pmtmode.m

SDFGASFASFASFAS EDGSGA DGSFGSA

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);
    for i = 1 : size(image_data, 3)
        disp_single_image(image_data(:, :, i), fig_handle, image_par, new_file);

        % save image data if file is open
        if (~isempty(new_file.name_full) && ~strcmp(focus_flag, 'focus'))
            new_file.count_full = new_file.count_full + 1;
            imwrite(image_data(:, :, i), fullfile(new_file.file_path, new_file.name_full), ...
                'tif', 'WriteMode', 'append', 'Description', datestr(new_file.acq_time));
        end
    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:disp_single_image', 'unable to find image axes');
    return
end
h_text = fig_handle.h_text;
if (~istype(h_text(1), 'uicontrol'))
    warning('MATLAB:disp_single_image', '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

% create image mask if needed
% adjust mask if ROI selected
if (~isempty(image_par.roi_pmt))
    image_mask = feval(class(image_disp), ones(size(image_disp)));
    x(1) = min(max(image_par.roi_pmt.s1 - image_par.roi_coord(1) + 2, 1), size(image_disp, 2));
    x(2) = min(max(image_par.roi_pmt.s2 - image_par.roi_coord(1) + 2, 1), size(image_disp, 2));
    y(1) = min(max(image_par.roi_pmt.p1 - image_par.roi_coord(2) + 2, 1), size(image_disp, 1));
    y(2) = min(max(image_par.roi_pmt.p2 - image_par.roi_coord(2) + 2, 1), size(image_disp, 1));
    image_mask(y(1) : y(2), x(1) : x(2)) = feval(class(image_disp), 0);
    image_disp = image_disp .* image_mask;
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', ...
        'ButtonDownFcn', 'pmtmode(gcf, ''select pixel'')', ...
        '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.count_full, ...
    elapsed_time, double(min(min(image_data))), double(max(max(image_data))), image_par.image_size);
set(h_text(1), '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:pmtmode', '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', 'pmtmode(gcf, ''colormap'')');
    set(h_axes, 'XDir', 'normal', ...
        'XTick', [], ...
        'YDir', 'normal', ...
        'YTick', [], ...
        'Tag', 'colorbar', ...
        'UserData', h_image);
end
return



% % CREATE_ICL_SCRIPT
% function icl_script = create_icl_script(image_par, pvcam_get, pvcam_set)
% 
% % obtain ICL coordinates from ROI structure
% s_offset = [image_par.roi_pmt(:).s1];
% s_size = [image_par.roi_pmt(:).s2] - [image_par.roi_pmt(:).s1] + 1;
% s_bin = [image_par.roi_pmt(:).sbin];
% x_size = floor(s_size ./ s_bin);
% if (length(image_par.roi_pmt) > 1)
%     p_shift = [image_par.roi_pmt.p1] - [-1 image_par.roi_pmt(1 : end - 1).p2] - 1;
% else
%     p_shift = image_par.roi_pmt.p1;
% end
% p_size = [image_par.roi_pmt(:).p2] - [image_par.roi_pmt(:).p1] + 1;
% p_bin = [image_par.roi_pmt(:).pbin];
% y_size = floor(p_size ./ p_bin);
% 
% % create scripts to open & close shutter
% % clear CCD array after shutter opens & closes
% icl_script = {'script_begin( );', ...
%     'shutter_open( );', ...
%     sprintf('clear_parallel( %d );', pvcam_set.PARAM_CLEAR_CYCLES), ...
%     sprintf('clear_serial( %d );', pvcam_set.PARAM_CLEAR_CYCLES)};
% 
% % begin exposure loop
% icl_script{end + 1} = sprintf('loop_begin( %d );', image_par.total_pmt);
% if (image_par.expose_pmt > 0)
%     icl_script{end + 1} = sprintf('expose( %d );', image_par.expose_pmt);
% end
% 
% % use frame transfer to maximize exposure time during shifting and readout
% % otherwise shift pixels directly into serial register
% if (pvcam_get.PARAM_FRAME_CAPABLE)
%     icl_script{end + 1} = 'shift_image_to_storage( );';
% else
%     p_shift(1) = p_shift(1) + pvcam_get.PARAM_PREMASK - 1;
% end
% 
% % shift exposed pixels into serial register if needed
% if (p_shift(1) > 0)
%     icl_script{end + 1} = sprintf('shift( %d );', p_shift(1));
% end
% 
% % readout pixels from serial register
% % shift subsequent ROIs into serial register if present
% for i = 1 : length(image_par.roi_pmt)
%     icl_script{end + 1} = sprintf('pixel_readout( %d, %d, %d, %d, %d );', s_offset(i), s_size(i), s_bin(i), p_size(i), p_bin(i));
%     if (i < length(image_par.roi_pmt))
%         if (p_shift(i + 1) > 0)
%             icl_script{end + 1} = sprintf('shift( %d );', p_shift(i + 1));
%         end
%     end
% end
% 
% % readout pixels as a matrix with one row per exposure
% % column size equals number of pixels in all ROIs
% icl_script{end + 1} = 'loop_end( );';
% icl_script{end + 1} = sprintf('pixel_display( %d, %d );', sum(x_size .* y_size), image_par.total_pmt);
% 
% % reset shift mode if frame transfer capable
% if (pvcam_get.PARAM_FRAME_CAPABLE)
%     icl_script{end + 1} = 'shift_mode_is( );';
% end
% 
% % close shutter and terminate script
% icl_script{end + 1} = 'shutter_close( );';
% icl_script{end + 1} = sprintf('clear_parallel( %d );', pvcam_set.PARAM_CLEAR_CYCLES);
% icl_script{end + 1} = sprintf('clear_serial( %d );', pvcam_set.PARAM_CLEAR_CYCLES);
% icl_script{end + 1} = 'script_end( 0 );';
% return



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

% enable all buttons except stop
set(h_button, 'Enable', 'on');
set(h_button(5), 'Enable', 'off');

% image sequence button
if (image_par.total_full < 2)
    set(h_button(2), 'Enable', 'off');
else
    set(h_button(2), 'Enable', 'on');
end

% PMT sequence button
if (isempty(image_par.roi_pmt) || isempty(image_par.offset_pmt))
    set(h_button(3), 'Enable', 'off');
else
    set(h_button(3), 'Enable', 'on');
end

% camera setup button
if (isscalar(image_par.h_cam))
    set(h_button(9), 'Enable', 'on');
else
    set(h_button(9), 'Enable', 'off');
end

% open/close file button
if (isempty(file_par.name_full))
    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 new_par = create_roi_struct(old_par)
new_par = old_par;
field_name = {'s1', 's2', 'sbin', 'p1', 'p2', 'pbin'};

% initialize full field ROI
field_value = {new_par.roi_coord(1) - 1, ...
    new_par.roi_coord(3) - mod(diff(new_par.roi_coord([1 3])) + 1, new_par.bin_full(1)) - 1, ...
    new_par.bin_full(1), ...
    new_par.roi_coord(2) - 1, ...
    new_par.roi_coord(4) - mod(diff(new_par.roi_coord([2 4])) + 1, new_par.bin_full(2)) - 1, ...
    new_par.bin_full(2)};
new_par.roi_full = cell2struct(field_value, field_name, 2);

% create PMT ROI
if (isempty(new_par.offset_pmt))
    new_par.roi_pmt = [];
else
    new_par.offset_pmt = round(min([max([new_par.offset_pmt; floor(new_par.bin_pmt .* new_par.pixel_pmt / 2)]); ...
        (new_par.image_size - floor(new_par.bin_pmt .* new_par.pixel_pmt / 2) - 1)]));
    first_pixel = new_par.offset_pmt - floor(new_par.bin_pmt .* new_par.pixel_pmt / 2);
    last_pixel = new_par.offset_pmt + floor(new_par.bin_pmt .* new_par.pixel_pmt / 2) - 1;
    field_value = {first_pixel(1), last_pixel(1), new_par.bin_pmt(1), first_pixel(end), last_pixel(end), new_par.bin_pmt(end)};
    new_par.roi_pmt = cell2struct(field_value, field_name, 2);
end
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', 'pmtmode(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', 'Image Sequence', 'PMT Sequence', 'Start Focus', 'Stop Focus', 'Clear Pixel', ...
    'Draw Line', 'Parameters', 'Camera Setup', 'ROI Setup', 'Reset Graph', 'Open File', 'Close File'};
h_button = guipanel(h_fig, button_pos, 'vertical', ...
    'Enable', 'off', ...
    'FontName', 'Helvetica', ...
    'FontSize', 8, ...
    'Style', 'pushbutton', ...
    'Callback', 'pmtmode(gcf, get(gcbo, ''Tag''))', ...
    'String', labels, ...
    'Tag', labels);
set(h_button(5), '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