From 19e0d130162dafe2a08bd3aa0e60e1e975555778 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Sun, 28 Jul 2024 14:09:58 -0400
Subject: [PATCH] STYLE: Factor out itkOMEZarrNGFFCommon.h

For re-use across ImageIO and TransformIO.

OMEZarrNGFFAxis is renamed to OMEZarrAxis for brevity. Also, what was
previously ambigiously ome-zarr-ngff is now OME-Zarr.
---
 CMakeLists.txt                     |  3 +-
 include/itkOMEZarrNGFFCommon.h     | 46 ++++++++++++++++++++++++++++++
 include/itkOMEZarrNGFFImageIO.h    | 20 +++----------
 src/itkOMEZarrNGFFImageIO.cxx      |  2 +-
 wrapping/CMakeLists.txt            |  3 ++
 wrapping/itkOMEZarrNGFFCommon.wrap |  4 +++
 6 files changed, 59 insertions(+), 19 deletions(-)
 create mode 100644 include/itkOMEZarrNGFFCommon.h
 create mode 100644 wrapping/itkOMEZarrNGFFCommon.wrap

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 56351dd..d48ab5c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -8,11 +8,10 @@ set(CMAKE_CXX_STANDARD 17)
 set_property(GLOBAL PROPERTY USE_FOLDERS ON)
 
 project(IOOMEZarrNGFF CXX C ASM_NASM ASM)
-
 set(IOOMEZarrNGFF_LIBRARIES IOOMEZarrNGFF)
 
 if(NOT ITK_SOURCE_DIR)
-  find_package(ITK 5.0 REQUIRED)
+  find_package(ITK 5.4 REQUIRED)
   list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
   set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
   include(ITKModuleExternal)
diff --git a/include/itkOMEZarrNGFFCommon.h b/include/itkOMEZarrNGFFCommon.h
new file mode 100644
index 0000000..1054ecf
--- /dev/null
+++ b/include/itkOMEZarrNGFFCommon.h
@@ -0,0 +1,46 @@
+/*=========================================================================
+ *
+ *  Copyright NumFOCUS
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         https://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *=========================================================================*/
+
+#ifndef itkOMEZarrNGFFCommon_h
+#define itkOMEZarrNGFFCommon_h
+#include "IOOMEZarrNGFFExport.h"
+
+
+#include <string>
+
+namespace itk
+{
+/** \class OMEZarrNGFFAxis
+ *
+ * \brief Represent an OME-Zarr NGFF axis
+ *
+ * Open Microscopy Environment Zarr Next Generation File Format
+ * specification can be found at https://github.com/ome/ngff
+ *
+ * \ingroup IOOMEZarrNGFF
+ */
+struct IOOMEZarrNGFF_EXPORT OMEZarrAxis
+{
+  std::string name;
+  std::string type;
+  std::string unit;
+};
+
+} // end namespace itk
+
+#endif // itkOMEZarrNGFFCommon_h
diff --git a/include/itkOMEZarrNGFFImageIO.h b/include/itkOMEZarrNGFFImageIO.h
index e31d541..b8e5e71 100644
--- a/include/itkOMEZarrNGFFImageIO.h
+++ b/include/itkOMEZarrNGFFImageIO.h
@@ -24,25 +24,13 @@
 #include <fstream>
 #include <string>
 #include <vector>
+
 #include "itkImageIOBase.h"
 
+#include "itkOMEZarrNGFFCommon.h"
+
 namespace itk
 {
-/** \class OMEZarrNGFFAxis
- *
- * \brief Represent an OME-Zarr NGFF axis
- *
- * Open Microscopy Environment Zarr Next Generation File Format
- * specification can be found at https://github.com/ome/ngff
- *
- * \ingroup IOOMEZarrNGFF
- */
-struct IOOMEZarrNGFF_EXPORT OMEZarrNGFFAxis
-{
-  std::string name;
-  std::string type;
-  std::string unit;
-};
 
 /** \class OMEZarrNGFFImageIO
  *
@@ -73,7 +61,7 @@ class IOOMEZarrNGFF_EXPORT OMEZarrNGFFImageIO : public ImageIOBase
 
   static constexpr unsigned MaximumDimension = 5; // OME-NGFF specifies up to 5D data
   static constexpr int      INVALID_INDEX = -1;   // for specifying enumerated axis slice indices
-  using AxesCollectionType = std::vector<OMEZarrNGFFAxis>;
+  using AxesCollectionType = std::vector<OMEZarrAxis>;
 
   /** The different types of ImageIO's can support data of varying
    * dimensionality. For example, some file formats are strictly 2D
diff --git a/src/itkOMEZarrNGFFImageIO.cxx b/src/itkOMEZarrNGFFImageIO.cxx
index 8dc9167..c63f99f 100644
--- a/src/itkOMEZarrNGFFImageIO.cxx
+++ b/src/itkOMEZarrNGFFImageIO.cxx
@@ -554,7 +554,7 @@ OMEZarrNGFFImageIO::ReadImageInformation()
     auto targetIt = m_StoreAxes.rbegin();
     for (const auto & axis : json.at("axes"))
     {
-      *targetIt = (OMEZarrNGFFAxis{ axis.at("name"), axis.at("type"), (axis.contains("unit") ? axis.at("unit") : "") });
+      *targetIt = (OMEZarrAxis{ axis.at("name"), axis.at("type"), (axis.contains("unit") ? axis.at("unit") : "") });
       ++targetIt;
     }
     itkAssertOrThrowMacro(targetIt == m_StoreAxes.rend(),
diff --git a/wrapping/CMakeLists.txt b/wrapping/CMakeLists.txt
index b3eaae0..750e02b 100644
--- a/wrapping/CMakeLists.txt
+++ b/wrapping/CMakeLists.txt
@@ -1,3 +1,6 @@
 itk_wrap_module(IOOMEZarrNGFF)
+set(WRAPPER_SUBMODULE_ORDER
+  itkOMEZarrNGFFCommon
+)
 itk_auto_load_submodules()
 itk_end_wrap_module()
diff --git a/wrapping/itkOMEZarrNGFFCommon.wrap b/wrapping/itkOMEZarrNGFFCommon.wrap
new file mode 100644
index 0000000..fd35ac9
--- /dev/null
+++ b/wrapping/itkOMEZarrNGFFCommon.wrap
@@ -0,0 +1,4 @@
+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
+itk_wrap_include("itkOMEZarrNGFFCommon.h")
+itk_wrap_simple_class("itk::OMEZarrAxis")
+set(WRAPPER_AUTO_INCLUDE_HEADERS ON)
\ No newline at end of file