svn to git migration

CWLocationString.m

@@ -0,0 +1,23 @@
+function locStr=CWLocationString(pt_name,tar_loc),
+
+locStr='';
+%# Patients with non-standard DVH names
+anom_pts = {'Cohen','Lapid','Menaker','Pisano','Sutton','Underkoffler'};
+
+matches = strcmp(anom_pts,pt_name);
+
+if sum(matches)>0,
+    if tar_loc(2)=='U',
+        locStr='CW2SUP';
+    else
+        locStr='CW2INF';
+    end
+else %# not anomoly, just determine L/R
+     if tar_loc(1)=='R',
+        locStr='CW2RT';
+    else
+        locStr='CW2LT';
+     end
+end
+
+end

CWPDataIntegration.m

@@ -0,0 +1,171 @@
+function CWPDataIntegration
+tic;
+% parameters
+    dvhdef={'2cmExp';'Colorado'};
+
+    b2a = 0;
+
+% load patient info stored in the spread sheet
+	fn='Z:/Fan/Andy/Ken/meta/20100424CWFinalCohort';
+    if isunix
+        fn=strrep(fn,'G:','/media/SKI_G');
+    end
+    try
+        load(fn,'xlsraw');
+    catch
+        [~,~,xlsraw]=xlsread([fn,'.xlsx'],'sheet1');
+        save(fn,'xlsraw');
+    end
+
+% pick up related data from the spread sheet
+    PtInfo = classDataFromXls();
+    PtInfo.mXlsRaw = xlsraw;
+    % identity
+    PtInfo.mColName = 'Patient Last Name';
+    PtInfo = PtInfo.fExtractColData();
+    flgptcode = PtInfo.mFlgDataRows;
+    ptcode = PtInfo.mColData;
+    % Number of Fractions
+    PtInfo.mColName = 'Number of Fractions';
+    PtInfo = PtInfo.fExtractColData();
+    flgfx = PtInfo.mFlgDataRows;
+    fx = zeros(size(flgfx));
+    fx(flgfx) = cell2mat(PtInfo.mColData(flgfx));
+    % Date of Birth
+    PtInfo.mColName = 'Date of Birth';
+    PtInfo = PtInfo.fExtractColData();
+    flgdatebirth = PtInfo.mFlgDataRows;
+    datebirth = zeros(size(flgdatebirth));
+    f = PtInfo.mColData(flgdatebirth);
+    datebirth(flgdatebirth) = datenum(f);
+    % IGRT Start Date
+    PtInfo.mColName = 'IGRT Start Date';
+    PtInfo = PtInfo.fExtractColData();
+    flgdateIGRT = PtInfo.mFlgDataRows;
+    dateIGRT = zeros(size(flgdateIGRT));
+    f = PtInfo.mColData(flgdateIGRT);
+    dateIGRT(flgdateIGRT) = datenum(f);
+    % Last Follow Up Date
+    PtInfo.mColName = 'Surv Date';
+    PtInfo = PtInfo.fExtractColData();
+    flgdatefu = PtInfo.mFlgDataRows;
+    datefu = zeros(size(flgdatefu));
+    datefu(flgdatefu) = datenum(PtInfo.mColData(flgdatefu));
+    % complication grade 3
+    PtInfo.mColName = 'Pain Grade 3';
+    PtInfo = PtInfo.fExtractColData();
+    datepain = inf(size(PtInfo.mColData));
+    flgcensor = true(size(datefu));
+    f = PtInfo.mFlgDataRows;
+    datepain(f) = datenum(PtInfo.mColData(f));
+    flgcensor(f) = false;
+    % complication grade 2
+    PtInfo.mColName = 'Pain Grade 2';
+    PtInfo = PtInfo.fExtractColData();
+    f = PtInfo.mFlgDataRows;
+    datepain(f) = datenum(PtInfo.mColData(f));
+    flgcensor(f) = false;
+    % relapse date
+    PtInfo.mColName = 'Local Failure';
+    PtInfo = PtInfo.fExtractColData();
+    f = PtInfo.mFlgDataRows;
+    flgfailure = false(size(f));
+    flgfailure(f) = cell2mat(PtInfo.mColData(f));
+    PtInfo.mColName = 'Local Failure Date';
+    PtInfo = PtInfo.fExtractColData();
+    flgrelapse = PtInfo.mFlgDataRows;
+    datefailure = inf(size(flgrelapse));
+    datefailure(flgrelapse&flgfailure) = datenum(PtInfo.mColData(flgrelapse&flgfailure));
+    flgrelapse = flgrelapse&f;
+    % gender
+    PtInfo.mColName = 'Sex';
+    PtInfo = PtInfo.fExtractColData();
+    flggender = PtInfo.mFlgDataRows;
+    ptgender = PtInfo.mColData;
+    % death date
+    PtInfo.mColName = 'Surv alive 0, dead 1';
+    PtInfo = PtInfo.fExtractColData();
+    f1 = PtInfo.mFlgDataRows;
+    flgdeath = false(size(f1));
+    flgdeath(f1) = cell2mat(PtInfo.mColData(f1));
+    PtInfo.mColName = 'death Date';
+    PtInfo = PtInfo.fExtractColData();
+    f = PtInfo.mFlgDataRows;
+    datedeath = inf(size(f));
+    datedeath(f&flgdeath) = datenum(PtInfo.mColData(f&flgdeath));
+    flgdeath = f1&f;
+
+    % common part of those data
+    flg = flgptcode & flgfx & flgdatebirth & flgdateIGRT & flgdatefu & flgrelapse & flggender & flgdeath;
+    ptcode=ptcode(flg);
+    fx=fx(flg);
+    datebirth=datebirth(flg);
+    dateIGRT=dateIGRT(flg);
+    datefu=datefu(flg);
+    datepain=datepain(flg);
+    flgcensor=flgcensor(flg);
+    datefailure = datefailure(flg);
+    ptgender = ptgender(flg);
+    datedeath = datedeath(flg);
+
+% patient DVH and objects
+    CGobj_org=classEndPointGroup();
+    CGobj_org.mBeta2Alpha = b2a;
+    for m=1:length(dvhdef) % iterate with each definition
+        % load dvh info
+        fn=['G:/MSKCC/Andy/Ken/meta/DVH_',dvhdef{m}];
+        if isunix
+            fn=strrep(fn,'G:','/media/SKI_G');
+        end
+        load(fn,'DVH');
+
+        % match patients DVH and .xls
+        [f1,g1]=ismember(ptcode,DVH(:,1));
+        [f2,g2]=ismember(DVH(:,1),ptcode);
+        if length(unique(g2(g2~=0)))~=length(find(g2))% || length(unique(g2~=0))~=length(find(g2))
+            error('The patient ids are not unique');
+        end
+        if ~( all(f1) && all(f2) )
+            disp('The patients in the spread sheet do not match with those in DVH curves, take the common part');
+            % use common part only
+            DVH=DVH(f2,:);
+            ptcode=ptcode(f1); fx=fx(f1); datebirth=datebirth(f1); dateIGRT=dateIGRT(f1); datefu=datefu(f1); datepain=datepain(f1); flgcensor=flgcensor(f1);
+            [~,g1]=ismember(ptcode,DVH(:,1));
+        end
+
+        % combine info from DVH and .xls to form complicationgroup object
+        CIobjs = classEndPointIndividual();
+        CIobjs = repmat(CIobjs,[size(DVH,1),1]);
+        for n = 1:size(DVH,1)
+            CIobjs(n,1).mID=ptcode{n};
+            CIobjs(n,1).mDoseBins_org=DVH{g1(n),2}(:,1);
+            CIobjs(n,1).mVolDiff=DVH{g1(n),2}(:,2);
+            CIobjs(n,1).mVolCum=DVH{g1(n),2}(:,3);
+            CIobjs(n,1).mFxNum=fx(n);
+            %                 CIobjs(n,1).DoseStep = dosestep;
+            %                 CIobjs(n,1).VolStep = volstep;
+            CIobjs(n,1).mDateBirth = datebirth(n);
+            CIobjs(n,1).mDateBaseline = dateIGRT(n);
+            CIobjs(n,1).mDateComp = datepain(n);
+            CIobjs(n,1).mDateLastFollowup = datefu(n);
+            CIobjs(n,1).mFlgCensor = flgcensor(n);
+            CIobjs(n,1).mDateRelapse = datefailure(n);
+            CIobjs(n,1).mGender = ptgender(n);
+            CIobjs(n,1).mDateDeath = datedeath(n);
+        end
+        if any([CIobjs.mFxNum]==0)
+            error('Fraction number is zeros');
+        end
+        CGobj = CGobj_org.fAddPatient(CIobjs);
+
+        % save result
+        CGstrct = ObjToStruct(CGobj);
+        fn=['G:/MSKCC/Andy/Ken/tom/CW_',dvhdef{m},'.mat'];
+        if isunix
+            fn=strrep(fn,'G:','/media/SKI_G');
+        end
+        save(fn,'CGobj','CGstrct');
+        disp(fn);
+    end
+toc;
+end