datastore error in dicom AI classification
2 views (last 30 days)
Show older comments
hi i get this error i need some help to fix it ?
Error using matlab.io.datastore.ImageDatastore
Files must be a valid string scalar, character vector, cell array of character vectors, string array, or a
matlab.io.datastore.FileSet.
on this row
imds = imageDatastore(dataSource,...
'IncludeSubfolders',true,...
'FileExtensions','.dcm',...
'ReadFcn',@(dcmfile) repmat(uint8(dicomread(dicominfo(dcmfile))),1,1,3));
pxds = pixelLabelDatastore(cellstr(labelData),labelDefs.Name,labelDefs.PixelLabelID,...
'IncludeSubfolders',true,...
'ReadFcn',@readFramesLabels,...
'FileExtensions','.mat');
pxlabeltbl = countEachLabel(pxds)
more over if someone can double check my code i whould realy appriciate it
this is the code
clear; close all; clc
%doTraining ;
try
prj = currentProject;
catch
OpenProject(pwd)
OpenPart01;
prj = currentProject;
end
datafolder = fullfile(prj.RootFolder,'Data');
load(fullfile(datafolder,"gTruthMed.mat"))
dataSource = gTruthMed.DataSource.Source;
labelData = gTruthMed.LabelData;
labelDefs = gTruthMed.LabelDefinitions;
imds = imageDatastore(dataSource,...
'IncludeSubfolders',true,...
'FileExtensions','.dcm',...
'ReadFcn',@(dcmfile) repmat(uint8(dicomread(dicominfo(dcmfile))),1,1,3));
pxds = pixelLabelDatastore(cellstr(labelData),labelDefs.Name,labelDefs.PixelLabelID,...
'IncludeSubfolders',true,...
'ReadFcn',@readFramesLabels,...
'FileExtensions','.mat');
pxlabeltbl = countEachLabel(pxds);
[net,info] = trainNetwork(datasource,lgraph,options);
augmenter = imageDataAugmenter('RandXReflection',true,...
'RandXTranslation',[-10 10], 'RandYTranslation',[-10 10],...
'RandRotation',[0 180]);
dataSource = pixelLabelImageDatastore(imds,pxds,...
'DataAugmentation',augmenter);
imtotal = numel(dataSource.Images);
trainidx = floor(imtotal*0.75);
validx = floor(imtotal*0.2);
testidx = floor(imtotal*0.05);
shuffleindx = randperm(imtotal);
trainds = partitionByIndex(datasource,shuffleindx(1:trainidx));
valds = partitionByIndex(dataSource,shuffleindx(trainidx+1:trainidx+validx));
testds = partitionByindex(dataSource,shuffleindx(trainidx+validx+1:end));
bar([numel(trainds.Images),numel(valds.Images),numel(testds.Images)])
title('Partitioned Dataset')
xticklabels({'Training Set','Validation Set','Testing Set'})
ylabel('Number of dicoms')
imageSize = [256 256 3];
numClasses = height(pxlabeltbl);
lgraph = segnetLayers(imageSize,numClasses,'vgg16');
analyzeNetwork(lgraph)
freaquency = pxlabeltbl.PixelCount ./ pxlabeltbl.ImagePixelCount;
bar(1:height(pxlabeltbl),frequency)
xticklabels(pxlabeltbl.Name); xtickangle(45)
ylabel('Frequency')
lgraph.Layers(end)
pxLayer = dicePixelClassificatoinLayer(...
'Name','Label');
lgraph = removeLayers(lgraph, lgraph.Layers(end).Name);
lgraph = addLayers(lgraph,pxLayer);
lgraph = connectLayers(lgraph,lgraph.Layers(end-1).Name,'labels');
lgraph.Layers(end)
if doTraining
options = trainingOptions('sgdm',...
'Momentum',0.9,...
'InitialLearnRate',0.0002,...
'L2Regularization',0.0005,...
'MaxEpochs',100,...
'MiniBatchSize',4,...
'Shuffle','every-epoch',...
'VerboseFrequency',100,...
'ValidationData',valds,...
'ValidationPatience',5,...
'Plots','training-progress',...
'ExecutionEnvironment','auto');
[net,info] = trainNetwork(tain,lgraph,options);
else
imshow(fullfile(prj.RootFolder,"HelperFunctions","images","SegnetTrainingProgressPlot.png"))
end
load mySemSegNetwork.mat
testimds = imageDatastore(testds.Images,...
'FileExtensions','.dcm',...
'ReadFcn',@(dcmfile) repmat(unit8(dicomread(dicominfo(dcmfile))),1,1,3));
testpxds = pixelLabelDatastore(testds.PixelLabelData,labelDefs.Name,labelDefs.PixelLabelID,...
'includeSubfolders',true,...
'readFcn',@readFramesLabels,...
'FileExtentions','.mat');
pxdsResults = semanticseg(testimds,net,...
'WriteLocation',fullfile(datafolder,'Results'),...
'verbose',true);
[B,imtitle] = overlayRndcontour(testimds,pxdsResults);
imshow(B)
title(imtitle)
metrics = evaluateSemanticSegmentation(pxdsResults,testpxds);
metrics.ClassMetrics
h = heatmap(labelDefs.Name,labelDefs.Name,metrics.NormalizedConfusionMatrix.Variables);
thank you
0 Comments
Answers (1)
Kojiro Saito
on 23 Jan 2023
Possibly,
dataSource = gTruthMed.DataSource.Source;
is N ×1 cell array.
Just converting it to "1 x N cell array" with single quatation (') would work.
imds = imageDatastore(dataSource',...
0 Comments
See Also
Community Treasure Hunt
Find the treasures in MATLAB Central and discover how the community can help you!
Start Hunting!