Write z interval metadata for correct display in Zen 2d viewer / dime…

…nsion slider (#8)

* cleanup

* create new guids for each z layer

* use guid only where necessary

* only activate acquisition tiles if command line parameter is set

* suggestions from code review

* cleanup

* cleanup

* fix linux build, more suggestions from code review

* missing files from previous commit

* suggestions from code review

* version number, documentation

* add changes

* cosmetic - remove some commented out code

* fix linter-issues

* copy attachments

* fix null pointer exception

* suggestions from code review

* add interval metadata, increase version number

* cleanup

* more cleanup

* more cleanup

* remove accidentially added files

* suggestions from code review

---------

Co-authored-by: ptahmose <jbohl@h-quer.de>

.gitignore

@@ -37,4 +37,6 @@ out/
 build/
 CMakeSettings.json
 cmake-build-*/
-.idea/
+.idea/
+.vscode/launch.json
+.vscode/settings.json

CMakeLists.txt

@@ -19,7 +19,7 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set (CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/modules" ${CMAKE_MODULE_PATH})
 
 project ("warpaffine"
-          VERSION 0.5.0
+          VERSION 0.5.1
           DESCRIPTION "experimental Deskew operation")
 
 option(WARPAFFINE_BUILD_CLANGTIDY "Build with Clang-Tidy" OFF)

documentation/version-history.md

@@ -7,4 +7,5 @@ version history                 {#version_history}
  0.3.1              |  [3](https://github.com/ZEISS/warpaffine/pull/3)     | bugfix for a crash for "CZIs containing a single brick but have an S-index"
  0.3.2              |  [5](https://github.com/ZEISS/warpaffine/pull/5)     | bugfix for a deadlock in rare case
  0.4.0              |  [6](https://github.com/ZEISS/warpaffine/pull/6)     | set re-tiling id of sub-blocks to allow for more sensible stitching of resulting CZI
- 0.5.0              |  [7](https://github.com/ZEISS/warpaffine/pull/7)     | copy attachments from source document
+ 0.5.0              |  [7](https://github.com/ZEISS/warpaffine/pull/7)     | copy attachments from source document
+ 0.5.1              |  [8](https://github.com/ZEISS/warpaffine/pull/8)     | fix z interval metadata

libwarpaffine/sliceswriter/SlicesWriterTbb.cpp

@@ -237,6 +237,18 @@ void CziSlicesWriterTbb::Close(const std::shared_ptr<libCZI::ICziMetadata>& sour
             MetadataUtils::WriteScalingInfo(metadata_builder_from_source.get(), *new_scaling_info);
         }
 
+        if (new_scaling_info->IsScaleZValid())
+        {
+            auto increment_node = metadata_builder_from_source->GetRootNode()->GetOrCreateChildNode("Metadata/Information/Image/Dimensions/Z/Positions/Interval/Increment");
+            if (increment_node)
+            {
+                const double original_scaling_meters = new_scaling_info->scaleZ;
+
+                // increment should be in micrometers
+                increment_node->SetValueDbl(original_scaling_meters * 1e6);
+            }
+        }
+
         // allow the caller to tweak the metadata before it is written out
         if (tweak_metadata_hook)
         {