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Merge pull request #96 from ORMIR-XCT/enhancement/incorporate_aimio_1
Restructure and Refactor Header Handling
2 parents 434b550 + 1308359 commit e815be6

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‎include/itkAIMHeaderIO.h‎

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/*=========================================================================
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*
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* Copyright NumFOCUS
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* https://www.apache.org/licenses/LICENSE-2.0.txt
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*=========================================================================*/
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#ifndef itkAIMHeaderIO_h
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#define itkAIMHeaderIO_h
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#include "itkScancoHeaderIO.h"
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#include <sstream>
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struct AIMV020StructHeader;
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struct AIMV030StructHeader;
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namespace itk
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{
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class AIMHeaderIO : public ScancoHeaderIO
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{
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public:
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using ScancoHeaderIO::ScancoHeaderIO;
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~AIMHeaderIO();
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/** Read the header from an infile.
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* Fills in the m_HeaderData structure with the header information.
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* \param infile The input file stream to read the header from.
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* \throws std::runtime_error if the file cannot be opened or read.
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* \note Overrides base class virtual method
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*/
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unsigned long
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ReadHeader(std::ifstream & infile) override;
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/** Write the header to an open file stream.
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* \param outfile Pointer to an open std::ofstream where the header will be written.
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* \param imageSize size of the image that will be written after the header, in bytes
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* \throws std::runtime_error if headerData is null.
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* \note overrides base class virtual method
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* \returns number of bytes written to the file.
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*/
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unsigned long
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WriteHeader(std::ofstream & outfile, unsigned long imageSize) override;
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protected:
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/** Read the AIM pre-header from the file stream.
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* \param file The input file stream to read the header from.
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* \param length The length of the pre-header to read.
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* \param offset The offset in the file to start reading from.
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* \note m_IntSize is used to determine the size of integers in the pre-header,
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* and should be set appropriately before calling
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* \returns -1 on failure, 0 on success.
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*/
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int
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ReadPreHeader(std::ifstream & file, unsigned long length, unsigned long offset = 0);
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/** Read the AIM v020 image structure header from a data structure.
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* \param headerData pointer to structure containing image structure header
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*/
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void
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ReadImgStructHeader(AIMV020StructHeader * headerData);
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/** Read the AIM v030 image structure header from a data structure.
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* \param headerData pointer to structure containing image structure header
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* \overload ReadImgStructHeader for AIM v020
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*/
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void
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ReadImgStructHeader(AIMV030StructHeader * headerData);
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/** Read the AIM processing log from the file stream.
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* \param file The input file stream to read the header from.
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* \param length The length of the processing log to read.
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* \param offset The offset in the file to start reading from.
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* \returns -1 on failure, 0 on success.
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*/
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int
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ReadProcessingLog(std::ifstream & infile, unsigned long offset, unsigned long length);
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/** Write the image structure header to an AIM v020 data structure
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* \returns AIMV020StructHeader structure filled with encoded header data
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*/
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AIMV020StructHeader
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WriteStructHeaderV020();
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/** Write the image structure header to an AIM v030 data structure
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* \returns AIMV030StructHeader structure filled with encoded header data
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*/
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AIMV030StructHeader
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WriteStructHeaderV030();
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/** Write the processing log to a string.
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* \returns std::string containing the processing log populated with the header data
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*/
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std::string
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WriteProcessingLog();
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/** Write the image pre-header to a file
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* \param outfile The output file stream to write the pre-header to
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* \param imageSize size of the image that will be written after the header, in bytes
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* \param version The AIM file version to write (default is AIM_020)
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* \returns number of bytes written to the file
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* \note pre-header is written into the current file pointer of the outfile stream
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* \note pre-header blocks are written based on imageSize, m_ImgStructSize, and m_ProcessingLogSize,
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* which should be set accordingly
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*/
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size_t
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WritePreHeader(std::ofstream & outfile, size_t imageSize, ScancoFileVersions version = ScancoFileVersions::AIM_020);
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private:
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unsigned int m_IntSize{ 4 }; // Size of integers in the header (4 for AIM v020, 8 for AIM v030)
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/** Header Size = m_PreHeaderSize + m_ImgStructSize + m_ProcessingLogSize */
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unsigned long m_PreHeaderSize{ 0 };
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unsigned long m_ImgStructSize{ 0 };
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unsigned long m_ProcessingLogSize{ 0 };
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};
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} // namespace itk
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#endif // itkAIMHeaderIO_h

‎include/itkISQHeaderIO.h‎

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/*=========================================================================
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*
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* Copyright NumFOCUS
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* https://www.apache.org/licenses/LICENSE-2.0.txt
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*=========================================================================*/
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#ifndef itkISQHeaderIO_h
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#define itkISQHeaderIO_h
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#include "itkScancoHeaderIO.h"
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struct ISQEncodedPreHeader;
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struct ISQEncodedHeaderBlock;
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struct RADEncodedHeaderBlock;
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namespace itk
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{
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class ISQHeaderIO : public ScancoHeaderIO
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{
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public:
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using ScancoHeaderIO::ScancoHeaderIO;
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/** Read the header from an infile.
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* Fills in the m_HeaderData structure with the header information.
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* \param infile The input file stream to read the header from.
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* \throws std::runtime_error if the file cannot be opened or read.
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* \note Overrides base class virtual method
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*/
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unsigned long
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ReadHeader(std::ifstream & infile) override;
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/** Write the header to an open file stream.
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* \param outfile Pointer to an open std::ofstream where the header will be written.
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* \throws std::runtime_error if headerData is null.
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* \returns number of bytes written to the file.
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*/
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unsigned long
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WriteHeader(std::ofstream & outfile, unsigned long imageSize) override;
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private:
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/** Read date into creation and modification date strings
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* \param year The Gregorian year.
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* \param month The Gregorian month (1-12).
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* \param day The Gregorian day (1-31).
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* \param hour The hour (0-23).
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* \param minute The minute (0-59).
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* \param second The second (0-59).
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* \param millis The milliseconds (0-999).
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*/
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void
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ReadDateValues(const int year,
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const int month,
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const int day,
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const int hour,
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const int minute,
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const int second,
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const int milli);
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/** Parse and Save pixel and physical dimension values
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* Values are converted into appropriate units
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* \see unit conversions in itkScancoImageIO.h
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* \param imageData encoded data of at least 24 bytes to read from
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* \returns true if the file is a RAD file based on the dimension data,
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* false otherise
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*/
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bool
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ReadDimensionData(ISQEncodedPreHeader * imageData);
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/** Read RAD header values and convert units appropriately
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* \see unit conversions in itkScancoImageIO.h
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* \param headerData struct holding encoded RAD header data
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*/
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void
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ReadRADHeader(RADEncodedHeaderBlock * headerData);
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/** Read ISQ header values and convert units appropriately
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* \see unit conversions in itkScancoImageIO.h
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* \param headerData struct holding encoded ISQ header data
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*/
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void
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ReadISQHeader(ISQEncodedHeaderBlock * headerData);
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/** Read in extended header data
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* This may include a multi-header section with calibration data
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* \param buffer pointer to start of extended header data
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* \param length length of extended header,
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* this can be calculated from the data offset found in the last 4 bytes of the main header block
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* \note length must be at least 3 blocks
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* \note buffer must be at least length bytes
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*/
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void
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ReadExtendedHeader(const char * buffer, unsigned long length);
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/** Write Calibration data to extended header blocks
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* \param outfile file to write data to
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* \note requires first block (512 bytes) to be written with header data
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* \returns number of bytes written to the file
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*/
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unsigned long
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WriteExtendedHeader(std::ofstream & outfile);
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unsigned long m_HeaderSize;
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};
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} // namespace itk
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#endif // itkISQHeaderIO_h

‎include/itkScancoDataManipulation.h‎

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*=========================================================================*/
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#ifndef itkScancoDataManipulation_h
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#define itkScancoDataManipulation_h
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#include "itkMacro.h"
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#include <cstddef>
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#include <array>
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struct itkScancoPixelData
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{
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int m_Dimensions[3]; // Dimensions of the pixel data
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float m_Origin[3]; // Origin of the pixel data in physical space
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double m_Spacing[3]; // Spacing between pixels in physical space
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int m_ComponentType; // Data Type (e.g., unsigned char, short, float)
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int m_PixelType;
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};
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struct itkScancoHeaderData
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{
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char m_Version[18]; // Version string, e.g., "AIMDATA_V020 "
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char m_PatientName[42];
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int m_PatientIndex;
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int m_ScannerID;
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char m_CreationDate[32];
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char m_ModificationDate[32];
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int m_ScanDimensionsPixels[3];
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double m_ScanDimensionsPhysical[3];
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double m_SliceThickness; // Slice thickness in mm
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double m_SliceIncrement; // Slice increment in mm
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double m_StartPosition;
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double m_EndPosition;
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double m_ZPosition;
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std::array<double, 2> m_DataRange;
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double m_MuScaling;
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int m_NumberOfSamples;
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int m_NumberOfProjections;
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double m_ScanDistance;
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double m_SampleTime;
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int m_ScannerType;
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int m_MeasurementIndex;
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int m_Site;
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int m_ReconstructionAlg;
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double m_ReferenceLine;
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double m_Energy;
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double m_Intensity;
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int m_RescaleType;
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char m_RescaleUnits[18];
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char m_CalibrationData[66];
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double m_RescaleSlope;
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double m_RescaleIntercept;
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double m_MuWater;
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char * m_RawHeader;
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itkScancoPixelData m_PixelData; // Pixel data information
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};
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#define ScancoGetConstMacro(name, type) \
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virtual type Get##name() const { return this->m_HeaderData.m_##name; } \
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ITK_MACROEND_NOOP_STATEMENT
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#define ScancoSetMacro(name, type) \
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virtual void Set##name(type _arg) \
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{ \
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itkDebugMacro("setting " #name " to " << _arg); \
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ITK_GCC_PRAGMA_PUSH \
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ITK_GCC_SUPPRESS_Wfloat_equal \
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if (this->m_HeaderData.m_##name != _arg) \
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{ \
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this->m_HeaderData.m_##name = std::move(_arg); \
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this->Modified(); \
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} \
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ITK_GCC_PRAGMA_POP \
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} \
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ITK_MACROEND_NOOP_STATEMENT
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constexpr int ScancoHeaderBlockSize = 512;
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/** Check the file header to see what type of file it is.
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*
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void
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EncodeInt(int data, void * target);
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/** Convert 64-bit int (little-endian) to char data.
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*
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* \param data The integer to convert.
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* \param target Pointer to a buffer of at least 8 bytes to store the result.
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*/
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void
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EncodeInt64(int64_t data, void * target);
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/** Convert char data to float (single precision).
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*
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* \param data Pointer to a buffer of at least 4 bytes.
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float
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DecodeFloat(const void * data);
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/** Convert float data to char data.
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*
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* \param data The float to convert.
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* \param target Pointer to a buffer of at least 4 bytes to store the result.
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*/
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void
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EncodeFloat(float data, void * target);
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/** Convert char data to float (double precision).
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*
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* \param data Pointer to a buffer of at least 8 bytes.
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double
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DecodeDouble(const void * data);
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void
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EncodeDouble(double data, void * target);
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/** Convert a VMS timestamp to a calendar date.
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*
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* \param data Pointer to a buffer of at least 8 bytes containing the VMS timestamp.
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void
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DecodeDate(const void * data, int & year, int & month, int & day, int & hour, int & minute, int & second, int & millis);
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/** Formats a date into a string of the form DD-MMM-YYYY HH:MM:SS:mmm
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* \param target Pointer to a buffer of at least 32 bytes to store the formatted date string.
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* \param year The year.
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* \param month The month (1-12).
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* \param day The day (1-31).
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* \param hour The hour (0-23).
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* \param minute The minute (0-59).
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* \param second The second (0-59).
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* \param millis The milliseconds (0-999).
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*/
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void
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DateToString(const void * target, int year, int month, int day, int hour, int minute, int second, int millis);
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/** Get the current date and time as a string in the format "YYYY-MM-DD HH:MM:SS.mmm".
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* \param target Pointer to a buffer of at least 32 bytes to store the current date string.
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*/
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void
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GetCurrentDateString(void * target);
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/** Convert the current calendar date to a VMS timestamp and store in target
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*
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* \param target Pointer to a buffer of at least 8 bytes to store the VMS timestamp.

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