readRawFileSegm.m

function obj = readRawFileSegm( obj )
%READRAWFILESEGM Read metadata for segment of type ZISRAWFILE
%   Extract information from ZISRAWFILE segments. For the moment, read all
%   fields, even the unnecessary ones, and use them for sanity check.
%
% AUTHOR: Stefano Masneri
% Date: 13.10.2016


  Major = int32(fread(obj.cziPtr, 1, 'int32')); % Should be always one
  Minor = int32(fread(obj.cziPtr, 1, 'int32')); % Should be always zero
  if (Major ~= 1 || Minor ~= 0)
    error('CZIReader.readRawFileSegm: Major and Minor fields are not correct')
  end
  
  Reserved = fread(obj.cziPtr, 2, 'int32');
  
  PrimaryFileGuid = fread(obj.cziPtr, 4, 'int32'); % Unique Guid of Master file (FilePart 0)
  FileGuid = fread(obj.cziPtr, 4, 'int32'); % Unique per file
  if ~isequal(PrimaryFileGuid, FileGuid)
    warning('CZIReader.readRawFileSegm: multifile dataset. Currently unsupported')
  end
  
  % FilePart: Part number in multi-file scenarios
  FilePart = int32(fread(obj.cziPtr, 1, 'int32'));
  
  % DirectoryPosition: File position of the SubBlockDirectory Segment
  DirectoryPosition = int64(fread(obj.cziPtr, 1, 'int64'));
  if DirectoryPosition ~= obj.offsetDirectorySegm - 32 %32 is the ehader size
    error('CZIReader.readRawFileSegm: Inconsistent offset for Directory segment')
  end
  
  %MetadataPosition: File position of the Metadata Segment
  MetadataPosition = int64(fread(obj.cziPtr, 1, 'int64')); 
  if MetadataPosition ~= obj.offsetMetadataSegm - 32 %32 is the ehader size
    error('CZIReader.readRawFileSegm: Inconsistent offset for Metadata segment')
  end
  
  % UpdatePending: % either 0 or 0xffff
  % This flag indicates a currently inconsistent
  % situation (e.g. updating Index, Directory or
  % Metadata segment).
  % Readers should either wait until this flag is
  % reset (in case that a writer is still accessing the
  % file), or try a recovery procedure by scanning
  % all segments.
  UpdatePending = int32(fread(obj.cziPtr, 1, 'int32'));                                              
  if 0 ~= UpdatePending
    error('CZIReader.readRawFileSegm: UpdatePending field set')
  end
       
  % AttachmentDirectoryPosition: File position of the AttachmentDirectory Segment
  AttachmentDirectoryPosition = int64(fread(obj.cziPtr, 1, 'int64'));
  if AttachmentDirectoryPosition ~= obj.offsetAttachDirSegm - 32 %32 is the ehader size
    error('CZIReader.readRawFileSegm: Inconsistent offset for AttachDirectory segment')
  end                                               
end