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 get_outputs(seg, seg_truth):
print seg.shape, seg_truth.shape
seg_thresh = utility.threshold(seg,THRESHOLD)
print seg_thresh.shape
contour = utility.listSegToContours(seg_thresh, meta_test[1,:],
meta_test[0,:], ISOVALUE)
errs = utility.listAreaOverlapError(contour, contours_test)
thresh,ts = utility.cum_error_dist(errs,DX)
roc = roc_curve(np.ravel(seg_truth),np.ravel(seg), pos_label=1)
pr = precision_recall_curve(np.ravel(seg_truth),np.ravel(seg), pos_label=1)
dorf = []
emd = []
asdl = []
dice = []
prec = []
for i in range(len(seg_truth)):
if np.sum(seg_thresh[i,:,:]) > 0.1 and np.sum(seg_truth[i,:,:,0]) > 0.1:
e= hd(seg_thresh[i,:,:],seg_truth[i,:,:,0],meta_test[0,i][0])
dorf.append(e)
e_asd= assd(seg_thresh[i,:,:],seg_truth[i,:,:,0],meta_test[0,i][0])
asdl.append(e_asd)
# if np.sum(seg_thresh[i,:,:]) < 600 and np.sum(seg_truth[i,:,:,0]) < 600:
# print i,np.sum(seg_thresh[i,:,:]),np.sum(seg_truth[i,:,:,0])
# e_emd = utility.EMDSeg(seg_truth[i,:,:,0],seg_thresh[i,:,:], meta_test[0,i][0])
# emd.append(e_emd)
edc = dc(seg_thresh[i,:,:],seg_truth[i,:,:,0])
dice.append(edc)
prec.append(precision(seg_thresh[i,:,:],seg_truth[i,:,:,0]))
acc,mean_acc = calc_accuracy(seg, seg_truth)
return (contour,errs,thresh,roc,pr,acc,mean_acc,dorf,dice, prec,asdl)
def binary_measures_numpy(result, target, binary_threshold=0.5):
result_binary = (result > binary_threshold).astype(numpy.uint8)
target_binary = (target > binary_threshold).astype(numpy.uint8)
result = BinaryMeasuresDto(mpm.dc(result_binary, target_binary), numpy.Inf,
numpy.Inf,
mpm.precision(result_binary, target_binary),
mpm.sensitivity(result_binary, target_binary),
mpm.specificity(result_binary, target_binary))
if result_binary.any() and target_binary.any():
result.hd = mpm.hd(result_binary, target_binary)
result.assd = mpm.assd(result_binary, target_binary)
return result
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
}
# ratio = non_zero_count / (lab.shape[0] * lab.shape[1])
# print(ratio)
input = Variable(
torch.from_numpy(img).type('torch.FloatTensor').cuda(gpu_id))
res = fcn(input).detach().cpu().numpy()
# res =res/res.max()
# res = (res-1)/res.max()
ret, res = cv2.threshold(res[0, 0, :, :], 0.8, 1, cv2.THRESH_BINARY)
# res = res[0,0,:,:]
dice = dc(lab, res)
jaccard = jc(lab, res)
sens = sensitivity(lab, res)
spec = specificity(lab, res)
pres = precision(lab, res)
rec = recall(lab, res)
print('dice:', dice)
print('jaccad:', jaccard)
print('sensitivity:', sens)
print('precision:', pres)
dc_list.append(dice)
jc_list.append(jaccard)
sens_list.append(sens)
spec_list.append(spec)
pres_list.append(pres)
recall_list.append(rec)
print('average dice:', sum(dc_list) / len(dc_list))
def calculate_precision():
dictindex = []
global prec
with open('./label.txt') as f:
content = f.readlines()
for symbol in content:
symbol = symbol.replace('\n', '')
split = symbol.split(' ')
dictindex.append(split[0])
print('\nPrecision')
net.eval()
global dice_score
global ite
target_boxes = testset.boxes
target_labels = testset.labels
for batch_idx, (images, loc_targets,
conf_targets) in enumerate(testloader):
if use_cuda:
images = images.cuda()
loc_targets = loc_targets.cuda()
conf_targets = conf_targets.cuda()
images = Variable(images, volatile=True)
loc_preds, conf_preds = net(images)
data_encoder = DataEncoder()
conf_preds_list = []
for i in range(batch_size):
s_conf = F.softmax(conf_preds[i]).data
conf_preds_list.append(s_conf)
try:
boxes, labels, scores = data_encoder.decodeforbatch(
loc_preds.data, conf_preds_list)
for b_id in range(batch_size):
predict_res = find_boxescoreslabel(labels[b_id], boxes[b_id])
target_res = find_boxescoreslabel(
target_labels[b_id + batch_idx * batch_size],
target_boxes[b_id + batch_idx * batch_size], False)
# pdb.set_trace()'
print('[I %d]:' % (batch_idx))
for box_id in range(len(predict_res)):
# pdb.set_trace()
t_label = [item[0] for item in target_res]
la = predict_res[box_id][0]
if la in t_label:
predict_img = create_binaryImageforPrec(
predict_res[box_id][1])
# pdb.set_trace()
# imgg = Image.fromarray(predict_img)
# imgg.show()
target_img = create_binaryImageforPrec(
target_res[t_label.index(la)][1], False)
# img = Image.fromarray(target_img)
# img.show()
# pdb.set_trace()
prec[0][la] += binary.precision(
predict_img, target_img)
print('[la %d: %.5f]' % (la, prec[0][la]))
# print(prec[0][la])
else:
print('no exist in t_label')
prec[1][la] += 1
except:
print('err')
metricsDir = './{}/metrics/'.format(dataset, indexName)
if not os.path.exists(metricsDir):
os.makedirs(metricsDir)
outputMetrics = metricsDir + '{}.csv'.format(indexName)
filenames = glob.glob("./{}/cortadas/labels/*.tif".format(dataset))
with open(outputMetrics, 'w') as csvfile:
fieldNames = ['Image', 'Dice', 'Jaccard', 'Precision', 'Recall', 'Sensitivity', 'Specificity']
writer = csv.writer(csvfile, delimiter=";")
writer.writerow(fieldNames)
for maskFileName in filenames:
fileName = maskFileName.replace('./{}/cortadas/labels/'.format(dataset), '')
mask = cv2.imread(maskFileName, cv2.IMREAD_COLOR)
processed = cv2.imread(processedDir + fileName, cv2.IMREAD_COLOR)
dc = str(mbin.dc(mask, processed)).replace(".", ",")
jc = str(mbin.jc(mask, processed)).replace(".", ",")
precision = str(mbin.precision(processed, mask)).replace(".", ",")
recall = str(mbin.recall(processed, mask)).replace(".", ",")
sensitivity = str(mbin.sensitivity(processed, mask)).replace(".", ",")
specificity = str(mbin.specificity(processed, mask)).replace(".", ",")
writer.writerow([fileName, dc, jc, precision, recall, sensitivity, specificity])
