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();
}
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);
}
public override void OnInspectorGUI()
{
VolumeRenderedObject myTarget = (VolumeRenderedObject)target;
RenderMode oldRenderMode = myTarget.GetRemderMode();
RenderMode newRenderMode = (RenderMode)EditorGUILayout.EnumPopup("Render mode", oldRenderMode);
if (newRenderMode != oldRenderMode)
{
myTarget.SetRenderMode(newRenderMode);
}
}
private void UpdateBrain(VolumeRenderedObject vro)
{
if (vro != null)
{
/* update renderer and bounds */
// volume data is stored in child gameobject
rend = vro.transform.GetChild(0).GetComponent <Renderer>();
Vector3 center = rend.bounds.center;
float radius = rend.bounds.extents.magnitude;
float x = rend.bounds.extents.x;
float y = rend.bounds.extents.y;
float z = rend.bounds.extents.z;
// update position so that the world origin point is at the corner of brain
vro.transform.position = new Vector3(x, y, z);
}
}
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();
}
private void OnGUI()
{
SlicingPlane[] spawnedPlanes = FindObjectsOfType <SlicingPlane>();
if (spawnedPlanes.Length > 0)
{
selectedPlaneIndex = selectedPlaneIndex % spawnedPlanes.Length;
}
float bgWidth = Mathf.Min(this.position.width - 20.0f, (this.position.height - 50.0f) * 2.0f);
Rect bgRect = new Rect(0.0f, 0.0f, bgWidth, bgWidth * 0.5f);
if (selectedPlaneIndex != -1 && spawnedPlanes.Length > 0)
{
SlicingPlane planeObj = spawnedPlanes[System.Math.Min(selectedPlaneIndex, spawnedPlanes.Length - 1)];
// Draw the slice view
Material mat = planeObj.GetComponent <MeshRenderer>().sharedMaterial;
Graphics.DrawTexture(bgRect, mat.GetTexture("_DataTex"), mat);
// Handle mouse click inside slice view (activates moving the plane with mouse)
if (Event.current.type == EventType.MouseDown && Event.current.button == 0 && bgRect.Contains(new Vector2(Event.current.mousePosition.x, Event.current.mousePosition.y)))
{
handleMouseMovement = true;
prevMousePos = Event.current.mousePosition;
}
// Handle mouse movement (move the plane)
if (handleMouseMovement)
{
Vector2 mouseOffset = (Event.current.mousePosition - prevMousePos) / new Vector2(bgRect.width, bgRect.height);
if (Mathf.Abs(mouseOffset.y) > 0.00001f)
{
planeObj.transform.Translate(Vector3.up * mouseOffset.y);
prevMousePos = Event.current.mousePosition;
}
}
}
if (Event.current.type == EventType.MouseUp)
{
handleMouseMovement = false;
}
// Show buttons for changing the active plane
if (spawnedPlanes.Length > 0)
{
if (GUI.Button(new Rect(0.0f, bgRect.y + bgRect.height + 20.0f, 100.0f, 30.0f), "previous\nplane"))
{
selectedPlaneIndex = (selectedPlaneIndex - 1) % spawnedPlanes.Length;
Selection.activeGameObject = spawnedPlanes[selectedPlaneIndex].gameObject;
}
if (GUI.Button(new Rect(120.0f, bgRect.y + bgRect.height + 20.0f, 100.0f, 30.0f), "next\nplane"))
{
selectedPlaneIndex = (selectedPlaneIndex + 1) % spawnedPlanes.Length;
Selection.activeGameObject = spawnedPlanes[selectedPlaneIndex].gameObject;
}
}
// Show button for adding new plane
if (GUI.Button(new Rect(240.0f, bgRect.y + bgRect.height + 20.0f, 100.0f, 30.0f), "add\nplane"))
{
VolumeRenderedObject volRend = FindObjectOfType <VolumeRenderedObject>();
if (volRend != null)
{
selectedPlaneIndex = spawnedPlanes.Length;
volRend.CreateSlicingPlane();
}
}
// Show hint
if (spawnedPlanes.Length > 0)
{
GUI.Label(new Rect(0.0f, bgRect.y + bgRect.height + 60.0f, 450.0f, 30.0f), "Move plane by left clicking in the above view and dragging the mouse,\n or simply move it in the object hierarchy.");
}
}
private void OnGUI()
{
VolumeRenderedObject volRend = FindObjectOfType <VolumeRenderedObject>();
if (volRend == null)
{
return;
}
tf = volRend.transferFunction;
Color oldColour = GUI.color;
float bgWidth = Mathf.Min(this.position.width - 20.0f, (this.position.height - 50.0f) * 2.0f);
Rect bgRect = new Rect(0.0f, 0.0f, bgWidth, bgWidth * 0.5f);
tf.GenerateTexture();
histogramMaterial.SetTexture("_TFTex", tf.GetTexture());
histogramMaterial.SetTexture("_HistTex", tf.histogramTexture);
Graphics.DrawTexture(bgRect, tf.GetTexture(), histogramMaterial);
Texture2D tfTexture = tf.GetTexture();
colorBarMaterial.SetTexture("_TFTex", tf.GetTexture());
Graphics.DrawTexture(new Rect(bgRect.x, bgRect.y + bgRect.height + 20, bgRect.width, 20.0f), tfTexture, colorBarMaterial);
// Colour control points
for (int iCol = 0; iCol < tf.colourControlPoints.Count; iCol++)
{
ControlPointColor colPoint = tf.colourControlPoints[iCol];
Rect ctrlBox = new Rect(bgRect.x + bgRect.width * colPoint.dataValue, bgRect.y + bgRect.height + 20, 10, 20);
GUI.color = Color.red;
GUI.skin.box.fontSize = 8;
GUI.Box(ctrlBox, "|");
if (Event.current.type == EventType.MouseDown && Event.current.button == 0 && ctrlBox.Contains(new Vector2(Event.current.mousePosition.x, Event.current.mousePosition.y)))
{
movingColPointIndex = iCol;
selectedColPointIndex = iCol;
}
else if (movingColPointIndex == iCol)
{
colPoint.dataValue = Mathf.Clamp((Event.current.mousePosition.x - bgRect.x) / bgRect.width, 0.0f, 1.0f);
}
tf.colourControlPoints[iCol] = colPoint;
}
// Alpha control points
for (int iAlpha = 0; iAlpha < tf.alphaControlPoints.Count; iAlpha++)
{
ControlPointAlpha alphaPoint = tf.alphaControlPoints[iAlpha];
Rect ctrlBox = new Rect(bgRect.x + bgRect.width * alphaPoint.dataValue, bgRect.y + (1.0f - alphaPoint.alphaValue) * bgRect.height, 10, 10);
GUI.color = oldColour;
GUI.skin.box.fontSize = 6;
GUI.Box(ctrlBox, "a");
if (Event.current.type == EventType.MouseDown && Event.current.button == 0 && ctrlBox.Contains(new Vector2(Event.current.mousePosition.x, Event.current.mousePosition.y)))
{
movingAlphaPointIndex = iAlpha;
}
else if (movingAlphaPointIndex == iAlpha)
{
alphaPoint.dataValue = Mathf.Clamp((Event.current.mousePosition.x - bgRect.x) / bgRect.width, 0.0f, 1.0f);
alphaPoint.alphaValue = Mathf.Clamp(1.0f - (Event.current.mousePosition.y - bgRect.y) / bgRect.height, 0.0f, 1.0f);
}
tf.alphaControlPoints[iAlpha] = alphaPoint;
}
if (Event.current.type == EventType.MouseUp)
{
movingColPointIndex = -1;
movingAlphaPointIndex = -1;
}
if (Event.current.type == EventType.MouseDown && Event.current.button == 1)
{
if (bgRect.Contains(new Vector2(Event.current.mousePosition.x, Event.current.mousePosition.y)))
{
tf.alphaControlPoints.Add(
tf.CreateControlPointAlpha(
Mathf.Clamp((Event.current.mousePosition.x - bgRect.x) / bgRect.width, 0.0f, 1.0f),
Mathf.Clamp(1.0f - (Event.current.mousePosition.y - bgRect.y) / bgRect.height, 0.0f, 1.0f)
));
}
else
{
tf.colourControlPoints.Add(tf.CreateControlPointColor(Mathf.Clamp((Event.current.mousePosition.x - bgRect.x) / bgRect.width, 0.0f, 1.0f), Random.ColorHSV()));
}
selectedColPointIndex = -1;
}
if (selectedColPointIndex != -1)
{
ControlPointColor colPoint = tf.colourControlPoints[selectedColPointIndex];
colPoint.colourValue = EditorGUI.ColorField(new Rect(bgRect.x, bgRect.y + bgRect.height + 50, 100.0f, 40.0f), colPoint.colourValue);
tf.colourControlPoints[selectedColPointIndex] = colPoint;
}
// TEST!!! TODO
volRend.GetComponent <MeshRenderer>().sharedMaterial.SetTexture("_TFTex", tfTexture);
volRend.GetComponent <MeshRenderer>().sharedMaterial.DisableKeyword("TF2D_ON");
GUI.color = oldColour;
}
public void OnSegmentationButtonClicked()
{
brainSeg = Import(completePath + "_seg");
brainSeg.transform.GetChild(0).GetComponent <Renderer>().material = matBrainSeg;
UpdateBrain(brainSeg);
}
public void OnImportButtonClicked()
{
brain = Import(completePath + "_flair");
UpdateBrain(brain);
}
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);
}
private void OnGUI()
{
VolumeRenderedObject volRend = FindObjectOfType <VolumeRenderedObject>();
if (volRend == null)
{
return;
}
if (hist2DTex == null)
{
hist2DTex = HistogramTextureGenerator.Generate2DHistogramTexture(volRend.dataset);
}
TransferFunction2D tf2d = volRend.transferFunction2D;
// Calculate GUI width (minimum of window width and window height * 2)
float bgWidth = Mathf.Min(this.position.width - 20.0f, (this.position.height - 250.0f) * 2.0f);
// Draw the histogram
Rect histRect = new Rect(0.0f, 0.0f, bgWidth, bgWidth * 0.5f);
Graphics.DrawTexture(histRect, hist2DTex);
// Draw the TF texture (showing the rectangles)
tfGUIMat.SetTexture("_TFTex", tf2d.GetTexture());
Graphics.DrawTexture(histRect, tf2d.GetTexture(), tfGUIMat);
// Handle mouse click in box
for (int iBox = 0; iBox < tf2d.boxes.Count; iBox++)
{
TransferFunction2D.TF2DBox box = tf2d.boxes[iBox];
Rect boxRect = new Rect(histRect.x + box.rect.x * histRect.width, histRect.y + (1.0f - box.rect.height - box.rect.y) * histRect.height, box.rect.width * histRect.width, box.rect.height * histRect.height);
if (Event.current.type == EventType.MouseDown && Event.current.button == 0 && boxRect.Contains(new Vector2(Event.current.mousePosition.x, Event.current.mousePosition.y)))
{
selectedBoxIndex = iBox;
}
}
float startX = histRect.x;
float startY = histRect.y + histRect.height + 10;
// Show GUI for editing selected rectangle
if (selectedBoxIndex != -1)
{
EditorGUI.BeginChangeCheck();
TransferFunction2D.TF2DBox box = tf2d.boxes[selectedBoxIndex];
float oldX = box.rect.x;
float oldY = box.rect.y;
box.rect.x = EditorGUI.Slider(new Rect(startX, startY, 200.0f, 20.0f), "x", box.rect.x, 0.0f, 0.99f);
box.rect.width = EditorGUI.Slider(new Rect(startX + 220.0f, startY, 200.0f, 20.0f), "width", oldX + box.rect.width, box.rect.x + 0.01f, 1.0f) - box.rect.x;
box.rect.y = EditorGUI.Slider(new Rect(startX, startY + 50, 200.0f, 20.0f), "y", box.rect.y, 0.0f, 1.0f);
box.rect.height = EditorGUI.Slider(new Rect(startX + 220.0f, startY + 50, 200.0f, 20.0f), "height", oldY + box.rect.height, box.rect.y + 0.01f, 1.0f) - box.rect.y;
box.colour = EditorGUI.ColorField(new Rect(startX + 450.0f, startY + 10, 100.0f, 20.0f), box.colour);
box.minAlpha = EditorGUI.Slider(new Rect(startX + 450.0f, startY + 30, 200.0f, 20.0f), "min alpha", box.minAlpha, 0.0f, 1.0f);
box.alpha = EditorGUI.Slider(new Rect(startX + 450.0f, startY + 60, 200.0f, 20.0f), "max alpha", box.alpha, 0.0f, 1.0f);
tf2d.boxes[selectedBoxIndex] = box;
needsRegenTexture |= EditorGUI.EndChangeCheck();
}
else
{
EditorGUI.LabelField(new Rect(startX, startY, this.position.width - startX, 50.0f), "Select a rectangle in the above view, or add a new one.");
}
// Add new rectangle
if (GUI.Button(new Rect(startX, startY + 100, 150.0f, 40.0f), "Add rectangle"))
{
tf2d.AddBox(0.1f, 0.1f, 0.8f, 0.8f, Color.white, 0.5f);
needsRegenTexture = true;
}
// Remove selected shape
if (selectedBoxIndex != -1)
{
if (GUI.Button(new Rect(startX, startY + 150, 150.0f, 40.0f), "Remove selected shape"))
{
tf2d.boxes.RemoveAt(selectedBoxIndex);
needsRegenTexture = true;
}
}
// TODO: regenerate on add/remove/modify (and do it async)
if (needsRegenTexture)
{
tf2d.GenerateTexture();
needsRegenTexture = false;
}
volRend.GetComponent <MeshRenderer>().sharedMaterial.SetTexture("_TFTex", tf2d.GetTexture());
volRend.GetComponent <MeshRenderer>().sharedMaterial.EnableKeyword("TF2D_ON");
return;
}
