%  With no arguments ViewRes opens the interactive window for viewing 
% the fMRI results saved earlier, or prodeced in batch jobs.
%
%
% [out_image,tab_image,BigOutImage] = ViewRes(setup_name,pair_list,t_cutoff,cluster_number,...
% slice_listVR,stat_nr,option)
%
% defaults : ViewRes(setup_name,[12 34 56],1.5,5,[1 2 3],2,'o',parameter1,parameter2,parameter3)
%
% to introduce different positive and negative cutoff enter cutoff = [cut_pos; cut_neg]
% to introduce different cutoffs for each pair enter cutoff [t1 t2 t3] (for 3 pairs)
% to introduce different cutoffs for each pair and slice enter
% cutoff = [t11 t12 t13; t21 t22 t23] - for 3 pairs and 2 slices
%
% option is a string of characters :
% if it contains :
%	n - no image is drawn (only variable out_image is returned
%	m - activation map is median filtered
%	l - no labels (x or y) are made
%	t - in plane talairach transformation is applied
%		this options performs Talairach transformation in plane ONLY
%		use ViewResTal to apply it in all 3 Dimensions
%	A - prints outline of the brain with green color for axial study
%	- changes the sign of t_tab1
%	C - prints outline of the brain with green color for coronal study
%	a - prints outline of the brain with green color for autism study
%	b - only with one of: a,A,C options instead of outline it blacks out everything outisde
%	B - same as b but blacks out only activation maps - not anatomical image
% 	digit N=(0:9) t_tab1 is replaced by t_tabN
%	+ and digit, t_tab1 is replaced by t_tab(N+10)
%	M - use "median_image" (that is in fact mean of the whole data_base) 
%		as anatomical image
%	y - surpress printing the Talairach grid on Talairach images
%	Y - surpress printing the Talairach grid on Talairach images, but leaves main AC-PC lines
%	H - create histogram image for the data distribution
%	p - slice by slice - sets variable thresholds to display t_cut percents of pixels positively activated
%	P -overall -  sets variable thresholds to display t_cut percents of pixels positively activated
% 	x - enhance gray scale contrast
% 	c - displays the mass center for ROIs (parameter1 must be ROI data filename (string including the directory path
%		but NOT including the pair_name)
% 	L - log (p2log) transform - to be used with probabilistcal SPMs
%	f - using fourier data	
% 	r - preserve the image ratio (the shape of the brain will not be squished or stretched)
% 	z - shows green whenever the statistical map equals zero
% 	! - organizes all images in one column
% 	_ - organizes all images in one raw
%	k - using mask defined by global variables
%	$ - will make color bars in corners of the image 
% 	R - create grean outline for talairach defined ROI as defined in global variable ROIfile_name
% 		in global variables : ROIfile_name ROInumber_list
%   global MaskStatNr MaskCutPos MaskCutNeg MaskCluster 
% 		MaskPairName MaskWorkSlice MaskSetupName
%
% 	global variable do_after load, if defined, will be executed right after
% 	loading data file, this can be used to further manipulate
%	data to be displayed 

function [out_image,tab_image,BigOutImage] = ViewRes(setup_name1,pair_list,t_cutoff1,cluster_number1, ...
slice_listVR,stat_nr1,option,parameter1,parameter2,parameter3)
out_image=[];
tab_image=[];
BigOutImage=[];
% globals
global c_gray1 c_gray2 OutImage TabImage SetupNameVR 
global save_directory image_directory save_directory_tab
global  t_cutoff cluster_number  tiff_name TiffImage col_map MatlabVersion
global col_map bw_col_map tif_col_map hot_color_map cool_color_map add_color_map
if isempty(col_map), colmap_setup; end
if nargout == 0,  out_image = [];end
if nargin == 0
	disp('WARNING : program changed to adapt to MATLAB5')
	disp('use ViewResOne to view data with interactive window wit fancy buttons');
end
% fmri_initialization
if isempty(MatlabVersion), MatlabVersion = version; end
BigOutImage = [];
if nargin <8, parameter1 = []; end;
if nargin <9, parameter2 = []; end;
if nargin <10, parameter3 = []; end;
if nargin <7, option = []; end;
if nargin <6, stat_nr1 = -1; end;
if nargin <5, slice_listVR = [1 2 3] ; end;
if nargin <4, cluster_number1 = 5, end;
if nargin <3, t_cutoff1 = 1.5, end;
if nargin <2, pair_list = [], end;

if size(setup_name1,1) >1
	[out_image,tab_image] = ViewResSetups1(setup_name1,pair_list,t_cutoff1,cluster_number1, ...
		slice_listVR,stat_nr1,option,parameter1,parameter2,parameter3);
else
if  ~isempty(findstr('P',option))
	option = option(find(option~='P'));
	percent_cutoff = t_cutoff1;
	disp(['(ViewRes)option  P  = ' num2str(percent_cutoff )])
	[out_image,tab_image] = ViewRes(setup_name1,pair_list,0,0, ...
		slice_listVR,stat_nr1,[option 'n'],parameter1,parameter2,parameter3);
	tmp = tab_image(find(tab_image));
	if ~isempty(tmp)
		tmp = tmp(find(tmp~=11));
		t_cutoff1= my_prctile(tmp,100-percent_cutoff );
	end
	disp(['(ViewRes)option  P tcutoff1 = ' num2str(t_cutoff1)])
[out_image,tab_image,BigOutImage] = ViewRes(setup_name1,pair_list,t_cutoff1,cluster_number1, ...
slice_listVR,stat_nr1,option,parameter1,parameter2,parameter3);
if nargout == 0,  out_image = [];end
return
end
setup_name = setup_name1(find(setup_name1~=' '));
if look_for_data(setup_name) == 0
	disp(['WARNING (ViewRes) cannot find the data for : ' setup_name]);
end
SetupNameVR = setup_name;
% t_cutoff = t_cutoff1;
cluster_number = cluster_number1;
stat_nr = stat_nr1;
if size(pair_list,1) ==1
	if isstr(pair_list)
		ViewSize = 1;
	else
		ViewSize = size(pair_list,2);
	end
else
	ViewSize = max(1,size(pair_list,1));
end
SliceNumber = size(slice_listVR,2);
stat_list = stat_nr;
if SliceNumber ==1 & length(stat_nr)>1
	SliceNumber =  length(stat_nr);
end
name1 = [setup_name ' T-cutoff = ' num2str(t_cutoff1(1)) ' stat_nr = ' ...
	num2str(stat_nr) ' cluster_number = ' num2str(cluster_number)];
if strcmp(size(t_cutoff),[2 1])
	cut_p = t_cutoff(1);
	cut_n = t_cutoff(2);
end
if SliceNumber>1 & ViewSize>1
	my_sub1 = SliceNumber;
	my_sub2 = ViewSize;
elseif isempty(findstr('!',option)) & isempty(findstr('_',option))
	my_sub2 = min(ceil(sqrt(SliceNumber*ViewSize)),SliceNumber*ViewSize);
	my_sub1 = ceil(SliceNumber * ViewSize/my_sub2);
elseif ~isempty(findstr('_',option)) 
	my_sub2 = SliceNumber*ViewSize;
	my_sub1 = 1;
elseif ~isempty(findstr('!',option)) 
	my_sub1 = SliceNumber*ViewSize;
	my_sub2 = 1;
end
if MatlabVersion(1) ~='4'
	out_image = 11*ones(SliceNumber,ViewSize,2,2);
	TabImage = 11*zeros(SliceNumber,ViewSize,2,2);
end
if isempty(findstr('n',option))
figEPI = figure('Position',[10 20 min(1200,300*my_sub2), ...
	min(900,300*my_sub1)],'NumberTitle','off','Name',name1);
end
for pair_nr = 1:ViewSize
pair_name = [];
if isstr(pair_list)
	pair_name = pair_list(pair_nr,:);
	pair_name = pair_name(pair_name~=' ');
elseif  ~isempty(pair_list)
	pair_name = num2str(pair_list(pair_nr),20);
end
	for is = 1:SliceNumber
		if (size(t_cutoff1,1)==SliceNumber) & (size(t_cutoff1,2)==ViewSize)
			cut_p = t_cutoff1(is,pair_nr);
			cut_n = -t_cutoff1(is,pair_nr);
		elseif (size(t_cutoff1,1)==1) & (size(t_cutoff1,2)==ViewSize)
			cut_p = t_cutoff1(pair_nr);
			cut_n = -t_cutoff1(pair_nr);
		elseif (size(t_cutoff1,1)==1) & (size(t_cutoff1,2)==1)
			cut_p = t_cutoff1;
			cut_n = -t_cutoff1;
		elseif (size(t_cutoff1,1)==2) & (size(t_cutoff1,2)==1)
			cut_p = t_cutoff1(1);
			cut_n = t_cutoff1(2);
		else
			error('(ViewRes) wrong dimension of t_cutoff')
		end
		if length(slice_listVR) > 1
			work_slice = slice_listVR(is);
		else
			work_slice = slice_listVR;
			if ~isempty(stat_list)
				stat_nr = stat_list(is);
			else
				stat_nr = [];
			end
		end
		if work_slice ~= 0
		if isempty(findstr('n',option))
		if SliceNumber>1 & ViewSize>1 & isempty(findstr('!',option)) 
			my_subplot(my_sub1,my_sub2,is,pair_nr);
		else
			my_subplot(my_sub1,my_sub2,is*pair_nr);
		end
		end
		if stat_nr1 == 21 & ~isempty(FreqList) &  isempty(findstr('n',option))
			if size(FreqList,2) == ViewSize
				freq = FreqList(pair_nr)
				phase_up = PhaseUpList(pair_nr);
				phase_down = PhaseDownList(pair_nr);
			elseif size(FreqList,2) == SliceNumber
				freq = FreqList(is);
				phase_up = PhaseUpList(is);
				phase_down = PhaseDownList(is);
			else
				error(['wrong size of FreqList ' ...
					num2str(size(FreqList))]);
			end			
		end
		if stat_nr1 == 21 &	~isempty(parameter1) &  isempty(findstr('n',option))
			disp(['freq=' num2str(parameter1) ...
				' phase_down=' num2str(parameter2) ...
				' phase_up=' num2str(parameter3)]);
			[out_image1,out_image2] = ViewResTool(setup_name,work_slice,stat_nr, ...
			pair_name,cut_p,cut_n,cluster_number,option, ...
			parameter1,parameter2,parameter3);
		else
			if ((is == 1) & (pair_nr == 1)) | ((is == my_sub1) & (pair_nr == my_sub2))
				[out_image1,out_image2] = ViewResTool(setup_name,work_slice,stat_nr, ...
				pair_name,cut_p,cut_n,cluster_number,option,parameter1,parameter2,parameter3);
			else
				[out_image1,out_image2] = ViewResTool(setup_name,work_slice,stat_nr, ...
				pair_name,cut_p,cut_n,cluster_number,[option 's'],parameter1,parameter2,parameter3);
			end
		end
		TiffImage = out_image1;
		if MatlabVersion(1) ~='4'
		if size(out_image1,1)>size(out_image,3) |  size(out_image1,2)>size(out_image,4)
			tmp = 11*ones(SliceNumber,ViewSize,max(size(out_image1,1),size(out_image,3)), ...
				max(size(out_image1,2),size(out_image,4)));
			tmp2 = 11*ones(SliceNumber,ViewSize,max(size(out_image2,1),size(out_image,3)), ...
				max(size(out_image2,2),size(out_image,4)));
			for i=1:SliceNumber
			for j=1:ViewSize
				tmp(i,j,1:size(out_image,3),1:size(out_image,4)) = ...
					out_image(i,j,1:size(out_image,3),1:size(out_image,4));
				tmp2(i,j,1:size(out_image1,3),1:size(out_image1,4)) = ...
					TabImage(i,j,1:size(out_image1,3),1:size(out_image1,4));
			end
			end
			tmp(is,pair_nr,1:size(out_image1,1),1:size(out_image1,2)) = ...
					out_image1;
			tmp2(is,pair_nr,1:size(out_image2,1),1:size(out_image2,2)) = ...
					out_image2;
			out_image = tmp;
			TabImage = tmp2;
		elseif ~isempty(out_image1)
			if size(out_image,3) == size(out_image1,1) & size(out_image,4) == size(out_image1,2) 
				out_image(is,pair_nr,:,:) = out_image1;
			end
			if ~isempty(out_image2)
				TabImage(is,pair_nr,:,:) = out_image2;
			end
		end
		else % if MatlabVersion(1) ~='4'
			out_image = out_image1;
			TabImage = out_image2;
		end % if MatlabVersion(1) ~='4'

		end	
	end
		end
if isempty(findstr('n',option))
c_gray1 = uicontrol('Style','Slider','Position',[5 11 300 8],...
'Min',1,'Max',200,'Value',10, 'Callback','set_gray_scale');

c_gray2 = uicontrol('Style','Slider','Position',[5 1 300 8],...
'Min',1,'Max',200,'Value',190, 'Callback','set_gray_scale');
set_gray_scale;
% c_spyglass = uicontrol('Style','Pushbutton','Position',[325 22 200 15],...
%	'String','make Spyglass directory', 'Callback',' SaveSpyGlassFolder');
c_ps = uicontrol('Style','Pushbutton','String','PostScript save',...
	'Position',[325 1 100 8],'Callback','ViewResPsSave');
tiff_name = [image_directory setup_name '.tiff'];
c_tiff = uicontrol('Style','Pushbutton','String','TIFF save',...
	'Position',[325 11 100 8],'Callback','TiffSave');
end
end
OutImage = out_image;
tab_image = TabImage;

if MatlabVersion(1) =='4'
tmp = 11*ones(SliceNumber*(1+size(out_image,4))-1,ViewSize*(1+size(out_image,3))-1);
tmp2 = 11*ones(SliceNumber*(1+size(out_image,4))-1,ViewSize*(1+size(out_image,3))-1);
for i=1:SliceNumber
for j=1:ViewSize
		tmp((i-1)*(1+size(out_image,4))+(1:size(out_image,4)),(j-1)*(1+size(out_image,3))+(1:size(out_image,3))) = ...
				squeeze(out_image(i,j,1:size(out_image,3),1:size(out_image,4)))';
		tmp2((i-1)*(1+size(out_image,4))+(1:size(out_image,4)),(j-1)*(1+size(out_image,3))+(1:size(out_image,3))) = ...
				squeeze(TabImage(i,j,1:size(out_image,3),1:size(out_image,4)))';
end
end

TabImage = tmp2;
OutImage = out_image;
TiffImage = out_image;
end % if MatlabVersion(1) ~='4'
TiffImage = out_image;


if nargout < 2,  tab_image = [];end

if ~isempty(findstr('T',option))
	plist = num2str(pair_list); plist = plist(find(plist~=' '));
	tiff_name = [image_directory setup_name1 plist 'BIG.tiff'];
	size_list = size(out_image);
	if length(size_list)==3, size_list = [1 size_list]; end
	if length(size(out_image))==3, out_image = reshape(out_image,1,size(out_image,1),size(out_image,2),size(out_image,3)); end
	big_image = 11*ones(5*(size_list(1)-1)+size_list(1)*size_list(3),5*(size_list(2)-1)+size_list(2)*size_list(4));
	for i=1:size_list(1)
	for j=1:size_list(2)
		big_image((i-1)*(5+size_list(3))+1:i*(5+size_list(3))-5,(j-1)*(5+size_list(4))+1:j*(5+size_list(4))-5) = ...
			squeeze(out_image(i,j,:,:)); 	
	end % for j=1:size_list(2)
	end % for i=1:size_list(1)

	if ~isempty(findstr('$',option))
		[bi_sizeY,bi_sizeX] = size(big_image);
		big_image_colorbar = 11*ones(bi_sizeY,floor(bi_sizeX/50));
		cb_skip = floor(bi_sizeY/25);
		for i=1:10
			big_image_colorbar(bi_sizeY-i*cb_skip:bi_sizeY-(i-1)*cb_skip,:) = ...
				(11-i)+0*big_image_colorbar(bi_sizeY-i*cb_skip:bi_sizeY-(i-1)*cb_skip,:);
		end
		for i=1:10
			big_image_colorbar(1+(i-1)*cb_skip:i*cb_skip,:) = ...
				221-i+0*big_image_colorbar(1+(i-1)*cb_skip:i*cb_skip,:);
		end
		big_image = [big_image big_image_colorbar];
	end
	big_image = min(big_image,224);
	if ~isempty(findstr('w',option)) 
		tiff_out = TiffSave(big_image',bw_col_map,tiff_name,'n');              
	else
		tiff_out = TiffSave(big_image',col_map,tiff_name,'n');
	end
end
if nargout == 0,  out_image = [];end

BigOutImage = zeros(size(OutImage,3)*size(OutImage,2),size(OutImage,1)*size(OutImage,4));
for i=1:size(OutImage,1)
for j=1:size(OutImage,2)
	counter1 = (i-1)*size(OutImage,4);
	counter2 = (j-1)*size(OutImage,3);
	BigOutImage(counter2+1:counter2+size(OutImage,3),counter1+1:counter1+size(OutImage,4)) = squeeze(OutImage(i,j,:,:));
end
end