def AverageSurfaceDist(pred, gt, replace_NaN=100):
ASD = {}
bg_asd = asd(pred == 0, gt == 0)
if 1 in np.unique(pred):
csf_asd = asd(pred == 1, gt == 1)
else:
csf_asd = replace_NaN
if 2 in np.unique(pred):
gm_asd = asd(pred == 2, gt == 2)
else:
gm_asd = replace_NaN
if 3 in np.unique(pred):
wm_asd = asd(pred == 3, gt == 3)
else:
wm_asd = replace_NaN
if 4 in np.unique(pred):
tm_asd = asd(pred == 4, gt == 4)
else:
tm_asd = replace_NaN
ASD['avg'] = (csf_asd + gm_asd + wm_asd + tm_asd) / 4
ASD['bg'] = bg_asd
ASD['csf'] = csf_asd
ASD['gm'] = gm_asd
ASD['wm'] = wm_asd
ASD['tm'] = tm_asd
return ASD
def update_eval_metrics(preds, labels, eval_metrics):
if len(labels.shape) == 2:
preds = np.expand_dims(preds, axis=0)
labels = np.expand_dims(labels, axis=0)
N = labels.shape[0]
for i in range(N):
pred = preds[i, :, :]
label = labels[i, :, :]
eval_metrics['dice score'].append(dc(pred, label))
eval_metrics['precision'].append(precision(pred, label))
eval_metrics['recall'].append(recall(pred, label))
eval_metrics['sensitivity'].append(sensitivity(pred, label))
eval_metrics['specificity'].append(specificity(pred, label))
if np.sum(pred) > 0 and np.sum(label) > 0:
eval_metrics['hausdorff'].append(hd(pred, label))
eval_metrics['hausdorff 95%'].append(hd95(pred, label))
eval_metrics['asd'].append(asd(pred, label))
eval_metrics['assd'].append(assd(pred, label))
eval_metrics['jaccard'].append(jc(pred, label))
else:
eval_metrics['hausdorff'].append('nan')
eval_metrics['hausdorff 95%'].append('nan')
eval_metrics['asd'].append('nan')
eval_metrics['assd'].append('nan')
eval_metrics['jaccard'].append('nan')
return eval_metrics
def metrics2(img_gt, img_pred, apply_hd=False, apply_asd=False):
"""
evaluate the models on mmwhs data in batches
:param img_gt: the ground truth
:param img_pred: the prediction
:param apply_hd: whether to evaluate Hausdorff Distance
:param apply_asd: whether to evaluate Average Surface Distance
:return:
"""
if img_gt.ndim != img_pred.ndim:
raise ValueError("The arrays 'img_gt' and 'img_pred' should have the "
"same dimension, {} against {}".format(img_gt.ndim,
img_pred.ndim))
res = {}
class_name = ["myo", "la", "lv", "aa"]
# Loop on each classes of the input images
for c, cls_name in zip([1, 2, 3, 4], class_name) :
gt_c_i = np.where(img_gt == c, 1, 0)
pred_c_i = np.where(img_pred == c, 1, 0)
# Compute the Dice
dice = dc(gt_c_i, pred_c_i)
h_d, a_sd = 0, 0
if apply_hd:
h_d = hd(gt_c_i, pred_c_i)
if apply_asd:
a_sd = asd (gt_c_i, pred_c_i)
res[cls_name] = [dice, h_d, a_sd]
return res
def asd(predictions, labels, num_classes):
"""Calculates the categorical Dice similarity coefficients for each class
between labels and predictions.
Args:
predictions (np.ndarray): predictions
labels (np.ndarray): labels
num_classes (int): number of classes to calculate the dice
coefficient for
Returns:
np.ndarray: dice coefficient per class
"""
dice_scores = np.zeros((num_classes))
import SimpleITK as sitk
p = sitk.GetImageFromArray(predictions.astype(np.uint8))
l = sitk.GetImageFromArray(labels.astype(np.uint8))
for i in range(num_classes):
lTestImage = sitk.BinaryThreshold(p, i, i, 1, 0)
lResultImage = sitk.BinaryThreshold(l, i, i, 1, 0)
pT = sitk.GetArrayFromImage(lTestImage)
lT = sitk.GetArrayFromImage(lResultImage)
from medpy.metric.binary import asd
asd_value = asd(pT, lT)
dice_scores[i] = asd_value
return dice_scores.astype(np.float32)
def metrics(img_gt, img_pred, ifhd=True, ifasd=True):
from medpy.metric.binary import hd, dc, asd
if img_gt.ndim != img_pred.ndim:
raise ValueError("The arrays 'img_gt' and 'img_pred' should have the "
"same dimension, {} against {}".format(
img_gt.ndim, img_pred.ndim))
res = []
cat = {'Myo', 'LA-blood', 'LV-blood', 'AA'}
for c in range(len(cat)):
# Copy the gt image to not alterate the input
gt_c_i = np.where(img_gt == c + 1, 1, 0)
# Copy the pred image to not alterate the input
pred_c_i = np.where(img_pred == c + 1, 1, 0)
# Clip the value to compute the volumes
gt_c_i = np.clip(gt_c_i, 0, 1)
pred_c_i = np.clip(pred_c_i, 0, 1)
# Compute the Dice
dice = dc(gt_c_i, pred_c_i)
try:
h_d = hd(gt_c_i, pred_c_i) if ifhd else -1
except:
h_d = -1
try:
a_sd = asd(gt_c_i, pred_c_i) if ifasd else -1
except:
a_sd = -1
res += [dice, h_d, a_sd]
return res
def channelwise_asd(pred, target):
""" calculate channel-wise average symmetric surface distance """
max_asd = 2 * target.shape[1]
channel_res = []
for c_inx in range(0, len(pred)):
if np.sum(target[c_inx]) != 0:
if np.sum(pred[c_inx]) == 0:
res = max_asd
else:
res = asd(pred[c_inx], target[c_inx])
channel_res.append(res)
mean_asd = sum(channel_res) / len(channel_res)
return mean_asd
def evaluate(img_gt, img_pred, apply_hd=False, apply_asd=False):
"""
Function to compute the metrics between two segmentation maps given as input.
:param img_gt: Array of the ground truth segmentation map.
:param img_pred: Array of the predicted segmentation map.
:param apply_hd: whether to compute Hausdorff Distance.
:param apply_asd: Whether to compute Average Surface Distance.
:return: A list of metrics in this order, [dice myo, hd myo, asd myo, dice lv, hd lv asd lv, dice rv, hd rv, asd rv]
"""
if img_gt.ndim != img_pred.ndim:
raise ValueError("The arrays 'img_gt' and 'img_pred' should have the "
"same dimension, {} against {}".format(img_gt.ndim,
img_pred.ndim))
res = {}
class_name = ["myo", "lv", "rv"]
# Loop on each classes of the input images
for c, cls_name in zip([1, 2, 3], class_name) :
# Copy the gt image to not alterate the input
gt_c_i = np.copy(img_gt)
gt_c_i[gt_c_i != c] = 0
# Copy the pred image to not alterate the input
pred_c_i = np.copy(img_pred)
pred_c_i[pred_c_i != c] = 0
# Clip the value to compute the volumes
gt_c_i = np.clip(gt_c_i, 0, 1)
pred_c_i = np.clip(pred_c_i, 0, 1)
# Compute the Dice
dice = dc(gt_c_i, pred_c_i)
h_d, a_sd = 0, 0
if apply_hd:
h_d = hd(gt_c_i, pred_c_i)
if apply_asd:
a_sd = asd (gt_c_i, pred_c_i)
# Compute volume
res[cls_name] = [dice, h_d, a_sd]
return res
def metrics(img_gt, img_pred, ifhd=True, ifasd=True):
"""
Function to compute the metrics between two segmentation maps given as input.
img_gt: Array of the ground truth segmentation map.
img_pred: Array of the predicted segmentation map.
Return: A list of metrics in this order, [Dice endo, HD endo, ASD endo, Dice RV, HD RV, ASD RV, Dice MYO, HD MYO, ASD MYO]
"""
if img_gt.ndim != img_pred.ndim:
raise ValueError("The arrays 'img_gt' and 'img_pred' should have the "
"same dimension, {} against {}".format(img_gt.ndim,
img_pred.ndim))
res = []
# cat = {500: 'endo', 600: 'rv', 200: 'myo'}
for c in [500, 600, 200]:
# Copy the gt image to not alterate the input
gt_c_i = np.copy(img_gt)
gt_c_i[gt_c_i != c] = 0
# Copy the pred image to not alterate the input
pred_c_i = np.copy(img_pred)
pred_c_i[pred_c_i != c] = 0
# Clip the value to compute the volumes
gt_c_i = np.clip(gt_c_i, 0, 1)
pred_c_i = np.clip(pred_c_i, 0, 1)
# Compute the Dice
dice = dc(gt_c_i, pred_c_i)
h_d, a_sd = -1, -1
if ifhd or ifasd:
if np.sum(gt_c_i) == 0 or np.sum(pred_c_i) == 0:
dice = -1
h_d = -1
a_sd = -1
else:
h_d = hd(gt_c_i, pred_c_i) if ifhd else h_d
a_sd = asd(gt_c_i, pred_c_i) if ifasd else a_sd
res += [dice, h_d, a_sd]
return res
def slicewise_asd(pred, target, n_classes=3):
""" calculate slice-wise average symmetric surface distance
:param pred: ndarray with size [H, W], predicted bound
:param target: ndarray with size [H, W], ground truth
:param n_classes: int, # of classes
"""
slice_res = []
max_asd = 2 * target.shape[0]
for c_inx in range(1, n_classes):
pred_cinx = (pred == c_inx)
target_cinx = (target == c_inx)
if np.sum(target_cinx) != 0:
if np.sum(pred_cinx) == 0:
res = max_asd
else:
res = asd(pred_cinx, target_cinx)
slice_res.append(res)
mean_res = sum(slice_res) / len(slice_res)
return mean_res
def compute_scores(preds, labels):
preds_data = preds.data.cpu().numpy()
labels_data = labels.data.cpu().numpy()
dice_score = dc(preds_data, labels_data)
jaccard_coef = jc(preds_data, labels_data)
hausdorff_dist = hd(preds_data, labels_data)
asd_score = asd(preds_data, labels_data)
assd_score = assd(preds_data, labels_data)
precision_value = precision(preds_data, labels_data)
recall_value = recall(preds_data, labels_data)
sensitivity_value = sensitivity(preds_data, labels_data)
specificity_value = specificity(preds_data, labels_data)
return {
'dice score': dice_score,
'jaccard': jaccard_coef,
'hausdorff': hausdorff_dist,
'asd': asd_score,
'assd': assd_score,
'precision': precision_value,
'recall': recall_value,
'sensitivity': sensitivity_value,
'specificity': specificity_value
}
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--model-file', type=str, default='./logs/test1/20190506_221021.177567/checkpoint_200.pth.tar', help='Model path')
parser.add_argument('--datasetTest', type=list, default=[1], help='test folder id contain images ROIs to test')
parser.add_argument('--dataset', type=str, default='test', help='test folder id contain images ROIs to test')
parser.add_argument('-g', '--gpu', type=int, default=0)
parser.add_argument('--data-dir', default='../../../../Dataset/Fundus/', help='data root path')
parser.add_argument('--out-stride', type=int, default=16, help='out-stride of deeplabv3+',)
parser.add_argument('--sync-bn', type=bool, default=False, help='sync-bn in deeplabv3+')
parser.add_argument('--freeze-bn', type=bool, default=False, help='freeze batch normalization of deeplabv3+')
parser.add_argument('--movingbn', type=bool, default=False, help='moving batch normalization of deeplabv3+ in the test phase',)
parser.add_argument('--test-prediction-save-path', type=str, default='./results/rebuttle-0401/', help='Path root for test image and mask')
args = parser.parse_args()
os.environ['CUDA_VISIBLE_DEVICES'] = str(args.gpu)
model_file = args.model_file
output_path = os.path.join(args.test_prediction_save_path, 'test' + str(args.datasetTest[0]), args.model_file.split('/')[-2])
# 1. dataset
composed_transforms_test = transforms.Compose([
tr.Normalize_tf(),
tr.ToTensor()
])
db_test = DL.FundusSegmentation(base_dir=args.data_dir, phase='test', splitid=args.datasetTest,
transform=composed_transforms_test, state='prediction')
batch_size = 12
test_loader = DataLoader(db_test, batch_size=batch_size, shuffle=False, num_workers=1)
# 2. model
model = DeepLab(num_classes=2, backbone='mobilenet', output_stride=args.out_stride,
sync_bn=args.sync_bn, freeze_bn=args.freeze_bn).cuda()
if torch.cuda.is_available():
model = model.cuda()
print('==> Loading %s model file: %s' %
(model.__class__.__name__, model_file))
# model_data = torch.load(model_file)
checkpoint = torch.load(model_file)
pretrained_dict = checkpoint['model_state_dict']
model_dict = model.state_dict()
# 1. filter out unnecessary keys
pretrained_dict = {k: v for k, v in pretrained_dict.items() if k in model_dict}
# 2. overwrite entries in the existing state dict
model_dict.update(pretrained_dict)
# 3. load the new state dict
model.load_state_dict(model_dict)
if args.movingbn:
model.train()
else:
model.eval()
val_cup_dice = 0.0
val_disc_dice = 0.0
total_hd_OC = 0.0
total_hd_OD = 0.0
total_asd_OC = 0.0
total_asd_OD = 0.0
timestamp_start = datetime.now(pytz.timezone('Asia/Hong_Kong'))
total_num = 0
OC = []
OD = []
for batch_idx, (sample) in tqdm.tqdm(enumerate(test_loader),total=len(test_loader),ncols=80, leave=False):
data = sample['image']
target = sample['label']
img_name = sample['img_name']
if torch.cuda.is_available():
data, target = data.cuda(), target.cuda()
data, target = Variable(data), Variable(target)
prediction, dc, sel, _ = model(data)
prediction = torch.nn.functional.interpolate(prediction, size=(target.size()[2], target.size()[3]), mode="bilinear")
data = torch.nn.functional.interpolate(data, size=(target.size()[2], target.size()[3]), mode="bilinear")
target_numpy = target.data.cpu()
imgs = data.data.cpu()
hd_OC = 100
asd_OC = 100
hd_OD = 100
asd_OD = 100
for i in range(prediction.shape[0]):
prediction_post = postprocessing(prediction[i], dataset=args.dataset)
cup_dice, disc_dice = dice_coeff_2label(prediction_post, target[i])
OC.append(cup_dice)
OD.append(disc_dice)
if np.sum(prediction_post[0, ...]) < 1e-4:
hd_OC = 100
asd_OC = 100
else:
hd_OC = binary.hd95(np.asarray(prediction_post[0, ...], dtype=np.bool),
np.asarray(target_numpy[i, 0, ...], dtype=np.bool))
asd_OC = binary.asd(np.asarray(prediction_post[0, ...], dtype=np.bool),
np.asarray(target_numpy[i, 0, ...], dtype=np.bool))
if np.sum(prediction_post[0, ...]) < 1e-4:
hd_OD = 100
asd_OD = 100
else:
hd_OD = binary.hd95(np.asarray(prediction_post[1, ...], dtype=np.bool),
np.asarray(target_numpy[i, 1, ...], dtype=np.bool))
asd_OD = binary.asd(np.asarray(prediction_post[1, ...], dtype=np.bool),
np.asarray(target_numpy[i, 1, ...], dtype=np.bool))
val_cup_dice += cup_dice
val_disc_dice += disc_dice
total_hd_OC += hd_OC
total_hd_OD += hd_OD
total_asd_OC += asd_OC
total_asd_OD += asd_OD
total_num += 1
for img, lt, lp in zip([imgs[i]], [target_numpy[i]], [prediction_post]):
img, lt = utils.untransform(img, lt)
save_per_img(img.numpy().transpose(1, 2, 0),
output_path,
img_name[i],
lp, lt, mask_path=None, ext="bmp")
print('OC:', OC)
print('OD:', OD)
import csv
with open('Dice_results.csv', 'a+') as result_file:
wr = csv.writer(result_file, dialect='excel')
for index in range(len(OC)):
wr.writerow([OC[index], OD[index]])
val_cup_dice /= total_num
val_disc_dice /= total_num
total_hd_OC /= total_num
total_asd_OC /= total_num
total_hd_OD /= total_num
total_asd_OD /= total_num
print('''\n==>val_cup_dice : {0}'''.format(val_cup_dice))
print('''\n==>val_disc_dice : {0}'''.format(val_disc_dice))
print('''\n==>average_hd_OC : {0}'''.format(total_hd_OC))
print('''\n==>average_hd_OD : {0}'''.format(total_hd_OD))
print('''\n==>ave_asd_OC : {0}'''.format(total_asd_OC))
print('''\n==>average_asd_OD : {0}'''.format(total_asd_OD))
with open(osp.join(output_path, '../test' + str(args.datasetTest[0]) + '_log.csv'), 'a') as f:
elapsed_time = (
datetime.now(pytz.timezone('Asia/Hong_Kong')) -
timestamp_start).total_seconds()
log = [['batch-size: '] + [batch_size] + [args.model_file] + ['cup dice coefficence: '] + \
[val_cup_dice] + ['disc dice coefficence: '] + \
[val_disc_dice] + ['average_hd_OC: '] + \
[total_hd_OC] + ['average_hd_OD: '] + \
[total_hd_OD] + ['ave_asd_OC: '] + \
[total_asd_OC] + ['average_asd_OD: '] + \
[total_asd_OD] + [elapsed_time]]
log = map(str, log)
f.write(','.join(log) + '\n')
def main(_):
if not FLAGS.dataset_dir:
raise ValueError('You must supply the dataset directory with --dataset_dir')
tf.logging.set_verbosity(tf.logging.INFO)
with tf.Graph().as_default():
tf_global_step = slim.get_or_create_global_step()
######################
# Gnerate the tfRecorder data #
######################
datareader,Volshape,rindex,spmap,labelOrg,imgOrg=EvalSample_Gnerate(FLAGS.dataset_dir, 'Glabel.nrrd')
Patchsize=len(rindex)
######################
# Select the dataset #
######################
dataset = dataset_factory.get_dataset(
FLAGS.dataset_name, FLAGS.dataset_split_name, FLAGS.dataset_dir,file_pattern=FLAGS.file_name,Datasize=Patchsize)
####################
# Select the model #
####################
#num_classes=2
with tf.Graph().as_default():
network_fn = nets_factory.get_network_fn(
FLAGS.model_name,
num_classes=(dataset.num_classes - FLAGS.labels_offset),
is_training=False)
##############################################################
# Create a dataset provider that loads data from the dataset #
##############################################################
provider = slim.dataset_data_provider.DatasetDataProvider(
dataset,
shuffle=False,
common_queue_capacity=2 * FLAGS.batch_size,
common_queue_min=FLAGS.batch_size)
[image, label] = provider.get(['image', 'label'])
# label -= FLAGS.labels_offset
#####################################
# Select the preprocessing function #
#####################################
preprocessing_name = FLAGS.preprocessing_name or FLAGS.model_name
image_preprocessing_fn = preprocessing_factory.get_preprocessing(
preprocessing_name,
is_training=False)
eval_image_size = FLAGS.eval_image_size or network_fn.default_image_size
image = image_preprocessing_fn(image, eval_image_size, eval_image_size)
images, labels = tf.train.batch(
[image, label],
batch_size=FLAGS.batch_size,
num_threads=FLAGS.num_preprocessing_threads,
capacity=5 * FLAGS.batch_size)
###################
# Define the model #
####################
logits, end_points = network_fn(images)
probabilities = tf.nn.softmax(logits)
pred = tf.argmax(logits, dimension=1)
# if FLAGS.moving_average_decay:
# variable_averages = tf.train.ExponentialMovingAverage(
# FLAGS.moving_average_decay, tf_global_step)
# variables_to_restore = variable_averages.variables_to_restore(
# slim.get_model_variables())
# variables_to_restore[tf_global_step.op.name] = tf_global_step
# else:
# variables_to_restore = slim.get_variables_to_restore()
# #predictions = tf.argmax(logits, 1)
# labels = tf.squeeze(labels)
#
# # Define the metrics:
# names_to_values, names_to_updates = slim.metrics.aggregate_metric_map({
# 'Accuracy': slim.metrics.streaming_accuracy(predictions, labels),
# 'Recall@5': slim.metrics.streaming_recall_at_k(
# logits, labels, 5),
# })
#
# # Print the summaries to screen.
# summary_ops = []
# for name, value in names_to_values.items():
# summary_name = 'eval/%s' % name
# op = tf.scalar_summary(summary_name, value, collections=[])
# op = tf.Print(op, [value], summary_name)
# tf.add_to_collection(tf.GraphKeys.SUMMARIES, op)
# summary_ops.append(op)
# # TODO(sguada) use num_epochs=1
# if FLAGS.max_num_batches:
# num_batches = FLAGS.max_num_batches
# else:
# # This ensures that we make a single pass over all of the data.
# num_batches = math.ceil(dataset.num_samples / float(FLAGS.batch_size))
if tf.gfile.IsDirectory(FLAGS.checkpoint_path):
checkpoint_path = tf.train.latest_checkpoint(FLAGS.checkpoint_path)
else:
checkpoint_path = FLAGS.checkpoint_path
tf.logging.info('Evaluating %s' % checkpoint_path)
init_fn = slim.assign_from_checkpoint_fn(
os.path.join(checkpoint_path),
slim.get_model_variables())# vriable name???
#Volshape=(50,61,61)
imgshape=spmap.shape
segResult=np.zeros(imgshape)
groundtruth=np.zeros(imgshape)
segPromap=np.zeros(imgshape)
segPromapEdge=np.zeros(imgshape)
PreMap=[]
labellist=[]
seglist=[]
conv1list=[]
conv2list=[]
imgorglist=[]
fclist=[]
with tf.Session() as sess:
# Load weights
init_fn(sess)
# sess.run(images.initializer, feed_dict)
# Start input enqueue threads.
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
num_iter = int(math.ceil(dataset.num_samples/float(FLAGS.batch_size)))
step = 0
try:
while step < num_iter and not coord.should_stop():
# Run evaluation steps or whatever
segmentation,log,pmap,labelmap,imgpre,conv1,conv2,fc3= sess.run([pred,logits,probabilities,labels,images,end_points['conv1'],end_points['conv3'],end_points['fc3']])
step+=1
PreMap.extend(pmap)
conv1list.extend(conv1)
conv2list.extend(conv2)
fclist.extend(fc3)
imgorglist.extend(imgpre)
seglist.append(segmentation)
labellist.append(labelmap)
print('The No. %d/%d caculation'%(step,num_iter))
#Miaimshow.subplots(Pro_imgs, num=step+2, cols=8)
except tf.errors.OutOfRangeError:
print('Done evalutaion -- epoch limit reached')
finally:
# When done, ask the threads to stop.
coord.request_stop()
PreMap = np.array(PreMap)
np.save(os.path.join(FLAGS.dataset_dir,'liverspProbmap.npy'), PreMap)
# PreMap=np.squeeze(PreMap,axis=1)
# PreMap_flat = PreMap.ravel()
# PreMap_flat=np.divide((PreMap_flat - np.amin(PreMap_flat)) * 255, (np.amax(PreMap_flat) - np.amin(PreMap_flat)))
m = 0
for i in range(len(rindex)):
segResult[spmap==rindex[i]]=np.array(seglist).ravel()[i]
segPromap[spmap==rindex[i]]=PreMap[i,1]
segPromapEdge[spmap==rindex[i]]=PreMap[i,2]
groundtruth[spmap==rindex[i]]=np.array(labellist).ravel()[i]
coord.join(threads)
fig,ax= plt.subplots(nrows=2,ncols=3)
from skimage.segmentation import mark_boundaries
ax[0,0].set_title('Segmentation with superpixel map')
ax[0,0].imshow(mark_boundaries(segResult, spmap))
ax[0,1].set_title('Segmentation with ground truth map')
ax[0,1].imshow(segResult)
ax[0,1].imshow(labelOrg,alpha=0.5,cmap='jet')
ax[0,2].set_title('Reading label')
ax[0,2].imshow(groundtruth)
ax[1,0].set_title('liver Probabilities map')
ax[1,0].imshow(segPromap)
ax[1,1].set_title('edge Probabilities map')
ax[1,1].imshow(segPromapEdge)
ax[1,2].set_title('liver +edge Probabilities map')
ax[1,2].imshow(segPromapEdge+segPromap)
segthpro=segPromapEdge+segPromap
segthpro[segthpro<0.8]=0
from skimage.segmentation import active_contour
from skimage.measure import find_contours
from skimage.filters import gaussian
from skimage import morphology
#edg=sobel(segResult.astype(int))
segmorp=morphology.remove_small_objects(segthpro.astype(bool),5000)
segopen=morphology.opening(segmorp,morphology.disk(3))
segclose=morphology.closing(segopen,morphology.disk(15))
fig,ax=plt.subplots(1,3)
ax=ax.ravel()
ax[0].imshow(segmorp)
ax[0].set_title('Removed the small objects')
ax[1].imshow(segopen)
ax[1].set_title('After open operation')
ax[2].imshow(segclose)
ax[2].imshow(labelOrg,alpha=0.5,cmap='jet')
ax[2].set_title('After close operation')
plt.axis('off')
from MiaUtils import Miametrics as metric
mt=metric.MiaMetrics(logger)
dsc=mt.DSCMetric(segclose,labelOrg.astype(bool))
print('The dice similarity coefficient score is {}'.format(dsc))
voe=mt.VOEMetric(segclose,labelOrg.astype(bool))
print('The Volume overlap Error score is {}'.format(voe))
rvd=mt.RVDMetric(segclose,labelOrg.astype(bool))
print('The Relative voume difference score is {}'.format(rvd))
from medpy.metric.binary import hd
from medpy.metric.binary import asd
from medpy.metric.binary import obj_fpr
from medpy.metric.binary import obj_tpr
Asd=asd(segclose,labelOrg.astype(bool))
print('The Asd score is {}'.format(Asd))
HD=hd(segclose,labelOrg.astype(bool))
print('The Hausdorff Distance score is {}'.format(HD))
###************************************************************************
####superpixel-graph cuts mehtod computation
#######********************************************************************
from skimage import segmentation, color,filters
from skimage.future import graph
img=DataNormalize(imgOrg)/255
img=np.dstack((np.dstack((img, img)), img))
labels1 = segmentation.slic(img, compactness=5, n_segments=2000,sigma=1)
#labels1=spmap
out1 = color.label2rgb(labels1, img, kind='avg')
edge_map = filters.sobel(color.rgb2gray(img))
g = graph.rag_boundary(labels1, edge_map)
#g = graph.rag_mean_color(img, labels1, mode='similarity')
labels2 = graph.cut_normalized(labels1, g)
out2 = color.label2rgb(labels2, img, kind='avg')
fig, ax = plt.subplots(nrows=2, sharex=True, sharey=True)
ax[0].imshow(out1)
ax[1].imshow(out2)
for a in ax:
a.axis('off')
plt.tight_layout()
