brainnmf.m

非负矩阵分解的matlab代码

function varargout = brainNMF(varargin)
% brainNMF M-file for nmf2.fig
%      NMF2, by itself, creates a new brainNMF or raises the existing
%      singleton*.
%
%      H = brainNMF returns the handle to a new brainNMF or the handle to
%      the existing singleton*.
%
%      brainNMF('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in brainNMF.M with the given input arguments.
%
%      brainNMF('Property','Value',...) creates a new brainNMF or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before brainNMF_OpeningFunction gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to brainNMF_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help brainNMF

% Last Modified by Bartlomiej Wilkowski ([e-mail]) 06-Nov-2007, ver.
% 1.4

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @brainNMF_OpeningFcn, ...
                   'gui_OutputFcn',  @brainNMF_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT


% --- Executes just before brainNMF is made visible.
function brainNMF_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to brainNMF (see VARARGIN)

% Choose default command line output for brainNMF
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);
addpath('../.');
% UIWAIT makes brainNMF wait for user response (see UIRESUME)
% uiwait(handles.figure1);


% --- Outputs from this function are returned to the command line.
function varargout = brainNMF_OutputFcn(hObject, eventdata, handles) 
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;


% --- Executes on button press in plot_thresshold.
function plot_thresshold_Callback(hObject, eventdata, handles)
% hObject    handle to plot_thresshold (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
if ~isfield(handles, 'img')
    errordlg('Load file first','Error');
    return
end
img = handles.img;
figure(2),
thresshold(1) = str2double(get(handles.lowerThress,'String'));
thresshold(2) = str2double(get(handles.upperThress,'String'));
plotThresshold(img,thresshold)

% --- Executes on button press in plot_spatial.
function plot_spatial_Callback(hObject, eventdata, handles)
% hObject    handle to plot_spatial (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
if ~isfield(handles, 'W')
    errordlg('Run NMF first','Error');
    return
end

W = handles.W;
indx = handles.indx;
%dim = size(handles.img);
plotSlices(W,indx,handles.imgSize)

% --- Executes on button press in rescale.
function rescale_Callback(hObject, eventdata, handles)
% hObject    handle to rescale (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of rescale



function set_sources_Callback(hObject, eventdata, handles)
% hObject    handle to set_sources (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of set_sources as text
%        str2double(get(hObject,'String')) returns contents of set_sources as a double

k = str2double(get(hObject,'String'));

if k<2 || isnan(k)
    errordlg('Not valid number','Error');
    set(handles.set_sources,'String',3);
    return
end

% --- Executes during object creation, after setting all properties.
function set_sources_CreateFcn(hObject, eventdata, handles)
% hObject    handle to set_sources (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function set_iterations_Callback(hObject, eventdata, handles)
% hObject    handle to set_iterations (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of set_iterations as text
%        str2double(get(hObject,'String')) returns contents of set_iterations as a double
iter = str2double(get(hObject,'String'));

if iter<1 || isnan(iter)
    errordlg('Not valid number','Error');
    set(handles.set_iterations,'String',1000);
    return
end

% --- Executes during object creation, after setting all properties.
function set_iterations_CreateFcn(hObject, eventdata, handles)
% hObject    handle to set_iterations (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- Executes on button press in load_data.
function load_data_Callback(hObject, eventdata, handles)
% hObject    handle to load_data (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

%checks if there exist earlier H and W matrices, plotErr and rescaledFlag in <handles> taken from the
%previous NMF calculation. If yes, it removes them.

[fn,pn]=uigetfile('*.img','Analyze file');
if fn~=0
    if isfield(handles, 'W')
        handles = rmfield(handles, 'W');
    end
    if isfield(handles, 'H')
        handles = rmfield(handles, 'H');
    end
    if isfield(handles, 'plotErr')
        handles = rmfield(handles, 'plotErr');
    end
    if isfield(handles, 'rescaledFlag')
        handles = rmfield(handles, 'rescaledFlag');
    end

    set(handles.rescale, 'Value', get(handles.rescale, 'Min'));

    set(handles.plot_samples,'Enable', 'on');
    set(handles.plot_thresshold,'Enable', 'on');
    set(handles.run_nmf,'Enable', 'on');
    set(handles.plot_spatial,'Enable', 'off');
    set(handles.plot_error,'Enable', 'off');
    
    %load([pn fn]);
    [img hdr] = ReadAnalyzeImg([pn fn]);
    img = reshape((img - hdr.offset).*hdr.scale,hdr.dim');
    handles.img = img;
    handles.imgSize = size(img);
    %set(choose_file,[pn fn])
    set(handles.info_text, 'String', 'DATA LOADED for image:');
    set(handles.Choose_file, 'String', [pn fn]);

    %Also read in .tim file to get frames
    [timFileExist]=fileattrib([pn fn(1:end-3) 'tim']);
    if timFileExist
        [time tmp] = textread([pn fn(1:end-3) 'tim']);
        xAxisLabel = 'Time';
    else
        time = 1:hdr.dim(4);
        xAxisLabel = 'Frame';
    end

    imgMean = mean(img,4);
    set(handles.minMean,'String',num2str(min(imgMean(:))));
    set(handles.maxMean,'String',num2str(max(imgMean(:))));
    set(handles.lowerThress,'String',num2str(min(imgMean(:))));
    set(handles.upperThress,'String',num2str(max(imgMean(:))));
    handles.time = time;
    handles.scanName = hdr.name;
    handles.xAxisLabel = xAxisLabel;

    % save the structure
    guidata(hObject, handles);
end

% --- Executes on button press in plot_samples.
function plot_samples_Callback(hObject, eventdata, handles)
% hObject    handle to plot_samples (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if ~isfield(handles, 'img')
    errordlg('Load file first','Error');
    return
end
img = handles.img;
time = handles.time;
xAxisLabel = handles.xAxisLabel;
[x y slice frame] = size(img);
img = reshape(img,x*y*slice,frame);
figure(1),plot(time,img(1:1000:end,:)');
xlabel(xAxisLabel), ylabel('Activity'), title('Sample of time curves')

% --- Executes on button press in run_nmf.
function run_nmf_Callback(hObject, eventdata, handles)
% hObject    handle to run_nmf (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
if ~isfield(handles, 'img')
    errordlg('Load file first','Error');
    return
end