From 1147cf872e235d818fc8599fcb16e77b3c359351 Mon Sep 17 00:00:00 2001
From: Hui Xie <hui-xie@uiowa.edu>
Date: Thu, 23 Feb 2017 18:59:09 -0600
Subject: [PATCH] BUG: The Z spacing was set using thickness

This addresses https://issues.itk.org/jira/browse/ITK-3527

According Dicom standard (DICOM PS3.6 2016b - Data Dictionary)
(0028, 0030) indicates physical X,Y spacing inside a slice;
(0018, 0088) indicates physical Z spacing between slices;
which above are also consistent with Dcom2iix software.

In current code, the zSpace is get from (0x0018,0x0050) which
actually is the thickness from which the signal is created,
not the separation of signal samplings.

This patch set resolves the problem by updating the Z get
spacing method by using (0018, 0088) when it is available.

If (0018, 0088) is not available, then the code reverts to
the previous behavior of using (0x0018,0x0050).

Change-Id: I1111c55dd9e15444411e31bd6f2f1e68b7cf7618
---
 Modules/IO/DCMTK/src/itkDCMTKFileReader.cxx | 38 +++++++++++++++++----
 1 file changed, 31 insertions(+), 7 deletions(-)

diff --git a/Modules/IO/DCMTK/src/itkDCMTKFileReader.cxx b/Modules/IO/DCMTK/src/itkDCMTKFileReader.cxx
index 4386ad411f1..daab6d9c212 100644
--- a/Modules/IO/DCMTK/src/itkDCMTKFileReader.cxx
+++ b/Modules/IO/DCMTK/src/itkDCMTKFileReader.cxx
@@ -1326,7 +1326,16 @@ ::GetSpacing(double * const spacing) const
     // slice thickness
     spacing[0] = _spacing[1];
     spacing[1] = _spacing[0];
-    if(this->GetElementDS<double>(0x0018,0x0050,1,&_spacing[2],false) == EXIT_SUCCESS)
+    /*
+     * According Dicom standard (DICOM PS3.6 2016b - Data Dictionary)
+     * (0028, 0030) indicates physical X,Y spacing inside a slice;
+     * (0018, 0088) indicates physical Z spacing between slices;
+     *  which above are also consistent with Dcom2iix software.
+     *  when we can not get (0018, 0088),we will revert to previous
+     *  behavior and use (0018, 0050) thickness as a proxy to spacing.
+     * */
+    if(GetElementDS<double>(0x0018,0x0088,1,&_spacing[2], false) == EXIT_SUCCESS
+       || GetElementDS<double>(0x0018,0x0050,1,&_spacing[2],false) == EXIT_SUCCESS)
       {
       spacing[2] = _spacing[2];
       }
@@ -1359,12 +1368,27 @@ ::GetSpacing(double * const spacing) const
         rval = item.GetElementSQ(0x0028,0x9110,subSequence,false);
         if(rval == EXIT_SUCCESS)
           {
-          if(subSequence.GetElementDS<double>(0x0028,0x0030,2,_spacing,false) == EXIT_SUCCESS
-             && subSequence.GetElementDS<double>(0x0018,0x0050,1,&_spacing[2]) == EXIT_SUCCESS)
-            {
-            spacing[0] = _spacing[1];
-            spacing[1] = _spacing[0];
-            spacing[2] = _spacing[2];
+           /*
+            * According Dicom standard (DICOM PS3.6 2016b - Data Dictionary)
+            * (0028, 0030) indicates physical X,Y spacing inside a slice;
+            * (0018, 0088) indicates physical Z spacing between slices;
+            *  which above are also consistent with Dcom2iix software.
+            *  when we can not get (0018, 0088),we will revert to previous
+            *  behavior and use (0018, 0050) thickness as a proxy to spacing.
+            * */
+           if(subSequence.GetElementDS<double>(0x0028,0x0030,2,_spacing,false) == EXIT_SUCCESS)
+           {
+               spacing[0] = _spacing[1];
+               spacing[1] = _spacing[0];
+               if (subSequence.GetElementDS<double>(0x0018,0x0088,1,&_spacing[2], false) == EXIT_SUCCESS
+                   || subSequence.GetElementDS<double>(0x0018,0x0050,1,&_spacing[2], false) == EXIT_SUCCESS){
+                   spacing[2] = _spacing[2];
+               }
+               else
+               {
+                   // punt, zSpace of 1
+                   spacing[2] = 1.0;
+               }
             break;
             }
           }