X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLungGenericFilter.txx;h=01455c84c3ba65d77ecb811da8e8a8afa442e029;hb=refs%2Fheads%2Fmaster;hp=64e7fb85f36513f3aa75febcddfc2a965bb2098f;hpb=5668d4a49a5a6b68dc80fa28f0f82b54187cb70c;p=clitk.git

diff --git a/segmentation/clitkExtractLungGenericFilter.txx b/segmentation/clitkExtractLungGenericFilter.txx
index 64e7fb8..01455c8 100644
--- a/segmentation/clitkExtractLungGenericFilter.txx
+++ b/segmentation/clitkExtractLungGenericFilter.txx
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 #ifndef CLITKEXTRACTLUNGSGENERICFILTER_TXX
 #define CLITKEXTRACTLUNGSGENERICFILTER_TXX
@@ -51,11 +51,74 @@ template<class ArgsInfoType>
 void clitk::ExtractLungGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a) 
 {
   mArgsInfo=a;
-  SetIOVerbose(mArgsInfo.verbose_flag);
+  this->SetIOVerbose(mArgsInfo.verbose_flag);
   if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
-  if (mArgsInfo.input_given)   AddInputFilename(mArgsInfo.input_arg);
-  if (mArgsInfo.output_given)  AddOutputFilename(mArgsInfo.output_arg);
-  if (mArgsInfo.outputTrachea_given)  AddOutputFilename(mArgsInfo.outputTrachea_arg);
+  if (mArgsInfo.input_given)   this->AddInputFilename(mArgsInfo.input_arg);
+  if (mArgsInfo.output_given)  this->AddOutputFilename(mArgsInfo.output_arg);
+  if (mArgsInfo.outputTrachea_given)  this->AddOutputFilename(mArgsInfo.outputTrachea_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void clitk::ExtractLungGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f) 
+{
+  //f->SetVerboseFlag(mArgsInfo.verbose_flag);
+  f->SetVerboseOptionFlag(mArgsInfo.verboseOption_flag);
+  f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag);
+  f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
+  f->SetVerboseWarningFlag(!mArgsInfo.verboseWarningOff_flag);
+  f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
+
+  if (mArgsInfo.afdb_given)
+    f->SetAFDBFilename(mArgsInfo.afdb_arg);
+  f->SetOutputLungFilename(mArgsInfo.output_arg);
+  f->SetOutputTracheaFilename(mArgsInfo.outputTrachea_arg);
+  
+  f->SetUpperThreshold(mArgsInfo.upper_arg);
+  f->SetLowerThreshold(mArgsInfo.lower_arg);
+  
+  f->SetNumberOfSlicesToSkipBeforeSearchingSeed(mArgsInfo.skipslices_arg);
+
+  f->SetTracheaVolumeMustBeCheckedFlag(!mArgsInfo.doNotCheckTracheaVolume_flag);
+  f->SetVerboseRegionGrowingFlag(mArgsInfo.verboseRG_flag);
+
+  f->SetUpperThresholdForTrachea(mArgsInfo.upperThresholdForTrachea_arg);
+  f->SetMultiplierForTrachea(mArgsInfo.multiplierForTrachea_arg);
+  f->SetThresholdStepSizeForTrachea(mArgsInfo.thresholdStepSizeForTrachea_arg);
+  f->SetTracheaSeedAlgorithm(mArgsInfo.type_arg);
+  f->SetNumSlices(mArgsInfo.numSlices_arg);
+  f->SetMaxElongation(mArgsInfo.maxElongation_arg);
+  f->SetSeedPreProcessingThreshold(mArgsInfo.seedPreProcessingThreshold_arg);
+
+  typename FilterType::InputImagePointType s;
+  if (mArgsInfo.seed_given) {
+    ConvertOptionMacro(mArgsInfo.seed, s, 3, false);
+    f->AddSeed(s);
+  }
+
+  f->SetMinimalComponentSize(mArgsInfo.minSize_arg);
+  f->SetNumberOfHistogramBins(mArgsInfo.bins_arg);
+  f->SetRadiusForTrachea(mArgsInfo.radius_arg);
+  
+  f->SetOpenCloseFlag(mArgsInfo.openclose_flag);
+  f->SetOpenCloseRadius(mArgsInfo.opencloseRadius_arg);
+  f->SetAutoCrop(!mArgsInfo.noAutoCrop_flag);
+  
+  if (mArgsInfo.doNotFillHoles_given)
+    f->SetFillHolesFlag(false);
+  else
+    f->SetFillHolesFlag(true);
+
+  f->SetRemoveSmallLabelBeforeSeparationFlag(mArgsInfo.removeSmallLabel_flag);
+
+  if (mArgsInfo.doNotSeparateLungs_given)
+    f->SetSeparateLungsFlag(false);
+  else
+    f->SetSeparateLungsFlag(true);
 }
 //--------------------------------------------------------------------
 
@@ -81,8 +144,8 @@ void clitk::ExtractLungGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
   this->SetFilterBase(filter);
     
   // Set global Options 
-  filter->SetArgsInfo(mArgsInfo);
   filter->SetInput(input);
+  SetOptionsFromArgsInfoToFilter<FilterType>(filter);
 
   // Go !
   filter->Update();