1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ======================================================================-====*/
19 #include "clitkImageCommon.h"
21 //--------------------------------------------------------------------
22 template<class ArgsInfoType>
23 clitk::CropImageGenericFilter<ArgsInfoType>::CropImageGenericFilter():
24 ImageToImageGenericFilter<Self>("CropImage")
27 cmdline_parser_clitkCropImage_init(&mArgsInfo);
28 InitializeImageType<2>();
29 InitializeImageType<3>();
30 InitializeImageType<4>();
32 //--------------------------------------------------------------------
35 //--------------------------------------------------------------------
36 template<class ArgsInfoType>
37 template<unsigned int Dim>
38 void clitk::CropImageGenericFilter<ArgsInfoType>::InitializeImageType()
40 ADD_DEFAULT_IMAGE_TYPES(Dim);
41 //ADD_IMAGE_TYPE(Dim, uchar);
42 //ADD_IMAGE_TYPE(Dim, short);
43 // ADD_IMAGE_TYPE(Dim, uint);
44 // ADD_IMAGE_TYPE(Dim, ulong);
45 // ADD_IMAGE_TYPE(Dim, int);
46 // ADD_IMAGE_TYPE(Dim, float);
48 //--------------------------------------------------------------------
51 //--------------------------------------------------------------------
52 template<class ArgsInfoType>
53 void clitk::CropImageGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a)
56 SetIOVerbose(mArgsInfo.verbose_flag);
57 if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
58 if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg);
59 if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
61 //--------------------------------------------------------------------
64 //--------------------------------------------------------------------
65 // Update with the number of dimensions and the pixeltype
66 //--------------------------------------------------------------------
67 template<class ArgsInfoType>
68 template<class ImageType>
69 void clitk::CropImageGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
72 typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
75 if (mArgsInfo.BG_given && mArgsInfo.like_given)
76 clitkExceptionMacro("Do not use --BG and --like at the same time");
79 typename ImageType::Pointer output;
81 // ------------------------------------------------
82 if (mArgsInfo.BG_given) { // AutoCrop filter
83 if (mArgsInfo.boundingBox_given)
84 clitkExceptionMacro("Do not use --BG and --boundingBox at the same time");
85 if (mArgsInfo.lower_given)
86 clitkExceptionMacro("Do not use --BG and --lower at the same time");
87 if (mArgsInfo.upper_given)
88 clitkExceptionMacro("Do not use --BG and --upper at the same time");
89 typedef clitk::AutoCropFilter<ImageType> FilterType;
90 typename FilterType::Pointer filter = FilterType::New();
91 filter->SetInput(input);
92 filter->SetBackgroundValue(mArgsInfo.BG_arg);
94 output = filter->GetOutput();
97 // ------------------------------------------------
98 if (mArgsInfo.like_given) { // CropLike filter
99 if (mArgsInfo.boundingBox_given)
100 clitkExceptionMacro("Do not use --like and --boundingBox at the same time");
101 if (mArgsInfo.lower_given)
102 clitkExceptionMacro("Do not use --like and --lower at the same time");
103 if (mArgsInfo.upper_given)
104 clitkExceptionMacro("Do not use --like and --upper at the same time");
105 typedef clitk::CropLikeImageFilter<ImageType> FilterType;
106 typename FilterType::Pointer filter = FilterType::New();
107 filter->SetInput(input);
108 filter->SetCropLikeFilename(mArgsInfo.like_arg);
109 filter->SetBackgroundValue(mArgsInfo.BGLike_arg);
111 output = filter->GetOutput();
114 // ------------------------------------------------
115 typename ImageType::SizeType lSize;
116 typename ImageType::SizeType uSize;
117 if (mArgsInfo.boundingBox_given) {
118 for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
119 lSize[i] = mArgsInfo.boundingBox_arg[2*i];
120 uSize[i] = input->GetLargestPossibleRegion().GetSize()[i]-mArgsInfo.boundingBox_arg[2*i+1]-1;
124 if (mArgsInfo.lower_given) {
125 for(unsigned int i=0; i<ImageType::ImageDimension; i++)
126 lSize[i]=static_cast<unsigned int >(mArgsInfo.lower_arg[i]);
129 if (mArgsInfo.upper_given) {
130 for(unsigned int i=0; i<ImageType::ImageDimension; i++)
131 uSize[i]=static_cast<unsigned int >(mArgsInfo.upper_arg[i]);
135 typedef itk::CropImageFilter<ImageType, ImageType> CropImageFilterType;
136 typename CropImageFilterType::Pointer filter=CropImageFilterType::New();
137 filter->SetInput(input);
138 filter->SetLowerBoundaryCropSize(lSize);
139 filter->SetUpperBoundaryCropSize(uSize);
141 output = filter->GetOutput();
145 // Force origin if needed
146 if (mArgsInfo.origin_flag) {
147 typename ImageType::PointType origin;
148 origin.Fill(itk::NumericTraits<double>::Zero);
149 output->SetOrigin(origin);
152 // Write/Save results
153 this->template SetNextOutput<ImageType>(output);
155 //--------------------------------------------------------------------