WiscPlan_olderMV/photonDoseCalc/scripts_m/geom2am.m

function geom2am(Geometry,AmiraMeshFile)
% geom2am(Geometry,AmiraMeshFile) converts a geometry structure to an 
% AmiraMesh (.am) file.  The Geometry structure has the form:
%
% Geometry = 
%          start: [3x1 double/single]
%     voxel_size: [3x1 double/single]
%           data: [MxNxQ double/single]
%
% AmiraMeshFile = name of resulting AmiraMesh file
%
% Ryan T Flynn 23 August 2007

% check validity of inputs
if ~isa(Geometry,'struct')
    error('Geometry must be a structure.');
else % ensure that all of the required fields are present
    if ~isfield(Geometry,'start')
        error('Geometry must have a ''start'' field.');
    elseif prod(size(Geometry.start)) ~= 3 | ~isnumeric(Geometry.start)
        error('Geometry.start must be a 3-element vector.');
    end

    if ~isfield(Geometry,'voxel_size')
        error('Geometry must have a ''voxel_size'' field.');
    elseif prod(size(Geometry.start)) ~= 3 | ~isnumeric(Geometry.start)
        error('Geometry.voxel_size field must be a 3-element vector.');
    end

    if ~isfield(Geometry,'data')
        error('Geometry must have a ''data'' field.');
    elseif ~isnumeric(Geometry.start)
        error('Geometry.data field must be a numeric array.');
    end
end

if ~isa(AmiraMeshFile,'char')
    error('AmiraMeshFile must be a character array.');
end

Xcount = size(Geometry.data,1);
Ycount = size(Geometry.data,2);
Zcount = size(Geometry.data,3);

inc = Geometry.voxel_size;

% bounding box coordinate vectors
boxstart = Geometry.start;
boxend = boxstart + [inc(1)*(Xcount-1) inc(2)*(Ycount-1) inc(3)*(Zcount-1)];

% conversion table for data types
% 6 allowed types for Amira:
% byte, short, ushort, int32, float, double

% Figure out what the data type is
for k=1:6
   if isa(Geometry.data,'int8')
       MatlabDataType = 'int8';
       AmiraDataType = 'byte';
   elseif isa(Geometry.data,'int16')
       MatlabDataType = 'int16';
       AmiraDataType = 'short';
   elseif isa(Geometry.data,'uint16')
       MatlabDataType = 'uint16';
       AmiraDataType = 'ushort';
   elseif isa(Geometry.data,'int32')
       MatlabDataType = 'int32';
       AmiraDataType = 'int32';
   elseif isa(Geometry.data,'float')
       MatlabDataType = 'float';
       AmiraDataType = 'float';
   elseif isa(Geometry.data,'double')
       MatlabDataType = 'double';
       AmiraDataType = 'double';
   else
       error('Geometry.data data type is not supported by Amira.');
   end  
end

% open the AmiraMesh file for writing text
fid = fopen(AmiraMeshFile,'w');

fprintf(fid,'# AmiraMesh 3D BINARY 2.0\n\n');
fprintf(fid,['# CreationDate: ' datestr(now,'ddd mmm') datestr(now,' dd HH:MM:SS yyyy') '\n\n']);
fprintf(fid,'define Lattice %g %g %g\n\n',Xcount,Ycount,Zcount);
fprintf(fid,'Parameters {\n');
fprintf(fid,'    Content "%gx%gx%g %s, uniform coordinates",',Xcount,Ycount,Zcount,AmiraDataType);
fprintf(fid,'    BoundingBox %g %g %g %g %g %g,\n',boxstart(1),boxend(1),boxstart(2),boxend(2),boxstart(3),boxend(3));
fprintf(fid,'    CoordType "uniform"\n');
fprintf(fid,'}\n\n');
fprintf(fid,'Lattice { %s Data } @1\n\n',AmiraDataType);
fprintf(fid,'# Data section follows\n');
fprintf(fid,'@1\n');
fclose(fid);  % close the text part of the file
% write the data in big endian format
fid = fopen(AmiraMeshFile,'ab','ieee-be');
fwrite(fid,Geometry.data,MatlabDataType);
fclose(fid);