I get this error trying to find Hausdorff dist Array formation and parentheses-style indexing with objects of class 'matlab.io.datastore.PixelLabelDatastore' is not allowed.

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Amira Youssef 2023-3-8

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https://ww2.mathworks.cn/matlabcentral/answers/1925285-i-get-this-error-trying-to-find-hausdorff-dist-array-formation-and-parentheses-style-indexing-with-o

I am trying to test the performance of my trained network and I get the following error:

[hd D] = HausdorffDist(pxdsResults,pxdsTruth,0);

Array formation and parentheses-style indexing with objects of

class 'matlab.io.datastore.PixelLabelDatastore' is not allowed.

Use objects of class 'matlab.io.datastore.PixelLabelDatastore'

only as scalars or use a cell array.

Error in HausdorffDist (line 120)

cP=P(combos(:,1),:);

This is my code :

clear all

close all

clc

dataSetDir = fullfile('LungTS','preprocessedDataset');

testImagesDir = fullfile(dataSetDir,'imagesTest');

imdReader = @(x) matRead(x);

imds = imageDatastore(testImagesDir, ...

'FileExtensions','.mat','ReadFcn',imdReader);

%imds = imageDatastore(testImagesDir);

% classNames = ["nodule" "background"];%The labels for results are ["background" "tumor"], so we should use the same label

classNames = ["background" "tumor"];%%%I add this line.

% labelIDs = [255 0];%The numbers in corresponding .mat data are 0 and 1 (not 0 and 255).

labelIDs = [0 1];%I add this line

labelReader = @(x) matRead(x);

testLabelsDir = fullfile(dataSetDir,'labelsTest');

pxdsTruth = pixelLabelDatastore(testLabelsDir,classNames,labelIDs, ...

'FileExtensions','.mat','ReadFcn',labelReader);

net = load('HybridNetwork-160');

net = net.net;

pxdsResults = semanticseg(imds,net,"WriteLocation",tempdir);

metrics = evaluateSemanticSegmentation(pxdsResults,pxdsTruth);

metrics.ClassMetrics

metrics.ConfusionMatrix

cm = confusionchart(metrics.ConfusionMatrix.Variables, ...

classNames, 'Normalization','row-normalized');%The format corrected.

% classNames, Normalization ='row-normalized');%Wrong format

cm.Title = 'Normalized Confusion Matrix (%)';

imageIoU = metrics.ImageMetrics.MeanIoU;

%figure

%histogram(imageIoU)

%title('Image Mean IoU')

[minIoU, worstImageIndex] = min(imageIoU);

minIoU = minIoU(1);

worstImageIndex = worstImageIndex(1);

worstTestImage = readimage(imds,worstImageIndex);%ehsan: %size is [32 32 32]

worstTrueLabels = readimage(pxdsTruth,worstImageIndex);

worstPredictedLabels = readimage(pxdsResults,worstImageIndex);

worstTrueLabelImage = im2uint8(worstTrueLabels == classNames(1));%ehsan: %size is [32 32 32]

worstPredictedLabelImage = im2uint8(worstPredictedLabels == classNames(1));%ehsan: %size is [32 32 32]

figure,subplot(1,3,1),montage(worstTestImage,'Size',[8 4]),title('Worst Test Image')

subplot(1,3,2),montage(worstTrueLabelImage,'Size',[8 4]),title('Truth')

subplot(1,3,3),montage(worstPredictedLabelImage,'Size',[8 4]),title(['Prediction. IoU = ', num2str(minIoU)])

% title(['Test Image vs. Truth vs. Prediction. IoU = ' num2str(minIoU)])

[maxIoU, bestImageIndex] = max(imageIoU);

maxIoU = maxIoU(1);

bestImageIndex = bestImageIndex(1);

bestTestImage = readimage(imds,bestImageIndex);

bestTrueLabels = readimage(pxdsTruth,bestImageIndex);

bestPredictedLabels = readimage(pxdsResults,bestImageIndex);

bestTrueLabelImage = im2uint8(bestTrueLabels == classNames(1));

bestPredictedLabelImage = im2uint8(bestPredictedLabels == classNames(1));

bestTrueLabelImage(bestTrueLabelImage==0)=2;

bestTrueLabelImage(bestTrueLabelImage==255)=0;

bestTrueLabelImage(bestTrueLabelImage==2)=255;

bestPredictedLabelImage(bestPredictedLabelImage==0)=2;

bestPredictedLabelImage(bestPredictedLabelImage==255)=0;

bestPredictedLabelImage(bestPredictedLabelImage==2)=255;

figure,subplot(1,3,1),montage(bestTestImage,'Size',[8 4]),title('Best Test Image')

subplot(1,3,2),montage(bestTrueLabelImage,'Size',[8 4]),title('Truth')

subplot(1,3,3),montage(bestPredictedLabelImage,'Size',[8 4]),title(['Prediction. IoU = ', num2str(maxIoU)])

% title(['Test Image vs. Truth vs. Prediction. IoU = ' num2str(maxIoU)])

evaluationMetrics = ["accuracy" "iou"];

metrics = evaluateSemanticSegmentation(pxdsResults,pxdsTruth,"Metrics",evaluationMetrics);

metrics.ClassMetrics

confmat = metrics.ConfusionMatrix ;

TP = table2array(confmat(2, 2));

TN = table2array(confmat(1, 1));

FP = table2array(confmat(1, 2));

FN = table2array(confmat(2, 1));

Accuracy = (TP + TN) / (TP + TN + FP + FN)

Sensitivity = TP / (FN + TP)

specificity = TN / (TN + FP)

precision = (TP)/(TP+FP)

Dice=(2*TP)/(2*TP+FP+FN)

MCC=(TP*TN-FP*FN)/sqrt((TP+FN)*(TP+FP)*(TN+FP)*(TN+FN))

Recall=(TP/(TP+FN))

F_score =(2*TP)/((2*TP)+FP+FN)

[hd D] = HausdorffDist(pxdsResults,pxdsTruth,0);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The folowing is the the hasdruf function I am using:

function [hd D] = HausdorffDist(P,Q,lmf,dv)

% Calculates the Hausdorff Distance between P and Q

%

% hd = HausdorffDist(P,Q)

% [hd D] = HausdorffDist(P,Q)

% [hd D] = HausdorffDist(...,lmf)

% [hd D] = HausdorffDist(...,[],'visualize')

%

% Calculates the Hausdorff Distance, hd, between two sets of points, P and

% Q (which could be two trajectories). Sets P and Q must be matrices with

% an equal number of columns (dimensions), though not necessarily an equal

% number of rows (observations).

%

% The Directional Hausdorff Distance (dhd) is defined as:

% dhd(P,Q) = max p c P [ min q c Q [ ||p-q|| ] ].

% Intuitively dhd finds the point p from the set P that is farthest from

% any point in Q and measures the distance from p to its nearest neighbor

% in Q.

%

% The Hausdorff Distance is defined as max{dhd(P,Q),dhd(Q,P)}

%

% D is the matrix of distances where D(n,m) is the distance of the nth

% point in P from the mth point in Q.

%

% lmf: If the size of P and Q are very large, the matrix of distances

% between them, D, will be too large to store in memory. Therefore, the

% function will check your available memory and not build the D matrix if

% it will exceed your available memory and instead use a faster version of

% the code. If this occurs, D will be returned as the empty matrix. You may

% force the code to forgo the D matrix even for small P and Q by calling the

% function with the optional 3rd lmf variable set to 1. You may also force

% the function to return the D matrix by setting lmf to 0. lmf set to []

% allows the code to automatically choose which mode is appropriate.

%

% Including the 'vis' or 'visualize' option plots the input data of

% dimension 1, 2 or 3 if the small dataset algorithm is used.

%

% Performance Note: Including the lmf input increases the speed of the

% algorithm by avoiding the overhead associated with checking memory

% availability. For the lmf=0 case, this may represent a sizeable

% percentage of the entire run-time.

%

% %%% ZCD Oct 2009 %%%

% Edits ZCD: Added the matrix of distances as an output. Fixed bug that

% would cause an error if one of the sets was a single point. Removed

% excess calls to "size" and "length". - May 2010

% Edits ZCD: Allowed for comparisons of N-dimensions. - June 2010

% Edits ZCD: Added large matrix mode to avoid insufficient memory errors

% and a user input to control this mode. - April 2012

% Edits ZCD: Using bsxfun rather than repmat in large matrix mode to

% increase performance speeds. [update recommended by Roel H on MFX] -

% October 2012

% Edits ZCD: Added a plotting function for visualization - October 2012

%

sP = size(P); sQ = size(Q);

if ~(sP(2)==sQ(2))

error('Inputs P and Q must have the same number of columns')

end

if nargin > 2 && ~isempty(lmf)

% the user has specified the large matrix flag one way or the other

largeMat = lmf;

if ~(largeMat==1 || largeMat==0)

error('3rd ''lmf'' input must be 0 or 1')

end

else

largeMat = 0; % assume this is a small matrix until we check

% If the result is too large, we will not be able to build the matrix of

% differences, we must loop.

if sP(1)*sQ(1) > 2e6

% ok, the resulting matrix or P-to-Q distances will be really big, lets

% check if our memory can handle the space we'll need

memSpecs = memory; % load in memory specifications

varSpecs = whos('P','Q'); % load in variable memory specs

sf = 10; % build in a saftey factor of 10 so we don't run out of memory for sure

if prod([varSpecs.bytes]./[sP(2) sQ(2)]) > memSpecs.MaxPossibleArrayBytes/sf

largeMat = 1; % we have now concluded this is a large matrix situation

end

if largeMat

% we cannot save all distances, so loop through every point saving only

% those that are the best value so far

maxP = 0; % initialize our max value

% loop through all points in P looking for maxes

for p = 1:sP(1)

% calculate the minimum distance from points in P to Q

minP = min(sum( bsxfun(@minus,P(p,:),Q).^2, 2));

if minP>maxP

% we've discovered a new largest minimum for P

maxP = minP;

end

% repeat for points in Q

maxQ = 0;

for q = 1:sQ(1)

minQ = min(sum( bsxfun(@minus,Q(q,:),P).^2, 2));

if minQ>maxQ

maxQ = minQ;

end

hd = sqrt(max([maxP maxQ]));

D = [];

else

% we have enough memory to build the distance matrix, so use this code

% obtain all possible point comparisons

iP = repmat(1:sP(1),[1,sQ(1)])';

iQ = repmat(1:sQ(1),[sP(1),1]);

combos = [iP,iQ(:)];

% get distances for each point combination

cP=P(combos(:,1),:);

cQ=Q(combos(:,2),:);

dists = sqrt(sum((cP - cQ).^2,2));

% Now create a matrix of distances where D(n,m) is the distance of the nth

% point in P from the mth point in Q. The maximum distance from any point

% in Q from P will be max(D,[],1) and the maximum distance from any point

% in P from Q will be max(D,[],2);

D = reshape(dists,sP(1),[]);

% Obtain the value of the point, p, in P with the largest minimum distance

% to any point in Q.

vp = max(min(D,[],2));

% Obtain the value of the point, q, in Q with the largets minimum distance

% to any point in P.

vq = max(min(D,[],1));

hd = max(vp,vq);

end

% - visualization ---

if nargin==4 && any(strcmpi({'v','vis','visual','visualize','visualization'},dv))

if largeMat == 1 || sP(2)>3

warning('MATLAB:actionNotTaken',...

'Visualization failed because data sets were too large or data dimensionality > 3.')

return;

end

% visualize the data

figure

subplot(1,2,1)

hold on

axis equal

% need some data for plotting

[mp ixp] = min(D,[],2);

[mq ixq] = min(D,[],1);

[mp ixpp] = max(mp);

[mq ixqq] = max(mq);

[m ix] = max([mq mp]);

if ix==2

ixhd = [ixp(ixpp) ixpp];

xyf = [Q(ixhd(1),:); P(ixhd(2),:)];

else

ixhd = [ixqq ixq(ixqq)];

xyf = [Q(ixhd(1),:); P(ixhd(2),:)];

end

% -- plot data --

if sP(2) == 2

h(1) = plot(P(:,1),P(:,2),'bx','markersize',10,'linewidth',3);

h(2) = plot(Q(:,1),Q(:,2),'ro','markersize',8,'linewidth',2.5);

% draw all minimum distances from set P

Xp = [P(1:sP(1),1) Q(ixp,1)];

Yp = [P(1:sP(1),2) Q(ixp,2)];

plot(Xp',Yp','-b');

% draw all minimum distances from set Q

Xq = [P(ixq,1) Q(1:sQ(1),1)];

Yq = [P(ixq,2) Q(1:sQ(1),2)];

plot(Xq',Yq','-r');

% denote the hausdorff distance

h(3) = plot(xyf(:,1),xyf(:,2),'-ks','markersize',12,'linewidth',2);

uistack(fliplr(h),'top')

xlabel('Dim 1'); ylabel('Dim 2');

title(['Hausdorff Distance = ' num2str(m)])

legend(h,{'P','Q','Hausdorff Dist'},'location','best')

elseif sP(2) == 1

ofst = hd/2; % plotting offset

h(1) = plot(P(:,1),ones(1,sP(1)),'bx','markersize',10,'linewidth',3);

h(2) = plot(Q(:,1),ones(1,sQ(1))+ofst,'ro','markersize',8,'linewidth',2.5);

% draw all minimum distances from set P

Xp = [P(1:sP(1)) Q(ixp)];

Yp = [ones(sP(1),1) ones(sP(1),1)+ofst];

plot(Xp',Yp','-b');

% draw all minimum distances from set Q

Xq = [P(ixq) Q(1:sQ(1))];

Yq = [ones(sQ(1),1) ones(sQ(1),1)+ofst];

plot(Xq',Yq','-r');

% denote the hausdorff distance

h(3) = plot(xyf(:,1),[1+ofst;1],'-ks','markersize',12,'linewidth',2);

uistack(fliplr(h),'top')

xlabel('Dim 1'); ylabel('visualization offset');

set(gca,'ytick',[])

title(['Hausdorff Distance = ' num2str(m)])

legend(h,{'P','Q','Hausdorff Dist'},'location','best')

elseif sP(2) == 3

h(1) = plot3(P(:,1),P(:,2),P(:,3),'bx','markersize',10,'linewidth',3);

h(2) = plot3(Q(:,1),Q(:,2),Q(:,3),'ro','markersize',8,'linewidth',2.5);

% draw all minimum distances from set P

Xp = [P(1:sP(1),1) Q(ixp,1)];

Yp = [P(1:sP(1),2) Q(ixp,2)];

Zp = [P(1:sP(1),3) Q(ixp,3)];

plot3(Xp',Yp',Zp','-b');

% draw all minimum distances from set Q

Xq = [P(ixq,1) Q(1:sQ(1),1)];

Yq = [P(ixq,2) Q(1:sQ(1),2)];

Zq = [P(ixq,3) Q(1:sQ(1),3)];

plot3(Xq',Yq',Zq','-r');

% denote the hausdorff distance

h(3) = plot3(xyf(:,1),xyf(:,2),xyf(:,3),'-ks','markersize',12,'linewidth',2);

uistack(fliplr(h),'top')

xlabel('Dim 1'); ylabel('Dim 2'); zlabel('Dim 3');

title(['Hausdorff Distance = ' num2str(m)])

legend(h,{'P','Q','Hausdorff Dist'},'location','best')

end

subplot(1,2,2)

% add offset because pcolor ignores final rows and columns

[X Y] = meshgrid(1:(sQ(1)+1),1:(sP(1)+1));

hpc = pcolor(X-0.5,Y-0.5,[[D; D(end,:)] [D(:,end); 0]]);

set(hpc,'edgealpha',0.25)

xlabel('ordered points in Q (o)')

ylabel('ordered points in P (x)')

title({'Distance (color) between points in P and Q';...

'Hausdorff distance outlined in white'})

colorbar('location','SouthOutside')

hold on

% bug: does not draw when hd is the very last point

rectangle('position',[ixhd(1)-0.5 ixhd(2)-0.5 1 1],...

'edgecolor','w','linewidth',2);

end

Can anyone help me how to modify these data please????????

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I get this error trying to find Hausdorff dist Array formation and parentheses-style indexing with objects of class 'matlab.io.datastore.PixelLabelDatastore' is not allowed.

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I get this error trying to find Hausdorff dist Array formation and parentheses-style indexing with objects of class 'matlab.io​.datastore​.PixelLabe​lDatastore​' is not allowed.

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I get this error trying to find Hausdorff dist Array formation and parentheses-style indexing with objects of class 'matlab.io.datastore.PixelLabelDatastore' is not allowed.

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