Merge pull request #27 from mlavik1/issue24-dicomfixes

Issue24: Misc dicomfixes

Assets/3rdparty/openDicom/Encoding/DT.cs

@@ -83,15 +83,15 @@ namespace openDicom.Encoding
                         }
                         catch (Exception e)
                         {
-                            throw new EncodingException(
-                                "Date time format is invalid.", Tag, 
-                                Name + "/item", item);
+                            UnityEngine.Debug.LogWarning($"Date time format is invalid. tag: {Tag}, name: {Name}");
+                            dateTime[i] = System.DateTime.Now;
                         }
                     }
                     else
-                        throw new EncodingException(
-                            "Date time format is invalid.", Tag, Name + "/item",
-                            item);
+                    {
+                        UnityEngine.Debug.LogWarning($"Date time format is invalid. tag: {Tag}, name: {Name}");
+                        dateTime[i] = System.DateTime.Now;
+                    }
                 }
             }
             return dateTime;
@@ -123,30 +123,30 @@ namespace openDicom.Encoding
                         string second = "0";
                         if (item.Length > 12) second = item.Substring(12, 2);
                         string millisecond = "0";
-                        if (item.Length > 14) 
+                        if (item.Length > 14)
                             millisecond = item.Substring(14, 6);
                         string timeZone = "+0";
-                        if (item.Length > 20) 
+                        if (item.Length > 20)
                             timeZone = item.Substring(20, 5);
                         // TODO: What to do with the time zone?
                         try
                         {
-                            dateTime[i] = new System.DateTime(int.Parse(year), 
+                            dateTime[i] = new System.DateTime(int.Parse(year),
                                 int.Parse(month), int.Parse(day), int.Parse(hour),
                                 int.Parse(minute), int.Parse(second),
                                 int.Parse(millisecond));
                         }
                         catch (Exception e)
                         {
-                            throw new EncodingException(
-                                "Date time format is invalid.", Tag, 
-                                Name + "/item", item);
+                            UnityEngine.Debug.LogWarning($"Date time format is invalid. tag: {Tag}, name: {Name}");
+                            dateTime[i] = System.DateTime.Now;
                         }
                     }
                     else
-                        throw new EncodingException(
-                            "Date time format is invalid.", Tag, Name + "/item",
-                            item);
+                    {
+                        UnityEngine.Debug.LogWarning($"Date time format is invalid. tag: {Tag}, name: {Name}");
+                        dateTime[i] = System.DateTime.Now;
+                    }
                 }
             }
             return dateTime;

Assets/Scripts/Importing/DICOMImporter.cs

@@ -24,6 +24,7 @@ namespace UnityVolumeRendering
             public float location = 0;
             public float intercept = 0.0f;
             public float slope = 1.0f;
+            public float pixelSpacing = 0.0f;
         }
 
         private string diroctoryPath;
@@ -108,6 +109,13 @@ namespace UnityVolumeRendering
                 }
             }
 
+            if(files[0].pixelSpacing > 0.0f)
+            {
+                dataset.scaleX = files[0].pixelSpacing * dataset.dimX;
+                dataset.scaleY = files[0].pixelSpacing * dataset.dimY;
+                dataset.scaleZ = Mathf.Abs(files[files.Count - 1].location - files[0].location);
+            }
+
             return dataset;
         }
 
@@ -149,6 +157,13 @@ namespace UnityVolumeRendering
                 }
                 else
                     Debug.LogWarning($"The file {filePath} is missing the intercept element. As a result, the default transfer function might not look good.");
+                // Read pixel spacing
+                Tag pixelSpacingTag = new Tag("(0028,0030)");
+                if (file.DataSet.Contains(pixelSpacingTag))
+                {
+                    DataElement elemPixelSpacing = file.DataSet[pixelSpacingTag];
+                    slice.pixelSpacing = (float)Convert.ToDouble(elemPixelSpacing.Value[0]);
+                }
 
                 return slice;
             }

Assets/Scripts/VolumeData/VolumeDataset.cs

@@ -10,6 +10,8 @@ namespace UnityVolumeRendering
         public int[] data = null;
         [SerializeField]
         public int dimX, dimY, dimZ;
+        [SerializeField]
+        public float scaleX = 0.0f, scaleY = 0.0f, scaleZ = 0.0f;
 
         [SerializeField]
         public string datasetName;

Assets/Scripts/VolumeObject/SlicingPlane.cs

@@ -15,7 +15,7 @@ namespace UnityVolumeRendering
         private void Update()
         {
             meshRenderer.sharedMaterial.SetMatrix("_parentInverseMat", transform.parent.worldToLocalMatrix);
-            meshRenderer.sharedMaterial.SetMatrix("_planeMat", Matrix4x4.TRS(transform.position, transform.rotation, Vector3.one)); // TODO: allow changing scale
+            meshRenderer.sharedMaterial.SetMatrix("_planeMat", Matrix4x4.TRS(transform.position, transform.rotation, transform.parent.lossyScale)); // TODO: allow changing scale
         }
     }
 }

Assets/Scripts/VolumeObject/VolumeObjectFactory.cs

@@ -42,6 +42,12 @@ namespace UnityVolumeRendering
             meshRenderer.sharedMaterial.DisableKeyword("MODE_MIP");
             meshRenderer.sharedMaterial.DisableKeyword("MODE_SURF");
 
+            if(dataset.scaleX != 0.0f && dataset.scaleY != 0.0f && dataset.scaleZ != 0.0f)
+            {
+                float maxScale = Mathf.Max(dataset.scaleX, dataset.scaleY, dataset.scaleZ);
+                volObj.transform.localScale = new Vector3(dataset.scaleX / maxScale, dataset.scaleY / maxScale, dataset.scaleZ / maxScale);
+            }
+
             return volObj;
         }
 

Assets/Scripts/VolumeObject/VolumeRenderedObject.cs

@@ -29,13 +29,14 @@ namespace UnityVolumeRendering
             sliceRenderingPlane.transform.parent = transform;
             sliceRenderingPlane.transform.localPosition = Vector3.zero;
             sliceRenderingPlane.transform.localRotation = Quaternion.identity;
+            sliceRenderingPlane.transform.localScale = Vector3.one * 0.1f; // TODO: Change the plane mesh instead and use Vector3.one
             MeshRenderer sliceMeshRend = sliceRenderingPlane.GetComponent<MeshRenderer>();
             sliceMeshRend.material = new Material(sliceMeshRend.sharedMaterial);
             Material sliceMat = sliceRenderingPlane.GetComponent<MeshRenderer>().sharedMaterial;
             sliceMat.SetTexture("_DataTex", dataset.GetDataTexture());
             sliceMat.SetTexture("_TFTex", transferFunction.GetTexture());
             sliceMat.SetMatrix("_parentInverseMat", transform.worldToLocalMatrix);
-            sliceMat.SetMatrix("_planeMat", Matrix4x4.TRS(sliceRenderingPlane.transform.position, sliceRenderingPlane.transform.rotation, Vector3.one)); // TODO: allow changing scale
+            sliceMat.SetMatrix("_planeMat", Matrix4x4.TRS(sliceRenderingPlane.transform.position, sliceRenderingPlane.transform.rotation, transform.lossyScale)); // TODO: allow changing scale
 
             return sliceRenderingPlane.GetComponent<SlicingPlane>();
         }

Assets/Shaders/SliceRenderingShader.shader

@@ -36,16 +36,18 @@ Shader "VolumeRendering/SliceRenderingShader"
 
             sampler3D _DataTex;
             sampler2D _TFTex;
+            // Parent's inverse transform (used to convert from world space to volume space)
             uniform float4x4 _parentInverseMat;
+            // Plane transform
             uniform float4x4 _planeMat;
 
             v2f vert (appdata v)
             {
                 v2f o;
-                float3 vert = float3(-v.uv.x, 0.0f, -v.uv.y) + float3(0.5f, 0.0f, 0.5f);
-                vert = mul(_planeMat, float4(vert, 1.0f));
-                //o.vertex = mul(UNITY_MATRIX_VP, float4(vert, 1.0f));
-                o.vertex = UnityObjectToClipPos(v.vertex);;
+                o.vertex = UnityObjectToClipPos(v.vertex);
+                // Calculate plane vertex world position.
+                float3 vert = mul(_planeMat, float4(0.5f -v.uv.x, 0.0f, 0.5f -v.uv.y, 1.0f));
+                // Convert from world space to volume space.
                 o.relVert = mul(_parentInverseMat, float4(vert, 1.0f));
                 o.uv = v.uv;
                 return o;
@@ -53,12 +55,21 @@ Shader "VolumeRendering/SliceRenderingShader"
             
             fixed4 frag (v2f i) : SV_Target
             {
-                float3 dataCoord = i.relVert +float3(0.5f, 0.5f, 0.5f);
-                float dataVal = tex3D(_DataTex, dataCoord);
-                float4 col = tex2D(_TFTex, float2(dataVal, 0.0f));
-                col.a = 1.0f;
-
-                return col;
+                float3 dataCoord = i.relVert + float3(0.5f, 0.5f, 0.5f);
+                // If the current fragment is outside the volume, simply colour it black.
+                // Note: Unity does not seem to have support for clamping texture coordinates to a border value, so we have to do this manually
+                if (dataCoord.x > 1.0f || dataCoord.y > 1.0f || dataCoord.z > 1.0f || dataCoord.x < 0.0f || dataCoord.y < 0.0f || dataCoord.z < 0.0f)
+                {
+                   return float4(0.0f, 0.0f, 0.0f, 1.0f);
+                }
+                else
+                {
+                   // Sample the volume texture.
+                   float dataVal = tex3D(_DataTex, dataCoord);
+                   float4 col = tex2D(_TFTex, float2(dataVal, 0.0f));
+                   col.a = 1.0f;
+                   return col;
+                }
             }
             ENDCG
         }