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Bugfixes
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Corrected issues with text fields.
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@robdahn
robdahn committed Jun 5, 2024
1 parent d39b20c commit ef7fec4
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Showing 2 changed files with 101 additions and 40 deletions.
14 changes: 11 additions & 3 deletions cat_io_struct2cell.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@

FN = fieldnames(S);
C = struct2cell(S);
for ci = numel(C):-1:1
for ci = numel(C)-1:-1:1
if isstruct(C{ci})
% recursive call
[FNi,Ci] = cat_io_struct2cell(C{ci});
Expand All @@ -43,9 +43,17 @@
FNi{FNii} = sprintf('%s%s%s',FN{ci},separator,FNi{FNii});
end

% update fieldnames and cell
% update fieldnames and cell if not empty
FN = [FN(1:ci-1); FNi; FN(ci+1:end)];
C = [C(1:ci-1); Ci; C(ci+1:end)];
if numel(Ci) > 0
try
if size(C,1) > size(C,2)
C = [C(1:ci-1,:); Ci; C(ci+1:end,:)];
else
C = [C(:,1:ci-1), Ci, C(:,ci+1:end)];
end
end
end
end
end

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127 changes: 90 additions & 37 deletions cat_stat_getCSVXMLfield.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,7 @@
};
if ~isempty( job.fields ) && ~isempty( job.fields{1} )
fields = genvarname(cat_io_strrep(cat_io_strrep(cat_io_strrep( job.fields ,replaceset{1,1},replaceset{1,2}),replaceset{2,1},replaceset{2,2}),'__','_'));
fields = cat_io_strrep(fields,'x0x2E','.');
fields = cat_io_strrep(fields,{'x0x2E','0x2E'},{'.','.'});
for si = numel(fields):-1:1
if ~isnan( str2double(job.fields{si}) ), fields(si) = []; end
end
Expand Down Expand Up @@ -273,7 +273,7 @@
[xmlfull,xmlcell] = cat_io_struct2cell( xml );

% match/select fields
if ~isempty( job.fields ) && isempty( job.fields{1} )
if ~isempty( job.fields ) && ~isempty( job.fields{1} ) %~isempty( fields )
xmlfull = xmlfull( cat_io_contains( xmlfull, fields ) );
end

Expand Down Expand Up @@ -454,7 +454,7 @@
pps = textscan(pp,'%s','Delimiter',filesep);
if numel(job.fnamefields(fi).filesel)>1
ff = pps{1}{job.fnamefields(fi).filesel(1):job.fnamefields(fi).filesel(2)};
elseif numel(job.fnamefields(fi).filesel)==1
elseif isscalar(job.fnamefields(fi).filesel)
try
ff = pps{1}{job.fnamefields(fi).filesel(1)};
catch
Expand Down Expand Up @@ -532,7 +532,7 @@
pps = textscan(pp,'%s','Delimiter',filesep);
if numel(job.idselector.filesel)>1
ff = pps{1}{job.idselector.filesel(1):job.idselector.filesel(2)};
elseif numel(job.idselector.filesel)==1
elseif isscalar( job.idselector.filesel )
ff = pps{1}{job.idselector.filesel(1)};
end
end
Expand All @@ -556,14 +556,14 @@
cat_io_cprintf('err',sprintf('Cannot find data for "%s". You selected "%s" of the filename.\n',P{si},ff));
out.(csvsvars{fi}){si,1} = nan;
elseif numel(ids)>1
if numel( unique( [csv{ids + 1,1}] ) )==1
if isscalar( unique( [csv{ids + 1,1}] ) )
warn = sprintf(' Found multiple possible entries for subject "%s". Take the first entry. Check your csv file! \n',P{si});
out.(csvsvars{fi}){si,1} = csv{ids + 1,csvsvari(fi)};
else
warn = sprintf(' Found multiple possible entries (index=[ %s]) for subject in "%s". Check file!\n',sprintf('%d ',ids),P{si});
out.(csvsvars{fi}){si,1} = nan;
end
if isempty( strfind(warns,warn) )
if cat_io_contains(warns,warn)
cat_io_cprintf('warn',warn);
warns = [warns warn];
end
Expand All @@ -575,7 +575,7 @@
if isnumeric( out.(csvsvars{fi}){1} )
clear temp
try
error
%error
temp = cell2mat(out.(csvsvars{fi}));
out = rmfield(out,csvsvars{fi});
out.(csvsvars{fi}) = temp;
Expand Down Expand Up @@ -605,8 +605,9 @@

% remove CSV fields
[xmlvars,xmlvarsi] = setdiff( xmlfields , csvsvars );
xmlvars0 = xmlvars; %fields(xmlvarsi);
xmlvarsf = cat_io_strrep(xmlvars,{'.','(',')','{','}'},{'_','','','',''});
xmlvars0 = xmlvars; %fields(xmlvarsi);
xmlvars00 = fieldnames(XML);
xmlvarsf = cat_io_strrep(xmlvars,{'.','(',')','{','}'},{'_','','','',''});

% check if fields exist
for fi = numel(xmlvars0):-1:1
Expand Down Expand Up @@ -638,9 +639,9 @@
val = NaN;
elseif iscell(out.(xmlvarsf{fi})(1))
if isnumeric(out.(xmlvarsf{fi}){1})
var = NaN;
var = NaN; %#ok<NASGU>
else
var = 'NaN';
var = 'NaN'; %#ok<NASGU>
end
else
val = 'NaN';
Expand All @@ -652,10 +653,19 @@
else
out.(xmlvarsf{fi}){si,1} = 'NA';
end
elseif ischar( val )
out.(xmlvarsf{fi}){si,1} = val;
else
out.(xmlvarsf{fi})(si,1) = val(1);
try
out.(xmlvarsf{fi})(si,1) = val(1);
catch
if si>2 & ischar(out.(xmlvarsf{fi}){si-1,1})
out.(xmlvarsf{fi}){si,1} = 'NA';
else
out.(xmlvarsf{fi}){si,1} = NaN;
end
end
end

end
end

Expand All @@ -666,18 +676,18 @@
else
missed = setdiff( job.fields , xmlvars0 );
end
if ~isempty(missed)
if numel(missed)>0 && ~isempty(missed{1})
if job.dep
fprintf('getCSVXML setup: Cannot find %d fields: ',numel(missed));
else
fprintf(' Missed %d fields: ',numel(missed));
end
for fni=1:numel(missed), cat_io_cprintf('r','%s \n',missed{fni}); end
fprintf('\n');
fprintf('\n');

fprintf('Further %d XML fields: ',numel(xmlvars));
for fni=1:numel(csvvars), cat_io_cprintf('b','%s \n',csvvars{fni}); end
fprintf('\n');
fprintf('Further %d XML fields: \n',numel(xmlvars00));
for fni=1:numel(xmlvars00), cat_io_cprintf('b',' %s... \n',xmlvars00{fni}); end
fprintf('\n\n');

end

Expand All @@ -687,6 +697,11 @@
return
end
end
if numel(out)==0
warning('cat_stat_getCSVXMLfields:dissMatch', ...
'No matching fields at all. Stop processing.');
return
end



Expand Down Expand Up @@ -746,22 +761,24 @@
if iscell(out.(FN{fni}))
for si = 1:numel(out.(FN{fni}))
if iscell(out.(FN{fni}){si})
for cii = 1:numel(out.(FN{fni}{si}))
if ischar(out.(FN{fni}){si})
scsv{si+1,li} = [scsv{si+1,li} sprintf('%s ',out.(FN{fni}){si})];
if h, fprintf(h ,'%s ',out.(FN{fni}){si}); end
elseif out.(FN{fni}){si} == round(out.(FN{fni}){si})
scsv{si+1,li} = [scsv{si+1,li} sprintf('%d ',out.(FN{fni}){si})];
if h, fprintf(h ,'%d ',out.(FN{fni}){si}); end
else
scsv{si+1,li} = [scsv{si+1,li} sprintf('%f ',out.(FN{fni}){si})];
if h, fprintf(h ,'%f ',out.(FN{fni}){si}); end
try
for cii = 1:numel(out.(FN{fni}{si}))
if ischar(out.(FN{fni}){si})
scsv{si+1,li} = [scsv{si+1,li} sprintf('%s ',out.(FN{fni}){si})];
if h, fprintf(h ,'%s ',out.(FN{fni}){si}); end
elseif out.(FN{fni}){si} == round(out.(FN{fni}){si})
scsv{si+1,li} = [scsv{si+1,li} sprintf('%d ',out.(FN{fni}){si})];
if h, fprintf(h ,'%d ',out.(FN{fni}){si}); end
else
scsv{si+1,li} = [scsv{si+1,li} sprintf('%f ',out.(FN{fni}){si})];
if h, fprintf(h ,'%f ',out.(FN{fni}){si}); end
end
end
end
if h, fprintf(h ,'\n'); end
elseif ischar(out.(FN{fni}){si})
scsv{si+1,fni} = sprintf('%s',out.(FN{fni}){si});
if h, fprintf(h ,'%s\n',out.(FN{fni}){si}); end
scsv{si+1,fni} = sprintf('"%s"',out.(FN{fni}){si,:});
if h, fprintf(h ,'"%s"\n',out.(FN{fni}){si,:}); end
elseif out.(FN{fni}){si} == round(out.(FN{fni}){si})
scsv{si+1,fni} = sprintf('%d',out.(FN{fni}){si});
if h, fprintf(h ,'%d\n',out.(FN{fni}){si}); end
Expand All @@ -770,20 +787,56 @@
if h, fprintf(h ,'%f\n',out.(FN{fni}){si}); end
end
end
elseif ischar(out.(FN{fni}))
elseif all( ischar(out.(FN{fni})) )
for si = 1:numel(out.(FN{fni}))
scsv{si+1,fni} = sprintf('%s',out.(FN{fni})(si));
if h, fprintf(h ,'%s\n',out.(FN{fni})(si,:)); end
scsv{si+1,fni} = sprintf('"%s"',out.(FN{fni})(si,:));
if h, fprintf(h ,'"%s"\n',out.(FN{fni})(si,:)); end
end
elseif out.(FN{fni}) == round(out.(FN{fni}))
elseif isnumeric(out.(FN{fni})) && all( out.(FN{fni}) == round(out.(FN{fni})) )
for si = 1:numel(out.(FN{fni}))
scsv{si+1,fni} = sprintf('%d',out.(FN{fni})(si));
if h, fprintf(h ,'%d\n',out.(FN{fni})(si,:)); end
end
else
elseif mean( isnumeric(out.(FN{fni})) > 0.5)
for si = 1:numel(out.(FN{fni}))
scsv{si+1,fni} = sprintf('%f',out.(FN{fni})(si));
if h, fprintf(h ,'%f\n',out.(FN{fni}){si}); end
if isnumeric(out.(FN{fni})(si))
scsv{si+1,fni} = sprintf('%f',out.(FN{fni})(si));
if h, fprintf(h ,'%f\n',out.(FN{fni}){si}); end
else
try
scsv{si+1,fni} = sprintf('%f',double(out.(FN{fni})(si)));
if h, fprintf(h ,'%f\n',double(out.(FN{fni}){si})); end
catch
scsv{si+1,fni} = nan;
if h, fprintf(h ,'%f\n',nan); end
end
end
end
else
if si>1
if isnumeric(out.(FN{fni})(si-1))
try
scsv{si+1,fni} = sprintf('%f',out.(FN{fni})(si));
if h, fprintf(h ,'%f\n',out.(FN{fni}){si}); end
catch
scsv{si+1,fni} = nan;
if h, fprintf(h ,'%f\n',nan); end
end
elseif ischar(out.(FN{fni})(si-1))
try
scsv{si+1,fni} = sprintf('"%s"',out.(FN{fni})(si,:));
if h, fprintf(h ,'"%s"\n',out.(FN{fni}){si,:}); end
catch
scsv{si+1,fni} = nan;
if h, fprintf(h ,'"NA"\n'); end
end
else
scsv{si+1,fni} = nan;
if h, fprintf(h ,'"NA"\n'); end
end
else
scsv{si+1,fni} = nan;
if h, fprintf(h ,'"NA"\n'); end
end
end
end
Expand Down

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