How can I label DICOM images for classification based on folder name
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Cameron Harris
el 10 de Mzo. de 2018
Editada: shivan artosh
el 2 de Abr. de 2020
I want to carry out transfer learning using AlexNet for a set of 128x128 DICOM images. It looks like on of the most efficient methods of storing and labeling images is using imageDatastore, however I don't think this supports DICOM formats, I can create the store with no errors using:
images = imageDatastore(fullfile(pwd,'Project_Segmentations'),...
'IncludeSubfolders',true,'FileExtensions','.dcm',...
'LabelSource','foldernames');
This correctly labels the DICOMs based on the name of the folder they are in, however, when I try to use this data for training I'm met with the error:
Error using matlab.io.datastore.ImageDatastore/readimage (line 32)
Error using ReadFcn @readDatastoreImage function handle for file
Which makes sense given imread doesn't support DICOM images.
Ideally I want to keep the DICOM file format, is there anyway I can achieve this data labeling for DICOM images?
Many Thanks.
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Image Analyst
el 10 de Mzo. de 2018
Perhaps write a utility that reads in all the images and stores them out in PNG format.
for k = 1 : numImages
thisImage = dicomread(....
outputFileName = strrep(lower(inputFileName), '.dcm', '.png');
imwrite(thisImage, outputFileName);
end
3 comentarios
ahmed adam
el 14 de Mayo de 2018
I have the same problem now , did you change the format to PNG or continue as dicom images ?
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Khalid
el 19 de En. de 2019
I have faced a similar issue in wich I had to create another readDatastoreImage function. You might solved it this way:
Create a copy of the readDatastoreImage function within the imageDatastore function and give it a different name, for example: readDicomDatastoreImage
Then change the imread(filename) function wihin the one you copyed to dicomread(filename)
finaly, use it with the imageDatastore function this way:
imds = imageDatastore(imageDir, 'FileExtensions','.dcm','ReadFcn',@readDicomDatastoreImage);
Hope this can help
Khalid
3 comentarios
Khalid Babutain
el 26 de Mzo. de 2020
1. write in your main code:
imds = imageDatastore('DataSet', ...
'IncludeSubfolders',true, 'LabelSource','foldernames', ... % this for labeling by folder names
'FileExtensions','.dcm','ReadFcn',@readDicomDatastoreImage);
2. create (readDicomDatastoreImage) function that include:
function I = readDicomDatastoreImage(filename)
onState = warning('off', 'backtrace');
c = onCleanup(@() warning(onState));
I = dicomread(filename);
in this way, each time you read an image from your (imds) it will be read using (readDicomDatastoreImage) function
Hope this is clear
Khalid
shivan artosh
el 26 de Mzo. de 2020
Editada: shivan artosh
el 2 de Abr. de 2020
thank you so much sir it is really helpful
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