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
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
- ======================================================================-====*/
+ ===========================================================================**/
#include "clitkImageCommon.h"
void clitk::ExtractPatientGenericFilter<ArgsInfoType>::InitializeImageType()
{
ADD_IMAGE_TYPE(Dim, short);
+ ADD_IMAGE_TYPE(Dim, unsigned short);
+ ADD_IMAGE_TYPE(Dim, float);
// ADD_IMAGE_TYPE(Dim, int);
// ADD_IMAGE_TYPE(Dim, float);
}
void clitk::ExtractPatientGenericFilter<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) SetInputFilename(mArgsInfo.input_arg);
- if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
+ if (mArgsInfo.input_given) this->SetInputFilename(mArgsInfo.input_arg);
+ if (mArgsInfo.output_given) this->AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void
+clitk::ExtractPatientGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+ f->SetVerboseOptionFlag(mArgsInfo.verbose_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->SetOutputPatientFilename(mArgsInfo.output_arg);
+
+ f->SetUpperThreshold(mArgsInfo.upper_arg);
+ f->SetLowerThreshold(mArgsInfo.lower_arg);
+ f->SetPrimaryOpeningRadius(mArgsInfo.openingRadius_arg);
+
+ f->SetDecomposeAndReconstructDuringFirstStep(mArgsInfo.erode1_flag);
+
+ // Convert to SizeType
+ typename FilterType::InputImageSizeType s;
+ if (mArgsInfo.radius1_given) {
+ ConvertOptionMacro(mArgsInfo.radius1, s, 3, false);
+ f->SetRadius1(s);
+ }
+
+ f->SetMaximumNumberOfLabels1(mArgsInfo.max1_arg);
+ f->SetNumberOfNewLabels1(mArgsInfo.new1_arg);
+
+ f->SetDecomposeAndReconstructDuringSecondStep(mArgsInfo.erode2_flag);
+
+ // Convert to SizeType
+ if (mArgsInfo.radius2_given) {
+ ConvertOptionMacro(mArgsInfo.radius2, s, 3, false);
+ f->SetRadius2(s);
+ }
+
+ f->SetMaximumNumberOfLabels2(mArgsInfo.max2_arg);
+ f->SetNumberOfNewLabels2(mArgsInfo.new2_arg);
+
+ f->SetFirstKeep(mArgsInfo.firstKeep_arg);
+ f->SetLastKeep(mArgsInfo.lastKeep_arg);
+
+ f->SetFinalOpenClose(mArgsInfo.openClose_flag);
+ f->SetAutoCrop(!mArgsInfo.noAutoCrop_flag);
}
//--------------------------------------------------------------------
typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
// Create filter
- typedef clitk::ExtractPatientFilter<ImageType, OutputImageType> FilterType;
+ typedef clitk::ExtractPatientFilter<ImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
// Set the filter (needed for example for threaded monitoring)
this->SetFilterBase(filter);
// Set global Options
- filter->SetArgsInfo(mArgsInfo);
filter->SetInput(input);
+ SetOptionsFromArgsInfoToFilter<FilterType>(filter);
// Go !
filter->Update();
-
- // // Check if error
- // if (filter->HasError()) {
- // SetLastError(filter->GetLastError());
- // // No output
- // return;
- // }
// Write/Save results
typename OutputImageType::Pointer output = filter->GetOutput();