my_stepCSD.asv

function varargout = my_stepCSD(varargin)
% MY_STEPCSD M-file for my_stepCSD.fig
%      MY_STEPCSD, by itself, creates a new MY_STEPCSD or raises the existing
%      singleton*.
%
%      H = MY_STEPCSD returns the handle to a new MY_STEPCSD or the
%      handle to
%      the existing singleton*.
%
%      MY_STEPCSD('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in MY_STEPCSD.M with the given input arguments.
%
%      MY_STEPCSD('Property','Value',...) creates a new MY_STEPCSD or raises the
%      existing singleton*.  Starting from the left, property value pairs
%      are
%      applied to the GUI before my_stepCSD_OpeningFunction gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to my_stepCSD_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 my_stepCSD

% Last Modified by GUIDE v2.5 18-Dec-2005 20:50:17

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @my_stepCSD_OpeningFcn, ...
                   'gui_OutputFcn',  @my_stepCSD_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 my_stepCSD is made visible.
function my_stepCSD_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 my_stepCSD (see VARARGIN)
handles.pot = varargin{2};
handles.dt = varargin{4};

%image(imread('CSD_plotter.png'))
axis off;

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

% Update handles structure
guidata(hObject, handles);

% UIWAIT makes my_stepCSD wait for user response (see UIRESUME)
% uiwait(handles.delta_CSD);


% --- Outputs from this function are returned to the command line.
function varargout = my_stepCSD_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;



function filter_b0_Callback(hObject, eventdata, handles)
% hObject    handle to filter_b0 (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 filter_b0 as text
%        str2double(get(hObject,'String')) returns contents of filter_b0 as a double


% --- Executes during object creation, after setting all properties.
function filter_b0_CreateFcn(hObject, eventdata, handles)
% hObject    handle to filter_b0 (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 filter_b1_Callback(hObject, eventdata, handles)
% hObject    handle to filter_b1 (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 filter_b1 as text
%        str2double(get(hObject,'String')) returns contents of filter_b1 as a double


% --- Executes during object creation, after setting all properties.
function filter_b1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to filter_b1 (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 ex_cond_Callback(hObject, eventdata, handles)
% hObject    handle to ex_cond (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 ex_cond as text
%        str2double(get(hObject,'String')) returns contents of ex_cond as a double


% --- Executes during object creation, after setting all properties.
function ex_cond_CreateFcn(hObject, eventdata, handles)
% hObject    handle to ex_cond (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 top_cond_Callback(hObject, eventdata, handles)
% hObject    handle to top_cond (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 top_cond as text
%        str2double(get(hObject,'String')) returns contents of top_cond as a double


% --- Executes during object creation, after setting all properties.
function top_cond_CreateFcn(hObject, eventdata, handles)
% hObject    handle to top_cond (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 diam_Callback(hObject, eventdata, handles)
% hObject    handle to diam (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 diam as text
%        str2double(get(hObject,'String')) returns contents of diam as a double


% --- Executes during object creation, after setting all properties.
function diam_CreateFcn(hObject, eventdata, handles)
% hObject    handle to diam (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 run_all.
function run_all_Callback(hObject, eventdata, handles)
% hObject    handle to run_all (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)


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

% filter parameters:
gauss_sigma = str2num(get(handles.gsigma,'String'))*1e-3; % mm -> m
filter_range = 5*gauss_sigma; % numeric filter must be finite in extent
if gauss_sigma<0
    errordlg('The gaussian filter width cannot be negative.')
    return
end;

% electrical parameters:
cond = str2num(get(handles.ex_cond,'String'));
if cond<=0
    errordlg('Ex. cond. has to be a positive number');
    return
end;
cond_top = str2num(get(handles.top_cond,'String'));

% size, potential (m1 has to equal number of electrode contacts)
[m1,m2] = size(handles.pot);

% geometrical parameters:
diam = str2num(get(handles.diam,'String'))*1e-3; %diameter in [m]
if diam<=0
    errordlg('Diameter has to be a positive number.');
    return
end;

el_pos = str2num(get(handles.electrode_pos,'String'))*1e-3;
if cond_top~=cond & (el_pos~=abs(el_pos) | length(el_pos)~=length(nonzeros(el_pos)))
    errordlg('Electrode contact positions must be positive when top cond. is different to ex. cond.')
    return;
end;
if m1~=length(el_pos)
    errordlg(['Number of electrode contacts has to equal number of rows in potential matrix. Currently there are ',...
        num2str(length(el_pos)),' electrodes contacts, while the potential matrix has ',num2str(m1),' rows.']) 
    return
end;

% compute step iCSD:
CSD = F_const(el_pos,diam,cond,cond_top)^-1*handles.pot;

% make CSD continous (200 points):
% npoints = 200; % number of points to plot in the vertical direction
% le = length(el_pos);
% first_z = el_pos(1)-(el_pos(2)-el_pos(1))/2; %plot starts at z1-h/2;
% last_z = el_pos(le)+(el_pos(le)-el_pos(le-1))/2; %ends at zN+h/2;
% zs = first_z:(last_z-first_z)/npoints:last_z;
% el_pos(le+1) = el_pos(le)+(el_pos(le)-el_pos(le-1)); % need an extra pos in for-loop
% j=1; %counter
% for i=1:length(zs) % all new positions
%     if zs(i)>(el_pos(j)+(el_pos(j+1)-el_pos(j))/2) % > el_pos(j) + h/2
%         j = min(j+1,le);
%     end;
%     new_CSD_matrix(i,:)=CSD(j,:);
% end;
le = length(el_pos);    % number of electrode contacts
mfactor = ceil(200/el_pos); % each row is expanded to mfatctor rows
npoints = le*mfactor; % number of points to plot in the vertical direction
h = el_pos(2)-el_pos(1);    % inter-contact distance
first_z = el_pos(1)-h/2;    % plot starts at z1-h/2;
dzs = h/mfactor;            % 
sub_zs = 0:dzs:(mfactor-1)*dzs;
for i=1:size(CSD,1) % all rows
    zs(1:mfactor+mfactor*(i-1)) = first_z+(i-1)*h+sub_zs;
    new_CSD_matrix((1:mfactor)+mfactor*(i-1),:) = repmat(CSD(i,:),mfactor,1);
end;

if gauss_sigma~=0 %filter iCSD
  [zs,new_CSD_matrix]=gaussian_filtering(zs,new_CSD_matrix,gauss_sigma,filter_range);
%  [new_positions,gfiltered_spline_CSD]=gaussian_filtering(zs,CSD_cs,gauss_sigma,filter_range);
end;

% if b1~=0 %filter iCSD
%   [n1,n2]=size(CSD);            
%   CSD_add(1,:) = zeros(1,n2);   %add top and buttom row with zeros
%   CSD_add(n1+2,:)=zeros(1,n2);
%   CSD_add(2:n1+1,:)=CSD;        %CSD_add has n1+2 rows
%   CSD = S_general(n1+2,b0,b1)*CSD_add; % CSD has n1 rows
% end;

% plot CSD
plot_CSD(new_CSD_matrix,zs,handles.dt,1,0) %length(el_pos) must equal rows of CSD! 


function electrode_pos_Callback(hObject, eventdata, handles)
% hObject    handle to electrode_pos (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 electrode_pos as text
%        str2double(get(hObject,'String')) returns contents of electrode_pos as a double


% --- Executes during object creation, after setting all properties.
function electrode_pos_CreateFcn(hObject, eventdata, handles)
% hObject    handle to electrode_pos (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 new_figure_Callback(hObject, eventdata, handles)
% hObject    handle to new_figure (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% filter parameters:
gauss_sigma = str2num(get(handles.gsigma,'String'))*1e-3; % mm -> m
filter_range = 5*gauss_sigma; % numeric filter must be finite in extent

% electrical parameters:
cond = str2num(get(handles.ex_cond,'String'));
cond_top = str2num(get(handles.top_cond,'String'));
% geometrical parameters:
diam = str2num(get(handles.diam,'String'))*1e-3; %diameter in [m]
el_pos = str2num(get(handles.electrode_pos,'String'))*1e-3;

% compute step iCSD:
CSD = F_const(el_pos,diam,cond,cond_top)^-1*handles.pot;

% make CSD continous (200 points):
npoints = 200; % number of points to plot in the vertical direction
le = length(el_pos);
first_z = el_pos(1)-(el_pos(2)-el_pos(1))/2; %plot starts at z1-h/2;
last_z = el_pos(le)+(el_pos(le)-el_pos(le-1))/2; %ends at zN+h/2;
zs = first_z:(last_z-first_z)/npoints:last_z;
el_pos(le+1) = el_pos(le)+(el_pos(le)-el_pos(le-1)); % need an extra pos in for-loop
j=1; %counter
for i=1:length(zs) % all new positions
    if zs(i)>(el_pos(j)+(el_pos(j+1)-el_pos(j))/2) % > el_pos(j) + h/2
        j = min(j+1,le);
    end;
    new_CSD_matrix(i,:)=CSD(j,:);
end;

if gauss_sigma~=0 %filter iCSD
  [zs,new_CSD_matrix]=gaussian_filtering(zs,new_CSD_matrix,gauss_sigma,filter_range);
%  [new_positions,gfiltered_spline_CSD]=gaussian_filtering(zs,CSD_cs,gauss_sigma,filter_range);
end;

% plot CSD
figure()
plot_CSD(new_CSD_matrix,zs,handles.dt,1,0) %length(el_pos) must equal rows of CSD! 


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





function gsigma_Callback(hObject, eventdata, handles)
% hObject    handle to gsigma (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 gsigma as text
%        str2double(get(hObject,'String')) returns contents of gsigma as a double


% --- Executes during object creation, after setting all properties.
function gsigma_CreateFcn(hObject, eventdata, handles)
% hObject    handle to gsigma (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