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Diffusion Imaris Cell Densities - Julie Meystre (master) Browse

xt-cell-densities/functions/manualAverageInterface.m
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manualAverageInterface.m
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function manualAverageInterface
global X;
global intensities;
global res;
% Get all the spots first
sCh = getFromTag('txt_channel_spot', 'Number');
spots = X.GetObject('Name', sprintf('Detected Spots from Channel %d', sCh));
stats = X.GetSelectedStatistics(spots, 'Intensity Mean');
selectedChannels = cell2mat(stats.factors(:,2));
intensities = [];
% for all the Ids and all Channels, will fill all values from the chosen statistic
for i = 1:length(stats.values)
intensities(stats.ids(i)+1, str2num(selectedChannels(i))) = stats.values(i);
end
f = figure('Name', 'BIOP - Spots Stats', ...
'NumberTitle', 'off', 'Visible', 'off', 'Position', [0 0 500 200], ...
'Tag', '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';
l = .05;
w = .4;
h = .1;
s = 0.1;
% Refresh button
uicontrol(f,'Style','pushbutton','String','Calculate',...
'Units','normalized', 'Tag', 'btn_stats_refresh', ...
'Position',[0.10 .75 0.8 h*2],...
'Callback', @btn_stats_refresh_callback);
% Info text
uicontrol(f,'Style','text','String','Spots Selected: ',...
'Units','normalized', ...
'HorizontalAlignment', 'right', ...
'Position',[l .60 0.32 h]);
uicontrol(f,'Style','text','String','',...
'Units','normalized', 'Tag', 'txt_spot_name', ...
'HorizontalAlignment', 'left', ...
'Position',[l+0.33 .60 0.5 h]);
uicontrol(f,'Style','text','String','',...
'Units','normalized', 'Tag', 'txt_spot_stats', ...
'FontWeight', 'bold', ...
'HorizontalAlignment', 'left', ...
'Position',[0.26 .44 0.9 h]);
% 'Add to' popup list
options = {};
chan={};
nChan = getChannelIndexes();
manCat = getFromTag('txt_manual_cat_num', 'Number');
for i=nChan
chan{end+1} = sprintf('Channel %d', i);
options{end+1} = sprintf('Channel %d BG',i);
for j=1:(manCat-1)
options{end+1} = sprintf('Channel %d Thr %d',i,j);
end
end
%Choose Channel
uicontrol(f, 'Style', 'popup',...
'Units','normalized', 'Tag', 'popup_chan', ...
'String', chan,...
'Position',[l .45 0.2 h]);
uicontrol(f, 'Style', 'popup',...
'Units','normalized', 'Tag', 'popup_add_to', ...
'String', options,...
'Position',[l .15 0.5 h]);
% Add to button
uicontrol(f,'Style','pushbutton','String','Add',...
'Units','normalized', 'Tag', 'btn_add', ...
'Position',[l+0.55 .15 0.2 .1],...
'Callback', @btn_add_callback);
end
function btn_stats_refresh_callback(hObject, eventdata, handles)
global X;
global intensities;
global res;
choices = get(findobj('Tag', 'popup_chan'),'String');
choice = choices{getFromTag('popup_chan')};
expression = 'Channel (?<channel>\d+)';
tokenNames = regexp(choice,expression,'names');
ch = str2num(tokenNames.channel(1));
spots = X.GetObject();
idx = spots.GetSelectedIndices()+1;
size(intensities);
res = intensities(idx,ch);
setFromTag('txt_spot_name', X.GetName(spots));
setFromTag('txt_spot_stats', sprintf('%d Spots, Average Intensity %.2f, SD %.2f', numel(res), mean(res), std(res)));
end
function btn_add_callback(hObject, eventdata, handles)
% Get popup options
global intensities;
global res;
choices = get(findobj('Tag', 'popup_add_to'),'String');
choice = choices{getFromTag('popup_add_to')};
expression = ['Channel (?<channel>\d+) [BGThr ]+(?<cat>[\d]*).*'];
tokenNames = regexp(choice,expression,'names');
if isempty(tokenNames.cat)
%BG
setFromTag(sprintf('txt_manual_bg_ch_%s',tokenNames.channel(1)), sprintf('%.2f',mean(res)+2*std(res)));
else
setFromTag(sprintf('txt_manual_cat_%s_ch_%s',tokenNames.cat(1), tokenNames.channel(1)), sprintf('%.2f',mean(res)-2*std(res)));
end
end
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