An error when run Unet Model Deep learning

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mohd akmal masud
mohd akmal masud on 23 Jun 2022
Answered: Ben on 23 Jun 2022
Dear all,
I was develop my network thru apps design. then generate code. Like below.
But I got error.
clc
clear all
close all
%testDataimages
DATASetDir = fullfile('C:\Users\Akmal\Desktop\NEW 3D U NET 128X128');
IMAGEDir = fullfile(DATASetDir,'ImagesTr');
volReader = @(x) matRead(x);
volds = imageDatastore(IMAGEDir, ...
'FileExtensions','.mat','ReadFcn',volReader);
% labelReader = @(x) matread(x);
matFileDir = fullfile('C:\Users\Akmal\Desktop\NEW 3D U NET 128X128\LabelsTr');
classNames = ["background", "tumor"];
pixelLabelID = [0 1];
% pxds = (LabelDirr,classNames,pixelLabelID, ...
% 'FileExtensions','.mat','ReadFcn',labelReader);
pxds = pixelLabelDatastore(matFileDir,classNames,pixelLabelID, ...
'FileExtensions','.mat','ReadFcn',@matRead);
ds = pixelLabelImageDatastore(volds,pxds);
volume = preview(volds);
label = preview(pxds);
patchSize = [128 128 64];
patchPerImage = 16;
miniBatchSize = 8;
patchds = randomPatchExtractionDatastore(volds,pxds,patchSize, ...
'PatchesPerImage',patchPerImage);
patchds.MiniBatchSize = miniBatchSize;
dsTrain = transform(patchds,@augment3dPatch);
volLocVal = fullfile('C:\Users\Akmal\Desktop\NEW 3D U NET 128X128\imagesVal');
voldsVal = imageDatastore(volLocVal, ...
'FileExtensions','.mat','ReadFcn',volReader);
lblLocVal = fullfile('C:\Users\Akmal\Desktop\NEW 3D U NET 128X128\labelsVal');
pxdsVal = pixelLabelDatastore(lblLocVal,classNames,pixelLabelID, ...
'FileExtensions','.mat','ReadFcn',volReader);
dsVal = randomPatchExtractionDatastore(voldsVal,pxdsVal,patchSize, ...
'PatchesPerImage',patchPerImage);
dsVal.MiniBatchSize = miniBatchSize;
lgraph = layerGraph();
tempLayers = [
image3dInputLayer([128 128 64 1],"Name","image3dinput")
convolution3dLayer([3 3 3],64,"Name","Encoder-Stage-1-Conv-1","Padding","same")
reluLayer("Name","Encoder-Stage-1-ReLU-1_1")
%126x126
convolution3dLayer([3 3 3],64,"Name","Encoder-Stage-1-Conv-2","Padding","same")
reluLayer("Name","Encoder-Stage-1-ReLU-1_2")];
%124x124
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
maxPooling3dLayer([2 2 2],"Name","Encoder-Stage-1-MaxPool_1","Padding","same")
%62x62
convolution3dLayer([3 3 3],128,"Name","Encoder-Stage-1-MaxPool_2","Padding","same")
reluLayer("Name","Encoder-Stage-2-ReLU-1")
%60x60
convolution3dLayer([3 3 3],128,"Name","Encoder-Stage-2-Conv-2","Padding","same")
reluLayer("Name","Encoder-Stage-2-ReLU-2")];
%58x58
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
maxPooling3dLayer([2 2 2],"Name","Encoder-Stage-2-MaxPool","Padding","same")
%29x29
convolution3dLayer([3 3 3],256,"Name","Encoder-Stage-3-Conv-1","Padding","same")
reluLayer("Name","Encoder-Stage-3-ReLU-1")
%27x27
convolution3dLayer([3 3 3],256,"Name","conv3d","Padding","same")
reluLayer("Name","Encoder-Stage-3-ReLU-2")];
%25x25
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
dropoutLayer(0.5,"Name","Encoder-Stage-3-DropOut")
maxPooling3dLayer([2 2 2],"Name","Encoder-Stage-3-MaxPool_1","Padding","same")
%12x12
convolution3dLayer([3 3 3],512,"Name","Bridge-Conv-1","Padding","same")
reluLayer("Name","Bridge-ReLU-1")
%10x10
convolution3dLayer([3 3 3],512,"Name","Bridge-Conv-2","Padding","same")
reluLayer("Name","Bridge-ReLU-2")
%8x8
dropoutLayer(0.5,"Name","Bridge-DropOut")
transposedConv3dLayer([2 2 2],256,"Name","Decoder-Stage-1-UpConv","Cropping","same")
reluLayer("Name","Decoder-Stage-1-UpReLU")];
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
depthConcatenationLayer(2,"Name","Decoder-Stage-1-DepthConcatenation")
convolution3dLayer([3 3 3],256,"Name","Decoder-Stage-1-Conv-1","Padding","same")
reluLayer("Name","Decoder-Stage-1-ReLU-1")
convolution3dLayer([3 3 3],256,"Name","Decoder-Stage-1-Conv-2","Padding","same")
reluLayer("Name","Decoder-Stage-1-ReLU-2")
transposedConv3dLayer([2 2 2],128,"Name","Decoder-Stage-2-UpConv","Cropping","same")
reluLayer("Name","Decoder-Stage-2-UpReLU")];
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
depthConcatenationLayer(2,"Name","Decoder-Stage-2-DepthConcatenation")
convolution3dLayer([3 3 3],128,"Name","Decoder-Stage-2-Conv-1","Padding","same")
reluLayer("Name","Decoder-Stage-2-ReLU-1")
convolution3dLayer([3 3 3],128,"Name","Decoder-Stage-2-Conv-2","Padding","same")
reluLayer("Name","Decoder-Stage-2-ReLU-2")
transposedConv3dLayer([2 2 2],64,"Name","Decoder-Stage-3-UpConv","Cropping","same")
reluLayer("Name","Decoder-Stage-3-UpReLU")];
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
depthConcatenationLayer(2,"Name","Decoder-Stage-3-DepthConcatenation")
convolution3dLayer([3 3 3],64,"Name","Decoder-Stage-3-Conv-1","Padding","same")
reluLayer("Name","Decoder-Stage-3-ReLU-1")
convolution3dLayer([3 3 3],64,"Name","Decoder-Stage-3-Conv-2","Padding","same")
reluLayer("Name","Decoder-Stage-3-ReLU-2")
convolution3dLayer([2 2 2],32,"Name","Final-ConvolutionLayer","Padding","same")
softmaxLayer("Name","softmax")
pixelClassificationLayer("Name","pixel-class")];
lgraph = addLayers(lgraph,tempLayers);
% clean up helper variable
clear tempLayers;
lgraph = connectLayers(lgraph,"Encoder-Stage-1-ReLU-1_2","Encoder-Stage-1-MaxPool_1");
lgraph = connectLayers(lgraph,"Encoder-Stage-1-ReLU-1_2","Decoder-Stage-3-DepthConcatenation/in2");
lgraph = connectLayers(lgraph,"Encoder-Stage-2-ReLU-2","Encoder-Stage-2-MaxPool");
lgraph = connectLayers(lgraph,"Encoder-Stage-2-ReLU-2","Decoder-Stage-2-DepthConcatenation/in2");
lgraph = connectLayers(lgraph,"Encoder-Stage-3-ReLU-2","Encoder-Stage-3-DropOut");
lgraph = connectLayers(lgraph,"Encoder-Stage-3-ReLU-2","Decoder-Stage-1-DepthConcatenation/in1");
lgraph = connectLayers(lgraph,"Decoder-Stage-1-UpReLU","Decoder-Stage-1-DepthConcatenation/in2");
lgraph = connectLayers(lgraph,"Decoder-Stage-2-UpReLU","Decoder-Stage-2-DepthConcatenation/in1");
lgraph = connectLayers(lgraph,"Decoder-Stage-3-UpReLU","Decoder-Stage-3-DepthConcatenation/in1");
plot(lgraph);
maxEpochs = 10;
options = trainingOptions('adam', ...
'MaxEpochs',maxEpochs, ...
'InitialLearnRate',1e-3, ...
'LearnRateSchedule','piecewise', ...
'LearnRateDropPeriod',5, ...
'LearnRateDropFactor',0.97, ...
'ValidationData',dsVal, ...
'ValidationFrequency',50, ...
'Plots','training-progress', ...
'Verbose',false, ...
'MiniBatchSize',miniBatchSize);
doTraining = true;
if doTraining
modelDateTime = datestr(now,'dd-mmm-yyyy-HH-MM-SS');
[net,info] = trainNetwork(dsTrain,lgraph,options);
save(['trained3DUNet-' modelDateTime '-Epoch-' num2str(maxEpochs) '.mat'],'net');
else
load('trained3DVNet-07-Jun-2022-13-45-30-Epoch-250.mat');
end
ERROR
Error using trainNetwork
Invalid training data. The output size (32) of the last layer does not match the number of
classes of the responses (2).
Error in basicunetmodel3D (line 170)
[net,info] = trainNetwork(dsTrain,lgraph,options);
Anyone can help me?
  2 Comments

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Accepted Answer

Ben
Ben on 23 Jun 2022
You should set the number of filters on the final convolution layer to match the number of pixel classes for your problem. Tt looks like you have 2 classes, so I would swap convolution3dLayer([2 2 2],32,"Name","Final-ConvolutionLayer","Padding","same") for convolution3dLayer([2 2 2],2,"Name","Final-ConvolutionLayer","Padding","same").
You might also be able to use unetLayers to construct your network, which allows you to specify the numClasses as an input.

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