% creates mask files for plotting in Amira

load GeometryProstate.mat;   % geometry file of interest

amira_folder = 'amira2';   % folder for Amira data

amira_file = 'prostateBoost.hx';

curr_dir = pwd;   % current directory

mkdir(amira_folder);   % create the amira folder

cd(amira_folder);      % go to amira folder

Nroi = length(Geometry.ROIS);  % get number of ROIS from Geometry structure

% icon position vectors
xIcon = [0:2]*200 + 50;
yIcon = [0:1]*50;
yShift = [0:Nroi]*120 + 400;

% get the names of the rois
roi_names = cell(1,Nroi);
for k=1:Nroi
    roi_names{k} = Geometry.ROIS{k}.name;
end

% set up a mask structure
mask.start = Geometry.start;
mask.voxel_size = Geometry.voxel_size;
siz = size(Geometry.data);  % mask dimensions

% create the Amira .hx file
fid = fopen(amira_file,'w');

fprintf(fid,'# Amira Script\n');
fprintf(fid,'remove -all\n');
fprintf(fid,['remove physics.icol glow.col dose.am BoundingBox OrthoSlice0 OrthoSlice1 OrthoSlice2 Colorwash0 Colorwash1 Colorwash2 Isolines0 Isolines1 Isolines2 GlobalAxis CastField\n']);
fprintf(fid,'\n');

% viewer parameters
fprintf(fid,'# Create viewers\n');
fprintf(fid,'viewer setVertical 0\n');
fprintf(fid,'\n');
fprintf(fid,'viewer 0 setBackgroundMode 1\n');
fprintf(fid,'viewer 0 setBackgroundColor 0.06 0.13 0.24\n');
fprintf(fid,'viewer 0 setBackgroundColor2 0.72 0.72 0.78\n');
fprintf(fid,'viewer 0 setTransparencyType 5\n');
fprintf(fid,'viewer 0 setAutoRedraw 0\n');
fprintf(fid,'viewer 0 show\n');
fprintf(fid,'mainWindow show\n');
fprintf(fid,'\n');

% create files for each mask region
for k=1:Nroi
    mask_filename = [roi_names{k} '.am'];
    mask_filename = regexprep(mask_filename,' ','');  % remove spaces
    mask.data = zeros(siz,'int8');
    mask.data(Geometry.ROIS{k}.ind) = 1;  % fill in the mask
    geom2am(mask,mask_filename);  % save the structure to an Amira file
    
    fprintf(fid,'set hideNewModules 0\n');
    fprintf(fid,['[ load ${SCRIPTDIR}/' mask_filename ' ] setLabel ' mask_filename '\n']);
    fprintf(fid,[mask_filename ' setIconPosition ' num2str(xIcon(1)) ' ' num2str(yIcon(1)+yShift(k)) '\n']);
    fprintf(fid,[mask_filename ' fire\n']);
    fprintf(fid,[mask_filename ' fire\n']);
    fprintf(fid,[mask_filename ' setViewerMask 65535\n']);
    fprintf(fid,'\n');
    
    % set up a CastField module for a LabelField for the mask
    fprintf(fid,'set hideNewModules 0\n');
    castFieldName = ['CastField' num2str(k)];
    fprintf(fid,['create HxCastField {' castFieldName '}\n']);
    fprintf(fid,[castFieldName ' setIconPosition ' num2str(xIcon(2)) ' ' num2str(yIcon(1)+yShift(k)) '\n']);
    fprintf(fid,[castFieldName ' data connect ' mask_filename '\n']);
    fprintf(fid,[castFieldName ' colormap setDefaultColor 1 0.8 0.5\n']);
    fprintf(fid,[castFieldName ' colormap setDefaultAlpha 0.500000\n']);
    fprintf(fid,[castFieldName ' fire\n']);
    fprintf(fid,[castFieldName ' outputType setValue 0 6\n']);
    fprintf(fid,[castFieldName ' scaling setMinMax 0 -1.00000001384843e+024 1.00000001384843e+024\n']);
    fprintf(fid,[castFieldName ' scaling setValue 0 1\n']);
    fprintf(fid,[castFieldName ' scaling setMinMax 1 -1.00000001384843e+024 1.00000001384843e+024\n']);
    fprintf(fid,[castFieldName ' scaling setValue 1 0\n']);
    fprintf(fid,[castFieldName ' voxelGridOptions setValue 0 1\n']);
    fprintf(fid,[castFieldName ' colorFieldOptions setValue 0 0\n']);
    fprintf(fid,[castFieldName ' fire\n']);
    fprintf(fid,[castFieldName ' setViewerMask 65535\n']);
    fprintf(fid,[castFieldName ' deselect\n']);
    fprintf(fid,'\n');
    
    % set up mask plotting routines
    mask_labelfield_name = regexprep(mask_filename,'am','Labelfield'); 
    fprintf(fid,'set hideNewModules 0\n');
    fprintf(fid,['[ {' castFieldName '} create\n']);
    fprintf(fid,['    ] setLabel {' mask_labelfield_name '}\n']);
    fprintf(fid,[mask_labelfield_name ' setIconPosition ' num2str(xIcon(1)) ' ' num2str(yIcon(2)+yShift(k)) '\n']);
    fprintf(fid,[mask_labelfield_name ' master connect ' castFieldName '\n']);
    fprintf(fid,[mask_labelfield_name ' fire\n']);
    fprintf(fid,[mask_labelfield_name ' primary setValue 0 0\n']);
    fprintf(fid,[mask_labelfield_name ' fire\n']);
    fprintf(fid,[mask_labelfield_name ' setViewerMask 65535\n']);
    fprintf(fid,'\n');
    
    surfaceGenName = ['SurfaceGen' num2str(k)];
    fprintf(fid,'set hideNewModules 0\n');
    fprintf(fid,['create HxGMC {' surfaceGenName '}\n']);
    fprintf(fid,[surfaceGenName ' setIconPosition ' num2str(xIcon(3)) ' ' num2str(yIcon(1)+yShift(k)) '\n']);
    fprintf(fid,[surfaceGenName ' data connect ' mask_labelfield_name '\n']);
    fprintf(fid,[surfaceGenName ' fire\n']);
    fprintf(fid,[surfaceGenName ' smoothing setValue 0 3\n']);
    fprintf(fid,[surfaceGenName ' options setValue 0 1\n']);
    fprintf(fid,[surfaceGenName ' options setValue 1 0\n']);
    fprintf(fid,[surfaceGenName ' border setValue 0 1\n']);
    fprintf(fid,[surfaceGenName ' border setValue 1 0\n']);
    fprintf(fid,[surfaceGenName ' minEdgeLength setMinMax 0 0 0.800000011920929\n']);
    fprintf(fid,[surfaceGenName ' minEdgeLength setValue 0 0\n']);
    fprintf(fid,[surfaceGenName ' materialList setValue 0 0\n']);
    fprintf(fid,[surfaceGenName ' fire\n']);
    fprintf(fid,[surfaceGenName ' setViewerMask 65535\n']);
    fprintf(fid,'\n');
    
    mask_surf_name = regexprep(mask_filename,'am','surf'); 
    fprintf(fid,'set hideNewModules 0\n');
    fprintf(fid,['[ {' surfaceGenName '} create {' mask_surf_name '}\n']);
    fprintf(fid,['    ] setLabel {' mask_surf_name '}\n']);
    fprintf(fid,[mask_surf_name ' setIconPosition ' num2str(xIcon(2)) ' ' num2str(yIcon(2)+yShift(k)) '\n']);
    fprintf(fid,[mask_surf_name ' master connect ' surfaceGenName '\n']);
    fprintf(fid,[mask_surf_name ' fire\n']);
    fprintf(fid,[mask_surf_name ' LevelOfDetail setMinMax -1 -1\n']);
    fprintf(fid,[mask_surf_name ' LevelOfDetail setButtons 1\n']);
    fprintf(fid,[mask_surf_name ' LevelOfDetail setIncrement 1\n']);
    fprintf(fid,[mask_surf_name ' LevelOfDetail setValue -1\n']);
    fprintf(fid,[mask_surf_name ' LevelOfDetail setSubMinMax -1 -1\n']);
    fprintf(fid,[mask_surf_name ' fire\n']);
    fprintf(fid,[mask_surf_name ' setViewerMask 65535\n']);
    fprintf(fid,[mask_surf_name ' deselect\n']);
    fprintf(fid,'\n');
    fprintf(fid,'set hideNewModules 0\n');
    fprintf(fid,'\n');
    
    surfaceViewName = ['SurfaceView' num2str(k)];
    fprintf(fid,'set hideNewModules 0\n');
    fprintf(fid,['create HxDisplaySurface {' surfaceViewName '}\n']);
    fprintf(fid,[surfaceViewName ' setIconPosition ' num2str(xIcon(3)) ' ' num2str(yIcon(2)+yShift(k)) '\n']);
    fprintf(fid,[surfaceViewName ' data connect ' mask_surf_name '\n']);
    fprintf(fid,[surfaceViewName ' colormap setDefaultColor 1 0.1 0.1\n']);
    fprintf(fid,[surfaceViewName ' colormap setDefaultAlpha 0.500000\n']);
    fprintf(fid,[surfaceViewName ' fire\n']);
    fprintf(fid,[surfaceViewName '  drawStyle setValue 4\n']);
    fprintf(fid,[surfaceViewName '  drawStyle setSpecularLighting 1\n']);
    fprintf(fid,[surfaceViewName '  drawStyle setTexture 0\n']);
    fprintf(fid,[surfaceViewName '  drawStyle setAlphaMode 3\n']);
    fprintf(fid,[surfaceViewName '  drawStyle setNormalBinding 0\n']);
    fprintf(fid,[surfaceViewName '  drawStyle setCullingMode 0\n']);
    fprintf(fid,[surfaceViewName '  selectionMode setValue 0 0\n']);
    fprintf(fid,[surfaceViewName '  Patch setMinMax 0 1\n']);
    fprintf(fid,[surfaceViewName '  Patch setButtons 1\n']);
    fprintf(fid,[surfaceViewName '  Patch setIncrement 1\n']);
    fprintf(fid,[surfaceViewName '  Patch setValue 1\n']);
    fprintf(fid,[surfaceViewName '  Patch setSubMinMax 0 1\n']);
    fprintf(fid,[surfaceViewName '  BoundaryId setValue 0 -1\n']);
    fprintf(fid,[surfaceViewName '  materials setValue 0 1\n']);
    fprintf(fid,[surfaceViewName '  materials setValue 1 0\n']);
    fprintf(fid,[surfaceViewName '  colorMode setValue 0\n']);
    fprintf(fid,[surfaceViewName '  baseTrans setMinMax 0 1\n']);
    fprintf(fid,[surfaceViewName '  baseTrans setButtons 0\n']);
    fprintf(fid,[surfaceViewName '  baseTrans setIncrement 0.1\n']);
    fprintf(fid,[surfaceViewName '  baseTrans setValue 0.53\n']);
    fprintf(fid,[surfaceViewName '  baseTrans setSubMinMax 0 1\n']);
    fprintf(fid,[surfaceViewName '  VRMode setValue 0 0\n']);
    fprintf(fid,[surfaceViewName '  fire\n']);
    fprintf(fid,[surfaceViewName '  hideBox 1\n']);
    fprintf(fid,['{' surfaceViewName '} selectTriangles zab HIJMPLPPHPGAABDPBAADAACGHIICIN\n']);
    fprintf(fid,[surfaceViewName '  fire\n']);
    fprintf(fid,[surfaceViewName '  setViewerMask 65535\n']);
    fprintf(fid,[surfaceViewName '  deselect\n']);
    fprintf(fid,'\n');
end

fclose(fid);