inbreastBuilder.m

%         	INbreast Release 1.0
%Breast Research Group, INESC Porto, Portugal
%http://medicalresearch.inescporto.pt/breastresearch/
%     	medicalresearch@inescporto.pt
xlsdata= read_mixed_csv('../INBreast.csv',';');
biradsclass = xlsdata(2:end,8);
biradsclassFilename=xlsdata(2:end,6);
date=xlsdata(2:end,5);
[sortedFilenames,idx]=sort(biradsclassFilename);
biradsclass=biradsclass(idx);
date=date(idx);
DIR = dir('.\*.dcm');
nn=numel(DIR);
INbreast=cell(nn,8);
for k=1:nn
	disp(num2str(k))
	info=dicominfo(DIR(k).name);
	INbreast{k,1}=k;

	lineData = textscan(DIR(k).name, '%s', 'Delimiter','_');
	lineData = lineData{1};
	%INbreast{k,2} is empty - name
	INbreast{k,3}=lineData{2};%patient ID
	INbreast{k,4}=lineData{3}; %Modality - MG
	INbreast{k,5}=lineData{5}; %ViewPosition CC or ML(O)
	%INbreast{k,6} is empty - date
	INbreast{k,7}=DIR(k).name;
	%INbreast{k,8} is empty - birads
end
dicomFilename=INbreast(:,7);
[sortedFilenames,idx]=sort(dicomFilename);
INbreast=INbreast(idx,:);
INbreast(:,8)=biradsclass;
INbreast(:,6)=date;

%organize by cases: a case is the set of all views for a single patient for
%a single day. We have 117 cases.
%IMPORTANT NOTE: in the Academic Radiology publication the number is wrongly presented as 115.
PatientInfo=strcat(INbreast(:,3),INbreast(:,6));
uniquePatientInfo=unique(PatientInfo);
for n=1:length(uniquePatientInfo)
	idx = find(ismember(PatientInfo, uniquePatientInfo(n))==1);
	INbreastCase{n}=idx;
end

%just usage example
caseBirads =-10*ones(length(INbreastCase),1);
caseLen = zeros(length(INbreastCase),1);
for n=1:length(INbreastCase)
% 	disp(['case ', num2str(n)]);
	curr_case = INbreastCase{n};
	curr_biradsSet=[];
	caseLen(n)=length(curr_case);
	for i=1:length(curr_case)
    	filename = INbreast{curr_case(i),7};
    	birads= INbreast{curr_case(i),8};
    	negFolder = 'neg';
    	posFolder = 'pos';
    	if contains(birads, "1") || contains(birads, "2")
        	copyfile([filename],[negFolder]);
    	end

    	if contains(birads, "4") || contains(birads, "5") || contains(birads, "6")
        	copyfile([filename],[posFolder]);
    	end

    	curr_biradsSet=[curr_biradsSet,sscanf(birads, '%g')];

    	%img=dicomread(filename);
    	%imshow(img,[]);
	end
	caseBirads(n)=max(curr_biradsSet);
end
%[caseLen caseBirads]
% figure, hist(caseLen, 1:8)
% figure, hist(caseBirads, 0:6)