names the class to be instantiated, currently this can be one of
- DICOMITKSeriesGDCMReader
- ThreeDnTDICOMSeriesReader
Both classes bring simple configuration flags with them and a description of how images are sorted prior to loading.
Flag for DICOMITKSeriesGDCMReader:
fixTiltByShearing="true|false"
Determines whether a potential gantry tilt should be "fixed" by shearing the output image.
Flag for ThreeDnTDICOMSeriesReader:
group3DnT="true|false"
Determines whether images at the same spatial position should be interpreted as 3D+t images.
The tags and describe the basic loading strategy of both
reader mentioned above: first images are divided into incompatible groups (),
and afterwards the images within each group are sorted by means of DICOMSortCriterion, which
most commonly mentions a tag.
Tag element and group are interpreted as the exadecimal numbers
found all around the DICOM standard. The numbers can be prepended by a "0x" if this is preferred
by the programmer (but they are taken as hexadecimal in all cases).
\section DICOMReaderConfigurator_AboutTheFuture About the future evolution of this class
This first version is hard coded for the current state of the implementation.
If things should evolve in a way that needs us to splitt off readers for "old" versions,
time should be taken to refactor this class.
Basically, a serializer class should accompany each of the configurable classes. Such
serializer classes should be registered and discovered via micro-services (to support extensions).
A serializer should offer both methods to serialize a class and to desirialize it again.
A "version" attribute at the top-level tag should be used to distinguish versions.
Usually it should be enough to keep DE-serializers for all versions. Writers for the most
recent version should be enough.
*/
-class MITKDICOMREADER_EXPORT DICOMReaderConfigurator : public itk::LightObject
+class MITKDICOM_EXPORT DICOMReaderConfigurator : public itk::LightObject
{
public:
mitkClassMacroItkParent( DICOMReaderConfigurator, itk::LightObject );
itkNewMacro( DICOMReaderConfigurator );
DICOMFileReader::Pointer CreateFromConfigFile(const std::string& filename) const;
DICOMFileReader::Pointer CreateFromUTF8ConfigString(const std::string& xmlContents) const;
std::string CreateConfigStringFromReader(DICOMFileReader::ConstPointer reader) const;
protected:
DICOMReaderConfigurator();
~DICOMReaderConfigurator() override;
private:
DICOMFileReader::Pointer CreateFromTiXmlDocument(TiXmlDocument& doc) const;
DICOMTag tagFromXMLElement(TiXmlElement*) const;
std::string requiredStringAttribute(TiXmlElement* xmlElement, const std::string& key) const;
unsigned int hexStringToUInt(const std::string& s) const;
ThreeDnTDICOMSeriesReader::Pointer ConfigureThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, TiXmlElement*) const;
DICOMITKSeriesGDCMReader::Pointer ConfigureDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, TiXmlElement*) const;
void ConfigureCommonPropertiesOfDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, TiXmlElement* element) const;
void ConfigureCommonPropertiesOfThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, TiXmlElement* element) const;
DICOMSortCriterion::Pointer CreateDICOMSortByTag(TiXmlElement* xmlElement, DICOMSortCriterion::Pointer secondaryCriterion) const;
DICOMSortCriterion::Pointer CreateSortByImagePositionPatient(TiXmlElement* xmlElement, DICOMSortCriterion::Pointer secondaryCriterion) const;
mitk::DICOMTagBasedSorter::Pointer CreateDICOMTagBasedSorter(TiXmlElement* element) const;
TiXmlElement* CreateConfigStringFromReader(const DICOMITKSeriesGDCMReader* reader) const;
TiXmlElement* CreateConfigStringFromReader(const ThreeDnTDICOMSeriesReader* reader) const;
TiXmlElement* CreateConfigStringFromReader(const ClassicDICOMSeriesReader* reader) const;
TiXmlElement* CreateConfigStringFromDICOMDatasetSorter(const DICOMTagBasedSorter* sorter) const;
TiXmlElement* CreateConfigStringFromDICOMTag(const DICOMTag& tag) const;
TiXmlElement* CreateDICOMFileReaderTag(const DICOMFileReader* reader) const;
const char* toString(bool) const;
std::string toHexString(unsigned int i) const;
/** Helper that queries an boolean xml attribute. If the attribute does not exist, the passed default value is used.*/
bool QueryBooleanAttribute(const TiXmlElement* element, const char* attributeName, bool defaultValue) const;
};
} // namespace
#endif // mitkDICOMReaderConfigurator_h
diff --git a/Modules/DICOMReader/include/mitkDICOMSortByTag.h b/Modules/DICOM/include/mitkDICOMSortByTag.h
similarity index 95%
rename from Modules/DICOMReader/include/mitkDICOMSortByTag.h
rename to Modules/DICOM/include/mitkDICOMSortByTag.h
index b97726f3f1..e84efb6435 100644
--- a/Modules/DICOMReader/include/mitkDICOMSortByTag.h
+++ b/Modules/DICOM/include/mitkDICOMSortByTag.h
@@ -1,68 +1,68 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDICOMSortByTag_h
#define mitkDICOMSortByTag_h
#include "mitkDICOMSortCriterion.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief Compare two datasets by the value of a single tag (for use in DICOMTagBasedSorter).
The class will compare the tag values by
1. numerical value if possible (i.e. both datasets have a value that is numerical)
2. alphabetical order otherwise
If the comparison results in equalness, it is refered to the secondary criterion, see
DICOMSortByTag::NextLevelIsLeftBeforeRight().
*/
-class MITKDICOMREADER_EXPORT DICOMSortByTag : public DICOMSortCriterion
+class MITKDICOM_EXPORT DICOMSortByTag : public DICOMSortCriterion
{
public:
mitkClassMacro( DICOMSortByTag, DICOMSortCriterion );
mitkNewMacro1Param( DICOMSortByTag, const DICOMTag& );
mitkNewMacro2Param( DICOMSortByTag, const DICOMTag&, DICOMSortCriterion::Pointer );
DICOMTagList GetTagsOfInterest() const override;
bool IsLeftBeforeRight(const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right) const override;
double NumericDistance(const mitk::DICOMDatasetAccess* from, const mitk::DICOMDatasetAccess* to) const override;
void Print(std::ostream& os) const override;
bool operator==(const DICOMSortCriterion& other) const override;
protected:
DICOMSortByTag( const DICOMTag& tag, DICOMSortCriterion::Pointer secondaryCriterion = nullptr );
~DICOMSortByTag() override;
DICOMSortByTag(const DICOMSortByTag& other);
DICOMSortByTag& operator=(const DICOMSortByTag& other);
bool StringCompare(const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right, const DICOMTag& tag) const;
bool NumericCompare(const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right, const DICOMTag& tag) const;
private:
DICOMTag m_Tag;
};
}
#endif
diff --git a/Modules/DICOMReader/include/mitkDICOMSortCriterion.h b/Modules/DICOM/include/mitkDICOMSortCriterion.h
similarity index 96%
rename from Modules/DICOMReader/include/mitkDICOMSortCriterion.h
rename to Modules/DICOM/include/mitkDICOMSortCriterion.h
index 7997de89c1..4fa2aebff1 100644
--- a/Modules/DICOMReader/include/mitkDICOMSortCriterion.h
+++ b/Modules/DICOM/include/mitkDICOMSortCriterion.h
@@ -1,78 +1,78 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDICOMSortCriterion_h
#define mitkDICOMSortCriterion_h
#include "itkObjectFactory.h"
#include "mitkCommon.h"
#include "mitkDICOMDatasetAccess.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief A tag based sorting criterion for use in DICOMTagBasedSorter.
This class is used within std::sort (see DICOMTagBasedSorter::Sort())
and has to answer a simple question by implementing IsLeftBeforeRight().
Each time IsLeftBeforeRight() is called, the method should return whether
the left dataset should be sorted before the right dataset.
Because there are identical tags values quite oftenly, a DICOMSortCriterion
will always hold a secondary DICOMSortCriterion. In cases of equal tag
values, the decision is refered to the secondary criterion.
*/
-class MITKDICOMREADER_EXPORT DICOMSortCriterion : public itk::LightObject
+class MITKDICOM_EXPORT DICOMSortCriterion : public itk::LightObject
{
public:
mitkClassMacroItkParent( DICOMSortCriterion, itk::LightObject );
/// \brief Tags used for comparison (includes seconary criteria).
DICOMTagList GetAllTagsOfInterest() const;
/// \brief Tags used for comparison.
virtual DICOMTagList GetTagsOfInterest() const = 0;
/// \brief Answer the sorting question.
virtual bool IsLeftBeforeRight(const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right) const = 0;
/// \brief Calculate a distance between two datasets.
/// This ansers the question of consecutive datasets.
virtual double NumericDistance(const mitk::DICOMDatasetAccess* from, const mitk::DICOMDatasetAccess* to) const = 0;
/// \brief The fallback criterion.
DICOMSortCriterion::ConstPointer GetSecondaryCriterion() const;
/// brief describe this class in given stream.
virtual void Print(std::ostream& os) const = 0;
virtual bool operator==(const DICOMSortCriterion& other) const = 0;
protected:
DICOMSortCriterion( DICOMSortCriterion::Pointer secondaryCriterion );
~DICOMSortCriterion() override;
bool NextLevelIsLeftBeforeRight(const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right) const;
explicit DICOMSortCriterion(const DICOMSortCriterion& other);
DICOMSortCriterion& operator=(const DICOMSortCriterion& other);
DICOMSortCriterion::Pointer m_SecondaryCriterion;
};
}
#endif
diff --git a/Modules/DICOMReader/include/mitkDICOMTag.h b/Modules/DICOM/include/mitkDICOMTag.h
similarity index 95%
rename from Modules/DICOMReader/include/mitkDICOMTag.h
rename to Modules/DICOM/include/mitkDICOMTag.h
index 19b67c2e1e..b62289a587 100644
--- a/Modules/DICOMReader/include/mitkDICOMTag.h
+++ b/Modules/DICOM/include/mitkDICOMTag.h
@@ -1,86 +1,86 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkTag_h
#define mitkTag_h
#include "mitkPoint.h"
#include "mitkVector.h"
-#include "MitkDICOMReaderExports.h"
+#include "MitkDICOMExports.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief Representation of a DICOM tag.
This class is just meant to combine group and element
numbers for better readability and make handling tags
more easy by offering comparison methods.
*/
-class MITKDICOMREADER_EXPORT DICOMTag
+class MITKDICOM_EXPORT DICOMTag
{
public:
DICOMTag(unsigned int group, unsigned int element);
DICOMTag(const DICOMTag& other);
DICOMTag& operator=(const DICOMTag& other);
bool operator==(const DICOMTag& other) const;
bool operator<(const DICOMTag& other) const;
unsigned int GetGroup() const;
unsigned int GetElement() const;
/// Return the name of this tag (e.g. "SeriesDescription" instead of "(0008,103e)")
std::string GetName() const;
/// add "(group-id,element-id) name" to given stream
void Print(std::ostream& os) const;
private:
std::string toHexString(unsigned int i) const;
unsigned int m_Group;
unsigned int m_Element;
};
typedef std::vector DICOMTagList;
/**
\brief Convert DICOM string describing a point two Vector3D.
DICOM tags like ImageOrientationPatient contain two vectors as float numbers separated by backslashes:
\verbatim
42.7131\13.77\0.7\137.76\0.3
\endverbatim
*/
void DICOMStringToOrientationVectors(const std::string& s, Vector3D& right, Vector3D& up, bool& successful);
bool DICOMStringToSpacing(const std::string& s, ScalarType& spacingX, ScalarType& spacingY);
/**
\brief Convert DICOM string describing a point to Point3D.
DICOM tags like ImagePositionPatient contain a position as float numbers separated by backslashes:
\verbatim
42.7131\13.77\0.7
\endverbatim
*/
Point3D DICOMStringToPoint3D(const std::string& s, bool& successful);
}
#endif
diff --git a/Modules/DICOMReader/include/mitkDICOMTagBasedSorter.h b/Modules/DICOM/include/mitkDICOMTagBasedSorter.h
similarity index 96%
rename from Modules/DICOMReader/include/mitkDICOMTagBasedSorter.h
rename to Modules/DICOM/include/mitkDICOMTagBasedSorter.h
index efc2b46121..b708bf53c1 100644
--- a/Modules/DICOMReader/include/mitkDICOMTagBasedSorter.h
+++ b/Modules/DICOM/include/mitkDICOMTagBasedSorter.h
@@ -1,202 +1,202 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDICOMTagBasedSorter_h
#define mitkDICOMTagBasedSorter_h
#include "mitkDICOMDatasetSorter.h"
#include "mitkDICOMSortCriterion.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief Sort DICOM datasets based on configurable tags.
This class implements sorting of input DICOM datasets into multiple outputs
as described in \ref DICOMITKSeriesGDCMReader_LoadingStrategy.
The logic of sorting and splitting is most simple and most generic:
1. Datasets will be put into different groups, if they differ in their value of specific tags (defined by AddDistinguishingTag())
- there might be multiple distinguishing tags defined
- tag values might be processed before comparison by means of TagValueProcessor (e.g. round to a number of decimal places)
2. Each of the groups will be sorted by comparing their tag values using multiple DICOMSortCriterion
- DICOMSortCriterion might evaluate a single tag (e.g. Instance Number) or multiple values (as in SortByImagePositionPatient)
- only a single DICOMSortCriterion is defined for DICOMTagBasedSorter, because each DICOMSortCriterion holds a "secondary sort criterion", i.e. an application can define multiple tags for sorting by chaining \link DICOMSortCriterion DICOMSortCriteria \endlink
- applications should make sure that sorting is always defined (to avoid problems with standard containers), e.g. by adding a comparison of filenames or instance UIDs as a last sorting fallback.
*/
-class MITKDICOMREADER_EXPORT DICOMTagBasedSorter : public DICOMDatasetSorter
+class MITKDICOM_EXPORT DICOMTagBasedSorter : public DICOMDatasetSorter
{
public:
/**
\brief Processes tag values before they are compared.
These classes could do some kind of normalization such as rounding, lower case formatting, etc.
*/
- class MITKDICOMREADER_EXPORT TagValueProcessor
+ class MITKDICOM_EXPORT TagValueProcessor
{
public:
/// \brief Implements the "processing".
virtual std::string operator()(const std::string&) const = 0;
virtual TagValueProcessor* Clone() const = 0;
virtual ~TagValueProcessor() {}
};
/**
\brief Cuts a number after configured number of decimal places.
An instance of this class can be used to avoid errors when comparing minimally different image orientations.
*/
- class MITKDICOMREADER_EXPORT CutDecimalPlaces : public TagValueProcessor
+ class MITKDICOM_EXPORT CutDecimalPlaces : public TagValueProcessor
{
public:
CutDecimalPlaces(unsigned int precision);
CutDecimalPlaces(const CutDecimalPlaces& other);
unsigned int GetPrecision() const;
std::string operator()(const std::string&) const override;
TagValueProcessor* Clone() const override;
private:
unsigned int m_Precision;
};
mitkClassMacro( DICOMTagBasedSorter, DICOMDatasetSorter );
itkNewMacro( DICOMTagBasedSorter );
/**
\brief Datasets that differ in given tag's value will be sorted into separate outputs.
*/
void AddDistinguishingTag( const DICOMTag&, TagValueProcessor* tagValueProcessor = nullptr );
DICOMTagList GetDistinguishingTags() const;
const TagValueProcessor* GetTagValueProcessorForDistinguishingTag(const DICOMTag&) const;
/**
\brief Define the sorting criterion (which holds seconardy criteria)
*/
void SetSortCriterion( DICOMSortCriterion::ConstPointer criterion );
DICOMSortCriterion::ConstPointer GetSortCriterion() const;
/**
\brief A list of all the tags needed for processing (facilitates scanning).
*/
DICOMTagList GetTagsOfInterest() override;
/**
\brief Whether or not groups should be checked for consecutive tag values.
When this flag is set (default in constructor=off), the sorter will
not only sort in a way that the values of a configured tag are ascending
BUT in addition the sorter will enforce a constant numerical distance
between values.
Having this flag is useful for handling of series with missing slices,
e.g. Instance Numbers 1 2 3 5 6 7 8. With the flag set to true, the sorter
would split this group into two, because the initial distance of 1 is
not kept between Instance Numbers 3 and 5.
A special case of this behavior can be configured by SetExpectDistanceOne().
When this additional flag is set to true, the sorter will expect distance
1 exactly. This can help if the second slice is missing already. Without
this additional flag, we would "learn" about a wrong distance of 2 (or similar)
and then sort completely wrong.
*/
void SetStrictSorting(bool strict);
bool GetStrictSorting() const;
/**
\brief Flag for a special case in "strict sorting".
Please see documentation of SetStrictSorting().
\sa SetStrictSorting
*/
void SetExpectDistanceOne(bool strict);
bool GetExpectDistanceOne() const;
/**
\brief Actually sort as described in the Detailed Description.
*/
void Sort() override;
/**
\brief Print configuration details into given stream.
*/
void PrintConfiguration(std::ostream& os, const std::string& indent = "") const override;
bool operator==(const DICOMDatasetSorter& other) const override;
static bool GetDefaultStrictSorting()
{
return m_DefaultStrictSorting;
}
static bool GetDefaultExpectDistanceOne()
{
return m_DefaultExpectDistanceOne;
}
protected:
/**
\brief Helper struct to feed into std::sort, configured via DICOMSortCriterion.
*/
struct ParameterizedDatasetSort
{
ParameterizedDatasetSort(DICOMSortCriterion::ConstPointer);
bool operator() (const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right);
DICOMSortCriterion::ConstPointer m_SortCriterion;
};
DICOMTagBasedSorter();
~DICOMTagBasedSorter() override;
DICOMTagBasedSorter(const DICOMTagBasedSorter& other);
DICOMTagBasedSorter& operator=(const DICOMTagBasedSorter& other);
/**
\brief Helper for SplitInputGroups().
*/
std::string BuildGroupID( DICOMDatasetAccess* dataset );
typedef std::map GroupIDToListType;
/**
\brief Implements the "distiguishing tags".
To sort datasets into different groups, a long string will be built for each dataset. The string concatenates all tags and their respective values.
Datasets that match in all values will end up with the same string.
*/
GroupIDToListType SplitInputGroups();
/**
\brief Implements the sorting step.
Relatively simple implementation thanks to std::sort and a parameterization via DICOMSortCriterion.
*/
GroupIDToListType& SortGroups(GroupIDToListType& groups);
DICOMTagList m_DistinguishingTags;
typedef std::map TagValueProcessorMap;
TagValueProcessorMap m_TagValueProcessor;
DICOMSortCriterion::ConstPointer m_SortCriterion;
bool m_StrictSorting;
bool m_ExpectDistanceOne;
const static bool m_DefaultStrictSorting = false;
const static bool m_DefaultExpectDistanceOne = false;
};
}
#endif
diff --git a/Modules/DICOMReader/include/mitkDICOMTagCache.h b/Modules/DICOM/include/mitkDICOMTagCache.h
similarity index 92%
rename from Modules/DICOMReader/include/mitkDICOMTagCache.h
rename to Modules/DICOM/include/mitkDICOMTagCache.h
index e16a2b28bb..1e70ae3478 100644
--- a/Modules/DICOMReader/include/mitkDICOMTagCache.h
+++ b/Modules/DICOM/include/mitkDICOMTagCache.h
@@ -1,63 +1,63 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDICOMTagCache_h
#define mitkDICOMTagCache_h
#include "itkObjectFactory.h"
#include "mitkCommon.h"
#include "mitkDICOMTag.h"
#include "mitkDICOMDatasetAccess.h"
#include "mitkDICOMEnums.h"
#include "mitkDICOMDatasetAccessingImageFrameInfo.h"
-#include "MitkDICOMReaderExports.h"
+#include "MitkDICOMExports.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief ...
*/
- class MITKDICOMREADER_EXPORT DICOMTagCache : public itk::Object
+ class MITKDICOM_EXPORT DICOMTagCache : public itk::Object
{
public:
mitkClassMacroItkParent( DICOMTagCache, itk::Object );
typedef std::list FindingsListType;
/**
\brief Define the list of files that were scanned to populate the cache.
*/
virtual void SetInputFiles(const StringList& filenames);
virtual DICOMDatasetFinding GetTagValue(DICOMImageFrameInfo* frame, const DICOMTag& tag) const = 0;
virtual FindingsListType GetTagValue(DICOMImageFrameInfo* frame, const DICOMTagPath& path) const = 0;
/**
\brief Retrieve a result list for file-by-file tag access.
*/
virtual DICOMDatasetAccessingImageFrameList GetFrameInfoList() const = 0;
protected:
StringList m_InputFilenames;
DICOMTagCache();
DICOMTagCache(const DICOMTagCache&);
~DICOMTagCache() override;
};
}
#endif
diff --git a/Modules/DICOMReader/include/mitkDICOMTagPath.h b/Modules/DICOM/include/mitkDICOMTagPath.h
similarity index 88%
rename from Modules/DICOMReader/include/mitkDICOMTagPath.h
rename to Modules/DICOM/include/mitkDICOMTagPath.h
index b758384c4a..7c82a56fb7 100644
--- a/Modules/DICOMReader/include/mitkDICOMTagPath.h
+++ b/Modules/DICOM/include/mitkDICOMTagPath.h
@@ -1,176 +1,176 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDICOMTagPath_h
#define mitkDICOMTagPath_h
#include
#include
-#include
+#include
namespace mitk
{
/** @brief Class is used to identify (nested) attributes in a DICOM dataset.
* In contrast to the class DICOMTag, which only specifies one specific tag,
* the tag path can identify nested attributes (like items in a DICOM sequence).
* In addition you may also specify wildcards for the selection index or
* complete elements of the path.
* @remark If you want to keep the DICOMTagPath compatible to the dcmtk search path
* format, you may *not* use element wild cards (this IsExplicit() or HasItemSelectionWildcardsOnly()
* must return true).
*/
- class MITKDICOMREADER_EXPORT DICOMTagPath
+ class MITKDICOM_EXPORT DICOMTagPath
{
public:
typedef int ItemSelectionIndex;
- struct MITKDICOMREADER_EXPORT NodeInfo
+ struct MITKDICOM_EXPORT NodeInfo
{
enum class NodeType
{
Invalid = 0, //*< Node is non existant or invalid.
Element, //*< Selects an specific element given the node name.
SequenceSelection, //*< Selects an specific item in a sequence of items and has a item selector ("[n]").
AnySelection, //*< Selects all items of a specific element ("[*]").
AnyElement, //*< Selects any element/item. Node name is wildcarded ("*"); item selection as well implictily.
};
NodeType type;
DICOMTag tag;
ItemSelectionIndex selection;
NodeInfo();
NodeInfo(const DICOMTag& tag, NodeType type = NodeType::Element, ItemSelectionIndex index = 0);
bool Matches(const NodeInfo& right) const;
bool operator == (const NodeInfo& right) const;
};
typedef std::vector NodeInfoVectorType;
typedef NodeInfoVectorType::size_type PathIndexType;
/** Returns if the DICOMTagPath is empty.*/
bool IsEmpty() const;
/** Returns if the path is explicit (has no wildcards).*/
bool IsExplicit() const;
/** Returns if the path has any nodes with item selection wild cards ([*]).*/
bool HasItemSelectionWildcardsOnly() const;
/** Number of path nodes the DICOMTagPath contains.*/
PathIndexType Size() const;
/** Adds a new node to the end of the path.
\param [in] newNode Reference to the node that should be added.
\return Returns the index of the newly added node.*/
PathIndexType AddNode(const NodeInfo& newNode);
/** Function returns the node info of a path node specified by the index
* within the DICOMTagPath.
* \pre Passed index must not be out of bound.
* \param [in] index Index of the node whose info should be retrieved.
* \return Info of the specified path node. If the index is out of bound an InvalidPathNode exception will be thrown.*/
const NodeInfo& GetNode(const PathIndexType& index) const;
/** Function returns the node info of a path node specified by the index
* within the DICOMTagPath.
* \pre Passed index must not be out of bound.
* \param [in] index Index of the node whose info should be retrieved.
* \return Info of the specified path node. If the index is out of bound an InvalidPathNode exception will be thrown.*/
NodeInfo& GetNode(const PathIndexType& index);
/** Function returns the node info of the first path node within the DICOMTagPath.
* \pre DICOMTagPath must not be empty.
* \return Info of the first path node. If the path is empty, an InvalidPathNode exception will be thrown.*/
NodeInfo& GetFirstNode();
/** Function returns the node info of the first path node within the DICOMTagPath.
* \pre DICOMTagPath must not be empty.
* \return Info of the first path node. If the path is empty, an InvalidPathNode exception will be thrown.*/
const NodeInfo& GetFirstNode() const;
/** Function returns the node info of the last path node within the DICOMTagPath.
* \pre DICOMTagPath must not be empty.
* \return Info of the first path node. If the path is empty, an InvalidPathNode exception will be thrown.*/
NodeInfo& GetLastNode();
/** Function returns the node info of the last path node within the DICOMTagPath.
* \pre DICOMTagPath must not be empty.
* \return Info of the first path node. If the path is empty, an InvalidPathNode exception will be thrown.*/
const NodeInfo& GetLastNode() const;
const NodeInfoVectorType& GetNodes() const;
std::string ToStr() const;
DICOMTagPath& FromStr(const std::string& pathStr);
/**Compares two DICOMTagPaths for real equality. So its a string compare of their string conversion*/
bool operator == (const DICOMTagPath& path) const;
/**Operation equals like comparing the ToStr() results with operator <.*/
bool operator < (const DICOMTagPath& right) const;
/**Checks if to DICOMTagPathes are specify the same node. Hence all wildcards will be processed.\n
* E.G.: "item1/child1/grandChild2" == ".//item1//grandChild2" is true.
* \remark If you want to check if to pathes are "truely" equal and not only equal in terms of
* pointing to the same node, use the member function Equals()*/
bool Equals(const DICOMTagPath& path) const;
DICOMTagPath& operator = (const DICOMTagPath& path);
DICOMTagPath& AddAnyElement();
DICOMTagPath& AddElement(unsigned int group, unsigned int element);
DICOMTagPath& AddAnySelection(unsigned int group, unsigned int element);
DICOMTagPath& AddSelection(unsigned int group, unsigned int element, ItemSelectionIndex index);
DICOMTagPath();
DICOMTagPath(const DICOMTagPath& path);
DICOMTagPath(const DICOMTag& tag);
explicit DICOMTagPath(unsigned int group, unsigned int element);
virtual ~DICOMTagPath();
virtual void Reset();
protected:
NodeInfoVectorType m_NodeInfos;
static bool DICOMTagPathesMatch(const DICOMTagPath& left, const DICOMTagPath& right);
};
typedef std::vector DICOMTagPathList;
- MITKDICOMREADER_EXPORT std::ostream& operator<<(std::ostream& os, const DICOMTagPath& path);
+ MITKDICOM_EXPORT std::ostream& operator<<(std::ostream& os, const DICOMTagPath& path);
- MITKDICOMREADER_EXPORT std::string DICOMTagPathToPropertyRegEx(const DICOMTagPath& tagPath);
- MITKDICOMREADER_EXPORT std::string DICOMTagPathToPersistenceKeyRegEx(const DICOMTagPath& tagPath);
- MITKDICOMREADER_EXPORT std::string DICOMTagPathToPersistenceKeyTemplate(const DICOMTagPath& tagPath);
- MITKDICOMREADER_EXPORT std::string DICOMTagPathToPersistenceNameTemplate(const DICOMTagPath& tagPath);
+ MITKDICOM_EXPORT std::string DICOMTagPathToPropertyRegEx(const DICOMTagPath& tagPath);
+ MITKDICOM_EXPORT std::string DICOMTagPathToPersistenceKeyRegEx(const DICOMTagPath& tagPath);
+ MITKDICOM_EXPORT std::string DICOMTagPathToPersistenceKeyTemplate(const DICOMTagPath& tagPath);
+ MITKDICOM_EXPORT std::string DICOMTagPathToPersistenceNameTemplate(const DICOMTagPath& tagPath);
/** Converts a passed path into a search string for the DCMTK DcmPathProcessor.
@pre tagPath must be an explicit (DICOMTagPath::IsExplicit()) path or
must only contain selection wild cards (DICOMTagPath::HasItemSelectionWildcardsOnly()).*/
- MITKDICOMREADER_EXPORT std::string DICOMTagPathToDCMTKSearchPath(const DICOMTagPath& tagPath);
+ MITKDICOM_EXPORT std::string DICOMTagPathToDCMTKSearchPath(const DICOMTagPath& tagPath);
/** Converts the passed property name into a tag path. If the property name cannot be converted
into a valid path, the returned path is empty.*/
- MITKDICOMREADER_EXPORT DICOMTagPath PropertyNameToDICOMTagPath(const std::string& propertyName);
+ MITKDICOM_EXPORT DICOMTagPath PropertyNameToDICOMTagPath(const std::string& propertyName);
/** returns the correct property name for a given DICOMTagPath instance. */
- MITKDICOMREADER_EXPORT std::string DICOMTagPathToPropertyName(const DICOMTagPath& tagPath);
+ MITKDICOM_EXPORT std::string DICOMTagPathToPropertyName(const DICOMTagPath& tagPath);
}
#endif
diff --git a/Modules/DICOMReader/include/mitkDICOMTagScanner.h b/Modules/DICOM/include/mitkDICOMTagScanner.h
similarity index 97%
rename from Modules/DICOMReader/include/mitkDICOMTagScanner.h
rename to Modules/DICOM/include/mitkDICOMTagScanner.h
index 84a9a9defd..374899f943 100644
--- a/Modules/DICOMReader/include/mitkDICOMTagScanner.h
+++ b/Modules/DICOM/include/mitkDICOMTagScanner.h
@@ -1,118 +1,118 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDICOMTagScanner_h
#define mitkDICOMTagScanner_h
#include
#include "itkMutexLock.h"
#include "mitkDICOMEnums.h"
#include "mitkDICOMTagPath.h"
#include "mitkDICOMTagCache.h"
#include "mitkDICOMDatasetAccessingImageFrameInfo.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief Abstracts the tag scanning process for a set of DICOM files.
Formerly integrated as a part of DICOMITKSeriesGDCMReader, the tag
scanning part has been factored out into DICOMTagScanner classes
in order to allow a single scan for multiple reader alternatives. This
helps much in the selection process of e.g. DICOMFileReaderSelector.
This is an abstract base class for concrete scanner implementations.
@remark When used in a process where multiple classes will access the scan
results, care should be taken that all the tags and files of interest
are communicated to DICOMTagScanner before requesting the results!
*/
- class MITKDICOMREADER_EXPORT DICOMTagScanner : public itk::Object
+ class MITKDICOM_EXPORT DICOMTagScanner : public itk::Object
{
public:
mitkClassMacroItkParent(DICOMTagScanner, itk::Object);
/**
\brief Add this tag to the scanning process.
*/
virtual void AddTag(const DICOMTag& tag) = 0;
/**
\brief Add a list of tags to the scanning process.
*/
virtual void AddTags(const DICOMTagList& tags) = 0;
/**
\brief Add this tag path to the scanning process.
*/
virtual void AddTagPath(const DICOMTagPath& path) = 0;
/**
\brief Add a list of tag pathes to the scanning process.
*/
virtual void AddTagPaths(const DICOMTagPathList& paths) = 0;
/**
\brief Define the list of files to scan.
This does not ADD to an internal list, but it replaces the
whole list of files.
*/
virtual void SetInputFiles(const StringList& filenames) = 0;
/**
\brief Start the scanning process.
Calling Scan() will invalidate previous scans, forgetting
all about files and tags from files that have been scanned
previously.
*/
virtual void Scan() = 0;
/**
\brief Retrieve a result list for file-by-file tag access.
*/
virtual DICOMDatasetAccessingImageFrameList GetFrameInfoList() const = 0;
/**
\brief Retrieve Pointer to the complete cache of the scan.
*/
virtual DICOMTagCache::Pointer GetScanCache() const = 0;
protected:
/** \brief Return active C locale */
static std::string GetActiveLocale();
/**
\brief Remember current locale on stack, activate "C" locale.
"C" locale is required for correct parsing of numbers by itk::ImageSeriesReader
*/
void PushLocale() const;
/**
\brief Activate last remembered locale from locale stack
"C" locale is required for correct parsing of numbers by itk::ImageSeriesReader
*/
void PopLocale() const;
DICOMTagScanner();
~DICOMTagScanner() override;
private:
static itk::MutexLock::Pointer s_LocaleMutex;
mutable std::stack m_ReplacedCLocales;
mutable std::stack m_ReplacedCinLocales;
DICOMTagScanner(const DICOMTagScanner&);
};
}
#endif
diff --git a/Modules/DICOMReader/include/mitkDICOMTagsOfInterestAddHelper.h b/Modules/DICOM/include/mitkDICOMTagsOfInterestAddHelper.h
similarity index 95%
rename from Modules/DICOMReader/include/mitkDICOMTagsOfInterestAddHelper.h
rename to Modules/DICOM/include/mitkDICOMTagsOfInterestAddHelper.h
index d5cb9cceb4..e2160057de 100644
--- a/Modules/DICOMReader/include/mitkDICOMTagsOfInterestAddHelper.h
+++ b/Modules/DICOM/include/mitkDICOMTagsOfInterestAddHelper.h
@@ -1,72 +1,72 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDICOMTagsOfInterestAddHelper_h
#define mitkDICOMTagsOfInterestAddHelper_h
#include
#include
#include
#include
#include
-#include "MitkDICOMReaderExports.h"
+#include "MitkDICOMExports.h"
namespace us
{
class ModuleContext;
}
namespace mitk
{
class IDICOMTagsOfInterest;
/** Helper class that can be used to ensure that a given list
of DICOM tags will be registered at existing DICOMTagsOfInterest
services. If the services are available the tags will be directly
added. As long as the helper is active, it will add the given tags to
all new DICOMTagsOfInterest services as soon as they are registered.
This helper class is e.g. used in module activators where the
DICOMTagsOfInterest service might not be registered when a module
is loaded but the module wants to ensure that the tags are added
as soon as possible.
The helper must be deactivated before the module context used on activation
gets invalid (e.g. in the Unload function of the module activator that
uses the helper to ensure that the tags will be added).
*/
- class MITKDICOMREADER_EXPORT DICOMTagsOfInterestAddHelper
+ class MITKDICOM_EXPORT DICOMTagsOfInterestAddHelper
{
public:
using TagsOfInterestVector = std::vector;
~DICOMTagsOfInterestAddHelper();
void Activate(us::ModuleContext* context, TagsOfInterestVector tags);
void Deactivate();
private:
void RegisterTagsOfInterest(IDICOMTagsOfInterest* toiService) const;
void DICOMTagsOfInterestServiceChanged(const us::ServiceEvent event);
TagsOfInterestVector m_TagsOfInterest;
bool m_Active = false;
us::ModuleContext* m_Context = nullptr;
/**mutex to guard the service listening */
std::mutex m_Mutex;
};
}
#endif
diff --git a/Modules/DICOMReader/include/mitkDICOMTagsOfInterestHelper.h b/Modules/DICOM/include/mitkDICOMTagsOfInterestHelper.h
similarity index 87%
rename from Modules/DICOMReader/include/mitkDICOMTagsOfInterestHelper.h
rename to Modules/DICOM/include/mitkDICOMTagsOfInterestHelper.h
index 9068284967..f9dc423f51 100644
--- a/Modules/DICOMReader/include/mitkDICOMTagsOfInterestHelper.h
+++ b/Modules/DICOM/include/mitkDICOMTagsOfInterestHelper.h
@@ -1,41 +1,41 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDICOMTagsOfInterestHelper_h
#define mitkDICOMTagsOfInterestHelper_h
#include
#include
-#include "MitkDICOMReaderExports.h"
+#include "MitkDICOMExports.h"
namespace mitk
{
/** Type specifies tags of interest. Key is the tag path of interest.
* The value is an optional user defined name for the property that should be used to store the tag value(s).
* Empty value is default and will imply to use the found DICOMTagPath as property name.*/
typedef std::map DICOMTagPathMapType;
/** Returns the list of tags that are by default of interest and should
* be extracted when loading DICOM data. This can for instance be used
* to with DICOMFileReader::SetAdditionalTagsOfInterest().*/
- DICOMTagPathMapType MITKDICOMREADER_EXPORT GetCurrentDICOMTagsOfInterest();
+ DICOMTagPathMapType MITKDICOM_EXPORT GetCurrentDICOMTagsOfInterest();
/** Returns the list of tags that are by default of interest and should
* be extracted when loading DICOM data. This can for instance be used
* to with DICOMFileReader::SetAdditionalTagsOfInterest().*/
- DICOMTagPathMapType MITKDICOMREADER_EXPORT GetDefaultDICOMTagsOfInterest();
+ DICOMTagPathMapType MITKDICOM_EXPORT GetDefaultDICOMTagsOfInterest();
}
#endif
diff --git a/Modules/DICOMReader/include/mitkEquiDistantBlocksSorter.h b/Modules/DICOM/include/mitkEquiDistantBlocksSorter.h
similarity index 98%
rename from Modules/DICOMReader/include/mitkEquiDistantBlocksSorter.h
rename to Modules/DICOM/include/mitkEquiDistantBlocksSorter.h
index d80ecc1a78..03bc4f5476 100644
--- a/Modules/DICOMReader/include/mitkEquiDistantBlocksSorter.h
+++ b/Modules/DICOM/include/mitkEquiDistantBlocksSorter.h
@@ -1,211 +1,211 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkEquiDistantBlocksSorter_h
#define mitkEquiDistantBlocksSorter_h
#include "mitkDICOMDatasetSorter.h"
#include "mitkDICOMSortCriterion.h"
#include "mitkGantryTiltInformation.h"
#include "mitkVector.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief Split inputs into blocks of equidistant slices (for use in DICOMITKSeriesGDCMReader).
Since inter-slice distance is not recorded in DICOM tags, we must ensure that blocks are made up of
slices that have equal distances between neighboring slices. This is especially necessary because itk::ImageSeriesReader
is later used for the actual loading, and this class expects (and does nocht verify) equal inter-slice distance (see \ref DICOMITKSeriesGDCMReader_ForcedConfiguration).
To achieve such grouping, the inter-slice distance is calculated from the first two different slice positions of a block.
Following slices are added to a block as long as they can be added by adding the calculated inter-slice distance to the
last slice of the block. Slices that do not fit into the expected distance pattern, are set aside for further analysis.
This grouping is done until each file has been assigned to a group.
Slices that share a position in space are also sorted into separate blocks during this step.
So the result of this step is a set of blocks that contain only slices with equal z spacing
and uniqe slices at each position.
During sorting, the origins (documented in tag image position patient) are compared
against expected origins (from former origin plus moving direction). As there will
be minor differences in numbers (from both calculations and unprecise tag values),
we must be a bit tolerant here. The default behavior is to expect that an origin is
not further away from the expected position than 30% of the inter-slice distance.
To support a legacy behavior of a former loader (DicomSeriesReader), this default can
be restricted to a constant number of millimeters by calling SetToleratedOriginOffset(mm).
Detailed implementation in AnalyzeFileForITKImageSeriesReaderSpacingAssumption().
*/
-class MITKDICOMREADER_EXPORT EquiDistantBlocksSorter : public DICOMDatasetSorter
+class MITKDICOM_EXPORT EquiDistantBlocksSorter : public DICOMDatasetSorter
{
public:
mitkClassMacro( EquiDistantBlocksSorter, DICOMDatasetSorter );
itkNewMacro( EquiDistantBlocksSorter );
DICOMTagList GetTagsOfInterest() override;
/**
\brief Delegates work to AnalyzeFileForITKImageSeriesReaderSpacingAssumption().
AnalyzeFileForITKImageSeriesReaderSpacingAssumption() is called until it does not
create multiple blocks anymore.
*/
void Sort() override;
/**
\brief Whether or not to accept images from a tilted acquisition in a single output group.
*/
void SetAcceptTilt(bool accept);
bool GetAcceptTilt() const;
/**
\brief See class description and SetToleratedOriginOffset().
*/
void SetToleratedOriginOffsetToAdaptive(double fractionOfInterSliceDistanct = 0.3);
/**
\brief See class description and SetToleratedOriginOffsetToAdaptive().
Default value of 0.005 is calculated so that we get a maximum of 1/10mm
error when having a measurement crosses 20 slices in z direction (too strict? we don't know better..).
*/
void SetToleratedOriginOffset(double millimeters = 0.005);
double GetToleratedOriginOffset() const;
bool IsToleratedOriginOffsetAbsolute() const;
void SetAcceptTwoSlicesGroups(bool accept);
bool GetAcceptTwoSlicesGroups() const;
void PrintConfiguration(std::ostream& os, const std::string& indent = "") const override;
bool operator==(const DICOMDatasetSorter& other) const override;
protected:
/**
\brief Return type of AnalyzeFileForITKImageSeriesReaderSpacingAssumption().
Class contains the grouping result of method AnalyzeFileForITKImageSeriesReaderSpacingAssumption(),
which takes as input a number of images, which are all equally oriented and spatially sorted along their normal direction.
The result contains of two blocks: a first one is the grouping result, all of those images can be loaded
into one image block because they have an equal origin-to-origin distance without any gaps in-between.
*/
class SliceGroupingAnalysisResult
{
public:
SliceGroupingAnalysisResult();
/**
\brief Grouping result, all same origin-to-origin distance w/o gaps.
*/
DICOMDatasetList GetBlockDatasets();
void SetFirstFilenameOfBlock(const std::string& filename);
std::string GetFirstFilenameOfBlock() const;
void SetLastFilenameOfBlock(const std::string& filename);
std::string GetLastFilenameOfBlock() const;
/**
\brief Remaining files, which could not be grouped.
*/
DICOMDatasetList GetUnsortedDatasets();
/**
\brief Wheter or not the grouped result contain a gantry tilt.
*/
bool ContainsGantryTilt();
/**
\brief Detailed description of gantry tilt.
*/
const GantryTiltInformation& GetTiltInfo() const;
/**
\brief Meant for internal use by AnalyzeFileForITKImageSeriesReaderSpacingAssumption only.
*/
void AddFileToSortedBlock(DICOMDatasetAccess* dataset);
/**
\brief Meant for internal use by AnalyzeFileForITKImageSeriesReaderSpacingAssumption only.
*/
void AddFileToUnsortedBlock(DICOMDatasetAccess* dataset);
void AddFilesToUnsortedBlock(const DICOMDatasetList& datasets);
/**
\brief Meant for internal use by AnalyzeFileForITKImageSeriesReaderSpacingAssumption only.
\todo Could make sense to enhance this with an instance of GantryTiltInformation to store the whole result!
*/
void FlagGantryTilt(const GantryTiltInformation& tiltInfo);
/**
\brief Only meaningful for use by AnalyzeFileForITKImageSeriesReaderSpacingAssumption.
*/
void UndoPrematureGrouping();
protected:
DICOMDatasetList m_GroupedFiles;
DICOMDatasetList m_UnsortedFiles;
GantryTiltInformation m_TiltInfo;
std::string m_FirstFilenameOfBlock;
std::string m_LastFilenameOfBlock;
};
/**
\brief Ensure an equal z-spacing for a group of files.
Takes as input a number of images, which are all equally oriented and spatially sorted along their normal direction.
Internally used by GetSeries. Returns two lists: the first one contins slices of equal inter-slice spacing.
The second list contains remaining files, which need to be run through AnalyzeFileForITKImageSeriesReaderSpacingAssumption again.
Relevant code that is matched here is in
itkImageSeriesReader.txx (ImageSeriesReader::GenerateOutputInformation(void)), lines 176 to 245 (as of ITK 3.20)
*/
SliceGroupingAnalysisResult
AnalyzeFileForITKImageSeriesReaderSpacingAssumption(const DICOMDatasetList& files, bool groupsOfSimilarImages);
/**
\brief Safely convert const char* to std::string.
*/
std::string
ConstCharStarToString(const char* s);
EquiDistantBlocksSorter();
~EquiDistantBlocksSorter() override;
EquiDistantBlocksSorter(const EquiDistantBlocksSorter& other);
EquiDistantBlocksSorter& operator=(const EquiDistantBlocksSorter& other);
bool m_AcceptTilt;
typedef std::vector ResultsList;
ResultsList m_SliceGroupingResults;
double m_ToleratedOriginOffset;
bool m_ToleratedOriginOffsetIsAbsolute;
bool m_AcceptTwoSlicesGroups;
};
}
#endif
diff --git a/Modules/DICOMReader/include/mitkGantryTiltInformation.h b/Modules/DICOM/include/mitkGantryTiltInformation.h
similarity index 98%
rename from Modules/DICOMReader/include/mitkGantryTiltInformation.h
rename to Modules/DICOM/include/mitkGantryTiltInformation.h
index a213495372..550e9de731 100644
--- a/Modules/DICOMReader/include/mitkGantryTiltInformation.h
+++ b/Modules/DICOM/include/mitkGantryTiltInformation.h
@@ -1,143 +1,143 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkGantryTiltInformation_h
#define mitkGantryTiltInformation_h
#include "mitkPoint.h"
#include "mitkVector.h"
#include "mitkPoint.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief Gantry tilt analysis result.
Takes geometry information for two slices of a DICOM series and
calculates whether these fit into an orthogonal block or not.
If NOT, they can either be the result of an acquisition with
gantry tilt OR completly broken by some shearing transformation.
Most calculations are done in the constructor, results can then
be read via the remaining methods.
This class is a helper to DICOMITKSeriesGDCMReader and can
- not be used outside of \ref DICOMReaderModule
+ not be used outside of \ref DICOMModule
*/
class GantryTiltInformation
{
public:
// two types to avoid any rounding errors
typedef itk::Point Point3Dd;
typedef itk::Vector Vector3Dd;
/**
\brief Just so we can create empty instances for assigning results later.
*/
GantryTiltInformation();
void Print(std::ostream& os) const;
/**
\brief THE constructor, which does all the calculations.
Determining the amount of tilt is done by checking the distances
of origin1 from planes through origin2. Two planes are considered:
- normal vector along normal of slices (right x up): gives the slice distance
- normal vector along orientation vector "up": gives the shift parallel to the plane orientation
The tilt angle can then be calculated from these distances
\param origin1 origin of the first slice
\param origin2 origin of the second slice
\param right right/up describe the orientatation of borth slices
\param up right/up describe the orientatation of borth slices
\param numberOfSlicesApart how many slices are the given origins apart (1 for neighboring slices)
*/
GantryTiltInformation( const Point3D& origin1,
const Point3D& origin2,
const Vector3D& right,
const Vector3D& up, unsigned int numberOfSlicesApart);
/**
\brief Factory method to create GantryTiltInformation from tag values (strings).
Parameters as the regular c'tor.
*/
static
GantryTiltInformation
MakeFromTagValues( const std::string& origin1String,
const std::string& origin2String,
const std::string& orientationString,
unsigned int numberOfSlicesApart);
/**
\brief Whether the slices were sheared.
True if any of the shifts along right or up vector are non-zero.
*/
bool IsSheared() const;
/**
\brief Whether the shearing is a gantry tilt or more complicated.
Gantry tilt will only produce shifts in ONE orientation, not in both.
Since the correction code currently only coveres one tilt direction
AND we don't know of medical images with two tilt directions, the
loading code wants to check if our assumptions are true.
*/
bool IsRegularGantryTilt() const;
/**
\brief The offset distance in Y direction for each slice in mm (describes the tilt result).
*/
double GetMatrixCoefficientForCorrectionInWorldCoordinates() const;
/**
\brief The z / inter-slice spacing. Needed to correct ImageSeriesReader's result.
*/
double GetRealZSpacing() const;
/**
\brief The shift between first and last slice in mm.
Needed to resize an orthogonal image volume.
*/
double GetTiltCorrectedAdditionalSize(unsigned int imageSizeZ) const;
/**
\brief Calculated tilt angle in degrees.
*/
double GetTiltAngleInDegrees() const;
private:
/**
\brief Projection of point p onto line through lineOrigin in direction of lineDirection.
*/
Point3D projectPointOnLine( Point3Dd p, Point3Dd lineOrigin, Vector3Dd lineDirection );
double m_ShiftUp;
double m_ShiftRight;
double m_ShiftNormal;
double m_ITKAssumedSliceSpacing;
unsigned int m_NumberOfSlicesApart;
};
} // namespace
#endif
diff --git a/Modules/DICOMReader/include/mitkIDICOMTagsOfInterest.h b/Modules/DICOM/include/mitkIDICOMTagsOfInterest.h
similarity index 96%
rename from Modules/DICOMReader/include/mitkIDICOMTagsOfInterest.h
rename to Modules/DICOM/include/mitkIDICOMTagsOfInterest.h
index 410fdb5f40..6b968deaee 100644
--- a/Modules/DICOMReader/include/mitkIDICOMTagsOfInterest.h
+++ b/Modules/DICOM/include/mitkIDICOMTagsOfInterest.h
@@ -1,64 +1,64 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkIDICOMTagsOfInterest_h
#define mitkIDICOMTagsOfInterest_h
#include
#include
#include
#include
-#include
+#include
namespace mitk
{
/**
* \ingroup MicroServices_Interfaces
* \brief Interface of DICOM tags of interest service.
*
* This service allows you to manage the tags of interest (toi).
* All registred toi will be extracted when loading dicom data and stored as properties in the corresponding
* base data object. In addition the service can (if available) use IPropertyPersistance and IPropertyAliases
* to ensure that the tags of interests are also persisted and have a human readable alias.
*/
- class MITKDICOMREADER_EXPORT IDICOMTagsOfInterest
+ class MITKDICOM_EXPORT IDICOMTagsOfInterest
{
public:
virtual ~IDICOMTagsOfInterest();
/** \brief Add an tag to the TOI.
* If the tag was already added it will be overwritten with the passed values.
* \param[in] tag Tag that should be added.
* \param[in] makePersistant Indicates if the tag should be made persistant if possible via the IPropertyPersistence service.
*/
virtual void AddTagOfInterest(const DICOMTagPath& tag, bool makePersistant = true) = 0;
/** Returns the map of all tags of interest. Key is the property name. Value is the DICOM tag.*/
virtual DICOMTagPathMapType GetTagsOfInterest() const = 0;
/** Indicates if the given tag is already a tag of interest.*/
virtual bool HasTag(const DICOMTagPath& tag) const = 0;
/** \brief Remove specific tag. If it not exists the function will do nothing.
* \param[in] tag Tag that should be removed.
*/
virtual void RemoveTag(const DICOMTagPath& tag) = 0;
/** \brief Remove all tags.
*/
virtual void RemoveAllTags() = 0;
};
}
MITK_DECLARE_SERVICE_INTERFACE(mitk::IDICOMTagsOfInterest, "org.mitk.IDICOMTagsOfInterest")
#endif
diff --git a/Modules/DICOMReader/include/mitkITKDICOMSeriesReaderHelper.h b/Modules/DICOM/include/mitkITKDICOMSeriesReaderHelper.h
similarity index 100%
rename from Modules/DICOMReader/include/mitkITKDICOMSeriesReaderHelper.h
rename to Modules/DICOM/include/mitkITKDICOMSeriesReaderHelper.h
diff --git a/Modules/DICOMReader/include/mitkITKDICOMSeriesReaderHelper.txx b/Modules/DICOM/include/mitkITKDICOMSeriesReaderHelper.txx
similarity index 100%
rename from Modules/DICOMReader/include/mitkITKDICOMSeriesReaderHelper.txx
rename to Modules/DICOM/include/mitkITKDICOMSeriesReaderHelper.txx
diff --git a/Modules/DICOMReader/include/mitkNormalDirectionConsistencySorter.h b/Modules/DICOM/include/mitkNormalDirectionConsistencySorter.h
similarity index 94%
rename from Modules/DICOMReader/include/mitkNormalDirectionConsistencySorter.h
rename to Modules/DICOM/include/mitkNormalDirectionConsistencySorter.h
index 6f62620098..a870e7a134 100644
--- a/Modules/DICOMReader/include/mitkNormalDirectionConsistencySorter.h
+++ b/Modules/DICOM/include/mitkNormalDirectionConsistencySorter.h
@@ -1,71 +1,71 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkNormalDirectionConsistencySorter_h
#define mitkNormalDirectionConsistencySorter_h
#include "mitkDICOMDatasetSorter.h"
#include "mitkGantryTiltInformation.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief Makes sure that the order of files is along the image plane normals.
When loading with ImageSeriesReader and initializing an mitk::Image with the result
we need to make sure that the order of inputs for the ImageSeriesReader is along the
normal of the images. I.e. The direction of the normal needs to be the same direction
as the vector from the first to the last image origin.
Since this class is used as a last sorting step before loading, it will also
calculate (and return) an updated GantryTiltInformation object.
\note This class might be a workaround for another bug in MITK, but until this issue
is completely understood, the workaround fixes the problem of images that
appear upside-down.
*/
-class MITKDICOMREADER_EXPORT NormalDirectionConsistencySorter : public DICOMDatasetSorter
+class MITKDICOM_EXPORT NormalDirectionConsistencySorter : public DICOMDatasetSorter
{
public:
mitkClassMacro( NormalDirectionConsistencySorter, DICOMDatasetSorter );
itkNewMacro( NormalDirectionConsistencySorter );
DICOMTagList GetTagsOfInterest() override;
/// See class description.
void Sort() override;
/// See class description and DICOMITKSeriesGDCMReader.
GantryTiltInformation GetTiltInformation() const;
void PrintConfiguration(std::ostream& os, const std::string& indent = "") const override;
bool operator==(const DICOMDatasetSorter& other) const override;
protected:
NormalDirectionConsistencySorter();
~NormalDirectionConsistencySorter() override;
NormalDirectionConsistencySorter(const NormalDirectionConsistencySorter& other);
NormalDirectionConsistencySorter& operator=(const NormalDirectionConsistencySorter& other);
GantryTiltInformation m_TiltInfo;
};
}
#endif
diff --git a/Modules/DICOMReader/include/mitkSortByImagePositionPatient.h b/Modules/DICOM/include/mitkSortByImagePositionPatient.h
similarity index 94%
rename from Modules/DICOMReader/include/mitkSortByImagePositionPatient.h
rename to Modules/DICOM/include/mitkSortByImagePositionPatient.h
index 4806155ea7..988ee3cfaa 100644
--- a/Modules/DICOMReader/include/mitkSortByImagePositionPatient.h
+++ b/Modules/DICOM/include/mitkSortByImagePositionPatient.h
@@ -1,64 +1,64 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkSortByImagePositionPatient_h
#define mitkSortByImagePositionPatient_h
#include "mitkDICOMSortCriterion.h"
#include "mitkVector.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief Sort by distance of image origin along image normal (for use in DICOMTagBasedSorter).
To compare two datasets, their distance to the world origin is calculated.
This distance is calculated along the image normals because we do not know
the image orientation in advance, to any of the three coordinates could be identical for all datasets.
\note This class assumes that the datasets have identical orientations!
*/
-class MITKDICOMREADER_EXPORT SortByImagePositionPatient : public DICOMSortCriterion
+class MITKDICOM_EXPORT SortByImagePositionPatient : public DICOMSortCriterion
{
public:
mitkClassMacro( SortByImagePositionPatient, DICOMSortCriterion );
mitkNewMacro1Param( SortByImagePositionPatient, DICOMSortCriterion::Pointer );
DICOMTagList GetTagsOfInterest() const override;
bool IsLeftBeforeRight(const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right) const override;
double NumericDistance(const mitk::DICOMDatasetAccess* from, const mitk::DICOMDatasetAccess* to) const override;
void Print(std::ostream& os) const override;
bool operator==(const DICOMSortCriterion& other) const override;
protected:
SortByImagePositionPatient( DICOMSortCriterion::Pointer secondaryCriterion = nullptr );
~SortByImagePositionPatient() override;
SortByImagePositionPatient(const SortByImagePositionPatient& other);
SortByImagePositionPatient& operator=(const SortByImagePositionPatient& other);
double InternalNumericDistance(const mitk::DICOMDatasetAccess* from, const mitk::DICOMDatasetAccess* to, bool& possible) const;
private:
};
}
#endif
diff --git a/Modules/DICOMReader/include/mitkThreeDnTDICOMSeriesReader.h b/Modules/DICOM/include/mitkThreeDnTDICOMSeriesReader.h
similarity index 96%
rename from Modules/DICOMReader/include/mitkThreeDnTDICOMSeriesReader.h
rename to Modules/DICOM/include/mitkThreeDnTDICOMSeriesReader.h
index 6bbb263c93..1a903eeef8 100644
--- a/Modules/DICOMReader/include/mitkThreeDnTDICOMSeriesReader.h
+++ b/Modules/DICOM/include/mitkThreeDnTDICOMSeriesReader.h
@@ -1,99 +1,99 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkThreeDnTDICOMSeriesReader_h
#define mitkThreeDnTDICOMSeriesReader_h
#include "mitkDICOMITKSeriesGDCMReader.h"
-#include "MitkDICOMReaderExports.h"
+#include "MitkDICOMExports.h"
namespace mitk
{
/**
\ingroup DICOMReader
\brief Extends DICOMITKSeriesGDCMReader by sorting/grouping into 3D+t image blocks.
This class reuses the DICOMITKSeriesGDCMReader class and adds the option of
grouping 3D blocks at the same spatial position into a single block, which
is loaded as a 3D+t mitk::Image (compare to \ref DICOMITKSeriesGDCMReader_Condensing).
To group two output blocks into a single 3D+t block, this class tests a number
of requirements that the two blocks must fulfill:
- the origin of the first slice must be identical
- the origin of the last slice must be identical
- the number of slices must be identical
The output blocks described by DICOMImageBlockDescriptor will contains the following properties:
- \b "3D+t": true if the image is 3D+t
- \b "timesteps": number of timesteps of an image (only defined if "3D+t" is true)
*/
-class MITKDICOMREADER_EXPORT ThreeDnTDICOMSeriesReader : public DICOMITKSeriesGDCMReader
+class MITKDICOM_EXPORT ThreeDnTDICOMSeriesReader : public DICOMITKSeriesGDCMReader
{
public:
mitkClassMacro( ThreeDnTDICOMSeriesReader, DICOMITKSeriesGDCMReader );
mitkCloneMacro( ThreeDnTDICOMSeriesReader );
itkNewMacro( ThreeDnTDICOMSeriesReader );
mitkNewMacro1Param( ThreeDnTDICOMSeriesReader, unsigned int );
/// \brief Control whether 3D+t grouping shall actually be attempted.
void SetGroup3DandT(bool on);
bool GetGroup3DandT() const;
itkBooleanMacro(OnlyCondenseSameSeries);
itkSetMacro(OnlyCondenseSameSeries, bool);
itkGetConstMacro(OnlyCondenseSameSeries, bool);
// void AllocateOutputImages();
/// \brief Load via multiple calls to itk::ImageSeriesReader.
bool LoadImages() override;
bool operator==(const DICOMFileReader& other) const override;
static bool GetDefaultGroup3DandT()
{
return m_DefaultGroup3DandT;
}
static bool GetDefaultOnlyCondenseSameSeries()
{
return m_DefaultOnlyCondenseSameSeries;
}
protected:
ThreeDnTDICOMSeriesReader(unsigned int decimalPlacesForOrientation = Superclass::m_DefaultDecimalPlacesForOrientation);
~ThreeDnTDICOMSeriesReader() override;
ThreeDnTDICOMSeriesReader(const ThreeDnTDICOMSeriesReader& other);
ThreeDnTDICOMSeriesReader& operator=(const ThreeDnTDICOMSeriesReader& other);
/**
\brief Analyze the groups produced by DICOMITKSeriesGDCMReader for 3D+t properties.
This method tests whether some blocks are at the same spatial position and groups
them into single blocks.
*/
SortingBlockList Condense3DBlocks(SortingBlockList&) override;
bool LoadMitkImageForImageBlockDescriptor(DICOMImageBlockDescriptor& block) const override;
bool m_Group3DandT;
bool m_OnlyCondenseSameSeries;
const static bool m_DefaultGroup3DandT = true;
const static bool m_DefaultOnlyCondenseSameSeries = true;
};
}
#endif
diff --git a/Modules/DICOMReader/resource/configurations/3D/classicreader.xml b/Modules/DICOM/resource/configurations/3D/classicreader.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3D/classicreader.xml
rename to Modules/DICOM/resource/configurations/3D/classicreader.xml
diff --git a/Modules/DICOMReader/resource/configurations/3D/imageposition.xml b/Modules/DICOM/resource/configurations/3D/imageposition.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3D/imageposition.xml
rename to Modules/DICOM/resource/configurations/3D/imageposition.xml
diff --git a/Modules/DICOMReader/resource/configurations/3D/imageposition_byacquisition.xml b/Modules/DICOM/resource/configurations/3D/imageposition_byacquisition.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3D/imageposition_byacquisition.xml
rename to Modules/DICOM/resource/configurations/3D/imageposition_byacquisition.xml
diff --git a/Modules/DICOMReader/resource/configurations/3D/imagetime.xml b/Modules/DICOM/resource/configurations/3D/imagetime.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3D/imagetime.xml
rename to Modules/DICOM/resource/configurations/3D/imagetime.xml
diff --git a/Modules/DICOMReader/resource/configurations/3D/instancenumber.xml b/Modules/DICOM/resource/configurations/3D/instancenumber.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3D/instancenumber.xml
rename to Modules/DICOM/resource/configurations/3D/instancenumber.xml
diff --git a/Modules/DICOMReader/resource/configurations/3D/instancenumber_soft.xml b/Modules/DICOM/resource/configurations/3D/instancenumber_soft.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3D/instancenumber_soft.xml
rename to Modules/DICOM/resource/configurations/3D/instancenumber_soft.xml
diff --git a/Modules/DICOMReader/resource/configurations/3D/simpleinstancenumber_soft.xml b/Modules/DICOM/resource/configurations/3D/simpleinstancenumber_soft.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3D/simpleinstancenumber_soft.xml
rename to Modules/DICOM/resource/configurations/3D/simpleinstancenumber_soft.xml
diff --git a/Modules/DICOMReader/resource/configurations/3D/slicelocation.xml b/Modules/DICOM/resource/configurations/3D/slicelocation.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3D/slicelocation.xml
rename to Modules/DICOM/resource/configurations/3D/slicelocation.xml
diff --git a/Modules/DICOMReader/resource/configurations/3DnT/classicreader.xml b/Modules/DICOM/resource/configurations/3DnT/classicreader.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3DnT/classicreader.xml
rename to Modules/DICOM/resource/configurations/3DnT/classicreader.xml
diff --git a/Modules/DICOMReader/resource/configurations/3DnT/imageposition.xml b/Modules/DICOM/resource/configurations/3DnT/imageposition.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3DnT/imageposition.xml
rename to Modules/DICOM/resource/configurations/3DnT/imageposition.xml
diff --git a/Modules/DICOMReader/resource/configurations/3DnT/imageposition_byacquisition.xml b/Modules/DICOM/resource/configurations/3DnT/imageposition_byacquisition.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3DnT/imageposition_byacquisition.xml
rename to Modules/DICOM/resource/configurations/3DnT/imageposition_byacquisition.xml
diff --git a/Modules/DICOMReader/resource/configurations/3DnT/imageposition_bytriggertime.xml b/Modules/DICOM/resource/configurations/3DnT/imageposition_bytriggertime.xml
similarity index 100%
rename from Modules/DICOMReader/resource/configurations/3DnT/imageposition_bytriggertime.xml
rename to Modules/DICOM/resource/configurations/3DnT/imageposition_bytriggertime.xml
diff --git a/Modules/DICOMReader/src/legacy/mitkDicomSR_GantryTiltInformation.cpp b/Modules/DICOM/src/legacy/mitkDicomSR_GantryTiltInformation.cpp
similarity index 100%
rename from Modules/DICOMReader/src/legacy/mitkDicomSR_GantryTiltInformation.cpp
rename to Modules/DICOM/src/legacy/mitkDicomSR_GantryTiltInformation.cpp
diff --git a/Modules/DICOMReader/src/legacy/mitkDicomSR_ImageBlockDescriptor.cpp b/Modules/DICOM/src/legacy/mitkDicomSR_ImageBlockDescriptor.cpp
similarity index 100%
rename from Modules/DICOMReader/src/legacy/mitkDicomSR_ImageBlockDescriptor.cpp
rename to Modules/DICOM/src/legacy/mitkDicomSR_ImageBlockDescriptor.cpp
diff --git a/Modules/DICOMReader/src/legacy/mitkDicomSR_LoadDICOMRGBPixel.cpp b/Modules/DICOM/src/legacy/mitkDicomSR_LoadDICOMRGBPixel.cpp
similarity index 100%
rename from Modules/DICOMReader/src/legacy/mitkDicomSR_LoadDICOMRGBPixel.cpp
rename to Modules/DICOM/src/legacy/mitkDicomSR_LoadDICOMRGBPixel.cpp
diff --git a/Modules/DICOMReader/src/legacy/mitkDicomSR_LoadDICOMRGBPixel4D.cpp b/Modules/DICOM/src/legacy/mitkDicomSR_LoadDICOMRGBPixel4D.cpp
similarity index 100%
rename from Modules/DICOMReader/src/legacy/mitkDicomSR_LoadDICOMRGBPixel4D.cpp
rename to Modules/DICOM/src/legacy/mitkDicomSR_LoadDICOMRGBPixel4D.cpp
diff --git a/Modules/DICOMReader/src/legacy/mitkDicomSR_LoadDICOMScalar.cpp b/Modules/DICOM/src/legacy/mitkDicomSR_LoadDICOMScalar.cpp
similarity index 100%
rename from Modules/DICOMReader/src/legacy/mitkDicomSR_LoadDICOMScalar.cpp
rename to Modules/DICOM/src/legacy/mitkDicomSR_LoadDICOMScalar.cpp
diff --git a/Modules/DICOMReader/src/legacy/mitkDicomSR_LoadDICOMScalar4D.cpp b/Modules/DICOM/src/legacy/mitkDicomSR_LoadDICOMScalar4D.cpp
similarity index 100%
rename from Modules/DICOMReader/src/legacy/mitkDicomSR_LoadDICOMScalar4D.cpp
rename to Modules/DICOM/src/legacy/mitkDicomSR_LoadDICOMScalar4D.cpp
diff --git a/Modules/DICOMReader/src/legacy/mitkDicomSR_SliceGroupingResult.cpp b/Modules/DICOM/src/legacy/mitkDicomSR_SliceGroupingResult.cpp
similarity index 100%
rename from Modules/DICOMReader/src/legacy/mitkDicomSR_SliceGroupingResult.cpp
rename to Modules/DICOM/src/legacy/mitkDicomSR_SliceGroupingResult.cpp
diff --git a/Modules/DICOMReader/src/legacy/mitkDicomSeriesReader.cpp b/Modules/DICOM/src/legacy/mitkDicomSeriesReader.cpp
similarity index 100%
rename from Modules/DICOMReader/src/legacy/mitkDicomSeriesReader.cpp
rename to Modules/DICOM/src/legacy/mitkDicomSeriesReader.cpp
diff --git a/Modules/DICOMReader/src/legacy/mitkDicomSeriesReader.h b/Modules/DICOM/src/legacy/mitkDicomSeriesReader.h
similarity index 100%
rename from Modules/DICOMReader/src/legacy/mitkDicomSeriesReader.h
rename to Modules/DICOM/src/legacy/mitkDicomSeriesReader.h
diff --git a/Modules/DICOMReader/src/legacy/mitkDicomSeriesReader.txx b/Modules/DICOM/src/legacy/mitkDicomSeriesReader.txx
similarity index 100%
rename from Modules/DICOMReader/src/legacy/mitkDicomSeriesReader.txx
rename to Modules/DICOM/src/legacy/mitkDicomSeriesReader.txx
diff --git a/Modules/DICOMReader/src/mitkBaseDICOMReaderService.cpp b/Modules/DICOM/src/mitkBaseDICOMReaderService.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkBaseDICOMReaderService.cpp
rename to Modules/DICOM/src/mitkBaseDICOMReaderService.cpp
diff --git a/Modules/DICOMReader/src/mitkClassicDICOMSeriesReader.cpp b/Modules/DICOM/src/mitkClassicDICOMSeriesReader.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkClassicDICOMSeriesReader.cpp
rename to Modules/DICOM/src/mitkClassicDICOMSeriesReader.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMDCMTKTagScanner.cpp b/Modules/DICOM/src/mitkDICOMDCMTKTagScanner.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMDCMTKTagScanner.cpp
rename to Modules/DICOM/src/mitkDICOMDCMTKTagScanner.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMDatasetAccessingImageFrameInfo.cpp b/Modules/DICOM/src/mitkDICOMDatasetAccessingImageFrameInfo.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMDatasetAccessingImageFrameInfo.cpp
rename to Modules/DICOM/src/mitkDICOMDatasetAccessingImageFrameInfo.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMDatasetSorter.cpp b/Modules/DICOM/src/mitkDICOMDatasetSorter.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMDatasetSorter.cpp
rename to Modules/DICOM/src/mitkDICOMDatasetSorter.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMEnums.cpp b/Modules/DICOM/src/mitkDICOMEnums.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMEnums.cpp
rename to Modules/DICOM/src/mitkDICOMEnums.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMFileReader.cpp b/Modules/DICOM/src/mitkDICOMFileReader.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMFileReader.cpp
rename to Modules/DICOM/src/mitkDICOMFileReader.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMFileReaderSelector.cpp b/Modules/DICOM/src/mitkDICOMFileReaderSelector.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMFileReaderSelector.cpp
rename to Modules/DICOM/src/mitkDICOMFileReaderSelector.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMFilesHelper.cpp b/Modules/DICOM/src/mitkDICOMFilesHelper.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMFilesHelper.cpp
rename to Modules/DICOM/src/mitkDICOMFilesHelper.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMGDCMImageFrameInfo.cpp b/Modules/DICOM/src/mitkDICOMGDCMImageFrameInfo.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMGDCMImageFrameInfo.cpp
rename to Modules/DICOM/src/mitkDICOMGDCMImageFrameInfo.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMGDCMTagCache.cpp b/Modules/DICOM/src/mitkDICOMGDCMTagCache.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMGDCMTagCache.cpp
rename to Modules/DICOM/src/mitkDICOMGDCMTagCache.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMGDCMTagScanner.cpp b/Modules/DICOM/src/mitkDICOMGDCMTagScanner.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMGDCMTagScanner.cpp
rename to Modules/DICOM/src/mitkDICOMGDCMTagScanner.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMGenericImageFrameInfo.cpp b/Modules/DICOM/src/mitkDICOMGenericImageFrameInfo.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMGenericImageFrameInfo.cpp
rename to Modules/DICOM/src/mitkDICOMGenericImageFrameInfo.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMGenericTagCache.cpp b/Modules/DICOM/src/mitkDICOMGenericTagCache.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMGenericTagCache.cpp
rename to Modules/DICOM/src/mitkDICOMGenericTagCache.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMIOHelper.cpp b/Modules/DICOM/src/mitkDICOMIOHelper.cpp
similarity index 97%
rename from Modules/DICOMReader/src/mitkDICOMIOHelper.cpp
rename to Modules/DICOM/src/mitkDICOMIOHelper.cpp
index be7a272a0f..648d18a6c6 100644
--- a/Modules/DICOMReader/src/mitkDICOMIOHelper.cpp
+++ b/Modules/DICOM/src/mitkDICOMIOHelper.cpp
@@ -1,71 +1,71 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkDICOMIOHelper.h"
#include
#include
#include
#include
namespace mitk
{
mitk::IDICOMTagsOfInterest *GetDicomTagsOfInterestService()
{
mitk::IDICOMTagsOfInterest *result = nullptr;
us::ModuleContext *context = us::GetModuleContext();
if (context == nullptr)
{
- MITK_WARN << "No MitkDICOMReader module context found.";
+ MITK_WARN << "No MitkDICOM module context found.";
return result;
}
std::vector> toiRegisters =
context->GetServiceReferences();
if (!toiRegisters.empty())
{
if (toiRegisters.size() > 1)
{
MITK_WARN << "Multiple DICOM tags of interest services found. Using just one.";
}
result = us::GetModuleContext()->GetService(toiRegisters.front());
}
return result;
}
FindingsListVectorType ExtractPathsOfInterest(const DICOMTagPathList &pathsOfInterest,
const DICOMDatasetAccessingImageFrameList &frames)
{
std::vector findings;
for (const auto &entry : pathsOfInterest)
{
findings.push_back(frames.front()->GetTagValueAsString(entry));
}
return findings;
}
void SetProperties(BaseDataPointer image, const FindingsListVectorType &findings)
{
for (const auto &finding : findings)
{
for (const auto &entry : finding)
{
const std::string propertyName = mitk::DICOMTagPathToPropertyName(entry.path);
auto property = mitk::TemporoSpatialStringProperty::New();
property->SetValue(entry.value);
image->SetProperty(propertyName.c_str(), property);
}
}
}
}
diff --git a/Modules/DICOMReader/src/mitkDICOMIOMetaInformationPropertyConstants.cpp b/Modules/DICOM/src/mitkDICOMIOMetaInformationPropertyConstants.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMIOMetaInformationPropertyConstants.cpp
rename to Modules/DICOM/src/mitkDICOMIOMetaInformationPropertyConstants.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMITKSeriesGDCMReader.cpp b/Modules/DICOM/src/mitkDICOMITKSeriesGDCMReader.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMITKSeriesGDCMReader.cpp
rename to Modules/DICOM/src/mitkDICOMITKSeriesGDCMReader.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMImageBlockDescriptor.cpp b/Modules/DICOM/src/mitkDICOMImageBlockDescriptor.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMImageBlockDescriptor.cpp
rename to Modules/DICOM/src/mitkDICOMImageBlockDescriptor.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMImageFrameInfo.cpp b/Modules/DICOM/src/mitkDICOMImageFrameInfo.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMImageFrameInfo.cpp
rename to Modules/DICOM/src/mitkDICOMImageFrameInfo.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMProperty.cpp b/Modules/DICOM/src/mitkDICOMProperty.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMProperty.cpp
rename to Modules/DICOM/src/mitkDICOMProperty.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMReaderConfigurator.cpp b/Modules/DICOM/src/mitkDICOMReaderConfigurator.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMReaderConfigurator.cpp
rename to Modules/DICOM/src/mitkDICOMReaderConfigurator.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMSortByTag.cpp b/Modules/DICOM/src/mitkDICOMSortByTag.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMSortByTag.cpp
rename to Modules/DICOM/src/mitkDICOMSortByTag.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMSortCriterion.cpp b/Modules/DICOM/src/mitkDICOMSortCriterion.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMSortCriterion.cpp
rename to Modules/DICOM/src/mitkDICOMSortCriterion.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMTag.cpp b/Modules/DICOM/src/mitkDICOMTag.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMTag.cpp
rename to Modules/DICOM/src/mitkDICOMTag.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMTagBasedSorter.cpp b/Modules/DICOM/src/mitkDICOMTagBasedSorter.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMTagBasedSorter.cpp
rename to Modules/DICOM/src/mitkDICOMTagBasedSorter.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMTagCache.cpp b/Modules/DICOM/src/mitkDICOMTagCache.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMTagCache.cpp
rename to Modules/DICOM/src/mitkDICOMTagCache.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMTagPath.cpp b/Modules/DICOM/src/mitkDICOMTagPath.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMTagPath.cpp
rename to Modules/DICOM/src/mitkDICOMTagPath.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMTagScanner.cpp b/Modules/DICOM/src/mitkDICOMTagScanner.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMTagScanner.cpp
rename to Modules/DICOM/src/mitkDICOMTagScanner.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMTagsOfInterestAddHelper.cpp b/Modules/DICOM/src/mitkDICOMTagsOfInterestAddHelper.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMTagsOfInterestAddHelper.cpp
rename to Modules/DICOM/src/mitkDICOMTagsOfInterestAddHelper.cpp
diff --git a/Modules/DICOMReader/src/mitkDICOMTagsOfInterestHelper.cpp b/Modules/DICOM/src/mitkDICOMTagsOfInterestHelper.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkDICOMTagsOfInterestHelper.cpp
rename to Modules/DICOM/src/mitkDICOMTagsOfInterestHelper.cpp
diff --git a/Modules/DICOMReader/src/mitkEquiDistantBlocksSorter.cpp b/Modules/DICOM/src/mitkEquiDistantBlocksSorter.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkEquiDistantBlocksSorter.cpp
rename to Modules/DICOM/src/mitkEquiDistantBlocksSorter.cpp
diff --git a/Modules/DICOMReader/src/mitkGantryTiltInformation.cpp b/Modules/DICOM/src/mitkGantryTiltInformation.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkGantryTiltInformation.cpp
rename to Modules/DICOM/src/mitkGantryTiltInformation.cpp
diff --git a/Modules/DICOMReader/src/mitkIDICOMTagsOfInterest.cpp b/Modules/DICOM/src/mitkIDICOMTagsOfInterest.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkIDICOMTagsOfInterest.cpp
rename to Modules/DICOM/src/mitkIDICOMTagsOfInterest.cpp
diff --git a/Modules/DICOMReader/src/mitkITKDICOMSeriesReaderHelper.cpp b/Modules/DICOM/src/mitkITKDICOMSeriesReaderHelper.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkITKDICOMSeriesReaderHelper.cpp
rename to Modules/DICOM/src/mitkITKDICOMSeriesReaderHelper.cpp
diff --git a/Modules/DICOMReader/src/mitkNormalDirectionConsistencySorter.cpp b/Modules/DICOM/src/mitkNormalDirectionConsistencySorter.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkNormalDirectionConsistencySorter.cpp
rename to Modules/DICOM/src/mitkNormalDirectionConsistencySorter.cpp
diff --git a/Modules/DICOMReader/src/mitkSortByImagePositionPatient.cpp b/Modules/DICOM/src/mitkSortByImagePositionPatient.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkSortByImagePositionPatient.cpp
rename to Modules/DICOM/src/mitkSortByImagePositionPatient.cpp
diff --git a/Modules/DICOMReader/src/mitkThreeDnTDICOMSeriesReader.cpp b/Modules/DICOM/src/mitkThreeDnTDICOMSeriesReader.cpp
similarity index 100%
rename from Modules/DICOMReader/src/mitkThreeDnTDICOMSeriesReader.cpp
rename to Modules/DICOM/src/mitkThreeDnTDICOMSeriesReader.cpp
diff --git a/Modules/DICOMReader/test/CMakeLists.txt b/Modules/DICOM/test/CMakeLists.txt
similarity index 100%
rename from Modules/DICOMReader/test/CMakeLists.txt
rename to Modules/DICOM/test/CMakeLists.txt
diff --git a/Modules/DICOMReader/test/files.cmake b/Modules/DICOM/test/files.cmake
similarity index 100%
rename from Modules/DICOMReader/test/files.cmake
rename to Modules/DICOM/test/files.cmake
diff --git a/Modules/DICOMReader/test/mitkDICOMDCMTKTagScannerTest.cpp b/Modules/DICOM/test/mitkDICOMDCMTKTagScannerTest.cpp
similarity index 100%
rename from Modules/DICOMReader/test/mitkDICOMDCMTKTagScannerTest.cpp
rename to Modules/DICOM/test/mitkDICOMDCMTKTagScannerTest.cpp
diff --git a/Modules/DICOMReader/test/mitkDICOMFileReaderTest.cpp b/Modules/DICOM/test/mitkDICOMFileReaderTest.cpp
similarity index 100%
rename from Modules/DICOMReader/test/mitkDICOMFileReaderTest.cpp
rename to Modules/DICOM/test/mitkDICOMFileReaderTest.cpp
diff --git a/Modules/DICOMReader/test/mitkDICOMFileReaderTestHelper.h b/Modules/DICOM/test/mitkDICOMFileReaderTestHelper.h
similarity index 100%
rename from Modules/DICOMReader/test/mitkDICOMFileReaderTestHelper.h
rename to Modules/DICOM/test/mitkDICOMFileReaderTestHelper.h
diff --git a/Modules/DICOMReader/test/mitkDICOMFilenameSorter.cpp b/Modules/DICOM/test/mitkDICOMFilenameSorter.cpp
similarity index 100%
rename from Modules/DICOMReader/test/mitkDICOMFilenameSorter.cpp
rename to Modules/DICOM/test/mitkDICOMFilenameSorter.cpp
diff --git a/Modules/DICOMReader/test/mitkDICOMFilenameSorter.h b/Modules/DICOM/test/mitkDICOMFilenameSorter.h
similarity index 97%
rename from Modules/DICOMReader/test/mitkDICOMFilenameSorter.h
rename to Modules/DICOM/test/mitkDICOMFilenameSorter.h
index d788595937..2f44c9fdea 100644
--- a/Modules/DICOMReader/test/mitkDICOMFilenameSorter.h
+++ b/Modules/DICOM/test/mitkDICOMFilenameSorter.h
@@ -1,57 +1,57 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDICOMFilenameSorter_h
#define mitkDICOMFilenameSorter_h
#include "mitkDICOMDatasetSorter.h"
namespace mitk
{
/**
- \ingroup DICOMReaderModule
+ \ingroup DICOMModule
\brief sort files based on filename (last resort).
*/
class DICOMFilenameSorter : public DICOMDatasetSorter
{
public:
mitkClassMacro( DICOMFilenameSorter, DICOMDatasetSorter );
itkNewMacro( DICOMFilenameSorter );
DICOMTagList GetTagsOfInterest() override;
void Sort() override;
void PrintConfiguration(std::ostream& os, const std::string& indent = "") const override;
bool operator==(const DICOMDatasetSorter& other) const override;
protected:
struct FilenameSort
{
bool operator() (const mitk::DICOMDatasetAccess* left, const mitk::DICOMDatasetAccess* right);
};
DICOMFilenameSorter();
~DICOMFilenameSorter() override;
DICOMFilenameSorter(const DICOMFilenameSorter& other);
DICOMFilenameSorter& operator=(const DICOMFilenameSorter& other);
};
}
#endif
diff --git a/Modules/DICOMReader/test/mitkDICOMITKSeriesGDCMReaderBasicsTest.cpp b/Modules/DICOM/test/mitkDICOMITKSeriesGDCMReaderBasicsTest.cpp
similarity index 100%
rename from Modules/DICOMReader/test/mitkDICOMITKSeriesGDCMReaderBasicsTest.cpp
rename to Modules/DICOM/test/mitkDICOMITKSeriesGDCMReaderBasicsTest.cpp
diff --git a/Modules/DICOMReader/test/mitkDICOMNullFileReader.cpp b/Modules/DICOM/test/mitkDICOMNullFileReader.cpp
similarity index 100%
rename from Modules/DICOMReader/test/mitkDICOMNullFileReader.cpp
rename to Modules/DICOM/test/mitkDICOMNullFileReader.cpp
diff --git a/Modules/DICOMReader/test/mitkDICOMNullFileReader.h b/Modules/DICOM/test/mitkDICOMNullFileReader.h
similarity index 100%
rename from Modules/DICOMReader/test/mitkDICOMNullFileReader.h
rename to Modules/DICOM/test/mitkDICOMNullFileReader.h
diff --git a/Modules/DICOMReader/test/mitkDICOMPropertyTest.cpp b/Modules/DICOM/test/mitkDICOMPropertyTest.cpp
similarity index 100%
rename from Modules/DICOMReader/test/mitkDICOMPropertyTest.cpp
rename to Modules/DICOM/test/mitkDICOMPropertyTest.cpp
diff --git a/Modules/DICOMReader/test/mitkDICOMReaderConfiguratorTest.cpp b/Modules/DICOM/test/mitkDICOMReaderConfiguratorTest.cpp
similarity index 100%
rename from Modules/DICOMReader/test/mitkDICOMReaderConfiguratorTest.cpp
rename to Modules/DICOM/test/mitkDICOMReaderConfiguratorTest.cpp
diff --git a/Modules/DICOMReader/test/mitkDICOMSimpleVolumeImportTest.cpp b/Modules/DICOM/test/mitkDICOMSimpleVolumeImportTest.cpp
similarity index 96%
rename from Modules/DICOMReader/test/mitkDICOMSimpleVolumeImportTest.cpp
rename to Modules/DICOM/test/mitkDICOMSimpleVolumeImportTest.cpp
index 535bec6d12..712d226183 100644
--- a/Modules/DICOMReader/test/mitkDICOMSimpleVolumeImportTest.cpp
+++ b/Modules/DICOM/test/mitkDICOMSimpleVolumeImportTest.cpp
@@ -1,106 +1,106 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkDICOMFileReaderSelector.h"
#include "mitkDICOMFileReaderTestHelper.h"
#include
#include
#include
#include
#include
#include
#include "mitkImageToItk.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "mitkTestingMacros.h"
/**
\brief Verify single block reading of SimpleDICOMvolumeImport for sloppily tagged data.
*/
int mitkDICOMSimpleVolumeImportTest(int argc, char* argv[])
{
typedef mitk::DICOMFileReaderSelector::ReaderList ReaderList;
typedef itk::Image< short, 3 > ImageType;
typedef itk::ImageRegionConstIteratorWithIndex< ImageType > IteratorType;
MITK_TEST_BEGIN("mitkDICOMSimpleVolumeImportTest");
us::ModuleResource resource =
- us::ModuleRegistry::GetModule("MitkDICOMReader")->GetResource("configurations/3D/simpleinstancenumber_soft.xml");
+ us::ModuleRegistry::GetModule("MitkDICOM")->GetResource("configurations/3D/simpleinstancenumber_soft.xml");
std::string descr;
if ( resource.IsValid() )
{
us::ModuleResourceStream stream(resource);
stream.seekg(0, std::ios::end);
descr.reserve(stream.tellg());
stream.seekg(0, std::ios::beg);
descr.assign((std::istreambuf_iterator(stream)),
std::istreambuf_iterator());
}
mitk::DICOMFileReaderSelector::Pointer readerSelector = mitk::DICOMFileReaderSelector::New();
readerSelector->AddConfig( descr );
ReaderList readers = readerSelector->GetAllConfiguredReaders();
mitk::DICOMFileReader::Pointer simpleReader;
for ( ReaderList::const_iterator it = readers.begin(); it != readers.end(); ++it )
{
mitk::DICOMFileReader::Pointer reader = *it;
std::string configLabel = reader->GetConfigurationLabel();
if ( configLabel == "Instance Number, non-consecutive, simple import" )
{
simpleReader = reader;
}
}
MITK_TEST_CONDITION_REQUIRED( simpleReader.IsNotNull(), "DICOMFileReaderSelector is able to create simple reader from XML");
if ( argc > 1 )
{
mitk::DICOMFileReaderTestHelper::SetTestInputFilenames( argc,argv );
mitk::DICOMFileReaderTestHelper::TestInputFilenames( simpleReader );
mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs( simpleReader );
mitk::DICOMFileReaderTestHelper::TestSingleBlockIsRead( simpleReader );
const mitk::DICOMImageBlockDescriptor block = simpleReader->GetOutput( 0 );
const mitk::Image::Pointer mitkImage = block.GetMitkImage();
ImageType::Pointer itkImage = mitk::ImageToItkImage( mitkImage );
IteratorType it( itkImage, itkImage->GetLargestPossibleRegion() );
bool success = true;
while ( !it.IsAtEnd() )
{
ImageType::PixelType val = it.Get();
ImageType::IndexType ind = it.GetIndex();
if ( !(val == ind[2]) )
{
success = false;
break;
}
++it;
}
MITK_TEST_CONDITION( success, "Single block image composed as expected.");
}
MITK_TEST_END();
}
diff --git a/Modules/DICOMReader/test/mitkDICOMTagPathTest.cpp b/Modules/DICOM/test/mitkDICOMTagPathTest.cpp
similarity index 100%
rename from Modules/DICOMReader/test/mitkDICOMTagPathTest.cpp
rename to Modules/DICOM/test/mitkDICOMTagPathTest.cpp
diff --git a/Modules/DICOMPM/CMakeLists.txt b/Modules/DICOMPM/CMakeLists.txt
index bb13df19c1..aa17f28473 100644
--- a/Modules/DICOMPM/CMakeLists.txt
+++ b/Modules/DICOMPM/CMakeLists.txt
@@ -1,6 +1,6 @@
MITK_CREATE_MODULE(DICOMPM
- DEPENDS MitkCore MitkDICOMReader MitkModelFit MitkDICOMQI
+ DEPENDS MitkCore MitkDICOM MitkModelFit MitkDICOMQI
PACKAGE_DEPENDS
PRIVATE DCMTK
)
-add_subdirectory(autoload/DICOMPMIO)
\ No newline at end of file
+add_subdirectory(autoload/DICOMPMIO)
diff --git a/Modules/DICOMQI/CMakeLists.txt b/Modules/DICOMQI/CMakeLists.txt
index b02baee9ea..eee1639517 100644
--- a/Modules/DICOMQI/CMakeLists.txt
+++ b/Modules/DICOMQI/CMakeLists.txt
@@ -1,5 +1,5 @@
MITK_CREATE_MODULE(
- DEPENDS MitkCore MitkDICOMReader
+ DEPENDS MitkCore MitkDICOM
PACKAGE_DEPENDS
PRIVATE DCMTK
)
diff --git a/Modules/DICOMTesting/CMakeLists.txt b/Modules/DICOMTesting/CMakeLists.txt
index 256daf6b3b..d0d96f0e67 100644
--- a/Modules/DICOMTesting/CMakeLists.txt
+++ b/Modules/DICOMTesting/CMakeLists.txt
@@ -1,43 +1,43 @@
if(BUILD_TESTING)
if(GDCM_DIR)
# clear variables from prior files.cmake
# Else CMake would use the content of these variables and would try to create tests (which are not present in DICOMTesting).
set(MODULE_TESTS)
set(MODULE_IMAGE_TESTS)
set(MODULE_SURFACE_TESTS)
set(MODULE_TESTIMAGE)
set(MODULE_TESTSURFACE)
set(MODULE_CUSTOM_TESTS)
set(H_FILES)
set(CPP_FILES)
# now create a new module only for testing purposes
MITK_CREATE_MODULE(
- DEPENDS MitkDICOMReader
+ DEPENDS MitkDICOM
PACKAGE_DEPENDS
PRIVATE GDCM DCMTK ITK|ITKIOGDCM
)
mitk_check_module_dependencies(MODULES MitkDICOMTesting MISSING_DEPENDENCIES_VAR _missing_deps)
if(_missing_deps)
message(STATUS "mitkDICOMTesting module helper applications won't be built. Missing: ${_missing_deps}")
else(_missing_deps)
# dumps out image information
add_executable(DumpDICOMMitkImage src/DumpDICOMMitkImage.cpp)
mitk_use_modules(TARGET DumpDICOMMitkImage MODULES MitkDICOMTesting)
# compares dumped out image information against reference dump
add_executable(VerifyDICOMMitkImageDump src/VerifyDICOMMitkImageDump.cpp)
mitk_use_modules(TARGET VerifyDICOMMitkImageDump MODULES MitkDICOMTesting)
set_property(TARGET DumpDICOMMitkImage VerifyDICOMMitkImageDump PROPERTY FOLDER
"${MITK_ROOT_FOLDER}/Modules/Tests")
add_subdirectory(test)
endif()
endif()
endif()
diff --git a/Modules/DicomUI/CMakeLists.txt b/Modules/DICOMUI/CMakeLists.txt
similarity index 100%
rename from Modules/DicomUI/CMakeLists.txt
rename to Modules/DICOMUI/CMakeLists.txt
diff --git a/Modules/DicomUI/files.cmake b/Modules/DICOMUI/files.cmake
similarity index 100%
rename from Modules/DicomUI/files.cmake
rename to Modules/DICOMUI/files.cmake
diff --git a/Modules/DicomUI/include/QmitkDicomExternalDataWidget.h b/Modules/DICOMUI/include/QmitkDicomExternalDataWidget.h
similarity index 99%
rename from Modules/DicomUI/include/QmitkDicomExternalDataWidget.h
rename to Modules/DICOMUI/include/QmitkDicomExternalDataWidget.h
index 4c689b3b5b..588628e1a4 100644
--- a/Modules/DicomUI/include/QmitkDicomExternalDataWidget.h
+++ b/Modules/DICOMUI/include/QmitkDicomExternalDataWidget.h
@@ -1,120 +1,120 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QmitkDicomExternalDataWidget_h
#define QmitkDicomExternalDataWidget_h
#include "ui_QmitkDicomExternalDataWidgetControls.h"
-#include
+#include
// include ctk
#include
#include
// include QT
#include
#include
#include
#include
#include
#include
#include
class ctkFileDialog;
/**
* \brief QmitkDicomExternalDataWidget is a QWidget providing functionality for dicom import.
*
* \sa QmitkFunctionality
* \ingroup Functionalities
*/
class MITKDICOMUI_EXPORT QmitkDicomExternalDataWidget : public QWidget
{
// this is needed for all Qt objects that should have a Qt meta-object
// (everything that derives from QObject and wants to have signal/slots)
Q_OBJECT
public:
static const std::string Widget_ID;
/**
* \brief QmitkDicomExternalDataWidget(QWidget *parent) constructor.
*
* \param parent is a pointer to the parent widget
*/
QmitkDicomExternalDataWidget(QWidget *parent);
/**
* \brief QmitkDicomExternalDataWidget destructor.
*/
~QmitkDicomExternalDataWidget() override;
/**
* \brief CreateQtPartControl(QWidget *parent) sets the view objects from ui_QmitkDicomExternalDataWidgetControls.h.
*
* \param parent is a pointer to the parent widget
*/
virtual void CreateQtPartControl(QWidget *parent);
/**
* \brief Initializes the widget. This method has to be called before widget can start.
*/
void Initialize();
signals:
/// @brief emitted when import into database is finished.
void SignalStartDicomImport(const QStringList &);
/// @brief emitted when view button is clicked.
void SignalDicomToDataManager(QHash);
public slots:
/// @brief Called when download button was clicked.
void OnDownloadButtonClicked();
/// @brief Called when view button was clicked.
void OnViewButtonClicked();
/// @brief Called when adding a dicom directory. Starts a thread adding the directory.
void OnStartDicomImport(const QString &);
void OnSeriesSelectionChanged(const QStringList &s);
protected slots:
void OnProgressStep(const QString&);
void OnProgressDetail(const QString&);
protected:
/// \brief Get the list of filepath from current selected index in TreeView. All file paths referring to the index
/// will be returned.
QStringList GetFileNamesFromIndex();
/// \brief SetupImportDialog Sets up import dialog.
void SetupImportDialog();
void SetupProgressDialog();
ctkDICOMDatabase *m_ExternalDatabase;
ctkDICOMIndexer *m_ExternalIndexer;
ctkFileDialog *m_ImportDialog;
QProgressDialog *m_ProgressDialog;
QString m_LastImportDirectory;
QString m_ProgressStep;
Ui::QmitkDicomExternalDataWidgetControls *m_Controls;
};
#endif // _QmitkDicomExternalDataWidget_H_INCLUDED
diff --git a/Modules/DicomUI/include/QmitkDicomLocalStorageWidget.h b/Modules/DICOMUI/include/QmitkDicomLocalStorageWidget.h
similarity index 99%
rename from Modules/DicomUI/include/QmitkDicomLocalStorageWidget.h
rename to Modules/DICOMUI/include/QmitkDicomLocalStorageWidget.h
index 40b275e01a..cd8b541fbc 100644
--- a/Modules/DicomUI/include/QmitkDicomLocalStorageWidget.h
+++ b/Modules/DICOMUI/include/QmitkDicomLocalStorageWidget.h
@@ -1,117 +1,117 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QmitkDicomLocalStorageWidget_h
#define QmitkDicomLocalStorageWidget_h
// #include
#include "ui_QmitkDicomLocalStorageWidgetControls.h"
-#include
+#include
// include ctk
#include
#include
#include
// include QT
#include
#include
#include
#include
#include
class QProgressDialog;
class QLabel;
/**
* \brief QmitkDicomLocalStorageWidget is a QWidget providing functionality for dicom storage and import.
*
* \sa QmitkFunctionality
* \ingroup Functionalities
*/
class MITKDICOMUI_EXPORT QmitkDicomLocalStorageWidget : public QWidget
{
// this is needed for all Qt objects that should have a Qt meta-object
// (everything that derives from QObject and wants to have signal/slots)
Q_OBJECT
public:
static const std::string Widget_ID;
/**
* \brief QmitkDicomLocalStorageWidget(QWidget *parent) constructor.
*
* \param parent is a pointer to the parent widget
*/
QmitkDicomLocalStorageWidget(QWidget *parent);
/**
* \brief QmitkDicomExternalDataWidget destructor.
*/
~QmitkDicomLocalStorageWidget() override;
/**
* \brief CreateQtPartControl(QWidget *parent) sets the view objects from ui_QmitkDicomExternalDataWidgetControls.h.
*
* \param parent is a pointer to the parent widget
*/
virtual void CreateQtPartControl(QWidget *parent);
/**
* \brief SetDatabaseDirectory sets database directory.
*
* \param newDatabaseDirectory contains path to new database directoy.
*/
void SetDatabaseDirectory(QString newDatabaseDirectory);
signals:
/// @brief emitted when import into database is finished.
void SignalFinishedImport();
/**
* @brief emitted when view button is clicked.
* @param QHash containing dicom UIDs properties.
*/
void SignalDicomToDataManager(QHash);
/// \brief emitted if cancel button is pressed.
void SignalCancelImport();
public slots:
/// @brief Called when view button was clicked.
void OnViewButtonClicked();
/// @brief Called delete button was clicked.
void OnDeleteButtonClicked();
/// @brief Called when adding a dicom directory. Starts a thread adding the directory.
void OnStartDicomImport(const QString &dicomData);
/// @brief Called when adding a list of dicom files. Starts a thread adding the dicom files.
void OnStartDicomImport(const QStringList &dicomData);
/// @brief Called when the selection in the series table has changed
void OnSeriesSelectionChanged(const QStringList &);
protected:
void SetDatabase(QString databaseFile);
bool DeletePatients();
bool DeleteStudies();
bool DeleteSeries();
ctkDICOMDatabase *m_LocalDatabase;
ctkDICOMIndexer *m_LocalIndexer;
Ui::QmitkDicomLocalStorageWidgetControls *m_Controls;
};
#endif // _QmitkDicomLocalStorageWidget_H_INCLUDED
diff --git a/Modules/DicomUI/src/QmitkDicomExternalDataWidget.cpp b/Modules/DICOMUI/src/QmitkDicomExternalDataWidget.cpp
similarity index 100%
rename from Modules/DicomUI/src/QmitkDicomExternalDataWidget.cpp
rename to Modules/DICOMUI/src/QmitkDicomExternalDataWidget.cpp
diff --git a/Modules/DicomUI/src/QmitkDicomExternalDataWidgetControls.ui b/Modules/DICOMUI/src/QmitkDicomExternalDataWidgetControls.ui
similarity index 86%
rename from Modules/DicomUI/src/QmitkDicomExternalDataWidgetControls.ui
rename to Modules/DICOMUI/src/QmitkDicomExternalDataWidgetControls.ui
index 154d4cdd0d..483d6ab6f0 100644
--- a/Modules/DicomUI/src/QmitkDicomExternalDataWidgetControls.ui
+++ b/Modules/DICOMUI/src/QmitkDicomExternalDataWidgetControls.ui
@@ -1,138 +1,138 @@
QmitkDicomExternalDataWidgetControls
0
0
754
633
Form
-
External Dicom Data
-
true
0
0
QFrame::Box
QFrame::Sunken
-
Scan directory
-
- :/org.mitk.gui.qt.dicom/folder_32.png:/org.mitk.gui.qt.dicom/folder_32.png
+
+ :/org.mitk.gui.qt.dicombrowser/folder_32.png:/org.mitk.gui.qt.dicombrowser/folder_32.png
-
true
Add to local storage
-
- :/org.mitk.gui.qt.dicom/import_32.png:/org.mitk.gui.qt.dicom/import_32.png
+
+ :/org.mitk.gui.qt.dicombrowser/import_32.png:/org.mitk.gui.qt.dicombrowser/import_32.png
-
false
View
-
- :/org.mitk.gui.qt.dicom/viewIcon.png:/org.mitk.gui.qt.dicom/viewIcon.png
+
+ :/org.mitk.gui.qt.dicombrowser/viewIcon.png:/org.mitk.gui.qt.dicombrowser/viewIcon.png
16
20
-
Qt::Horizontal
40
20
-
0
QLayout::SetNoConstraint
0
0
-
ctkDICOMTableManager
QWidget
1
-
+
diff --git a/Modules/DicomUI/src/QmitkDicomLocalStorageWidget.cpp b/Modules/DICOMUI/src/QmitkDicomLocalStorageWidget.cpp
similarity index 100%
rename from Modules/DicomUI/src/QmitkDicomLocalStorageWidget.cpp
rename to Modules/DICOMUI/src/QmitkDicomLocalStorageWidget.cpp
diff --git a/Modules/DicomUI/src/QmitkDicomLocalStorageWidgetControls.ui b/Modules/DICOMUI/src/QmitkDicomLocalStorageWidgetControls.ui
similarity index 93%
rename from Modules/DicomUI/src/QmitkDicomLocalStorageWidgetControls.ui
rename to Modules/DICOMUI/src/QmitkDicomLocalStorageWidgetControls.ui
index 4087d11a4a..540f1bdad8 100644
--- a/Modules/DicomUI/src/QmitkDicomLocalStorageWidgetControls.ui
+++ b/Modules/DICOMUI/src/QmitkDicomLocalStorageWidgetControls.ui
@@ -1,128 +1,128 @@
QmitkDicomLocalStorageWidgetControls
0
0
754
633
Form
-
Local Dicom Storage
12
-
0
0
QFrame::Box
QFrame::Sunken
-
false
View
-
- :/org.mitk.gui.qt.dicom/viewIcon.png:/org.mitk.gui.qt.dicom/viewIcon.png
+
+ :/org.mitk.gui.qt.dicombrowser/viewIcon.png:/org.mitk.gui.qt.dicombrowser/viewIcon.png
16
20
-
true
Delete
:/org.mitk.gui.qt.datamanager/Remove_48.png:/org.mitk.gui.qt.datamanager/Remove_48.png
-
Qt::Horizontal
40
20
-
0
QLayout::SetNoConstraint
0
0
-
ctkDICOMTableManager
QWidget
1
-
+
diff --git a/Modules/DicomRT/CMakeLists.txt b/Modules/DicomRT/CMakeLists.txt
deleted file mode 100644
index 7fe08ffd4e..0000000000
--- a/Modules/DicomRT/CMakeLists.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-if(NOT DEFINED DCMTK_dcmrt_LIBRARY OR DCMTK_dcmrt_LIBRARY)
- mitk_create_module(
- DEPENDS MitkSceneSerializationBase MitkDICOMReader
- PACKAGE_DEPENDS PUBLIC DCMTK
- )
- add_subdirectory(autoload/IO)
- add_subdirectory(test)
-else()
- message("MITK DicomRT Support disabled because the DCMTK dcmrt library not found")
-endif()
diff --git a/Modules/ModuleList.cmake b/Modules/ModuleList.cmake
index d65ee8faa4..e9a5d07801 100644
--- a/Modules/ModuleList.cmake
+++ b/Modules/ModuleList.cmake
@@ -1,86 +1,85 @@
# The entries in the mitk_modules list must be
# ordered according to their dependencies.
set(MITK_MODULES
Core
CommandLine
CoreCmdApps
AppUtil
LegacyIO
DataTypesExt
Annotation
LegacyGL
AlgorithmsExt
MapperExt
- DICOMReader
- DICOMReaderServices
+ DICOM
DICOMQI
DICOMTesting
SceneSerializationBase
PlanarFigure
ImageDenoising
ImageExtraction
SceneSerialization
Gizmo
GraphAlgorithms
Multilabel
Chart
ImageStatistics
ContourModel
SurfaceInterpolation
Segmentation
QtWidgets
QtWidgetsExt
ImageStatisticsUI
SegmentationUI
MatchPointRegistration
MatchPointRegistrationUI
Classification
OpenIGTLink
IGTBase
IGT
CameraCalibration
OpenCL
OpenCVVideoSupport
QtOverlays
ToFHardware
ToFProcessing
ToFUI
PhotoacousticsHardware
PhotoacousticsAlgorithms
PhotoacousticsLib
US
USUI
- DicomUI
+ DICOMUI
Remeshing
Python
QtPython
Persistence
OpenIGTLinkUI
IGTUI
- DicomRT
+ RT
RTUI
IOExt
XNAT
TubeGraph
BiophotonicsHardware
BoundingShape
RenderWindowManager
RenderWindowManagerUI
SemanticRelations
SemanticRelationsUI
CEST
BasicImageProcessing
ModelFit
ModelFitUI
Pharmacokinetics
PharmacokineticsUI
DICOMPM
REST
RESTService
DICOMweb
)
if(MITK_ENABLE_PIC_READER)
list(APPEND MITK_MODULES IpPicSupportIO)
endif()
diff --git a/Modules/RT/CMakeLists.txt b/Modules/RT/CMakeLists.txt
new file mode 100644
index 0000000000..753686d460
--- /dev/null
+++ b/Modules/RT/CMakeLists.txt
@@ -0,0 +1,10 @@
+if(NOT DEFINED DCMTK_dcmrt_LIBRARY OR DCMTK_dcmrt_LIBRARY)
+ mitk_create_module(
+ DEPENDS MitkSceneSerializationBase MitkDICOM
+ PACKAGE_DEPENDS PUBLIC DCMTK
+ )
+ add_subdirectory(autoload/DICOMRTIO)
+ add_subdirectory(test)
+else()
+ message("MITK RT Support disabled because the DCMTK dcmrt library not found")
+endif()
diff --git a/Modules/DicomRT/autoload/IO/CMakeLists.txt b/Modules/RT/autoload/DICOMRTIO/CMakeLists.txt
similarity index 59%
rename from Modules/DicomRT/autoload/IO/CMakeLists.txt
rename to Modules/RT/autoload/DICOMRTIO/CMakeLists.txt
index d449c318cf..54d3ff5335 100644
--- a/Modules/DicomRT/autoload/IO/CMakeLists.txt
+++ b/Modules/RT/autoload/DICOMRTIO/CMakeLists.txt
@@ -1,8 +1,8 @@
-MITK_CREATE_MODULE(DicomRTIO
+MITK_CREATE_MODULE(DICOMRTIO
INCLUDE_DIRS
PRIVATE src/IO
DEPENDS
- PUBLIC MitkDicomRT MitkContourModel
+ PUBLIC MitkRT MitkContourModel
PACKAGE_DEPENDS PUBLIC DCMTK
AUTOLOAD_WITH MitkCore
)
diff --git a/Modules/DicomRT/autoload/IO/files.cmake b/Modules/RT/autoload/DICOMRTIO/files.cmake
similarity index 79%
rename from Modules/DicomRT/autoload/IO/files.cmake
rename to Modules/RT/autoload/DICOMRTIO/files.cmake
index e05e20b944..0e04027394 100644
--- a/Modules/DicomRT/autoload/IO/files.cmake
+++ b/Modules/RT/autoload/DICOMRTIO/files.cmake
@@ -1,6 +1,6 @@
set(CPP_FILES
- mitkDicomRTIOActivator.cpp
+ mitkDICOMRTIOActivator.cpp
mitkRTDoseReaderService.cpp
mitkRTPlanReaderService.cpp
mitkRTStructureSetReaderService.cpp
)
diff --git a/Modules/DicomRT/autoload/IO/mitkDicomRTIOActivator.cpp b/Modules/RT/autoload/DICOMRTIO/mitkDICOMRTIOActivator.cpp
similarity index 83%
rename from Modules/DicomRT/autoload/IO/mitkDicomRTIOActivator.cpp
rename to Modules/RT/autoload/DICOMRTIO/mitkDICOMRTIOActivator.cpp
index 4ac2ab74f3..af0e65cd38 100644
--- a/Modules/DicomRT/autoload/IO/mitkDicomRTIOActivator.cpp
+++ b/Modules/RT/autoload/DICOMRTIO/mitkDICOMRTIOActivator.cpp
@@ -1,56 +1,56 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include
#include
-#include
+#include
#include
#include
#include
namespace mitk
{
- class DicomRTIOActivator : public us::ModuleActivator
+ class DICOMRTIOActivator : public us::ModuleActivator
{
public:
- DicomRTIOActivator()
+ DICOMRTIOActivator()
{
}
- ~DicomRTIOActivator() = default;
+ ~DICOMRTIOActivator() = default;
void Load(us::ModuleContext* context) override
{
us::ServiceProperties props;
props[us::ServiceConstants::SERVICE_RANKING()] = 100;
- for (const auto& mimeType : DicomRTMimeTypes::Get())
+ for (const auto& mimeType : DICOMRTMimeTypes::Get())
context->RegisterService(mimeType.get(), props);
m_RTDoseReader = std::make_unique();
m_RTPlanReader = std::make_unique();
m_RTStructureSetReader = std::make_unique();
}
void Unload(us::ModuleContext*) override
{
}
private:
std::unique_ptr m_RTDoseReader;
std::unique_ptr m_RTPlanReader;
std::unique_ptr m_RTStructureSetReader;
};
}
-US_EXPORT_MODULE_ACTIVATOR(mitk::DicomRTIOActivator)
+US_EXPORT_MODULE_ACTIVATOR(mitk::DICOMRTIOActivator)
diff --git a/Modules/DicomRT/autoload/IO/mitkRTDoseReaderService.cpp b/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp
similarity index 97%
rename from Modules/DicomRT/autoload/IO/mitkRTDoseReaderService.cpp
rename to Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp
index 7406172d13..921e4d6556 100644
--- a/Modules/DicomRT/autoload/IO/mitkRTDoseReaderService.cpp
+++ b/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp
@@ -1,168 +1,168 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
-#include
+#include
#include
#include
#include
#include
namespace mitk
{
- RTDoseReaderService::RTDoseReaderService() : AbstractFileReader(CustomMimeType(mitk::DicomRTMimeTypes::DICOMRT_DOSE_MIMETYPE_NAME()), mitk::DicomRTMimeTypes::DICOMRT_DOSE_MIMETYPE_DESCRIPTION()) {
+ RTDoseReaderService::RTDoseReaderService() : AbstractFileReader(CustomMimeType(mitk::DICOMRTMimeTypes::DICOMRT_DOSE_MIMETYPE_NAME()), mitk::DICOMRTMimeTypes::DICOMRT_DOSE_MIMETYPE_DESCRIPTION()) {
m_FileReaderServiceReg = RegisterService();
}
RTDoseReaderService::RTDoseReaderService(const RTDoseReaderService& other) : mitk::AbstractFileReader(other)
{
}
RTDoseReaderService::~RTDoseReaderService() {}
template
void RTDoseReaderService::MultiplyGridScaling(itk::Image* image, float gridscale)
{
typedef itk::Image OutputImageType;
typedef itk::Image InputImageType;
typedef itk::CastImageFilter CastFilterType;
typedef itk::ShiftScaleImageFilter ScaleFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
typename ScaleFilterType::Pointer scaleFilter = ScaleFilterType::New();
castFilter->SetInput(image);
scaleFilter->SetInput(castFilter->GetOutput());
scaleFilter->SetScale(gridscale);
scaleFilter->Update();
typename OutputImageType::Pointer scaledOutput = scaleFilter->GetOutput();
this->scaledDoseImage = mitk::Image::New();
mitk::CastToMitkImage(scaledOutput, this->scaledDoseImage);
}
std::vector > RTDoseReaderService::DoRead()
{
std::vector > result;
mitk::IDICOMTagsOfInterest* toiSrv = GetDicomTagsOfInterestService();
auto tagsOfInterest = toiSrv->GetTagsOfInterest();
DICOMTagPathList tagsOfInterestList;
for (const auto& tag : tagsOfInterest) {
tagsOfInterestList.push_back(tag.first);
}
std::string location = GetInputLocation();
mitk::DICOMFileReaderSelector::Pointer selector = mitk::DICOMFileReaderSelector::New();
selector->LoadBuiltIn3DConfigs();
selector->SetInputFiles({ location });
mitk::DICOMFileReader::Pointer reader = selector->GetFirstReaderWithMinimumNumberOfOutputImages();
reader->SetAdditionalTagsOfInterest(toiSrv->GetTagsOfInterest());
reader->SetInputFiles({ location });
reader->AnalyzeInputFiles();
reader->LoadImages();
if (reader->GetNumberOfOutputs() == 0) {
MITK_ERROR << "Could not determine a DICOM reader for this file" << std::endl;
return result;
}
mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New();
scanner->SetInputFiles({ location });
scanner->AddTagPaths(tagsOfInterestList);
scanner->Scan();
mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList();
if (frames.empty()) {
MITK_ERROR << "Error reading the RTDOSE file" << std::endl;
return result;
}
const mitk::DICOMImageBlockDescriptor& desc = reader->GetOutput(0);
mitk::Image::Pointer originalImage = desc.GetMitkImage();
if (originalImage.IsNull())
{
MITK_ERROR << "Error reading the RTDOSE file in mitk::DicomFileReader" << std::endl;
return result;
}
DcmFileFormat fileformat;
OFCondition outp = fileformat.loadFile(location.c_str(), EXS_Unknown);
if (outp.bad())
{
MITK_ERROR << "Error reading the RTDOSE file in DCMTK" << std::endl;
return result;
}
DcmDataset *dataset = fileformat.getDataset();
DRTDoseIOD doseObject;
OFCondition DCMTKresult = doseObject.read(*dataset);
if (DCMTKresult.bad())
{
MITK_ERROR << "Error reading the RTDOSE file in DCMTK" << std::endl;
return result;
}
auto findingsGridScaling = frames.front()->GetTagValueAsString(DICOMTagPath(0x3004, 0x000e)); //(0x3004, 0x000e) is grid scaling
double gridScaling;
if (findingsGridScaling.empty()) {
MITK_ERROR << "Could not find DoseGridScaling tag" << std::endl;
return result;
}
else {
gridScaling = boost::lexical_cast(findingsGridScaling.front().value);
}
AccessByItk_1(originalImage, MultiplyGridScaling, gridScaling);
auto statistics = this->scaledDoseImage->GetStatistics();
double maxDose = statistics->GetScalarValueMax();
this->scaledDoseImage->SetPropertyList(originalImage->GetPropertyList());
this->scaledDoseImage->SetProperty(mitk::RTConstants::PRESCRIBED_DOSE_PROPERTY_NAME.c_str(), mitk::GenericProperty::New(0.8*maxDose));
auto findings = ExtractPathsOfInterest(tagsOfInterestList, frames);
SetProperties(this->scaledDoseImage, findings);
result.push_back(this->scaledDoseImage.GetPointer());
return result;
}
RTDoseReaderService* RTDoseReaderService::Clone() const
{
return new RTDoseReaderService(*this);
}
}
diff --git a/Modules/DicomRT/autoload/IO/mitkRTDoseReaderService.h b/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.h
similarity index 98%
rename from Modules/DicomRT/autoload/IO/mitkRTDoseReaderService.h
rename to Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.h
index ad24fd6011..720c43cd3f 100644
--- a/Modules/DicomRT/autoload/IO/mitkRTDoseReaderService.h
+++ b/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.h
@@ -1,66 +1,66 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkRTDoseReaderService_h
#define mitkRTDoseReaderService_h
#include
#include
#include
-#include
+#include
namespace mitk
{
/**
* \brief RTDoseReaderService reads DICOM files of modality RTDOSE.
*/
class MITKDICOMRTIO_EXPORT RTDoseReaderService : public mitk::AbstractFileReader
{
public:
RTDoseReaderService(const RTDoseReaderService& other);
RTDoseReaderService();
~RTDoseReaderService() override;
using AbstractFileReader::Read;
protected:
/**
* @brief Reads a dicom dataset from a RTDOSE file
* The method reads the PixelData from the DicomRT dose file and scales
* them with a factor for getting Gray-values instead of pixel-values.
* The Gray-values are stored in a mitkImage with a vtkColorTransferFunc.
* Relative values are used for coloring the image. The relative values are
* relative to a PrescriptionDose defined in the RT-Plan. If there is no
* RT-Plan file PrescriptionDose is set to 80% of the maximum dose.
*/
std::vector> DoRead() override;
private:
RTDoseReaderService* Clone() const override;
/**
* \brief Scales an image with a factor
*
* \param gridscale the factor to scale with
*/
template
void MultiplyGridScaling(itk::Image< TPixel, VImageDimension>* image, float gridscale);
mitk::Image::Pointer scaledDoseImage;
us::ServiceRegistration m_FileReaderServiceReg;
};
}
#endif
diff --git a/Modules/DicomRT/autoload/IO/mitkRTPlanReaderService.cpp b/Modules/RT/autoload/DICOMRTIO/mitkRTPlanReaderService.cpp
similarity index 93%
rename from Modules/DicomRT/autoload/IO/mitkRTPlanReaderService.cpp
rename to Modules/RT/autoload/DICOMRTIO/mitkRTPlanReaderService.cpp
index c1d8686b03..9952d979b7 100644
--- a/Modules/DicomRT/autoload/IO/mitkRTPlanReaderService.cpp
+++ b/Modules/RT/autoload/DICOMRTIO/mitkRTPlanReaderService.cpp
@@ -1,82 +1,82 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include
#include
#include
#include
#include
#include
#include
#include
-#include
+#include
namespace mitk
{
- RTPlanReaderService::RTPlanReaderService() : AbstractFileReader(CustomMimeType(mitk::DicomRTMimeTypes::DICOMRT_PLAN_MIMETYPE_NAME()), mitk::DicomRTMimeTypes::DICOMRT_PLAN_MIMETYPE_DESCRIPTION()) {
+ RTPlanReaderService::RTPlanReaderService() : AbstractFileReader(CustomMimeType(mitk::DICOMRTMimeTypes::DICOMRT_PLAN_MIMETYPE_NAME()), mitk::DICOMRTMimeTypes::DICOMRT_PLAN_MIMETYPE_DESCRIPTION()) {
m_FileReaderServiceReg = RegisterService();
}
RTPlanReaderService::RTPlanReaderService(const RTPlanReaderService& other) : mitk::AbstractFileReader(other)
{
}
RTPlanReaderService::~RTPlanReaderService() {}
std::vector > RTPlanReaderService::DoRead()
{
std::vector > result;
auto DICOMTagsOfInterestService = GetDicomTagsOfInterestService();
auto tagsOfInterest = DICOMTagsOfInterestService->GetTagsOfInterest();
DICOMTagPathList tagsOfInterestList;
for (const auto& tag : tagsOfInterest) {
tagsOfInterestList.push_back(tag.first);
}
std::string location = GetInputLocation();
mitk::StringList files = { location };
mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New();
scanner->SetInputFiles(files);
scanner->AddTagPaths(tagsOfInterestList);
scanner->Scan();
mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList();
if (frames.empty()) {
MITK_ERROR << "Error reading the RTPLAN file" << std::endl;
return result;
}
auto findings = ExtractPathsOfInterest(tagsOfInterestList, frames);
//just create empty image. No image information available in RTPLAN. But properties will be attached.
Image::Pointer dummyImage = Image::New();
mitk::PixelType pt = mitk::MakeScalarPixelType();
unsigned int dim[] = { 1,1};
dummyImage->Initialize(pt, 2, dim);
SetProperties(dummyImage, findings);
result.push_back(dummyImage.GetPointer());
return result;
}
RTPlanReaderService* RTPlanReaderService::Clone() const
{
return new RTPlanReaderService(*this);
}
}
diff --git a/Modules/DicomRT/autoload/IO/mitkRTPlanReaderService.h b/Modules/RT/autoload/DICOMRTIO/mitkRTPlanReaderService.h
similarity index 98%
rename from Modules/DicomRT/autoload/IO/mitkRTPlanReaderService.h
rename to Modules/RT/autoload/DICOMRTIO/mitkRTPlanReaderService.h
index c2653f2991..f1171b57b0 100644
--- a/Modules/DicomRT/autoload/IO/mitkRTPlanReaderService.h
+++ b/Modules/RT/autoload/DICOMRTIO/mitkRTPlanReaderService.h
@@ -1,63 +1,63 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkRTPlanReaderService_h
#define mitkRTPlanReaderService_h
#include "mitkAbstractFileReader.h"
#include
#include "mitkIDICOMTagsOfInterest.h"
#include "mitkDICOMDatasetAccessingImageFrameInfo.h"
#include
-#include "MitkDicomRTIOExports.h"
+#include "MitkDICOMRTIOExports.h"
namespace mitk
{
/**
* \brief RTPlanReaderService reads DICOM files of modality RTPLAN.
\details The tags are defined in mitk::GetDefaultDICOMTagsOfInterest() in Module MitkDicomReader. They are stored as TemporoSpatialStringProperty.
with the key as their respective DICOM tags.
\note No image information is in RTPLAN.
*/
class MITKDICOMRTIO_EXPORT RTPlanReaderService : public mitk::AbstractFileReader
{
public:
RTPlanReaderService();
RTPlanReaderService(const RTPlanReaderService& other);
using AbstractFileReader::Read;
~RTPlanReaderService() override;
protected:
/**
* \brief Reads the file (only tags).
@details DICOMDCMTKTagScanner is used to read the tags
\note No image information is in RTPLAN.
\sa mitk::GetDefaultDICOMTagsOfInterest() for tags that are read
*/
std::vector> DoRead() override;
private:
RTPlanReaderService* Clone() const override;
us::ServiceRegistration m_FileReaderServiceReg;
};
}
#endif
diff --git a/Modules/DicomRT/autoload/IO/mitkRTStructureSetReaderService.cpp b/Modules/RT/autoload/DICOMRTIO/mitkRTStructureSetReaderService.cpp
similarity index 98%
rename from Modules/DicomRT/autoload/IO/mitkRTStructureSetReaderService.cpp
rename to Modules/RT/autoload/DICOMRTIO/mitkRTStructureSetReaderService.cpp
index f4c4bcb794..5455f4112e 100644
--- a/Modules/DicomRT/autoload/IO/mitkRTStructureSetReaderService.cpp
+++ b/Modules/RT/autoload/DICOMRTIO/mitkRTStructureSetReaderService.cpp
@@ -1,288 +1,288 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkRTStructureSetReaderService.h"
-#include
+#include
#include
#include
#include
#include "dcmtk/dcmrt/drtstrct.h"
namespace mitk
{
- RTStructureSetReaderService::RTStructureSetReaderService() : AbstractFileReader(CustomMimeType(mitk::DicomRTMimeTypes::DICOMRT_STRUCT_MIMETYPE_NAME()), mitk::DicomRTMimeTypes::DICOMRT_STRUCT_MIMETYPE_DESCRIPTION()) {
+ RTStructureSetReaderService::RTStructureSetReaderService() : AbstractFileReader(CustomMimeType(mitk::DICOMRTMimeTypes::DICOMRT_STRUCT_MIMETYPE_NAME()), mitk::DICOMRTMimeTypes::DICOMRT_STRUCT_MIMETYPE_DESCRIPTION()) {
m_FileReaderServiceReg = RegisterService();
}
RTStructureSetReaderService::RTStructureSetReaderService(const RTStructureSetReaderService& other) : mitk::AbstractFileReader(other)
{
}
RTStructureSetReaderService::~RTStructureSetReaderService() {}
RTStructureSetReaderService::RoiEntry::RoiEntry()
{
Number = 0;
DisplayColor[0] = 1.0;
DisplayColor[1] = 0.0;
DisplayColor[2] = 0.0;
ContourModelSet = mitk::ContourModelSet::New();
}
RTStructureSetReaderService::RoiEntry::RoiEntry(const RoiEntry& src)
{
Number = src.Number;
Name = src.Name;
Description = src.Description;
DisplayColor[0] = src.DisplayColor[0];
DisplayColor[1] = src.DisplayColor[1];
DisplayColor[2] = src.DisplayColor[2];
ContourModelSet = mitk::ContourModelSet::New();
SetPolyData(src.ContourModelSet);
}
RTStructureSetReaderService::RoiEntry::~RoiEntry() {}
RTStructureSetReaderService::RoiEntry& RTStructureSetReaderService::
RoiEntry::operator =(const RoiEntry& src)
{
Number = src.Number;
Name = src.Name;
Description = src.Description;
DisplayColor[0] = src.DisplayColor[0];
DisplayColor[1] = src.DisplayColor[1];
DisplayColor[2] = src.DisplayColor[2];
SetPolyData(src.ContourModelSet);
return (*this);
}
void RTStructureSetReaderService::RoiEntry::
SetPolyData(mitk::ContourModelSet::Pointer roiPolyData)
{
if (roiPolyData == this->ContourModelSet)
{
return;
}
this->ContourModelSet = roiPolyData;
}
size_t RTStructureSetReaderService::GetNumberOfROIs() const
{
return this->ROISequenceVector.size();
}
RTStructureSetReaderService::RoiEntry* RTStructureSetReaderService::
FindRoiByNumber(unsigned int roiNum)
{
for (unsigned int i = 0; i < this->ROISequenceVector.size(); ++i)
{
if (this->ROISequenceVector[i].Number == roiNum)
{
return &this->ROISequenceVector[i];
}
}
return nullptr;
}
std::vector > RTStructureSetReaderService::DoRead()
{
std::vector > result;
std::string location = GetInputLocation();
auto DICOMTagsOfInterestService = GetDicomTagsOfInterestService();
auto tagsOfInterest = DICOMTagsOfInterestService->GetTagsOfInterest();
DICOMTagPathList tagsOfInterestList;
for (const auto& tag : tagsOfInterest) {
tagsOfInterestList.push_back(tag.first);
}
mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New();
scanner->SetInputFiles({ location });
scanner->AddTagPaths(tagsOfInterestList);
scanner->Scan();
mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList();
if (frames.empty()) {
MITK_ERROR << "Error reading the RTSTRUCT file" << std::endl;
return result;
}
auto findings = ExtractPathsOfInterest(tagsOfInterestList, frames);
DcmFileFormat file;
OFCondition output = file.loadFile(location.c_str(), EXS_Unknown);
if (output.bad())
{
MITK_ERROR << "Can't read the file" << std::endl;
return result;
}
DcmDataset* dataset = file.getDataset();
DRTStructureSetIOD structureSetObject;
OFCondition outp = structureSetObject.read(*dataset);
if (!outp.good())
{
MITK_ERROR << "Error reading the file" << std::endl;
return result;
}
DRTStructureSetROISequence& roiSequence =
structureSetObject.getStructureSetROISequence();
if (!roiSequence.gotoFirstItem().good())
{
MITK_ERROR << "Error reading the structure sequence" << std::endl;
return result;
}
do
{
DRTStructureSetROISequence::Item& currentSequence =
roiSequence.getCurrentItem();
if (!currentSequence.isValid())
{
continue;
}
OFString roiName;
OFString roiDescription;
Sint32 roiNumber;
RoiEntry roi;
currentSequence.getROIName(roiName);
currentSequence.getROIDescription(roiDescription);
currentSequence.getROINumber(roiNumber);
roi.Name = roiName.c_str();
roi.Description = roiDescription.c_str();
roi.Number = roiNumber;
this->ROISequenceVector.push_back(roi);
} while (roiSequence.gotoNextItem().good());
Sint32 refRoiNumber;
DRTROIContourSequence& roiContourSeqObject =
structureSetObject.getROIContourSequence();
if (!roiContourSeqObject.gotoFirstItem().good())
{
MITK_ERROR << "Error reading the contour sequence" << std::endl;
return result;
}
do
{
mitk::ContourModelSet::Pointer contourSet = mitk::ContourModelSet::New();
DRTROIContourSequence::Item& currentRoiObject =
roiContourSeqObject.getCurrentItem();
if (!currentRoiObject.isValid())
{
continue;
}
currentRoiObject.getReferencedROINumber(refRoiNumber);
DRTContourSequence& contourSeqObject =
currentRoiObject.getContourSequence();
if (contourSeqObject.getNumberOfItems() > 0 && contourSeqObject.gotoFirstItem().good())
{
do
{
DRTContourSequence::Item& contourItem =
contourSeqObject.getCurrentItem();
if (!contourItem.isValid())
{
continue;
}
OFString contourNumber;
OFString numberOfPoints;
OFVector contourData_LPS;
mitk::ContourModel::Pointer contourSequence =
mitk::ContourModel::New();
contourItem.getContourNumber(contourNumber);
contourItem.getNumberOfContourPoints(numberOfPoints);
contourItem.getContourData(contourData_LPS);
for (unsigned int i = 0; i < contourData_LPS.size() / 3; i++)
{
mitk::Point3D point;
point[0] = contourData_LPS.at(3 * i);
point[1] = contourData_LPS.at(3 * i + 1);
point[2] = contourData_LPS.at(3 * i + 2);
contourSequence->AddVertex(point);
}
contourSequence->Close();
contourSet->AddContourModel(contourSequence);
} while (contourSeqObject.gotoNextItem().good());
}
else
{
MITK_WARN << "contourSeqObject has no items in sequence. Object is neglected and not read. Struct name: " << this->FindRoiByNumber(refRoiNumber)->Name << std::endl;
}
RoiEntry* refROI = this->FindRoiByNumber(refRoiNumber);
if (refROI == nullptr)
{
MITK_ERROR << "Can not find references ROI" << std::endl;
continue;
}
Sint32 roiColor;
for (unsigned int j = 0; j < 3; j++)
{
currentRoiObject.getROIDisplayColor(roiColor, j);
refROI->DisplayColor[j] = roiColor / 255.0;
}
refROI->ContourModelSet = contourSet;
contourSet->SetProperty("name", mitk::StringProperty::New(refROI->Name));
contourSet->SetProperty("contour.color", mitk::ColorProperty::New(
refROI->DisplayColor[0],
refROI->DisplayColor[1],
refROI->DisplayColor[2]));
} while (roiContourSeqObject.gotoNextItem().good());
for (auto const& aROI : ROISequenceVector)
{
result.push_back(aROI.ContourModelSet.GetPointer());
result.at(result.size() - 1)->SetProperty("name", aROI.ContourModelSet->GetProperty("name"));
result.at(result.size() - 1)->SetProperty("color", aROI.ContourModelSet->GetProperty("contour.color"));
result.at(result.size() - 1)->SetProperty("contour.color", aROI.ContourModelSet->GetProperty("contour.color"));
SetProperties(result.at(result.size() - 1).GetPointer(), findings);
}
return result;
}
RTStructureSetReaderService* RTStructureSetReaderService::Clone() const
{
return new RTStructureSetReaderService(*this);
}
}
diff --git a/Modules/DicomRT/autoload/IO/mitkRTStructureSetReaderService.h b/Modules/RT/autoload/DICOMRTIO/mitkRTStructureSetReaderService.h
similarity index 98%
rename from Modules/DicomRT/autoload/IO/mitkRTStructureSetReaderService.h
rename to Modules/RT/autoload/DICOMRTIO/mitkRTStructureSetReaderService.h
index 8fcf2e8efb..25871642b1 100644
--- a/Modules/DicomRT/autoload/IO/mitkRTStructureSetReaderService.h
+++ b/Modules/RT/autoload/DICOMRTIO/mitkRTStructureSetReaderService.h
@@ -1,87 +1,87 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef MITKRTSTRUCTURESETREADER_H
#define MITKRTSTRUCTURESETREADER_H
#include
-#include "MitkDicomRTIOExports.h"
+#include "MitkDICOMRTIOExports.h"
#include
#include
namespace mitk
{
class MITKDICOMRTIO_EXPORT RTStructureSetReaderService : public mitk::AbstractFileReader
{
/**
* Represent a region of interest (ROI)
*/
class RoiEntry
{
public:
RoiEntry();
RoiEntry(const RoiEntry& src);
virtual ~RoiEntry();
RoiEntry& operator=(const RoiEntry& src);
void SetPolyData(ContourModelSet::Pointer roiPolyData);
unsigned int Number;
std::string Name;
std::string Description;
double DisplayColor[3];
mitk::ContourModelSet::Pointer ContourModelSet;
};
public:
RTStructureSetReaderService();
RTStructureSetReaderService(const RTStructureSetReaderService& other);
~RTStructureSetReaderService() override;
/**
* @brief Reading a RT StructureSet from the DICOM file and returns the ROIs
* (region of interest) as a ContourModelSet. One ContourModelSet represent
* one ROI. A ContourModelSet contains ContourModels which represent the
* single structures.
*/
using AbstractFileReader::Read;
protected:
std::vector> DoRead() override;
private:
RTStructureSetReaderService* Clone() const override;
/**
* containing the ROIs meta information like name number and description
*/
std::vector ROISequenceVector;
/**
* Returns the number of ROIs from the ROISequenceVector
*/
size_t GetNumberOfROIs() const;
/**
* Returns the relevant ROI from the ROISequenceVector by its number
*/
RoiEntry* FindRoiByNumber(unsigned int roiNum);
us::ServiceRegistration m_FileReaderServiceReg;
};
}
#endif // MITKRTSTRUCTURESETREADER_H
diff --git a/Modules/DicomRT/files.cmake b/Modules/RT/files.cmake
similarity index 93%
rename from Modules/DicomRT/files.cmake
rename to Modules/RT/files.cmake
index b7fe17c979..e1b6f55ab8 100644
--- a/Modules/DicomRT/files.cmake
+++ b/Modules/RT/files.cmake
@@ -1,19 +1,19 @@
file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*")
SET(CPP_FILES
mitkRTConstants.cpp
mitkIsoDoseLevel.cpp
mitkIsoDoseLevelCollections.cpp
mitkIsoDoseLevelSetProperty.cpp
mitkIsoDoseLevelVectorProperty.cpp
mitkDoseImageVtkMapper2D.cpp
mitkIsoLevelsGenerator.cpp
mitkDoseNodeHelper.cpp
- mitkDicomRTMimeTypes.cpp
+ mitkDICOMRTMimeTypes.cpp
)
set(TPP_FILES
)
set(MOC_H_FILES
)
diff --git a/Modules/DicomRT/include/mitkDicomRTMimeTypes.h b/Modules/RT/include/mitkDICOMRTMimeTypes.h
similarity index 79%
rename from Modules/DicomRT/include/mitkDicomRTMimeTypes.h
rename to Modules/RT/include/mitkDICOMRTMimeTypes.h
index d57d821f0d..37522ba7bf 100644
--- a/Modules/DicomRT/include/mitkDicomRTMimeTypes.h
+++ b/Modules/RT/include/mitkDICOMRTMimeTypes.h
@@ -1,79 +1,79 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
-#ifndef MITKDicomRTMimeTypes_H
-#define MITKDicomRTMimeTypes_H
+#ifndef MITKDICOMRTMimeTypes_H
+#define MITKDICOMRTMimeTypes_H
#include
#include
-#include
+#include
#include
#include
#include
namespace mitk {
-class MITKDICOMRT_EXPORT DicomRTMimeTypes
+class MITKRT_EXPORT DICOMRTMimeTypes
{
public:
- class MITKDICOMRT_EXPORT RTDoseMimeType : public CustomMimeType
+ class MITKRT_EXPORT RTDoseMimeType : public CustomMimeType
{
public:
RTDoseMimeType();
bool AppliesTo(const std::string &path) const override;
RTDoseMimeType* Clone() const override;
};
- class MITKDICOMRT_EXPORT RTStructMimeType : public CustomMimeType
+ class MITKRT_EXPORT RTStructMimeType : public CustomMimeType
{
public:
RTStructMimeType();
bool AppliesTo(const std::string &path) const override;
RTStructMimeType* Clone() const override;
};
- class MITKDICOMRT_EXPORT RTPlanMimeType : public CustomMimeType
+ class MITKRT_EXPORT RTPlanMimeType : public CustomMimeType
{
public:
RTPlanMimeType();
bool AppliesTo(const std::string &path) const override;
RTPlanMimeType* Clone() const override;
};
// Get all DicomRT Mime Types
static std::array, 3> Get();
static RTDoseMimeType DICOMRT_DOSE_MIMETYPE();
static RTStructMimeType DICOMRT_STRUCT_MIMETYPE();
static RTPlanMimeType DICOMRT_PLAN_MIMETYPE();
static std::string DICOMRT_DOSE_MIMETYPE_NAME();
static std::string DICOMRT_STRUCT_MIMETYPE_NAME();
static std::string DICOMRT_PLAN_MIMETYPE_NAME();
static std::string DICOMRT_DOSE_MIMETYPE_DESCRIPTION();
static std::string DICOMRT_STRUCT_MIMETYPE_DESCRIPTION();
static std::string DICOMRT_PLAN_MIMETYPE_DESCRIPTION();
- DicomRTMimeTypes() = delete;
- DicomRTMimeTypes(const DicomRTMimeTypes&) = delete;
+ DICOMRTMimeTypes() = delete;
+ DICOMRTMimeTypes(const DICOMRTMimeTypes&) = delete;
static mitk::IDICOMTagsOfInterest* GetDicomTagsOfInterestService();
static bool canReadByDicomFileReader(const std::string & path);
static std::string GetModality(const std::string & path);
};
}
-#endif // MITKDicomRTMimeTypes_H
+#endif // MITKDICOMRTMimeTypes_H
diff --git a/Modules/DicomRT/include/mitkDoseImageVtkMapper2D.h b/Modules/RT/include/mitkDoseImageVtkMapper2D.h
similarity index 98%
rename from Modules/DicomRT/include/mitkDoseImageVtkMapper2D.h
rename to Modules/RT/include/mitkDoseImageVtkMapper2D.h
index 636f1a9ffe..cb0f7bbded 100644
--- a/Modules/DicomRT/include/mitkDoseImageVtkMapper2D.h
+++ b/Modules/RT/include/mitkDoseImageVtkMapper2D.h
@@ -1,309 +1,309 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef MITKDoseImageVtkMapper2D2D_H_HEADER_INCLUDED
#define MITKDoseImageVtkMapper2D2D_H_HEADER_INCLUDED
//MITK
#include
-#include