function cloudmask = readModisCloudMask(maskFilename, byteList, area)

% function cloudmask = readModisCloudMask(maskFilename, byteList)
%
% DESCRIPTION:
% Read cloud mask product information from a MODIS MOD35 HDF file
%
% REQUIRED INPUT:
%    maskFilename (string) 	Name of MODIS MOD35 HDF file
%
% ------------------------------------------------------------------------
%
% OPTIONAL INPUT: 
%    byteList 	Byte numbers of data to return.  If this argument is 
%               specified, all bits of the selected byte are 
%               returned.  If this argument is not specified, ONLY
%               bits 1 & 2 of byte 1 (cloud mask probability of clear,
%               with QA) is returned.
%
%               byteList can be either an array of byte #s
%               (1 through 6) or the string 'all' to return all
%               bytes.  Note that to get the 250m cloud mask, only 
%               byte 5 or 6 (not both) needs to be requested.  
%            
%               See list below (under "Output") for a description of the 
%               bits in each byte.
%               
%               For each byte requested, QA information is also read in 
%               A separate QA array is not returned, instead this information
%               is incorporated into the cloud mask fields that are returned.
%               The cloud mask values corresponding to QA "not useful" or
%               "not applied" are set to -1.   
%
% ------------------------------------------------------------------------
%
% OUTPUT:
%    cloudmask (struct) with contents determined by the byte 
%    numbers selected in byteList:
%
%    BYTE 1
%      cloudmask.flag (bit 0)
%			0 = Not determined 
%			1 = Determined
%		.mask (bits 1 & 2)
%                      -1 = Not Useful (from QA) 
%			0 = Cloud
%			1 = 66% Probability of clear
%			2 = 95% Probability of clear
%			3 = 99% Probability of clear
%               .confidenceQA (QA byte 1, bits 1,2,3)
%                       0 - 7 confidence level for cloudmask.mask
%		.dayOrNight (bit 3)
%			0 = Night   1 = Day  -1 = Not Useful (from QA)
%		.sunglint (bit 4)
%			0 = Yes     1 = No   -1 = Not Useful (from QA)
%		.snowIce (bit 5)
%			0 = Yes     1 = No   -1 = Not Useful (from QA)
%		.landWater (bits 6 & 7)
%                      -1 = Not Useful (from QA)
%			0 = Water
%			1 = Coastal
%			2 = Desert
%			3 = Land
%
%    BYTE 2 (0 = Yes;  1 = No; -1 = Not Applied, from QA)
%      cloudmask.bit0 (Non-cloud obstruction flag)
%		.bit1 (Thin cirrus detected, solar)
%		.bit2 (Shadow found)
%		.bit3 (Thin cirrus detected, IR)
%		.bit4 (Adjacent cloud detected -- implemented
%		       post-launch to indicate cloud found within
%		       surrounding 1km pixels)
%		.bit5 (Cloud Flag, IR threshold)
%		.bit6 (High cloud flag, CO2 test)
%		.bit7 (High cloud flag, 6.7 micron test)
%
%    BYTE 3 (0 = Yes;  1 = No; -1 = Not Applied, from QA)
%      cloudmask.bit0 (High cloud flag, 1.38 micron test)
%		.bit1 (High cloud flag, 3.7-12 micron test)
%		.bit2 (Cloud flag, IR temperature difference)
%		.bit3 (Cloud flag, 3.7-11 micron test)
%		.bit4 (Cloud flag, visible reflectance test)
%		.bit5 (Cloud flag, visible reflectance ratio test)
%		.bit6 (0.935/0.87 reflectance test)
%		.bit7 (3.7-3.9 micron test)
%
%    BYTE 4 (0 = Yes;  1 = No; -1 = Not Applied, from QA)
%      cloudmask.bit0 (Cloud flag, temporal consistency)
%		.bit1 (Cloud flag, spatial variability)
%		.bit2 (Final confidence confirmation test)
%		.bit3 (Cloud flag, night water spatial variability)
%		.bit4 (Suspended dust flag)
%
%    BYTES 5 & 6 250m Cloud Flag Visible Tests
%                (0 = Yes;  1 = No; -1 = Not Applied, from QA) 
%      cloudmask.visibleTest250m 	250m resolution array 
%
%     
%  24 April: removed this field, it is memory intensive and not
%            too useful so far.  
%      		.sumVisibleTest250m 	1km resolution, sum of all
%                                       16 elements in each 1km grid
%
% ------------------------------------------------------------------------
%
% Time to run this code for:   Byte 1        1 minute
%                              Bytes 1-4     1.5 minutes
%                              Bytes 5 & 6   3.3 minutes
% 
% Note: With 1G of RAM, I run out of memory if I try to read all bytes at
%       once.  Instead, I read bytes 1-4, then 5-6 separately. 
%
% ------------------------------------------------------------------------
%
% Written By:
%    Suzanne Wetzel Seemann   
%    swetzel@ssec.wisc.edu
%    April 2001
%
% update 23 April 2001 -- added QA for bytes 5 & 6
% update 24 April 2001 -- removed .sumVisibleTest250m field because it
%                         is memory intensive and not very useful so far
%
% Code History: Based on a code by Shaima Nasiri (modis_mask_read.m) that 
%               reads Byte 1 of the cloud mask.  
%
% RESTRICTIONS:
%    Only tested on Matlab version 5.3.1 (R11.1) - performance under
%    other versions of Matlab is unknown
%
% ------------------------------------------------------------------------
%
% SAMPLE RUN STATEMENTS:
%  dataPath = '/home/swetzel/data/gomo310/';
%
%  readModisCloudMask([dataPath 'MOD35_L2.A2000310.1750.002.2000332030507.hdf'], ...
%                     [1 4]);                     
%  readModisCloudMask([dataPath 'MOD35_L2.A2000310.1750.002.2000332030507.hdf'], ...
%                     5);                     
%  readModisCloudMask([dataPath 'MOD35_L2.A2000310.1750.002.2000332030507.hdf'], ...
%                     1,'all');                     

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Error check inputs
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
onlyBits1and2 = 0;

 if nargin < 1
    error(['readModisCloudMask requires at least one input: maskFilename']);
 elseif nargin == 1
    byteList = 1;
    onlyBits1and2 = 1;
 elseif nargin > 1
    if ischar(byteList) 
       if strcmp(byteList,'all')
            byteList = [1:6];
       else
            error(['Second input argument, byteList must either ' ...
	           'be an array of integers 1-6 or the string ''all''']);
       end
    else
       if any(byteList > 6) | any(byteList < 1)
            error(['Second input argument, byteList must either ' ...
	           'be an array of integers 1-6 or the string ''all''']);
       end
    end
 end

% Check for valid MOD35 HDF file
 if (~exist(maskFilename,'file'))
    error(['Filename : ' maskFilename ' was not found']);
 end

 len_filename = length(maskFilename);
 if (~strcmp( maskFilename(len_filename-3:len_filename), '.hdf'))
    error(['Filename: ' maskFilename ' is not an HDF file']);
 end

%% Add byte 5 to byteList if byte 6 was given or add
%% byte 6 to byteList if byte 5 was given

  if ismember(5,byteList) & ~ismember(6,byteList)
	  byteList = [byteList 6];
  elseif ~ismember(5,byteList) & ismember(6,byteList)
	  byteList = [byteList 5];
  end

%% Find the largest cloud mask and QA byte number, to minimize
%% the amount of data we need to read in.  

  minBytes = min(byteList);
  maxBytes = max(byteList);
  cloudMaskDataByteList = [minBytes:1:maxBytes];

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Open cloud mask file and read data, dimensions, and attributes
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 SD_id = hdfsd( 'start', maskFilename, 'read' );
 if (SD_id < 0)
    error(['HDF file' maskFilename ' was not opened.']);
 end

% data we want is 'Cloud_Mask'
 mask_ex = hdfsd('nametoindex', SD_id, 'Cloud_Mask');
 mask_id = hdfsd('select',SD_id, mask_ex);
 [name,rank,dimsizes,data_type,nattrs,status(1)] = hdfsd('getinfo',mask_id );

nbytes = dimsizes(1);
npixels_across =  dimsizes(2);
npixels_along = dimsizes(3); 

start = [minBytes-1; 0 ; 0]; 
count = [1 ; 1 ; 1];
edge = [1 ; npixels_across ;  npixels_along];


 if (nargin == 3)
    start(2) = min( [max([area(1) 0]) (npixels_across - 1)] );
    start(3) = min( [max([area(2) 0]) (npixels_along - 1)] );
    edge(2) = min( [max([area(3) 0]) (npixels_across - start(2))] );
    edge(3) = min( [max([area(4) 0]) (npixels_along - start(3))] );
 end
  
%  if maxBytes <= nbytes 
%    edge = [maxBytes-minBytes+1; npixels_along; npixels_across];
%  else 
%    error(['maxBytes cannot be greater than the number of bytes in the file']);
%  end

 [cloudMaskData,status(2)] = hdfsd('readdata',mask_id,start,count,edge);
%[cloudMaskData,status(2)] = hdfsd('readdata',mask_id);

 cloudMaskData  = double(cloudMaskData);
 attr_ex = hdfsd('findattr', mask_id, 'scale_factor');
 [scale, status(3)] = hdfsd('readattr', mask_id,attr_ex) ;
 
 attr_ex = hdfsd('findattr', mask_id, 'long_name');
 [longname, status(4)] = hdfsd('readattr', mask_id,attr_ex) ;

 attr_ex = hdfsd('findattr', mask_id, 'Cell_Along_Swath_Sampling');
 [sampling, status(5)] = hdfsd('readattr', mask_id,attr_ex) ;

 attr_ex = hdfsd('findattr', mask_id, 'add_offset');
 [offset, status(6)] = hdfsd('readattr', mask_id,attr_ex) ;
 if offset ~= 0 | scale ~= 1
    error(['Cloud_Mask offset ~= 0 or slope ~= 1']);
 end 

% stop accessing data 
 status(7) = hdfsd('endaccess',mask_id);

 if any(status == -1)
   error('Trouble reading Cloud_Mask data, dimensions, or attributes');
 end

 clear status

% close HDF file
 status = hdfsd('end', SD_id);
 if (status < 0)
    warning(['HDF file' maskFilename ' was not closed.']);
 end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Read all bits from the selected bytes
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% For each byte, before reading the bits, we must separate
%% the bytes and adjust image array for use in Matlab : 
%% 	convert values to double precision 
%%	rotate and flip the image
%% 	convert from MOD35's signed integers to Matlab's unsigned 
%%         integers where [0:127 -128:-1] is mapped to [0:1:255]

  clear cloudmask 
  cloudmask.filename = maskFilename; 

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  %% Cloud_Mask: BYTE 1
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  if any(byteList == 1) 

     byteInd = find(1 == cloudMaskDataByteList);
%    byte1 = flipud(rot90(squeeze(cloudMaskData(:,:,byteInd)) ));
     byte1 = squeeze(cloudMaskData(:,:,byteInd));
     % find negative integers and remap them
     ind = find(byte1 < 0);
     byte1(ind) = 256 + byte1(ind);
     clear ind

     %% BITS 1,2 - Unobstructed FOV Quality Flag
     %%   0 = Cloud
     %%   1 = 66% Probability of clear
     %%   2 = 95% Probability of clear
     %%   3 = 99% Probability of clear
  
     bit3 = bitget(byte1,3); 
     bit2 = bitget(byte1, 2);
     clear99prob_ind = find(bit3 & bit2);
     clear95prob_ind = find(bit3 & ~bit2);
     clear66prob_ind = find(~bit3 & bit2);
     cloud_ind = find(~bit3 & ~bit2);
  
     cloudmask.byte1.mask = NaN * ones(size(byte1));
     cloudmask.byte1.mask(clear99prob_ind) = 3;
     cloudmask.byte1.mask(clear95prob_ind) = 2;
     cloudmask.byte1.mask(clear66prob_ind) = 1;
     cloudmask.byte1.mask(cloud_ind) = 0;

     clear bit3 bit2 clear99prob_ind clear95prob_ind clear66prob_ind cloud_ind

     if onlyBits1and2 == 0
        %% BIT 0 - CloudMask Flag
        %%   0 = Not determined
        %%   1 = Determined
        cloudmask.byte1.flag = bitget(byte1, 1);

        %% BIT 3 - Day or Night Path
        %%   0 = Night   1 = Day
        cloudmask.byte1.dayOrNight = bitget(byte1,4);

        %% BIT 4 - Sunglint Path
        %%   0 = Yes     1 = No
        cloudmask.byte1.sunglint = bitget(byte1,5);

        %% BIT 5 - Snow/Ice Background Path
        %%   0 = Yes     1 = No
        cloudmask.byte1.snowIce = bitget(byte1,6);
  
        %% BITS 6,7 - Land or Water Path
        %%   0 = Water
        %%   1 = Coastal
        %%   2 = Desert
        %%   3 = Land
        cloudmask.byte1.landWater = NaN * ones(size(byte1));

        bit7 = bitget(byte1,7); bit8 = bitget(byte1,8);
        land_ind  = find(bit8 & bit7);
        desert_ind = find(bit8 & ~bit7);
        coastal_ind = find(~bit8 & bit7);
        water_ind = find(~bit8 & ~bit7);

        cloudmask.byte1.landWater(land_ind) = 3;
        cloudmask.byte1.landWater(desert_ind) = 2;
        cloudmask.byte1.landWater(coastal_ind) = 1;
        cloudmask.byte1.landWater(water_ind) = 0;

        clear bit7 bit8 land_ind desert_ind coastal_ind water_ind
     end
     clear byte1
  end % byte 1

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  %% Cloud_Mask: BYTES 2-4 
  %%   0 = Yes     1 = No
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

  if any(byteList == 2 | byteList == 3 | byteList == 4)
     indBytes234 = find(byteList == 2 | byteList == 3 | byteList == 4);
indBytes234
     for j = 1:length(indBytes234)

        byteInd = find(byteList(indBytes234(j)) == cloudMaskDataByteList);
byteInd
%       byteData = flipud(rot90(squeeze(cloudMaskData(:,:,byteInd)) ));
        byteData = squeeze(cloudMaskData(:,:,byteInd));
	clear byteInd

        % find negative integers and remap them
        ind = find(byteData < 0);
        byteData(ind) = 256 + byteData(ind);
        clear ind

        if byteList(indBytes234(j)) < 4 
           %% 8 bits (0-7) in bytes 2 and 3	
           numBits = 8;
        else
           %% 5 bits (0-4) in byte 4
           numBits = 5;
        end

        % assign data to cloudmask structure: cloudmask.byte#.bit#
        for k = 1:numBits
           eval(['cloudmask.byte' num2str(byteList(indBytes234(j))) ...
	         '.bit' num2str(k-1) ' = bitget(byteData,k);']);
        end
        clear byteData 

      end %% for
  end  %% bytes 2, 3, 4

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  %% Cloud_Mask: BYTES 5 & 6: 250-m Cloud Flag, Visible Tests
  %%   0 = Yes     1 = No
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  if any(byteList == 5) | any(byteList == 6)

  %% BYTE 5

     byteInd = find(5 == cloudMaskDataByteList);
%    byte5 = flipud(rot90(squeeze(cloudMaskData(:,:,byteInd)) ));
     byte5 = squeeze(cloudMaskData(:,:,byteInd));
     clear byteInd

     % find negative integers and remap them
     ind = find(byte5 < 0);
     byte5(ind) = 256 + byte5(ind);
     clear ind

     %% create an array of all NaNs 4x the size of one element 
     %% repmat is faster than ones*NaN
     elementSize = size(bitget(byte5,1));
     cloudmask.visibleTest250m = repmat(0,elementSize*4);

     xStartInds = [1 1 1 1 2 2 2 2];
     yStartInds = [1 2 3 4 1 2 3 4];

     %% insert each element into the array of NaNs.
     for j = 1:8
        %allbits(j,:,:) = bitget(byte5,j);
        cloudmask.visibleTest250m([xStartInds(j):4:elementSize(1)*4], ...
                     [yStartInds(j):4:elementSize(2)*4]) = bitget(byte5,j); 
     end

     clear byte5

  %% BYTE 6

     byteInd = find(6 == cloudMaskDataByteList);
%    byte6 = flipud(rot90(squeeze(cloudMaskData(:,:,byteInd)) ));
     byte6 = squeeze(cloudMaskData(:,:,byteInd));
     clear byteInd

     % find negative integers and remap them
     ind = find(byte6 < 0);
     byte6(ind) = 256 + byte6(ind);
     clear ind

     byte6bits = [9:16];
     xStartInds = [3 3 3 3 4 4 4 4];
     yStartInds = [1 2 3 4 1 2 3 4];

     %% insert each element into the array of NaNs.
     for j = 1:8 
        %allbits(byte6bits(j),:,:) = bitget(byte6,j);
        cloudmask.visibleTest250m([xStartInds(j):4:elementSize(1)*4], ...
               [yStartInds(j):4:elementSize(2)*4]) = bitget(byte6,j); 

     end
     clear byte6

     %cloudmask.sumVisibleTest250m = squeeze(sum(allbits,1)); 

  end  %% byte 5,6

  clear cloudMaskData

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% QA: Open cloud mask file and read QA data, dimensions, and attributes
%
% NOTE: It is repetitive to do QA separately after all of the 'Cloud_Mask'
%        data, however it would take too much memory to keep 
%        'Quality_Assurance' and 'Cloud_Mask' (qaData and cloudMaskData) 
%        arrays around simultaneously
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 SD_id = hdfsd( 'start', maskFilename, 'read' );
 if (SD_id < 0)
    error(['HDF file' maskFilename ' was not opened.']);
 end

% data we want is 'Quality_Assurance'
 mask_ex = hdfsd('nametoindex', SD_id, 'Quality_Assurance');
 mask_id = hdfsd('select',SD_id, mask_ex);
 [name,rank,dimsizes,data_type,nattrs,status(1)] = hdfsd('getinfo',mask_id );

%  npixels_along = dimsizes(1);
%  npixels_across = dimsizes(2); 
%  nbytes = dimsizes(3);
  start = [0 ; 0 ; minBytes-1]; 
  count = [1 ; 1 ; 1];
% 
%  if maxBytes <= nbytes 
%    edge = [npixels_along; npixels_across; maxBytes-minBytes+1];
%  else 
%    error(['maxBytes cannot be greater than the number of bytes in the file']);
%  end

 edge = [npixels_across ;  npixels_along; maxBytes-minBytes+1];

 if (nargin == 3)
    start(1) = min( [max([area(1) 0]) (npixels_across - 1)] );
    start(2) = min( [max([area(2) 0]) (npixels_along - 1)] );
    edge(1) = min( [max([area(3) 0]) (npixels_across - start(2))] );
    edge(2) = min( [max([area(4) 0]) (npixels_along - start(3))] );
end
 
 [qaData,status(2)] = hdfsd('readdata',mask_id,start,count,edge);

 qaData  = double(qaData);

 attr_ex = hdfsd('findattr', mask_id, 'scale_factor');
 [qascale, status(3)] = hdfsd('readattr', mask_id,attr_ex) ;
 
 attr_ex = hdfsd('findattr', mask_id, 'long_name');
 [qalongname, status(4)] = hdfsd('readattr', mask_id,attr_ex) ;

 attr_ex = hdfsd('findattr', mask_id, 'Cell_Along_Swath_Sampling');
 [qasampling, status(5)] = hdfsd('readattr', mask_id,attr_ex) ;

 attr_ex = hdfsd('findattr', mask_id, 'add_offset');
 [qaoffset, status(6)] = hdfsd('readattr', mask_id,attr_ex) ;
 if qaoffset ~= 0 | qascale ~= 1
    error(['Quality_Assurance offset ~= 0 or slope ~= 1']);
 end 

% stop accessing data 
 status(7) = hdfsd('endaccess',mask_id);

 if any(status == -1)
   error('Trouble reading Quality_Assurance data, dimensions, or attributes');
 end

 clear status

% close HDF file
 status = hdfsd('end', SD_id);
 if (status < 0)
    warning(['HDF file' maskFilename ' was not closed.']);
 end

 if any(byteList == 1) 

     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     %% 'Quality_Assurance': BYTE 1
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     byteInd = find(1 == cloudMaskDataByteList);
%    qabyte1 = flipud(rot90(squeeze(qaData(byteInd,:,:)) ));
     qabyte1 = squeeze(qaData(byteInd,:,:));
     % find negative integers and remap them
     ind = find(qabyte1 < 0);
     qabyte1(ind) = 256 + qabyte1(ind);
     clear ind

     %% BIT 0 - Cloud Mask QA
     %% 0 = not useful    1 = useful
     %% Assign all not useful values to -1 byte1 fields 
     notUsefulInds = find(~bitget(qabyte1,1));
     cloudmask.byte1.mask(notUsefulInds) = -1;

     if onlyBits1and2 == 0
        cloudmask.byte1.dayOrNight(notUsefulInds) = -1;
        cloudmask.byte1.sunglint(notUsefulInds) = -1;
        cloudmask.byte1.snowIce(notUsefulInds) = -1;
        cloudmask.byte1.landWater(notUsefulInds) = -1;

        %% BITS 1,2,3 - Cloud Mask Confidence
        bit2 = bitget(qabyte1,2); 
        bit3 = bitget(qabyte1,3); 
        bit4 = bitget(qabyte1,4); 
        ind0 = find(~bit4 & ~bit3 & ~bit2);
        ind1 = find(~bit4 & ~bit3 & bit2);
        ind2 = find(~bit4 & bit3 & ~bit2);
        ind3 = find(~bit4 & bit3  & bit2);
        ind4 = find(bit4 & ~bit3 & ~bit2);
        ind5 = find(bit4 & ~bit3 & bit2);
        ind6 = find(bit4 & bit3 & ~bit2);
        ind7 = find(bit4 & bit3 & bit2);
        clear bit2 bit3 bit4

        cloudmask.byte1.confidenceQA = NaN * ones(size(qabyte1)); 
        cloudmask.byte1.confidenceQA(ind0) = 0; 
        cloudmask.byte1.confidenceQA(ind1) = 1; 
        cloudmask.byte1.confidenceQA(ind2) = 2; 
        cloudmask.byte1.confidenceQA(ind3) = 3; 
        cloudmask.byte1.confidenceQA(ind4) = 4; 
        cloudmask.byte1.confidenceQA(ind5) = 5; 
        cloudmask.byte1.confidenceQA(ind6) = 6; 
        cloudmask.byte1.confidenceQA(ind7) = 7; 

        clear ind0 ind1 ind2 ind3 ind4 ind5 ind6 ind7 
    end
    clear qabyte1 notUsefulInds

  end  %% qa byte 1

  if any(byteList == 2 | byteList == 3 | byteList == 4)

     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     %% Quality_Assurance: BYTES 2-4
     %% 
     %% 0 = Not Applied   1 = Applied
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     indBytes234 = find(byteList == 2 | byteList == 3 | byteList == 4);
     for j = 1:length(indBytes234)

        qaByteInd = find(byteList(indBytes234(j)) == cloudMaskDataByteList);
%       qaByteData = flipud(rot90(squeeze(qaData(qaByteInd,:,:)) ));
        qaByteData = squeeze(qaData(qaByteInd,:,:));
	clear qaByteInd

        % find negative integers and remap them
        ind = find(qaByteData < 0);
        qaByteData(ind) = 256 + qaByteData(ind);
        clear ind

        if byteList(indBytes234(j)) < 4 
           %% 8 qa bits (0-7) in qa bytes 2 and 3	
           numBits = 8;
        else
           %% 5 qa bits (0-4) in qa byte 4
           numBits = 5;
        end

        %% For QA "not applied", set corresponding value in   
        %% cloudmask.byte#.bit# to -1 
        for k = 1:numBits
           eval(['cloudmask.byte' num2str(byteList(indBytes234(j))) ...
	         '.bit' num2str(k-1) '(find(~bitget(qaByteData,k))) = -1;']);
        end % for k

        clear qaByteData 

      end %% for j
  end  %% bytes 2, 3, 4

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  %% Quality_Assurance: BYTES 5 & 6: 250-m Cloud Flag, Visible Tests
  %%   0 = Not Applied     1 = Applied 
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  if any(byteList == 5) | any(byteList == 6)
	  
  save tempCMdata 
%  keep2 cloudMaskDataByteList qaData
  clear cloudmask

  %% BYTE 5

     qaByteInd = find(5 == cloudMaskDataByteList);
%    qaByteData = flipud(rot90(squeeze(qaData(qaByteInd,:,:)) ));
     qaByteData = squeeze(qaData(qaByteInd,:,:));
     clear qaByteInd

     % find negative integers and remap them
     ind = find(qaByteData < 0);
     qaByteData(ind) = 256 + qaByteData(ind);
     clear ind

     %% create an array of all NaNs 4x the size of one element 
     %% repmat is faster than ones*NaN
     elementSize = size(bitget(qaByteData,1));
     temporaryQA = repmat(0,elementSize*4);

     xStartInds = [1 1 1 1 2 2 2 2];
     yStartInds = [1 2 3 4 1 2 3 4];

     %% insert each element into the array of NaNs.
     for j = 1:8
        temporaryQA([xStartInds(j):4:elementSize(1)*4], ...
                      [yStartInds(j):4:elementSize(2)*4]) = bitget(qaByteData,j); 
     end

     clear qaByteData 

  %% BYTE 6

     qaByteInd = find(6 == cloudMaskDataByteList);
%    qaByteData = flipud(rot90(squeeze(qaData(qaByteInd,:,:)) ));
     qaByteData = squeeze(qaData(qaByteInd,:,:));
     clear qaByteInd

     % find negative integers and remap them
     ind = find(qaByteData < 0);
     qaByteData(ind) = 256 + qaByteData(ind);
     clear ind

     xStartInds = [3 3 3 3 4 4 4 4];
     yStartInds = [1 2 3 4 1 2 3 4];

     %% insert each element into the array of NaNs.
     for j = 1:8 
        temporaryQA([xStartInds(j):4:elementSize(1)*4], ...
                    [yStartInds(j):4:elementSize(2)*4]) = bitget(qaByteData,j); 
     end

     clear qaByteData qaData

     notAppliedInds = find(~temporaryQA);

     load tempCMdata
     cloudmask.visibleTest250m(notAppliedInds) = -1;

     clear notAppliedInds temporaryQA

  end  %% byte 5,6

