Merge pull request #1 from pyushkevich/JLasserv-master

J lasserv master

Author: JLasserv

CMakeLists.txt

@@ -1,3 +1,4 @@
+
 #--------------------------------------------------------------------------------
 # PROJECT: SNAP                             
 #--------------------------------------------------------------------------------

Common/Minzip/crypt.h

@@ -64,7 +64,7 @@ static int update_keys(unsigned long* pkeys,const z_crc_t* pcrc_32_tab,int c)
     (*(pkeys+1)) += (*(pkeys+0)) & 0xff;
     (*(pkeys+1)) = (*(pkeys+1)) * 134775813L + 1;
     {
-      register int keyshift = (int)((*(pkeys+1)) >> 24);
+      int keyshift = (int)((*(pkeys+1)) >> 24);
       (*(pkeys+2)) = CRC32((*(pkeys+2)), keyshift);
     }
     return c;

Common/Minzip/miniunz.c

@@ -15,6 +15,10 @@
 #include <errno.h>
 #include <fcntl.h>
 
+#ifdef __APPLE__
+#include <sys/stat.h>
+#endif
+
 #ifdef unix
 # include <unistd.h>
 # include <utime.h>
@@ -336,7 +340,7 @@ int do_extract_currentfile(uf,popt_extract_without_path,popt_overwrite,password)
             {
                 char c=*(filename_withoutpath-1);
                 *(filename_withoutpath-1)='\0';
-                makedir(write_filename);
+                makedir((char *)(write_filename));
                 *(filename_withoutpath-1)=c;
                 fout=fopen(write_filename,"wb");
             }

Common/Minzip/miniunz.h

@@ -1,11 +1,15 @@
-#ifndef _miniumz_H
+#ifndef _miniunz_H
 #define _miniunz_H
 
 
 #ifdef __cplusplus
 extern "C" {
 #endif
 
+#ifdef __APPLE__
+#define unix
+#endif
+
 #ifdef unix
 # include <unistd.h>
 # include <utime.h>

Common/SNAPOpenGL.h

@@ -35,6 +35,8 @@
 #ifndef __SNAPOpenGL_h_
 #define __SNAPOpenGL_h_
 
+// Prevent errors due to OpenGL having moved on...
+#define GL_SILENCE_DEPRECATION
 
 #include "IRISVectorTypes.h"
 

GUI/Model/InterpolateLabelModel.cxx

@@ -5,6 +5,7 @@
 #include "ScalarImageWrapper.h"
 #include "itkMorphologicalContourInterpolator.h"
 #include "SegmentationUpdateIterator.h"
+#include "itkBinaryThresholdImageFilter.h"
 
 void InterpolateLabelModel::SetParentModel(GlobalUIModel *parent)
 {
@@ -23,6 +24,18 @@ void InterpolateLabelModel::UpdateOnShow()
   this->SetDrawOverFilter(m_Parent->GetGlobalState()->GetDrawOverFilter());
 }
 
+template <class TLabel>
+class BinarizeFunctor
+{
+public:
+  void SetLabel(const TLabel &l) { m_Label = l; }
+  
+  TLabel operator()(const TLabel &in) { return (in == m_Label) ? m_Label : 0; }
+  bool operator != (const BinarizeFunctor<TLabel> &other ) { return m_Label != other.m_Label; }
+private:
+  TLabel m_Label;
+};
+
 void InterpolateLabelModel::Interpolate()
 {
   // Get the segmentation wrapper
@@ -35,11 +48,28 @@ void InterpolateLabelModel::Interpolate()
   // Are we interpolating all labels?
   bool interp_all = this->GetInterpolateAll();
 
-  mci->SetInput(liw->GetImage());
-
-  // Should we be interpolating a specific label?
-  if (!interp_all)
+  // Should we be interpolating a specific label or all labels?
+  if(interp_all)
+    {
+    mci->SetInput(liw->GetImage());
+    }
+  else
+    {
+    // We need to extract a single component from the segmentation image to interpolate
+    typedef GenericImageData::LabelImageType LabelImageType;
+    typedef BinarizeFunctor<LabelType> FunctorType;
+    typedef itk::UnaryFunctorImageFilter<LabelImageType, LabelImageType, FunctorType> BinarizeFilterType;
+    typename BinarizeFilterType::Pointer flt = BinarizeFilterType::New();
+    
+    FunctorType fn;
+    fn.SetLabel(this->GetInterpolateLabel());
+    flt->SetInput(liw->GetImage());
+    flt->SetFunctor(fn);
+    flt->Update();
+
+    mci->SetInput(flt->GetOutput());
     mci->SetLabel(this->GetInterpolateLabel());
+    }
 
   // Should we interpolate only one axis?
   if (this->GetMorphologyInterpolateOneAxis())
@@ -56,7 +86,7 @@ void InterpolateLabelModel::Interpolate()
 
   // Update the filter
   mci->Update();
-
+  
   // Apply the labels back to the segmentation
   SegmentationUpdateIterator it_trg(liw->GetImage(), liw->GetImage()->GetBufferedRegion(),
                                     this->GetDrawingLabel(), this->GetDrawOverFilter());
@@ -74,17 +104,19 @@ void InterpolateLabelModel::Interpolate()
     }
   else
     {
+    LabelType l_interp = this->GetInterpolateLabel();
     LabelType l_replace = this->GetDrawingLabel();
     for(; !it_trg.IsAtEnd(); ++it_trg, ++it_src)
-      it_trg.PaintLabelWithExtraProtection(it_src.Get(), l_replace);
+      if(it_src.Get() == l_interp)
+        it_trg.PaintLabelWithExtraProtection(l_interp, l_replace);
     }
 
   // Finish the segmentation editing and create an undo point
   it_trg.Finalize();
   liw->StoreUndoPoint("Interpolate label", it_trg.RelinquishDelta());
 
-  // TODO: this should not be needed because this should propagate from wrapper
-  // this->m_Parent->GetDriver()->InvokeEvent(SegmentationChangeEvent());
+  // Fire event to inform GUI that segmentation has changed
+  this->m_Parent->GetDriver()->InvokeEvent(SegmentationChangeEvent());
 }
 
 

GUI/Model/InterpolateLabelModel.h

@@ -93,7 +93,9 @@ class InterpolateLabelModel : public AbstractPropertyContainerModel
 
   typedef ConcretePropertyModel<InterpolationType, TrivialDomain> ConcreteInterpolationType;
   SmartPtr<ConcreteInterpolationType> m_InterpolationMethodModel;
-
+  
+  // Templated code to interpolate an image
+  template <class TImage> void DoInterpolate(TImage *image);
 
   // The parent model
   GlobalUIModel *m_Parent;

GUI/Qt/Windows/InterpolateLabelsDialog.cxx

@@ -28,6 +28,7 @@ void InterpolateLabelsDialog::SetModel(InterpolateLabelModel *model)
 
   makeCoupling(ui->inActiveLabel, m_Model->GetDrawingLabelModel());
   makeCoupling(ui->inLabelToInterpolate, m_Model->GetInterpolateLabelModel());
+  makeCoupling(ui->inDrawOverFilter, m_Model->GetDrawOverFilterModel());
 
   makeRadioGroupCoupling(ui->btnInterpolateAll, ui->btnInterpolateOne, m_Model->GetInterpolateAllModel());
 

GUI/Qt/Windows/InterpolateLabelsDialog.ui

@@ -89,7 +89,7 @@ color: gray;</string>
       <item row="3" column="0">
        <widget class="QLabel" name="label_4">
         <property name="text">
-         <string>Interpolate with:</string>
+         <string>Paint with label:</string>
         </property>
        </widget>
       </item>
@@ -100,6 +100,20 @@ color: gray;</string>
         </property>
        </widget>
       </item>
+      <item row="4" column="1">
+       <widget class="QComboBox" name="inDrawOverFilter">
+        <property name="toolTip">
+         <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Select which label of set of labels will be painted over during interpolation. You can paint over all labels, clear voxels, or a specific label.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+        </property>
+       </widget>
+      </item>
+      <item row="4" column="0">
+       <widget class="QLabel" name="label_5">
+        <property name="text">
+         <string>Paint over label(s):</string>
+        </property>
+       </widget>
+      </item>
      </layout>
     </widget>
    </item>

GUI/Qt/Windows/MainImageWindow.cxx

@@ -1068,115 +1068,12 @@ SliceViewPanel * MainImageWindow::GetSlicePanel(unsigned int i)
 
 void MainImageWindow::remove_dir(const std::string path)
 {
-#ifdef WIN32
-    WIN32_FIND_DATA ffd;
-    TCHAR szDir[MAX_PATH];
-    HANDLE hFind = INVALID_HANDLE_VALUE;
-
-    // Prepare string for use with FindFile functions.  First, copy the
-    // string to a buffer, then append '\*' to the directory name.
-    StringCchCopy(szDir, MAX_PATH, path.c_str());
-    StringCchCat(szDir, MAX_PATH, TEXT("\\*"));
-
-    // Find the first file in the directory.
-    hFind = FindFirstFile(szDir, &ffd);
-
-
-    while (FindNextFile(hFind, &ffd) != 0)
-    {
-        // If the directory contains a directory, we empty it
-        if (ffd.dwFileAttributes & FILE_ATTRIBUTE_DIRECTORY)
-        {
-            if (strcmp(ffd.cFileName, ".") != 0 & strcmp(ffd.cFileName, "..") != 0) {
-                std::string new_path = path + "\\" + ffd.cFileName;
-                if (_rmdir(new_path.c_str()) == -1) { // Error while removing the directory
-                    if (errno == ENOTEMPTY) {
-                        //Open the subdirectory to delete files
-                        remove_dir(new_path);
-                    }
-                }
-            }
-        }
-        else //Remove files
-        {
-            std::string new_path = path + "\\" + ffd.cFileName;
-            remove(new_path.c_str());
-        }
-    }
-    //Remove the folder once it's empty
-    if (FindNextFile(hFind, &ffd) == 0) {
-        _rmdir(path.c_str());
-    }
-    FindClose(hFind);
-
-#else
-    DIR* dir;
-    DIR* subdir;
-    struct dirent* ent;
-    if ((dir = opendir(path.c_str())) != NULL) {
-        while ((ent = readdir(dir)) != NULL) {
-            std::string file = std::string(path) + "/" + std::string(ent->d_name);
-            // If the folder contains a folder:
-            if ((subdir = opendir(file.c_str())) != NULL) {
-                closedir(subdir);
-                remove_dir(file.c_str());
-
-            }
-            else {
-                remove(file.c_str());
-            }
-        }
-        closedir(dir);
-    }
-#endif
+  m_Model->GetDriver()->remove_dir(path);
 }
 
 void MainImageWindow::cleanUp_tempdir(void)
 {
-#ifdef WIN32
-  char tempDir[_MAX_PATH + 1] = "";
-  // First call return a directory only
-  DWORD length = GetTempPath(_MAX_PATH+1, tempDir);
-  WIN32_FIND_DATA ffd;
-  TCHAR szDir[MAX_PATH];
-  HANDLE hFind = INVALID_HANDLE_VALUE;
-
-  // Prepare string for use with FindFile functions.  First, copy the
-  // string to a buffer, then append '\*' to the directory name.
-  StringCchCopy(szDir, MAX_PATH, tempDir);
-  StringCchCat(szDir, MAX_PATH, TEXT("\\*"));
-
-  // Find the first file in the directory.
-  hFind = FindFirstFile(szDir, &ffd);
-
-
-  while (FindNextFile(hFind, &ffd) != 0)
-  {
-	  std::size_t find_zip = std::string(ffd.cFileName).find("ZIP");
-	  if (find_zip != std::string::npos) {
-		  std::string path = tempDir + std::string(ffd.cFileName);
-		  remove_dir(path);
-	  }
-  }
-
-
-#else
-  //Find the folders extracted into temp directory
-  DIR* dir;
-  struct dirent* ent;
-  std::string path;
-  if ((dir = opendir("/tmp")) != NULL) {
-      while ((ent = readdir (dir)) != NULL) {
-          //Find the extracted folders
-          std::size_t find_zip = std::string(ent->d_name).find("ZIPDIR");
-          if (find_zip != std::string::npos) {
-              path = "/tmp/" + std::string(ent->d_name);
-              remove_dir(path);
-          }
-      }
-      closedir(dir);
-  }
-#endif
+  m_Model->GetDriver()->cleanUp_tempdir();
 }
 
 void MainImageWindow::closeEvent(QCloseEvent *event)