From 3b43831bd78c3e152dd4988747ba7007daaebe36 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.

Change-Id: I1111c55dd9e15444411e31bd6f2f1e68b7cf7618
---
 Modules/IO/DCMTK/src/itkDCMTKFileReader.cxx | 35 +++++++++++++++++----
 1 file changed, 29 insertions(+), 6 deletions(-)

diff --git a/Modules/IO/DCMTK/src/itkDCMTKFileReader.cxx b/Modules/IO/DCMTK/src/itkDCMTKFileReader.cxx
index e2e72c1407d..d068bb9bfed 100644
--- a/Modules/IO/DCMTK/src/itkDCMTKFileReader.cxx
+++ b/Modules/IO/DCMTK/src/itkDCMTKFileReader.cxx
@@ -1326,7 +1326,15 @@ ::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)
       {
       spacing[2] = _spacing[2];
       }
@@ -1341,8 +1349,8 @@ ::GetSpacing(double * const spacing) const
   // functional group, and then the per-frame functional group
   unsigned short candidateSequences[2] =
     {
-      0x9229, // check for Shared Functional Group Sequence first
-      0x9230, // check the Per-frame Functional Groups Sequence
+    0x9229, // check for Shared Functional Group Sequence first
+    0x9230, // check the Per-frame Functional Groups Sequence
     };
   for(unsigned short candidateSequence : candidateSequences)
     {
@@ -1359,12 +1367,27 @@ ::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)
+          /*
+           * 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];
-            spacing[2] = _spacing[2];
+            if (subSequence.GetElementDS<double>(0x0018,0x0088,1,&_spacing[2], false) == EXIT_SUCCESS)
+              {
+              spacing[2] = _spacing[2];
+              }
+            else
+              {
+              // punt, zSpace of 1
+              spacing[2] = 1.0;
+              }
             break;
             }
           }