Merge pull request pyushkevich#128 from jilei-hao/dev/mesh-wt

Dev/mesh wt

CMakeLists.txt

@@ -89,13 +89,13 @@ ENDIF()
 
 # These four fields should be modified when versions change
 SET(SNAP_VERSION_MAJOR 4)
-SET(SNAP_VERSION_MINOR 0)
-SET(SNAP_VERSION_PATCH 1)
-SET(SNAP_VERSION_QUALIFIER "")
+SET(SNAP_VERSION_MINOR 1)
+SET(SNAP_VERSION_PATCH 0)
+SET(SNAP_VERSION_QUALIFIER "-dev")
 
 # These fields should also be modified each time
-SET(SNAP_VERSION_RELEASE_DATE "20230320")
-SET(SNAP_VERSION_RELEASE_DATE_FORMATTED "March 20, 2023")
+SET(SNAP_VERSION_RELEASE_DATE "20230523")
+SET(SNAP_VERSION_RELEASE_DATE_FORMATTED "May 23, 2023")
 
 # This field should only change when the format of the settings files changes
 # in a non backwards-compatible way

Common/Registry.cxx

@@ -41,6 +41,7 @@
 #include <cstdarg>
 #include <fstream>
 #include <iomanip>
+#include <regex>
 #include "itksys/SystemTools.hxx"
 #include "IRISException.h"
 
@@ -491,6 +492,23 @@ ::FindValue(const StringType& value)
   return "";
 }
 
+Registry::StringListType
+Registry
+::FindFoldersFromPattern(const StringType &_pattern) const
+{
+  StringListType ret;
+  std::regex pattern(_pattern);
+  std::smatch match;
+
+  for (auto &kv : m_FolderMap)
+    {
+    if (std::regex_search(kv.first, match, pattern))
+      ret.push_back(kv.first);
+    }
+
+  return ret;
+}
+
 void 
 Registry
 ::RemoveKeys(const char *match)

Common/Registry.h

@@ -460,6 +460,9 @@ class Registry
   /** Find a value in a folder or return "" */
   StringType FindValue(const StringType& value);
 
+  /** Find a list of folders keys with string pattern */
+  StringListType FindFoldersFromPattern(const StringType& _pattern) const;
+
   /** Empty the contents of the registry */
   void Clear();
 

GUI/Qt/Windows/SplashPanel.ui

@@ -110,7 +110,7 @@ color:rgb(109, 109, 109);</string>
       <string>Copyright (C) 1998-2022
 Paul A. Yushkevich 
 Guido Gerig 
-Alison Pouch 
+Alison M. Pouch 
 Jilei Hao</string>
      </property>
      <property name="alignment">

Logic/Framework/GenericImageData.cxx

@@ -649,6 +649,13 @@ int GenericImageData::GetNumberOfOverlays()
   return m_Wrappers[OVERLAY_ROLE].size();
 }
 
+unsigned int
+GenericImageData
+::GetNumberOfTimePoints() const
+{
+  return m_Parent->GetNumberOfTimePoints();
+}
+
 ImageWrapperBase *GenericImageData::GetLastOverlay()
 {
   return m_Wrappers[OVERLAY_ROLE].back();

Logic/Framework/GenericImageData.h

@@ -187,6 +187,11 @@ class GenericImageData : public itk::Object
 
   int GetNumberOfOverlays();
 
+  /**
+   * Get Number of Timepoints in the workspace
+   */
+  unsigned int GetNumberOfTimePoints() const;
+
   ImageWrapperBase *GetLastOverlay();
 
   // virtual ImageWrapperBase* GetLayer(unsigned int layer) const;

Logic/Mesh/GuidedMeshIO.h

@@ -79,7 +79,7 @@ class GuidedMeshIO
   FileFormat GetFileFormat(Registry &folder, FileFormat dflt = FORMAT_COUNT);
 
   /** Set the file format in a registry */
-  void SetFileFormat(Registry &folder, FileFormat format);
+  static void SetFileFormat(Registry &folder, FileFormat format);
 
   /** Get enum description */
   std::string GetFormatDescription(FileFormat formatEnum);

Logic/Mesh/ImageMeshLayers.cxx

@@ -226,7 +226,8 @@ ::LoadFromRegistry(Registry &project, std::string &project_dir_orig,
     {
     auto folder_crnt_layer = folder_layers.Folder(layer_key);
     auto mesh_wrapper = StandaloneMeshWrapper::New();
-    mesh_wrapper->LoadFromRegistry(folder_crnt_layer, project_dir_orig, project_dir_crnt);
+    mesh_wrapper->LoadFromRegistry(folder_crnt_layer, project_dir_orig,
+                                   project_dir_crnt, m_ImageData->GetNumberOfTimePoints());
     AddLayer(mesh_wrapper, true);
 
     ++layer_id;

Logic/Mesh/LevelSetMeshWrapper.cxx

@@ -178,7 +178,7 @@ ::SaveToRegistry(Registry &)
 
 void
 LevelSetMeshWrapper
-::LoadFromRegistry(Registry &, std::string &, std::string &)
+::LoadFromRegistry(Registry &, std::string &, std::string &, unsigned int)
 {
 
 }

Logic/Mesh/LevelSetMeshWrapper.h

@@ -66,7 +66,8 @@ class LevelSetMeshWrapper : public MeshWrapperBase
   virtual void SaveToRegistry(Registry &folder) override;
 
   /** Build the layer from registry */
-  virtual void LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_dir) override;
+  virtual void LoadFromRegistry(Registry &folder, std::string &orig_dir,
+                                std::string &crnt_dir, unsigned int nT) override;
 
   /** Get Pipeline Modified Time */
   unsigned long GetAssemblyMTime(unsigned int tp);

Logic/Mesh/MeshWrapperBase.cxx

@@ -2,6 +2,7 @@
 #include "MeshDisplayMappingPolicy.h"
 #include "Rebroadcaster.h"
 #include "IRISApplication.h"
+#include "IRISException.h"
 #include <vtkPointData.h>
 #include <vtkCellData.h>
 #include <vtkDataSetAttributes.h>
@@ -432,7 +433,8 @@ ::GetNumberOfMeshes(unsigned int timepoint)
 
 void
 MeshWrapperBase
-::LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_dir)
+::LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_dir,
+                   unsigned int nT)
 {
   GuidedMeshIO io;
   bool moved = (orig_dir.compare(crnt_dir) != 0);
@@ -444,13 +446,17 @@ ::LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_di
   // Load mesh timepoint assembly
   auto folder_assembly = folder.Folder("MeshTimePoints");
   bool fnSet = false;
-  unsigned int crnt_tp = 1;
-  std::string key_tp = Registry::Key("TimePoint[%03d]", crnt_tp);
+  bool has_poly = false;
 
-  while (folder_assembly.HasFolder(key_tp))
+  for (unsigned int tp = 1; tp <= nT; ++tp)
     {
+    std::string key_tp = Registry::Key("TimePoint[%03d]", tp);
+
+    if (!folder_assembly.HasFolder(key_tp))
+      continue;
+
     auto folder_tp = folder_assembly.Folder(key_tp);
-    unsigned int crnt_poly = 0;
+    unsigned int crnt_poly = 0; // polydata must start with index 0
     std::string key_poly = Registry::Key("PolyData[%03d]", crnt_poly);
 
     while (folder_tp.HasFolder(key_poly))
@@ -471,15 +477,16 @@ ::LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_di
           .GetEnum(GuidedMeshIO::GetEnumFileFormat(), FileFormat::FORMAT_COUNT);
 
       // Load with tp = j-1. The storeing of time point index is zero-based
-      io.LoadMesh(poly_file_full.c_str(), format, this, crnt_tp - 1, crnt_poly);
+      io.LoadMesh(poly_file_full.c_str(), format, this, tp - 1, crnt_poly);
 
       ++crnt_poly;
+      has_poly = true;
       key_poly = Registry::Key("TimePoint[%03d]", crnt_poly);
       }
-
-    ++crnt_tp;
-    key_tp = Registry::Key("TimePoint[%03d]", crnt_tp);
     }
+
+  if (!has_poly)
+    throw IRISException("Mesh polydata not found in the workspace file!");
 }
 
 void

Logic/Mesh/MeshWrapperBase.h

@@ -268,8 +268,11 @@ class MeshWrapperBase : public WrapperBase
   /** Save the layer to registry */
   virtual void SaveToRegistry(Registry &folder);
 
-  /** Build the layer from registry */
-  virtual void LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_dir);
+  /**
+   *  Build the layer from registry
+   */
+  virtual void LoadFromRegistry(Registry &folder, std::string &orig_dir,
+                                std::string &crnt_dir, unsigned int nT);
 
   // End of virtual methods definition
   //------------------------------------------------

Logic/Mesh/SegmentationMeshWrapper.cxx

@@ -159,7 +159,7 @@ ::SaveToRegistry(Registry &)
 
 void
 SegmentationMeshWrapper
-::LoadFromRegistry(Registry &, std::string &, std::string &)
+::LoadFromRegistry(Registry &, std::string &, std::string &, unsigned int)
 {
 
 }

Logic/Mesh/SegmentationMeshWrapper.h

@@ -54,7 +54,8 @@ class SegmentationMeshWrapper : public MeshWrapperBase
   virtual void SaveToRegistry(Registry &folder) override;
 
   /** Build the layer from registry */
-  virtual void LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_dir) override;
+  virtual void LoadFromRegistry(Registry &folder, std::string &orig_dir,
+                                std::string &crnt_dir, unsigned int nT) override;
 
   //  End of virtual methods implementation
   //-----------------------------------------------------

Logic/Mesh/StandaloneMeshWrapper.cxx

@@ -35,8 +35,11 @@ ::SetMesh(vtkPolyData *mesh, unsigned int timepoint, LabelType id)
       m_MeshAssemblyMap[timepoint] = assembly.GetPointer();
     }
 
+  int propId = (m_CombinedDataPropertyMap.size() > 0) ?
+        m_CombinedDataPropertyMap.cbegin()->first : -1;
+
   // Set Default active array id
-  SetActiveMeshLayerDataPropertyId(m_CombinedDataPropertyMap.cbegin()->first);
+  SetActiveMeshLayerDataPropertyId(propId);
 
   InvokeEvent(ValueChangedEvent());
 }
@@ -88,9 +91,10 @@ ::SaveToRegistry(Registry &folder)
 
 void
 StandaloneMeshWrapper
-::LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_dir)
+::LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_dir,
+                   unsigned int nT)
 {
-  Superclass::LoadFromRegistry(folder, orig_dir, crnt_dir); // Load basic structures using parent method
+  Superclass::LoadFromRegistry(folder, orig_dir, crnt_dir, nT); // Load basic structures using parent method
 
   auto folder_data = folder.Folder("DataArrayProperties");
   unsigned int array_id = 0;
@@ -130,7 +134,5 @@ ::LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_di
     ++array_id;
     key_data = Registry::Key("DataArray[%03d]", array_id);
     }
-
-  SetActiveMeshLayerDataPropertyId(0);
 }
 

Logic/Mesh/StandaloneMeshWrapper.h

@@ -45,7 +45,8 @@ class StandaloneMeshWrapper : public MeshWrapperBase
   virtual void SaveToRegistry(Registry &folder) override;
 
   /** Build the layer from registry */
-  virtual void LoadFromRegistry(Registry &folder, std::string &orig_dir, std::string &crnt_dir)override;
+  virtual void LoadFromRegistry(Registry &folder, std::string &orig_dir,
+                                std::string &crnt_dir, unsigned int nT) override;
 
   // End of virtual methods definition
   //-------------------------------------------------