public static GameBoard CreateGame(Guid guid, int complexityLevel)
{
int width, height, colorCount;
switch (complexityLevel)
{
case 2:
width = 20;
height = 20;
colorCount = 12;
break;
case 1:
width = 15;
height = 15;
colorCount = 9;
break;
case 0:
default:
width = 10;
height = 10;
colorCount = 6;
break;
}
var boardData = RandomFieldGenerator.Create(width, height, colorCount);
return(new GameBoard(width, height, boardData, guid, ColorPaletteGenerator.CreateHexPalette(colorCount)));
}
public static int[,] ToIndexArray(this CellDto[] cells, String[] palette)
{
int axisX = cells.Select <CellDto, int>(x => x.Pos.X).Max();
int axisY = cells.Select <CellDto, int>(y => y.Pos.Y).Max();
int[,] indexArray = new int[axisX, axisY];
foreach (CellDto cell in cells)
{
indexArray[cell.Pos.X, cell.Pos.Y] = ColorPaletteGenerator.IndexInPalette(palette, cell.Content);
}
return(indexArray);
}
public static void LoadIngredients(string recipePath)
{
Debug.Log("*****");
Debug.Log("Loading scene: " + recipePath);
var cellPackSceneJsonPath = recipePath;//Application.dataPath + "/../Data/HIV/cellPACK/BloodHIV1.0_mixed_fixed_nc1.json";
if (!File.Exists(cellPackSceneJsonPath))
{
throw new Exception("No file found at: " + cellPackSceneJsonPath);
}
var resultData = Helper.ParseJson(cellPackSceneJsonPath);
//we can traverse the json dictionary and gather ingredient source (PDB,center), sphereTree, instance.geometry if we want.
//the recipe is optional as it will gave more information than just the result file.
//idea: use secondary color scheme for compartments, and analogous color for ingredient from the recipe baseColor
current_color = 0;
//first grab the total number of object
int nIngredients = 0;
if (resultData["cytoplasme"] != null)
{
nIngredients += resultData["cytoplasme"]["ingredients"].Count;
}
for (int i = 0; i < resultData["compartments"].Count; i++)
{
nIngredients += resultData["compartments"][i]["interior"]["ingredients"].Count;
nIngredients += resultData["compartments"][i]["surface"]["ingredients"].Count;
}
//generate the palette
//ColorsPalette = ColorGenerator.Generate(nIngredients).Skip(2).ToList();
ColorsPalette = ColorGenerator.Generate(8).Skip(2).ToList();//.Skip(2).ToList();
List <Vector3> startKmeans = new List <Vector3>(ColorsPalette);
//paletteGenerator.initKmeans (startKmeans);
usedColors = new Dictionary <int, List <int> >();
ColorsPalette2 = ColorPaletteGenerator.generate(
6, // Colors
ColorPaletteGenerator.testfunction,
false, // Using Force Vector instead of k-Means
50 // Steps (quality)
);
// Sort colors by differenciation first
//ColorsPalette2 = paletteGenerator.diffSort(ColorsPalette2);
//check if cytoplasme present
Color baseColor = new Color(1.0f, 107.0f / 255.0f, 66.0f / 255.0f);
if (resultData["cytoplasme"] != null)
{
usedColors.Add(current_color, new List <int>());
baseColor = new Color(1.0f, 107.0f / 255.0f, 66.0f / 255.0f);
AddRecipeIngredients(resultData["cytoplasme"]["ingredients"], baseColor, "cytoplasme");
current_color += 1;
}
for (int i = 0; i < resultData["compartments"].Count; i++)
{
baseColor = new Color(148.0f / 255.0f, 66.0f / 255.0f, 255.0f / 255.0f);
usedColors.Add(current_color, new List <int>());
AddRecipeIngredients(resultData["compartments"][i]["interior"]["ingredients"], baseColor, "interior" + i.ToString());
current_color += 1;
baseColor = new Color(173.0f / 255.0f, 255.0f / 255.0f, 66.0f / 255.0f);
usedColors.Add(current_color, new List <int>());
AddRecipeIngredients(resultData["compartments"][i]["surface"]["ingredients"], baseColor, "surface" + i.ToString());
current_color += 1;
}
}
public static void AddProteinIngredient(JSONNode ingredientDictionary, string prefix)
{
var name = prefix + "_" + ingredientDictionary["name"];
var biomt = (bool)ingredientDictionary["source"]["biomt"].AsBool;
var center = (bool)ingredientDictionary["source"]["transform"]["center"].AsBool;
var pdbName = ingredientDictionary["source"]["pdb"].Value.Replace(".pdb", "");
if (pdbName == "")
{
return;
}
if (pdbName == "null")
{
return;
}
if (pdbName == "None")
{
return;
}
if (pdbName.StartsWith("EMDB"))
{
return;
}
if (pdbName.Contains("1PI7_1vpu_biounit"))
{
return;
}
// Disable biomts until loading problem is resolved
if (biomt)
{
return;
}
// Load atom set from pdb file
var atomSet = PdbLoader.LoadAtomSet(pdbName);
// If the set is empty return
if (atomSet.Count == 0)
{
return;
}
var atomSpheres = AtomHelper.GetAtomSpheres(atomSet);
var centerPosition = AtomHelper.ComputeBounds(atomSpheres).center;
var biomtTransforms = biomt ? PdbLoader.LoadBiomtTransforms(pdbName) : new List <Matrix4x4>();
var biomtCenter = AtomHelper.GetBiomtCenter(biomtTransforms);
var containsACarbonOnly = AtomHelper.ContainsACarbonOnly(atomSet);
// Center atoms
AtomHelper.OffsetSpheres(ref atomSpheres, centerPosition);
// Compute bounds
var bounds = AtomHelper.ComputeBounds(atomSpheres);
// Get ingredient color
// TODO: Move color palette code into dedicated function
var cid = ColorPaletteGenerator.GetRandomUniqFromSample(current_color, usedColors[current_color]);
usedColors[current_color].Add(cid);
var sample = ColorPaletteGenerator.colorSamples[cid];
var c = ColorPaletteGenerator.lab2rgb(sample) / 255.0f;
var color = new Color(c[0], c[1], c[2]);
// Define cluster decimation levels
var clusterLevels = (containsACarbonOnly)
? new List <float>()
{
0.85f, 0.25f, 0.1f
}
: new List <float>()
{
0.10f, 0.05f, 0.01f
};
// Add ingredient type
//SceneManager.Instance.AddIngredient(name, bounds, atomSpheres, color);
SceneManager.Instance.AddIngredient(name, bounds, atomSpheres, color, clusterLevels);
int instanceCount = 0;
for (int k = 0; k < ingredientDictionary["results"].Count; k++)
{
var p = ingredientDictionary["results"][k][0];
var r = ingredientDictionary["results"][k][1];
var position = new Vector3(-p[0].AsFloat, p[1].AsFloat, p[2].AsFloat);
var rotation = new Quaternion(r[0].AsFloat, r[1].AsFloat, r[2].AsFloat, r[3].AsFloat);
var mat = Helper.quaternion_matrix(rotation);
var euler = Helper.euler_from_matrix(mat);
rotation = Helper.MayaRotationToUnity(euler);
if (!biomt)
{
// Find centered position
if (!center)
{
position += Helper.QuaternionTransform(rotation, centerPosition);
}
SceneManager.Instance.AddIngredientInstance(name, position, rotation);
instanceCount++;
}
else
{
foreach (var transform in biomtTransforms)
{
var biomtOffset = Helper.RotationMatrixToQuaternion(transform) * centerPosition;
var biomtInstanceRot = rotation * Helper.RotationMatrixToQuaternion(transform);
var biomtInstancePos = rotation * (new Vector3(transform.m03, transform.m13, transform.m23) + biomtOffset) + position - biomtCenter;
SceneManager.Instance.AddIngredientInstance(name, biomtInstancePos, biomtInstanceRot);
instanceCount++;
}
}
}
Debug.Log("*****");
Debug.Log("Added ingredient: " + name);
if (containsACarbonOnly)
{
Debug.Log("Alpha-carbons only");
}
Debug.Log("Pdb name: " + pdbName + " *** " + "Num atoms: " + atomSpheres.Count + " *** " + "Num instances: " + instanceCount + " *** " + "Total atom count: " + atomSpheres.Count * instanceCount);
}
public static void AddProteinIngredient(JSONNode ingredientDictionary, params string[] pathElements)
{
var name = ingredientDictionary["name"];
var path = MyUtility.GetUrlPath(pathElements.ToList(), name);
var biomt = (bool)ingredientDictionary["source"]["biomt"].AsBool;
var center = (bool)ingredientDictionary["source"]["transform"]["center"].AsBool;
var pdbName = ingredientDictionary["source"]["pdb"].Value.Replace(".pdb", "");
List <Vector4> atomSpheres;
List <Matrix4x4> biomtTransforms = new List <Matrix4x4>();
Vector3 biomtCenter = Vector3.zero;
bool containsACarbonOnly = false;
bool oneLOD = false;
if ((pdbName == "") || (pdbName == "null") || (pdbName == "None") || pdbName.StartsWith("EMDB"))
{
return;
////check for sphere file//information in the file. if not in file is it on disk ? on repo ?
////possibly read the actuall recipe definition ?
////check if bin exist
//var filePath = PdbLoader.DefaultPdbDirectory + ingredientDictionary["name"] + ".bin";
//if (File.Exists(filePath)){
// atomSpheres = new List<Vector4>();
// var points = MyUtility.ReadBytesAsFloats(filePath);
// for (var i = 0; i < points.Length; i += 4) {
// var currentAtom = new Vector4 (points [i], points [i + 1], points [i + 2], points [i + 3]);
// atomSpheres.Add (currentAtom);
// }
// containsACarbonOnly = true;
// oneLOD = true;
//}
//else if (ingredientDictionary ["radii"] != null) {
// atomSpheres = MyUtility.gatherSphereTree(ingredientDictionary)[0];
// Debug.Log ("nbprim "+atomSpheres.Count.ToString());//one sphere
// oneLOD = true;
//} else {
// float radius = 30.0f;
// if (name.Contains("dLDL"))
// radius = 108.08f;//or use the mesh? or make sphere from the mesh ?
// if (name.Contains("iLDL"))
// radius = 105.41f;//or use the mesh? or make sphere from the mesh ?
// atomSpheres = new List<Vector4>();
// atomSpheres.Add (new Vector4(0,0,0,radius));
// //No LOD since only one sphere
// oneLOD = true;
//}
}
else
{
//if (pdbName.StartsWith("EMDB")) return;
//if (pdbName.Contains("1PI7_1vpu_biounit")) return;//??
// Load atom set from pdb file
var atomSet = PdbLoader.LoadAtomSet(pdbName);
// If the set is empty return
if (atomSet.Count == 0)
{
return;
}
atomSpheres = AtomHelper.GetAtomSpheres(atomSet);
containsACarbonOnly = AtomHelper.ContainsCarbonAlphaOnly(atomSet);
}
var centerPosition = AtomHelper.ComputeBounds(atomSpheres).center;
// Center atoms
AtomHelper.OffsetSpheres(ref atomSpheres, centerPosition);
// Compute bounds
var bounds = AtomHelper.ComputeBounds(atomSpheres);
biomtTransforms = biomt ? PdbLoader.LoadBiomtTransforms(pdbName) : new List <Matrix4x4>();
biomtCenter = AtomHelper.GetBiomtCenter(biomtTransforms, centerPosition);
//if (!pdbName.Contains("1TWT_1TWV")) return;
// Disable biomts until loading problem is resolved
//if (!biomt) return;
// Get ingredient color
// TODO: Move color palette code into dedicated function
var cid = ColorPaletteGenerator.GetRandomUniqFromSample(current_color, usedColors[current_color]);
usedColors[current_color].Add(cid);
var sample = ColorPaletteGenerator.colorSamples[cid];
var c = ColorPaletteGenerator.lab2rgb(sample) / 255.0f;
var color = new Color(c[0], c[1], c[2]);
// Define cluster decimation levels
var clusterLevels = (containsACarbonOnly)
? new List <float>()
{
0.85f, 0.25f, 0.1f
}
: new List <float>()
{
0.15f, 0.10f, 0.05f
};
if (oneLOD)
{
clusterLevels = new List <float> ()
{
1, 1, 1
}
}
;
// Add ingredient type
//SceneManager.Instance.AddIngredient(name, bounds, atomSpheres, color);
SceneManager.Get.AddProteinIngredient(path, bounds, atomSpheres, color, clusterLevels, oneLOD);
int instanceCount = 0;
for (int k = 0; k < ingredientDictionary["results"].Count; k++)
{
var p = ingredientDictionary["results"][k][0];
var r = ingredientDictionary["results"][k][1];
var position = new Vector3(-p[0].AsFloat, p[1].AsFloat, p[2].AsFloat);
var rotation = new Quaternion(r[0].AsFloat, r[1].AsFloat, r[2].AsFloat, r[3].AsFloat);
var mat = MyUtility.quaternion_matrix(rotation);
var euler = MyUtility.euler_from_matrix(mat);
rotation = MyUtility.MayaRotationToUnity(euler);
if (!biomt)
{
// Find centered position
if (!center)
{
position += MyUtility.QuaternionTransform(rotation, centerPosition);
}
SceneManager.Get.AddProteinInstance(path, position, rotation);
instanceCount++;
}
else
{
foreach (var transform in biomtTransforms)
{
var biomteuler = MyUtility.euler_from_matrix(transform);
var rotBiomt = MyUtility.MayaRotationToUnity(biomteuler);
var offset = MyUtility.QuaternionTransform(rotBiomt, centerPosition); //Helper.RotationMatrixToQuaternion(matBiomt), GetCenter());
var posBiomt = new Vector3(-transform.m03, transform.m13, transform.m23) + offset - biomtCenter;
var biomtOffset = MyUtility.RotationMatrixToQuaternion(transform) * centerPosition;
var biomtInstanceRot = rotation * rotBiomt; //Helper.RotationMatrixToQuaternion(transform);
var biomtInstancePos = rotation * posBiomt + position;
SceneManager.Get.AddProteinInstance(path, biomtInstancePos, biomtInstanceRot);
instanceCount++;
}
}
}
SceneManager.Get.AddIngredientProperties(atomSpheres.Count, instanceCount);
Debug.Log("*****");
Debug.Log("Added ingredient: " + path);
//if (isCarbonAlphaOnly) Debug.Log("Alpha-carbons only");
//Debug.Log("Pdb name: " + pdbName + " *** " + "Num atoms: " + atomSet.Count + " *** " + "Num instances: " + instanceCount + " *** " + "Total atom count: " + atomSet.Count * instanceCount);
}
