MeVisLab Toolbox Reference
mlMLToDicomTools.h
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1 // Copyright (c) Fraunhofer MEVIS, Germany. All rights reserved.
2 // **InsertLicense** code
3 //----------------------------------------------------------------------------------
5 
10 //----------------------------------------------------------------------------------
11 
12 #pragma once
13 
14 #include "MLMLToDicomToolsSystem.h"
15 #include <mlModuleIncludes.h>
16 #include <DCMTree_Lib.h>
17 
18 ML_START_NAMESPACE
19 
20 // Forward of volume representation of DirectDicomImport module.
21 class _DicomDateTimeTagIds;
22 class BitImage;
23 
26 namespace MLToDicomTools {
27 
46  ML_MLToDicomTools_EXPORT void getSpacingImagePositionAndOrientationPatientFromMLWorldMatrix(MedicalImageProperties imgProps,
47  Vector3 &pixelSpacing,
48  Vector3 &imagePositionPatient,
49  Vector6 &imageOrientationPatient,
50  std::string *issueMessages=nullptr);
51 
75  ML_MLToDicomTools_EXPORT void setPixelData(DCMTree::TagPtr pixelDataTag,
76  PagedImage &inImg,
77  MLDataType overrideDataType=ML_INVALID_DATA_TYPE,
78  double *minVal=nullptr,
79  double *maxVal=nullptr,
80  const SubImageBox *overrideBox=nullptr);
81 
97  ML_MLToDicomTools_EXPORT void setVectorGridData(DCMTree::TagPtr vecGridDataTag,
98  PagedImage &inImg);
99 
109  ML_MLToDicomTools_EXPORT std::string addAndSetSEGPixelDataTag(DCMTree::TreePtr dcmTree,
110  const BitImage &bitImage,
111  bool writePadded);
112 
120  ML_MLToDicomTools_EXPORT std::string appendImagePixelModuleTags(DCMTree::TreePtr resultTree,
121  unsigned int samplesPerPixel,
122  const std::string &photometricInterpretation,
123  unsigned int rows,
124  unsigned int columns,
125  unsigned int bitsAllocated,
126  unsigned int bitsStored,
127  unsigned int highBit,
128  unsigned int pixelRepresentation,
129  bool writePlanarConfiguration=false,
130  unsigned int planarConfiguration=0,
131  bool writeMinMaxPixelValue=false,
132  double smallestPixelValue=0,
133  double largestPixelValue=0,
134  MLint numberOfColorChannels=0,
135  const std::vector<std::string> &cDimInfos=std::vector<std::string>());
136 
143  ML_MLToDicomTools_EXPORT std::string setSegmentationBinaryImagePixelTags(DCMTree::TreePtr &dcmTree,
144  const BitImage &inputBitImage);
145 
146 
153  ML_MLToDicomTools_EXPORT std::string setSegmentationFractionalImagePixelTags(DCMTree::TreePtr &dcmTree,
154  const PagedImage &inputBitImage);
155 
156  // Forward to the internally used parameter container describing for
157  // example additional multiframe parameters.
158  class AdvancedTagSetUpArgs;
159 
195  ML_MLToDicomTools_EXPORT SubImageBox determineFrameRegion(DCMTree::TreePtr dcmTree,
196  const FieldContainer *treeInfos,
197  PagedImage &inImg,
198  Vector3 *srcImgPosPatient = nullptr,
199  Vector3 *dstImgPosPatient = nullptr,
200  std::string *errorMessage = nullptr,
201  bool useFullTUDimExtentFromInImgInSliceWiseUpdate=false,
202  AdvancedTagSetUpArgs *configParams = nullptr);
203 
215  ML_MLToDicomTools_EXPORT bool setUpPhotometricInterpretation(DCMTree::TreePtr dcmTree,
216  MLint numColorChannels,
217  const std::vector<std::string> &cDimInfos);
218 
262  // TODO: Support DCMTree_FloatPixelData and DCMTree_DoubleFloatPixelData
298  ML_MLToDicomTools_EXPORT std::string setImagePixelTags(DCMTree::TreePtr dcmTree,
299  const FieldContainer *treeInfos,
300  PagedImage &inImg,
301  bool adjustSliceWise,
302  bool reportNonOrthoWorldMatrix,
303  AdvancedTagSetUpArgs *configParams=nullptr);
304 };
305 
306 ML_END_NAMESPACE
DCMTree_Lib.h
MLMLToDicomToolsSystem.h
Project global and OS specific declarations.
ML_MLToDicomTools_EXPORT
#define ML_MLToDicomTools_EXPORT
Only for diagnostic purposes.
Definition: MLMLToDicomToolsSystem.h:22
ml::BitImage
Class to manage a binary image.
Definition: mlBitImage.h:67
ml::FieldContainer
Defines the class FieldContainer to encapsulate a vector of fields for (see class Field).
Definition: mlFieldContainer.h:62
ml::MLToDicomTools::AdvancedTagSetUpArgs
Some dedicated parameters for advanced tag setups when setting pixel data and related tags in DICOM f...
Definition: mlMLToDicomTagSetUpArguments.h:31
ml::MedicalImageProperties
This class encapsulates basic medical image properties:
Definition: mlMedicalImageProperties.h:69
ml::PagedImage
Class which represents an image, which manages properties of an image and image data which is located...
Definition: mlPagedImage.h:70
ML_INVALID_DATA_TYPE
#define ML_INVALID_DATA_TYPE
Defines an invalid MLDataType.
Definition: mlTypeDefs.h:715
MLDataType
MLint32 MLDataType
MLDataType.
Definition: mlTypeDefs.h:684
MLint
MLint64 MLint
A signed ML integer type with at least 64 bits used for index calculations on very large images even ...
Definition: mlTypeDefs.h:578
DCMTree::TagPtr
boost::shared_ptr< Tag > TagPtr
shared-pointer to tag
Definition: DCMTree_Lib.h:59
DCMTree::TreePtr
boost::shared_ptr< Tree > TreePtr
shared pointer to a DCMTree::Tree
Definition: DCMTree_Lib.h:70
ml::MLToDicomTools::determineFrameRegion
ML_MLToDicomTools_EXPORT SubImageBox determineFrameRegion(DCMTree::TreePtr dcmTree, const FieldContainer *treeInfos, PagedImage &inImg, Vector3 *srcImgPosPatient=nullptr, Vector3 *dstImgPosPatient=nullptr, std::string *errorMessage=nullptr, bool useFullTUDimExtentFromInImgInSliceWiseUpdate=false, AdvancedTagSetUpArgs *configParams=nullptr)
If possible then determine and return the region in inImg which corresponds to the region the dcmTree...
ml::MLToDicomTools::setVectorGridData
ML_MLToDicomTools_EXPORT void setVectorGridData(DCMTree::TagPtr vecGridDataTag, PagedImage &inImg)
Gets a floating point vector field with getTile from inImg and sets it as OF value of the vecGridData...
ml::MLToDicomTools::appendImagePixelModuleTags
ML_MLToDicomTools_EXPORT std::string appendImagePixelModuleTags(DCMTree::TreePtr resultTree, unsigned int samplesPerPixel, const std::string &photometricInterpretation, unsigned int rows, unsigned int columns, unsigned int bitsAllocated, unsigned int bitsStored, unsigned int highBit, unsigned int pixelRepresentation, bool writePlanarConfiguration=false, unsigned int planarConfiguration=0, bool writeMinMaxPixelValue=false, double smallestPixelValue=0, double largestPixelValue=0, MLint numberOfColorChannels=0, const std::vector< std::string > &cDimInfos=std::vector< std::string >())
Appends required DICOM tags to resultTree according to DICOM standard, C.7.6.3 Image Pixel Module Att...
ml::MLToDicomTools::setSegmentationBinaryImagePixelTags
ML_MLToDicomTools_EXPORT std::string setSegmentationBinaryImagePixelTags(DCMTree::TreePtr &dcmTree, const BitImage &inputBitImage)
Set Image Pixel / Segmentation Image Module Attribute tags for a binary segmentation image using setI...
ml::MLToDicomTools::setPixelData
ML_MLToDicomTools_EXPORT void setPixelData(DCMTree::TagPtr pixelDataTag, PagedImage &inImg, MLDataType overrideDataType=ML_INVALID_DATA_TYPE, double *minVal=nullptr, double *maxVal=nullptr, const SubImageBox *overrideBox=nullptr)
Gets an input image as pixel data with getTile from inImg and sets it as value of pixelDataTag.
ml::MLToDicomTools::getSpacingImagePositionAndOrientationPatientFromMLWorldMatrix
ML_MLToDicomTools_EXPORT void getSpacingImagePositionAndOrientationPatientFromMLWorldMatrix(MedicalImageProperties imgProps, Vector3 &pixelSpacing, Vector3 &imagePositionPatient, Vector6 &imageOrientationPatient, std::string *issueMessages=nullptr)
Gets DICOM compliant values for tags Pixel Spacing, Image Position Patient, and Image Orientation Pat...
ml::MLToDicomTools::setSegmentationFractionalImagePixelTags
ML_MLToDicomTools_EXPORT std::string setSegmentationFractionalImagePixelTags(DCMTree::TreePtr &dcmTree, const PagedImage &inputBitImage)
Set Image Pixel / Segmentation Image Module Attribute tags for a fractional segmentation image using ...
ml::MLToDicomTools::setUpPhotometricInterpretation
ML_MLToDicomTools_EXPORT bool setUpPhotometricInterpretation(DCMTree::TreePtr dcmTree, MLint numColorChannels, const std::vector< std::string > &cDimInfos)
Evaluates the number of color channels and the cDimInfos of the input image, checks for valid setting...
ml::MLToDicomTools::setImagePixelTags
ML_MLToDicomTools_EXPORT std::string setImagePixelTags(DCMTree::TreePtr dcmTree, const FieldContainer *treeInfos, PagedImage &inImg, bool adjustSliceWise, bool reportNonOrthoWorldMatrix, AdvancedTagSetUpArgs *configParams=nullptr)
Gets the input image and its properties, checks whether it is DICOM-like and if yes it sets image pix...
ml::MLToDicomTools::addAndSetSEGPixelDataTag
ML_MLToDicomTools_EXPORT std::string addAndSetSEGPixelDataTag(DCMTree::TreePtr dcmTree, const BitImage &bitImage, bool writePadded)
Stores the bit mask given by BitImage in newly created PixelData tag in dcmTree; it does not set any ...