Add support for reading/writing VTK XML ImageData (.vti) format

Modules/Core/TestKernel/src/itkTestDriverIncludeRequiredFactories.cxx

@@ -26,6 +26,7 @@
 #include "itkTIFFImageIOFactory.h"
 #include "itkBMPImageIOFactory.h"
 #include "itkVTKImageIOFactory.h"
+#include "itkVTIImageIOFactory.h"
 #include "itkNrrdImageIOFactory.h"
 #include "itkGiplImageIOFactory.h"
 #include "itkNiftiImageIOFactory.h"
@@ -72,6 +73,7 @@ RegisterRequiredIOFactories()
   itk::ObjectFactoryBase::RegisterFactory(itk::GDCMImageIOFactory::New());
   itk::ObjectFactoryBase::RegisterFactory(itk::JPEGImageIOFactory::New());
   itk::ObjectFactoryBase::RegisterFactory(itk::VTKImageIOFactory::New());
+  itk::ObjectFactoryBase::RegisterFactory(itk::VTIImageIOFactory::New());
   itk::ObjectFactoryBase::RegisterFactory(itk::PNGImageIOFactory::New());
   itk::ObjectFactoryBase::RegisterFactory(itk::TIFFImageIOFactory::New());
   itk::ObjectFactoryBase::RegisterFactory(itk::BMPImageIOFactory::New());

Modules/IO/VTK/include/itkVTIImageIO.h

@@ -0,0 +1,178 @@
+/*=========================================================================
+ *
+ *  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 itkVTIImageIO_h
+#define itkVTIImageIO_h
+#include "ITKIOVTKExport.h"
+
+#include <fstream>
+#include "itkImageIOBase.h"
+
+namespace itk
+{
+/**
+ * \class VTIImageIO
+ *
+ *  \brief ImageIO class for reading and writing VTK XML ImageData (.vti) files.
+ *
+ * Supports the VTK XML ImageData format (version 0.1 and 2.2), including
+ * ASCII, binary (base64-encoded), and raw-appended data formats.
+ * Scalar, vector (3-component), RGB, RGBA, and symmetric second rank tensor
+ * pixel types are supported.
+ *
+ * The XML structure is parsed using the expat XML library (provided by
+ * ITKExpat / ITKIOXML), so the parser is robust to attribute ordering,
+ * whitespace, comments, and CDATA sections.  The raw appended data section
+ * (which is XML-illegal binary content following an `_` marker) is read
+ * directly from the file at the byte offset recorded by the parser when
+ * it encountered the `<AppendedData>` element.
+ *
+ * \ingroup IOFilters
+ * \ingroup ITKIOVTK
+ */
+class ITKIOVTK_EXPORT VTIImageIO : public ImageIOBase
+{
+public:
+  ITK_DISALLOW_COPY_AND_MOVE(VTIImageIO);
+
+  /** Standard class type aliases. */
+  using Self = VTIImageIO;
+  using Superclass = ImageIOBase;
+  using Pointer = SmartPointer<Self>;
+  using ConstPointer = SmartPointer<const Self>;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** \see LightObject::GetNameOfClass() */
+  itkOverrideGetNameOfClassMacro(VTIImageIO);
+
+  /*-------- This part of the interface deals with reading data. ------ */
+
+  /** Determine the file type. Returns true if this ImageIO can read the
+   * file specified. */
+  bool
+  CanReadFile(const char *) override;
+
+  /** Set the spacing and dimension information for the current filename. */
+  void
+  ReadImageInformation() override;
+
+  /** Reads the data from disk into the memory buffer provided. */
+  void
+  Read(void * buffer) override;
+
+  /*-------- This part of the interfaces deals with writing data. ----- */
+
+  /** Determine the file type. Returns true if this ImageIO can write the
+   * file specified. */
+  bool
+  CanWriteFile(const char *) override;
+
+  /** Writes the spacing and dimensions of the image.
+   * Assumes SetFileName has been called with a valid file name. */
+  void
+  WriteImageInformation() override
+  {}
+
+  /** Writes the data to disk from the memory buffer provided. Make sure
+   * that the IORegion has been set properly. */
+  void
+  Write(const void * buffer) override;
+
+protected:
+  VTIImageIO();
+  ~VTIImageIO() override;
+
+  void
+  PrintSelf(std::ostream & os, Indent indent) const override;
+
+private:
+  /** Parse the XML header to fill image information. */
+  void
+  InternalReadImageInformation();
+
+  /** Map VTK type string to ITK IOComponentEnum. */
+  static IOComponentEnum
+  VTKTypeStringToITKComponent(const std::string & vtkType);
+
+  /** Map ITK IOComponentEnum to VTK type string. */
+  static std::string
+  ITKComponentToVTKTypeString(IOComponentEnum t);
+
+  /** Decode a base64-encoded string into raw bytes.  Returns the number
+   *  of decoded bytes. */
+  static SizeType
+  DecodeBase64(const std::string & encoded, std::vector<unsigned char> & decoded);
+
+  /** Encode raw bytes as a base64 string. */
+  static std::string
+  EncodeBase64(const unsigned char * data, SizeType numBytes);
+
+  /** Trim leading/trailing whitespace from a string. */
+  static std::string
+  TrimString(const std::string & s);
+
+  // Encoding format of the data array found in the file.
+  // (Plain comment, not doxygen, to satisfy KWStyle's `\class` rule for
+  // class-like declarations.)
+  enum class DataEncoding : std::uint8_t
+  {
+    ASCII,
+    Base64,      // binary data encoded in base64 (format="binary")
+    RawAppended, // raw binary appended data (format="appended" with raw encoding)
+    ZLibBase64,  // zlib-compressed data encoded in base64
+    ZLibAppended // zlib-compressed raw appended data
+  };
+
+  DataEncoding m_DataEncoding{ DataEncoding::Base64 };
+
+  /** Cached ASCII data text content captured by the expat parser when the
+   *  active DataArray is in ASCII format.  Empty otherwise. */
+  std::string m_AsciiDataContent{};
+
+  /** Cached base64 data text content captured by the expat parser when the
+   *  active DataArray is in base64 ("binary") format.  Empty otherwise. */
+  std::string m_Base64DataContent{};
+
+  /** Byte offset into the file where the appended data section begins
+   *  (only relevant when m_DataEncoding == RawAppended). */
+  std::streampos m_AppendedDataOffset{ 0 };
+
+  /** Offset within the appended data block for this DataArray (in bytes,
+   *  not counting the leading block-size UInt32/UInt64). */
+  SizeType m_DataArrayOffset{ 0 };
+
+  /** Whether the header uses 64-bit block-size integers (header_type="UInt64"). */
+  bool m_HeaderTypeUInt64{ false };
+
+  /** Whether the file uses zlib compression (compressor="vtkZLibDataCompressor"). */
+  bool m_IsZLibCompressed{ false };
+
+  /** Decompress a VTK zlib-compressed block sequence into raw bytes.
+   *  The input buffer begins with the VTK multi-block compression header
+   *  (nblocks / uncompressed_blocksize / last_partial_size / compressed_sizes[]).
+   *  Header integers are UInt32 or UInt64 per \a headerUInt64. */
+  static void
+  DecompressZLib(const unsigned char *        compressedData,
+                 std::size_t                  compressedDataSize,
+                 bool                         headerUInt64,
+                 std::vector<unsigned char> & uncompressed);
+};
+} // end namespace itk
+
+#endif // itkVTIImageIO_h

Modules/IO/VTK/include/itkVTIImageIOFactory.h

@@ -0,0 +1,71 @@
+/*=========================================================================
+ *
+ *  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 itkVTIImageIOFactory_h
+#define itkVTIImageIOFactory_h
+#include "ITKIOVTKExport.h"
+
+#include "itkObjectFactoryBase.h"
+#include "itkImageIOBase.h"
+
+namespace itk
+{
+/**
+ * \class VTIImageIOFactory
+ * \brief Create instances of VTIImageIO objects using an object factory.
+ * \ingroup ITKIOVTK
+ */
+class ITKIOVTK_EXPORT VTIImageIOFactory : public ObjectFactoryBase
+{
+public:
+  ITK_DISALLOW_COPY_AND_MOVE(VTIImageIOFactory);
+
+  /** Standard class type aliases. */
+  using Self = VTIImageIOFactory;
+  using Superclass = ObjectFactoryBase;
+  using Pointer = SmartPointer<Self>;
+  using ConstPointer = SmartPointer<const Self>;
+
+  /** Class Methods used to interface with the registered factories. */
+  const char *
+  GetITKSourceVersion() const override;
+
+  const char *
+  GetDescription() const override;
+
+  /** Method for class instantiation. */
+  itkFactorylessNewMacro(Self);
+
+  /** \see LightObject::GetNameOfClass() */
+  itkOverrideGetNameOfClassMacro(VTIImageIOFactory);
+
+  /** Register one factory of this type  */
+  static void
+  RegisterOneFactory()
+  {
+    auto vtiFactory = VTIImageIOFactory::New();
+
+    ObjectFactoryBase::RegisterFactoryInternal(vtiFactory);
+  }
+
+protected:
+  VTIImageIOFactory();
+  ~VTIImageIOFactory() override;
+};
+} // end namespace itk
+
+#endif

Modules/IO/VTK/itk-module.cmake

@@ -1,18 +1,24 @@
 set(
   DOCUMENTATION
   "This module contains classes for reading and writing image
-files in the \"legacy\" (non-XML) VTK file format."
+files in the \"legacy\" (non-XML) VTK file format and the VTK XML
+ImageData (.vti) file format."
 )
 
 itk_module(
   ITKIOVTK
   ENABLE_SHARED
   DEPENDS
     ITKIOImageBase
+  PRIVATE_DEPENDS
+    ITKExpat
+    ITKZLIB
   TEST_DEPENDS
     ITKTestKernel
     ITKImageSources
+    ITKZLIB
   FACTORY_NAMES
     ImageIO::VTK
+    ImageIO::VTI
   DESCRIPTION "${DOCUMENTATION}"
 )

Modules/IO/VTK/src/CMakeLists.txt

@@ -2,6 +2,8 @@ set(
   ITKIOVTK_SRCS
   itkVTKImageIO.cxx
   itkVTKImageIOFactory.cxx
+  itkVTIImageIOFactory.cxx
+  itkVTIImageIO.cxx
 )
 
 itk_module_add_library(ITKIOVTK ${ITKIOVTK_SRCS})