Merge pull request #240 from mldiego/master

Fix bug on ImageStar.estimateRanges

code/nnv/engine/set/ImageStar.m

@@ -857,10 +857,13 @@
 
             if isempty(obj.im_lb) || isempty(obj.im_ub)
 
-                x1 = obj.V(:,:,:,1) + tensorprod(obj.V(:,:,:,2:end), obj.pred_lb, 4, 1);
-                x2 = obj.V(:,:,:,1) + tensorprod(obj.V(:,:,:,2:end), obj.pred_ub, 4, 1);
-                image_lb = min(x1,x2);
-                image_ub = max(x1,x2);
+                gens = obj.V(:,:,:,2:end);
+                pos_gens = gens;
+                pos_gens(gens < 0) = 0;
+                neg_gens = gens;
+                neg_gens(gens > 0) = 0;
+                image_lb = obj.V(:,:,:,1) + tensorprod(pos_gens, obj.pred_lb, 4, 1) + tensorprod(neg_gens, obj.pred_ub, 4, 1);
+                image_ub = obj.V(:,:,:,1) + tensorprod(pos_gens, obj.pred_ub, 4, 1) + tensorprod(neg_gens, obj.pred_lb, 4, 1);
 
                 obj.im_lb = image_lb;
                 obj.im_ub = image_ub;

code/nnv/examples/Submission/WiP_3d/verify_adrenal.m

@@ -11,7 +11,7 @@
 load(dataset);
 
 % data to verify (test set)
-test_images = permute(test_images, [2 3 4 5 1]);
+test_images = squeeze(permute(test_images, [2 3 4 5 1]));
 test_labels = test_labels + 1;
 
 % load network
@@ -21,8 +21,22 @@
 
 % select volumes to verify
 N = 50;
-inputs = single(test_images(:,:,:,:,1:N));
-targets = single(test_labels(1:N));
+idxs = zeros(N,1);
+count = 1;
+
+for i = 1:length(test_labels)
+    y = classify(matlabNet,test_images(:,:,:,i));
+    if single(y) == test_labels(i)
+        idxs(count) = i;
+        count = count + 1;
+    end
+    if count > N
+        break
+    end
+end
+
+inputs = single(test_images(:,:,:,idxs));
+targets = single(test_labels(idxs));
 
 % Reachability parameters
 reachOptions = struct;
@@ -54,7 +68,7 @@
 
             % 3) Begin verification analysis
             for i=1:N
-                img = squeeze(inputs(:,:,:,:,i));
+                img = inputs(:,:,:,i);
                 target = targets(i);
                 results(i,:) = verify_instance_shape(net, img, target, adv_attack, reachOptions);
             end

code/nnv/examples/Submission/WiP_3d/verify_fracture.m

@@ -20,9 +20,23 @@
 net = matlab2nnv(net);
 
 % select volumes to verify
-N = 50; % even for numCores
-inputs = single(test_images(:,:,:,:,1:N));
-targets = single(test_labels(1:N));
+N = 50;
+idxs = zeros(N,1);
+count = 1;
+
+for i = 1:length(test_labels)
+    y = classify(matlabNet,test_images(:,:,:,i));
+    if single(y) == test_labels(i)
+        idxs(count) = i;
+        count = count + 1;
+    end
+    if count > N
+        break
+    end
+end
+
+inputs = single(test_images(:,:,:,idxs));
+targets = single(test_labels(idxs));
 
 % Reachability parameters
 reachOptions = struct;
@@ -57,7 +71,7 @@
 
             % 3) Begin verification analysis
             for i=1:N
-                img = squeeze(inputs(:,:,:,:,i));
+                img = inputs(:,:,:,i);
                 target = targets(i);
                 results(i,:) = verify_instance_3d(net, img, target, adv_attack, reachOptions);
             end

code/nnv/examples/Submission/WiP_3d/verify_nodule.m

@@ -20,9 +20,23 @@
 net = matlab2nnv(net);
 
 % select volumes to verify
-N = 50; % even for numCores
-inputs = single(test_images(:,:,:,:,1:N));
-targets = single(test_labels(1:N));
+N = 50;
+idxs = zeros(N,1);
+count = 1;
+
+for i = 1:length(test_labels)
+    y = classify(matlabNet,test_images(:,:,:,i));
+    if single(y) == test_labels(i)
+        idxs(count) = i;
+        count = count + 1;
+    end
+    if count > N
+        break
+    end
+end
+
+inputs = single(test_images(:,:,:,idxs));
+targets = single(test_labels(idxs));
 
 % Reachability parameters
 reachOptions = struct;
@@ -58,7 +72,7 @@
 
             % 3) Begin verification analysis
             for i=1:N
-                img = squeeze(inputs(:,:,:,:,i));
+                img = inputs(:,:,:,i);
                 target = targets(i);
                 results(i,:) = verify_instance_3d(net, img, target, adv_attack, reachOptions);
             end

code/nnv/examples/Submission/WiP_3d/verify_organ.m

@@ -21,8 +21,22 @@
 
 % select volumes to verify
 N = 50;
-inputs = single(test_images(:,:,:,:,1:N));
-targets = single(test_labels(1:N));
+idxs = zeros(N,1);
+count = 1;
+
+for i = 1:length(test_labels)
+    y = classify(matlabNet,test_images(:,:,:,i));
+    if single(y) == test_labels(i)
+        idxs(count) = i;
+        count = count + 1;
+    end
+    if count > N
+        break
+    end
+end
+
+inputs = single(test_images(:,:,:,idxs));
+targets = single(test_labels(idxs));
 
 % Reachability parameters
 reachOptions = struct;
@@ -57,7 +71,7 @@
 
             % 3) Begin verification analysis
             for i=1:N
-                img = squeeze(inputs(:,:,:,:,i));
+                img = inputs(:,:,:,i);
                 target = targets(i);
                 results(i,:) = verify_instance_3d(net, img, target, adv_attack, reachOptions);
             end

code/nnv/examples/Submission/WiP_3d/verify_synapse.m

@@ -20,9 +20,23 @@
 net = matlab2nnv(net);
 
 % select volumes to verify
-N = 50; % even for numCores
-inputs = single(test_images(:,:,:,:,1:N));
-targets = single(test_labels(1:N));
+N = 50;
+idxs = zeros(N,1);
+count = 1;
+
+for i = 1:length(test_labels)
+    y = classify(matlabNet,test_images(:,:,:,i));
+    if single(y) == test_labels(i)
+        idxs(count) = i;
+        count = count + 1;
+    end
+    if count > N
+        break
+    end
+end
+
+inputs = single(test_images(:,:,:,idxs));
+targets = single(test_labels(idxs));
 
 % Reachability parameters
 reachOptions = struct;
@@ -57,7 +71,7 @@
 
             % 3) Begin verification analysis
             for i=1:N
-                img = squeeze(inputs(:,:,:,:,i));
+                img = inputs(:,:,:,i);
                 target = targets(i);
                 results(i,:) = verify_instance_3d(net, img, target, adv_attack, reachOptions);
             end

code/nnv/examples/Submission/WiP_3d/verify_vessel.m

@@ -20,9 +20,23 @@
 net = matlab2nnv(net);
 
 % select volumes to verify
-N = 50; % even for numCores
-inputs = single(test_images(:,:,:,:,1:N));
-targets = single(test_labels(1:N));
+N = 50;
+idxs = zeros(N,1);
+count = 1;
+
+for i = 1:length(test_labels)
+    y = classify(matlabNet,test_images(:,:,:,i));
+    if single(y) == test_labels(i)
+        idxs(count) = i;
+        count = count + 1;
+    end
+    if count > N
+        break
+    end
+end
+
+inputs = single(test_images(:,:,:,idxs));
+targets = single(test_labels(idxs));
 
 % Reachability parameters
 reachOptions = struct;
@@ -52,7 +66,7 @@
 
             % 3) Begin verification analysis
             for i=1:N
-                img = squeeze(inputs(:,:,:,:,i));
+                img = inputs(:,:,:,i);
                 target = targets(i);
                 results(i,:) = verify_instance_shape(net, img, target, adv_attack, reachOptions);
             end