generateNinjaCap.m

%% CODE FOR NINJACAP GENERATION
% Instructions to the user:
% 0. set up and install everything as described in the github HELP file
% here: https://github.com/neuluce/ninjaCap
% 1. provide probe file with name "probe.SD" in dir \userinput\probe.SD
% 2. run generateNinjaCap.m with head circumference(HC) in cm as input argument: e.g. generateNinjaCap(56)
% 3. when the files are generated, a blender workspace will be opened. Run
% the default python script (click <Text> -> <Run Script>, or press Alt+P.
% 4. your generated and assembled cap is saved in the folder \print\. Here
% you also find a default 3D printing profile for Cura LULZBOT TAZ 6 using
% ninjaflex.
function [] = generateNinjaCap(HC, head_model)

if ~exist('head_model','var')
    head_model = 'Colin';
end

dirSave = pwd;
rootDir = fileparts(which(mfilename));

%% Change the current folder to the folder of this m-file.
% if(~isdeployed)
%     rootDir = fileparts(which(mfilename));
%     cd(rootDir);
% end

%% add this folder and subfolders to paths
% addpath(genpath(pwd))

%% AUTOMATED PANEL CREATION FROM SD FILES
% if you renamed your files, update the path and names here
if ~exist('HC','var')
    HC = 56; % default cap size
end
circumference = HC; % cm (actual circumference, correction applied automatically)

%% CHECK FOR EXISTING AltasViewer FILE?
if exist([pwd filesep 'atlasViewer.mat'], 'file')
    disp('An "atlasViewer.mat" file already exists.');
    prompt = ['To overwrite file press Y/y otherwise N/n and confirm with Enter:'];
    x = input(prompt,'s');
    if (x == 'y') || (x=='Y')
        delete([pwd filesep 'atlasViewer.mat'])
    else
        error('Stopped')
    end
end

%% PREPARE ATLASVIEWER.MAT

% launch AtlasViewer
% DEPENDENCY HOMER 3 >> getAppDir()
%AtlasViewerGUI(pwd, [getAppDir() 'PACKAGES' filesep 'AtlasViewerGUI' filesep 'Data' filesep 'Colin'], 'userargs');     
% appdir hardcoded
avMainFilepath = which('AtlasViewerGUI.m');
avAppDir = fileparts(avMainFilepath);
if strcmp(head_model,'Colin')
    avDataDir = filesepStandard([avAppDir, '/Data/Colin']);
elseif strcmp(head_model,'ICBM')
    avDataDir = filesepStandard([rootDir, '/Data/ICBM']);
else
    disp('Specified head model does not exist')
    return
end
AtlasViewerGUI(pwd, avDataDir, 'userargs');

% scale head to corrected circumference
generateScaleCircumference(circumference);

% load 10-10 points into AtlasViewer
generateLoad10_5();

% align to head surface
generateRegisterProbe();

% save state file
generateSaveViewerState();

%% RUN PANEL.m
cd(rootDir);
copyfile( [dirSave filesep 'atlasViewer.mat'],'.' );
panel('atlasViewer.mat', circumference);
drawnow

%% DELETE FILES
delete([pwd filesep 'atlasViewer.mat']);
% delete([pwd filesep 'digpts.txt']);
% delete([pwd filesep 'digpts2mc.txt']);

delete([dirSave filesep 'atlasViewer.mat']);
delete([dirSave filesep 'digpts.txt']);
delete([dirSave filesep 'digpts2mc.txt']);

%% RUN blender
system('wrkspace.blend')


%% Fix negitive z-coordinates issue with stl file
% I think this happens in Blender. This is a simple fix here but in the
% future need to fix in blender.

stl_files = dir(['print' filesep '*.stl']);
for u = 1:length(stl_files)
    TR = stlread([stl_files(u).folder filesep stl_files(u).name]);
    v = TR.Points;
    idx = find(v(:,3) < 0);
    v(idx,3) = 0;
    f = TR.ConnectivityList;
    TR = triangulation(f,v);
    stlwrite( TR,[stl_files(u).folder filesep stl_files(u).name],'text');
end

%% COPY BLENDER OUTPUT TO WORKING DIRECTORY
if ~isdir([dirSave filesep 'print'])
    mkdir([dirSave filesep 'print']);
end
copyfile( ['print' filesep '*.stl'], [dirSave filesep 'print'] );
copyfile( ['print' filesep '*.curaprofile'], [dirSave filesep 'print'] );
copyfile( 'stl_image.png', [dirSave filesep 'print'] );
cd(dirSave)

end