public static Texture2D GenerateHistogramTexture(VolumeDataset dataset)
{
int numSamples = dataset.GetMaxDataValue() + 1;
int[] values = new int[numSamples];
Color[] cols = new Color[numSamples];
Texture2D texture = new Texture2D(numSamples, 1, TextureFormat.RGBAFloat, false);
int maxFreq = 0;
for (int iData = 0; iData < dataset.data.Length; iData++)
{
values[dataset.data[iData]] += 1;
maxFreq = System.Math.Max(values[dataset.data[iData]], maxFreq);
}
for (int iSample = 0; iSample < numSamples; iSample++)
{
cols[iSample] = new Color(Mathf.Log10((float)values[iSample]) / Mathf.Log10((float)maxFreq), 0.0f, 0.0f, 1.0f);
}
texture.SetPixels(cols);
texture.Apply();
return(texture);
}
private VolumeRenderedObject Import(string dir)
{
if (Directory.Exists(dir))
{
bool recursive = true;
// Read all files
IEnumerable <string> fileCandidates = Directory.EnumerateFiles(dir, "*.*", recursive ? SearchOption.AllDirectories : SearchOption.TopDirectoryOnly)
.Where(p => p.EndsWith(".dcm", StringComparison.InvariantCultureIgnoreCase) || p.EndsWith(".dicom", StringComparison.InvariantCultureIgnoreCase) || p.EndsWith(".dicm", StringComparison.InvariantCultureIgnoreCase));
if (fileCandidates.Any())
{
DICOMImporter importer = new DICOMImporter(fileCandidates, Path.GetFileName(dir));
VolumeDataset dataset = importer.Import();
if (dataset != null)
{
VolumeRenderedObject vo = VolumeObjectFactory.CreateObject(dataset);
vo.transform.Rotate(new Vector3(180, 0, 0));
return(vo);
}
}
else
{
Debug.LogError("Could not find any DICOM files to import.");
}
}
return(null);
}
private void ImportDataset()
{
DatasetImporterBase importer = null;
switch (datasetType)
{
case DatasetType.Raw:
{
importer = new RawDatasetImporter(fileToImport, dimX, dimY, dimZ, DataContentFormat.Int16, 6);
break;
}
}
VolumeDataset dataset = null;
if (importer != null)
{
dataset = importer.Import();
}
if (dataset != null)
{
VolumeRenderedObject obj = VolumeObjectFactory.CreateObject(dataset);
}
else
{
Debug.LogError("Failed to import datset");
}
this.Close();
}
public override VolumeDataset Import()
{
VolumeDataset dataset = new VolumeDataset();
dataset.dimX = dimX;
dataset.dimY = dimY;
dataset.dimZ = dimZ;
FileStream fs = new FileStream(filePath, FileMode.Open);
BinaryReader reader = new BinaryReader(fs);
if (skipBytes > 0)
{
reader.ReadBytes(skipBytes);
}
int uDimension = dimX * dimY * dimZ;
dataset.data = new int[uDimension];
int val = 0;
for (int i = 0; i < uDimension; i++)
{
switch (contentFormat)
{
case DataContentFormat.Int8:
val = (int)reader.ReadByte();
break;
case DataContentFormat.Int16:
val = (int)reader.ReadInt16();
break;
case DataContentFormat.Int32:
val = (int)reader.ReadInt32();
break;
case DataContentFormat.Uint8:
val = (int)reader.ReadByte();
break;
case DataContentFormat.Uint16:
val = (int)reader.ReadUInt16();
break;
case DataContentFormat.Uint32:
val = (int)reader.ReadUInt32();
break;
}
dataset.data[i] = val;
}
Debug.Log("Loaded dataset in range: " + dataset.GetMinDataValue() + " - " + dataset.GetMaxDataValue());
return(dataset);
}
public async Task <IActionResult> ImportFromOfficial()
{
List <VolumeData> newVolumeDatas = await VolumeDataset.GetAllVolumes();
newVolumeDatas.ForEach(data =>
{
_context.VolumeData.Add(data);
_context.SaveChanges();
});
return(RedirectToAction(nameof(Index)));
}
public static Texture2D Generate2DHistogramTexture(VolumeDataset dataset)
{
int numSamples = dataset.GetMaxDataValue() + 1;
int numGradientSamples = 256;
Color[] cols = new Color[numSamples * numGradientSamples];
Texture2D texture = new Texture2D(numSamples, numGradientSamples, TextureFormat.RGBAFloat, false);
for (int iCol = 0; iCol < cols.Length; iCol++)
{
cols[iCol] = new Color(0.0f, 0.0f, 0.0f, 0.0f);
}
int maxRange = dataset.GetMaxDataValue() - dataset.GetMinDataValue();
const float maxNormalisedMagnitude = 1.75f; // sqrt(1^2 + 1^2 + 1^2) = swrt(3) = a bit less than 1.75
for (int x = 1; x < dataset.dimX - 1; x++)
{
for (int y = 1; y < dataset.dimY - 1; y++)
{
for (int z = 1; z < dataset.dimZ - 1; z++)
{
int iData = x + y * dataset.dimX + z * (dataset.dimX * dataset.dimY);
int density = dataset.data[iData];
int x1 = dataset.data[(x + 1) + y * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int x2 = dataset.data[(x - 1) + y * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int y1 = dataset.data[x + (y + 1) * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int y2 = dataset.data[x + (y - 1) * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int z1 = dataset.data[x + y * dataset.dimX + (z + 1) * (dataset.dimX * dataset.dimY)];
int z2 = dataset.data[x + y * dataset.dimX + (z - 1) * (dataset.dimX * dataset.dimY)];
Vector3 grad = new Vector3((x2 - x1) / (float)maxRange, (y2 - y1) / (float)maxRange, (z2 - z1) / (float)maxRange);
cols[density + (int)(grad.magnitude * numGradientSamples / maxNormalisedMagnitude) * numSamples] = Color.white;
}
}
}
texture.SetPixels(cols);
texture.Apply();
return(texture);
}
private void ImportDataset()
{
DatasetImporterBase importer = null;
switch (datasetType)
{
case DatasetType.Raw:
{
importer = new RawDatasetImporter(fileToImport, dimX, dimY, dimZ, DataContentFormat.Int16, 6);
break;
}
case DatasetType.DICOM:
{
throw new System.NotImplementedException("TODO: implement support for DICOM files");
}
}
VolumeDataset dataset = null;
if (importer != null)
{
dataset = importer.Import();
}
if (dataset != null)
{
VolumeRenderedObject obj = VolumeObjectFactory.CreateObject(dataset);
}
else
{
Debug.LogError("Failed to import datset");
}
this.Close();
}
public VolumeDataset CreateDataset()
{
VolumeDataset dataset = new VolumeDataset();
dataset.dimX = dimX;
dataset.dimY = dimY;
dataset.dimZ = dimZ;
FileStream fs = new FileStream(System.IO.Path.Combine(Application.streamingAssetsPath, filePath), FileMode.Open);
BinaryReader reader = new BinaryReader(fs);
if (skipBytes > 0)
{
reader.ReadBytes(skipBytes);
}
int uDimension = dimX * dimY * dimZ;
dataset.texture = new Texture3D(dimX, dimY, dimZ, TextureFormat.RGBAFloat, false);
dataset.texture.wrapMode = TextureWrapMode.Clamp;
dataset.data = new int[uDimension];
int minVal = int.MaxValue;
int maxVal = int.MinValue;
int val = 0;
for (int i = 0; i < uDimension; i++)
{
switch (contentFormat)
{
case DataContentFormat.Int8:
val = (int)reader.ReadByte();
break;
case DataContentFormat.Int16:
val = (int)reader.ReadInt16();
break;
case DataContentFormat.Int32:
val = (int)reader.ReadInt32();
break;
case DataContentFormat.Uint8:
val = (int)reader.ReadByte();
break;
case DataContentFormat.Uint16:
val = (int)reader.ReadUInt16();
break;
case DataContentFormat.Uint32:
val = (int)reader.ReadUInt32();
break;
}
minVal = Mathf.Min(minVal, val);
maxVal = Mathf.Max(maxVal, val);
dataset.data[i] = val;
}
Debug.Log("Loaded dataset in range: " + minVal + " - " + maxVal);
Debug.Log(minVal + " - " + maxVal);
dataset.minDataValue = minVal;
dataset.maxDataValue = maxVal;
return(dataset);
}
public void Import()
{
dataset = CreateDataset();
Program.instance.volumeRenderedObject = CreateVolumeRenderedObject(dataset);
}
public VolumeRenderedObject CreateVolumeRenderedObject(VolumeDataset dataset)
{
GameObject go = GameObject.Instantiate(volumeObjectPrefab) as GameObject;
go.transform.SetParent(Program.instance.operationOverlay.transform);
go.transform.localPosition = new Vector3(-0.0083f, 0.0426f, 0.0083f);
go.transform.rotation = Quaternion.Euler(-20f, 180f, 180f);
VolumeRenderedObject volObj = go.GetComponent <VolumeRenderedObject>();
MeshRenderer meshRenderer = go.GetComponent <MeshRenderer>();
volObj.dataset = dataset;
int dimX = dataset.dimX;
int dimY = dataset.dimY;
int dimZ = dataset.dimZ;
int maxRange = dataset.maxDataValue - dataset.minDataValue;
Color[] cols = new Color[dataset.data.Length];
for (int x = 0; x < dataset.dimX; x++)
{
for (int y = 0; y < dataset.dimY; y++)
{
for (int z = 0; z < dataset.dimZ; z++)
{
int iData = x + y * dimX + z * (dimX * dimY);
int x1 = dataset.data[Mathf.Min(x + 1, dimX - 1) + y * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int x2 = dataset.data[Mathf.Max(x - 1, 0) + y * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int y1 = dataset.data[x + Mathf.Min(y + 1, dimY - 1) * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int y2 = dataset.data[x + Mathf.Max(y - 1, 0) * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int z1 = dataset.data[x + y * dataset.dimX + Mathf.Min(z + 1, dimZ - 1) * (dataset.dimX * dataset.dimY)];
int z2 = dataset.data[x + y * dataset.dimX + Mathf.Max(z - 1, 0) * (dataset.dimX * dataset.dimY)];
Vector3 grad = new Vector3((x2 - x1) / (float)maxRange, (y2 - y1) / (float)maxRange, (z2 - z1) / (float)maxRange);
cols[iData] = new Color(grad.x, grad.y, grad.z, (float)dataset.data[iData] / (float)dataset.maxDataValue);
}
}
}
dataset.texture.SetPixels(cols);
dataset.texture.Apply();
Texture3D tex = dataset.texture;
const int noiseDimX = 512;
const int noiseDimY = 512;
Texture2D noiseTexture = NoiseTextureGenerator.GenerateNoiseTexture(noiseDimX, noiseDimY);
TransferFunction tf = Program.instance.transferFunctionManager.CreateTransferFunction();
Texture2D tfTexture = tf.GetTexture();
volObj.transferFunction = tf;
tf.histogramTexture = HistogramTextureGenerator.GenerateHistogramTexture(dataset);
TransferFunction2D tf2D = new TransferFunction2D();
tf2D.AddBox(0.05f, 0.1f, 0.8f, 0.7f, Color.white, 0.4f);
volObj.transferFunction2D = tf2D;
meshRenderer.sharedMaterial.SetTexture("_DataTex", tex);
meshRenderer.sharedMaterial.SetTexture("_NoiseTex", noiseTexture);
meshRenderer.sharedMaterial.SetTexture("_TFTex", tfTexture);
meshRenderer.sharedMaterial.EnableKeyword("MODE_DVR");
meshRenderer.sharedMaterial.DisableKeyword("MODE_MIP");
meshRenderer.sharedMaterial.DisableKeyword("MODE_SURF");
return(volObj);
}
public static VolumeRenderedObject CreateObject(VolumeDataset dataset)
{
GameObject obj = GameObject.Instantiate((GameObject)Resources.Load("VolumeRenderedObject"));
VolumeRenderedObject volObj = obj.GetComponent <VolumeRenderedObject>();
MeshRenderer meshRenderer = obj.GetComponent <MeshRenderer>();
volObj.dataset = dataset;
int dimX = dataset.dimX;
int dimY = dataset.dimY;
int dimZ = dataset.dimZ;
int maxRange = dataset.maxDataValue - dataset.minDataValue;
Color[] cols = new Color[dataset.data.Length];
for (int x = 0; x < dataset.dimX; x++)
{
for (int y = 0; y < dataset.dimY; y++)
{
for (int z = 0; z < dataset.dimZ; z++)
{
int iData = x + y * dimX + z * (dimX * dimY);
int x1 = dataset.data[Math.Min(x + 1, dimX - 1) + y * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int x2 = dataset.data[Math.Max(x - 1, 0) + y * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int y1 = dataset.data[x + Math.Min(y + 1, dimY - 1) * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int y2 = dataset.data[x + Math.Max(y - 1, 0) * dataset.dimX + z * (dataset.dimX * dataset.dimY)];
int z1 = dataset.data[x + y * dataset.dimX + Math.Min(z + 1, dimZ - 1) * (dataset.dimX * dataset.dimY)];
int z2 = dataset.data[x + y * dataset.dimX + Math.Max(z - 1, 0) * (dataset.dimX * dataset.dimY)];
Vector3 grad = new Vector3((x2 - x1) / (float)maxRange, (y2 - y1) / (float)maxRange, (z2 - z1) / (float)maxRange);
cols[iData] = new Color(grad.x, grad.y, grad.z, (float)dataset.data[iData] / (float)dataset.maxDataValue);
}
}
}
dataset.texture.SetPixels(cols);
dataset.texture.Apply();
Texture3D tex = dataset.texture;
const int noiseDimX = 512;
const int noiseDimY = 512;
Texture2D noiseTexture = NoiseTextureGenerator.GenerateNoiseTexture(noiseDimX, noiseDimY);
TransferFunction tf = new TransferFunction();
tf.AddControlPoint(new TFColourControlPoint(0.0f, new Color(0.11f, 0.14f, 0.13f, 1.0f)));
tf.AddControlPoint(new TFColourControlPoint(0.2415f, new Color(0.469f, 0.354f, 0.223f, 1.0f)));
tf.AddControlPoint(new TFColourControlPoint(0.3253f, new Color(1.0f, 1.0f, 1.0f, 1.0f)));
tf.AddControlPoint(new TFAlphaControlPoint(0.0f, 0.0f));
tf.AddControlPoint(new TFAlphaControlPoint(0.1787f, 0.0f));
tf.AddControlPoint(new TFAlphaControlPoint(0.2f, 0.024f));
tf.AddControlPoint(new TFAlphaControlPoint(0.28f, 0.03f));
tf.AddControlPoint(new TFAlphaControlPoint(0.4f, 0.546f));
tf.AddControlPoint(new TFAlphaControlPoint(0.547f, 0.5266f));
tf.GenerateTexture();
Texture2D tfTexture = tf.GetTexture();
volObj.transferFunction = tf;
tf.histogramTexture = HistogramTextureGenerator.GenerateHistogramTexture(dataset);
TransferFunction2D tf2D = new TransferFunction2D();
tf2D.AddBox(0.05f, 0.1f, 0.8f, 0.7f, Color.white, 0.4f);
volObj.transferFunction2D = tf2D;
meshRenderer.sharedMaterial.SetTexture("_DataTex", tex);
meshRenderer.sharedMaterial.SetTexture("_NoiseTex", noiseTexture);
meshRenderer.sharedMaterial.SetTexture("_TFTex", tfTexture);
meshRenderer.sharedMaterial.EnableKeyword("MODE_DVR");
meshRenderer.sharedMaterial.DisableKeyword("MODE_MIP");
meshRenderer.sharedMaterial.DisableKeyword("MODE_SURF");
return(volObj);
}
