STYLE: Factor out itkOMEZarrNGFFCommon.h

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)

include/itkOMEZarrNGFFCommon.h

@@ -0,0 +1,134 @@
+/*=========================================================================
+ *
+ *  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>
+
+#include "itkIOCommon.h"
+
+#include "tensorstore/container_kind.h"
+#include "tensorstore/context.h"
+#include "tensorstore/index_space/dim_expression.h"
+#include "tensorstore/open.h"
+#include "tensorstore/index_space/index_domain.h"
+#include "tensorstore/index_space/index_domain_builder.h"
+#include "tensorstore/index_space/dim_expression.h"
+
+#include <nlohmann/json.hpp>
+
+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;
+};
+
+// Update an existing "read" specification for an "http" driver to retrieve remote files.
+// Note that an "http" driver specification may operate on an HTTP or HTTPS connection.
+void
+makeKVStoreHTTPDriverSpec(nlohmann::json & spec, const std::string & fullPath);
+
+tensorstore::DataType
+itkToTensorstoreComponentType(const IOComponentEnum itkComponentType);
+
+// Returns TensorStore KvStore driver name appropriate for this path.
+// Options are file, zip. TODO: http, gcs (GoogleCouldStorage), etc.
+std::string
+getKVstoreDriver(std::string path);
+
+// JSON file path, e.g. "C:/Dev/ITKIOOMEZarrNGFF/v0.4/cyx.ome.zarr/.zgroup"
+void
+writeJson(nlohmann::json json, std::string path, std::string driver);
+
+// JSON file path, e.g. "C:/Dev/ITKIOOMEZarrNGFF/v0.4/cyx.ome.zarr/.zattrs"
+bool
+jsonRead(const std::string path, nlohmann::json & result, std::string driver);
+
+// We call tensorstoreToITKComponentType for each type.
+// Hopefully compiler will optimize it away via constant propagation and inlining.
+#define READ_ELEMENT_IF(typeName)                                                                     \
+  else if (tensorstoreToITKComponentType(tensorstore::dtype_v<typeName>) == this->GetComponentType()) \
+  {                                                                                                   \
+    ReadFromStore<typeName>(store, storeIORegion, reinterpret_cast<typeName *>(buffer));              \
+  }
+
+// We need to specify dtype for opening. As dtype is dependent on component type, this macro is long.
+#define ELEMENT_WRITE(typeName)                                                                       \
+  else if (tensorstoreToITKComponentType(tensorstore::dtype_v<typeName>) == this->GetComponentType()) \
+  {                                                                                                   \
+    if (sizeof(typeName) == 1)                                                                        \
+    {                                                                                                 \
+      dtype = "|";                                                                                    \
+    }                                                                                                 \
+    if (std::numeric_limits<typeName>::is_integer)                                                    \
+    {                                                                                                 \
+      if (std::numeric_limits<typeName>::is_signed)                                                   \
+      {                                                                                               \
+        dtype += 'i';                                                                                 \
+      }                                                                                               \
+      else                                                                                            \
+      {                                                                                               \
+        dtype += 'u';                                                                                 \
+      }                                                                                               \
+    }                                                                                                 \
+    else                                                                                              \
+    {                                                                                                 \
+      dtype += 'f';                                                                                   \
+    }                                                                                                 \
+    dtype += std::to_string(sizeof(typeName));                                                        \
+                                                                                                      \
+    auto openFuture = tensorstore::Open(                                                              \
+      {                                                                                               \
+        { "driver", "zarr" },                                                                         \
+        { "kvstore", { { "driver", driver }, { "path", this->m_FileName + "/" + path } } },           \
+        { "metadata",                                                                                 \
+          {                                                                                           \
+            { "compressor", { { "id", "blosc" } } },                                                  \
+            { "dtype", dtype },                                                                       \
+            { "shape", shape },                                                                       \
+          } },                                                                                        \
+      },                                                                                              \
+      tsContext,                                                                                      \
+      tensorstore::OpenMode::create | tensorstore::OpenMode::delete_existing,                         \
+      tensorstore::ReadWriteMode::read_write);                                                        \
+    TS_EVAL_CHECK(openFuture);                                                                        \
+                                                                                                      \
+    auto   writeStore = openFuture.value();                                                           \
+    auto * p = reinterpret_cast<typeName const *>(buffer);                                            \
+    auto   arr = tensorstore::Array(p, shape, tensorstore::c_order);                                  \
+    auto   writeFuture = tensorstore::Write(tensorstore::UnownedToShared(arr), writeStore);           \
+    TS_EVAL_CHECK(writeFuture);                                                                       \
+  }
+
+} // end namespace itk
+
+#endif // itkOMEZarrNGFFCommon_h

include/itkOMEZarrNGFFTransformIO.h

@@ -0,0 +1,133 @@
+/*=========================================================================
+ *
+ *  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 itkOMEZarrNGFFImageIO_h
+#define itkOMEZarrNGFFImageIO_h
+#include "IOOMEZarrNGFFExport.h"
+
+
+#include <fstream>
+#include <string>
+#include <vector>
+
+#include "itkImageIOBase.h"
+
+#include "itkOMEZarrNGFFCommon.h"
+
+namespace itk
+{
+
+/** \class OMEZarrNGFFTransformIO
+ *
+ * \brief Read and write OME-Zarr coordinate transformations.
+ *
+ * Open Microscopy Environment Zarr Next Generation File Format
+ * specification can be found at https://github.com/ome/ngff
+ *
+ * \ingroup IOFilters
+ * \ingroup IOOMEZarrNGFF
+ */
+template <typename TParametersValueType>
+class ITK_TEMPLATE_EXPORT OMEZarrNGFFTransformIOTemplate : public TransformIOBaseTemplate<TParametersValueType>
+{
+public:
+  /** Standard class typedefs. */
+  using Self = OMEZarrNGFFTransformIOTemplate;
+  using Superclass = TransformIOBaseTemplate<TParametersValueType>;
+  using Pointer = SmartPointer<Self>;
+  using typename Superclass::TransformListType;
+  using typename Superclass::TransformPointer;
+  using typename Superclass::TransformType;
+  using ParametersType = typename TransformType::ParametersType;
+  using ParametersValueType = typename TransformType::ParametersValueType;
+  using FixedParametersType = typename TransformType::FixedParametersType;
+  using FixedParametersValueType = typename TransformType::FixedParametersValueType;
+
+  using ConstTransformListType = typename TransformIOBaseTemplate<ParametersValueType>::ConstTransformListType;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(OMEZarrNGFFTransformIOTemplate, TransformIOBaseTemplate);
+
+  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<OMEZarrAxis>;
+
+  /** Special in-memory zip interface. An address needs to be provided in
+   * the "file name", using pattern address.memory, where address is a
+   * decimal representation of BufferInfo's address.
+   * Sample filename: "12341234.memory". */
+  using BufferInfo = struct
+  {
+    char * pointer;
+    size_t size;
+  };
+
+  /** Construct a "magic" file name from the provided bufferInfo. */
+  static std::string
+  MakeMemoryFileName(const BufferInfo & bufferInfo)
+  {
+    size_t bufferInfoAddress = reinterpret_cast<size_t>(&bufferInfo);
+    return std::to_string(bufferInfoAddress) + ".memory";
+  }
+
+  /*-------- This part of the interfaces deals with reading data. ----- */
+
+  /** Reads the data from disk into the memory buffer provided. */
+  void
+  Read() override;
+
+  bool
+  CanReadFile(const char *) override;
+
+  /*-------- This part of the interfaces deals with writing data. ----- */
+
+  /** Determine the file type. Returns true if this TransformIO can write the
+   * file specified. */
+  bool
+  CanWriteFile(const char *) override;
+
+  void
+  Write() override;
+
+protected:
+  OMEZarrNGFFTransformIOTemplate();
+  ~OMEZarrNGFFTransformIOTemplate() override = default;
+
+  void
+  PrintSelf(std::ostream & os, Indent indent) const override;
+
+  /** Read a single array and set relevant metadata. */
+  void
+  ReadArrayMetadata(std::string path, std::string driver);
+
+private:
+  // An empty zip file consists of 22 bytes of "end of central directory" record. More:
+  // https://github.com/google/tensorstore/blob/45565464b9f9e2567144d780c3bef365ee3c125a/tensorstore/internal/compression/zip_details.h#L64-L76
+  constexpr static unsigned m_EmptyZipSize = 22;
+  char                      m_EmptyZip[m_EmptyZipSize] = "PK\x05\x06"; // the rest is filled with zeroes
+  const BufferInfo          m_EmptyZipBufferInfo{ m_EmptyZip, m_EmptyZipSize };
+  const std::string         m_EmptyZipFileName = MakeMemoryFileName(m_EmptyZipBufferInfo);
+
+  ITK_DISALLOW_COPY_AND_MOVE(OMEZarrNGFFTransformIOTemplate);
+};
+} // end namespace itk
+
+#endif // itkOMEZarrNGFFImageIO_h

include/itkOMEZarrNGFFTransformIOFactory.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 itkOMEZarrNGFFTransformIOFactory_h
+#define itkOMEZarrNGFFTransformIOFactory_h
+#include "IOOMEZarrNGFFExport.h"
+
+#include "itkObjectFactoryBase.h"
+#include "itkTransformIOBase.h"
+
+namespace itk
+{
+/** \class OMEZarrNGFFTransformIOFactory
+ * \brief Create instances of OMEZarrNGFFTransformIO objects using an object factory.
+ * \ingroup ITKIOOMEZarrNGFF
+ */
+class IOOMEZarrNGFF_EXPORT OMEZarrNGFFTransformIOFactory : public ObjectFactoryBase
+{
+public:
+  /** Standard class typedefs. */
+  using Self = OMEZarrNGFFTransformIOFactory;
+  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);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(OMEZarrNGFFTransformIOFactory, ObjectFactoryBase);
+
+  /** Register one factory of this type  */
+  static void
+  RegisterOneFactory()
+  {
+    OMEZarrNGFFTransformIOFactory::Pointer zarrFactory = OMEZarrNGFFTransformIOFactory::New();
+
+    ObjectFactoryBase::RegisterFactoryInternal(zarrFactory);
+  }
+
+protected:
+  OMEZarrNGFFTransformIOFactory();
+  ~OMEZarrNGFFTransformIOFactory() override = default;
+
+private:
+  ITK_DISALLOW_COPY_AND_MOVE(OMEZarrNGFFTransformIOFactory);
+};
+} // end namespace itk
+
+#endif

itk-module.cmake

@@ -11,13 +11,15 @@ file(READ "${MY_CURRENT_DIR}/README.md" DOCUMENTATION)
 itk_module(IOOMEZarrNGFF
   DEPENDS
     ITKIOImageBase
+    ITKIOTransformBase
     ITKIOHDF5
     ITKZLIB
   TEST_DEPENDS
     ITKTestKernel
     ITKMetaIO
   FACTORY_NAMES
     ImageIO::OMEZarrNGFF
+    TransformIO::OMEZarrNGFF
   DESCRIPTION
     "IO for images stored in zarr-backed OME-NGFF"
   EXCLUDE_FROM_DEFAULT

src/CMakeLists.txt

@@ -1,6 +1,9 @@
 set(IOOMEZarrNGFF_SRCS
+  itkOMEZarrNGFFCommon.cxx
   itkOMEZarrNGFFImageIO.cxx
   itkOMEZarrNGFFImageIOFactory.cxx
+  itkOMEZarrNGFFTransformIO.cxx
+  itkOMEZarrNGFFTransformIOFactory.cxx
   )