From: tbaudier <thomas.baudier@creatis.insa-lyon.fr>
Date: Fri, 11 Jan 2019 10:55:04 +0000 (+0100)
Subject: Remove extract_series option
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=d647919fe732d73ed24138daaec16080c00df892;p=clitk.git

Remove extract_series option

With the itk::GDCMSeriesFileNames, we automatically have the dicom sorted according series, so this option is not necessary anymore.
So I removed the option in the .ggo file and I remove the if conditions.

I add .c_str() to series_UID to remove trailling white spaces
---

diff --git a/tools/clitkDicom2Image.cxx b/tools/clitkDicom2Image.cxx
index 54ab6bd..066aaf8 100644
--- a/tools/clitkDicom2Image.cxx
+++ b/tools/clitkDicom2Image.cxx
@@ -93,11 +93,9 @@ int main(int argc, char * argv[])
     hreader.Read();
     gdcm::DataSet& ds = hreader.GetFile().GetDataSet();
 
-    if (args_info.extract_series_flag) {
-      gdcm::Attribute<0x20,0x000e> series_UID_att;
-      series_UID_att.SetFromDataSet(ds);
-      series_UID = series_UID_att.GetValue();
-    }
+    gdcm::Attribute<0x20,0x000e> series_UID_att;
+    series_UID_att.SetFromDataSet(ds);
+    series_UID = series_UID_att.GetValue().c_str();
 
     series_UIDs.insert(series_UID);
     theorigin[series_UID] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
@@ -132,9 +130,7 @@ int main(int argc, char * argv[])
   header->SetMaxSizeLoadEntry(16384); // required ?
   header->Load();
 
-  if (args_info.extract_series_flag) {
-    series_UID = header->GetEntryValue(0x20,0x000e).c_str();
-  }
+  series_UID = header->GetEntryValue(0x20,0x000e).c_str();
 
   series_UIDs.insert(series_UID);
   theorigin[series_UID].resize(3);
diff --git a/tools/clitkDicom2Image.ggo b/tools/clitkDicom2Image.ggo
index 7cf454f..fd678f9 100644
--- a/tools/clitkDicom2Image.ggo
+++ b/tools/clitkDicom2Image.ggo
@@ -1,6 +1,6 @@
 # file clitkDicom2Image.ggo
 package "clitk"
-version "Try to convert a DICOM into an image (.hdr, .vox...)"
+version "Try to convert a DICOM into an image (.hdr, .vox...) identifying all available series"
 
 option "config"	  	    -	"Config file"		 string  	no
 option "verbose"	      v "Verbose"		 	 flag off
@@ -8,5 +8,4 @@ option "tolerance"	    t "Tolerance for slice position"	 double default="0" no
 option "output"         o "Output image filename"		string 	yes
 option "std_input"      - "Take the like of input file from stdin, to support huge lists of filenames" flag off
 option "focal_origin"   - "Output files with FOCAL-like origin, instead of the origin present in the dicom files" flag off
-option "extract_series" s "Identify different series in the file list and create the MHDs accordinly" flag off
 option "patientSystem"  p "Open the image with patient coordinate system" flag off