#include <mitkCustomTagParser.h>

Collaboration diagram for mitk::CustomTagParser:

Public Member Functions
	CustomTagParser (std::string relevantFile)
	the constructor expects a path to one of the files to be loaded or the directory of the dicom files More...

mitk::PropertyList::Pointer	ParseDicomProperty (mitk::TemporoSpatialStringProperty *dicomProperty)
	parse the provided dicom property and return a property list based on the closest revision parameter mapping More...

mitk::PropertyList::Pointer	ParseDicomPropertyString (std::string dicomPropertyString)
	parse the provided string and return a property list based on the closest revision parameter mapping More...

void	SetParseStrategy (std::string parseStrategy)

void	SetRevisionMappingStrategy (std::string revisionMappingStrategy)

Static Public Member Functions
static std::string	ExtractRevision (std::string sequenceFileName)

Static Public Attributes
static const std::string	m_OffsetsPropertyName
	name of the property for the offsets, including normalization offsets More...

static const std::string	m_RevisionPropertyName
	name of the property for the data acquisition revision More...

static const std::string	m_JSONRevisionPropertyName
	name of the property for the json parameter mapping revision More...

static const std::string	m_CESTPropertyPrefix
	prefix for all CEST related property names More...

Protected Member Functions
std::string	GetRevisionAppropriateJSONString (std::string revisionString)

void	GetClosestLowerRevision (std::string revisionString)

std::string	GetClosestLowerRevision (std::string revisionString, std::vector< int > availableRevisionsVector)

bool	IsT1Sequence (std::string preparationType, std::string recoveryMode, std::string spoilingType, std::string revisionString)
	Decides whether or not the image is likely to be a T1Map, if not it is assumed to be a CEST sequence. More...

std::string	GetOffsetString (std::string samplingType, std::string offset, std::string measurements)
	Get a string filled with the properly formated offsets based on the sampling type and offset. More...

std::vector< int >	GetExternalRevisions ()
	returns a vector revision numbers of all REVISIONNUMBER.json found beside the MitkCEST library More...

std::vector< int >	GetInternalRevisions ()
	returns a vector revision numbers of all REVISIONNUMBER.json provided as resources during the compile More...

std::string	GetExternalJSONDirectory ()
	returns the path where external jsons are expected to be located More...

Protected Attributes
std::string	m_ClosestInternalRevision
	the closest lower revision provided as resource, empty if none found More...

std::string	m_ClosestExternalRevision
	the closest lower revision provided as a json beside the library, empty if none found More...

std::string	m_DicomDataPath
	path to the dicom data More...

std::string	m_ParseStrategy
	Should the kind of data be automatically determined or should it be parsed as a specific one. More...

std::string	m_RevisionMappingStrategy
	How to handle parameter mapping based on absent revision jsons. More...

Static Protected Attributes
static const std::string	m_RevisionIndependentMapping
	revision independent mapping to inject into the revision dependent json string More...

static const std::string	m_DefaultJsonString
	default revision dependent json string if none is found More...

Detailed Description

The custom tag parser can be used to parse the custom dicom tag of the siemens private tag (0x0029, 0x1020) to extract relevant CEST data.

An initial parsing determines whether the provided string belongs to CEST data at all. To make the check and extract the revision number the following rules are aplied:

Sequence name (tSequenceFileName) must either
1. start with the substring "CEST" (case insensitiv), or
2. contain the substring "_CEST" (case insensitiv).
Sequence name (tSequenceFileName) must contain the substring "_Rev" (case insensitiv).
All numbers after "_Rev" represent the revision number; until either
1. the next _, or
2. end of sequence name.

Which custom parameters to save and to which property name can be controlled by a json file. This file can be either provided as a resource for the MitkCEST module during compilation or placed next to the MitkCEST library in your binary folder.

The expected format for the file "REVISIONNUMBER.json":
{
"REVISIONNUMBER" : "revision_json",
"sWiPMemBlock.alFree[1]" : "AdvancedMode",
"sWiPMemBlock.alFree[2]" : "RetreatMode"
}

where :

REVISIONNUMBER is the revision number of this json parameter mapping (files with non digit characters in their name will be ignored)
sWiPMemBlock.alFree[1] is the name of one parameter in the private dicom tag
AdvancedMode is the name of the property the content of sWiPMemBlock.alFree[1] should be saved to

Note: It is assumed that the entire content of tag (0x0029, 0x1020) is provided and that it es hex encoded (12\23\04...).

If the sampling type is list it will try to access LIST.txt at the location provided in the constructor to read the offsets.

Definition at line 70 of file mitkCustomTagParser.h.

Constructor & Destructor Documentation

◆ CustomTagParser()

mitk::CustomTagParser::CustomTagParser ( std::string relevantFile )

the constructor expects a path to one of the files to be loaded or the directory of the dicom files

Definition at line 118 of file mitkCustomTagParser.cpp.

References m_DicomDataPath, m_ParseStrategy, and m_RevisionMappingStrategy.

Member Function Documentation

◆ ExtractRevision()

std::string mitk::CustomTagParser::ExtractRevision ( std::string sequenceFileName )

static

Extract the revision out of the passed sequenceFileName. If the file name is not a valid CEST file name (see rules in the class documentation) exceptions will be thrown. If the file name is valid but contains no revision number an empty string will be returned.

Definition at line 128 of file mitkCustomTagParser.cpp.

References mitkThrow.

Referenced by ParseDicomPropertyString().

◆ GetClosestLowerRevision() [1/2]

void mitk::CustomTagParser::GetClosestLowerRevision ( std::string revisionString )

protected

Definition at line 575 of file mitkCustomTagParser.cpp.

References GetExternalJSONDirectory(), GetExternalRevisions(), GetInternalRevisions(), m_ClosestExternalRevision, m_ClosestInternalRevision, m_RevisionMappingStrategy, and mitkThrow.

Referenced by GetRevisionAppropriateJSONString().

◆ GetClosestLowerRevision() [2/2]

std::string mitk::CustomTagParser::GetClosestLowerRevision	(	std::string	revisionString,
		std::vector< int >	availableRevisionsVector
	)

protected

Definition at line 540 of file mitkCustomTagParser.cpp.

◆ GetExternalJSONDirectory()

std::string mitk::CustomTagParser::GetExternalJSONDirectory ( )

protected

returns the path where external jsons are expected to be located

Definition at line 831 of file mitkCustomTagParser.cpp.

References ModuleContext::GetModule(), and us::GetModuleContext().

Referenced by GetClosestLowerRevision(), GetExternalRevisions(), and GetRevisionAppropriateJSONString().

◆ GetExternalRevisions()

std::vector< int > mitk::CustomTagParser::GetExternalRevisions ( )

protected

returns a vector revision numbers of all REVISIONNUMBER.json found beside the MitkCEST library

Definition at line 510 of file mitkCustomTagParser.cpp.

References GetExternalJSONDirectory().

Referenced by GetClosestLowerRevision().

◆ GetInternalRevisions()

std::vector< int > mitk::CustomTagParser::GetInternalRevisions ( )

protected

returns a vector revision numbers of all REVISIONNUMBER.json provided as resources during the compile

Definition at line 495 of file mitkCustomTagParser.cpp.

References ModuleContext::GetModule(), and us::GetModuleContext().

Referenced by GetClosestLowerRevision().

◆ GetOffsetString()

std::string mitk::CustomTagParser::GetOffsetString	(	std::string	samplingType,
		std::string	offset,
		std::string	measurements
	)

protected

Get a string filled with the properly formated offsets based on the sampling type and offset.

Definition at line 693 of file mitkCustomTagParser.cpp.

References m_DicomDataPath, MITK_ERROR, and MITK_WARN.

Referenced by ParseDicomPropertyString().

◆ GetRevisionAppropriateJSONString()

std::string mitk::CustomTagParser::GetRevisionAppropriateJSONString ( std::string revisionString )

protected

Definition at line 608 of file mitkCustomTagParser.cpp.

References GetClosestLowerRevision(), GetExternalJSONDirectory(), ModuleContext::GetModule(), us::GetModuleContext(), us::ModuleResource::IsFile(), us::ModuleResource::IsValid(), m_ClosestExternalRevision, m_ClosestInternalRevision, m_DefaultJsonString, m_RevisionIndependentMapping, MITK_INFO, and MITK_WARN.

Referenced by ParseDicomPropertyString().

◆ IsT1Sequence()

bool mitk::CustomTagParser::IsT1Sequence	(	std::string	preparationType,
		std::string	recoveryMode,
		std::string	spoilingType,
		std::string	revisionString
	)

protected

Decides whether or not the image is likely to be a T1Map, if not it is assumed to be a CEST sequence.

Definition at line 175 of file mitkCustomTagParser.cpp.

References m_ParseStrategy.

Referenced by ParseDicomPropertyString().

◆ ParseDicomProperty()

mitk::PropertyList::Pointer mitk::CustomTagParser::ParseDicomProperty ( mitk::TemporoSpatialStringProperty * dicomProperty )

parse the provided dicom property and return a property list based on the closest revision parameter mapping

Definition at line 478 of file mitkCustomTagParser.cpp.

References mitk::TemporoSpatialStringProperty::GetValue(), MITK_ERROR, mitk::PropertyList::New(), and ParseDicomPropertyString().

◆ ParseDicomPropertyString()

mitk::PropertyList::Pointer mitk::CustomTagParser::ParseDicomPropertyString ( std::string dicomPropertyString )

parse the provided string and return a property list based on the closest revision parameter mapping

Definition at line 246 of file mitkCustomTagParser.cpp.

References mitk::IPropertyPersistence::AddInfo(), mitk::CEST_PROPERTY_NAME_PREPERATIONTYPE(), mitk::CEST_PROPERTY_NAME_RECOVERYMODE(), mitk::CEST_PROPERTY_NAME_SPOILINGTYPE(), mitk::CEST_PROPERTY_NAME_TREC(), ExtractRevision(), GetOffsetString(), GetPersistenceService(), GetRevisionAppropriateJSONString(), info(), IsT1Sequence(), m_CESTPropertyPrefix, m_DicomDataPath, m_JSONRevisionPropertyName, m_OffsetsPropertyName, m_RevisionPropertyName, MITK_ERROR, MITK_INFO, MITK_WARN, mitkThrow, mitk::PropertyPersistenceInfo::New(), mitk::StringProperty::New(), mitk::PropertyList::New(), offset, and mbilog::replace.

Referenced by mitk::MitkCESTIOMimeTypes::MitkCESTDicomMimeType::AppliesTo(), ParseDicomProperty(), and mitk::CESTDICOMReaderService::Read().

◆ SetParseStrategy()

void mitk::CustomTagParser::SetParseStrategy ( std::string parseStrategy )

Definition at line 821 of file mitkCustomTagParser.cpp.

References m_ParseStrategy.

Referenced by mitk::CESTDICOMReaderService::Read().

◆ SetRevisionMappingStrategy()

void mitk::CustomTagParser::SetRevisionMappingStrategy ( std::string revisionMappingStrategy )

Definition at line 826 of file mitkCustomTagParser.cpp.

References m_RevisionMappingStrategy.

Referenced by mitk::CESTDICOMReaderService::Read().

Member Data Documentation

◆ m_CESTPropertyPrefix

const std::string mitk::CustomTagParser::m_CESTPropertyPrefix

static

prefix for all CEST related property names

Definition at line 100 of file mitkCustomTagParser.h.

Referenced by ParseDicomPropertyString().

◆ m_ClosestExternalRevision

std::string mitk::CustomTagParser::m_ClosestExternalRevision

protected

the closest lower revision provided as a json beside the library, empty if none found

Definition at line 124 of file mitkCustomTagParser.h.

Referenced by GetClosestLowerRevision(), and GetRevisionAppropriateJSONString().

◆ m_ClosestInternalRevision

std::string mitk::CustomTagParser::m_ClosestInternalRevision

protected

the closest lower revision provided as resource, empty if none found

Definition at line 122 of file mitkCustomTagParser.h.

Referenced by GetClosestLowerRevision(), and GetRevisionAppropriateJSONString().

◆ m_DefaultJsonString

const std::string mitk::CustomTagParser::m_DefaultJsonString

staticprotected

default revision dependent json string if none is found

Definition at line 129 of file mitkCustomTagParser.h.

Referenced by GetRevisionAppropriateJSONString().

◆ m_DicomDataPath

std::string mitk::CustomTagParser::m_DicomDataPath

protected

path to the dicom data

Definition at line 131 of file mitkCustomTagParser.h.

Referenced by CustomTagParser(), GetOffsetString(), and ParseDicomPropertyString().

◆ m_JSONRevisionPropertyName

const std::string mitk::CustomTagParser::m_JSONRevisionPropertyName

static

name of the property for the json parameter mapping revision

Definition at line 97 of file mitkCustomTagParser.h.

Referenced by ParseDicomPropertyString().

◆ m_OffsetsPropertyName

const std::string mitk::CustomTagParser::m_OffsetsPropertyName

static

name of the property for the offsets, including normalization offsets

Definition at line 91 of file mitkCustomTagParser.h.

Referenced by ExtractOffsets(), mitk::CESTImageNormalizationFilter::GenerateData(), and ParseDicomPropertyString().

◆ m_ParseStrategy

std::string mitk::CustomTagParser::m_ParseStrategy

protected

Should the kind of data be automatically determined or should it be parsed as a specific one.

Definition at line 133 of file mitkCustomTagParser.h.

Referenced by CustomTagParser(), IsT1Sequence(), and SetParseStrategy().

◆ m_RevisionIndependentMapping

const std::string mitk::CustomTagParser::m_RevisionIndependentMapping

staticprotected

revision independent mapping to inject into the revision dependent json string

Definition at line 127 of file mitkCustomTagParser.h.

Referenced by GetRevisionAppropriateJSONString().

◆ m_RevisionMappingStrategy

std::string mitk::CustomTagParser::m_RevisionMappingStrategy

protected

How to handle parameter mapping based on absent revision jsons.

Definition at line 135 of file mitkCustomTagParser.h.

Referenced by CustomTagParser(), GetClosestLowerRevision(), and SetRevisionMappingStrategy().

◆ m_RevisionPropertyName

const std::string mitk::CustomTagParser::m_RevisionPropertyName

static

name of the property for the data acquisition revision

Definition at line 94 of file mitkCustomTagParser.h.

Referenced by ParseDicomPropertyString().

The documentation for this class was generated from the following files:

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CustomTagParser()

Member Function Documentation

◆ ExtractRevision()

◆ GetClosestLowerRevision() [1/2]

◆ GetClosestLowerRevision() [2/2]

◆ GetExternalJSONDirectory()

◆ GetExternalRevisions()

◆ GetInternalRevisions()

◆ GetOffsetString()

◆ GetRevisionAppropriateJSONString()

◆ IsT1Sequence()

◆ ParseDicomProperty()

◆ ParseDicomPropertyString()

◆ SetParseStrategy()

◆ SetRevisionMappingStrategy()

Member Data Documentation

◆ m_CESTPropertyPrefix

◆ m_ClosestExternalRevision

◆ m_ClosestInternalRevision

◆ m_DefaultJsonString

◆ m_DicomDataPath

◆ m_JSONRevisionPropertyName

◆ m_OffsetsPropertyName

◆ m_ParseStrategy

◆ m_RevisionIndependentMapping

◆ m_RevisionMappingStrategy

◆ m_RevisionPropertyName