Hello everyone,
I want to inform about an internal discussion concerning the handling of DICOM
tags as BaseData properties and the changes we are planning to do in the
context of finally switching to the DICOM reading infrastructure of the Module
DICOMReader. Please feel free to comment on that topic, if you have thoughts
about it. This would give us the possibility to make the refactorization as
beneficial as possible for everyone.
Background/motivation:
* At the moment we store extracted DICOM tags as properties. => Good :)
* At the moment the properties naming style for DICOM tags is very
heterogeneous/individualized [1]. And that's putting it nicely. => Bad! :(
* At the moment you have no standardized possibility to access DICOM
tag values stored in properties. Especially if a value is slice or time point
specific.
Planned changes:
1. DICOM tags (or generally spoken, information that should be stored in
properties semantically encoded with DICOM tags as names) will be stored with
the following property naming convention: "DICOM.<Group Number>.<Element
Number>". E.g.: the values of the DICOM tag "Modality" would be stored with the
property name "DICOM.0008.0060". The storing location of the information will
be the (Base)Data instance (not the node!).
2. To support human readability the following strategies will be used.
a. Dedicated Plugin and/or overlay information. See Bug
19476<https://dkfzowa0.dkfz-heidelberg.de/owa/redir.aspx?SURL=DLGc3uSBeZwIhFBYJIHiNh9VlNxinevOFo1VP87MwkV_-NFru0jTCGgAdAB0AHAAOgAvAC8AYgB1AGcAcwAuAG0AaQB0AGsALgBvAHIAZwAvAHMAaABvAHcAXwBiAHUAZwAuAGMAZwBpAD8AaQBkAD0AMQA5ADQANwA2AA..&URL=http%3a%2f%2fbugs.mitk.org%2fshow_bug.cgi%3fid%3d19476>
- Create a way to show selected DICOM tags of a node.
b. The PropertyDescriptions service will be used to add the human readable
DICOM tag names as description for the respective properties. (Therefore it
will also automatically displayed in the PropertyView)
3. We will introduce non-member functions that allow to query the value of
a DICOM tag from the properties of a BaseData instance. They will also allow
querying for certain slices or time points. Additionally there will be some
helper function for name management. The draft for the function signatures is
something like [2].
4. The content of the property will be stored as a JSON string. The
function introduced in bullet point 3 can be used as a convenient access to the
values. The hide implementation details and allow easier refactorization later
one (e.g. if we move to microservice for more configurability of the
encoding/decoding/storing of the information.
Planned implementation process:
1. The above mentioned points will be implemented and the default.
2. The old property naming becomes deprecated. This will additionally
indicated by adding a PropertyDescription to all old names, saying
"DEPRECATED!!!" (or something like this ;).
3. The mitk code base will be checked and usage of old names will be
corrected
4. Removal of the old style from the code (e.g. DICOMSeriesReader,
DICOMReaderModule...) after one release cycle.
If you have any comments or thoughts on this topic, please let us know. Thanks.
Best regards,
Ralf
[1] Currrent naming style zoo:
* Some have the root "dicom", some "dicomSeriesReader
* Some are stored by name
* Some are stored by numbers
* Different upper and lower case styles
[2] Draft of the non member function signatures
/** Convenience function to get the value of a certain DICOM tag from an data
object.
@param data BaseData instance that may contain the DICOM tag as property
@param tag DICOM tag of the wanted value.
@param value The retrieved value as string (only valid if return is true)
@param timePoint Value for the given time point. (If undefined for the time
point (e.g. only one value at all), the last suitable value will be used)
@param z Slice index/ z indicating the slice the value should correspond to.
(If undefined for the time point (e.g. only one value at all), the last
suitable value will be used)
@param strict If strict equals "true", the query will only be successful, when
there is really a value stored for the given time point and slice. If strict
equals "false" it will return the value that matches best. If no perfect match
is possible, it will be the "default" value for the time point (1st order) and
slice index (2nd order), if defined.
@return Indicates if the tag was found and the out parameter value is valid.
Only use "value" if return value is true.**/
bool mitk::GetDICOMValueFromDataProperty ( const mitk::BaseData* data, const
mitk::DICOMTag& tag, std::string& value, int timePoint = 0, int z = 0 , bool
strict = false)
/**Overloaded convenience function that returns the value as double. If the
value was found, but cannot be returned as double, the return value will be
false and the content of "value" is invalid.*/
bool mitk::GetDICOMValueFromDataProperty ( const mitk::BaseData* data, const
mitk::DICOMTag& tag, double& value, int timePoint = 0, int z = 0 , bool strict
= false)
/**Overloaded convenience function that returns the value as int. If the value
was found, but cannot be returned as int, the return value will be false and
the content of "value" is invalid.*/
bool mitk::GetDICOMValueFromDataProperty ( const mitk::BaseData* data, const
mitk::DICOMTag& tag, double& int, int timePoint = 0, int z = 0 , bool strict =
false)
/** Returns the property for a given DICOM tag. If no property is found a NULL
pointer is returned. */
mitk::BaseProperty::Pointer mitk::GetDICOMDataProperty ( const mitk::BaseData*
data, const mitk::DICOMTag& tag)
/** Checks if the value of a certain DICOM tag is stored for the passed data
instance.
@param data BaseData instance that may contain the DICOM tag as property
@param tag DICOM tag of the wanted value.
@param timePoint Value for the given time point. (If undefined for the time
point (e.g. only one value at all), the last suitable value will be used)
@param z Slice index/ z indicating the slice the value should correspond to.
(If undefined for the time point (e.g. only one value at all), the last
suitable value will be used)
@param strict If strict equals "true", the query will only be successful, when
there is really a value stored for the given time point and slice. If strict
equals "false" it will return the value that matches best. If no perfect match
is possible, it will be the "default" value for the time point (1st order) and
slice index (2nd order), if defined.
@return Indicates if the tag was found and the out parameter value is valid.
Only use "value" if return value is true.**/
bool mitk::isExistingDICOMValueInDataProperty ( const mitk::BaseData* data,
const mitk::DICOMTag& tag, int timePoint = 0, int z = 0 , bool strict = false)
/** returns the correct property name for a given DICOMTag instance. */
std::string mitk::GeneratPropertyNameForDICOMTag(const mitk::DICOMTag& tag);
------------------------------------------------------------------------------------------------------
Dr. Ralf Floca
Software development for Integrated Diagnostic and Therapy (SIDT)
Group leader
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 280
69120 Heidelberg
Germany
phone: +49 6221 42-2560
r.fl...@dkfz.de
www.dkfz.de<http://www.dkfz.de/>
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