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niftiRead.m: Include an option to call different functions depending on nifti file size #257

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niftiRead.m: Include an option to call different functions depending on nifti file size #257

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43 changes: 35 additions & 8 deletions fileFilters/nifti/niftiRead.m
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
function ni = niftiRead(fileName, volumesToLoad)
% Matlab wrapper to call the mex readFileNifti
function ni = niftiRead(fileName, volumesToLoad, threshold)
% Matlab wrapper to call the mex readFileNifti or niftiReadMatlab
%
% niftiImage = niftiRead(fileName,volumesToLoad)
%
Expand All @@ -9,6 +9,13 @@
% If volumesToLoad is not included in the arguments, all the data
% are returned. If volumesToLoad is empty ([]) returns only the header
%
% This function calls
% readFileNifti: memory efficient
% or
% niftiReadMatlab: slow, but robust for nifti file with large size
% depending on the file size. (We can define the selection criteria by
% using parameter "threshold")
%
% Web Resources
% web('http://nifti.nimh.nih.gov/nifti-1/','-browser')
%
Expand All @@ -19,6 +26,16 @@
% ni = niftiRead(niFile);
%
% Copyright, Vista Team Stanford, 2011
% History:
% 2017.07: HT included the option to call two functions depending on file
% size

% Default threshold = 3GB. If the file size exceeds this limit, we use
% niftiReadMatlab, not readFileNifti
if notDefined('threshold'), threshold = 3221225472; end

% Get file size
fileinfo = dir(fileName);

% This normally calls the mex file for your system
if ~exist('fileName','var') || isempty(fileName)
Expand All @@ -36,22 +53,32 @@
% ni = niftiRead('foo.nii.gz',1:20);
% We let readFileNifti complain about not implemented for
% now.
ni = readFileNifti(fileName,volumesToLoad);
if fileinfo.bytes < threshold
ni = readFileNifti(fileName,volumesToLoad);
else
ni = niftiReadMatlab(fileName,volumesToLoad);
end
else
% ni = niftiRead('foo.nii.gz');
ni = readFileNifti(fileName);
if fileinfo.bytes < threshold
ni = readFileNifti(fileName);
else
ni = niftiReadMatlab(fileName);
end
end
else
% Did the person not include the .nii.gz extensions?
[~,n,e] = fileparts(r);
if isempty(e), fileNameExtended = [n,'.nii.gz']; end
if exist('fileNameExtended', 'var') ...
&& exist(fileNameExtended,'file')
ni = readFileNifti(fileNameExtended);
&& exist(fileNameExtended,'file')
if fileinfo.bytes < threshold
ni = readFileNifti(fileNameExtended);
else
ni = niftiReadMatlab(fileNameExtended);
end
else
error('Cannot find the file %s or %s\n',fileName,fileNameExtended);
end
end


end