Merge branch 'release/4.1.0'

Assets/Scripts/HBP/Core/Data/Loaded/DynamicData.cs

@@ -1,6 +1,7 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using UnityEngine;
 
 namespace HBP.Core.Data
 {
@@ -76,8 +77,16 @@ public DynamicData(DataInfo dataInfo) : this()
             List<DLL.EEG.Electrode> channels = file.Electrodes;
             foreach (var channel in channels)
             {
-                ValuesByChannel.Add(channel.Label, channel.Data);
-                UnitByChannel.Add(channel.Label, channel.Unit);
+                try
+                {
+                    ValuesByChannel.Add(channel.Label, channel.Data);
+                    UnitByChannel.Add(channel.Label, channel.Unit);
+                }
+                catch (ArgumentException e)
+                {
+                    Debug.LogException(e);
+                    throw new Exception(string.Format("The data file contains multiple {0} channels.", channel.Label));
+                }
             }
             Frequency = file.SamplingFrequency;
             m_OccurencesByCode = new Dictionary<int, List<EventOccurence>>();

Assets/Scripts/HBP/Core/Data/Patient/BaseMesh.cs

@@ -147,11 +147,12 @@ public static BaseMesh[] LoadFromDirectory(string path)
         {
             List<BaseMesh> meshes = new List<BaseMesh>();
             DirectoryInfo parent = new DirectoryInfo(path);
-            DirectoryInfo t1mr1 = new DirectoryInfo(Path.Combine(path, "t1mri"));
+            DirectoryInfo t1mri = new DirectoryInfo(Path.Combine(path, "t1mri"));
+            DirectoryInfo ct = new DirectoryInfo(Path.Combine(path, "ct"));
 
             DirectoryInfo preimplantationDirectory = null, preTransformationsDirectory = null;
             FileInfo preTransformation = null;
-            preimplantationDirectory = t1mr1.GetDirectories("T1pre_*").FirstOrDefault();
+            if (t1mri.Exists) preimplantationDirectory = t1mri.GetDirectories("T1pre_*").FirstOrDefault();
             if (preimplantationDirectory != null && preimplantationDirectory.Exists)
             {
                 preTransformationsDirectory = new DirectoryInfo(Path.Combine(preimplantationDirectory.FullName, "registration"));
@@ -165,7 +166,7 @@ public static BaseMesh[] LoadFromDirectory(string path)
             // Post
             DirectoryInfo postimplantationDirectory = null, postTransformationsDirectory = null;
             FileInfo postTransformation = null;
-            postimplantationDirectory = t1mr1.GetDirectories("T1post_*").FirstOrDefault();
+            if (t1mri.Exists) postimplantationDirectory = t1mri.GetDirectories("T1post_*").FirstOrDefault();
             if (postimplantationDirectory != null && postimplantationDirectory.Exists)
             {
                 postTransformationsDirectory = new DirectoryInfo(Path.Combine(postimplantationDirectory.FullName, "registration"));
@@ -176,6 +177,20 @@ public static BaseMesh[] LoadFromDirectory(string path)
             }
             string postTransformationPath = string.Empty;
             if (postTransformation != null && postTransformation.Exists) postTransformationPath = postTransformation.FullName;
+            // CT
+            DirectoryInfo ctDirectory = null, ctTransformationsDirectory = null;
+            FileInfo ctTransformation = null;
+            if (ct.Exists) ctDirectory = ct.GetDirectories("CTpost_*").FirstOrDefault();
+            if (ctDirectory != null && ctDirectory.Exists)
+            {
+                ctTransformationsDirectory = new DirectoryInfo(Path.Combine(ctDirectory.FullName, "registration"));
+                if (ctTransformationsDirectory != null && ctTransformationsDirectory.Exists)
+                {
+                    ctTransformation = ctTransformationsDirectory.GetFiles("CT-" + parent.Name + "_" + ctDirectory.Name + "_TO_Scanner_Based.trm").FirstOrDefault();
+                }
+            }
+            string ctTransformationPath = string.Empty;
+            if (ctTransformation != null && ctTransformation.Exists) ctTransformationPath = ctTransformation.FullName;
             // Mesh
             DirectoryInfo meshDirectory = new DirectoryInfo(Path.Combine(preimplantationDirectory.FullName, "default_analysis", "segmentation", "mesh"));
             if(meshDirectory.Exists)
@@ -189,6 +204,10 @@ public static BaseMesh[] LoadFromDirectory(string path)
                     {
                         meshes.Add(new LeftRightMesh("Grey matter post", postTransformationPath, greyMatterLeftHemisphere.FullName, greyMatterRightHemisphere.FullName, string.Empty, string.Empty));
                     }
+                    if (!string.IsNullOrEmpty(ctTransformationPath))
+                    {
+                        meshes.Add(new LeftRightMesh("Grey matter CT", ctTransformationPath, greyMatterLeftHemisphere.FullName, greyMatterRightHemisphere.FullName, string.Empty, string.Empty));
+                    }
                 }
 
                 FileInfo whiteMatterLeftHemisphere = new FileInfo(Path.Combine(meshDirectory.FullName, parent.Name + "_Lwhite" + MESH_EXTENSION));
@@ -205,6 +224,10 @@ public static BaseMesh[] LoadFromDirectory(string path)
                     {
                         meshes.Add(new LeftRightMesh("White matter post", postTransformationPath, whiteMatterLeftHemisphere.FullName, whiteMatterRightHemisphere.FullName, marsAtlasLeftHemispherePath, marsAtlasRightHemispherePath));
                     }
+                    if (!string.IsNullOrEmpty(ctTransformationPath))
+                    {
+                        meshes.Add(new LeftRightMesh("White matter CT", ctTransformationPath, whiteMatterLeftHemisphere.FullName, whiteMatterRightHemisphere.FullName, marsAtlasLeftHemispherePath, marsAtlasRightHemispherePath));
+                    }
                 }
             }
             return meshes.ToArray();

Assets/Scripts/HBP/Core/Data/Patient/MRI.cs

@@ -141,6 +141,7 @@ public static MRI[] LoadFromDirectory(string path)
             if (string.IsNullOrEmpty(path) || !Directory.Exists(path)) return MRIs.ToArray();
             DirectoryInfo directoryInfo = new DirectoryInfo(path);
             DirectoryInfo t1mriDirectoy = directoryInfo.GetDirectories("t1mri", SearchOption.TopDirectoryOnly).FirstOrDefault();
+            DirectoryInfo ct = directoryInfo.GetDirectories("ct", SearchOption.TopDirectoryOnly).FirstOrDefault();
 
             if (t1mriDirectoy != null && t1mriDirectoy.Exists)
             {
@@ -165,6 +166,20 @@ public static MRI[] LoadFromDirectory(string path)
                         MRIs.Add(new MRI("Postimplantation", postimplantationMRIFile.FullName));
                     }
                 }
+
+                // CT
+                if (ct != null && ct.Exists)
+                {
+                    DirectoryInfo ctDirectory = ct.GetDirectories("CTpost_*", SearchOption.TopDirectoryOnly).FirstOrDefault();
+                    if (ctDirectory != null && ctDirectory.Exists)
+                    {
+                        FileInfo ctMRIFile = ctDirectory.GetFiles(directoryInfo.Name + "-CTPost_*" + EXTENSION).FirstOrDefault();
+                        if (ctMRIFile != null && ctMRIFile.Exists)
+                        {
+                            MRIs.Add(new MRI("CT", ctMRIFile.FullName));
+                        }
+                    }
+                }
             }
             return MRIs.ToArray();
         }

Assets/Scripts/HBP/Core/Data/Patient/Site.cs

@@ -123,6 +123,10 @@ public static List<Site> LoadFromIntranatDirectory(string path)
                 {
                     referenceSystem = "Post";
                 }
+                else if (referenceSystem.Contains("CTPost"))
+                {
+                    referenceSystem = "CT";
+                }
                 var ptsSites = LoadSitesFromPTSFile(referenceSystem, file.FullName);
                 foreach (var site in ptsSites)
                 {
@@ -175,11 +179,11 @@ public static List<Site> LoadImplantationFromBIDSFile(string referenceSystem, st
                         int marsAtlasIndex = splittedLines[0].IndexOf("MarsAtlas");
                         if (marsAtlasIndex != -1)
                         {
-                            splittedLines[0].Insert(marsAtlasIndex + 1, "Hemisphere (MarsAtlas)");
-                            splittedLines[0].Insert(marsAtlasIndex + 2, "Lobe (MarsAtlas)");
-                            splittedLines[0].Insert(marsAtlasIndex + 3, "Name_FS (MarsAtlas)");
-                            splittedLines[0].Insert(marsAtlasIndex + 4, "Full name (MarsAtlas)");
-                            splittedLines[0].Insert(marsAtlasIndex + 5, "Brodmann Area (MarsAtlas)");
+                            splittedLines[0].Insert(marsAtlasIndex + 1, "Hemisphere-MarsAtlas");
+                            splittedLines[0].Insert(marsAtlasIndex + 2, "Lobe-MarsAtlas");
+                            splittedLines[0].Insert(marsAtlasIndex + 3, "NameFS-MarsAtlas");
+                            splittedLines[0].Insert(marsAtlasIndex + 4, "Fullname-MarsAtlas");
+                            splittedLines[0].Insert(marsAtlasIndex + 5, "BrodmannArea-MarsAtlas");
                             for (int i = 1; i < splittedLines.Count; ++i)
                             {
                                 int marsAtlasLabel = Object3DManager.MarsAtlas.Label(splittedLines[i][marsAtlasIndex]);
@@ -410,11 +414,11 @@ public static List<Site> LoadSitesFromCSVFile(string csvFile)
                             int marsAtlasIndex = splittedLines[0].IndexOf("MarsAtlas");
                             if (marsAtlasIndex != -1)
                             {
-                                splittedLines[0].Insert(marsAtlasIndex + 1, "Hemisphere (MarsAtlas)");
-                                splittedLines[0].Insert(marsAtlasIndex + 2, "Lobe (MarsAtlas)");
-                                splittedLines[0].Insert(marsAtlasIndex + 3, "Name_FS (MarsAtlas)");
-                                splittedLines[0].Insert(marsAtlasIndex + 4, "Full name (MarsAtlas)");
-                                splittedLines[0].Insert(marsAtlasIndex + 5, "Brodmann Area (MarsAtlas)");
+                                splittedLines[0].Insert(marsAtlasIndex + 1, "Hemisphere-MarsAtlas");
+                                splittedLines[0].Insert(marsAtlasIndex + 2, "Lobe-MarsAtlas");
+                                splittedLines[0].Insert(marsAtlasIndex + 3, "NameFS-MarsAtlas");
+                                splittedLines[0].Insert(marsAtlasIndex + 4, "Fullname-MarsAtlas");
+                                splittedLines[0].Insert(marsAtlasIndex + 5, "Brodmann-MarsAtlas");
                                 for (int i = 1; i < splittedLines.Count; ++i)
                                 {
                                     int marsAtlasLabel = Object3DManager.MarsAtlas.Label(splittedLines[i][marsAtlasIndex]);

Assets/Scripts/HBP/Core/Data/Project/Alias.cs

@@ -33,10 +33,12 @@ public Alias(string key, string value) : base()
         #region Public Methods
         public void ConvertKeyToValue(ref string s)
         {
+            if (string.IsNullOrEmpty(Value)) return;
             s = s.Replace(Key, Value);
         }
         public void ConvertValueToKey(ref string s)
         {
+            if (string.IsNullOrEmpty(Value)) return;
             s = s.Replace(Value, Key);
         }
         #endregion

Assets/Scripts/HBP/Core/Data/Project/Project.cs

@@ -9,6 +9,7 @@
 using UnityEngine;
 using HBP.Core.Exceptions;
 using HBP.Core.Tools;
+using HBP.Core.Interfaces;
 
 namespace HBP.Core.Data
 {
@@ -404,6 +405,89 @@ public string GetProject(string path, string ID)
             }
             return projectsDirectories.FirstOrDefault((project) => new ProjectInfo(project).Settings.ID == ID);
         }
+        public Dictionary<string, List<Tuple<BaseData, string>>> CheckProjectIDs()
+        {
+            Dictionary<string, List<Tuple<BaseData, string>>> dataByID = new Dictionary<string, List<Tuple<BaseData, string>>>();
+            void addToDict(BaseData data, string name)
+            {
+                if (dataByID.ContainsKey(data.ID)) dataByID[data.ID].Add(new Tuple<BaseData, string>(data, name));
+                else dataByID.Add(data.ID, new List<Tuple<BaseData, string>>(new Tuple<BaseData, string>[] { new Tuple<BaseData, string>(data, name) }));
+            }
+            string getName(INameable data)
+            {
+                return string.Format("{0} ({1})", data.Name, getType(data as BaseData));
+            }
+            string getType(BaseData data)
+            {
+                return data.GetType().ToString().Split('.').Last();
+            }
+            // Settings
+            addToDict(Preferences, getType(Preferences));
+            foreach (var alias in Preferences.Aliases) addToDict(alias, string.Format("{0} ({1})", alias.Key, getType(alias)));
+            foreach (var tag in Preferences.Tags) addToDict(tag, getName(tag));
+            // Patients
+            foreach (var patient in m_Patients)
+            {
+                addToDict(patient, getName(patient));
+                foreach (var mesh in patient.Meshes) addToDict(mesh, string.Format("{0} / {1}", getName(patient), getName(mesh)));
+                foreach (var mri in patient.MRIs) addToDict(mri, string.Format("{0} / {1}", getName(patient), getName(mri)));
+                foreach (var site in patient.Sites)
+                {
+                    addToDict(site, string.Format("{0} / {1}", getName(patient), getName(site)));
+                    foreach (var coordinate in site.Coordinates) addToDict(coordinate, string.Format("{0} / {1} / {2}", getName(patient), getName(site), string.Format("{0} ({1})", coordinate.ReferenceSystem, getType(coordinate))));
+                    foreach (var tagValue in site.Tags) addToDict(tagValue, string.Format("{0} / {1} / {2}", getName(patient), getName(site), string.Format("{0} ({1})", tagValue.Tag.Name, getType(tagValue))));
+                }
+                foreach (var tagValue in patient.Tags) addToDict(tagValue, string.Format("{0} / {1}", getName(patient), string.Format("{0} ({1})", tagValue.Tag.Name, getType(tagValue))));
+            }
+            // Groups
+            foreach (var group in m_Groups) addToDict(group, getName(group));
+            // Protocols
+            foreach (var protocol in m_Protocols)
+            {
+                addToDict(protocol, getName(protocol));
+                foreach (var bloc in protocol.Blocs)
+                {
+                    addToDict(bloc, string.Format("{0} / {1}", getName(protocol), getName(bloc)));
+                    foreach (var subBloc in bloc.SubBlocs)
+                    {
+                        addToDict(subBloc, string.Format("{0} / {1} / {2}", getName(protocol), getName(bloc), getName(subBloc)));
+                        foreach (var ev in subBloc.Events) addToDict(ev, string.Format("{0} / {1} / {2} / {3}", getName(protocol), getName(bloc), getName(subBloc), getName(ev)));
+                        foreach (var icon in subBloc.Icons) addToDict(icon, string.Format("{0} / {1} / {2} / {3}", getName(protocol), getName(bloc), getName(subBloc), getName(icon)));
+                        foreach (var treatment in subBloc.Treatments) addToDict(treatment, string.Format("{0} / {1} / {2} / {3}", getName(protocol), getName(bloc), getName(subBloc), getType(treatment)));
+                    }
+                }
+            }
+            // Datasets
+            foreach (var dataset in m_Datasets)
+            {
+                addToDict(dataset, getName(dataset));
+                foreach (var data in dataset.Data)
+                {
+                    addToDict(data, string.Format("{0} / {1}", getName(dataset), getName(data)));
+                    addToDict(data.DataContainer, string.Format("{0} / {1} / {2}", getName(dataset), getName(data), getType(data.DataContainer)));
+                }
+            }
+            // Visualizations
+            foreach (var visualization in m_Visualizations)
+            {
+                addToDict(visualization, getName(visualization));
+                foreach (var column in visualization.Columns)
+                {
+                    addToDict(column, string.Format("{0} / {1}", getName(visualization), getName(column)));
+                    addToDict(column.BaseConfiguration, string.Format("{0} / {1} / {2}", getName(visualization), getName(column), getType(column.BaseConfiguration)));
+                    foreach (var siteConfig in column.BaseConfiguration.ConfigurationBySite) addToDict(siteConfig.Value, string.Format("{0} / {1} / {2})", getName(visualization), getName(column), string.Format("{0} ({1})", siteConfig.Key, getType(siteConfig.Value))));
+                }
+                foreach (var anatomicColumn in visualization.AnatomicColumns) addToDict(anatomicColumn.AnatomicConfiguration, string.Format("{0} / {1} / {2}", getName(visualization), getName(anatomicColumn), getType(anatomicColumn.AnatomicConfiguration)));
+                foreach (var ieegColumn in visualization.IEEGColumns) addToDict(ieegColumn.DynamicConfiguration, string.Format("{0} / {1} / {2}", getName(visualization), getName(ieegColumn), getType(ieegColumn.DynamicConfiguration)));
+                foreach (var ccepColumn in visualization.CCEPColumns) addToDict(ccepColumn.DynamicConfiguration, string.Format("{0} / {1} / {2}", getName(visualization), getName(ccepColumn), getType(ccepColumn.DynamicConfiguration)));
+                foreach (var fmriColumn in visualization.FMRIColumns) addToDict(fmriColumn.FMRIConfiguration, string.Format("{0} / {1} / {2}", getName(visualization), getName(fmriColumn), getType(fmriColumn.FMRIConfiguration)));
+                foreach (var megColumn in visualization.MEGColumns) addToDict(megColumn.MEGConfiguration, string.Format("{0} / {1} / {2}", getName(visualization), getName(megColumn), getType(megColumn.MEGConfiguration)));
+            }
+            // Check unicity and return error string
+            Dictionary<string, List<Tuple<BaseData, string>>> problematicData = new Dictionary<string, List<Tuple<BaseData, string>>>();
+            foreach (var kv in dataByID) if (kv.Value.Count > 1) problematicData.Add(kv.Key, kv.Value);
+            return problematicData;
+        }
 
         public IEnumerator c_Load(ProjectInfo projectInfo, Action<float, float, LoadingText> onChangeProgress)
         {

Assets/Scripts/HBP/Core/Data/Project/ProjectInfo.cs

@@ -2,6 +2,7 @@
 using Ionic.Zip;
 using HBP.Core.Exceptions;
 using HBP.Core.Tools;
+using UnityEngine;
 
 namespace HBP.Core.Data
 {
@@ -64,7 +65,16 @@ public ProjectInfo(string path) : base()
                             FileInfo settingsFile = new FileInfo(System.IO.Path.Combine(ApplicationState.TMPFolder, entry.FileName));
                             if (settingsFile.Exists) settingsFile.Delete();
                             entry.Extract(ApplicationState.TMPFolder);
-                            Settings = ClassLoaderSaver.LoadFromJson<ProjectPreferences>(settingsFile.FullName);
+                            try
+                            {
+                                Settings = ClassLoaderSaver.LoadFromJson<ProjectPreferences>(settingsFile.FullName);
+                            }
+                            catch (System.Exception e)
+                            {
+                                Debug.LogException(e);
+                                Settings = new ProjectPreferences(System.IO.Path.GetFileNameWithoutExtension(path));
+                                Settings.CanLoadProject = false;
+                            }
                             settingsFile.Directory.Delete(true);
                         }
                     }

Assets/Scripts/HBP/Core/Data/Project/ProjectPreferences.cs

@@ -47,6 +47,7 @@ public ReadOnlyCollection<BaseTag> Tags
         [IgnoreDataMember] public static string DefaultName = "New Project";
         [IgnoreDataMember] public static string DefaultPatientDatabase = "";
         [IgnoreDataMember] public static string DefaultLocalizerDatabase = "";
+        [IgnoreDataMember] public bool CanLoadProject = true;
         #endregion
 
         #region Constructors