def calculate_metric_percase(pred, gt, num_classes):
"二分类、多分类的指标统计"
if num_classes is None:
num_classes = len(np.unique(gt))#注意：gt不是onehot编码
print('np.unique(gt):',np.unique(gt))
if num_classes==2:
dice = metric.binary.dc(pred, gt)
jc = metric.binary.jc(pred, gt)
hd = metric.binary.hd95(pred, gt)
asd = metric.binary.asd(pred, gt)
elif num_classes>2:
gt_onehot = to_categorical(gt, num_classes)
pred_onehot = to_categorical(pred, num_classes)
dice = []
jc = []
hd = []
asd = []
for k in range(num_classes):
pred_k = pred_onehot[...,k]
gt_k = gt_onehot[...,k]
dice += [metric.dc(result=pred_k, reference=gt_k)]
jc += [metric.jc(result=pred_k, reference=gt_k)]
hd += [metric.hd95(result=pred_k, reference=gt_k)]
asd += [metric.asd(result=pred_k, reference=gt_k)]
else:
raise ValueError("pred和gt不能是onehot编码")
return dice, jc, hd, asd
def calculate_metrics(mask1, mask2):
true_positives = metric.obj_tpr(mask1, mask2)
false_positives = metric.obj_fpr(mask1, mask2)
dc = metric.dc(mask1, mask2)
hd = metric.hd(mask1, mask2)
precision = metric.precision(mask1, mask2)
recall = metric.recall(mask1, mask2)
ravd = metric.ravd(mask1, mask2)
assd = metric.assd(mask1, mask2)
asd = metric.asd(mask1, mask2)
return true_positives, false_positives, dc, hd, precision, recall, ravd, assd, asd
def calculate_metrics(mask1, mask2):
true_positives = metric.obj_tpr(mask1, mask2)
false_positives = metric.obj_fpr(mask1, mask2)
dc = metric.dc(mask1, mask2)
hd = metric.hd(mask1, mask2)
precision = metric.precision(mask1, mask2)
recall = metric.recall(mask1, mask2)
ravd = metric.ravd(mask1, mask2)
assd = metric.assd(mask1, mask2)
asd = metric.asd(mask1, mask2)
return true_positives, false_positives, dc, hd, precision, recall, ravd, assd, asd
def avg_surface_distance(test=None, reference=None, confusion_matrix=None, nan_for_nonexisting=True, voxel_spacing=None, connectivity=1, **kwargs):
if confusion_matrix is None:
confusion_matrix = ConfusionMatrix(test, reference)
test_empty, test_full, reference_empty, reference_full = confusion_matrix.get_existence()
if test_empty or test_full or reference_empty or reference_full:
if nan_for_nonexisting:
return float("NaN")
else:
return 0
test, reference = confusion_matrix.test, confusion_matrix.reference
return metric.asd(test, reference, voxel_spacing, connectivity)
def calculate_validation_metrics(probas_pred,
image_gt,
class_labels=None,
num_classes=5):
classes = np.arange(probas_pred.shape[-1])
# determine valid classes (those that actually appear in image_gt). Some images may miss some classes
classes = [c for c in classes if np.sum(image_gt == c) != 0]
image_pred = probas_pred.argmax(-1)
assert image_gt.shape == image_pred.shape
accuracy = np.sum(image_gt == image_pred) / float(image_pred.size)
class_metrics = {}
y_true = convert_seg_flat_to_binary_label_indicator_array(
image_gt.ravel(), num_classes).astype(int)[:, classes]
y_pred = probas_pred.transpose(3, 0, 1,
2).reshape(num_classes,
-1).transpose(1, 0)[:, classes]
scores = roc_auc_score(y_true, y_pred, None)
for i, c in enumerate(classes):
true_positives = metric.obj_tpr(image_gt == c, image_pred == c)
false_positives = metric.obj_fpr(image_gt == c, image_pred == c)
dc = metric.dc(image_gt == c, image_pred == c)
hd = metric.hd(image_gt == c, image_pred == c)
precision = metric.precision(image_gt == c, image_pred == c)
recall = metric.recall(image_gt == c, image_pred == c)
ravd = metric.ravd(image_gt == c, image_pred == c)
assd = metric.assd(image_gt == c, image_pred == c)
asd = metric.asd(image_gt == c, image_pred == c)
label = c
if class_labels is not None and c in class_labels.keys():
label = class_labels[c]
class_metrics[label] = {
'true_positives': true_positives,
'false_positives': false_positives,
'DICE\t\t': dc,
'Hausdorff dist': hd,
'precision\t': precision,
'recall\t\t': recall,
'rel abs vol diff': ravd,
'avg surf dist symm': assd,
'avg surf dist\t': asd,
'roc_auc\t\t': scores[i]
}
return accuracy, class_metrics
batch_y = Y_test[i_c:i_c + 1, :, :, :, :].copy()
for j_c in range(n_class):
dice_c[i_c, j_c] = dk_seg.dice(batch_y[0, :, :, :, j_c] == 1, y_tr_pr_c == j_c)
y_t_c = np.argmax( batch_y[0, :, :, :, :], axis=-1)
#dk_aux.save_pred_thumbs(batch_x[0,:,:,:,0], y_t_c, y_tr_pr_c, False, i_c, i_eval, images_dir )
'''if i_eval==0:
save_pred_mhds(batch_x[0,:,:,:,0], y_t_c, y_tr_pr_c, False, i_c, i_eval)
else:
save_pred_mhds(None, None, y_tr_pr_c, False, i_c, i_eval)'''
dice_c[i_c, n_class] = hd95(y_t_c, y_tr_pr_c)
dice_c[i_c, n_class+1] = asd(y_t_c, y_tr_pr_c)
dice_c[i_c, n_class+2] = assd(y_t_c, y_tr_pr_c)
y_tr_pr_soft= y_tr_pr_sum[:,:,:,1]/(y_tr_pr_cnt+1e-10)
#dk_aux.save_pred_soft_thumbs(batch_x[0,:,:,:,0], y_t_c, y_tr_pr_c, y_tr_pr_soft, False, i_c, i_eval, images_dir)
error_mask= dk_aux.seg_2_anulus(y_t_c, radius= 2.0)
plot_save_path= None
ECE, MCE, ECE_curve= dk_aux.estimate_ECE_and_MCE(y_t_c, y_tr_pr_soft, plot_save_path=plot_save_path)
dice_c[i_c, n_class+3]= ECE
dice_c[i_c, n_class+4]= MCE
plot_save_path= None
ECE, MCE, ECE_curve= dk_aux.estimate_ECE_and_MCE_masked(y_t_c, y_tr_pr_soft, error_mask, plot_save_path=plot_save_path)
dice_c[i_c, n_class+5]= ECE
print(' ')
# =============================================================================
# Distancia Hausdorff
# =============================================================================
distanceHD1 = mdm.hd(cHull_binary,cHull_Mbinary,connectivity=1)
print('Distancia Hausdorff',distanceHD1)
# =============================================================================
# Distancia media entre superficies
# =============================================================================
distanceASD = mdm.asd(cHull_binary,cHull_Mbinary,connectivity=1)
print('Distancia Media',distanceASD)
# =============================================================================
# Distancia media simétrica entre superficies
# =============================================================================
distanceASSD = mdm.assd(cHull_binary,cHull_Mbinary,connectivity=1)
print('Distancia Media Simétrica',distanceASSD)
# =============================================================================
# Distancia media entre superficie de objetos
lbl_p[..., idx] = utils.preprocess_lbl_slice(lbl[..., idx])
# predict
pred = []
for idx in xrange(img.shape[2]):
net1.blobs['data'].data[0, 0, ...] = img_p[..., idx]
pred.append(net1.forward()['prob'][0, 1] > 0.5)
pred = np.array(pred).transpose(1, 2, 0)
# create volume instance from medpy
v = volume.Volume(pred, lbl_p)
# calculate metrics as in the oritinal paper
voe = v.get_volumetric_overlap_error()
rvd = v.get_relative_volume_difference()
asd = metric.asd(pred, lbl_p)
msd = metric.hd(pred, lbl_p)
dice = metric.dc(pred, lbl_p) * 100 # convert to percentage
perf_metrics.append([voe, rvd, asd, msd, dice])
print('subject %d: %s' % (idx_subject, str([voe, rvd, asd, msd, dice])))
perf_metrics = np.array(perf_metrics)
perf_metrics_mean = np.mean(perf_metrics, axis=0)
print('inference complete: mean of performance metrics')
print(perf_metrics_mean)
"""
# visualize the results
for idx in xrange(30, 100, 20):
utils.imshow(img[...,idx], img_p[..., idx], lbl_p[...,idx], pred[...,idx])