% <FILLSTACK> - Simple function to fill a stack with images
%
%    [ImStack] = fillstack (path, filename, format, images, dim, <colorDepth>)
%    ImStack   : 3D array containing the images
%    path      : String containing the path
%    filename  : String containing the filename without the numbers
%    format    : 'img'  - tvx .img format
%                'tif'  - tif format with extension .tif
%                'tiff' - tif format with extension .tiff
%                'ff'   - tvx flatfield tif format (= float tif)
%                         with extension .tif
%                'edf'  - edf: ESRF data format as .edf 
%    images    : Integer vector of the format images = [start end]
%    dim       : Matrix dimension as vector, e.g. dim = [xdim, ydim]
%    colorDepth: Color depth of the .img file in number of bits
%                (default 32). colorDepth can be
%                -  8
%                - 16 (for PILATUS 1 images)
%                - 32 (for PILATUS 2 images) or
%                - 64


%==========================================================================
% 
% FUNCTION: fillstack.m 
%           ===========
%
% $Date: 2006/12/11 12:39:13 $
% $Author: pauli_s $
% $Revision: 1.6 $
% $Source: /import/cvs/X/PILATUS/App/lib/X_PILATUS_Matlab/fillstack.m,v $
% $Tag: $
%
%
% <FILLSTACK> - Simple function to fill a stack with images
% 
% Author(s):            R. Herger (RH)
% Co-author(s):         C.M. Schlepuetz (CS)
%                       S.A. Pauli (SAP)
% Address:              Swiss Light Source (SLS)
%                       Paul Scherrer Institute
%                       CH - 5232 Villigen PSI
% Created:              2004/09/16
% 
% Change Log:
% -----------
% 
% 2005/11/11 (RH):
% - first version
%
% 2006/02/17 (SAP):
% - added format to input arguments
%
% 2006/10/20 (SAP):
% - added edf to format-input-arguments and corrected the orange-errors.

%==========================================================================
%  Main function - fillstack
%                  =========

function [ImStack] = fillstack(path, filename, format, images, dim, colorDepth)

% start the cpu clock
% clockstart = cputime;


%----------------------
% check input arguments

% are there 5 ... 6 input arguments?
error(nargchk(5, 6, nargin));

% is path of type string?
if(~ischar(path))
  error(strcat('Invalid input for ''path'' in function fillstack.m.\n', ...
               'Use ''help fillstack'' for further information.'), ...
               '');
end


% is filename of type string?
if(~ischar(filename))
  error(strcat('Invalid input for ''filename'' in function fillstack.m.\n', ...
               'Use ''help fillstack'' for further information.'), ...
               '');
end

% is format img, tif, tiff or ff?
if ((strcmpi(format,'img')  | strcmpi(format,'tif') | ...
     strcmpi(format,'tiff') | strcmpi(format,'ff')  | ...
     strcmpi(format,'edf')) ~= 1)
  error(strcat('Invalid input for ''format'' in function imageread.\n', ...
               'Use ''help imageread'' for further information.'), ...
               '');
end 

% is dim a images an integer array of size [1 2]?
if (isnumeric(images))
  if (~isequal(size(images), [1 2]))
    error(strcat('Invalid input for ''images'' in function fillstack.m.\n', ...
                 'Use ''help fillstack'' for further information.'), ...
                 '');
  end;
else
  error(strcat('Invalid input for ''images'' in function fillstack.m.\n', ...
                 'Use ''help fillstack'' for further information.'), ...
                 '');
end;

% is dim a vector of size [1 2]?
if (~isequal(size(dim), [1 2]))
  error(strcat('Invalid input for ''dim'' in function fillstack.\n', ...
               'Use ''help fillstack'' for further information.'), ...
               '');
end

% is colorDepth equal to 8, 16, 32, or 64?
if (nargin < 6)
  colorDepth = 32;
end;
if (colorDepth ~= 8 && colorDepth ~= 16 &&...
    colorDepth ~= 32 && colorDepth ~= 64)
  error(strcat('Invalid input for ''colorDepth'' in function fillstack.m.', ...
               '\nUse ''help imageread'' for further information.'), ...
               '');
end;

% is colorDepth an integer value?
if (~isnumeric(colorDepth))
  error(strcat('Invalid input for ''colorDepth'' in function ', ...
               ' fillstack.m.\n Use ''help fillstack'' for further ', ...
               ' information.'), ...
               '');
end;


%----------------------
% check output argument

% is 1 output argument specified?
error(nargoutchk(1, 1, nargout));


%---------------
% fill the stack

% initialize some variables
q = 1;

zdim = length(images(1,1):images(1,2));
ImStack = zeros(dim(2),dim(1),zdim);

% create the stack
for i=images(1,1):images(1,2)
  no = sprintf ('%05d', i);
  actualImage = strcat (path, filename, no);
  ImStack (:, :, q) = imageread (actualImage, format, dim, colorDepth);
  q = q + 1;
end;


% clear some variables
clear q no actualimage format clockstart clockend time;



%==========================================================================
%
%---------------------------------------------------%
% emacs setup:  force text mode to get no help with %
%               indentation and force use of spaces %
%               when tabbing.                       %
% Local Variables:                                  %
% mode:text                                         %
% indent-tabs-mode:nil                              %
% End:                                              %
%---------------------------------------------------%
%
% $Log: fillstack.m,v $
% Revision 1.6  2006/12/11 12:39:13  pauli_s
% added tag
%
% Revision 1.5  2006/11/21 15:45:58  pauli_s
% added edf, corrected orange errors
%
% Revision 1.4  2006/08/17 14:30:57  pauli_s
% ubcalc.m
%
% Revision 1.3  2006/02/17 13:11:02  pauli_s
% added format to imput arguments
%
% Revision 1.2  2005/11/14 12:36:00  herger
% changed wrong argument in the help text
%
% Revision 1.1  2005/11/11 11:45:48  herger
% matlab function to create a stack of images
%
%
%================================= End of <functionName>.m ================