reshape([1] + list(exp_config.image_size))
if exp_config.data_identifier == 'lidc':
s_b = data.test.labels[index, ...]
if np.sum(s_b[..., 0]) > 0:
s_b = s_b[..., 0]
elif np.sum(s_b[..., 1]) > 0:
s_b = s_b[..., 1]
elif np.sum(s_b[..., 2]) > 0:
s_b = s_b[..., 2]
else:
s_b = s_b[..., 3]
s_b = s_b.reshape([1] + list(exp_config.image_size[0:2]))
elif exp_config.data_identifier == 'uzh_prostate':
s_b = data.test.labels[index, ...]
s_b = s_b[..., 0]
s_b = s_b.reshape([1] + list(exp_config.image_size[0:2]))
else:
s_b = data.test.labels[index,
...].reshape([1] +
list(exp_config.image_size[0:2]))
#
# print(x_b.shape)
# print(s_b.shape)
# x_b[:,30:64+10,64:64+10,:] = np.mean(x_b)
#
# x_b = utils.add_motion_artefacts(np.squeeze(x_b), 15)
# x_b = x_b.reshape([1]+list(exp_config.image_size))
x_b_d = utils.convert_to_uint8(np.squeeze(x_b))
x_b_d = utils.resize_image(x_b_d, video_target_size)
s_b_d = np.squeeze(np.uint8((s_b / exp_config.nlabels) * 255))
s_b_d = utils.resize_image(s_b_d,
video_target_size,
interp=cv2.INTER_NEAREST)
_, mu_list_init, _ = segvae_model.generate_prior_samples(
x_b, return_params=True)
if SAVE_VIDEO:
fourcc = cv2.VideoWriter_fourcc(*'XVID')
outfile = os.path.join(model_path, 'samplevid_id%d.avi' % index)
out = cv2.VideoWriter(outfile, fourcc, 10.0,
(3 * video_target_size[1], video_target_size[0]))
for lvl in reversed(range(lat_lvls)):
samps = 50 if lat_lvls > 1 else 200
for _ in range(samps):
# z_list, mu_list, sigma_list = segvae_model.generate_prior_samples(x_b, return_params=True)
print('doing level %d/%d' % (lvl, lat_lvls))
# fix all below current level
# for jj in range(lvl,lat_lvls-1):
# z_list[jj+1] = mu_list_init[jj+1] # fix jj's level to mu
# sample only current level
# z_list_new = z_list.copy()
# for jj in range(lat_lvls):
# z_list_new[jj] = mu_list_init[jj]
# z_list_new[lvl] = z_list[lvl]
# z_list = z_list_new
#
# print('z means')
# for jj, z in enumerate(z_list):
# print('lvl %d: %.3f' % (jj, np.mean(z)))
#
#
# feed_dict = {i: d for i, d in zip(segvae_model.prior_z_list_gen, z_list)}
# feed_dict[segvae_model.training_pl] = False
#
# fix all below current level (the correct implementation)
feed_dict = {}
for jj in range(lvl, lat_lvls - 1):
feed_dict[segvae_model.prior_z_list_gen[jj +
1]] = mu_list_init[jj +
1]
feed_dict[segvae_model.training_pl] = False
feed_dict[segvae_model.x_inp] = x_b
s_p, s_p_list = segvae_model.sess.run(
[segvae_model.s_out_eval, segvae_model.s_out_eval_list],
feed_dict=feed_dict)
s_p = np.argmax(s_p, axis=-1)
print(np.unique(s_p))
# print('mean logits for myo cardium per level')
# fig = plt.figure()
#
# cumsum = np.zeros((128,128))
# cumsum_all = np.zeros((128,128,4))
# for i, s in enumerate(reversed(s_p_list)):
#
# cumsum += s[0,:,:,2]
# cumsum_all += s[0,:,:,:]
#
# fig.add_subplot(4,4,i+1)
# plt.imshow(s[0,:,:,2])
#
# fig.add_subplot(4,4,i+1+4)
# plt.imshow(cumsum)
#
# fig.add_subplot(4,4,i+1+8)
# plt.imshow(1./(1+np.exp(-cumsum)))
#
# fig.add_subplot(4,4,i+1+12)
# plt.imshow(np.argmax(cumsum_all, axis=-1))
#
#
# plt.show()
# DEUBG
# cum_img = np.squeeze(s_p_list[lat_lvls-1])
# cum_img_disp = softmax(cum_img)
#
# indiv_img = np.squeeze(s_p_list[lat_lvls-1])
# indiv_img_disp = softmax(indiv_img)
#
# for ii in reversed(range(lat_lvls-1)):
# cum_img += np.squeeze(s_p_list[ii])
# indiv_img = np.squeeze(s_p_list[ii])
#
# cum_img_disp = np.concatenate([cum_img_disp, softmax(cum_img)], axis=1)
# indiv_img_disp = np.concatenate([indiv_img_disp, softmax(indiv_img)], axis=1)
#
#
# cum_img_disp = utils.convert_to_uint8(np.argmax(cum_img_disp, axis=-1))
# indiv_img_disp = utils.convert_to_uint8(indiv_img_disp[:,:,2])
#
# cum_img_disp = np.concatenate([cum_img_disp, indiv_img_disp], axis=0)
#
#
# print('cum img shape')
# print(cum_img_disp.shape)
# cv2.imshow('debug', cum_img_disp)
# END DEBUG
# s_p_d = utils.convert_to_uint8(np.squeeze(s_p))
s_p_d = np.squeeze(np.uint8((s_p / exp_config.nlabels) * 255))
s_p_d = utils.resize_image(s_p_d,
video_target_size,
interp=cv2.INTER_NEAREST)
img = np.concatenate([x_b_d, s_b_d, s_p_d], axis=1)
img = cv2.cvtColor(img, cv2.COLOR_GRAY2BGR)
img = histogram_equalization(img)
if exp_config.data_identifier == 'acdc':
# labels (0 85 170 255)
rv = cv2.inRange(s_p_d, 84, 86)
my = cv2.inRange(s_p_d, 169, 171)
rv_cnt, hierarchy = cv2.findContours(rv, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
my_cnt, hierarchy = cv2.findContours(my, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
cv2.drawContours(img, rv_cnt, -1, (0, 255, 0), 1)
cv2.drawContours(img, my_cnt, -1, (0, 0, 255), 1)
if exp_config.data_identifier == 'uzh_prostate':
# labels (0 85 170 255)
print(np.unique(s_p_d))
s1 = cv2.inRange(s_p_d, 84, 86)
s2 = cv2.inRange(s_p_d, 169, 171)
# s3 = cv2.inRange(s_p_d, 190, 192)
s1_cnt, hierarchy = cv2.findContours(s1, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
s2_cnt, hierarchy = cv2.findContours(s2, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
# s3_cnt, hierarchy = cv2.findContours(s3, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
cv2.drawContours(img, s1_cnt, -1, (0, 255, 0), 1)
cv2.drawContours(img, s2_cnt, -1, (0, 0, 255), 1)
# cv2.drawContours(img, s3_cnt, -1, (255, 0, 255), 1)
elif exp_config.data_identifier == 'lidc':
thresh = cv2.inRange(s_p_d, 127, 255)
lesion, hierarchy = cv2.findContours(thresh, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
cv2.drawContours(img, lesion, -1, (0, 255, 0), 1)
font = cv2.FONT_HERSHEY_SIMPLEX
cv2.putText(img, 'Sampling level %d/%d' % (lvl + 1, lat_lvls),
(30, 256 - 30), font, 1, (255, 255, 255), 1,
cv2.LINE_AA)
print('actual size')
print(img.shape)
if SAVE_VIDEO:
out.write(img)
cv2.imshow('frame', img)
if cv2.waitKey(1) & 0xFF == ord('q'):
break
if SAVE_VIDEO:
out.release()
cv2.destroyAllWindows()
