Copy attachments from source file to output file (#7)

* 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 --------- Co-authored-by: ptahmose <[email protected]>
ZEISS · Aug 21, 2024 · 0722536 · 0722536
1 parent 55462e6
commit 0722536
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Showing 8 changed files with 36 additions and 3 deletions.
diff --git a/CMakeLists.txt b/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 0.4.0
+          VERSION 0.5.0
           DESCRIPTION "experimental Deskew operation")
 
 option(WARPAFFINE_BUILD_CLANGTIDY "Build with Clang-Tidy" OFF)

diff --git a/documentation/version-history.md b/documentation/version-history.md
@@ -6,4 +6,5 @@ version history                 {#version_history}
  0.3.0              |  N/A                                                 | initial release
  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
+ 0.4.0              |  [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
diff --git a/libwarpaffine/main.cpp b/libwarpaffine/main.cpp
@@ -481,6 +481,7 @@ int libmain(int argc, char** _argv)
         }
 
         auto reader_and_stream = CreateCziReader(app_context);
+
         if (!get<0>(reader_and_stream) || !get<1>(reader_and_stream))
         {
             return EXIT_FAILURE;
@@ -494,6 +495,7 @@ int libmain(int argc, char** _argv)
         }
 
         auto writer = CreateCziWriter(app_context);
+
         auto brick_source = CreateCziBrickSource(app_context, get<0>(reader_and_stream), get<1>(reader_and_stream));
         auto warp_affine_engine = CreateWarpAffineEngine(app_context);
 
@@ -533,6 +535,13 @@ int libmain(int argc, char** _argv)
         doWarp.DoOperation();
         WaitUntilDone(app_context, doWarp);
 
+        get<0>(reader_and_stream)->EnumerateAttachments(
+            [&writer, &reader_and_stream](int index, const libCZI::AttachmentInfo& info) -> bool
+            {
+                writer->AddAttachment(get<0>(reader_and_stream)->ReadAttachment(index));
+                return true;
+            });
+
         switch (const auto type_of_operation = app_context.GetCommandLineOptions().GetTypeOfOperation())
         {
         case OperationType::Deskew:

diff --git a/libwarpaffine/sliceswriter/ISlicesWriter.h b/libwarpaffine/sliceswriter/ISlicesWriter.h
@@ -63,6 +63,10 @@ class ICziSlicesWriter
     /// Adds a slice (or subblock).
     /// \param  add_slice_info Information describing the add slice.
     virtual void AddSlice(const AddSliceInfo& add_slice_info) = 0;
+
+    /// Adds an attachment, i.e. a copy from a source document.
+    /// \param attachment The attachment to be added.
+    virtual void AddAttachment(const std::shared_ptr<libCZI::IAttachment>& attachment) = 0;
 
     /// Closes the output CZI-files. The specified metadata object (of the source document) is used
     /// to update the metadata of the output CZI-file.

diff --git a/libwarpaffine/sliceswriter/NullSlicesWriter.cpp b/libwarpaffine/sliceswriter/NullSlicesWriter.cpp
@@ -17,6 +17,10 @@ void NullSlicesWriter::AddSlice(const AddSliceInfo& add_slice_info)
 {
 }
 
+void NullSlicesWriter::AddAttachment(const std::shared_ptr<libCZI::IAttachment>& attachment)
+{
+}
+
 void NullSlicesWriter::Close(const std::shared_ptr<libCZI::ICziMetadata>&, const libCZI::ScalingInfo*, const std::function<void(libCZI::IXmlNodeRw*)>&)
 {
 }
diff --git a/libwarpaffine/sliceswriter/NullSlicesWriter.h b/libwarpaffine/sliceswriter/NullSlicesWriter.h
@@ -14,6 +14,7 @@ class NullSlicesWriter : public ICziSlicesWriter
 public:
     std::uint32_t GetNumberOfPendingSliceWriteOperations() override;
     void AddSlice(const AddSliceInfo& add_slice_info) override;
+    void AddAttachment(const std::shared_ptr<libCZI::IAttachment>& attachment) override;
     void Close(const std::shared_ptr<libCZI::ICziMetadata>& source_metadata,
                 const libCZI::ScalingInfo* new_scaling_info,
                 const std::function<void(libCZI::IXmlNodeRw*)>& tweak_metadata_hook) override;

diff --git a/libwarpaffine/sliceswriter/SlicesWriterTbb.cpp b/libwarpaffine/sliceswriter/SlicesWriterTbb.cpp
@@ -40,6 +40,20 @@ void CziSlicesWriterTbb::AddSlice(const AddSliceInfo& add_slice_info)
     ++this->number_of_slicewrite_operations_in_flight_;
 }
 
+void CziSlicesWriterTbb::AddAttachment(const std::shared_ptr<libCZI::IAttachment>& attachment)
+{
+    AddAttachmentInfo add_attachment_info;
+    const auto& attachment_info = attachment->GetAttachmentInfo();
+    add_attachment_info.contentGuid = attachment_info.contentGuid;
+    add_attachment_info.SetContentFileType(attachment_info.contentFileType);
+    add_attachment_info.SetName(attachment_info.name.c_str());
+    size_t size_of_data;
+    auto raw_data = attachment->GetRawData(&size_of_data);
+    add_attachment_info.ptrData = raw_data.get();
+    add_attachment_info.dataSize = static_cast<uint32_t>(size_of_data);
+    this->writer_->SyncAddAttachment(add_attachment_info);
+}
+
 void CziSlicesWriterTbb::WriteWorker()
 {
     try

diff --git a/libwarpaffine/sliceswriter/SlicesWriterTbb.h b/libwarpaffine/sliceswriter/SlicesWriterTbb.h
@@ -41,7 +41,7 @@ class CziSlicesWriterTbb : public ICziSlicesWriter
     std::uint32_t GetNumberOfPendingSliceWriteOperations() override;
 
     void AddSlice(const AddSliceInfo& add_slice_info) override;
-
+    void AddAttachment(const std::shared_ptr<libCZI::IAttachment>& attachment) override;
     void Close(const std::shared_ptr<libCZI::ICziMetadata>& source_metadata,
                 const libCZI::ScalingInfo* new_scaling_info,
                 const std::function<void(libCZI::IXmlNodeRw*)>& tweak_metadata_hook) override;
-Original file line number
+Diff line change
@@ Expand Up @@
     {
     }
+    void NullSlicesWriter::AddAttachment(const std::shared_ptr<libCZI::IAttachment>& attachment)
+    {
+    }
     void NullSlicesWriter::Close(const std::shared_ptr<libCZI::ICziMetadata>&, const libCZI::ScalingInfo*, const std::function<void(libCZI::IXmlNodeRw*)>&)
     {
     }