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retinaNN_predict.py
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###################################################
#
# Script to
# - Calculate prediction of the test dataset
# - Calculate the parameters to evaluate the prediction
#``
##################################################
#Python
import numpy as np
import configparser,os
import scipy.io
import time
import numpy as np
from matplotlib import pyplot as plt
import tensorflow as tf
#Keras
import tensorflow.keras as keras
from tensorflow.keras.models import model_from_json
from tensorflow.keras import Model
from tensorflow.keras import backend as K
#scikit learn
from sklearn.metrics import roc_curve
from sklearn.metrics import roc_auc_score
from sklearn.metrics import confusion_matrix
from sklearn.metrics import precision_recall_curve
from sklearn.metrics import jaccard_score
from sklearn.metrics import f1_score
import sys
sys.path.insert(0, './lib/')
# help_functions.py
from help_functions import *
# extract_patches.py
from extract_patches import recompone
from extract_patches import recompone_overlap
from extract_patches import paint_border
from extract_patches import kill_border
from extract_patches import pred_only_FOV
from extract_patches import get_data_testing
from extract_patches import get_data_testing_overlap
# pre_processing.py
from pre_processing import my_PreProc
from DropBlock import DropBlock2D, Mish
# from freeze_session import freeze_session
#========= CONFIG FILE TO READ FROM =======
config = configparser.RawConfigParser()
config.read('configuration.txt')
#===========================================
#run the training on invariant or local
path_data = config.get('data paths', 'path_local')
#original test images (for FOV selection)
DRIVE_test_imgs_original = path_data + config.get('data paths', 'test_imgs_original')
test_imgs_orig = load_hdf5(DRIVE_test_imgs_original)
full_img_height = test_imgs_orig.shape[2]
full_img_width = test_imgs_orig.shape[3]
#the border masks provided by the DRIVE
DRIVE_test_border_masks = path_data + config.get('data paths', 'test_border_masks')
test_border_masks = load_hdf5(DRIVE_test_border_masks)
# dimension of the patches
patch_height = int(config.get('data attributes', 'patch_height'))
patch_width = int(config.get('data attributes', 'patch_width'))
#the stride in case output with average
stride_height = int(config.get('testing settings', 'stride_height'))
stride_width = int(config.get('testing settings', 'stride_width'))
assert (stride_height < patch_height and stride_width < patch_width)
#model name
name_experiment = config.get('experiment name', 'name')
path_experiment = './' +name_experiment +'/'
#N full images to be predicted
Imgs_to_test = int(config.get('testing settings', 'full_images_to_test'))
#Grouping of the predicted images
N_visual = int(config.get('testing settings', 'N_group_visual'))
#====== average mode ===========
average_mode = config.getboolean('testing settings', 'average_mode')
# #ground truth
# gtruth= path_data + config.get('data paths', 'test_groundTruth')
# img_truth= load_hdf5(gtruth)
# visualize(group_images(test_imgs_orig[0:20,:,:,:],5),'original')#.show()
# visualize(group_images(test_border_masks[0:20,:,:,:],5),'borders')#.show()
# visualize(group_images(img_truth[0:20,:,:,:],5),'gtruth')#.show()
#============ Load the data and divide in patches
start_time = time.time()
patches_imgs_test = None
new_height = None
new_width = None
masks_test = None
patches_masks_test = None
if average_mode == True:
patches_imgs_test, new_height, new_width, masks_test = get_data_testing_overlap(
DRIVE_test_imgs_original = DRIVE_test_imgs_original, #original
DRIVE_test_groudTruth = path_data + config.get('data paths', 'test_groundTruth'), #masks
Imgs_to_test = int(config.get('testing settings', 'full_images_to_test')),
patch_height = patch_height,
patch_width = patch_width,
stride_height = stride_height,
stride_width = stride_width
)
else:
patches_imgs_test, patches_masks_test = get_data_testing(
DRIVE_test_imgs_original = DRIVE_test_imgs_original, #original
DRIVE_test_groudTruth = path_data + config.get('data paths', 'test_groundTruth'), #masks
Imgs_to_test = int(config.get('testing settings', 'full_images_to_test')),
patch_height = patch_height,
patch_width = patch_width,
)
#================ Run the prediction of the patches ==================================
load_data_time = time.time() - start_time
best_last = config.get('testing settings', 'best_last')
#Load the saved model
model = model_from_json(open(path_experiment+name_experiment +'_architecture.json').read(), custom_objects={'DropBlock2D': DropBlock2D, 'Mish': Mish})
model.load_weights(path_experiment+name_experiment + '_'+best_last+'_weights.h5')
load_model_time = time.time() - start_time
#Calculate the predictions
layer_name = 'res2a_branch2a'
predictions = model.predict(patches_imgs_test, batch_size=64, verbose=2)
print ("predicted images size :")
print (predictions.shape)
predict_time = time.time() - start_time
#===== Convert the prediction arrays in corresponding images
pred_patches = pred_to_imgs(predictions, patch_height, patch_width, "original")
#========== Elaborate and visualize the predicted images ====================
pred_imgs = None
orig_imgs = None
gtruth_masks = None
if average_mode == True:
pred_imgs = recompone_overlap(pred_patches, new_height, new_width, stride_height, stride_width)# predictions
start_proc = time.time()
orig_imgs = my_PreProc(test_imgs_orig[0:pred_imgs.shape[0],:,:,:]) #originals
proc_time = time.time() - start_proc
gtruth_masks = masks_test #ground truth masks
else:
pred_imgs = recompone(pred_patches,13,12) # predictions
orig_imgs = recompone(patches_imgs_test,13,12) # originals
gtruth_masks = recompone(patches_masks_test,13,12) #masks
# apply the DRIVE masks on the repdictions #set everything outside the FOV to zero!!
kill_border(pred_imgs, test_border_masks) #DRIVE MASK #only for visualization
convert_time = time.time() - start_time
## back to original dimensions
orig_imgs = orig_imgs[:,:,0:full_img_height,0:full_img_width]
pred_imgs = pred_imgs[:,:,0:full_img_height,0:full_img_width]
gtruth_masks = gtruth_masks[:,:,0:full_img_height,0:full_img_width]
print ("Orig imgs shape: " +str(orig_imgs.shape))
print ("pred imgs shape: " +str(pred_imgs.shape))
print ("Gtruth imgs shape: " +str(gtruth_masks.shape))
visualize(group_images(orig_imgs,N_visual),path_experiment+"all_originals")#.show()
visualize(group_images(pred_imgs,N_visual),path_experiment+"all_predictions")#.show()
visualize(group_images(gtruth_masks,N_visual),path_experiment+"all_groundTruths")#.show()
#visualize results comparing mask and prediction:
assert (orig_imgs.shape[0]==pred_imgs.shape[0] and orig_imgs.shape[0]==gtruth_masks.shape[0])
N_predicted = orig_imgs.shape[0]
group = N_visual
assert (N_predicted%group==0)
for i in range(int(N_predicted/group)):
orig_stripe = group_images(orig_imgs[i*group:(i*group)+group,:,:,:],group)
masks_stripe = group_images(gtruth_masks[i*group:(i*group)+group,:,:,:],group)
pred_stripe = group_images(pred_imgs[i*group:(i*group)+group,:,:,:],group)
total_img = np.concatenate((orig_stripe,masks_stripe,pred_stripe),axis=0)
visualize(total_img,path_experiment+name_experiment +"_Original_GroundTruth_Prediction"+str(i))#.show()
duration = time.time() - start_time
#====== Evaluate the results
print("\n\n======== Time =======================")
print("Overall time: " + str(duration) + 's')
print('Signal image time: ' + str(duration/Imgs_to_test) + 's')
print('Convert time:' + str(convert_time) + 's')
print('Predict time:' + str(predict_time) + 's')
print('Load model time:' + str(load_model_time) + 's')
print('Load data time:' + str(load_data_time) + 's')
print('Preproc data time:' + str(proc_time) + 's')
print ("\n\n======== Evaluate the results =======================")
#predictions only inside the FOV
y_scores, y_true = pred_only_FOV(pred_imgs,gtruth_masks, test_border_masks) #returns data only inside the FOV
print ("Calculating results only inside the FOV:")
print ("y scores pixels: " +str(y_scores.shape[0]) +" (radius 270: 270*270*3.14==228906), including background around retina: " +str(pred_imgs.shape[0]*pred_imgs.shape[2]*pred_imgs.shape[3]) +" (584*565==329960)")
print ("y true pixels: " +str(y_true.shape[0]) +" (radius 270: 270*270*3.14==228906), including background around retina: " +str(gtruth_masks.shape[2]*gtruth_masks.shape[3]*gtruth_masks.shape[0])+" (584*565==329960)")
#Area under the ROC curve
fpr, tpr, thresholds = roc_curve((y_true), y_scores)
AUC_ROC = roc_auc_score(y_true, y_scores)
scipy.io.savemat('./test/roc.mat', {'fpr':fpr, 'tpr':tpr, 'th':thresholds, 'auc':AUC_ROC})
# test_integral = np.trapz(tpr,fpr) #trapz is numpy integration
print ("\nArea under the ROC curve: " +str(AUC_ROC))
roc_curve =plt.figure()
plt.plot(fpr,tpr,'-',label='Area Under the Curve (AUC = %0.4f)' % AUC_ROC)
plt.title('ROC curve')
plt.xlabel("FPR (False Positive Rate)")
plt.ylabel("TPR (True Positive Rate)")
plt.legend(loc="lower right")
plt.savefig(path_experiment+"ROC.png")
#Precision-recall curve
precision, recall, thresholds = precision_recall_curve(y_true, y_scores)
precision = np.fliplr([precision])[0] #so the array is increasing (you won't get negative AUC)
recall = np.fliplr([recall])[0] #so the array is increasing (you won't get negative AUC)
AUC_prec_rec = np.trapz(precision,recall)
print ("\nArea under Precision-Recall curve: " +str(AUC_prec_rec))
prec_rec_curve = plt.figure()
plt.plot(recall,precision,'-',label='Area Under the Curve (AUC = %0.4f)' % AUC_prec_rec)
plt.title('Precision - Recall curve')
plt.xlabel("Recall")
plt.ylabel("Precision")
plt.legend(loc="lower right")
plt.savefig(path_experiment+"Precision_recall.png")
#Confusion matrix
threshold_confusion = 0.5
print( "\nConfusion matrix: Costum threshold (for positive) of " +str(threshold_confusion))
y_pred = np.empty((y_scores.shape[0]))
for i in range(y_scores.shape[0]):
if y_scores[i]>=threshold_confusion:
y_pred[i]=1
else:
y_pred[i]=0
confusion = confusion_matrix(y_true, y_pred)
print (confusion)
accuracy = 0
if float(np.sum(confusion))!=0:
accuracy = float(confusion[0,0]+confusion[1,1])/float(np.sum(confusion))
s = float(confusion[1,1]+confusion[1,0])/float(np.sum(confusion))
p = float(confusion[1,1]+confusion[0,1])/float(np.sum(confusion))
inter = float(confusion[1,1])/float(np.sum(confusion))
print ("Global Accuracy: " +str(accuracy))
specificity = 0
if float(confusion[0,0]+confusion[0,1])!=0:
specificity = float(confusion[0,0])/float(confusion[0,0]+confusion[0,1])
print ("Specificity: " +str(specificity))
sensitivity = 0
if float(confusion[1,1]+confusion[1,0])!=0:
sensitivity = float(confusion[1,1])/float(confusion[1,1]+confusion[1,0])
print ("Sensitivity: " +str(sensitivity))
precision = 0
if float(confusion[1,1]+confusion[0,1])!=0:
precision = float(confusion[1,1])/float(confusion[1,1]+confusion[0,1])
print ("Precision: " +str(precision))
G = 0
G = float(np.sqrt(sensitivity * specificity))
print ("G score: " +str(G))
MCC = 0
MCC = float(inter-s*p)/float(np.sqrt(p*s*(1-s)*(1-p)))
print("MCC: " +str(MCC))
#Jaccard similarity index
jaccard_index = jaccard_score(y_true, y_pred)
print ("\nJaccard similarity score: " +str(jaccard_index))
#F1 score
F1_score = f1_score(y_true, y_pred, labels=None, average='binary', sample_weight=None)
print ("\nF1 score (F-measure): " +str(F1_score))
#Save the results
file_perf = open(path_experiment+'performances.txt', 'w')
file_perf.write("Area under the ROC curve: "+str(AUC_ROC)
+ "\nArea under Precision-Recall curve: " +str(AUC_prec_rec)
+ "\nJaccard similarity score: " +str(jaccard_index)
+ "\nF1 score (F-measure): " +str(F1_score)
+"\n\nConfusion matrix:"
+str(confusion)
+"\nthreshold_confusion:" +str(threshold_confusion)
+"\nACCURACY: " +str(accuracy)
+"\nSENSITIVITY: " +str(sensitivity)
+"\nSPECIFICITY: " +str(specificity)
+"\nPRECISION: " +str(precision)
+"\nG: " + str(G)
+"\nMCC: " + str(MCC)
)
file_perf.close()