download_cutout_multichannel_HDF5.m

%% get multi-channel hdf5 file

% settings
clear_all = 1;
if clear_all
    clear all
end

% download hdf5 file to current directory
download_hdf5 = 1;

% for available projects
% view http://openconnecto.me/ocp/ocpca/public_tokens/

% token for desired project
project_token = 'Ex10R55';

% for project-specific channel list and dimensions
% view http://openconnecto.me/ocp/ca/[project_token]/info/

% channels to download:
chan_list = {'Synapsin1-2','PSD95-1','GFP-4','DAPI-1'};

% load contents of hdf5 file into workspace as variable 'data'
hdf5_getvar = 1;

% show single z-section of each channel in 'data'
hdf5_show = 1;

% resolution: (0 - full-scale, 1 - half-scale, 2 - quarter scale)
res = '0';

% data ranges to display: (must be within dataset dimensions @ res)
xbounds = '400,900';
ybounds = '400,900';
zbounds = '15,20';

% output filename
hdf5_file = 'Ex10R55_C-Syn1-M-PSD-G-GFP-B-DAPI_100-400_100-400_15-20.hdf5';

% load data from hdf5 file?
hdf5_getfile = 1;

% show slices (separately) from each downloaded channel
hdf5_show = 1;
show_slices = [3,5];


%%

if download_hdf5
    
    % url arguments
    server_base = 'openconnecto.me';
    webservice_name = 'ocp/ca';
    
    chan_str = strjoin(chan_list,',');
    
    restful_str = strjoin({res,xbounds,ybounds,zbounds},'/');
    
    % compose url from arguments above:
    hdf5_url = sprintf('http://%s/%s/%s/hdf5/%s/%s/',...
        server_base, webservice_name, project_token, chan_str,restful_str)
    
    % download cutout
    urlwrite(hdf5_url,hdf5_file);
end

%% extract hdf5 file contents to variable 'data' (if file exists)
if hdf5_getvar && exist(hdf5_file,'file')
    for i=1:numel(chan_list)
        chan_name = chan_list{i};
        %chan_base = chan_name(1:strfind(chan_name,'-')-1);
        chan_base = regexprep(chan_name,'-','_');
        data.(chan_base) = hdf5read ( hdf5_file, chan_name);
    end
end

%% show each channel in data variable (if it exists)
if hdf5_show && exist('data','var')
    channels = fields(data);
    
    
    for chan_num = 1:numel(channels)
        for slice = show_slices
            chan_token = channels{chan_num};
            
            figure
            imshow(data.(chan_token)(:,:,slice))
            
            title_str = sprintf('%s  %s  slice %d',...
                project_token, regexprep(chan_token,'_','-'), slice);
            title(title_str)
        end
    end
end