ENH: Ingest ITKIOScanco into Modules/IO

Modules/IO/IOScanco/CMakeLists.txt

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+project(IOScanco)
+set(IOScanco_LIBRARIES IOScanco)
+
+itk_module_impl()

Modules/IO/IOScanco/include/itkAIMHeaderIO.h

@@ -0,0 +1,127 @@
+/*=========================================================================
+ *
+ *  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 itkAIMHeaderIO_h
+#define itkAIMHeaderIO_h
+#include "itkScancoHeaderIO.h"
+#include <sstream>
+
+struct AIMV020StructHeader;
+struct AIMV030StructHeader;
+
+namespace itk
+{
+class AIMHeaderIO : public ScancoHeaderIO
+{
+public:
+  using ScancoHeaderIO::ScancoHeaderIO;
+
+  ~AIMHeaderIO();
+
+  /** Read the header from an infile.
+   * Fills in the m_HeaderData structure with the header information.
+   * \param infile The input file stream to read the header from.
+   * \throws std::runtime_error if the file cannot be opened or read.
+   * \note Overrides base class virtual method
+   */
+  unsigned long
+  ReadHeader(std::ifstream & infile) override;
+
+  /** Write the header to an open file stream.
+   * \param outfile Pointer to an open std::ofstream where the header will be written.
+   * \param imageSize size of the image that will be written after the header, in bytes
+   * \throws std::runtime_error if headerData is null.
+   * \note overrides base class virtual method
+   * \returns number of bytes written to the file.
+   */
+  unsigned long
+  WriteHeader(std::ofstream & outfile, unsigned long imageSize) override;
+
+protected:
+  /** Read the AIM pre-header from the file stream.
+   * \param file The input file stream to read the header from.
+   * \param offset The offset in the file to start reading from.
+   * \note m_IntSize is used to determine the size of integers in the pre-header,
+   *      and should be set appropriately before calling
+   * \returns -1 on failure, 0 on success.
+   */
+  int
+  ReadPreHeader(std::ifstream & file, size_t offset = 0);
+
+  /** Read the AIM v020 image structure header from a data structure.
+   * \param headerData pointer to structure containing image structure header
+   */
+  void
+  ReadImgStructHeader(AIMV020StructHeader * headerData);
+
+  /** Read the AIM v030 image structure header from a data structure.
+   * \param headerData pointer to structure containing image structure header
+   * \overload ReadImgStructHeader for AIM v020
+   */
+  void
+  ReadImgStructHeader(AIMV030StructHeader * headerData);
+
+  /** Read the AIM processing log from the file stream.
+   * \param file The input file stream to read the header from.
+   * \param length The length of the processing log to read.
+   * \param offset The offset in the file to start reading from.
+   * \returns size of the processing log read
+   */
+  size_t
+  ReadProcessingLog(std::ifstream & infile, size_t offset, size_t length);
+
+  /** Write the image structure header to an AIM v020 data structure
+   * \returns AIMV020StructHeader structure filled with encoded header data
+   */
+  AIMV020StructHeader
+  WriteStructHeaderV020();
+
+  /** Write the image structure header to an AIM v030 data structure
+   * \returns AIMV030StructHeader structure filled with encoded header data
+   */
+  AIMV030StructHeader
+  WriteStructHeaderV030();
+
+  /** Write the processing log to a string.
+   * \returns std::string containing the processing log populated with the header data
+   */
+  std::string
+  WriteProcessingLog();
+
+  /** Write the image pre-header to a file
+   * \param outfile The output file stream to write the pre-header to
+   * \param imageSize size of the image that will be written after the header, in bytes
+   * \param version The AIM file version to write (default is AIM_020)
+   * \returns number of bytes written to the file
+   * \note pre-header is written into the current file pointer of the outfile stream
+   * \note pre-header blocks are written based on imageSize, m_ImgStructSize, and m_ProcessingLogSize,
+   *       which should be set accordingly
+   */
+  size_t
+  WritePreHeader(std::ofstream & outfile, size_t imageSize, ScancoFileVersions version = ScancoFileVersions::AIM_020);
+
+private:
+  unsigned int m_IntSize{ 4 }; // Size of integers in the header (4 for AIM v020, 8 for AIM v030)
+
+  /** Header Size = m_PreHeaderSize + m_ImgStructSize + m_ProcessingLogSize */
+  size_t m_PreHeaderSize{ 0 };
+  size_t m_ImgStructSize{ 0 };
+  size_t m_ProcessingLogSize{ 0 };
+};
+} // namespace itk
+#endif // itkAIMHeaderIO_h

Modules/IO/IOScanco/include/itkISQHeaderIO.h

@@ -0,0 +1,118 @@
+/*=========================================================================
+ *
+ *  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 itkISQHeaderIO_h
+#define itkISQHeaderIO_h
+#include "itkScancoHeaderIO.h"
+
+struct ISQEncodedPreHeader;
+struct ISQEncodedHeaderBlock;
+struct RADEncodedHeaderBlock;
+
+namespace itk
+{
+class ISQHeaderIO : public ScancoHeaderIO
+{
+public:
+  using ScancoHeaderIO::ScancoHeaderIO;
+
+  /** Read the header from an infile.
+   * Fills in the m_HeaderData structure with the header information.
+   * \param infile The input file stream to read the header from.
+   * \throws std::runtime_error if the file cannot be opened or read.
+   * \note Overrides base class virtual method
+   */
+  unsigned long
+  ReadHeader(std::ifstream & infile) override;
+
+  /** Write the header to an open file stream.
+   * \param outfile Pointer to an open std::ofstream where the header will be written.
+   * \throws std::runtime_error if headerData is null.
+   * \returns number of bytes written to the file.
+   */
+  unsigned long
+  WriteHeader(std::ofstream & outfile, unsigned long imageSize) override;
+
+private:
+  /** Read date into creation and modification date strings
+   * \param year The Gregorian year.
+   * \param month The Gregorian month (1-12).
+   * \param day The Gregorian day (1-31).
+   * \param hour The hour (0-23).
+   * \param minute The minute (0-59).
+   * \param second The second (0-59).
+   * \param millis The milliseconds (0-999).
+   */
+  void
+  ReadDateValues(const int year,
+                 const int month,
+                 const int day,
+                 const int hour,
+                 const int minute,
+                 const int second,
+                 const int milli);
+
+  /** Parse and Save pixel and physical dimension values
+   * Values are converted into appropriate units
+   * \see unit conversions in itkScancoImageIO.h
+   * \param imageData encoded data of at least 24 bytes to read from
+   * \returns true if the file is a RAD file based on the dimension data,
+   *          false otherise
+   */
+  bool
+  ReadDimensionData(ISQEncodedPreHeader * imageData);
+
+  /** Read RAD header values and convert units appropriately
+   * \see unit conversions in itkScancoImageIO.h
+   * \param headerData struct holding encoded RAD header data
+   */
+  void
+  ReadRADHeader(RADEncodedHeaderBlock * headerData);
+
+  /** Read ISQ header values and convert units appropriately
+   * \see unit conversions in itkScancoImageIO.h
+   * \param headerData struct holding encoded ISQ header data
+   */
+  void
+  ReadISQHeader(ISQEncodedHeaderBlock * headerData);
+
+  /** Read in extended header data
+   * This may include a multi-header section with calibration data
+   * \param buffer pointer to start of extended header data
+   * \param length length of extended header,
+   *               this can be calculated from the data offset found in the last 4 bytes of the main header block
+   * \note length must be at least 3 blocks
+   * \note buffer must be at least length bytes
+   */
+  void
+  ReadExtendedHeader(const char * buffer, unsigned long length);
+
+  /** Write Calibration data to extended header blocks
+   * \param outfile file to write data to
+   * \note requires first block (512 bytes) to be written with header data
+   * \returns number of bytes written to the file
+   */
+  unsigned long
+  WriteExtendedHeader(std::ofstream & outfile);
+
+  unsigned long m_HeaderSize;
+};
+
+} // namespace itk
+
+#endif // itkISQHeaderIO_h