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IntrinsicImaging/WidgetIntrinsicAnalysis.m
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| classdef WidgetIntrinsicAnalysis < handle | |
| %WIDGETINTRINSICANALYSIS analyse streaming image data | |
| properties | |
| stream | |
| adaptor | |
| fps | |
| bitdepth | |
| resolution | |
| clim | |
| period | |
| window | |
| offset | |
| filter | |
| threshold | |
| binning | |
| frame | |
| end | |
| %% --- Export properties --- %% | |
| properties (Access = private) | |
| export_path | |
| export_name | |
| export_flag | |
| export_writerVideo | |
| export_writerMetaData | |
| export_fileVideo | |
| export_fileMetaData | |
| export_fileBackground | |
| export_fileSignal | |
| export_fileIntrinsic | |
| export_fileReference | |
| export_fileROI | |
| end | |
| %% --- Analysis properties --- %% | |
| properties (Access = public) | |
| buffer_size | |
| buffer_frames | |
| buffer_stamps | |
| buffer_baseline | |
| buffer_signal | |
| buffer_mask | |
| index_trial | |
| index_baselineFirst | |
| index_baselineLast | |
| index_signalFirst | |
| index_signalLast | |
| thread_analysis | |
| thread_export | |
| thread_present | |
| end | |
| %% --- visualization properties --- %% | |
| properties (Access = private) | |
| vw_parent | |
| vw_axes | |
| vw_image | |
| vw_patch | |
| vw_ellipse | |
| vw_roi | |
| vw_mask | |
| bg_parent | |
| bg_axes | |
| bg_bars | |
| bg_plot | |
| end | |
| %% --- UI properties --- %% | |
| properties (Access = private) | |
| ui_parent | |
| ui_panel | |
| ui_grid | |
| ui_text_export | |
| ui_checkbox_export | |
| ui_pushbutton_export | |
| ui_popup_binning | |
| ui_edit_period | |
| ui_edit_windowBefore | |
| ui_edit_windowAfter | |
| ui_edit_offsetBefore | |
| ui_edit_offsetAfter | |
| ui_text_threshold | |
| ui_slider_threshold | |
| ui_pushbutton_start | |
| ui_pushbutton_stop | |
| end | |
| %% --- constant properties --- %% | |
| properties (Constant = true, Access = private, Hidden = true) | |
| UIWINDOW_SIZE = [1, 1, 256, 267]; | |
| GRID_VGAP = [12, 2, 5]; | |
| GRID_HGAP = [5, 2, 5]; | |
| BACKGROUND_COLOR = [1, 1, 1]; | |
| FOREGROUND_COLOR = [0.5, 0.5, 0.5]; | |
| PATCH_COLOR = [0,255,0]; | |
| ALPHA_VALUE = 0.5; | |
| PUSHBUTTON_SIZE = [1, 1, 90, 26]; | |
| EDITBOX_SIZE = [1, 1, 60, 20]; | |
| CHECKBOX_SIZE = [1, 1, 90, 20]; | |
| SLIDER_SIZE = [1, 1, 240, 20]; | |
| BIN_SIZE = 100; | |
| DEVICE_ID = 1; | |
| BIT_MAX = [2^8, 2^12, 2^16] - 1; | |
| GAUSSFILTER_SIZE = 32; | |
| GAUSSFILTER_SIGMA = 5; | |
| KEY_ENTER = 13; | |
| BINNING_TYPE = {'x1', 'x2', 'x4'}; | |
| BINNING_VALUE = [1,2,4]; | |
| end | |
| %% --- events --- %% | |
| events (NotifyAccess = protected) | |
| event_start | |
| event_stop | |
| event_trigger | |
| end | |
| %% --- constructor / destructor --- %% | |
| methods | |
| function obj = WidgetIntrinsicAnalysis(varargin) | |
| %WIDGETINTRINSICANALYSIS class constructor | |
| parserObj = inputParser; | |
| addParameter(parserObj, 'Parent', [], @isgraphics); | |
| parse(parserObj, varargin{:}); | |
| % set parent graphics objects | |
| if isempty(parserObj.Results.Parent) | |
| obj.ui_parent = figure(... | |
| 'Visible', 'on',... | |
| 'Tag', 'hIntrinsicAnalysis',... | |
| 'Name', 'Intrinsic Analysis',... | |
| 'MenuBar', 'none',... | |
| 'ToolBar', 'none',... | |
| 'NumberTitle', 'off',... | |
| 'Color', obj.BACKGROUND_COLOR,... | |
| 'Resize', 'off',... | |
| 'Units', 'pixels',... | |
| 'Position', obj.UIWINDOW_SIZE,... | |
| 'CloseRequestFcn', @obj.fcnCallback_closeUserInterface); | |
| movegui(obj.ui_parent, 'northwest'); | |
| else | |
| obj.ui_parent = parserObj.Results.Parent; | |
| end | |
| % set defaults values | |
| obj.defaults(); | |
| % render user interface | |
| obj.renderUserInterface(); | |
| end | |
| function obj = dispose(obj) | |
| %DISPOSE class destructor | |
| % remove threads | |
| if isa(obj.thread_analysis, 'timer') | |
| delete(obj.thread_analysis); | |
| end | |
| if isa(obj.thread_export, 'timer') | |
| delete(obj.thread_export); | |
| end | |
| % remove user interface grid | |
| if isa(obj.ui_grid, 'uiGridLayout') | |
| delete(obj.ui_grid); | |
| end | |
| % destroy bar graph figure | |
| if isgraphics(obj.bg_parent, 'figure') | |
| delete(obj.bg_parent); | |
| end | |
| % destroy viewer figure | |
| if isgraphics(obj.vw_parent, 'figure') | |
| delete(obj.vw_parent); | |
| end | |
| % check if parent is figure or was inherit | |
| if isgraphics(obj.ui_parent, 'figure') | |
| delete(obj.ui_parent); | |
| end | |
| % dispose class object | |
| delete(obj); | |
| end | |
| function obj = defaults(obj) | |
| %DEFAULTS | |
| % allocate properties | |
| obj.period = 8; | |
| obj.window = [2, 2]; | |
| obj.offset = [0.5, 0.5]; | |
| obj.filter = fspecial('gaussian', [obj.GAUSSFILTER_SIZE, obj.GAUSSFILTER_SIZE], obj.GAUSSFILTER_SIGMA); | |
| obj.export_name = sprintf('%s_IntrinsicExport', datestr(now,'yyyymmdd-HHMMSS')); | |
| obj.export_path = pwd; | |
| obj.export_flag = 0; | |
| obj.threshold = 0.50; | |
| % set threads | |
| obj.thread_analysis = timer(... | |
| 'ExecutionMode', 'singleShot',... | |
| 'Name', 'ThreadIntrinsicAnalysis',... | |
| 'TimerFcn', @obj.fcnThread_analysis,... | |
| 'TasksToExecute', 1); | |
| obj.thread_export = timer(... | |
| 'ExecutionMode', 'singleShot',... | |
| 'Name', 'ThreadVideoExport',... | |
| 'TimerFcn', @obj.fcnThread_export,... | |
| 'TasksToExecute', 1); | |
| obj.thread_present = timer(... | |
| 'ExecutionMode', 'singleShot',... | |
| 'Name', 'ThreadAnalysisPresent',... | |
| 'TimerFcn', @obj.fcnThread_present,... | |
| 'TasksToExecute', 1); | |
| end | |
| function obj = renderUserInterface(obj) | |
| %RENDERUSERINTERFACE | |
| %%% --- create widget panel --- %%% | |
| obj.ui_panel = uipanel(... | |
| 'Parent', obj.ui_parent,... | |
| 'Title', 'Analysis',... | |
| 'TitlePosition', 'lefttop',... | |
| 'BorderType', 'line',... | |
| 'HighlightColor', obj.FOREGROUND_COLOR,... | |
| 'ForegroundColor', obj.FOREGROUND_COLOR,... | |
| 'BackgroundColor', obj.BACKGROUND_COLOR,... | |
| 'Units', 'normalized',... | |
| 'Position', [0, 0, 1, 1],... | |
| 'Units', 'pixels'); | |
| %%% --- create grid object --- %%% | |
| obj.ui_grid = uiGridLayout(... | |
| 'Parent', obj.ui_panel,... | |
| 'VGrid', 9,... | |
| 'HGrid', 4,... | |
| 'VGap', obj.GRID_VGAP,... | |
| 'HGap', obj.GRID_HGAP); | |
| %%% --- export properties --- %%% | |
| exportPath = fullfile(obj.export_path, obj.export_name); | |
| obj.ui_text_export = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'text',... | |
| 'String', ['...',exportPath(end-45:end)],... | |
| 'BackgroundColor', obj.BACKGROUND_COLOR,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.ui_grid.getGrid('VIndex', 1, 'HIndex', 1:4)); | |
| obj.ui_grid.align(obj.ui_text_export,... | |
| 'VIndex', 1,... | |
| 'HIndex', 1:4,... | |
| 'Anchor', 'center'); | |
| obj.ui_pushbutton_export = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'pushbutton',... | |
| 'String', 'set export',... | |
| 'Enable', 'on',... | |
| 'Callback', @obj.fcnCallback_setExport,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.PUSHBUTTON_SIZE); | |
| obj.ui_grid.align(obj.ui_pushbutton_export,... | |
| 'VIndex', 2,... | |
| 'HIndex', 1:2,... | |
| 'Anchor', 'center'); | |
| obj.ui_checkbox_export = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'checkbox',... | |
| 'String', 'keep video',... | |
| 'Value', 0,... | |
| 'BackgroundColor', obj.BACKGROUND_COLOR,... | |
| 'Callback', @obj.fcnCallback_check,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.CHECKBOX_SIZE); | |
| obj.ui_grid.align(obj.ui_checkbox_export,... | |
| 'VIndex', 2,... | |
| 'HIndex', 3:4,... | |
| 'Anchor', 'center'); | |
| %%% --- software binning --- %%% | |
| ui_text = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'text',... | |
| 'String', 'binning',... | |
| 'BackgroundColor', obj.BACKGROUND_COLOR,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.ui_grid.getGrid('VIndex', 3, 'HIndex', 3)); | |
| obj.ui_grid.align(ui_text,... | |
| 'VIndex', 3,... | |
| 'HIndex', 3,... | |
| 'Anchor', 'east'); | |
| obj.ui_popup_binning = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'popup',... | |
| 'String', obj.BINNING_TYPE,... | |
| 'Value', 1,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.EDITBOX_SIZE); | |
| obj.ui_grid.align(obj.ui_popup_binning,... | |
| 'VIndex', 3,... | |
| 'HIndex', 4,... | |
| 'Anchor', 'east'); | |
| %%% --- stimuli properties --- %%% | |
| ui_text = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'text',... | |
| 'String', 'period [sec]',... | |
| 'BackgroundColor', obj.BACKGROUND_COLOR,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.ui_grid.getGrid('VIndex', 3, 'HIndex', 1)); | |
| obj.ui_grid.align(ui_text,... | |
| 'VIndex', 3,... | |
| 'HIndex', 1,... | |
| 'Anchor', 'east'); | |
| obj.ui_edit_period = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'edit',... | |
| 'String', sprintf('%.2f', obj.period),... | |
| 'Callback', @obj.fcnCallback_parse,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.EDITBOX_SIZE); | |
| obj.ui_grid.align(obj.ui_edit_period,... | |
| 'VIndex', 3,... | |
| 'HIndex', 2,... | |
| 'Anchor', 'west'); | |
| %%% --- buffer properties --- %%% | |
| ui_text = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'text',... | |
| 'String', 'before',... | |
| 'BackgroundColor', obj.BACKGROUND_COLOR,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.ui_grid.getGrid('VIndex', 4, 'HIndex', 3)); | |
| obj.ui_grid.align(ui_text,... | |
| 'VIndex', 4,... | |
| 'HIndex', 3,... | |
| 'Anchor', 'south'); | |
| ui_text = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'text',... | |
| 'String', 'after',... | |
| 'BackgroundColor', obj.BACKGROUND_COLOR,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.ui_grid.getGrid('VIndex', 4, 'HIndex', 4)); | |
| obj.ui_grid.align(ui_text,... | |
| 'VIndex', 4,... | |
| 'HIndex', 4,... | |
| 'Anchor', 'south'); | |
| ui_text = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'text',... | |
| 'String', 'window size [sec]',... | |
| 'BackgroundColor', obj.BACKGROUND_COLOR,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.ui_grid.getGrid('VIndex', 5, 'HIndex', 1:2)); | |
| obj.ui_grid.align(ui_text,... | |
| 'VIndex', 5,... | |
| 'HIndex', 1:2,... | |
| 'Anchor', 'east'); | |
| obj.ui_edit_windowBefore = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'edit',... | |
| 'String', sprintf('%.2f', obj.window(1)),... | |
| 'Callback', @obj.fcnCallback_parse,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.EDITBOX_SIZE); | |
| obj.ui_grid.align(obj.ui_edit_windowBefore,... | |
| 'VIndex', 5,... | |
| 'HIndex', 3,... | |
| 'Anchor', 'center'); | |
| obj.ui_edit_windowAfter = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'edit',... | |
| 'String', sprintf('%.2f', obj.window(2)),... | |
| 'Callback', @obj.fcnCallback_parse,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.EDITBOX_SIZE); | |
| obj.ui_grid.align(obj.ui_edit_windowAfter,... | |
| 'VIndex', 5,... | |
| 'HIndex', 4,... | |
| 'Anchor', 'center'); | |
| ui_text = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'text',... | |
| 'String', 'stimuli offset [sec]',... | |
| 'BackgroundColor', obj.BACKGROUND_COLOR,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.ui_grid.getGrid('VIndex', 6, 'HIndex', 1:2)); | |
| obj.ui_grid.align(ui_text,... | |
| 'VIndex', 6,... | |
| 'HIndex', 1:2,... | |
| 'Anchor', 'east'); | |
| obj.ui_edit_offsetBefore = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'edit',... | |
| 'String', sprintf('%.2f', obj.offset(1)),... | |
| 'Callback', @obj.fcnCallback_parse,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.EDITBOX_SIZE); | |
| obj.ui_grid.align(obj.ui_edit_offsetBefore,... | |
| 'VIndex', 6,... | |
| 'HIndex', 3,... | |
| 'Anchor', 'center'); | |
| obj.ui_edit_offsetAfter = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'edit',... | |
| 'String', sprintf('%.2f', obj.offset(2)),... | |
| 'Callback', @obj.fcnCallback_parse,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.EDITBOX_SIZE); | |
| obj.ui_grid.align(obj.ui_edit_offsetAfter,... | |
| 'VIndex', 6,... | |
| 'HIndex', 4,... | |
| 'Anchor', 'center'); | |
| %%% --- threshold slider --- %%% | |
| obj.ui_text_threshold = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'text',... | |
| 'String', sprintf('mask threshold %.2f',obj.threshold),... | |
| 'BackgroundColor', obj.BACKGROUND_COLOR,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.ui_grid.getGrid('VIndex', 7, 'HIndex', 1:4)); | |
| obj.ui_grid.align(obj.ui_text_threshold,... | |
| 'VIndex', 7,... | |
| 'HIndex', 1:4,... | |
| 'Anchor', 'south'); | |
| obj.ui_slider_threshold = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'slider',... | |
| 'Min', 0,... | |
| 'Max', 1,... | |
| 'Value', 0.5,... | |
| 'SliderStep', [1/obj.BIN_SIZE, 1/(obj.BIN_SIZE/5)],... | |
| 'Callback', @obj.fcnCallback_slider,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.SLIDER_SIZE); | |
| obj.ui_grid.align(obj.ui_slider_threshold,... | |
| 'VIndex', 8,... | |
| 'HIndex', 1:4,... | |
| 'Anchor', 'center'); | |
| %%% --- push buttons --- %%% | |
| obj.ui_pushbutton_start = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'pushbutton',... | |
| 'String', 'Start',... | |
| 'Enable', 'on',... | |
| 'Callback', @obj.fcnCallback_start,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.PUSHBUTTON_SIZE); | |
| obj.ui_grid.align(obj.ui_pushbutton_start,... | |
| 'VIndex', 9,... | |
| 'HIndex', 1:2,... | |
| 'Anchor', 'center'); | |
| obj.ui_pushbutton_stop = uicontrol(... | |
| 'Parent', obj.ui_panel,... | |
| 'Style', 'pushbutton',... | |
| 'String', 'Stop',... | |
| 'Enable', 'off',... | |
| 'Callback', @obj.fcnCallback_stop,... | |
| 'Units', 'pixels',... | |
| 'Position', obj.PUSHBUTTON_SIZE); | |
| obj.ui_grid.align(obj.ui_pushbutton_stop,... | |
| 'VIndex', 9,... | |
| 'HIndex', 3:4,... | |
| 'Anchor', 'center'); | |
| end | |
| function obj = renderVisualWindow(obj) | |
| %RENDERVISUALWINDOW | |
| % get screen resolution | |
| screenResolution = get(0, 'ScreenSize'); | |
| screenResolution = floor(0.4 * screenResolution(3:4)); | |
| aspectRatioCam = obj.resolution(1) ./ obj.resolution(2); | |
| previewWidth = screenResolution(1); | |
| previewHeight = floor(aspectRatioCam * previewWidth); | |
| obj.clim = [min(obj.frame(:)), max(obj.frame(:))]; | |
| % apply initial binning | |
| obj.binning = obj.BINNING_VALUE(get(obj.ui_popup_binning, 'Value')); | |
| if obj.binning > 1 | |
| obj.frame = imbinning(obj.frame, obj.binning, obj.binning); | |
| obj.resolution = size(obj.frame); | |
| end | |
| % render image window handlers | |
| obj.vw_parent = figure(... | |
| 'Visible','on',... | |
| 'MenuBar','none',... | |
| 'ToolBar','none',... | |
| 'Name','Reference Frame',... | |
| 'NumberTitle','off',... | |
| 'Resize', 'off',... | |
| 'Units','pixels',... | |
| 'Position', [1, 1, previewWidth, previewHeight],... | |
| 'WindowKeyPressFcn', @obj.fcnCallback_acceptROI,... | |
| 'CloseRequestFcn', @obj.fcnCallback_closeViewerWindow); | |
| movegui(obj.vw_parent, 'north'); | |
| obj.vw_axes = axes(... | |
| 'Parent', obj.vw_parent,... | |
| 'Visible','off',... | |
| 'Units', 'pixels',... | |
| 'Position', [1, 1, previewWidth, previewHeight]); | |
| obj.vw_image = image(... | |
| obj.frame,... | |
| 'Parent', obj.vw_axes,... | |
| 'CDataMapping', 'scaled'); | |
| set(obj.vw_axes,... | |
| 'XTick', [],... | |
| 'YTick', [],... | |
| 'CLim', obj.clim); | |
| colormap(obj.vw_axes, 'gray'); | |
| obj.vw_mask = false(obj.resolution); | |
| hold(obj.vw_axes, 'on'); | |
| obj.vw_patch = image(... | |
| repmat(shiftdim(obj.PATCH_COLOR, -1), obj.resolution(1), obj.resolution(2)),... | |
| 'Parent', obj.vw_axes,... | |
| 'CDataMapping', 'scaled',... | |
| 'AlphaData', obj.vw_mask); | |
| hold(obj.vw_axes,'off'); | |
| % user defined ROI | |
| obj.vw_ellipse = imellipse(obj.vw_axes); | |
| end | |
| function obj = renderBarGraph(obj) | |
| %RENDERBARGRAPH interactive signal difference graph | |
| viewerPosition = get(obj.vw_parent, 'Position'); | |
| graphHeight = floor(viewerPosition(4) / 2); | |
| graphWidth = floor(viewerPosition(3) / 2); | |
| % create a figure output | |
| obj.bg_parent = figure(... | |
| 'Visible', 'on',... | |
| 'MenuBar', 'none',... | |
| 'ToolBar', 'none',... | |
| 'Name', 'Difference Histogram',... | |
| 'NumberTitle', 'off',... | |
| 'Color', obj.BACKGROUND_COLOR,... | |
| 'Resize', 'on',... | |
| 'Units', 'pixels',... | |
| 'Position', [1, 1, graphWidth, graphHeight],... | |
| 'CloseRequestFcn', @obj.fcnCallback_closeBarGraph); | |
| movegui(obj.bg_parent, 'southeast'); | |
| obj.bg_axes = axes('Parent', obj.bg_parent); | |
| obj.buffer_mask = double(obj.frame) ./ obj.BIT_MAX(obj.bitdepth); | |
| data = obj.buffer_mask(obj.vw_roi); | |
| obj.vw_mask = obj.buffer_mask; | |
| [y,x] = histcounts( data(:), obj.BIN_SIZE); | |
| x = x(1:end-1)+diff(x)./2; | |
| step = max(x)*0.01; | |
| obj.bg_bars = bar(x, y, 0.6, 'EdgeColor',[.4,.4,.4], 'FaceColor',[.75,.75,.75]); | |
| set(obj.bg_axes,'XLim',[min(x)-step, max(x)+step]); | |
| set(obj.ui_slider_threshold, 'Value', obj.threshold); | |
| hold(obj.bg_axes, 'on'); | |
| obj.bg_plot = plot(obj.bg_axes, [obj.threshold, obj.threshold], get(obj.bg_axes,'YLim'), 'r-.','LineWidth', 1.2); | |
| hold(obj.bg_axes, 'off'); | |
| xlabel(obj.bg_axes,'baseline / signal','FontSize',12); | |
| ylabel(obj.bg_axes,'frequency','FontSize', 12); | |
| end | |
| function obj = enable(obj, varstate) | |
| %ENABLE toggle on/off enable property | |
| if strcmp('on', varstate) || strcmp('off', varstate) | |
| set(obj.ui_edit_period, 'Enable', varstate); | |
| set(obj.ui_edit_windowBefore, 'Enable', varstate); | |
| set(obj.ui_edit_windowAfter, 'Enable', varstate); | |
| set(obj.ui_edit_offsetBefore, 'Enable', varstate); | |
| set(obj.ui_edit_offsetAfter, 'Enable', varstate); | |
| set(obj.ui_checkbox_export, 'Enable', varstate); | |
| set(obj.ui_popup_binning, 'Enable', varstate); | |
| set(obj.ui_pushbutton_export, 'Enable', varstate); | |
| end | |
| end | |
| end | |
| %% --- user callbacks --- %% | |
| methods | |
| function obj = fcnCallback_closeUserInterface(obj, ~, ~) | |
| %FCNCALLBACK_CLOSEUSERINTERFACE request destructor | |
| obj.dispose(); | |
| end | |
| function obj = fcnCallback_closeViewerWindow(obj, ~, ~) | |
| %FCNCALLBACK_CLOSEVIEWERWINDOW toggle viewer property | |
| set(obj.vw_parent, 'Visible', 'off'); | |
| end | |
| function obj = fcnCallback_closeBarGraph(obj, ~, ~) | |
| %FCNCALLBACK_CLOSEBARGRAPH toggle viewer property | |
| set(obj.bg_parent, 'Visible', 'off'); | |
| end | |
| function obj = fcnCallback_parse(obj, hSrc, ~) | |
| %FCNCALLBACK_PARSE parse edit box | |
| % parse edin box | |
| varchar = get(hSrc, 'String'); | |
| varnum = str2double(regexp(varchar, '[0-9]+\.?[0-9]*', 'match')); | |
| varnum(isempty(varnum)) = 0; | |
| % assign to property | |
| switch hSrc | |
| case obj.ui_edit_period | |
| % check for min period available | |
| minValue = sum(obj.window) + sum(obj.offset); | |
| if varnum < minValue | |
| varnum = minValue; | |
| end | |
| set(obj.ui_edit_period, 'String', sprintf('%.2f', varnum)); | |
| obj.period = varnum; | |
| case obj.ui_edit_windowBefore | |
| % check if window fits in period | |
| maxValue = obj.period - obj.window(2) - sum(obj.offset); | |
| if varnum > maxValue | |
| varnum = maxValue; | |
| end | |
| set(obj.ui_edit_windowBefore, 'String', sprintf('%.2f', varnum)); | |
| obj.window(1) = varnum; | |
| case obj.ui_edit_windowAfter | |
| % check if window fits in period | |
| maxValue = obj.period - obj.window(1) - sum(obj.offset); | |
| if varnum > maxValue | |
| varnum = maxValue; | |
| end | |
| set(obj.ui_edit_windowAfter, 'String', sprintf('%.2f', varnum)); | |
| obj.window(2) = varnum; | |
| case obj.ui_edit_offsetBefore | |
| % check if window fits in period | |
| maxValue = obj.period - obj.offset(2) - sum(obj.window); | |
| if varnum > maxValue | |
| varnum = maxValue; | |
| end | |
| set(obj.ui_edit_offsetBefore, 'String', sprintf('%.2f', varnum)); | |
| obj.offset(1) = varnum; | |
| case obj.ui_edit_offsetAfter | |
| % check if window fits in period | |
| maxValue = obj.period - obj.offset(1) - sum(obj.window); | |
| if varnum > maxValue | |
| varnum = maxValue; | |
| end | |
| set(obj.ui_edit_offsetAfter, 'String', sprintf('%.2f', varnum)); | |
| obj.offset(2) = varnum; | |
| end | |
| end | |
| function obj = fcnCallback_check(obj, ~, ~) | |
| %FCNCALLBACK_CHECKBOX toggle use state | |
| obj.export_flag = get(obj.ui_checkbox_export, 'Value'); | |
| end | |
| function obj = fcnCallback_slider(obj, ~, ~) | |
| %FCNCALLBACK_SLIDER | |
| obj.threshold = get(obj.ui_slider_threshold, 'Value'); | |
| set(obj.ui_text_threshold,... | |
| 'String', sprintf('mask threshold %.2f',obj.threshold)); | |
| obj.ui_grid.align(obj.ui_text_threshold,... | |
| 'VIndex', 7,... | |
| 'HIndex', 1:4,... | |
| 'Anchor', 'south'); | |
| if isgraphics(obj.bg_plot, 'line') | |
| set(obj.bg_plot, 'XData', [obj.threshold, obj.threshold]); | |
| obj.adjustMask(); | |
| end | |
| end | |
| function obj = fcnCallback_setExport(obj, ~, ~) | |
| %FCNCALLBACK_SETEXPORT set user defined export | |
| % open dialog box for saving files | |
| obj.export_name = sprintf('%s_IntrinsicExport', datestr(now,'yyyymmdd-HHMMSS')); | |
| [fileName, pathName] = uiputfile('*.*', 'Save experiment as', obj.export_name); | |
| % set new file name | |
| if (fileName ~= 0) | |
| obj.export_name = fileName; | |
| end | |
| % set new path | |
| if (pathName ~= 0) | |
| obj.export_path = pathName; | |
| end | |
| % update export message | |
| exportPath = fullfile(obj.export_path, obj.export_name); | |
| if length(exportPath) > 45 | |
| exportPath = ['...', exportPath(end-45:end)]; | |
| end | |
| set(obj.ui_text_export, 'String', exportPath); | |
| obj.ui_grid.align(obj.ui_text_export,... | |
| 'VIndex', 1,... | |
| 'HIndex', 1:4,... | |
| 'Anchor', 'south'); | |
| end | |
| function obj = fcnCallback_acceptROI(obj, ~, ~) | |
| %FCNCALLBACK_ACCEPTROI | |
| key_char = get(obj.vw_parent, 'CurrentCharacter'); | |
| if uint8(key_char) == obj.KEY_ENTER | |
| obj.vw_roi = createMask(obj.vw_ellipse, obj.vw_image); | |
| delete(obj.vw_ellipse); | |
| obj.start(); | |
| end | |
| end | |
| function obj = fcnCallback_start(obj, ~, ~) | |
| %FCNCALLBACK_START initialize run | |
| % emit start event | |
| notify(obj, 'event_start'); | |
| end | |
| function obj = fcnCallback_stop(obj, ~, ~) | |
| %FCNCALLBACK_STOP stop run | |
| % emit stop event | |
| notify(obj, 'event_stop'); | |
| obj.stop(); | |
| end | |
| end | |
| %% --- functional methods --- %% | |
| methods | |
| function obj = initialize(obj) | |
| %START initialize and start experiment | |
| % toggle UI components | |
| obj.enable('off'); | |
| set(obj.ui_pushbutton_start, 'enable', 'off'); | |
| set(obj.ui_pushbutton_stop, 'enable', 'on'); | |
| % initialize Run | |
| obj.initializeBuffers(); | |
| % initialize Export | |
| obj.initializeExport(); | |
| % initialize Stream | |
| obj.initializeStream(); | |
| % render visual window | |
| obj.renderVisualWindow(); | |
| end | |
| function obj = start(obj) | |
| %START experiment | |
| % render bar graph | |
| obj.renderBarGraph(); | |
| % adjust mask | |
| obj.adjustMask(); | |
| % start video stream | |
| if isa(obj.stream, 'videoinput') | |
| start(obj.stream); | |
| end | |
| end | |
| function obj = stop(obj) | |
| %STOP user requested experiment stop | |
| % toggle UI components | |
| obj.enable('on'); | |
| set(obj.ui_pushbutton_start, 'enable', 'on'); | |
| set(obj.ui_pushbutton_stop, 'enable', 'off'); | |
| % stop video object | |
| if isa(obj.stream, 'videoinput') | |
| stop(obj.stream); | |
| end | |
| % terminate export | |
| obj.terminateExport(); | |
| % reset properties | |
| obj.frame = []; | |
| obj.export_name = sprintf('%s_IntrinsicExport', datestr(now,'yyyymmdd-HHMMSS')); | |
| % update export message | |
| exportPath = fullfile(obj.export_path, obj.export_name); | |
| if length(exportPath) > 45 | |
| exportPath = ['...', exportPath(end-45:end)]; | |
| end | |
| set(obj.ui_text_export, 'String', exportPath); | |
| obj.ui_grid.align(obj.ui_text_export,... | |
| 'VIndex', 1,... | |
| 'HIndex', 1:4,... | |
| 'Anchor', 'south'); | |
| % close windows | |
| delete(obj.vw_parent); | |
| delete(obj.bg_parent); | |
| end | |
| function obj = initializeExport(obj) | |
| %INITIALIZEEXPORT prepare output files | |
| % create export folder | |
| exportFolder = fullfile(obj.export_path, obj.export_name); | |
| if exist(exportFolder, 'dir') == 0 | |
| mkdir(exportFolder); | |
| else | |
| % export name alread exist, update | |
| obj.export_name = sprintf('%s_%s',... | |
| datestr(now,'yyyymmdd-HHMMSS'),... | |
| obj.export_name); | |
| % new export folder | |
| exportFolder = fullfile(obj.export_path, obj.export_name); | |
| mkdir(exportFolder); | |
| end | |
| % set filenames | |
| obj.export_fileBackground = [exportFolder, filesep,... | |
| obj.export_name,... | |
| '_background.tif']; | |
| obj.export_fileSignal = [exportFolder, filesep,... | |
| obj.export_name,... | |
| '_signal.tif']; | |
| obj.export_fileReference = [exportFolder, filesep,... | |
| obj.export_name,... | |
| '_reference.tif']; | |
| obj.export_fileROI = [exportFolder, filesep,... | |
| obj.export_name,... | |
| '_roi.tif']; | |
| obj.export_fileMetaData = [exportFolder, filesep,... | |
| obj.export_name,... | |
| '_metadata.txt']; | |
| obj.export_fileIntrinsic = [exportFolder, filesep,... | |
| obj.export_name,... | |
| '_intrinsic.png']; | |
| % export meta data | |
| obj.export_writerMetaData = fopen(obj.export_fileMetaData, 'w'); | |
| % log current settings | |
| fprintf(obj.export_writerMetaData, '# experiment\t%s\n', obj.export_name); | |
| fprintf(obj.export_writerMetaData, '# stimuli_period\t%.2f\n', obj.period); | |
| fprintf(obj.export_writerMetaData, '# analysis_window\t%.2f, %.2f\n', obj.window); | |
| fprintf(obj.export_writerMetaData, '# analysis_offset\t%.2f, %.2f\n', obj.offset); | |
| fprintf(obj.export_writerMetaData, '# fps\t%.4f\n', obj.fps); | |
| fprintf(obj.export_writerMetaData, '# frames_per_trial\t%d\n', obj.buffer_size); | |
| fprintf(obj.export_writerMetaData, '# background averages\t%s_background.tif\n', obj.export_name); | |
| fprintf(obj.export_writerMetaData, '# signal averages\t%s_signal.tif\n', obj.export_name); | |
| fprintf(obj.export_writerMetaData, '# reference frame\t%s_reference.tif\n', obj.export_name); | |
| fprintf(obj.export_writerMetaData, '# ROI\t%s_roi.tif\n', obj.export_name); | |
| fprintf(obj.export_writerMetaData, '# intrinsic result\t%s_intrinsic.tif\n', obj.export_name); | |
| % set video writer if specified | |
| if obj.export_flag == 1 | |
| % log video export file | |
| fprintf(obj.export_writerMetaData, '# video stream\t%s_videostream.mj2\n', obj.export_name); | |
| % open video writer object | |
| obj.export_fileVideo = [exportFolder, filesep,... | |
| obj.export_name,... | |
| '_videostream.avi']; | |
| obj.export_writerVideo = VideoWriter(obj.export_fileVideo, 'Grayscale AVI'); | |
| set(obj.export_writerVideo, 'FrameRate', ceil(obj.fps)); | |
| open(obj.export_writerVideo); | |
| end | |
| end | |
| function obj = terminateExport(obj) | |
| %TERMINATEEXPORT close all files | |
| % save reference frame | |
| imwrite(obj.frame, obj.export_fileReference); | |
| % save reference mask | |
| imwrite(uint8(255.*obj.vw_roi), obj.export_fileROI); | |
| % scale frame | |
| frameRaw = double(obj.frame); | |
| frameMax = max(frameRaw(:)); | |
| frameMin = min(frameRaw(:)); | |
| frameScaled = (frameRaw - frameMin) ./ (frameMax - frameMin); | |
| % adjust mask | |
| obj.adjustMask(); | |
| mask = obj.vw_mask > 0; | |
| alpha = (frameScaled + obj.ALPHA_VALUE .* obj.vw_mask) ./ 2; | |
| % convert output frame to 8bit | |
| frameOut = uint8(255 .* frameScaled); | |
| resultFrame = repmat(frameOut, 1, 1, 3); | |
| % apply alpha mask | |
| for c = 1 : 3 | |
| tmp = resultFrame(:,:,c); | |
| tmp(mask) = obj.PATCH_COLOR(c) .* alpha(mask); | |
| resultFrame(:,:,c) = tmp; | |
| end | |
| imwrite(resultFrame, obj.export_fileIntrinsic); | |
| % close metadata file | |
| fclose(obj.export_writerMetaData); | |
| % check if video writer was active | |
| if (obj.export_flag == 1) | |
| % wait for export thread to finish | |
| while strcmp(obj.thread_export, 'on') | |
| pause(0.1); | |
| end | |
| % close video writer | |
| close(obj.export_writerVideo); | |
| end | |
| end | |
| function obj = initializeBuffers(obj) | |
| %INITIALIZEBUFFERS set buffers and stream properties | |
| % define indexes | |
| obj.buffer_size = ceil(obj.period * obj.fps); | |
| obj.index_trial = 0; | |
| obj.index_baselineFirst = floor((obj.period - obj.window(1) - obj.offset(1)) * obj.fps); | |
| obj.index_baselineLast = floor((obj.period - obj.offset(1)) * obj.fps); | |
| obj.index_signalFirst = ceil(obj.offset(2) * obj.fps); | |
| obj.index_signalLast = ceil((obj.offset(2) + obj.window(2)) * obj.fps); | |
| end | |
| function obj = initializeStream(obj) | |
| % set video stream | |
| obj.stream = videoinput(obj.adaptor, obj.DEVICE_ID); | |
| % set camera properties | |
| set(obj.stream,... | |
| 'ReturnedColorSpace', 'grayscale',... | |
| 'LoggingMode', 'memory',... | |
| 'FramesAcquiredFcn', @obj.fcnCamera_acquire,... | |
| 'FramesAcquiredFcnCount', obj.buffer_size,... | |
| 'FramesPerTrigger', obj.buffer_size,... | |
| 'StartFcn', @obj.fcnCamera_start,... | |
| 'StopFcn', @obj.fcnCamera_stop,... | |
| 'TriggerRepeat', Inf); | |
| triggerconfig(obj.stream, 'immediate'); | |
| end | |
| function obj = adjustMask(obj) | |
| % adjust mask | |
| obj.vw_mask(obj.vw_mask < obj.threshold) = 0; | |
| obj.vw_mask(~obj.vw_roi) = 0; | |
| set(obj.vw_patch, 'AlphaData', obj.vw_mask .* obj.ALPHA_VALUE); | |
| end | |
| end | |
| %% --- camera callbacks --- %% | |
| methods | |
| function obj = fcnCamera_start(obj, ~, ~) | |
| %FCNCAMERA_START starts camera acquisition | |
| eventLog = get(obj.stream, 'EventLog'); | |
| fprintf('Start rec :: %s\n', ... | |
| datestr(eventLog(1).Data.AbsTime,... | |
| 'dd-mmm-yyyy HH:MM:SS.FFF')); | |
| end | |
| function obj = fcnCamera_acquire(obj, hSrc, ~) | |
| %FCNCAMERA_ACQUIRE | |
| % trigger external stimuli | |
| notify(obj, 'event_trigger'); | |
| % update trial index | |
| obj.index_trial = obj.index_trial + 1; | |
| % read all available frames from buffer | |
| framesCount = get(hSrc, 'FramesAvailable'); | |
| [frames, obj.buffer_stamps] = getdata(hSrc, framesCount); | |
| obj.buffer_frames = squeeze(frames); | |
| % start analysis thread | |
| start(obj.thread_analysis); | |
| end | |
| function obj = fcnCamera_stop(obj, ~, ~) | |
| %FCNCAMERA_STOP starts camera acquisition | |
| eventLog = get(obj.stream, 'EventLog'); | |
| fprintf('Stop rec :: %s\n', ... | |
| datestr(eventLog(end).Data.AbsTime,... | |
| 'dd-mmm-yyyy HH:MM:SS.FFF')); | |
| end | |
| end | |
| %% --- Threads Callbacks --- %% | |
| methods | |
| function obj = fcnThread_analysis(obj, ~, ~) | |
| %FCNTHREAD_evalAVERAGE calculate average difference | |
| % calculate average frames | |
| obj.buffer_baseline = mean(obj.buffer_frames(:,:,obj.index_baselineFirst : obj.index_baselineLast), 3); | |
| obj.buffer_signal = mean(obj.buffer_frames(:, :, obj.index_signalFirst : obj.index_signalLast), 3); | |
| % apply binning | |
| if obj.binning > 1 | |
| obj.buffer_baseline = imbinning(obj.buffer_baseline, obj.binning, obj.binning); | |
| obj.buffer_signal = imbinning(obj.buffer_signal, obj.binning, obj.binning); | |
| end | |
| % calculate weights | |
| weightHistory = (obj.index_trial - 1)/obj.index_trial; | |
| weightCurrent = 1 / obj.index_trial; | |
| % update current difference | |
| diffMask = double(obj.buffer_signal) ./ double(obj.buffer_baseline); | |
| diffMask = imfilter(diffMask, obj.filter, 'replicate'); | |
| diffMask = max(diffMask(:)) - diffMask; % invert mask | |
| % accumulate mask difference | |
| if obj.index_trial == 1 | |
| obj.buffer_mask = diffMask; | |
| else | |
| obj.buffer_mask = weightHistory .* obj.buffer_mask + ... | |
| weightCurrent .* diffMask; | |
| end | |
| % start visualising thread | |
| start(obj.thread_present); | |
| % start export thread | |
| start(obj.thread_export); | |
| end | |
| function obj = fcnThread_export(obj, ~, ~) | |
| %FCNTHREAD_EXPORT records video stream | |
| % retrieve event Log | |
| eventLog = get(obj.stream, 'EventLog'); | |
| % user message | |
| fprintf('Trial %03d :: %s\n', ... | |
| obj.index_trial,... | |
| datestr(eventLog(obj.index_trial + 1).Data.AbsTime,... | |
| 'dd-mmm-yyyy HH:MM:SS.FFF')); | |
| % write to meta data | |
| fprintf(obj.export_writerMetaData, ... | |
| '# trial%03d\t%s\n', ... | |
| obj.index_trial,... | |
| datestr(eventLog(obj.index_trial + 1).Data.AbsTime,... | |
| 'dd-mmm-yyyy HH:MM:SS.FFF')); | |
| % rescale image for export | |
| if obj.bitdepth == 1 | |
| exportBackground = uint8(floor(obj.buffer_baseline)); | |
| exportSignal = uint8(floor(obj.buffer_signal)); | |
| else | |
| exportBackground = uint16(floor(obj.buffer_baseline)); | |
| exportSignal = uint16(floor(obj.buffer_signal)); | |
| end | |
| % check trial | |
| if obj.index_trial == 1 | |
| % write current trial | |
| imwrite(exportBackground, obj.export_fileBackground); | |
| imwrite(exportSignal, obj.export_fileSignal); | |
| else | |
| % write current trial | |
| imwrite(exportBackground, obj.export_fileBackground, 'WriteMode','append'); | |
| imwrite(exportSignal, obj.export_fileSignal, 'WriteMode','append'); | |
| end | |
| % export video stream | |
| if obj.export_flag == 1 | |
| framesCount = size(obj.buffer_frames, 3); | |
| for k = 1 : framesCount | |
| % 16 bit format | |
| lowerBits = uint8(bitand(obj.buffer_frames(:,:,k), 255)); | |
| higherBits = uint8(bitand(bitshift(obj.buffer_frames(:,:,k),-8), 255)); | |
| writeVideo(obj.export_writerVideo, lowerBits); | |
| writeVideo(obj.export_writerVideo, higherBits); | |
| fprintf(obj.export_writerMetaData, 'trial%d\tframe%d\t%.2f\n',... | |
| obj.index_trial,... | |
| k,... | |
| obj.buffer_stamps(k)); | |
| end | |
| fprintf(obj.export_writerMetaData, 'trial%d\ttrigger\t%.2f\n',... | |
| obj.index_trial,... | |
| obj.buffer_stamps(k)); | |
| end | |
| end | |
| function obj = fcnThread_present(obj, ~, ~) | |
| %FCNTHREAD_PRESENT | |
| % scale difference frame | |
| maskMin = min(obj.buffer_mask(obj.vw_roi)); | |
| maskMax = max(obj.buffer_mask(obj.vw_roi)); | |
| obj.vw_mask = (obj.buffer_mask - maskMin) ./ (maskMax - maskMin); | |
| % update current bar graph | |
| [y, x] = histcounts(obj.vw_mask(obj.vw_roi), obj.BIN_SIZE); | |
| x = x(1:end-1) + diff(x)./2; | |
| set(obj.bg_bars, 'XData', x); | |
| set(obj.bg_bars, 'YData', y); | |
| step = 0.01 * max(x); | |
| set(obj.bg_axes, 'XLim',[min(x) - step, max(x) + step]); | |
| set(obj.bg_plot, 'XData', [obj.threshold, obj.threshold]); | |
| set(obj.bg_plot, 'YData', [0, max(y)]); | |
| % adjust mask presentation | |
| obj.adjustMask(); | |
| end | |
| end | |
| end | |
| function [img] = imbinning(img, hbin, wbin) | |
| %IMBINNING software image binning | |
| [h, w]=size(img); | |
| % horizontal binning | |
| img = sum(reshape(img, hbin, []) , 1); | |
| img = reshape(img , h/hbin, []).'; | |
| % vertical binning | |
| img = sum(reshape(img, wbin, []) ,1); | |
| img = reshape(img, w/wbin, []).'; | |
| % renormalize sum | |
| img = img / (hbin * wbin); | |
| end |