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captainjtx committed Jun 23, 2017
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47 changes: 42 additions & 5 deletions README.md
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# CNELAB
Multi-channel reviewing Matlab GUI
Million thanks to BioSigPlot
#CNELab

Our official website (under constructing)
www.cnelab.org
Getting started with CNELab

Getting started with CNELab is fairly easy. It only took a few minutes to complete this tutorial step by step.

Preparations

We recommend using the latest Matlab release version, currently R2016a. However, most features of CNELab should be backward compatible up to R2014a. Starting R2014b, Matlab updated on its graphic system. CNELab experienced a major performance drop (especially in plotting speed) in R2014b and R2015a. Thus, it is not recommended to use R2014b, R2015a or any version before R2014a.

CNELab depends on several basic toolboxes of Matlab. Most of time they already come with your license.

Signal Processing Toolbox.

Statistics and Machine Learning Toolbox.
Wavelet Toolbox.
You can type ver in Matlab command window to verify.

Install CNELab

If do not have CNELab yet, please refer to our download page. Once you download the zip file, unzip it and put it anywhere you prefer.

Change your current Matlab path to the root folder of CNELab, where you can see files such as cnelab.m and setup.m.

Run setup.m by typing it in command window (ignore the prompt sign >>):

>> setup
If you receive no error message, congratulations !

More on setup.m

Although setup automatically removes existed CNELab from Matlab Path, it is always a good practice to manually delete the CNELab folder.

setup will check if your java JVM version used in Matlab lands in 1 . 7 . * . Most of time you should not worry about it as Matlab shipped its version with specific JVM after R2013b. Type version -java to verify yourself.

setup tries to recompile c++ mexfunctions in CNELab to your system environment. However, our release already contains compiled mexfunctions that can be immediately used in 64-bit of MacOS/Windows computer. Only if it is a unix or 32-bit system should you be careful. If you received a mex compile error, you would have to check your c++ compiler on maltab and manually compile them. Type mex -setup c++ to verify yourself.

Start with demo

The best way to learn CNELab is to use it:

>> cnelab
Open $CNELAB_ROOT/demo/demo.cds to explore yourself.
Binary file modified db/cfg/defaultconfig.cfg
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21 changes: 21 additions & 0 deletions lib/FDR/FDR.m
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function [pID,pN] = FDR(p,q)
% FORMAT pt = FDR(p,q)
%
% p - vector of p-values
% q - False Discovery Rate level
%
% pID - p-value threshold based on independence or positive dependence
% pN - Nonparametric p-value threshold
%______________________________________________________________________________
% @(#)FDR.m 1.3 Tom Nichols 02/01/18

p = sort(p(:));
V = length(p);
I = (1:V)';

cVID = 1;
cVN = sum(1./(1:V));

pID = p(max(find(p<=I/V*q/cVID)));
pN = p(max(find(p<=I/V*q/cVN)));

98 changes: 80 additions & 18 deletions src/class/AverageMapWindow.m
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Expand Up @@ -74,7 +74,7 @@
peak_
contact_
unit
interp_method
interp_scatter_
extrap_method

pos_t
Expand All @@ -92,6 +92,9 @@

export_picture_win
cmax
style_menu
map_interp_menu
map_scatter_menu
end

properties (Dependent=true)
Expand Down Expand Up @@ -121,7 +124,7 @@
neg
map_val


interp_scatter
end

methods
Expand Down Expand Up @@ -149,7 +152,7 @@ function varinitial(obj)
obj.width=300;
obj.height=300;
obj.unit='dB';
obj.interp_method='natural';
obj.interp_scatter='interp';
obj.extrap_method='linear';
obj.interp_missing_=0;
obj.symmetric_scale_=1;
Expand Down Expand Up @@ -195,6 +198,9 @@ function buildfig(obj)

obj.save_map_menu=uimenu(obj.save_menu,'label','Map','callback',@(src,evts) ExportMapCallback(obj));

obj.style_menu=uimenu(obj.fig,'label','Style');
obj.map_interp_menu=uimenu(obj.style_menu,'label','Interpolate','callback',@(src,evt) MapCallback(obj,src));
obj.map_scatter_menu=uimenu(obj.style_menu,'label','Scatter','callback',@(src,evt) MapCallback(obj,src));
columnName={'Selected','FileName'};
columnFormat={'logical','char'};
columnEditable=[true,false];
Expand Down Expand Up @@ -309,7 +315,7 @@ function buildfig(obj)
'units','normalized','position',[0.5,0.25,0.45,0.25],'value',obj.peak,...
'callback',@(src,evts) PeakCallback(obj,src));

obj.contact_radio=uicontrol('parent',hp_display,'style','radiobutton','string','Contact',...
obj.contact_radio=uicontrol('parent',hp_display,'style','radiobutton','string','Channel Name',...
'units','normalized','position',[0.5,0,0.45,0.25],'value',obj.contact,...
'callback',@(src,evts) ContactCallback(obj,src));

Expand All @@ -325,6 +331,7 @@ function buildfig(obj)

obj.pos=obj.pos_;
obj.neg=obj.neg_;
obj.interp_scatter=obj.interp_scatter_;
end

function OnClose(obj)
Expand Down Expand Up @@ -388,6 +395,9 @@ function loadMap(obj)

end
len=length(obj.MapFiles);
if ischar(FileName)
FileName={FileName};
end
for i=1:length(FileName)
obj.MapFiles_{len+i}=fullfile(FilePath,FileName{i});
end
Expand Down Expand Up @@ -442,6 +452,7 @@ function ComputeCallback(obj)
mv=obj.map_val;
%**************************************************************
vmax=-inf;
chanpos=obj.all_chan_pos(obj.chan_ind,:);
for i=1:size(mv,2)
%*********************
if obj.interp_missing
Expand All @@ -450,13 +461,25 @@ function ComputeCallback(obj)
val=mv(:,i);
end
%*********************
spatialmap_grid(obj.SpatialMapFig(i),val,obj.interp_method,...
obj.extrap_method,map_channames,map_pos(:,1),map_pos(:,2),map_pos(:,3),obj.width,obj.height,...
spatialmap_grid(obj.SpatialMapFig(i),val,obj.interp_scatter,...
map_pos(:,1),map_pos(:,2),obj.width,obj.height,...
obj.min_clim,obj.max_clim,obj.color_bar,obj.resize);
h=findobj(obj.SpatialMapFig(i),'-regexp','tag','SpatialMapAxes');
if obj.contact
plot_contact(h,allchanpos(:,1),allchanpos(:,2),allchanpos(:,3),obj.height,obj.width,[],...
~ismember(allchanpos,map_pos,'rows'),[],[]);

if obj.contact||strcmp(obj.interp_scatter,'scatter')
if obj.contact
cn=map_channames;
else
cn=[];
end

if strcmp(obj.interp_scatter,'scatter')
plot_contact(h,mapv,allchanpos(:,1),allchanpos(:,2),allchanpos(:,3),obj.height,obj.width,cn,...
~ismember(allchanpos,chanpos,'rows'),[],[]);
else
plot_contact(h,[],allchanpos(:,1),allchanpos(:,2),allchanpos(:,3),obj.height,obj.width,cn,...
~ismember(allchanpos,chanpos,'rows'),[],[]);
end
end

if obj.peak
Expand Down Expand Up @@ -776,7 +799,7 @@ function deleteMap(obj)
obj.height=round(obj.height/oldval*val);

chanpos=obj.all_chan_pos(obj.chan_ind,:);

allchanpos=obj.all_chan_pos;
if ~NoSpatialMapFig(obj)
for i=1:length(obj.SpatialMapFig)
if ishandle(obj.SpatialMapFig(i))
Expand All @@ -786,9 +809,20 @@ function deleteMap(obj)
if ~isempty(h)
delete(findobj(h,'Tag','contact'));
figure(obj.SpatialMapFig(i))
if obj.contact
plot_contact(h,obj.all_chan_pos(:,1),obj.all_chan_pos(:,2),obj.all_chan_pos(:,3),obj.height,obj.width,[],...
~ismember(obj.all_chan_pos,chanpos,'rows'));
if obj.contact||strcmp(obj.interp_scatter,'scatter')
if obj.contact
cn=obj.channames;
else
cn=[];
end

if strcmp(obj.interp_scatter,'scatter')
plot_contact(h,obj.map_val,allchanpos(:,1),allchanpos(:,2),allchanpos(:,3),obj.height,obj.width,cn,...
~ismember(allchanpos,chanpos,'rows'),[],[]);
else
plot_contact(h,[],allchanpos(:,1),allchanpos(:,2),allchanpos(:,3),obj.height,obj.width,cn,...
~ismember(allchanpos,chanpos,'rows'),[],[]);
end
end
end
end
Expand Down Expand Up @@ -829,7 +863,24 @@ function deleteMap(obj)
set(obj.pos_slider,'enable','off');
end
end
function val=get.interp_scatter(obj)
val=obj.interp_scatter_;
end

function set.interp_scatter(obj,val)
obj.interp_scatter_=val;

if obj.valid
switch val
case 'interp'
set(obj.map_interp_menu,'checked','on');
set(obj.map_scatter_menu,'checked','off');
case 'scatter'
set(obj.map_scatter_menu,'checked','on');
set(obj.map_interp_menu,'checked','off');
end
end
end
function val=get.neg(obj)
val=obj.neg_;
end
Expand Down Expand Up @@ -971,11 +1022,11 @@ function ContactCallback(obj,src)
for i=1:length(obj.SpatialMapFig)
h=findobj(obj.SpatialMapFig(i),'-regexp','Tag','SpatialMapAxes');
if ~isempty(h)
delete(findobj(h,'Tag','contact'));
figure(obj.SpatialMapFig(i))
delete(findobj(h,'Tag','names'));
if obj.contact
plot_contact(h,obj.all_chan_pos(:,1),obj.all_chan_pos(:,2),obj.all_chan_pos(:,3),obj.height,obj.width,[],...
~ismember(obj.all_chan_pos,chanpos,'rows'),[],[]);
plot_contact(h,[],obj.all_chan_pos(:,1),obj.all_chan_pos(:,2),obj.all_chan_pos(:,3),obj.height,obj.width,obj.channames,...
~ismember(obj.all_chan_pos,chanpos,'rows'));
end

end
Expand Down Expand Up @@ -1099,10 +1150,10 @@ function UpdateFigure(obj,src)
%*********************
h=findobj(obj.SpatialMapFig(i),'-regexp','Tag','SpatialMapAxes');
if ~isempty(h)
if strcmpi(obj.interp_method,'natural')
if strcmpi(obj.interp_scatter,'natural')
[x,y]=meshgrid((1:obj.width)/obj.width,(1:obj.height)/obj.height);

F= scatteredInterpolant(map_pos(:,1),map_pos(:,2),val,obj.interp_method,obj.extrap_method);
F= scatteredInterpolant(map_pos(:,1),map_pos(:,2),val,obj.interp_scatter,obj.extrap_method);
mapvq=F(x,y);
% mapvq = gaussInterpolant(col,row,mapv{i}',x,y);
else
Expand Down Expand Up @@ -1182,6 +1233,17 @@ function ExportMapCallback(obj)
fclose(fid);
end
end
function MapCallback(obj,src)
switch src
case obj.map_interp_menu
obj.interp_scatter='interp';
case obj.map_scatter_menu
obj.interp_scatter='scatter';
end

UpdateFigure(obj,src);

end
end

end
2 changes: 1 addition & 1 deletion src/methods/plot_contact.m
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Expand Up @@ -178,7 +178,7 @@ function plot_contact(axe,mapv,col,row,r,h,w,channames,varargin)
offset=rotation_m*offset;
for i=1:length(all_channames)
if badchan(i)
c=[0.5,0.5,0.5];
c=[1,1,1];
else
c=[0,0,0];
end
Expand Down

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