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minor fixes to SNIRF import code #3

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minor fixes to SNIRF import code #3

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23 changes: 21 additions & 2 deletions DataFiles/FileLoadSaveClass.m
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@


% ---------------------------------------------------------
function Load(obj, filename, format)
function varargout=Load(obj, filename, format)
if ~exist('filename','var')
filename = obj.filename;
end
Expand All @@ -41,9 +41,28 @@ function Load(obj, filename, format)
end
case obj.supportedFomats.hdf5
if ismethod(obj, 'LoadHdf5')
obj.LoadHdf5(filename);

flds=ListHDF5fields(filename);
cnt=1; parent={};
for i=1:length(flds)
f=strsplit(flds{i},'/');
if(length(f)>1 && ~isempty(strfind(f{2},'nirs')))
parent{cnt}=['/' f{2}];
cnt=cnt+1;
end
end
parent=unique(parent);
for i=1:length(parent)
obj(i)=obj(1);
obj(i).LoadHdf5(filename,parent{i});
end
end
end
if(nargout>0)
varargout={obj};
elseif(length(parent)>1)
warning(['multiple /nirs entries found; use snirf=snirf.load(''' filename ''');']);
end
end


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33 changes: 33 additions & 0 deletions DataFiles/Hdf5/hd5read_safeStrArray.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
function valout2 = hd5read_safeStrArray(fname, name, val)

valout2 = {};
try
try
valout2 = h5read(fname, name);
catch
cnt=1;
valout={};
while(1)
try
valout{cnt}= h5read(fname, [name num2str(cnt)]);
cnt=cnt+1;
catch
break;
end
end


for ii=1:length(valout)
valout2{ii,1} = convertH5StrToStr(valout{ii});
end
end
catch
switch(class(val))
case 'char'
valout2 = '';
case 'cell'
valout2 = {};
otherwise
valout2 = [];
end
end
6 changes: 3 additions & 3 deletions Snirf/DataClass.m
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Original file line number Diff line number Diff line change
Expand Up @@ -105,9 +105,9 @@
obj.time = h5read(fname, [parent, '/time']);
ii=1;
while 1
if ii > length(obj.measurementList)
obj.measurementList(ii) = MeasListClass;
end
if ii > length(obj.measurementList)
obj.measurementList(ii) = MeasListClass;
end
if obj.measurementList(ii).LoadHdf5(fname, [parent, '/measurementList', num2str(ii)]) < 0
obj.measurementList(ii).delete();
obj.measurementList(ii) = [];
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56 changes: 56 additions & 0 deletions Snirf/ListHDF5fields.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,56 @@
function [names,val] = ListHDF5fields(filename);

% Ted Added 4/8/2020
info=hdf5info(filename);

names={};
for i=1:length(info.GroupHierarchy)
for j=1:length(info.GroupHierarchy.Groups)
n=getgroups(info.GroupHierarchy.Groups(j));
names={names{:} n{:}};
end
for j=1:length(info.GroupHierarchy.Datasets)
n=getdatasets(info.GroupHierarchy.Datasets(j));
names={names{:} n{:}};
end
end

names=unique(names)';



if(nargout>1)
for i=1:length(names)
val{i}=hdf5read(filename,names{i});
end
varargout{1}=val;
end

function names= getgroups(in)

names={};
if(~isempty(in))
% names={names{:} in.Name};
for j=1:length(in.Groups)
n=getgroups(in.Groups(j));
names={names{:} n{:}};
end
for j=1:length(in.Datasets)
n=getdatasets(in.Datasets(j));
names={names{:} n{:}};
end
end


function names= getdatasets(in)

names={};
if(~isempty(in))
names={names{:} in.Name};
% for j=1:length(in.Groups)
% names={names{:} getgroups(in.Groups(j))};
% end
% for j=1:length(in.Datasets)
% names={names{:} getdatasets(in.Datasets(j))};
% end
end
2 changes: 1 addition & 1 deletion Snirf/MeasListClass.m
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@
obj.detectorIndex = hdf5read(fname, [parent, '/detectorIndex']);
obj.wavelengthIndex = hdf5read(fname, [parent, '/wavelengthIndex']);
obj.dataType = hdf5read(fname, [parent, '/dataType']);
obj.dataTypeLabel = convertH5StrToStr(hdf5read_safe(fname, [parent, '/dataTypeLabel'], obj.dataTypeLabel));
obj.dataTypeLabel = convertH5StrToStr(h5read_safe(fname, [parent, '/dataTypeLabel'], obj.dataTypeLabel));
obj.dataTypeIndex = hdf5read(fname, [parent, '/dataTypeIndex']);
obj.sourcePower = hdf5read_safe(fname, [parent, '/sourcePower'], obj.sourcePower);
obj.detectorGain = hdf5read_safe(fname, [parent, '/detectorGain'], obj.detectorGain);
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12 changes: 4 additions & 8 deletions Snirf/ProbeClass.m
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Original file line number Diff line number Diff line change
Expand Up @@ -100,14 +100,10 @@
obj.momentOrder = hdf5read_safe(fname, [parent, '/momentOrder'], obj.momentOrder);
obj.correlationTimeDelay = hdf5read_safe(fname, [parent, '/correlationTimeDelay'], obj.correlationTimeDelay);
obj.correlationTimeDelayWidth = hdf5read_safe(fname, [parent, '/correlationTimeDelayWidth'], obj.correlationTimeDelayWidth);
obj.sourceLabels = h5read_safe(fname, [parent, '/sourceLabels'], obj.sourceLabels);
for ii=1:length(obj.sourceLabels)
obj.sourceLabels{ii} = convertH5StrToStr(obj.sourceLabels{ii});
end
obj.detectorLabels = h5read_safe(fname, [parent, '/detectorLabels'], obj.detectorLabels);
for ii=1:length(obj.detectorLabels)
obj.detectorLabels{ii} = convertH5StrToStr(obj.detectorLabels{ii});
end
obj.sourceLabels = hd5read_safeStrArray(fname, [parent, '/sourceLabels'], obj.sourceLabels);

obj.detectorLabels = hd5read_safeStrArray(fname, [parent, '/detectorLabels'], obj.detectorLabels);

catch
err=-1;
return;
Expand Down