anatseq.m

SDFGASFASFASFAS EDGSGA DGSFGSA

        if (edit_flag)
            for i = 1 : length(pvcam_setpar)
                pvcam_set.(pvcam_setpar{i}) = pvcamgetvalue(image_par.h_cam, pvcam_setpar{i});
            end
            set(h_fig, 'UserData', {fig_handle, image_par, file_par, pvcam_get, pvcam_set, lambda_par, focus_par});
        end
        
    case 'roi setup'        % create/remove ROI
        set(h_fig, 'WindowButtonMotionFcn', '');
        [x1, y1, x2, y2, roi_flag] = guirbsel(h_fig, fig_handle.h_axes(1));
        if (roi_flag)
            image_par.roi_coord = round([x1, y1, x2, y2]);
        else
            image_par.roi_coord = [1 1 image_par.image_size];
        end
%         ans_cell = inputdlg('Enter ROI coords', 'ROI setup', 1, {num2str(image_par.roi_coord)});
%         if (isempty(ans_cell))
%             return
%         else
%             image_par.roi_coord = str2num(ans_cell{1});
%         end
        image_par.roi_full = create_roi_struct(image_par.roi_coord, image_par.bin_full);
        set(h_fig, 'UserData', {fig_handle, image_par, file_par, pvcam_get, pvcam_set, lambda_par, focus_par});
        set(h_fig, 'WindowButtonMotionFcn', motion_fcn);

    case 'open file'        % save images to TIF file
        % generate file name
        % filename example:  scm07feb03a.tif
        file_date = lower([datestr(datenum(date),'dd') datestr(datenum(date),'mmmyy')]);
        for file_char = double('a') : double('z')
            file_name = [file_par.file_prefix file_date char(file_char) '.tif'];
            if (~exist(fullfile(file_par.file_path, file_name), 'file'))
                break
            end
        end

        % have user select file name
        old_dir = pwd;
        if (exist(file_par.file_path, 'dir'))
            cd(file_par.file_path);
            [file_name, file_path] = uiputfile(file_name, 'Save Images to File');
            cd(old_dir);
        else
            [file_name, file_path] = uiputfile(file_name, 'Save Images to File');
            warning('MATLAB:anatseq', '%s not found, saving file to %s',  file_par.file_path, old_dir)
        end
        if ((file_name(1) ~= 0) && (file_path(1) ~= 0))
            % reset clock and filename display
            % enable appropriate buttons
            file_par.file_name = file_name;
            file_par.file_path = file_path;
            file_par.image_count = 0;
            file_par.start_time = clock;
            set(h_fig, 'Name', file_par.file_name);
            set(h_fig, 'UserData', {fig_handle, image_par, file_par, pvcam_get, pvcam_set, lambda_par, focus_par});
            enable_buttons(fig_handle.h_button, file_par, image_par);
        end

    case 'close file'       % stop saving images to TIF file
        file_par.file_name = '';
        enable_buttons(fig_handle.h_button, file_par, image_par);
        set(h_fig, 'Name', 'No file open');
        set(h_fig, 'UserData', {fig_handle, image_par, file_par, pvcam_get, pvcam_set, lambda_par, focus_par});

    case 'colormap'         % select a new colormap
        palette_list = {'autumn', 'bone', 'cool', 'copper', ...
            'gray', 'hot', 'hsv', 'invgray', ...
            'invhsv', 'jet', 'jetshift', 'lucifer', ...
            'pink', 'spectrum', 'spring', 'summer', 'winter'};
        [new_value, select_flag] = guilist('Palette', palette_list, func2str(image_par.color_map));
        if (select_flag)
            image_par.color_map = str2func(new_value);
            disp_colorbar(h_fig, fig_handle.h_axes(2), image_par.color_map);
            set(h_fig, 'UserData', {fig_handle, image_par, file_par, pvcam_get, pvcam_set, lambda_par, focus_par});
        end

    case 'finish'           % close figure window, camera and filter wheel
        if (isempty(image_par.h_cam))
            pvcamclose(0);
        else
            pvcamclose(image_par.h_cam);
        end
        lambdactrl(lambda_par.port, 'clear');
        if (isa(image_par.h_lambda, 'timer'))
            stop(image_par.h_lambda);
            delete(image_par.h_lambda);
        end
        delete(h_fig);

    otherwise               % invalid command
        warning('MATLAB:anatseq', '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:anatseq', 'unable to find image axes');
    return
end
h_text = fig_handle.h_text;
if (~istype(h_text, 'uicontrol'))
    warning('MATLAB:anatseq', '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:anatseq', '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', 'anatseq(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(3), 'Enable', 'off');

% camera setup button
if (isscalar(image_par.h_cam))
    set(h_button(5), 'Enable', 'on');
else
    set(h_button(5), 'Enable', 'off');
end

% open/close file button
if (isempty(file_par.file_name))
    set(h_button(7), 'Enable', 'on');
    set(h_button(8), 'Enable', 'off');
else
    set(h_button(7), 'Enable', 'off');
    set(h_button(8), '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 = [0.03 0.95 0.87 0.03];   % text label position (% of figure)
button_pos = [0.08 0.03 0.72 0.05]; % button panel position (% of figure)
image_pos = [0.03 0.10 0.87 0.85];  % image display position (% of figure)
color_pos = [0.92 0.10 0.06 0.85];  % colorbar display position (% of figure)

% create figure window
h_fig = figure('Color', figure_bkgnd, ...
    'Units', 'normalized', ...
    'Position', figure_pos, ...
    'BackingStore', 'off', ...
    'CloseRequestFcn', 'anatseq(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 Focus', 'Stop Focus', 'Parameters', 'Camera Setup', 'ROI Setup', 'Open File', 'Close File'};
h_button = guipanel(h_fig, button_pos, 'horizontal', ...
    'Enable', 'off', ...
    'FontName', 'Helvetica', ...
    'FontSize', 8, ...
    'Style', 'pushbutton', ...
    'Callback', 'anatseq(gcf, get(gcbo, ''Tag''))', ...
    'String', labels, ...
    'Tag', labels);
set(h_button(3), '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');

% 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