fluoseq.m

SDFGASFASFASFAS EDGSGA DGSFGSA

            delete(image_par.h_lambda);
        end
        if (isa(image_par.h_fluoseq, 'timer'))
            stop(image_par.h_fluoseq);
            delete(image_par.h_fluoseq);
        end
        delete(h_fig);

    otherwise               % invalid command
        warning('MATLAB:fluoseq', 'command ''%s'' not recognized', control_command);
end
return



function [image_data, new_file] = get_single_image(h_fig, fig_handle, image_par, file_par, lambda_par, focus_flag)

% initialize outputs
new_file = file_par;

% acquire image if device available
% otherwise generate random image
% wait for exposure time to pass in DEMO mode
% prevents Lambda 10-2 confusion during byte read from serial port
new_file.acq_time = clock;
if (isempty(image_par.h_cam))
    roi_size = diff(reshape(image_par.roi_coord, 2, 2), 1, 2)' + 1;
    image_data = uint16((2 ^ image_par.bit_depth - 1) * rand(1, prod(floor(roi_size ./ image_par.bin_full))));
    start_time = clock;
    while (1000 * etime(clock, start_time) < (image_par.expose_time + 100))
    end
else
    image_data = pvcamacq(image_par.h_cam, 1, image_par.roi_full, image_par.expose_time, 'timed');
end

% close shutter if Lambda 10-2 present
if (strcmp(image_par.filter_name, 'lambda 10-2') && ~strcmp(focus_flag, 'focus'))
    set(h_fig, 'Tag', 'close');
    lambdactrl(lambda_par.port, 'close');
end

% convert image stream into 2-D array
if (~isempty(image_data) && isnumeric(image_data))
    image_data = roiparse(image_data, image_par.roi_full);
    disp_single_image(image_data, fig_handle, image_par, new_file);

    % save image data if file is open
    if (~isempty(new_file.file_name) && ~strcmp(focus_flag, 'focus'))
        new_file.image_count = new_file.image_count + 1;
        imwrite(image_data, fullfile(new_file.file_path, new_file.file_name), ...
            'tif', 'WriteMode', 'append', 'Description', datestr(new_file.acq_time));
    end
end
return



function [] = disp_single_image(image_data, fig_handle, image_par, file_par)

% obtain image axes and text
h_axes = fig_handle.h_axes(1);
if (istype(h_axes, 'axes'))
    axes(h_axes);
    h_image = get(h_axes, 'UserData');
else
    warning('MATLAB:fluoseq', 'unable to find image axes');
    return
end
h_text = fig_handle.h_text;
if (~istype(h_text, 'uicontrol'))
    warning('MATLAB:fluoseq', 'unable to find text label');
    return
end

% display image
% shift image down to 8 bits before display
if (isa(image_data, 'uint8'))
    image_disp = image_data;
else
    image_disp = uint8(image_data / feval(class(image_data), max(1, 2 ^ (image_par.bit_depth - 8))));
end
if (istype(h_image, 'image'))
    set(h_image, 'CData', image_disp, 'UserData', image_data);
    set(h_axes, 'XLim', [1 size(image_disp, 2)], 'YLim', [1 size(image_disp, 1)]);
else
    h_image = image(image_disp);
    set(h_image, 'EraseMode', 'none', 'UserData', image_data);
    set(h_axes, 'XDir', 'reverse', ...
        'XTick', [], ...
        'YDir', 'normal', ...
        'YTick', [], ...
        'Tag', 'image', ...
        'UserData', h_image);
end

% update text label with times, counts, etc.
elapsed_time = datestr(datenum(file_par.acq_time) - datenum(file_par.start_time), 13);
text_string = sprintf('Image: %d    Elapsed Time: %s    Min: %d    Max: %d    Size: %d x %d', ...
    file_par.image_count, elapsed_time, double(min(min(image_data))), double(max(max(image_data))), ...
    floor(image_par.image_size ./ image_par.bin_full));
set(h_text, 'String', text_string);
drawnow;
return



function [] = disp_colorbar(h_fig, h_axes, color_func)

% obtain colorbar axes
if (istype(h_axes, 'axes'))
    axes(h_axes);
    h_image = get(h_axes, 'UserData');
else
    warning('MATLAB:fluoseq', 'unable to find colorbar axes');
    return
end

% obtain colormap
color_map = feval(color_func, 256);
set(h_fig, 'Colormap', color_map);
display_map = uint8(255 * reshape(color_map, [size(color_map, 1) 1 size(color_map, 2)]));

% display colorbar
if (istype(h_image, 'image'))
    set(h_image, 'CData', display_map);
else
    h_image = image(display_map);
    set(h_image, 'EraseMode', 'none', ...
        'ButtonDownFcn', 'fluoseq(gcf, ''colormap'')');
    set(h_axes, 'XDir', 'normal', ...
        'XTick', [], ...
        'YDir', 'normal', ...
        'YTick', [], ...
        'Tag', 'colorbar', ...
        'UserData', h_image);
end
return



function [] = enable_buttons(h_button, file_par, image_par)

% enable all buttons except stop
set(h_button, 'Enable', 'on');
set(h_button(4), 'Enable', 'off');

% camera setup button
if (isscalar(image_par.h_cam))
    set(h_button(10), 'Enable', 'on');
else
    set(h_button(10), 'Enable', 'off');
end

% open/close file button
if (isempty(file_par.file_name))
    set(h_button(12), 'Enable', 'on');
    set(h_button(13), 'Enable', 'off');
else
    set(h_button(12), 'Enable', 'off');
    set(h_button(13), 'Enable', 'on');
end
return



function roi_struct = create_roi_struct(roi_coord, image_bin)

% create valid ROI
% round pixels to provide exact binning
field_name = {'s1', 's2', 'sbin', 'p1', 'p2', 'pbin'};
field_value = {roi_coord(1) - 1, roi_coord(3) - mod(diff(roi_coord([1 3])) + 1, image_bin(1)) - 1, image_bin(1), ...
    roi_coord(2) - 1, roi_coord(4) - mod(diff(roi_coord([2 4])) + 1, image_bin(2)) - 1, image_bin(2)};
roi_struct = cell2struct(field_value, field_name, 2);
return



function h_fig = make_image_win(figure_tag)

% default parameters
figure_bkgnd = [0.8 0.8 0.8];       % figure window background colorspec
figure_pos = [0.10 0.10 0.80 0.80]; % figure window position (% of screen)
text_pos = [0.17 0.95 0.73 0.03];   % text label position (% of figure)
button_pos = [0.02 0.23 0.13 0.72]; % button panel position (% of figure)
image_pos = [0.17 0.23 0.73 0.72];  % image display position (% of figure)
color_pos = [0.92 0.23 0.06 0.72];  % colorbar display position (% of figure)
graph_pos = [0.08 0.05 0.90 0.15];  % graph display position (% of figure)

% create figure window
h_fig = figure('Color', figure_bkgnd, ...
    'Units', 'normalized', ...
    'Position', figure_pos, ...
    'BackingStore', 'off', ...
    'CloseRequestFcn', 'fluoseq(gcf, ''finish'')', ...
    'MenuBar', 'none', ...
    'Name', 'No file open', ...
    'NumberTitle', 'off', ...
    'Pointer', 'arrow', ...
    'UserData', [], ...
    'Tag', figure_tag);

% create text label
h_text = uicontrol('Parent', h_fig, ...
    'Units', 'normalized', ...
    'Position', text_pos, ...
    'BackgroundColor', figure_bkgnd, ...
    'ForegroundColor', [0.0 0.0 0.0], ...
    'FontName', 'Helvetica', ...
    'FontSize', 8, ...
    'String', '', ...
    'Style', 'text', ...
    'Tag', 'imagetext');

% create button panel
labels = {'Snap Image', 'Start Sequence', 'Start Focus', 'Stop Focus', 'Select Region', 'Show Region', ...
    'Clear Region', 'Reset Graph', 'Parameters', 'Camera Setup', 'ROI Setup', 'Open File', 'Close File'};
h_button = guipanel(h_fig, button_pos, 'vertical', ...
    'Enable', 'off', ...
    'FontName', 'Helvetica', ...
    'FontSize', 8, ...
    'Style', 'pushbutton', ...
    'Callback', 'fluoseq(gcf, get(gcbo, ''Tag''))', ...
    'String', labels, ...
    'Tag', labels);
set(h_button(4), 'Callback', 'set(gcf, ''Tag'', ''stop'')');

% create image axes
h_axes(1) = axes('Parent', h_fig, ...
    'Units', 'normalized', ...
    'Position', image_pos, ...
    'Box', 'on', ...
    'XDir', 'reverse', ...
    'XTick', [], ...
    'YDir', 'normal', ...
    'YTick', [], ...
    'Tag', 'image');

% create colorbar axes
h_axes(2) = axes('Parent', h_fig, ...
    'Units', 'normalized', ...
    'Position', color_pos, ...
    'Box', 'on', ...
    'XDir', 'normal', ...
    'XTick', [], ...
    'YDir', 'normal', ...
    'YTick', [], ...
    'Tag', 'colorbar');

% create graph axes
h_axes(3) = axes('Parent', h_fig, ...
    'Units', 'normalized', ...
    'Position', graph_pos, ...
    'Box', 'on', ...
    'FontName', 'helvetica', ...
    'FontSize', 8, ...
    'Tag', 'graph');

% save handles to figure UserData structure
fig_handle = cell2struct({h_axes, h_text, h_button}, {'h_axes', 'h_text', 'h_button'}, 2);
set(h_fig, 'UserData', fig_handle);
return