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xt-cell-densities/BIOP_Clustering.m
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BIOP_Clustering.m
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function BIOP_Clustering
%Start EasyXT
addpath('EasyXT');
addpath('functions');
global X;
X = EasyXT();
f = figure('Name', 'BIOP - Clustering', ...
'NumberTitle', 'off', 'Visible', 'off', 'Position', [0 0 700 512], ...
'Tag', 'clustetring_main_f', ...
'DockControls', 'off', 'ToolBar', 'none', 'MenuBar', 'none');
% Move the window to the center of the screen.
movegui(f,'center');
% Make the window visible.
f.Visible = 'on';
% Add 1 panel on the left and one on the right
settingsp = uipanel(f,'Title','Settings', 'Tag', 'p_settings',...
'Position',[.05 .05 .65 .9]);
commandsp = uipanel(f,'Title','Actions', 'Tag', 'p_commands',...
'Position',[.70 .05 .25 .9]);
% Settings Tab
uitabgroup('Parent', settingsp, 'Tag', 'tab_channels');
% Add buttons for refreshing data, and batch
h = .1;
w = .9;
l = .05;
uicontrol(commandsp,'Style','pushbutton','String','Refresh',...
'Units','normalized', 'Tag', 'btn_refresh', ...
'Position',[l .90 w h],...
'Callback', @btn_refresh_callback);
uicontrol(commandsp,'Style','pushbutton','String','Get Sum Channel',...
'Units','normalized', 'Tag', 'btn_sum', ...
'Position',[l .8 w h],...
'Callback', @btn_sum_callback);
uicontrol(commandsp,'Style','pushbutton','String','Clear Outside Sum Channel',...
'Units','normalized', 'Tag', 'btn_clear_outside', ...
'Position',[l .7 w h],...
'Callback', @btn_clear_outside_callback);
uicontrol(commandsp,'Style','pushbutton','String','Detect Spots',...
'Units','normalized', 'Tag', 'btn_detect_spots', ...
'Position',[l .6 w h],...
'Callback', @btn_detect_spots_callback);
uicontrol(commandsp,'Style','pushbutton','String','Cluster Spots',...
'Units','normalized', 'Tag', 'btn_cluster_spots', ...
'Position',[l .5 w h],...
'Callback', @btn_cluster_spots_callback);
uicontrol(commandsp,'Style','pushbutton','String','Reassign Spots',...
'Units','normalized', 'Tag', 'btn_reassign_spots', ...
'Position',[l .4 w h],...
'Callback', @btn_reassign_spots_callback);
% Load WingJ
uicontrol(commandsp,'Style','pushbutton','String','Load WingJ Data',...
'Units','normalized', 'Tag', 'btn_wingj', ...
'Position',[l .3 w h],...
'Callback', @btn_wingj_callback);
uicontrol(commandsp,'Style','pushbutton','String','Export To CSV',...
'Units','normalized', 'Tag', 'btn_export', ...
'Position',[l .2 w h],...
'Callback', @btn_export_callback);
uicontrol(commandsp,'Style','text',...
'String','Settings',...
'Units','Normalized', ...
'HorizontalAlignment', 'center', ...
'Position',[l .10 w 0.05]);
uicontrol(commandsp,'Style','pushbutton','String','Save',...
'Units','normalized', 'Tag', 'btn_save', ...
'Position',[l .05 w/2 h/2],...
'Callback', @savebtn_callback);
uicontrol(commandsp,'Style','pushbutton','String','load',...
'Units','normalized', 'Tag', 'btn_load', ...
'Position',[l+w/2 .05 w/2 h/2],...
'Callback', @loadbtn_callback);
% Make all the settings
% Settings Tab
tgroup = uitabgroup('Parent', settingsp, 'Tag', 'tab_channels');
makeChanSumTab(tgroup);
makeCleanChanTab(tgroup);
makeSpotDetectionTab(tgroup);
makeClusteringTab(tgroup);
makeReassignTab(tgroup);
makeWingJTab(tgroup)
%makeExportTab(tgroup);
end
function makeChanSumTab(parent)
global X;
tabTag = 'tab_chan_sum';
tabName = 'Sum Channels';
thisTab = findobj('Tag',tabTag);
if isempty(thisTab)
thisTab = uitab('Parent', parent, 'Title', tabName, ...
'Tag', tabTag);
% Add all the controls
%Control settings
%Channels of interest as checkboxes
sp = 0.05;
nChan = X.GetSize('C');
uicontrol(thisTab,'Style','text',...
'String','Channels to Sum',...
'Units','Normalized', ...
'HorizontalAlignment', 'left', ...
'Position',[.05 0.9 .3 sp]);
for k=1:nChan;
cbh(k) = uicontrol(thisTab, 'Style','checkbox','String',sprintf('Channel %d',k), ...
'Tag', sprintf('is_sum_chan_%d',k), ...
'Value',1, ...
'Units', 'Normalized', ...
'Position',[.05 .9-sp*k .3 sp]);
end
% Ask if we perform normalization
uicontrol(thisTab, 'Style','checkbox','String','Normalize Channels Before Sum', ...
'Tag', 'is_chan_norm', ...
'Value',1, ...
'Units', 'Normalized', ...
'Position',[.05 0.9-sp*(nChan+3) .5 sp]);
end
end
function makeCleanChanTab(parent)
tabTag = 'tab_clean';
tabName = 'Clean Channel';
thisTab = findobj('Tag',tabTag);
if isempty(thisTab)
thisTab = uitab('Parent', parent, 'Title', tabName, ...
'Tag', tabTag);
% Add all the controls
%Control position
sp = 0.05;
py = 0.89;
% Channel for surface creation
uicontrol(thisTab,'Style','text',...
'String','Surface Channel',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','',...
'Units','Normalized', ...
'Tag', 'txt_channel_surface', ...
'Position',[.36 py+.01 .1 sp]);
% Smoothing Factor for Surface
uicontrol(thisTab,'Style','text',...
'String','Surface Smoothing',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-sp .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','5.0',...
'Units','Normalized', ...
'Tag', 'txt_surface_smooth', ...
'Position',[.36 py+.01-sp .1 sp]);
% Surface Intensity Threshold
uicontrol(thisTab,'Style','text',...
'String','Intensity Threshold',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-2*sp .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','15',...
'Units','Normalized', ...
'Tag', 'txt_surface_intensity_threshold', ...
'Position',[.36 py+.01-2*sp .1 sp]);
end
end
function makeSpotDetectionTab(parent)
tabTag = 'tab_detect';
tabName = 'Detect Spots';
thisTab = findobj('Tag',tabTag);
if isempty(thisTab)
thisTab = uitab('Parent', parent, 'Title', tabName, ...
'Tag', tabTag);
% Add all the controls
%Control position
sp = 0.05;
py = 0.89;
% Spot Detection Channel
uicontrol(thisTab,'Style','text',...
'String','Spot Channel',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','',...
'Units','Normalized', ...
'Tag', 'txt_channel_spot', ...
'Position',[.36 py+.01 .1 sp]);
% Spot Spot Sizes
uicontrol(thisTab,'Style','text',...
'String','Spot Size [um]',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-sp .3 sp]);
% XY
uicontrol(thisTab,'Style','edit',...
'String','2.8',...
'Units','Normalized', ...
'Tag', 'txt_spot_size_xy', ...
'Position',[.36 py+.01-sp .1 sp]);
% Z (Optional)
uicontrol(thisTab,'Style','edit',...
'String','2.8',...
'Units','Normalized', ...
'Tag', 'txt_spot_size_z', ...
'Position',[.47 py+.01-sp .1 sp]);
% Spot Quality Threshold
uicontrol(thisTab,'Style','text',...
'String','Spot Quality Threshold',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-2*sp .30 sp]);
uicontrol(thisTab,'Style','edit',...
'String','15',...
'Units','Normalized', ...
'Tag', 'txt_spot_quality_threshold', ...
'Position',[.36 py+.01-2*sp .1 sp]);
% Remove Spots Closer than
uicontrol(thisTab,'Style','checkbox',...
'String','Remove Spots if closer than',...
'Tag', 'is_remove_spots', ...
'Units','Normalized', ...
'Position',[.05 py-3*sp .40 sp]);
uicontrol(thisTab,'Style','edit',...
'String','1.0',...
'Units','Normalized', ...
'Tag', 'txt_spot_proximity_threshold', ...
'Position',[.45 py-3*sp .07 sp]);
uicontrol(thisTab,'Style','text',...
'String','um to image edge',...
'Units','Normalized', ...
'HorizontalAlignment', 'left', ...
'Position',[.53 py-3*sp-.01 .30 sp]);
end
end
function makeClusteringTab(parent)
tabTag = 'tab_cluster';
tabName = 'Cluster';
thisTab = findobj('Tag',tabTag);
if isempty(thisTab)
thisTab = uitab('Parent', parent, 'Title', tabName, ...
'Tag', tabTag);
% Add all the controls
% Need 3 tabs: Manual Clustering, Brute Force and KMeans
clusMode = uitabgroup('Parent', thisTab, 'Tag', 'tab_cluster_modes');
%Settings for clustering tab
makeSettingsClusterTab(clusMode);
% Manual Tab
makeManualClusterTab(clusMode);
% Brute Force
makeBruteClusterTab(clusMode);
% KMeans Tab
makeKMeansClusterTab(clusMode);
end
end
function makeManualClusterTab(parent)
tabTag = 'tab_cluster_manual';
tabName = 'Manual';
thisTab = findobj('Tag',tabTag);
sp = .05;
py = .89;
if isempty(thisTab)
thisTab = uitab('Parent', parent, 'Title', tabName, ...
'Tag', tabTag);
uicontrol(thisTab,'Style','checkbox',...
'String','Use Manual Clustering',...
'Tag', 'is_do_manual', ...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py+sp .4 sp]);
uicontrol(thisTab,'Style','text',...
'String','Number of Categories',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-sp .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','2',...
'Units','Normalized', ...
'Tag', 'txt_manual_cat_num', ...
'Position',[.36 py+.01-sp .1 sp], ...
'Callback', @txt_manual_cat_num_callback);
end
updateManualTab(thisTab);
end
function txt_manual_cat_num_callback(hObject, eventdata, handles)
parent = findobj('Tag', 'tab_cluster_manual');
updateManualTab(parent);
end
function updateManualTab(parent)
global X;
% Add all the controls
% Grab all the channels that we need to build the settings for
chanIdx = getChannelIndexes();
nChan = X.GetSize('C');
numcat = str2num(get(findobj('Tag', 'txt_manual_cat_num'), 'String'));
py = 0.89;
sp = 0.05;
% Make the labels for the columns but only if they do not exist already...
if isempty(findobj('Tag', 'txt_bg'))
uicontrol(parent,'Style','text',...
'String','BG',...
'Units','Normalized', ...
'Tag', sprintf('txt_bg') , ...
'HorizontalAlignment', 'center', ...
'Position',[.26 py-2*sp .1 sp]);
end
for n=1:(numcat-1)
l = findobj('Tag', sprintf('txt_thr_%d', n));
if isempty(l)
thrtxt(n) = uicontrol(parent,'Style','text',...
'String',sprintf('Thr %d', n),...
'Tag',sprintf('txt_thr_%d', n), ...
'Units','Normalized', ...
'HorizontalAlignment', 'center', ...
'Position',[.26+n*.1 py-2*sp .1 sp], ...
'Visible', 'on');
else
thrtxt(n) = l;
end
set(thrtxt(n),'Visible', 'on');
end
for k=1:nChan
if (any(chanIdx==k))
isEnabled = 'on';
else
isEnabled = 'off';
end
l = findobj('Tag', sprintf('txt_chan_%d', k));
if isempty(l)
txt(k) = uicontrol(parent,'Style','text',...
'String',sprintf('Channel %d', k),...
'Units','Normalized', ...
'Tag', sprintf('txt_chan_%d',k) , ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-sp*(k+2) .2 sp]);
else
txt(k) = l;
end
set(txt(k),'Enable', isEnabled);
l= findobj('Tag', sprintf('txt_manual_bg_ch_%d',k));
if isempty(l)
edt(k) = uicontrol(parent,'Style','edit',...
'String','',...
'Units','Normalized', ...
'Tag', sprintf('txt_manual_bg_ch_%d',k) , ...
'Position',[.26 py-sp*(k+2) .1 sp]);
else
edt(k) = l;
end
set(edt(k),'Enable', isEnabled);
for n=1:(numcat-1)
l = findobj('Tag', sprintf('txt_manual_cat_%d_ch_%d',n,k));
if isempty(l)
thr((k-1)*(numcat-1)+n) = uicontrol(parent,'Style','edit',...
'String','',...
'Units','Normalized', ...
'Tag', sprintf('txt_manual_cat_%d_ch_%d',n,k) , ...
'Position',[.26+n*.1 py-sp*(k+2) .1 sp], ...
'Visible', 'on');
else
thr((k-1)*(numcat-1)+n)= l;
end
set(thr((k-1)*(numcat-1)+n),'Enable', isEnabled);
set(thr((k-1)*(numcat-1)+n),'Visible', 'on');
end
% Delete any columns that are no longer useful
for n=(numcat):10
obj = findobj('Tag', sprintf('txt_manual_cat_%d_ch_%d',n,k));
if ~isempty(obj)
delete(obj);
end
obj = findobj('Tag', sprintf('txt_thr_%d', n));
if ~isempty(obj)
delete(obj);
end
end
% Add button for manual measurement
uicontrol(parent,'Style','pushbutton','String','Fill values from spots',...
'Units','normalized', 'Tag', 'btn_calculate_values', ...
'Position',[.2 py-sp*(nChan+6) .4 sp*3], ...
'Callback', @btn_calculate_values_callback);
end
end
function makeBruteClusterTab(parent)
tabTag = 'tab_cluster_brute_force';
tabName = 'Brute Force';
thisTab = findobj('Tag',tabTag);
sp = .05;
py = .89;
if isempty(thisTab)
thisTab = uitab('Parent', parent, 'Title', tabName, ...
'Tag', tabTag);
uicontrol(thisTab,'Style','checkbox',...
'String','Use Brute Force Clustering',...
'Tag', 'is_do_brute', ...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py+sp .4 sp]);
% Number of categories
uicontrol(thisTab,'Style','text',...
'String','Number of Categories',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-sp .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','2',...
'Units','Normalized', ...
'Tag', 'txt_brute_cat_num', ...
'Position',[.36 py+.01-sp .1 sp]);
% BG Value
uicontrol(thisTab,'Style','text',...
'String','Background',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-2*sp .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','5',...
'Units','Normalized', ...
'Tag', 'txt_brute_bg', ...
'Position',[.36 py+.01-2*sp .1 sp]);
% Max Value
uicontrol(thisTab,'Style','text',...
'String','Max Threshold',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-3*sp .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','160',...
'Units','Normalized', ...
'Tag', 'txt_brute_max', ...
'Position',[.36 py+.01-3*sp .1 sp]);
end
end
function makeKMeansClusterTab(parent)
tabTag = 'tab_cluster_kmeans';
tabName = 'K-Means';
thisTab = findobj('Tag',tabTag);
sp = .05;
py = .89;
if isempty(thisTab)
thisTab = uitab('Parent', parent, 'Title', tabName, ...
'Tag', tabTag);
uicontrol(thisTab,'Style','checkbox',...
'String','Use K-Means clustering',...
'Tag', 'is_do_kmeans', ...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py+sp .4 sp]);
uicontrol(thisTab,'Style','text',...
'String','Number of clusters',...
'Tag', 'txt_norm_kmeans', ...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-sp .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','15',...
'Units','Normalized', ...
'Tag', 'txt_kmeans_cluster_num', ...
'Position',[.36 py+.01-sp .1 sp]);
uicontrol(thisTab,'Style','checkbox',...
'String','Separate K-Means per channel',...
'Tag', 'is_sep_kmeans', ...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-3*sp .5 sp], ...
'Callback', @is_sep_kmeans_callback);
uicontrol(thisTab,'Style','text',...
'String','Clusters per channel',...
'Tag', 'txt_sep_kmeans', ...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-4*sp-.01 .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','2',...
'Units','Normalized', ...
'Tag', 'txt_kmeans_sep_cluster_num', ...
'Position',[.36 py-4*sp .1 sp]);
end
end
function is_sep_kmeans_callback(hObject, eventdata, handles)
%Get object to enable or not
sep(1) = findobj('Tag','txt_sep_kmeans');
sep(2) = findobj('Tag','txt_kmeans_sep_cluster_num');
knorm(1) = findobj('Tag','txt_norm_kmeans');
knorm(2) = findobj('Tag','txt_kmeans_cluster_num');
if get(hObject,'Value')
%Disable normal KMeans Values
knorm(1).Enable = 'off';
knorm(2).Enable = 'off';
%Enable independent KMeans Values
sep(1).Enable = 'on';
sep(2).Enable = 'on';
else
%Disable normal KMeans Values
knorm(1).Enable = 'on';
knorm(2).Enable = 'on';
%Disable independent KMeans Values
sep(1).Enable = 'off';
sep(2).Enable = 'off';
end
end
function makeSettingsClusterTab(parent)
tabTag = 'tab_cluster_settings';
tabName = 'Settings';
thisTab = findobj('Tag',tabTag);
sp = .05;
py = .89;
if isempty(thisTab)
thisTab = uitab('Parent', parent, 'Title', tabName, ...
'Tag', tabTag);
% Allow empty clusters?
uicontrol(thisTab,'Style','checkbox',...
'String','No Empty Custers',...
'Tag', 'is_no_empty_clusters', ...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py+sp .4 sp]);
% Grouping distance
uicontrol(thisTab,'Style','text',...
'HorizontalAlignment', 'right', ...
'String',sprintf('%s\n%s','Groups spots','if closer than [um]'),...
'Units','Normalized', ...
'Position',[.05 py-sp .3 sp+0.02]);
uicontrol(thisTab,'Style','edit',...
'String','8.5',...
'Units','Normalized', ...
'Tag', 'txt_grouping_distance', ...
'Position',[.36 py+.01-sp .1 sp]);
% Z Compensation
uicontrol(thisTab,'Style','text',...
'String','Z Compensation factor',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-2*sp .3 sp]);
uicontrol(thisTab,'Style','edit',...
'String','3',...
'Units','Normalized', ...
'Tag', 'txt_z_compensation_factor', ...
'Position',[.36 py+.01-2*sp .1 sp]);
end
end
function makeReassignTab(parent)
tabTag = 'tab_reassign';
tabName = 'Reassign';
thisTab = findobj('Tag',tabTag);
sp = .05;
h= 0.05;
py = .89;
if isempty(thisTab)
thisTab = uitab('Parent', parent, 'Title', tabName, ...
'Tag', tabTag);
% Make one spot per cluster, spot number is cluster size?
uicontrol(thisTab,'Style','checkbox',...
'String','Make 1 Spot / Subcluster',...
'Tag', 'is_reassign_single_spot', ...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py+sp .4 h]);
% Grouping distance
uicontrol(thisTab,'Style','text',...
'HorizontalAlignment', 'right', ...
'String','Maximum distance for reassignment [um]',...
'Units','Normalized', ...
'Position',[.05 py-sp .5 h]);
uicontrol(thisTab,'Style','edit',...
'String','8.5',...
'Units','Normalized', ...
'Tag', 'txt_reassign_max_distance', ...
'Position',[.56 py-sp .1 h]);
% Z Compensation
uicontrol(thisTab,'Style','text',...
'String','Maximum intensity distance [AU]',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-2*sp .5 h]);
uicontrol(thisTab,'Style','edit',...
'String','120',...
'Units','Normalized', ...
'Tag', 'txt_reassign_max_intensity', ...
'Position',[.56 py-2*sp .1 h]);
% Z Compensation
uicontrol(thisTab,'Style','text',...
'String','Reassign if smaller than',...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-3*sp .5 h]);
uicontrol(thisTab,'Style','edit',...
'String','10',...
'Units','Normalized', ...
'Tag', 'txt_reassign_cluster_min', ...
'Position',[.56 py-3*sp .1 h]);
end
end
function makeWingJTab(parent)
tabTag = 'tab_wing_j';
tabName = 'WingJ';
thisTab = findobj('Tag',tabTag);
sp = .05;
py = .89;
h = .05;
if isempty(thisTab)
thisTab = uitab('Parent', parent, 'Title', tabName, ...
'Tag', tabTag);
% Make one spot per cluster, spot number is cluster size?
uicontrol(thisTab,'Style','checkbox',...
'String','Remove Offset',...
'Tag', 'is_wingj_remove_offset', ...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py .4 h]);
uicontrol(thisTab,'Style','checkbox',...
'String','Flip Y Coordinate',...
'Tag', 'is_wingj_flip_y', ...
'Units','Normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[.05 py-sp .4 h]);
end
end
%% Callbacks for all buttons
function btn_refresh_callback(hObject, eventdata, handles)
end
function btn_sum_callback(hObject, eventdata, handles)
sumChannels();
end
function btn_clear_outside_callback(hObject, eventdata, handles)
clearOutside();
end
function btn_detect_spots_callback(hObject, eventdata, handles)
detectSpots();
end
function btn_cluster_spots_callback(hObject, eventdata, handles)
clusterSpots();
end
function btn_reassign_spots_callback(hObject, eventdata, handles)
reassignSpots();
end
function btn_export_callback(hObject, eventdata, handles)
exportToCSV();
end
function savebtn_callback(hObject, eventdata, handles)
saveSettings();
end
function loadbtn_callback(hObject, eventdata, handles)
% Make sure this function is generic enough
loadSettings();
end
function btn_calculate_values_callback(hObject, eventdata, handles)
manualAverageInterface();
end
function btn_wingj_callback(hObject, eventdata, handles)
loadWingJData();
end
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