first gui commit

kilosort.m

@@ -0,0 +1,17 @@
+function k = kilosort
+% Call this to open the kilosort gui. 
+
+f = figure('Name', 'Kilosort',...
+        'MenuBar', 'none',...
+        'Toolbar', 'none',...
+        'NumberTitle', 'off',...
+        'Units', 'normalized',...
+        'OuterPosition', [0.1 0.1 0.8 0.8]);
+h = ksGUI(f);
+
+if nargout > 0
+  k = h;
+end
+
+end
+

ksGUI.m

@@ -0,0 +1,243 @@
+
+
+classdef ksGUI < handle
+    % GUI for kilosort
+    %
+    % Purpose is to display some basic data and diagnostics, to make it easy to
+    % run kilosort
+    %
+    % Kilosort by M. Pachitariu
+    % This GUI by N. Steinmetz
+
+    properties
+        figHandle % handle to the figure
+
+        guiHandles % struct of handles to useful parts of the gui
+
+        ops % struct for kilosort to run
+
+        rez % struct of results of running
+
+    end
+
+    methods
+        function obj = ksGUI(parent)
+
+            obj.init();
+
+            obj.build(parent);
+
+        end
+
+        function init(obj)
+
+            % check that required functions are present
+            if ~exist('uiextras.HBox')
+                error('ksGUI:init:uix', 'You must have the "uiextras" toolbox to use this GUI. Choose Environment->Get Add-ons and search for "GUI Layout Toolbox" by David Sampson.\n')
+            end
+
+            % add paths
+            fprintf(1, '%s\n', mfilename);
+            if ~exist('preprocessDataSub')
+                addpath(genpath(fileparts(mfilename)));
+            end
+            if ~exist('readNPY')
+                githubDir = fileparts(fileparts(mfilename)); % taking a guess that they have a directory with all github repos
+                if exist(fullfile(githubDir, 'npy-matlab'))
+                    addpath(genpath(fullfile(githubDir, 'npy-matlab')));
+                end
+            end
+            if ~exist('readNPY')
+                warning('ksGUI:init:npy', 'In order to save data for phy, you must have the npy-matlab repository from https://github.com/kwikteam/npy-matlab in your matlab path\n');
+            end
+
+            % compile if necessary
+            if ~exist('mexWtW2')
+
+                fprintf(1, 'Compiled Kilosort files not found. Attempting to compile now.\n');
+                try
+                    oldDir = pwd;
+                    cd(fullfile(fileparts(mfilename), 'CUDA'));
+                    mexGPUall;
+                    fprintf(1, 'Success!\n');
+                    cd(oldDir);
+                catch ex
+                    fprintf(1, 'Compilation failed. Check installation instructions at https://github.com/cortex-lab/Kilosort\n');
+                    rethrow(ex);
+                end
+            end         
+
+            obj.ops = ksGUI.defaultOps();
+
+        end
+
+
+        function build(obj, f)
+            % construct the GUI with appropriate panels
+            obj.figHandle = f;
+
+            obj.guiHandles.root = uiextras.VBox('Parent', f,...
+                'DeleteFcn', @(~,~)obj.cleanup(), 'Visible', 'on', ...
+                'Padding', 5);
+
+            % - Root sections
+
+            obj.guiHandles.titleBar = uicontrol(...
+                'Parent', obj.guiHandles.root,...
+                'Style', 'text', 'HorizontalAlignment', 'left', ...
+                'String', 'Kilosort', 'FontSize', 36,...
+                'FontName', 'Myriad Pro', 'FontWeight', 'bold');
+
+            obj.guiHandles.mainSection = uiextras.HBox(...
+                'Parent', obj.guiHandles.root);
+
+            obj.guiHandles.logPanel = uiextras.Panel(...
+                'Parent', obj.guiHandles.root, ...
+                'Title', 'Message Log', 'FontSize', 18,...
+                'FontName', 'Myriad Pro');
+
+            obj.guiHandles.root.Sizes = [-1 -8 -2];
+
+            % -- Main section
+            obj.guiHandles.settingsPanel = uiextras.Panel(...
+                'Parent', obj.guiHandles.mainSection, ...
+                'Title', 'Settings', 'FontSize', 18,...
+                'FontName', 'Myriad Pro');
+
+            obj.guiHandles.probePanel = uiextras.Panel(...
+                'Parent', obj.guiHandles.mainSection, ...
+                'Title', 'Probe view', 'FontSize', 18,...
+                'FontName', 'Myriad Pro');
+
+            obj.guiHandles.dataPanel = uiextras.Panel(...
+                'Parent', obj.guiHandles.mainSection, ...
+                'Title', 'Data view', 'FontSize', 18,...
+                'FontName', 'Myriad Pro');
+
+            obj.guiHandles.mainSection.Sizes = [-1 -1 -2];
+
+            % --- Settings panel
+
+            obj.guiHandles.settingsVBox = uiextras.VBox(...
+                'Parent', obj.guiHandles.settingsPanel);
+
+            obj.guiHandles.settingsGrid = uiextras.Grid(...
+                'Parent', obj.guiHandles.settingsVBox);
+
+            % choose file
+            obj.guiHandles.settings.ChooseFileTxt = uicontrol(...
+                'Parent', obj.guiHandles.settingsGrid,...
+                'Style', 'pushbutton', 'HorizontalAlignment', 'left', ...
+                'String', 'Select data file');
+            obj.guiHandles.settings.ChooseFileEdt = uicontrol(...
+                'Parent', obj.guiHandles.settingsGrid,...
+                'Style', 'edit', 'HorizontalAlignment', 'left', ...
+                'String', '...');
+
+            % choose temporary directory
+
+            % choose output path
+
+            % set nChannels
+
+            % set Fs
+
+            % choose probe
+
+            % choose max number of clusters
+
+            set( obj.guiHandles.settingsGrid, ...
+                'ColumnSizes', [-1 -1], 'RowSizes', -1 );%-1*ones(1,7)
+
+
+            % button for advanced options
+
+            % button for run
+
+            % button for write script
+
+            % button for save defaults
+
+            % -- Message log
+            obj.guiHandles.logBox = uicontrol(...
+                'Parent', obj.guiHandles.logPanel,...
+                'Style', 'listbox', 'Enable', 'inactive', 'String', {}, ...
+                'Tag', 'Logging Display', 'FontSize', 14);
+
+            obj.log('Initialization success.');
+
+        end
+
+        function run(obj)
+
+            % check that everything is set up correctly to run
+
+            % do preprocessing
+            obj.ops.gui = obj; % for kilosort to access, e.g. calling "log"
+            try
+                obj.rez = preprocessDataSub(obj.ops);
+            catch ex
+                log(sprintf('Error preprocessing! %s', ex.message));
+            end
+
+            % update gui with results of preprocessing
+            obj.updateDataView();
+
+            % fit templates
+            try
+                obj.rez = learnAndSolve8(obj.rez);
+            catch ex
+                log(sprintf('Error running kilosort! %s', ex.message));
+            end
+
+            % save results
+            try
+                rezToPhy(obj.rez, obj.ops.saveDir);
+            catch ex
+                log(sprintf('Error saving data for phy! %s', ex.message));
+            end
+
+        end
+
+        function writeScript(obj)
+            % write a .m file script that the user can use later to run 
+            % directly, i.e. skipping the gui
+
+        end
+
+        function cleanup(obj)
+            fclose('all');
+        end
+
+        function log(obj, message)
+            % show a message to the user in the log box
+            timestamp = datestr(now, 'dd-mm-yyyy HH:MM:SS');
+            str = sprintf('[%s] %s', timestamp, message);
+            current = get(obj.guiHandles.logBox, 'String');
+            set(obj.guiHandles.logBox, 'String', [current; str], ...
+                'Value', numel(current) + 1);
+        end
+    end
+
+    methods(Static)
+        function ops = defaultOps()
+            % look for a default ops file and load it
+            if exist('defaultOps.mat')
+                load('defaultOps.mat', 'ops');
+            else
+                ops = [];
+            end
+        end
+
+        function docString = opDoc(opName)
+            switch opName
+                case 'NchanTOT'; docString = 'Total number of rows in the data file';
+                case 'Th'; docString = 'Threshold on projections (like in Kilosort1)';
+            end
+        end
+
+    end
+
+end
+
+