clitkDicomRTStruct2Image: new features

- support conversion given ROI name or substring

diff --git a/common/clitkDicomRT_StructureSet.cxx b/common/clitkDicomRT_StructureSet.cxx
index bbbcfd61274aebff7bb969dfc51d508d4ddca3a7..761ea23212920d7a5e7c69d8c3060748168e491d 100644 (file)
--- a/common/clitkDicomRT_StructureSet.cxx
+++ b/common/clitkDicomRT_StructureSet.cxx
@@ -118,6 +118,101 @@ clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROIFromROINumber(int n)
 }
 //--------------------------------------------------------------------
 
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROIFromROIName(const std::string& name)
+{
+  std::map<int, std::string>::iterator it = mMapOfROIName.begin();
+  int number = -1;
+  while (it != mMapOfROIName.end() && number == -1) {
+    if (it->second == name)
+      number = it->first;
+    else
+      it++;
+  }
+
+  if (number == -1) {
+    std::cerr << "No ROI name " << name << std::endl;
+    return NULL;
+  }
+  
+  return mROIs[number];
+}
+//--------------------------------------------------------------------
+/*
+// RP: 08/02/2013
+// RegEx version shall be available when C++x11 supports it propely
+//
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROIFromROINameRegEx(const std::string& regEx)
+{
+  std::map<int, std::string>::iterator it = mMapOfROIName.begin();
+  int number = -1;
+
+  while (it != mMapOfROIName.end() && number == -1) {
+    if (std::tr1::regex_match (it->second, std::tr1::regex(regEx)))
+      number = it->first;
+    else
+      it++;
+  }
+
+  if (number == -1) {
+    std::cerr << "No ROI name " << number << std::endl;
+    return NULL;
+  }
+  
+  return mROIs[number];
+}
+//--------------------------------------------------------------------
+*/
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROIFromROINameSubstr(const std::string& s)
+{
+  std::map<int, std::string>::iterator it = mMapOfROIName.begin();
+  int number = -1;
+
+  while (it != mMapOfROIName.end() && number == -1) {
+    if (it->second.find(s) != std::string::npos)
+      number = it->first;
+    else
+      it++;
+  }
+
+  if (number == -1) {
+    std::cerr << "No ROI name " << s << std::endl;
+    return NULL;
+  }
+  
+  return mROIs[number];
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+clitk::DicomRT_StructureSet::ROIMapContainer * 
+clitk::DicomRT_StructureSet::GetROIsFromROINameSubstr(const std::string& s)
+{
+  static ROIMapContainer rois;
+  rois.clear();
+  
+  ROIMapContainer::iterator it = mROIs.begin();
+  int number = -1;
+
+  while (it != mROIs.end()) {
+    if (it->second->GetName().find(s) != std::string::npos) {
+      number = it->first;
+      rois[number] = it->second;
+    }
+    it++;
+  }
+
+  if (number == -1) {
+    std::cerr << "No ROI name " << s << std::endl;
+    return NULL;
+  }
+  
+  return &rois;
+  
+}
+//--------------------------------------------------------------------
 
 //--------------------------------------------------------------------
 void clitk::DicomRT_StructureSet::Print(std::ostream & os) const

diff --git a/common/clitkDicomRT_StructureSet.h b/common/clitkDicomRT_StructureSet.h
index 5761e14dc28e167bf13ae0d3e92b68c5b448cc12..99946083f027153a5c0039a290d5719b8e0f6dcb 100644 (file)
--- a/common/clitkDicomRT_StructureSet.h
+++ b/common/clitkDicomRT_StructureSet.h
@@ -44,8 +44,9 @@ public:
   typedef itk::SmartPointer<Self> Pointer;
   itkNewMacro(Self);
 
-  typedef std::map<int, clitk::DicomRT_ROI::Pointer>::iterator ROIIteratorType;
-  typedef std::map<int, clitk::DicomRT_ROI::Pointer>::const_iterator ROIConstIteratorType;
+  typedef std::map<int, clitk::DicomRT_ROI::Pointer> ROIMapContainer;
+  typedef ROIMapContainer::iterator ROIIteratorType;
+  typedef ROIMapContainer::const_iterator ROIConstIteratorType;
 
   void Print(std::ostream & os = std::cout) const;
   void Read(const std::string & filename);
@@ -53,7 +54,11 @@ public:
   void Write(const std::string & filename);
 
   clitk::DicomRT_ROI * GetROIFromROINumber(int n);
-  std::map<int, clitk::DicomRT_ROI::Pointer> & GetROIs() { return mROIs; }
+  clitk::DicomRT_ROI* GetROIFromROIName(const std::string& name);
+  //clitk::DicomRT_ROI* GetROIFromROINameRegEx(const std::string& regEx);
+  clitk::DicomRT_ROI* GetROIFromROINameSubstr(const std::string& s);
+  ROIMapContainer * GetROIsFromROINameSubstr(const std::string& s);
+  ROIMapContainer & GetROIs() { return mROIs; }
   const std::string & GetStudyID() const;
   const std::string & GetStudyTime() const;
   const std::string & GetStudyDate() const;

diff --git a/tools/clitkDicomRTStruct2Image.cxx b/tools/clitkDicomRTStruct2Image.cxx
index 88d480d1f625d9016beff80ec72e256191a22efd..b713d9412d20897bea105aa16bcf596c941bfd72 100644 (file)
--- a/tools/clitkDicomRTStruct2Image.cxx
+++ b/tools/clitkDicomRTStruct2Image.cxx
@@ -38,34 +38,70 @@ int main(int argc, char * argv[]) {
   clitk::DicomRTStruct2ImageFilter filter;
   filter.SetCropMaskEnabled(args_info.crop_flag);
   filter.SetImageFilename(args_info.image_arg);  // Used to get spacing + origin
-  if (args_info.roi_arg != -1) {
+  if (args_info.roiName_given) {
+    filter.SetROI(s->GetROIFromROIName(args_info.roiName_arg)); 
+    filter.SetOutputImageFilename(args_info.output_arg);
+    filter.Update();  
+  }
+  else if (args_info.roi_given && args_info.roi_arg != -1) {
     filter.SetROI(s->GetROIFromROINumber(args_info.roi_arg)); 
     filter.SetOutputImageFilename(args_info.output_arg);
     filter.Update();  
   }
   else {
+    clitk::DicomRT_StructureSet::ROIMapContainer* rois;
+    if (args_info.roiNameSubstr_given)
+      rois = s->GetROIsFromROINameSubstr(args_info.roiNameSubstr_arg);
+    else
+      rois = &s->GetROIs();
+    
     clitk::DicomRT_StructureSet::ROIConstIteratorType iter;
-    for(iter = s->GetROIs().begin(); iter != s->GetROIs().end(); iter++) {
-      clitk::DicomRT_ROI::Pointer roi = iter->second;
-      // Create the filter
-      clitk::DicomRTStruct2ImageFilter filter;
-      filter.SetCropMaskEnabled(args_info.crop_flag);
-      filter.SetImageFilename(args_info.image_arg);  // Used to get spacing + origin
-      std::string name = roi->GetName();
-      int num = roi->GetROINumber();
-      filter.SetROI(roi); 
-      name.erase(remove_if(name.begin(), name.end(), isspace), name.end());
-      std::string n = std::string(args_info.output_arg).append
-        (clitk::toString(num)).append
-        ("_").append
-        (name).append
-        (".mhd");
-      if (args_info.verbose_flag) {
-        std::cout << num << " " << roi->GetName() << " num=" << num << " : " << n << std::endl;
+    if (rois) {
+      for(iter = rois->begin(); iter != rois->end(); iter++) {
+        clitk::DicomRT_ROI::Pointer roi = iter->second;
+        clitk::DicomRTStruct2ImageFilter filter;
+        std::string name = roi->GetName();
+        int num = roi->GetROINumber();
+        filter.SetROI(roi); 
+        filter.SetCropMaskEnabled(args_info.crop_flag);
+        filter.SetImageFilename(args_info.image_arg);  // Used to get spacing + origin
+        name.erase(remove_if(name.begin(), name.end(), isspace), name.end());
+        std::string n = std::string(args_info.output_arg).append
+          (clitk::toString(num)).append
+          ("_").append
+          (name).append
+          (".mhd");
+        if (args_info.verbose_flag) {
+          std::cout << num << " " << roi->GetName() << " num=" << num << " : " << n << std::endl;
+        }
+        filter.SetOutputImageFilename(n);
+        filter.Update();  
       }
-      filter.SetOutputImageFilename(n);
-      filter.Update();
     }
+  }
+//   else {
+//     clitk::DicomRT_StructureSet::ROIConstIteratorType iter;
+//     for(iter = s->GetROIs().begin(); iter != s->GetROIs().end(); iter++) {
+//       clitk::DicomRT_ROI::Pointer roi = iter->second;
+//       // Create the filter
+//       clitk::DicomRTStruct2ImageFilter filter;
+//       filter.SetCropMaskEnabled(args_info.crop_flag);
+//       filter.SetImageFilename(args_info.image_arg);  // Used to get spacing + origin
+//       std::string name = roi->GetName();
+//       int num = roi->GetROINumber();
+//       filter.SetROI(roi); 
+//       name.erase(remove_if(name.begin(), name.end(), isspace), name.end());
+//       std::string n = std::string(args_info.output_arg).append
+//         (clitk::toString(num)).append
+//         ("_").append
+//         (name).append
+//         (".mhd");
+//       if (args_info.verbose_flag) {
+//         std::cout << num << " " << roi->GetName() << " num=" << num << " : " << n << std::endl;
+//       }
+//       filter.SetOutputImageFilename(n);
+//       filter.Update();
+//     }
 
     /*
     for(unsigned int i=0; i<s->GetListOfROI().size(); i++) {
@@ -87,7 +123,7 @@ int main(int argc, char * argv[]) {
       filter.SetOutputImageFilename(n);
       filter.Update();  
       }*/
-  }
+  //}
 
   // This is the end my friend 
   return 0;

diff --git a/tools/clitkDicomRTStruct2Image.ggo b/tools/clitkDicomRTStruct2Image.ggo
index d403f069524b7b112ceb67d19bb7b3eaad718f0a..06211bb334b38902ae4ed679e4b24a83663c9eee 100644 (file)
--- a/tools/clitkDicomRTStruct2Image.ggo
+++ b/tools/clitkDicomRTStruct2Image.ggo
@@ -7,9 +7,13 @@ option "verbose"         v "Verbose"                        flag       off
 option "verboseFile"     - "Verbose file content"            flag      off
 option "input"          i "Input Dicom file"                string     yes
 option "image"          j "Used to read image info (spacing, origin)"    string        yes
-option "roi"            r "ROI to binarize (if -1 = all roi)"            int    no default="-1"
 option "output"                 o "Output image filename"       string yes
 
+defgroup "ROIoption" groupdesc="an option of this group is required" 
+groupoption "roi"     r "ROI to binarize (if -1 = all roi)"            int    no default="-1" group="ROIoption"
+groupoption "roiName"     n "ROI name to binarize (be wary of spaces in ROI names; if blank, use given 'roi' value)"            string    no default="" group="ROIoption"
+groupoption "roiNameSubstr"     s "Substring of ROI name to binarize (reuturns the first match; if blank, use given 'roiName' value)"            string    no default="" group="ROIoption"
+
 option "crop"           c "Crop binary mask"            flag off
 
 #option "roi"           r "ROI to print (ID)"           int            no