add options ('keep object', 'inverse', verbose etc)

diff --git a/tools/clitkRelativePosition.ggo b/tools/clitkRelativePosition.ggo
index 4f65fe23c96a4a4c90d07a7501e520c615fce820..2192012f6d496a94910efefab89e2b63f9e6134d 100644 (file)
--- a/tools/clitkRelativePosition.ggo
+++ b/tools/clitkRelativePosition.ggo
@@ -8,7 +8,7 @@ option "config"         -       "Config file"                     string        no
 option "verbose"       v       "Verbose"                         flag          off
 option "verboseStep"    -       "Verbose each step"              flag          off
 option "writeStep"      w       "Write image at each step"       flag          off
-option "verboseOption"  -       "Display options values"          flag          off
+option "verboseOptions" -       "Display options values"          flag          off
 option "imagetypes"     -       "Display allowed image types"     flag          off
 
 section "Input/Output"
@@ -17,19 +17,19 @@ option "object"             j       "Input mask object filename"      string        yes
 option "output"        o       "Output image filename"           string        yes
 
 section "Main options"
-option "orientation"           r       "L R A P I S (LeftRightAntPostInfSup)"          string no       default="L"
+option "orientation"           r       "L R A P I S (LeftRightAntPostInfSup)"          string no multiple      default="L"
 option "angle1"        a       "Angle 1 (deg)"                    double       no      default="0"
 option "angle2"        b       "Angle 2 (deg)"                    double       no      default="0"
 option "spacing"       s       "Resample before (faster)"         double       no
 option "threshold"     t       "Fuzzy threshold"                  double       no default="0.6"
-option "not"            n       "Not flag : inverse of the orientation"     flag   off
+option "inverse"        n       "Not flag : inverse of the orientation"     flag   off
+option "doNotRemoveObject"  -   "if flag is on, do not remove the object"   flag   off
 option "noAutoCrop"     c       "No auto crop at the end if set"            flag   off
+option "combineWithOr"  -       "Combine relpos map and support with OR"    flag   off
 
 section "Slice by slice processing"
 option "sliceBySlice"   -       "Slice by slice relative position"          flag   off
 option "direction"     d       "If SbS, indicate the slice direction"      int    no default="2"
+option "uniqueCCL"      u       "Keep only one CC in each slice"            flag   off
    
 
-
-
-

diff --git a/tools/clitkRelativePositionGenericFilter.txx b/tools/clitkRelativePositionGenericFilter.txx
index 2e62b42957846569b3b66fbfb86a58b169ab0f4d..7ed172deaeea9c239783d7516e22e37bb83f890d 100644 (file)
--- a/tools/clitkRelativePositionGenericFilter.txx
+++ b/tools/clitkRelativePositionGenericFilter.txx
@@ -65,12 +65,12 @@ template<class FilterType>
 void clitk::RelativePositionGenericFilter<ArgsInfoType>::
 SetOptionsFromArgsInfoToFilter(FilterType * f) 
 {
-  f->SetVerboseOption(mArgsInfo.verbose_flag);
-  f->SetVerboseStep(mArgsInfo.verboseStep_flag);
-  f->SetWriteStep(mArgsInfo.writeStep_flag);
+  f->SetVerboseOptionFlag(mArgsInfo.verboseOptions_flag);
+  f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag);
+  f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
 
-  if (mArgsInfo.orientation_given) {
-    f->SetOrientationTypeString(mArgsInfo.orientation_arg);
+  for(uint i=0; i<mArgsInfo.orientation_given; i++) {
+    f->AddOrientationTypeString(mArgsInfo.orientation_arg[i]);
   }
   
   if (mArgsInfo.spacing_given) {
@@ -79,8 +79,10 @@ SetOptionsFromArgsInfoToFilter(FilterType * f)
   }
 
   f->SetFuzzyThreshold(mArgsInfo.threshold_arg);
-  f->SetNotFlag(mArgsInfo.not_flag);
+  f->SetRemoveObjectFlag(!mArgsInfo.doNotRemoveObject_flag);
   f->SetAutoCropFlag(!mArgsInfo.noAutoCrop_flag);
+  f->SetCombineWithOrFlag(mArgsInfo.combineWithOr_flag);
+  f->SetInverseOrientationFlag(mArgsInfo.inverse_flag);
 }
 
 //--------------------------------------------------------------------
@@ -107,7 +109,10 @@ UpdateWithInputImageType()
     filter->SetInput(input);
     filter->SetInputObject(object);
     SetOptionsFromArgsInfoToFilter<FilterType>(filter);
-    filter->SetDirection(mArgsInfo.direction_arg); // only for SliceBySliceRelativePositionFilter
+
+    // Set options only for SliceBySliceRelativePositionFilter
+    filter->SetDirection(mArgsInfo.direction_arg);
+    filter->SetUniqueConnectedComponentBySlice(mArgsInfo.uniqueCCL_flag);
     
     // Go !
     filter->Update();
@@ -127,8 +132,8 @@ UpdateWithInputImageType()
     // Set global Options 
     filter->SetInput(input);
     filter->SetInputObject(object);
-    filter->SetAngle1(mArgsInfo.angle1_arg);// only for this filter
-    filter->SetAngle2(mArgsInfo.angle2_arg);
+    if (mArgsInfo.angle1_given && mArgsInfo.angle2_given)
+      filter->AddAngles(mArgsInfo.angle1_arg, mArgsInfo.angle2_arg);
     SetOptionsFromArgsInfoToFilter<FilterType>(filter);
    
     // Go !