def segmentation_combined_atlas_minmax_test(): task = 'brain' n = 5 all_subjects = np.arange(n) train_slice = 1 tmp_data, tmp_labels, tmp_feature_labels = util.create_dataset(1,train_slice,task) all_data_matrix = np.empty((tmp_data.shape[0], tmp_data.shape[1], n)) all_labels_matrix = np.empty((tmp_labels.shape[0], n)) #Load datasets once for i in all_subjects: train_data, train_labels, train_feature_labels = util.create_dataset(i+1,train_slice,task) all_data_matrix[:,:,i] = train_data all_labels_matrix[:,i] = train_labels.ravel() predicted_labels_min = seg.segmentation_combined_atlas(all_labels_matrix, combining='min') predicted_labels_max = seg.segmentation_combined_atlas(all_labels_matrix, combining='max') test_labels = all_labels_matrix[:,4].astype(bool) print('Combining method = min:') err = util.classification_error(test_labels, predicted_labels_min) print('Error:\n{}'.format(err)) dice = util.dice_overlap(test_labels, predicted_labels_min) print('Dice coefficient:\n{}'.format(dice)) print('Combining method = max:') err = util.classification_error(test_labels, predicted_labels_max) print('Error:\n{}'.format(err)) dice = util.dice_overlap(test_labels, predicted_labels_max) print('Dice coefficient:\n{}'.format(dice))
def nn_classifier_test_brains(testDice=False): # Subject 1, slice 1 is the train data X, Y, feature_labels_train = util.create_dataset(1,1,'brain') N = 1000 ix = np.random.randint(len(X), size=N) train_data = X[ix,:] train_labels = Y[ix,:] # Subject 3, slice 1 is the test data test_data, test_labels, feature_labels_test = util.create_dataset(3,1,'brain') predicted_labels = seg.nn_classifier(train_data, train_labels, test_data) predicted_labels = predicted_labels.astype(bool) test_labels = test_labels.astype(bool) err = util.classification_error(test_labels, predicted_labels) print('Error:\n{}'.format(err)) if testDice: dice = util.dice_overlap(test_labels, predicted_labels) print('Dice coefficient:\n{}'.format(dice)) else: I = plt.imread('../data/dataset_brains/3_1_t1.tif') GT = plt.imread('../data/dataset_brains/3_1_gt.tif') gt_mask = GT>0 gt_labels = gt_mask.flatten() # labels predicted_mask = predicted_labels.reshape(I.shape) fig = plt.figure(figsize=(15,5)) ax1 = fig.add_subplot(131) ax1.imshow(I) ax2 = fig.add_subplot(132) ax2.imshow(predicted_mask) ax3 = fig.add_subplot(133) ax3.imshow(gt_mask)
def segmentation_combined_atlas_test(): task = 'brain' n = 5 all_subjects = np.arange(n) train_slice = 1 tmp_data, tmp_labels, tmp_feature_labels = util.create_dataset(1,train_slice,task) all_data_matrix = np.empty((tmp_data.shape[0], tmp_data.shape[1], n)) all_labels_matrix = np.empty((tmp_labels.shape[0], n)) #Load datasets once for i in all_subjects: train_data, train_labels, train_feature_labels = util.create_dataset(i+1,train_slice,task) all_data_matrix[:,:,i] = train_data all_labels_matrix[:,i] = train_labels.ravel() #------------------------------------------------------------------# # TODO: Use provided code to Combine labels of training images, # Convert combined label into mask image, # Convert true label into mask image, and # View both masks on the same axis, # Also calculate dice coefficient and error prlabes=seg.segmentation_combined_atlas(all_labels_matrix) predicted_mask= prlabes.reshape(240,240) GT = plt.imread('../data/dataset_brains/1_1_gt.tif') gt_mask = GT > 0 gt_vec = gt_mask.flatten() # labels MSE= util.classification_error(gt_vec,prlabes) Dice=util.dice_overlap(gt_vec,prlabes) print('MSE',MSE,'Dice',Dice) plt.figure() plt.imshow(predicted_mask, cmap='gray', alpha=0.5) plt.imshow(gt_mask, cmap='jet', alpha=0.5) plt.show()
def segmentation_combined_atlas_test(): task = 'brain' n = 5 all_subjects = np.arange(n) train_slice = 1 tmp_data, tmp_labels, tmp_feature_labels = util.create_dataset(1, train_slice, task) all_data_matrix = np.empty((tmp_data.shape[0], tmp_data.shape[1], n)) all_labels_matrix = np.empty((tmp_labels.shape[0], n)) # Load datasets once for i in all_subjects: train_data, train_labels, train_feature_labels = util.create_dataset(i + 1, train_slice, task) all_data_matrix[:, :, i] = train_data all_labels_matrix[:, i] = train_labels.ravel() # Combine labels of training images: predicted_labels = seg.segmentation_combined_atlas(all_labels_matrix, combining='mode') # Convert combined label into mask image: predicted_mask = predicted_labels.reshape(240, 240) # Convert true label into mask image: true_mask = all_labels_matrix[:, 4].reshape(240, 240) plt.imshow(predicted_mask + true_mask) err = util.classification_error(true_mask, predicted_mask) dice = util.dice_overlap(true_mask, predicted_mask) print("error: {0}, dice: {1}".format(err, dice))
def feature_curve(use_random=False): # Load training and test data train_data, train_labels, train_feature_labels = util.create_dataset(1, 1, 'brain') test_data, test_labels, test_feature_labels = util.create_dataset(2, 1, 'brain') if use_random: train_data = np.random.randn(train_data.shape[0], train_data.shape[1]) # Normalize data train_data, test_data = seg.normalize_data(train_data, test_data) # Define parameters feature_sizes = np.arange(train_data.shape[1]) + 1 train_size = 10 k = 3 num_iter = 5 # Store errors test_error = np.empty([len(feature_sizes), num_iter]) test_error[:] = np.nan train_error = np.empty([len(feature_sizes), num_iter]) train_error[:] = np.nan # Train and test with different sizes for i in np.arange(len(feature_sizes)): for j in np.arange(num_iter): print('feature size = {}, iter = {}'.format(feature_sizes[i], j)) start_time = timeit.default_timer() # Subsample training set ix = np.random.randint(len(train_data), size=train_size) subset_train_data = train_data[ix, :] subset_train_labels = train_labels[ix, :] # Train classifier neigh = KNeighborsClassifier(n_neighbors=k) neigh.fit(subset_train_data[:, :feature_sizes[i]], subset_train_labels.ravel()) # Evaluate predicted_test_labels = neigh.predict(test_data[:, :feature_sizes[i]]) predicted_train_labels = neigh.predict(subset_train_data[:, :feature_sizes[i]]) test_error[i, j] = util.classification_error(test_labels, predicted_test_labels) train_error[i, j] = util.classification_error(subset_train_labels, predicted_train_labels) # Timer log elapsed = timeit.default_timer() - start_time # print('elapsed time = {}'.format(elapsed)) ## Display results fig = plt.figure(figsize=(8, 8)) ax1 = fig.add_subplot(111) x = feature_sizes y_test = np.mean(test_error, 1) yerr_test = np.std(test_error, 1) p1 = ax1.errorbar(x, y_test, yerr=yerr_test, label='Test error') ax1.set_xlabel('Number of features') ax1.set_ylabel('Error') ax1.grid() ax1.legend()
def knn_curve(): # Load training and test data train_data, train_labels, train_feature_labels = util.create_dataset( 1, 1, 'brain') test_data, test_labels, test_feature_labels = util.create_dataset( 2, 1, 'brain') # Normalize data train_data, test_data = seg.normalize_data(train_data, test_data) #Define parameters num_iter = 3 train_size = 100 k = np.array([1, 3, 5, 9, 15, 25, 100]) # k = np.array([1, 5, 9]) #Store errors test_error = np.empty([len(k), num_iter]) test_error[:] = np.nan dice = np.empty([len(k), num_iter]) dice[:] = np.nan ## Train and test with different values for i in np.arange(len(k)): for j in np.arange(num_iter): print('k = {}, iter = {}'.format(k[i], j)) #Subsample training set ix = np.random.randint(len(train_data), size=train_size) subset_train_data = train_data[ix, :] subset_train_labels = train_labels[ix, :] predicted_test_labels = seg.knn_classifier(subset_train_data, subset_train_labels, test_data, k[i]) # #Train classifier # neigh = KNeighborsClassifier(n_neighbors=k[i]) # neigh.fit(subset_train_data, subset_train_labels) # #Evaluate # predicted_test_labels = neigh.predict(test_data) test_error[i, j] = util.classification_error(test_labels, predicted_test_labels) dice[i, j] = util.dice_overlap(test_labels, predicted_test_labels) ## Display results fig = plt.figure(figsize=(8, 8)) ax1 = fig.add_subplot(111) p1 = ax1.plot(k, np.mean(test_error, 1), 'r', label='error') p2 = ax1.plot(k, np.mean(dice, 1), 'k', label='dice') ax1.set_xlabel('k') ax1.set_ylabel('error') ax1.grid() ax1.legend()
def segmentation_combined_atlas_test(): task = 'brain' n = 5 all_subjects = np.arange(n) train_slice = 1 tmp_data, tmp_labels, tmp_feature_labels = util.create_dataset(1,train_slice,task) all_data_matrix = np.empty((tmp_data.shape[0], tmp_data.shape[1], n)) all_labels_matrix = np.empty((tmp_labels.shape[0], n)) #Load datasets once for i in all_subjects: train_data, train_labels, train_feature_labels = util.create_dataset(i+1,train_slice,task) all_data_matrix[:,:,i] = train_data all_labels_matrix[:,i] = train_labels.ravel() #------------------------------------------------------------------# # TODO: Use provided code to Combine labels of training images, # Convert combined label into mask image, # Convert true label into mask image, and # View both masks on the same axis, # Also calculate dice coefficient and error # Combine labels of training images: predicted_labels = stats.mode(all_labels_matrix[:,:4], axis=1)[0] # Convert combined label into mask image: predicted_mask = predicted_labels.reshape(240,240) # Convert true label into mask image: true_mask = all_labels_matrix[:,4].reshape(240,240) # View both masks on the same axis using imshow() class_error = util.classification_error(all_labels_matrix[:,4], predicted_labels) dice_Overlap = util.dice_overlap(all_labels_matrix[:,4], predicted_labels) print("The error: {:.2f}".format(class_error)) print("Dice coefficient: {:.2f}".format(dice_Overlap)) fig = plt.figure(figsize=(10,13)) ax1 = fig.add_subplot(121) ax1.imshow(predicted_mask, cmap = 'Oranges_r') ax2 = fig.add_subplot(122) ax2.imshow(true_mask)
def segmentation_combined_atlas_test(): task = 'brain' n = 5 all_subjects = np.arange(n) train_slice = 1 tmp_data, tmp_labels, tmp_feature_labels = util.create_dataset(1,train_slice,task) all_data_matrix = np.empty((tmp_data.shape[0], tmp_data.shape[1], n)) all_labels_matrix = np.empty((tmp_labels.shape[0], n)) #Load datasets once for i in all_subjects: train_data, train_labels, train_feature_labels = util.create_dataset(i+1,train_slice,task) all_data_matrix[:,:,i] = train_data all_labels_matrix[:,i] = train_labels.ravel()
def PCA_features_demo(): task = 'tissue' n = 5 all_subjects = np.arange(n) train_slice = 1 tmp_data, tmp_labels, tmp_feature_labels = util.create_dataset( 1, train_slice, task) all_data_matrix = np.empty((tmp_data.shape[0], tmp_data.shape[1], n)) all_labels_matrix = np.empty((tmp_labels.shape[0], n)) # Load all datasets once and compile in all_data_matrix for i in all_subjects: train_data, train_labels, train_feature_labels = util.create_dataset( i + 1, train_slice, task) all_data_matrix[:, :, i] = train_data all_labels_matrix[:, i] = train_labels.ravel() # Perform PCA and plots the first patient's features against each other # Also calculates tha amount of features needed to account for at least 95% of the variance X_pca, v, w, fraction_variance = seg.mypca(all_data_matrix[:, :, 0]) fig = plt.figure(figsize=(40, 40)) plot = 1 for i in range(8): for j in range(8): ax = plt.subplot(8, 8, plot) ax = util.scatter_data(X_pca, all_labels_matrix[:, 0], feature0=i, feature1=j, ax=ax) plot += 1 needed_features = np.sum((fraction_variance < 0.95).astype(int)) + 1 print("needed features to account for 95% of variance: {0}".format( needed_features))
def kmeans_clustering_test(): #------------------------------------------------------------------# #TODO: Store errors for training data X_data, Y, feature_labels_train = util.create_dataset(1, 1, 'brain') predicted_labels = seg.kmeans_clustering(X_data, K=2) I = plt.imread('../data/dataset_brains/1_1_t1.tif') GT = plt.imread('../data/dataset_brains/1_1_gt.tif') gt_mask = GT > 0 gt_labels = gt_mask.flatten() # labels predicted_mask = predicted_labels.reshape(I.shape) fig = plt.figure(figsize=(15, 5)) ax1 = fig.add_subplot(131) ax1.imshow(I) ax2 = fig.add_subplot(132) ax2.imshow(predicted_mask) ax3 = fig.add_subplot(133) ax3.imshow(gt_mask) util.scatter_data(X_data, predicted_labels, 0, 1)
def segmentation_demo(): # Data name specification train_subject = 1 test_subject = 2 train_slice = 1 test_slice = 1 task = 'tissue' # Load data train_data, train_labels, train_feature_labels = util.create_dataset( train_subject, train_slice, task) test_data, test_labels, test_feature_labels = util.create_dataset( test_subject, test_slice, task) # find the predicted labels (here: the train_labels) predicted_labels = seg.segmentation_atlas(None, train_labels, None) # Calculate the error and dice score of these predicted labels in comparison to test labels err = util.classification_error(test_labels, predicted_labels) dice = util.dice_overlap(test_labels, predicted_labels) # Display results true_mask = test_labels.reshape(240, 240) predicted_mask = predicted_labels.reshape(240, 240) fig = plt.figure(figsize=(8, 8)) ax1 = fig.add_subplot(111) ax1.imshow(true_mask, 'gray') ax1.imshow(predicted_mask, 'viridis', alpha=0.5) print('Subject {}, slice {}.\nErr {}, dice {}'.format( test_subject, test_slice, err, dice)) # COMPARE METHODS num_images = 5 num_methods = 3 im_size = [240, 240] # make space for error and dice data all_errors = np.empty([num_images, num_methods]) all_errors[:] = np.nan all_dice = np.empty([num_images, num_methods]) all_dice[:] = np.nan # data name specification all_subjects = np.arange(num_images) train_slice = 1 task = 'tissue' # make space for data all_data_matrix = np.empty( [train_data.shape[0], train_data.shape[1], num_images]) # all_labels_matrix = np.empty([train_labels.size, num_images], dtype=bool) all_labels_matrix = np.empty([train_labels.size, num_images]) # Load datasets once print('Loading data for ' + str(num_images) + ' subjects...') for i in all_subjects: sub = i + 1 train_data, train_labels, train_feature_labels = util.create_dataset( sub, train_slice, task) all_data_matrix[:, :, i] = train_data all_labels_matrix[:, i] = train_labels.flatten() print('Finished loading data.\nStarting segmentation...') # Go through each subject, taking i-th subject as the test for i in np.arange(num_images): sub = i + 1 # Define training subjects as all, except the test subject train_subjects = all_subjects.copy() train_subjects = np.delete(train_subjects, i) # Obtain data about the chosen amount of subjects train_data_matrix = all_data_matrix[:, :, train_subjects] train_labels_matrix = all_labels_matrix[:, train_subjects] test_data = all_data_matrix[:, :, i] test_labels = all_labels_matrix[:, i] test_shape_1 = test_labels.reshape(im_size[0], im_size[1]) fig = plt.figure(figsize=(15, 5)) # Get predicted labels from atlas method predicted_labels = seg.segmentation_combined_atlas(train_labels_matrix) all_errors[i, 0] = util.classification_error(test_labels, predicted_labels) all_dice[i, 0] = util.dice_overlap(test_labels, predicted_labels) # Plot atlas method predicted_mask_1 = predicted_labels.reshape(im_size[0], im_size[1]) ax1 = fig.add_subplot(131) ax1.imshow(test_shape_1, 'gray') ax1.imshow(predicted_mask_1, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 0], all_dice[i, 0]) ax1.set_xlabel(text_str) ax1.set_title('Subject {}: Combined atlas'.format(sub)) # Get predicted labels from kNN method predicted_labels = seg.segmentation_combined_knn( train_data_matrix, train_labels_matrix, test_data) all_errors[i, 1] = util.classification_error(test_labels, predicted_labels) all_dice[i, 1] = util.dice_overlap(test_labels, predicted_labels) # Plot kNN method predicted_mask_2 = predicted_labels.reshape(im_size[0], im_size[1]) ax2 = fig.add_subplot(132) ax2.imshow(test_shape_1, 'gray') ax2.imshow(predicted_mask_2, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 1], all_dice[i, 1]) ax2.set_xlabel(text_str) ax2.set_title('Subject {}: Combined k-NN'.format(sub)) # Get predicted labels from my own method predicted_labels = segmentation_mymethod(train_data_matrix, train_labels_matrix, test_data, task) print(predicted_labels.shape) print(np.unique(predicted_labels)) all_errors[i, 2] = util.classification_error(test_labels, predicted_labels) all_dice[i, 2] = util.dice_overlap(test_labels, predicted_labels) # Plot my own method predicted_mask_3 = predicted_labels.reshape(im_size[0], im_size[1]) ax3 = fig.add_subplot(133) ax3.imshow(test_shape_1, 'gray') ax3.imshow(predicted_mask_3, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 2], all_dice[i, 2]) ax3.set_xlabel(text_str) ax3.set_title('Subject {}: My method'.format(sub))
from IPython.display import display, clear_output from scipy import ndimage, stats import scipy import segmentation_project as prj train_subjects = [0, 1, 3, 4] test_subject = 2 train_slice = 1 test_slice = 1 task = 'tissue' im_size = [240, 240] num_images = 5 features = [8, 9] #[1,4] and #[0,4] and [8,9] num_iter = 100 mu = 0.1 test_data, test_labels, test_feature_labels = util.create_dataset( test_subject + 1, train_slice, task) all_data_matrix = np.empty( [test_data.shape[0], test_data.shape[1], num_images]) train_labels_matrix = np.empty([test_data.shape[0], num_images]) #isn't used only for plotting for i in np.arange(num_images): sub = i + 1 train_data, train_labels, train_feature_labels = util.create_dataset( sub, train_slice, task) all_data_matrix[:, :, i] = train_data train_labels_matrix[:, i] = train_labels.flatten() #select certain data:
def segmentation_demo(): train_subject = 1 test_subject = 2 train_slice = 1 test_slice = 1 task = 'brain' #Load data train_data, train_labels, train_feature_labels = util.create_dataset( train_subject, train_slice, task) test_data, test_labels, test_feature_labels = util.create_dataset( test_subject, test_slice, task) predicted_labels = seg.segmentation_atlas(None, train_labels, None) err = util.classification_error(test_labels, predicted_labels) dice = util.dice_overlap(test_labels, predicted_labels) #Display results true_mask = test_labels.reshape(240, 240) predicted_mask = predicted_labels.reshape(240, 240) # fig = plt.figure(figsize=(8,8)) # ax1 = fig.add_subplot(111) # ax1.imshow(true_mask, 'gray') # ax1.imshow(predicted_mask, 'viridis', alpha=0.5) # print('Subject {}, slice {}.\nErr {}, dice {}'.format(test_subject, test_slice, err, dice)) ## Compare methods num_images = 5 num_methods = 3 im_size = [240, 240] all_errors = np.empty([num_images, num_methods]) all_errors[:] = np.nan all_dice = np.empty([num_images, num_methods]) all_dice[:] = np.nan all_subjects = np.arange(num_images) train_slice = 1 task = 'brain' all_data_matrix = np.empty( [train_data.shape[0], train_data.shape[1], num_images]) all_labels_matrix = np.empty([train_labels.size, num_images], dtype=bool) #Load datasets once print('Loading data for ' + str(num_images) + ' subjects...') for i in all_subjects: sub = i + 1 train_data, train_labels, train_feature_labels = util.create_dataset( sub, train_slice, task) all_data_matrix[:, :, i] = train_data all_labels_matrix[:, i] = train_labels.flatten() print('Finished loading data.\nStarting segmentation...') #Go through each subject, taking i-th subject as the test for i in np.arange(num_images): sub = i + 1 #Define training subjects as all, except the test subject train_subjects = all_subjects.copy() train_subjects = np.delete(train_subjects, i) train_data_matrix = all_data_matrix[:, :, train_subjects] train_labels_matrix = all_labels_matrix[:, train_subjects] test_data = all_data_matrix[:, :, i] test_labels = all_labels_matrix[:, i] test_shape_1 = test_labels.reshape(im_size[0], im_size[1]) fig = plt.figure(figsize=(15, 5)) predicted_labels = seg.segmentation_combined_atlas(train_labels_matrix) all_errors[i, 0] = util.classification_error(test_labels, predicted_labels) all_dice[i, 0] = util.dice_overlap(test_labels, predicted_labels) predicted_mask_1 = predicted_labels.reshape(im_size[0], im_size[1]) ax1 = fig.add_subplot(131) ax1.imshow(test_shape_1, 'gray') ax1.imshow(predicted_mask_1, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 0], all_dice[i, 0]) ax1.set_xlabel(text_str) ax1.set_title('Subject {}: Combined atlas'.format(sub)) predicted_labels = seg.segmentation_combined_knn( train_data_matrix, train_labels_matrix, test_data) all_errors[i, 1] = util.classification_error(test_labels, predicted_labels) all_dice[i, 1] = util.dice_overlap(test_labels, predicted_labels) predicted_mask_2 = predicted_labels.reshape(im_size[0], im_size[1]) ax2 = fig.add_subplot(132) ax2.imshow(test_shape_1, 'gray') ax2.imshow(predicted_mask_2, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 1], all_dice[i, 1]) ax2.set_xlabel(text_str) ax2.set_title('Subject {}: Combined k-NN'.format(sub)) predicted_labels = segmentation_mymethod(train_data_matrix, train_labels_matrix, test_data, task) all_errors[i, 2] = util.classification_error(test_labels, predicted_labels) all_dice[i, 2] = util.dice_overlap(test_labels, predicted_labels) predicted_mask_3 = predicted_labels.reshape(im_size[0], im_size[1]) ax3 = fig.add_subplot(133) ax3.imshow(test_shape_1, 'gray') ax3.imshow(predicted_mask_3, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 2], all_dice[i, 2]) ax3.set_xlabel(text_str) ax3.set_title('Subject {}: My method'.format(sub))
def segmentation_demo(): #only SECTION 2 is needed for what we want to do train_subject = 1 test_subject = 2 train_slice = 1 test_slice = 1 task = 'tissue' #SECTION 1 (this seciton has nothing to do with SECTION 2) #Load data from a train and testsubject train_data, train_labels, train_feature_labels = util.create_dataset( train_subject, train_slice, task) test_data, test_labels, test_feature_labels = util.create_dataset( test_subject, test_slice, task) util.scatter_data(train_data, train_labels, 0, 6) util.scatter_data(test_data, test_labels, 0, 6) predicted_labels = seg.segmentation_atlas(None, train_labels, None) err = util.classification_error(test_labels, predicted_labels) dice = util.dice_overlap(test_labels, predicted_labels) #Display results true_mask = test_labels.reshape(240, 240) predicted_mask = predicted_labels.reshape(240, 240) fig = plt.figure(figsize=(8, 8)) ax1 = fig.add_subplot(111) ax1.imshow(true_mask, 'gray') ax1.imshow(predicted_mask, 'viridis', alpha=0.5) print('Subject {}, slice {}.\nErr {}, dice {}'.format( test_subject, test_slice, err, dice)) ## SECTION 2:Compare methods num_images = 5 num_methods = 3 im_size = [240, 240] all_errors = np.empty([num_images, num_methods]) all_errors[:] = np.nan all_dice = np.empty([num_images, num_methods]) all_dice[:] = np.nan all_subjects = np.arange(5) #list of all subjects [0, 1, 2, 3, 4] train_slice = 2 task = 'tissue' all_data_matrix = np.empty( [train_data.shape[0], train_data.shape[1], num_images]) all_labels_matrix = np.empty([train_labels.size, num_images]) #Load datasets once print('Loading data for ' + str(num_images) + ' subjects...') for i in all_subjects: sub = i + 1 train_data, train_labels, train_feature_labels = util.create_dataset( sub, train_slice, task) all_data_matrix[:, :, i] = train_data all_labels_matrix[:, i] = train_labels.flatten() print('Finished loading data.\nStarting segmentation...') #Go through each subject, taking i-th subject as the test for i in all_subjects: sub = i + 1 #Define training subjects as all, except the test subject train_subjects = all_subjects.copy() train_subjects = np.delete(train_subjects, i) train_data_matrix = all_data_matrix[:, :, train_subjects] train_labels_matrix = all_labels_matrix[:, train_subjects] test_data = all_data_matrix[:, :, i] test_labels = all_labels_matrix[:, i] test_shape_1 = test_labels.reshape(im_size[0], im_size[1]) fig = plt.figure(figsize=(15, 5)) predicted_labels, predicted_labels2 = seg.segmentation_combined_atlas( train_labels_matrix) all_errors[i, 0] = util.classification_error(test_labels, predicted_labels2) all_dice[i, 0] = util.dice_multiclass(test_labels, predicted_labels2) predicted_mask_1 = predicted_labels2.reshape(im_size[0], im_size[1]) ax1 = fig.add_subplot(131) ax1.imshow(test_shape_1, 'gray') ax1.imshow(predicted_mask_1, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 0], all_dice[i, 0]) ax1.set_xlabel(text_str) ax1.set_title('Subject {}: Combined atlas'.format(sub)) predicted_labels, predicted_labels2 = seg.segmentation_combined_knn( train_data_matrix, train_labels_matrix, test_data) all_errors[i, 1] = util.classification_error(test_labels, predicted_labels2) all_dice[i, 1] = util.dice_multiclass(test_labels, predicted_labels2) predicted_mask_2 = predicted_labels2.reshape(im_size[0], im_size[1]) ax2 = fig.add_subplot(132) ax2.imshow(test_shape_1, 'gray') ax2.imshow(predicted_mask_2, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 1], all_dice[i, 1]) ax2.set_xlabel(text_str) ax2.set_title('Subject {}: Combined k-NN'.format(sub)) #OUR METHOD #predict the labels using our method predicted_labels_mymethod = segmentation_mymethod(train_data_matrix, train_labels_matrix, test_data, num_iter=100, mu=0.1) #determine error and dice (multiclass, since there are more classes) all_errors[i, 2] = util.classification_error(test_labels, predicted_labels_mymethod) all_dice[i, 2] = util.dice_multiclass(test_labels, predicted_labels_mymethod) #reshape the predicted labels in order to plot the results predicted_mask_3 = predicted_labels_mymethod.reshape( im_size[0], im_size[1]) #plot the predicted image over the real image plt.imshow(predicted_mask_3, 'viridis') ax3 = fig.add_subplot(133) ax3.imshow(test_shape_1, 'gray') ax3.imshow(predicted_mask_3, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 2], all_dice[i, 2]) ax3.set_xlabel(text_str) ax3.set_title('Subject {}: My method'.format(sub)) #save the figure after every loop (3 subimages/plots) fig.savefig("Results for test subject {}".format(sub), )
def segmentation_demo(): # Data name specification train_subject = 1 test_subject = 2 train_slice = 1 test_slice = 1 task = 'tissue' # Load data train_data, train_labels, train_feature_labels = util.create_dataset( train_subject, train_slice, task) test_data, test_labels, test_feature_labels = util.create_dataset( test_subject, test_slice, task) # Normalize and feed data through X_pca train_norm, _ = seg.normalize_data(train_data) Xpca, v, w, fraction_variance, ix = seg.mypca(train_norm) relevant_feature = int(np.sum(fraction_variance < 0.95)) + 1 train_norm_ord = train_norm[:, ix] train_norm = train_norm_ord[:, :relevant_feature] # find the predicted labels (here: the train_labels) predicted_labels = seg.segmentation_atlas(None, train_labels, None) # Calculate the error and dice score of these predicted labels in comparison to test labels err = util.classification_error(test_labels, predicted_labels) dice = util.dice_multiclass(test_labels, predicted_labels) # Display results true_mask = test_labels.reshape(240, 240) predicted_mask = predicted_labels.reshape(240, 240) fig = plt.figure(figsize=(8, 8)) ax1 = fig.add_subplot(111) ax1.imshow(true_mask, 'gray') ax1.imshow(predicted_mask, 'viridis', alpha=0.5) print('Subject {}, slice {}.\nErr {}, dice {}'.format( test_subject, test_slice, err, dice)) # COMPARE METHODS num_images = 5 num_methods = 3 im_size = [240, 240] # make space for error and dice data all_errors = np.empty([num_images, num_methods]) all_errors[:] = np.nan all_dice = np.empty([num_images, num_methods]) all_dice[:] = np.nan # data name specification all_subjects = np.arange(num_images) train_slice = 1 task = 'tissue' # make space for data all_data_matrix = np.empty( [train_norm.shape[0], train_norm.shape[1], num_images]) all_labels_matrix = np.empty([train_labels.size, num_images]) all_data_matrix_kmeans = np.empty( [train_norm.shape[0], train_norm.shape[1], num_images]) all_labels_matrix_kmeans = np.empty([train_labels.size, num_images]) # Load datasets once print('Loading data for ' + str(num_images) + ' subjects...') for i in all_subjects: sub = i + 1 train_data, train_labels, train_feature_labels = util.create_dataset( sub, train_slice, task) train_norm, _ = seg.normalize_data(train_data) Xpca, v, w, fraction_variance, ix = seg.mypca(train_norm) relevant_labels = int(np.sum(fraction_variance < 0.95)) + 1 train_norm_ord = train_norm[:, ix] train_norm = train_norm_ord[:, :relevant_labels] all_data_matrix[:, :, i] = train_norm all_labels_matrix[:, i] = train_labels.flatten() # Load datasets for kmeans print('Loading data for ' + str(num_images) + ' subjects...') for i in all_subjects: sub = i + 1 train_data_kmeans, train_labels_kmeans, train_feature_labels_kmeans = create_dataset( sub, train_slice, task) train_norm_kmeans, _ = seg.normalize_data(train_data_kmeans) all_data_matrix_kmeans[:, :, i] = train_norm_kmeans all_labels_matrix_kmeans[:, i] = train_labels_kmeans.flatten() print('Finished loading data.\nStarting segmentation...') # Go through each subject, taking i-th subject as the test for i in np.arange(num_images): sub = i + 1 # Define training subjects as all, except the test subject train_subjects = all_subjects.copy() train_subjects = np.delete(train_subjects, i) # Obtain data about the chosen amount of subjects train_data_matrix = all_data_matrix[:, :, train_subjects] train_labels_matrix = all_labels_matrix[:, train_subjects] test_data = all_data_matrix[:, :, i] test_labels = all_labels_matrix[:, i] test_shape_1 = test_labels.reshape(im_size[0], im_size[1]) fig = plt.figure(figsize=(15, 5)) # Get predicted labels from atlas method predicted_labels = seg.segmentation_combined_atlas(train_labels_matrix) all_errors[i, 0] = util.classification_error(test_labels, predicted_labels) all_dice[i, 0] = util.dice_multiclass(test_labels, predicted_labels) # Plot atlas method predicted_mask_1 = predicted_labels.reshape(im_size[0], im_size[1]) ax1 = fig.add_subplot(151) ax1.imshow(test_shape_1, 'gray') ax1.imshow(predicted_mask_1, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 0], all_dice[i, 0]) ax1.set_xlabel(text_str) ax1.set_title('Subject {}: Combined atlas'.format(sub)) # Get predicted labels from kNN method predicted_labels = seg.segmentation_combined_knn(train_data_matrix, train_labels_matrix, test_data, k=10) all_errors[i, 1] = util.classification_error(test_labels, predicted_labels) all_dice[i, 1] = util.dice_multiclass(test_labels, predicted_labels) # Plot kNN method predicted_mask_2 = predicted_labels.reshape(im_size[0], im_size[1]) ax2 = fig.add_subplot(152) ax2.imshow(test_shape_1, 'gray') ax2.imshow(predicted_mask_2, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 1], all_dice[i, 1]) ax2.set_xlabel(text_str) ax2.set_title('Subject {}: Combined k-NN'.format(sub)) # Get predicted labels from my own method # all_data_matrix_bnb = np.empty([train_norm.shape[0], train_norm.shape[1], num_images]) # all_labels_matrix_bnb = np.empty([train_labels.size, num_images]) # for ii in all_subjects: # sub = i + 1 # task = 'brain' # train_data_bnb, train_labels_bnb, train_feature_labels_bnb = util.create_dataset(sub, train_slice, task) # train_norm_bnb, _ = seg.normalize_data(train_data_bnb) # Xpca, v, w, fraction_variance, ix = seg.mypca(train_norm_bnb) # relevant_labels_bnb = int(np.sum(fraction_variance < 0.95)) + 1 # train_norm_ord_bnb = train_norm_bnb[:, ix] # train_norm_bnb = train_norm_ord_bnb[:, :relevant_labels_bnb] # all_data_matrix_bnb[:, :, ii] = train_norm_bnb # all_labels_matrix_bnb[:, ii] = train_labels_bnb.flatten() # # qw, we, er = all_data_matrix.shape # for iii in np.arange(qw): # for j in np.arange(er): # if all_labels_matrix_bnb[iii, j] == 0: # for k in np.arange(we): # all_data_matrix[iii, k, j] = 0 # train_data_matrix = all_data_matrix[:, :, train_subjects] # test_data = all_data_matrix[:, :, i] train_data_matrix_kmeans = all_data_matrix_kmeans[:, :, train_subjects] train_labels_matrix_kmeans = all_labels_matrix[:, train_subjects] test_data_kmeans = all_data_matrix_kmeans[:, :, i] predicted_labels = segmentation_mymethod(train_data_matrix_kmeans, train_labels_matrix_kmeans, test_data_kmeans, task) all_errors[i, 2] = util.classification_error(test_labels, predicted_labels) all_dice[i, 2] = util.dice_multiclass(test_labels, predicted_labels) # Plot my own method predicted_mask_3 = predicted_labels.reshape(im_size[0], im_size[1]) ax3 = fig.add_subplot(153) ax3.imshow(test_shape_1, 'gray') ax3.imshow(predicted_mask_3, 'viridis', alpha=0.5) text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 2], all_dice[i, 2]) ax3.set_xlabel(text_str) ax3.set_title('Subject {}: My method'.format(sub)) ax4 = fig.add_subplot(154) ax4.imshow(predicted_mask_3, 'viridis') text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 2], all_dice[i, 2]) ax4.set_xlabel(text_str) ax4.set_title('Subject {}: My method'.format(sub)) ax5 = fig.add_subplot(155) ax5.imshow(test_shape_1, 'gray') text_str = 'Err {:.4f}, dice {:.4f}'.format(all_errors[i, 2], all_dice[i, 2]) ax5.set_xlabel(text_str) ax5.set_title('Subject {}: My method'.format(sub))
def learning_curve(): # Load training and test data # train_data, train_labels = seg.generate_gaussian_data(1000) train_data, train_labels, _ = util.create_dataset(1, 1, 'brain') # test_data, test_labels = seg.generate_gaussian_data(1000) test_data, test_labels, _ = util.create_dataset(2, 1, 'brain') train_data, test_data = seg.normalize_data(train_data, test_data) # Define parameters train_sizes = np.logspace(0.1, 3.0, num=15).astype(int) k = 1 num_iter = 3 # How often to repeat the experiment # Store errors test_error = np.empty([len(train_sizes), num_iter]) test_error[:] = np.nan test_dice = np.empty([len(train_sizes), num_iter]) test_dice[:] = np.nan train_error = np.empty([len(train_sizes), num_iter]) train_error[:] = np.nan train_dice = np.empty([len(train_sizes), num_iter]) train_dice[:] = np.nan ## Train and test with different values for i in np.arange(len(train_sizes)): for j in np.arange(num_iter): print('train_size = {}, iter = {}'.format(train_sizes[i], j)) # Subsample training set ix = np.random.randint(len(train_data), size=train_sizes[i]) subset_train_data = train_data[ix, :] subset_train_labels = train_labels[ix, :] # Train classifier neigh = KNeighborsClassifier(n_neighbors=k) neigh.fit(subset_train_data, subset_train_labels.ravel()) # Evaluate predicted_test_labels = neigh.predict(test_data) test_labels = test_labels.astype(bool) predicted_test_labels = predicted_test_labels.astype(bool) test_error[i, j] = util.classification_error(test_labels, predicted_test_labels) test_dice[i, j] = util.dice_overlap(test_labels, predicted_test_labels) predicted_train_labels = neigh.predict(train_data).astype(bool) train_labels_bool = train_labels.astype(bool) train_error[i, j] = util.classification_error(train_labels_bool, predicted_train_labels) train_dice[i, j] = util.dice_overlap(train_labels_bool, predicted_train_labels) ## Display results fig = plt.figure(figsize=(8, 8)) gs = fig.add_gridspec(2, 2) ax1 = fig.add_subplot(gs[0, :]) ax2 = fig.add_subplot(gs[1, :]) x = np.log(train_sizes) ticks = list(x) tick_lbls = [str(i) for i in train_sizes] y_test = np.mean(test_error, 1) y_train = np.mean(train_error, 1) yerr_test = np.std(test_error, 1) yerr_train = np.std(train_error, 1) p1 = ax1.errorbar(x, y_test, yerr=yerr_test, label='Test error') p2 = ax2.errorbar(x, y_train, yerr=yerr_train, label='Train error') ax1.set_xlabel('Number of training samples (k)') ax1.set_ylabel('error') ax1.set_xticks(ticks) ax1.set_xticklabels(tick_lbls) ax1.grid() ax1.legend() ax2.set_xlabel('Number of training samples (k)') ax2.set_ylabel('error') ax2.set_xticks(ticks) ax2.set_xticklabels(tick_lbls) ax2.grid() ax2.legend()