Segment3DBrainTumorUsingDeepLearningExample/densenet_3d_small.m at master · ImageGuidedTherapyLab/Segment3DBrainTumorUsingDeepLearningExample · GitHub

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%% Create Layer Graph
% Create the layer graph variable to contain the network layers.
%define n as number of channels
n = 1;
lgraph = layerGraph();
%% Add Layer Branches
% Add the branches of the network to the layer graph. Each branch is a linear
% array of layers.

tempLayers = [
    image3dInputLayer([64 64 64 n],"Name","input","Normalization","none")
    batchNormalizationLayer("Name","BN_Module1_Level1")
    convolution3dLayer([3 3 3],32,"Name","conv_Module1_Level1","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module1_Level1")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    batchNormalizationLayer("Name","BN_Module1_Level2")
    convolution3dLayer([3 3 3],44,"Name","conv_Module1_Level2","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module1_Level2")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = concatenationLayer(4,2,"Name","concat_1");
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    maxPooling3dLayer([2 2 2],"Name","maxpool_Module1","Padding","same","Stride",[2 2 2])
    batchNormalizationLayer("Name","BN_Module2_Level1")
    convolution3dLayer([3 3 3],44,"Name","conv_Module2_Level1","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module2_Level1")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    batchNormalizationLayer("Name","BN_Module2_Level2")
    convolution3dLayer([3 3 3],56,"Name","conv_Module2_Level2","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module2_Level2")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = concatenationLayer(4,2,"Name","concat_2");
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    maxPooling3dLayer([2 2 2],"Name","maxpool_Module2","Padding","same","Stride",[2 2 2])
    batchNormalizationLayer("Name","BN_Module3_Level1")
    convolution3dLayer([3 3 3],56,"Name","conv_Module3_Level1","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module3_Level1")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    batchNormalizationLayer("Name","BN_Module3_Level2")
    convolution3dLayer([3 3 3],68,"Name","conv_Module3_Level2","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module3_Level2")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = concatenationLayer(4,2,"Name","concat_3");
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    maxPooling3dLayer([2 2 2],"Name","maxpool_Module3","Padding","same","Stride",[2 2 2])
    batchNormalizationLayer("Name","BN_Module4_Level1")
    convolution3dLayer([3 3 3],68,"Name","conv_Module4_Level1","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module4_Level1")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    batchNormalizationLayer("Name","BN_Module4_Level2")
    convolution3dLayer([3 3 3],80,"Name","conv_Module4_Level2","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module4_Level2")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    concatenationLayer(4,2,"Name","concat_4")
    upsample3dLayer([2 2 2],80,"Name","upsample_Module4","Stride",[2 2 2])];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    concatenationLayer(4,2,"Name","concat3")
    batchNormalizationLayer("Name","BN_Module5_Level1")
    convolution3dLayer([3 3 3],68,"Name","conv_Module5_Level1","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module5_Level1")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    batchNormalizationLayer("Name","BN_Module5_Level2")
    convolution3dLayer([3 3 3],68,"Name","conv_Module5_Level2","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module5_Level2")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    concatenationLayer(4,2,"Name","concat_5")
    upsample3dLayer([2 2 2],68,"Name","upsample_Module5","Stride",[2 2 2])];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    concatenationLayer(4,2,"Name","concat2")
    batchNormalizationLayer("Name","BN_Module6_Level1")
    convolution3dLayer([3 3 3],56,"Name","conv_Module6_Level1","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module6_Level1")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    batchNormalizationLayer("Name","BN_Module6_Level2")
    convolution3dLayer([3 3 3],56,"Name","conv_Module6_Level2","Padding","same","WeightsInitializer","narrow-normal")
    reluLayer("Name","relu_Module6_Level2")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    concatenationLayer(4,2,"Name","concat_6")
    upsample3dLayer([2 2 2],56,"Name","upsample_Module6","Stride",[2 2 2])];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    concatenationLayer(4,2,"Name","concat1")
    batchNormalizationLayer("Name","BN_Module7_Level1")
    convolution3dLayer([3 3 3],44,"Name","conv_Module7_Level1","Padding","same")
    reluLayer("Name","relu_Module7_Level1")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    batchNormalizationLayer("Name","BN_Module7_Level2")
    convolution3dLayer([3 3 3],44,"Name","conv_Module7_Level2","Padding","same")
    reluLayer("Name","relu_Module7_Level2")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    concatenationLayer(4,2,"Name","concat")
    batchNormalizationLayer("Name","BN_Module7_Level3")
    convolution3dLayer([1 1 1],2,"Name","ConvLast_Module7")
    softmaxLayer("Name","softmax")
    dicePixelClassification3dLayer("output")];
lgraph = addLayers(lgraph,tempLayers);

% clean up helper variable
clear tempLayers;
%% Connect Layer Branches
% Connect all the branches of the network to create the network graph.

lgraph = connectLayers(lgraph,"relu_Module1_Level1","BN_Module1_Level2");
lgraph = connectLayers(lgraph,"relu_Module1_Level1","concat_1/in1");
lgraph = connectLayers(lgraph,"relu_Module1_Level2","concat_1/in2");
lgraph = connectLayers(lgraph,"concat_1","maxpool_Module1");
lgraph = connectLayers(lgraph,"concat_1","concat1/in1");
lgraph = connectLayers(lgraph,"relu_Module2_Level1","BN_Module2_Level2");
lgraph = connectLayers(lgraph,"relu_Module2_Level1","concat_2/in1");
lgraph = connectLayers(lgraph,"relu_Module2_Level2","concat_2/in2");
lgraph = connectLayers(lgraph,"concat_2","maxpool_Module2");
lgraph = connectLayers(lgraph,"concat_2","concat2/in1");
lgraph = connectLayers(lgraph,"relu_Module3_Level1","BN_Module3_Level2");
lgraph = connectLayers(lgraph,"relu_Module3_Level1","concat_3/in1");
lgraph = connectLayers(lgraph,"relu_Module3_Level2","concat_3/in2");
lgraph = connectLayers(lgraph,"concat_3","maxpool_Module3");
lgraph = connectLayers(lgraph,"concat_3","concat3/in1");
lgraph = connectLayers(lgraph,"relu_Module4_Level1","BN_Module4_Level2");
lgraph = connectLayers(lgraph,"relu_Module4_Level1","concat_4/in1");
lgraph = connectLayers(lgraph,"relu_Module4_Level2","concat_4/in2");
lgraph = connectLayers(lgraph,"upsample_Module4","concat3/in2");
lgraph = connectLayers(lgraph,"relu_Module5_Level1","BN_Module5_Level2");
lgraph = connectLayers(lgraph,"relu_Module5_Level1","concat_5/in1");
lgraph = connectLayers(lgraph,"relu_Module5_Level2","concat_5/in2");
lgraph = connectLayers(lgraph,"upsample_Module5","concat2/in2");
lgraph = connectLayers(lgraph,"relu_Module6_Level1","BN_Module6_Level2");
lgraph = connectLayers(lgraph,"relu_Module6_Level1","concat_6/in1");
lgraph = connectLayers(lgraph,"relu_Module6_Level2","concat_6/in2");
lgraph = connectLayers(lgraph,"upsample_Module6","concat1/in2");
lgraph = connectLayers(lgraph,"relu_Module7_Level1","BN_Module7_Level2");
lgraph = connectLayers(lgraph,"relu_Module7_Level1","concat/in2");
lgraph = connectLayers(lgraph,"relu_Module7_Level2","concat/in1");
%% Plot Layers

plot(lgraph);