From: tbaudier <thomas.baudier@creatis.insa-lyon.fr>
Date: Thu, 20 Dec 2018 10:01:48 +0000 (+0100)
Subject: Change serie number to serie UID
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=e4970a5c24b53d6842e4f8f02d63b957f03bfbba;p=clitk.git

Change serie number to serie UID
In clitkDicom2Image, change serie number to serie UID.
Serie UID is more restrictive and better to separate series
Change number to string because series UID is a string

Series UID is better to use itk::GDCMSeriesFileNames
---

diff --git a/tools/clitkDicom2Image.cxx b/tools/clitkDicom2Image.cxx
index 5c9889b..b3bcc90 100644
--- a/tools/clitkDicom2Image.cxx
+++ b/tools/clitkDicom2Image.cxx
@@ -58,12 +58,12 @@ int main(int argc, char * argv[])
 
   //===========================================
   /// Get slices locations ...
-  int series_number = -1;
-  std::set<int> series_numbers;
-  std::map< int, std::vector<double> > theorigin;
-  std::map< int, std::vector<double> > theorientation;
-  std::map< int, std::vector<double> > sliceLocations;
-  std::map< int, std::vector<std::string> > seriesFiles;
+  std::string series_UID = "";
+  std::set<std::string> series_UIDs;
+  std::map< std::string, std::vector<double> > theorigin;
+  std::map< std::string, std::vector<double> > theorientation;
+  std::map< std::string, std::vector<double> > sliceLocations;
+  std::map< std::string, std::vector<std::string> > seriesFiles;
 #if GDCM_MAJOR_VERSION >= 2
   if (args_info.verbose_flag)
     std::cout << "Using GDCM-2.x" << std::endl;
@@ -83,28 +83,28 @@ int main(int argc, char * argv[])
     gdcm::DataSet& ds = hreader.GetFile().GetDataSet();
 
     if (args_info.extract_series_flag) {
-      gdcm::Attribute<0x20,0x11> series_number_att;
-      series_number_att.SetFromDataSet(ds);
-      series_number = series_number_att.GetValue();
+      gdcm::Attribute<0x20,0x000e> series_UID_att;
+      series_UID_att.SetFromDataSet(ds);
+      series_UID = series_UID_att.GetValue();
     }
 
-    series_numbers.insert(series_number);
-    theorigin[series_number] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
-    theorientation[series_number] = gdcm::ImageHelper::GetDirectionCosinesValue(hreader.GetFile());
+    series_UIDs.insert(series_UID);
+    theorigin[series_UID] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
+    theorientation[series_UID] = gdcm::ImageHelper::GetDirectionCosinesValue(hreader.GetFile());
     if (args_info.patientSystem_flag) {
-      double n1 = theorientation[series_number][1]*theorientation[series_number][5]-
-                  theorientation[series_number][2]*theorientation[series_number][4];
-      double n2 = theorientation[series_number][3]*theorientation[series_number][2]-
-                  theorientation[series_number][5]*theorientation[series_number][0];
-      double n3 = theorientation[series_number][0]*theorientation[series_number][4]-
-                  theorientation[series_number][1]*theorientation[series_number][3];
-      double sloc = theorigin[series_number][0]*n1+
-                    theorigin[series_number][1]*n2+
-                    theorigin[series_number][2]*n3;
-      sliceLocations[series_number].push_back(sloc);
+      double n1 = theorientation[series_UID][1]*theorientation[series_UID][5]-
+                  theorientation[series_UID][2]*theorientation[series_UID][4];
+      double n2 = theorientation[series_UID][3]*theorientation[series_UID][2]-
+                  theorientation[series_UID][5]*theorientation[series_UID][0];
+      double n3 = theorientation[series_UID][0]*theorientation[series_UID][4]-
+                  theorientation[series_UID][1]*theorientation[series_UID][3];
+      double sloc = theorigin[series_UID][0]*n1+
+                    theorigin[series_UID][1]*n2+
+                    theorigin[series_UID][2]*n3;
+      sliceLocations[series_UID].push_back(sloc);
     } else
-      sliceLocations[series_number].push_back(theorigin[series_number][2]);
-    seriesFiles[series_number].push_back(input_files[i]);
+      sliceLocations[series_UID].push_back(theorigin[series_UID][2]);
+    seriesFiles[series_UID].push_back(input_files[i]);
 
     gdcm::Attribute<0x28, 0x100> pixel_size;
     pixel_size.SetFromDataSet(ds);
@@ -122,16 +122,16 @@ int main(int argc, char * argv[])
   header->Load();
 
   if (args_info.extract_series_flag) {
-    series_number = atoi(header->GetEntryValue(0x20,0x11).c_str());
+    series_UID = header->GetEntryValue(0x20,0x000e).c_str();
   }
 
-  series_numbers.insert(series_number);
-  theorigin[series_number].resize(3);
-  theorigin[series_number][0] = header->GetXOrigin();
-  theorigin[series_number][1] = header->GetYOrigin();
-  theorigin[series_number][2] = header->GetZOrigin();
-  sliceLocations[series_number].push_back(theorigin[series_number][2]);
-  seriesFiles[series_number].push_back(input_files[i]);
+  series_UIDs.insert(series_UID);
+  theorigin[series_UID].resize(3);
+  theorigin[series_UID][0] = header->GetXOrigin();
+  theorigin[series_UID][1] = header->GetYOrigin();
+  theorigin[series_UID][2] = header->GetZOrigin();
+  sliceLocations[series_UID].push_back(theorigin[series_UID][2]);
+  seriesFiles[series_UID].push_back(input_files[i]);
   /*if (header->GetPixelSize() != 2) {
     std::cerr << "Pixel type 2 bytes ! " << std::endl;
     std::cerr << "In file " << input_files[i] << std::endl;
@@ -143,8 +143,8 @@ int main(int argc, char * argv[])
 
   //===========================================
   // Sort slices locations ...
-  std::set<int>::iterator sn = series_numbers.begin();
-  while ( sn != series_numbers.end() ) {
+  std::set<std::string>::iterator sn = series_UIDs.begin();
+  while ( sn != series_UIDs.end() ) {
     std::vector<double> locs = sliceLocations[*sn];
     std::vector<double> origin = theorigin[*sn];
     std::vector<std::string> files = seriesFiles[*sn];
@@ -229,7 +229,7 @@ int main(int argc, char * argv[])
     }
 
     std::string outfile;
-    if (series_numbers.size() == 1)
+    if (series_UIDs.size() == 1)
       outfile = args_info.output_arg;
     else {
       std::ostringstream name;