Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
89 lines (81 sloc) 3.26 KB
function imData=read_file(path_to_file,sframe,num2read,options,im_info)
% Reads uncompressed multipage .tiff, .hdf5, .avi or .raw files
% Usage: my_data=read_file('path_to_data_file, start frame, num to read);
% INPUTS:
% path_to_file: location of file to be read
% sframe: first frame to read (optional, default: 1)
% num2read: number of frames to read (optional, default: read the whole file)
% options: options for reading .raw or .bin files
% im_info: information about the file (if already present)
% OUTPUT:
% imData: data in array format
% Written by Eftychios A. Pnevmatikakis, Simons Foundation
if nargin<2 || isempty(sframe); sframe = 1; end
if nargin<3 || isempty(num2read); num2read = Inf; end
[~,~,ext] = fileparts(path_to_file);
if strcmpi(ext,'.tiff') || strcmpi(ext,'.tif') || strcmpi(ext,'.btf')
if ~exist('im_info','var')
im_info = imfinfo(path_to_file);
end
TifLink = Tiff(path_to_file, 'r');
num2read = min(num2read,length(im_info)-sframe+1);
imData = zeros(im_info(1).Height,im_info(1).Width,num2read,'like',TifLink.read());
for i=1:num2read
TifLink.setDirectory(i+sframe-1);
imData(:,:,i)=TifLink.read();
end
TifLink.close()
%imData = loadtiff(path_to_file,sframe,num2read);
elseif strcmpi(ext,'.hdf5') || strcmpi(ext,'.h5')
% info = hdf5info(path_to_file);
% dims = info.GroupHierarchy.Datasets.Dims;
% name = info.GroupHierarchy.Datasets.Name;
info = h5info(path_to_file);
dims = info.Datasets.Dataspace.Size;
name = info.Datasets.Name;
if nargin < 3
num2read = dims(end)-sframe+1;
end
num2read = min(num2read,dims(end)-sframe+1);
% imData = h5read(path_to_file,name,[ones(1,length(dims)-1),sframe],[dims(1:end-1),num2read]);
imData = h5read(path_to_file,['/',name],[ones(1,length(dims)-1),sframe],[dims(1:end-1),num2read]);
elseif strcmpi(ext,'.avi')
v = VideoReader(path_to_file);
if v.Duration*v.FrameRate < sframe
imData = [];
else
if nargin < 3
num2read = v.Duration*v.FrameRate-sframe+1;
end
num2read = min(num2read,v.Duration*v.FrameRate-sframe+1);
Y1 = readFrame(v);
imData = zeros(v.Height,v.Width,num2read,'like',Y1);
i = 1;
if sframe == 1
imData(:,:,i-sframe+1) = Y1;
end
while hasFrame(v) && (i - sframe + 1 < num2read)
video = readFrame(v);
i = i + 1;
if i >= sframe
imData(:,:,i-sframe+1) = video;
end
if i - sframe + 1 >= num2read
break;
end
end
end
elseif strcmpi(ext,'.raw')
if nargin < 4 || ~isfield(options,'d1') || isempty(options.d1);
options.d1 = input('What is the total number of rows? \n');
end
if nargin < 4 || ~isfield(options,'d2') || isempty(options.d2);
options.d2 = input('What is the total number of columns? \n');
end
if nargin < 4 || ~isfield(options,'bitsize') || isempty(options.bitsize);
options.bitsize = 2;
end
imData = read_raw_file(path_to_file,sframe,num2read,[options.d1,options.d2],options.bitsize);
else
error('Unknown file extension. Only .tiff, .avi and .hdf5 files are currently supported');
end
You can’t perform that action at this time.