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Added code for viewing supervoxel clustering.
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@kristinbranson
kristinbranson committed Jun 1, 2017
1 parent 6ca321e commit ed9bfda
Showing 1 changed file with 114 additions and 4 deletions.
118 changes: 114 additions & 4 deletions ExploreBehaviorAnatomyCorrelations.m
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Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,11 @@ function ExploreBehaviorAnatomyCorrelations_OpeningFcn(hObject, eventdata, handl

function handles = InitializeParameters(handles,varargin)

[handles.isanatomydir,leftovers] = myparse_nocheck(varargin,'isanatomydir',[]);

if ischar(handles.isanatomydir),
handles.isanatomydir = str2double(handles.isanatomydir);
end
handles.dologcmap = true;
handles.minpvalue_log = .0001;
handles.maxpvalue = .051;
Expand Down Expand Up @@ -101,7 +106,7 @@ function ExploreBehaviorAnatomyCorrelations_OpeningFcn(hObject, eventdata, handl
global EBAC_DATA;

EBAC_DATA = BehaviorAnatomyCorrData('SetStatusFcn',@(varargin) SetStatusCallback(handles.figure1,varargin{:}),...
'ClearStatusFcn',@(varargin) ClearStatusCallback(handles.figure1,varargin{:}),varargin{:});
'ClearStatusFcn',@(varargin) ClearStatusCallback(handles.figure1,varargin{:}),leftovers{:});

if isunix,
handles.rcfile = getenv('HOME');
Expand Down Expand Up @@ -210,7 +215,10 @@ function ExploreBehaviorAnatomyCorrelations_OpeningFcn(hObject, eventdata, handl
return;
end

if ~exist(EBAC_DATA.anatomydir,'dir'),
if ~isempty(handles.isanatomydir) && (handles.isanatomydir == 0),
EBAC_DATA.anatomydir = '';
fprintf('No access to per-line anatomy image directory.\n');
elseif ~exist(EBAC_DATA.anatomydir,'dir'),
res = questdlg('Do you have access to the per-line anatomy image directory?');
if strcmpi(res,'yes'),
fprintf('Select per-line anatomy image directory. Example: AverageAnatomyData20141028...\n');
Expand Down Expand Up @@ -419,6 +427,8 @@ function SetLogicControlVisibility(handles)

SetLogicControlVisibility(handles);
set(handles.text_map_expr_corr,'Visible','off');
set(handles.text_showsupervoxelclustering,'Visible','off');
set(handles.pushbutton_stop_showsupervoxelclustering,'Visible','off');

handles = ClearState(handles,{'cluster','supervoxel'});

Expand Down Expand Up @@ -1089,6 +1099,8 @@ function ClearStatusCallback(hObj,varargin)
[maxproj,idx] = max(EBAC_DATA.bamap.exprcorrmap,[],3);
case 'cluster',
[maxproj,idx] = max(EBAC_DATA.bamap.clustermap,[],3);
case 'supervoxel',
error('This should never happen!');
end

idx2 = sub2ind([handles.ysz*handles.xsz,handles.zsz],1:handles.ysz*handles.xsz,idx(:)');
Expand All @@ -1109,6 +1121,8 @@ function ClearStatusCallback(hObj,varargin)
set(handles.him_map,'CData',EBAC_DATA.bamap.exprcorrmap(:,:,handles.zslice));
case 'cluster'
set(handles.him_map,'CData',EBAC_DATA.bamap.clustermap(:,:,handles.zslice));
case 'supervoxels',
set(handles.him_map,'CData',EBAC_DATA.labeldata.imcolor(:,:,handles.zslice));
end

supervoxelid = EBAC_DATA.labeldata.labels(:,:,handles.zslice);
Expand Down Expand Up @@ -1138,6 +1152,8 @@ function ClearStatusCallback(hObj,varargin)
case 'cluster',
[maxsliceproj,handles.slice_z0s,handles.slice_z1s,idx] = SlicedMaxProjection(EBAC_DATA.bamap.clustermap,...
handles.nslices,'fun','max','dir',3);
case 'supervoxels',
error('This should never happen!');
%[maxproj,idx] = max(EBAC_DATA.bamap.clustermap,[],3);
end

Expand Down Expand Up @@ -1176,6 +1192,8 @@ function ClearStatusCallback(hObj,varargin)
[maxproj,idx] = max(EBAC_DATA.bamap.exprcorrmap,[],1);
case 'cluster',
[maxproj,idx] = max(EBAC_DATA.bamap.clustermap,[],1);
case 'supervoxels',
error('This should never happen!');
end

idx2 = sub2ind([handles.ysz,handles.xsz*handles.zsz],idx(:)',1:handles.xsz*handles.zsz);
Expand All @@ -1196,6 +1214,8 @@ function ClearStatusCallback(hObj,varargin)
set(handles.him_map,'CData',permute(EBAC_DATA.bamap.exprcorrmap(handles.yslice,:,:),[3,2,1]));
case 'cluster',
set(handles.him_map,'CData',permute(EBAC_DATA.bamap.clustermap(handles.yslice,:,:),[3,2,1]));
case 'supervoxels',
set(handles.him_map,'CData',permute(EBAC_DATA.labeldata.imcolor(handles.yslice,:,:),[3,2,1]));
end
supervoxelid = permute(EBAC_DATA.labeldata.labels(handles.yslice,:,:),[3,2,1]);
compartmentid = permute(single(EBAC_DATA.labeldata.maskdata.mask(handles.yslice,:,:)),[3,2,1]);
Expand Down Expand Up @@ -1223,6 +1243,8 @@ function ClearStatusCallback(hObj,varargin)
[maxsliceproj,handles.slice_y0s,handles.slice_y1s,idx] = SlicedMaxProjection(EBAC_DATA.bamap.clustermap,...
handles.nslices,'fun','max','dir',1);
%[maxproj,idx] = max(EBAC_DATA.bamap.clustermap,[],3);
case 'supervoxels',
error('This should never happen!');
end

handles.slicez = repmat((1:handles.zsz)',[handles.nslices,1]);
Expand Down Expand Up @@ -1264,6 +1286,15 @@ function ClearStatusCallback(hObj,varargin)
set(handles.pushbutton_stop_map_expr_corr,'Visible','off');
end

if strcmp(handles.datatype,'supervoxels'),
set(handles.text_showsupervoxelclustering,'Visible','on');
set(handles.pushbutton_stop_showsupervoxelclustering,'Visible','on');
else
set(handles.text_showsupervoxelclustering,'Visible','off');
set(handles.pushbutton_stop_showsupervoxelclustering,'Visible','off');
end


function handles = UpdateView(handles)

set(handles.menu_view_modes,'Checked','off');
Expand Down Expand Up @@ -1574,7 +1605,14 @@ function ClearStatusCallback(hObj,varargin)
set(handles.hmaskboundary,'Color','w');
set(handles.hsvboundary,'Color','w');

end
case 'supervoxels'
ncolors = max(EBAC_DATA.labeldata.coloring);
clim = [0,ncolors];
cm = jet(ncolors);
cm = [0,0,0;cm(randperm(ncolors),:)];
set(handles.hmaskboundary,'Color','w');
set(handles.hsvboundary,'Color','w');
end
set(handles.axes_main,'CLim',clim);
colormap(handles.axes_main,cm);

Expand Down Expand Up @@ -2505,7 +2543,9 @@ function figure1_ResizeFcn(hObject, eventdata, handles)
end

fns = {'uipanel_behavior','uipanel_supervoxel','uipanel_cluster',...
'text_map_expr_corr','pushbutton_stop_map_expr_corr'};
'text_map_expr_corr','pushbutton_stop_map_expr_corr',...
'text_showsupervoxelclustering','pushbutton_stop_showsupervoxelclustering',...
};

for i = 1:numel(fns),
fn = fns{i};
Expand Down Expand Up @@ -3379,3 +3419,73 @@ function edit_behavior_logicalexpr_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end


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

% set view mode to slice
if ismember(handles.viewmode,{'zslice','yslice'}),
% nothing to be done
else

res = questdlg('Need to switch to slice view mode to show supervoxels. Ok?');
if ~strcmpi(res,'Yes'),
return;
end
if any(handles.viewmode == 'z'),
% switch to zslice
handles.viewmode = 'zslice';
else
% switch to yslice
handles.viewmode = 'yslice';
end
handles = UpdateView(handles);
end

global EBAC_DATA;

if ~isfield(EBAC_DATA.labeldata,'imcolor'),

% compute correlation in expression between this supervoxel and all others
SetStatus(handles,'Computing colored version of supervoxel mapping...');

EBAC_DATA.labeldata.imcolor = zeros([size(EBAC_DATA.labeldata.labels),3],'uint8');
EBAC_DATA.labeldata.imcolor(EBAC_DATA.labeldata.labels>0) = EBAC_DATA.labeldata.coloring(EBAC_DATA.labeldata.labels(EBAC_DATA.labeldata.labels>0));

end

handles.datatype = 'supervoxels';

set(handles.text_showsupervoxelclustering,'Visible','on');
set(handles.pushbutton_stop_showsupervoxelclustering,'Visible','on');

set([handles.menu_view_maxzprojection,handles.menu_view_maxzsliceprojection,...
handles.menu_view_maxyprojection,handles.menu_view_maxysliceprojection],...
'Enable','off');

handles = UpdateMap(handles);
handles = UpdateMaskBoundary(handles);
handles = UpdateMapScaling(handles);
ClearStatus(handles);
guidata(hObject,handles);


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

set(handles.text_showsupervoxelclustering,'Visible','off');
set(handles.pushbutton_stop_showsupervoxelclustering,'Visible','off');
set(handles.menu_view_modes,'Enable','on');

handles.datatype = 'pvalue';
handles = UpdateMap(handles);
handles = UpdateMaskBoundary(handles);
handles = UpdateMapScaling(handles);
guidata(hObject,handles);

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