ENH: Add DICOMOrientation class from remote module #4791

blowekamp · 2024-07-31T13:09:06Z

The class provides anatomical orientation based enums for describing coordinate systems. In ITK the physical coordinate systems is the same as the DICOM standard. DICOM has the following specification:

If Anatomical Orientation Type (0010,2210) is absent or has a value of BIPED, the x-axis is increasing to the left hand side of the patient. The y-axis is increasing to the posterior side of the patient. The z-axis is increasing toward the head of the patient.

Which describes the direction of increasing. The above coordinate system is described as "LPS" with this enumeration and corresponds to an ITK image with an identity direction cosine matrix.

PR Checklist

No API changes were made (or the changes have been approved)
No major design changes were made (or the changes have been approved)
Added test (or behavior not changed)
Updated API documentation (or API not changed)
Added license to new files (if any)
Added Python wrapping to new files (if any) as described in ITK Software Guide Section 9.5
Added ITK examples for all new major features (if any)

Refer to the ITK Software Guide for
further development details if necessary.

Modules/Core/Common/include/itkDICOMOrientation.h

The class provides anatomical orientation based enums for describing coordinate systems. In ITK the physical coordinate systems is the same as the DICOM standard. DICOM has the following specification: If Anatomical Orientation Type (0010,2210) is absent or has a value of BIPED, the x-axis is increasing to the left hand side of the patient. The y-axis is increasing to the posterior side of the patient. The z-axis is increasing toward the head of the patient. Which describes the direction of increasing. The above coordidate system is described as "LPS" with this enumeration and corresponds to an ITK image with an identity direction cosine matrix.

This is a replacement for the OrientImageFilter, which used the DICOMOrientation enumerations and conventions for describing the patient orientation by the increasing anaomical axis.

Ensure matching byte codes between DICOM and legacy coordinate enums which have the same direction cosine interpretation. Add unambiguous CoordinateEnum duplication of the form LeftToRight. Add method to DICOMOrientationImageFilter which accepts DICOMOrientation object, which can be implicitly converted from legacy coordinate enums.

Replace usage of SpatialOrientationAdaptor with DICOMOrientation and unambiguous FROMToTO CoordinateEnums in GE related ImageIO classes.

dzenanz

Looking good so far.

dzenanz · 2024-08-06T14:41:03Z

Modules/IO/NIFTI/src/itkNiftiImageIO.cxx

      switch (this->m_NiftiImage->analyze75_orient)
      {
        case a75_transverse_unflipped:
-          orient = SpatialOrientationEnums::ValidCoordinateOrientations::ITK_COORDINATE_ORIENTATION_RPI;
+          orient = DICOMOrientation(DICOMOrientation::CoordinateEnum::RightToLeft,


In these long and and long-ish statements, it might make sense to using CE = DICOMOrientation::CoordinateEnum, then use CE::RightToLeft, CE::PosteriorToAnterior, CE::InferiorToSuperior on a single line. This applies to many places in the code, including previous commits.

dzenanz · 2024-08-06T14:44:32Z

One warning, Modules/IO/GE/src/itkGE5ImageIO.cxx:191:44: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct GEImageHeader'; use assignment or value-initialization instead [-Wclass-memaccess]

issakomi · 2024-08-07T14:10:49Z

In ITK the physical coordinate systems is the same as the DICOM standard.

It is not exactly the same, 1/2 of ITK orientations are not defined in DICOM.
DICOM defines only right-handed orientations. "Image Orientation (Patient) Attribute" defines "x" and "y" (6 values), "z" is right-handed cross-product.

The Patient-Based Coordinate System is a right handed system, i.e., the vector cross product of a unit vector along the positive x-axis and a unit vector along the positive y-axis is equal to a unit vector along the positive z-axis.

ITK defines "x", "y" and "z", so e.g. RAI-Code (from) LPS

-1  0  0
 0 -1  0
 0  0 -1

exists in ITK and is not applicable to DICOM definition.

issakomi · 2024-08-07T15:05:15Z

In fact I also think that something should be done with ITK's "from" orientation codes, it seems that surprisingly many users don't understand them at all. But how should they if there is no clear documentation and, even worse, at many places there are already "to" notations.
May be e.g. ITK_COORDINATE_ORIENTATION_RAI could be renamed to ITK_COORDINATE_ORIENTATION_NOTATION_FROM_RAI and be equal to ITK_COORDINATE_ORIENTATION_NOTATION_TO_LPS or something like that.
It will allow preserve AnatomicalOrientation field of Meta images (document properly!). Also the same for some methods returning orientation codes (clarify "to" and "from" in the name). And no need to kill OrientImageFilter and itkSpatial classes for the sake of "DICOM enums" which don't exist in DICOM.

Modules/Core/Common/include/itkDICOMOrientation.h

Co-Author: Niels Dekker <[email protected]>

Addresses: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct GEImageHeader'; use assignment or value-initialization instead [-Wclass-memaccess]

lassoan · 2024-08-15T10:29:47Z

Modules/Core/Common/test/CMakeLists.txt

@@ -1758,7 +1758,9 @@ set(ITKCommonGTests
    itkWeakPointerGTest.cxx
    itkCommonTypeTraitsGTest.cxx
    itkMetaDataDictionaryGTest.cxx
-    itkSpatialOrientationAdaptorGTest.cxx)
+    itkSpatialOrientationAdaptorGTest.cxx
+    itkDICOMOrientionGTest.cxx


Suggested change

itkDICOMOrientionGTest.cxx

itkDICOMOrientationGTest.cxx

lassoan · 2024-08-15T10:38:13Z

.github/workflows/itk_dict.txt

@@ -715,6 +715,7 @@ orthonormality
 opencl
 openjpeg
 oper
+osterior


This is word does not belong to the dictionary, because it should be rejected. It would be better to avoid using this word in the source code or disable spellchecking at the single place where this word is intentionally used.

This sounds like a misspelling of posterior.

blowekamp · 2024-08-15T14:56:56Z

Modules/Filtering/ImageGrid/include/itkDICOMOrientImageFilter.h

+ * \f[
+ * LPS = \begin{Bmatrix}
+ * from\ right\ to\ \textbf{L}eft \\
+ * from\ anterior\ towards\ \textbf{P}osterior  \\


@dzenanz It was added to the dictionary due to the mark up of P.

blowekamp · 2024-08-15T14:58:10Z

The work has evolved into another PR. I didn't expect the continued comments on this WIP, some were applied to the other PR still under development.

seanm · 2024-08-15T21:26:32Z

The work has evolved into another PR. I didn't expect the continued comments on this WIP, some were applied to the other PR still under development.

So wait, this one is dead? Should we only look at #4788 ? I'm confused with all these different PRs...

blowekamp · 2024-08-16T00:15:04Z

So wait, this one is dead? Should we only look at #4788 ? I'm confused with all these different PRs...

The original issue #4788 is the discussion. I have not yet directly asked for feedback on the other PR, its still approaching being finished and incorporating the feed back I have heard.

There was strong opposition for using the specific "DICOM" term ( and apparently overly specific/inappropriate association), and the opposition to replacing the OritenImageFilter class, a new PR with a updated title, and an updates description seemed appropriate to help reset everyone for the updated goals.

dzenanz · 2024-10-28T12:52:13Z

Should this PR be closed now?

blowekamp · 2024-10-28T13:00:02Z

See PR #4804 and #4895

blowekamp force-pushed the add_DICOMOrientImageFilter branch from f965299 to 908dd07 Compare July 31, 2024 14:29

github-actions bot added the area:Filtering Issues affecting the Filtering module label Jul 31, 2024

blowekamp mentioned this pull request Jul 31, 2024

WIP: Deprecate OrientImageFilter #4790

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blowekamp commented Jul 31, 2024

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Modules/Core/Common/include/itkDICOMOrientation.h Outdated Show resolved Hide resolved

blowekamp mentioned this pull request Jul 31, 2024

ITK's SpatialOrientation and OrientImageFilter have opposite definitions of the DICOM standard #4788

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blowekamp force-pushed the add_DICOMOrientImageFilter branch from 908dd07 to 90a76cd Compare July 31, 2024 15:54

github-actions bot added the area:IO Issues affecting the IO module label Jul 31, 2024

blowekamp requested a review from hjmjohnson August 1, 2024 09:51

blowekamp added 4 commits August 1, 2024 11:09

ENH: Add DICOMOrientImageFilter

f65805d

This is a replacement for the OrientImageFilter, which used the DICOMOrientation enumerations and conventions for describing the patient orientation by the increasing anaomical axis.

ENH: Conversion from SpatialOrientation to DICOMOrientation

b2a8968

ENH: Migrate MetaIO to DICOMOrientation

cb079f7

blowekamp force-pushed the add_DICOMOrientImageFilter branch from 90a76cd to 151519c Compare August 1, 2024 15:09

blowekamp added 2 commits August 1, 2024 16:39

ENH: Prefer usage of FROMToTO CoordinateEnum

f56ccbb

blowekamp force-pushed the add_DICOMOrientImageFilter branch from 151519c to c11dfb7 Compare August 1, 2024 21:03

blowekamp requested a review from dzenanz August 1, 2024 21:38

blowekamp added 2 commits August 2, 2024 07:59

ENH: Use DICOMOrientation with FROMToTO CoordinateEnums

a13d287

Replace usage of SpatialOrientationAdaptor with DICOMOrientation and unambiguous FROMToTO CoordinateEnums in GE related ImageIO classes.

ENH: Update NiftiImageIO to use DICOMOrientation

4d8bf5c

blowekamp force-pushed the add_DICOMOrientImageFilter branch from c11dfb7 to 4d8bf5c Compare August 2, 2024 12:10

dzenanz reviewed Aug 6, 2024

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N-Dekker reviewed Aug 8, 2024

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Modules/Core/Common/include/itkDICOMOrientation.h Outdated Show resolved Hide resolved

blowekamp added 2 commits August 12, 2024 12:00

ENH: Use Variable Templates for coordinate enum values.

4ae42c8

Co-Author: Niels Dekker <[email protected]>

BUG: Remove default initialization in struct

d7425ef

Addresses: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct GEImageHeader'; use assignment or value-initialization instead [-Wclass-memaccess]

lassoan reviewed Aug 15, 2024

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blowekamp commented Aug 15, 2024

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blowekamp closed this Oct 28, 2024

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ENH: Add DICOMOrientation class from remote module #4791

ENH: Add DICOMOrientation class from remote module #4791

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blowekamp commented Oct 28, 2024

ENH: Add DICOMOrientation class from remote module #4791

ENH: Add DICOMOrientation class from remote module #4791

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