Im2P_CreateFilesForFicTrac.m

%Im2P_CreateFilesForFicTrac checks if the las mask is correct, and if not - asks the
%user to create a new mask. Create a new folder for FicTrac input/output
%file for this date

%Nore: is CheckMask=0, the last modified *MASK* file in FicTracPath will be
%used, so do CheckMask=0 only if you are SURE that this mask is good.
%Any doubt? Do CheckMask = 1


%%To fix:
%It adds line to the config line each time a new one is created...
%Normalize VFOV?

function Im2P_CreateFilesForFicTrac(CheckMask)

%Parameters
FicTracPath = 'E:\FicTracWin64';
vfov = 2;%need to calibrate with ball radius!


%CheckMask must be 0 or 1
if ~(CheckMask == 0 || CheckMask == 1)
   disp('CheckMask must be 0 or 1. Returning')
   return
end


%FicTrac main folder path
CurrDir = cd(FicTracPath);
%Upload the last mask and snap files

%MASK
MASKfiles = dir('*mask*.png');
DateModified = zeros(1,size(MASKfiles,1));
for nMaskFile = 1:size(MASKfiles,1)
   DateModified(nMaskFile) = datenum(MASKfiles(nMaskFile).date);
end
MaskFile = fullfile(pwd,MASKfiles(DateModified == max(DateModified)).name);
MASK_filename = MaskFile;%use the last mask modified in FicTracPath (default, if not changed later)
MASK = imread(MaskFile);
if size(MASK,3) == 3%if the image file is a true RGB image file, convert
   MASK = rgb2gray(MASK);
end

if CheckMask
   %SNAP
   SNAPfiles = dir('*snap*');
   DateModified = zeros(1,size(SNAPfiles,1));
   for nSnapFile = 1:size(SNAPfiles,1)
      DateModified(nSnapFile) = datenum(SNAPfiles(nSnapFile).date);
   end
   
   SnapFile = fullfile(pwd,SNAPfiles(DateModified == max(DateModified)).name);
   SNAP = rgb2gray(imread(SnapFile));
   
   %show snap with transparent mask overlaid
   figure(1); clf
   colormap(gray)
   C = imfuse(SNAP,MASK,'blend');
   imshow(C)
   
   %Updated mask by user if needed
   prompt = 'Mask OK? Y/N [Y]: ';
   while 1
      IsOK = input(prompt,'s');
      if isempty(IsOK)
         IsOK = 'Y';
      end
      if strcmpi(IsOK,'N') || strcmpi(IsOK,'Y'), break, end
      disp('Wrong input value, Y/N only')
   end
else
   IsOK = 'Y';
end

%create new mask
if strcmpi(IsOK,'N')
   MaskOK = 0;
   imageSizeX = size(SNAP,2);
   imageSizeY = size(SNAP,1);
   [columnsInImage, rowsInImage] = meshgrid(1:imageSizeX, 1:imageSizeY);
   while 1
      %user defines ball circle
      disp('Define ball borders')
      fig = figure(1); clf(fig)
      imshow(SNAP)
      [x, y] = getpts(fig);
      [xc,yc,R,~] = circfit(x,y);
      config_shpere_centre_px = ['sphere_centre_px    ',num2str(round(xc,2)),' ',num2str(round(yc,2))];
      config_sphere_radius_px = ['sphere_radius_px    ',num2str(round(R,2))];
      disp(config_shpere_centre_px)
      disp(config_sphere_radius_px)
      BallPixels = (rowsInImage - yc).^2 ...
         + (columnsInImage - xc).^2 <= R.^2;
      BallMASK = BallPixels;% circlePixels is white - mask on
      
      %user defines glare circle
      disp('Define glare borders')
      fig = figure(1); clf(fig)
      imshow(SNAP)
      [x, y] = getpts(fig);
      [xc,yc,R,~] = circfit(x,y);
      
      glarePixels = (rowsInImage - yc).^2 ...
         + (columnsInImage - xc).^2 <= R.^2; % circlePixels is a 2D "logical" array.
      GlareMASK = 1 - glarePixels;%so that the glare is black - mask off
      
      %user defines ball holder
      while 1
         disp('Define holder rectangle (4 points)')
         fig = figure(1); clf(fig)
         imshow(SNAP)
         [x, y] = getpts(fig);
         if length(x) == 4
            break
         else
            disp('4 points please..')
         end
      end
      %fix x,y such that:
      %(1) straight line under the ball (in any image orientation)
      %(2) black all the way to the bottom (just in case the bottom was marked wrongly)
      if all(x>xc)%air stream axis: left
         [~,idx] = sort(x);
         x(idx(1:2)) = min(x(idx(1:2)));
         x(idx(3:4)) = size(SNAP,2);
      elseif all(x<xc)%air stream axis: right
         [~,idx] = sort(x);
         x(idx(3:4)) = max(x(idx(3:4)));
         x(idx(1:2)) = 1;
      elseif all(y<yc)%air stream axis: up
         [~,idx] = sort(y);
         y(idx(1:2)) = min(y(idx(1:2)));
         y(idx(3:4)) = size(SNAP,1);
         
      elseif all(y>yc)%air stream axis: down
         [~,idx] = sort(y);
         y(idx(3:4)) = max(y(idx(3:4)));
         y(idx(1:2)) = 1;
      else%don't change coordinates, but possibly something's wrong
         disp('ball orientation unclear, cant fix ball holder coordinates.')
      end
      
      BallHolder = poly2mask(x, y, size(SNAP,1), size(SNAP,2));
      BallHolderMASK = 1 - BallHolder; %so that the ball holder is black - mask off
      
      %make mask
      MASK = BallMASK & GlareMASK & BallHolderMASK;
      
      fig = figure(1); clf(fig)
      C = imfuse(SNAP,MASK,'blend');
      imshow(C)
      
      prompt = 'Mask OK? Y/N [Y]: ';
      while 1
         IsOK = input(prompt,'s');
         if isempty(IsOK)
            IsOK = 'Y';
         end
         if strcmpi(IsOK,'N') || strcmpi(IsOK,'Y'), break, end
         disp('Wrong input value, Y/N only')
      end
      
      if strcmpi(IsOK,'y'), MaskOK = 1; end
      
      if MaskOK == 1
         MASK_filename = fullfile(pwd,'online_MASK.png');%will be updated and used for FicTrac online tracking
         imwrite(MASK,MASK_filename)
         break
      end
   end
end



%create a folder for the current date and session
prompt = 'Session number? ';
while 1
   SessionNumber = input(prompt,'s');%I do it this way to prevent error for non numeric input
   SessionNumber = str2double(SessionNumber);
   if ~isnan(SessionNumber), break, end
   disp('Input must be a number')
end

DATE = char(datetime('now','Format','yyMMdd'));
Folder = [DATE,'_',num2str(SessionNumber)];

if isdir(Folder)
   prompt = ['Folder ',Folder,' already exist,override? Y/N [Y]: '];
   while 1
      IsContinue = input(prompt,'s');
      if isempty(IsContinue)
         IsContinue = 'Y';
      end
      if strcmpi(IsContinue,'N') || strcmpi(IsContinue,'Y'), break, end
      disp('Wrong input value - Y/N only')
   end
   
   if strcmpi(IsContinue,'N'), return, end
else
   mkdir(Folder)
end

%At this point the mask is updated and a folder was created for the session
config_filename = fullfile(pwd,'configOnline.txt');%will be updated and used for FicTrac online tracking
copyof_config_filename = fullfile(pwd,Folder,['configOnline_',DATE,'_',num2str(SessionNumber),'.txt']);%will be saved in the session folder

%MASK_filename is defined earlier as MASK_filename = fullfile(pwd,'online_MASK.png');%will be updated and used for FicTrac online tracking
copyof_MASK_filename = fullfile(pwd,Folder,['MASK_',DATE,'_',num2str(SessionNumber),'.png']);%will be saved in the session folder

calibration_filename = fullfile(pwd,'calibration-transform.dat');%will be updated and used for FicTrac online tracking
copyof_calibration_filename = fullfile(pwd,Folder,'calibration-transform.dat');%will be saved in the session folder

%modify config file
output_fn = ['.\output_',DATE,'_',num2str(SessionNumber)];
mask_fn = ['.\MASK_',DATE,'_',num2str(SessionNumber),'.png'];
transform_fn = '.\calibration-transform.dat';

%previous file: read
fid = fopen(config_filename);
%new file: right
new_fid = fopen(copyof_config_filename,'wt');

while 1
   tline = fgets(fid);
   if ~isempty(strfind(tline,'output_fn'))
      newline = ['output_fn           ',output_fn];
      fprintf(new_fid, '%s\n',newline);
   elseif ~isempty(strfind(tline,'mask_fn'))
      newline = ['mask_fn             ',mask_fn];
      fprintf(new_fid, '%s\n',newline);
   elseif ~isempty(strfind(tline,'transform_fn'))
      newline = ['transform_fn        ',transform_fn];
      fprintf(new_fid, '%s\n',newline);
   elseif (~isempty(strfind(tline,'vfov')) && exist('config_shpere_centre_px','var'))%MASK updated
      newline = ['vfov                ',num2str(vfov)];
      fprintf(new_fid, '%s\n',newline);
      newline = config_shpere_centre_px;
      fprintf(new_fid, '%s\n',newline);
      newline = config_sphere_radius_px;
      fprintf(new_fid, '%s\n',newline);
   elseif ~isempty(strfind(tline,'do_socket_out'))
      newline = 'do_socket_out      0';
      fprintf(new_fid, '%s\n',newline);
      break
   else
      fprintf(new_fid, '%s',tline);
   end
end

fclose(fid);
fclose(new_fid);

%copy files
copyfile(MASK_filename,copyof_MASK_filename)
copyfile(calibration_filename,copyof_calibration_filename)


cd(CurrDir)

end