pixelLabelDatastore only supports pixel label image files with uint8 data

I have built a Segnet (deep learning network) for tumor segmentation. My images are stored in 3D form with extension (.nii) i.e. medical file named NIFTI (Neuro imaging) file. each .nii file contains varying no of slices from 40 to 1200.

Can you please help me to clear this error?

Error using trainNetwork (line 165)
By default, pixelLabelDatastore only supports pixel label  image files with uint8 data. 
Use ReadFcn to specify a custom read function that returns categorical labels from non-uint8 image data.

[Md Shamim Hossain]

Same problem

[hla hla myint]

same problem

[quino]

Excuse me,have you solved this problem?

[Walter Roberson]

Which of the three possibilities I described matches for you? https://www.mathworks.com/matlabcentral/answers/490601-pixellabeldatastore-only-supports-pixel-label-image-files-with-uint8-data#answer_408483

Answer 1

[Walter Roberson]

There are three possibilities in this situation:

1)

If the image input file happens to not be uint8, but there are at most 256 different unique input values and each of them represents a different class, then construct a mapping list of the expected unique input values:

value_list = [17, 83:89, 293:295];   %the unique values that occur

Then have a custom ReadFcn that does:

InputImage = imread(filename);
[~, idx] = ismember(InputImage, value_list);
LabelOutput = uint8(idx-1);

2)

If the image input file happens to not be uint8, and there are more than 256 different unique input values, but multiple input values correspond to the same class, so there are at most 256 different classes, then construct a two-part mapping list:

value_list = [17, 83 84 84 86 87 88 89, 293 294 295];   %the unique values that occur
classnums  = [1,   2  2  2  3  4  4  4,   5   6   6];   %corresponding class numbers

and have a custom ReadFcn that does

InputImage = imread(filename);
[~, idx] = ismember(InputImage, value_list);
LabelOutput = uint8(classnums(idx));

3)

If the image input file happens to not be uint8, and there are more than 256 different classes, then use the technique shown in https://www.mathworks.com/help/matlab/ref/categorical.html#bt0w4ft-4 "Specify category names for integers" to construct a categorical array corresponding to the inputs. If you want multiple input values to correspond to the same category then you can list the same category name multiple times. For example,

>> A = categorical(1:10, [1;2;3;4;10],{'one', 'two', 'three', 'three', 'three'}), uint16(A)

A = 

  1×10 categorical array

     one      two      three      three      <undefined>      <undefined>      <undefined>      <undefined>      <undefined>      three 


ans =

  1×10 uint16 row vector

   1   2   3   3   0   0   0   0   0   3

Answer 2

[Gökay Karayegen]

Hello how can I fix the following error. Please help me to solve this problem ?

classNames = ["background","edema","nonEnhancingTumor","enhancingTumour"];
labelIDs   = [0 1 2 3];
dinfo = dir(fullfile(labelDir, '**', '*.nii'));
filenames = fullfile({dinfo.folder}, {dinfo.name});

pxds = pixelLabelDatastore(filenames,classNames,labelIDs);

pxds.ReadFcn = matReader;

ERROR

.bmp,.cur,.fts,.fits,.gif,.hdf,.ico,.j2c,.j2k,.jp2,.jpf,.jpx,.jpg,.jpeg,.pbm,.pcx,.pgm,.png,.pnm,.ppm,.ras,.tif,.tiff,.xwd

Error in pixelLabelDatastore (line 152)

ds = matlab.io.datastore.PixelLabelDatastore.create(location, classes, values, params);

Error in semantik_derinogrenme (line 118)

pxds = pixelLabelDatastore(filenames,classNames,labelIDs);

[Walter Roberson]

You seem to have left out the first line or two of the error message? Was it saying that only the given file types were accepted?

Ah, I see you posted the whole message over at https://www.mathworks.com/matlabcentral/answers/488024-input-folders-or-files-do-not-contain-specified-file-extensions#comment_849845 which is probably a better place to have the conversation.