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/*=========================================================================
*
* 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.
*
*=========================================================================*/
/**
* \file itkIPLCommonImageIO.h
* Much of the code for this file reader/writer was taken from
* the University of Iowa Imaging Group library with the
* permission of the authors, Milan Sonka, Joseph Reinhardt,
* Ryan Long, Hans Johnson, Gary Christensen, and others.
* The specification for this file format is taken from the
* web site https://analyzedirect.com/support/10.0Documents/Analyze_Resource_01.pdf
* \author Kent Williams
* The University of Iowa 2003
* \brief This file was written as a modification to the itkMetaImageIO
* as a new method for reading in files from the GE4 scanner.
*/
#ifndef itkIPLCommonImageIO_h
#define itkIPLCommonImageIO_h
#include "ITKIOIPLExport.h"
#include "itkImageIOBase.h"
#include "itkIPLFileNameList.h"
#include "itkGEImageHeader.h"
namespace itk
{
/**
* \class IPLCommonImageIO
*
* \author Hans J. Johnson
* \brief Class that defines how to read GE4 file format.
*
* \ingroup IOFilters
* \ingroup ITKIOIPL
*/
class ITKIOIPL_EXPORT IPLCommonImageIO : public ImageIOBase
{
public:
ITK_DISALLOW_COPY_AND_MOVE(IPLCommonImageIO);
/** Standard class type aliases. */
using Self = IPLCommonImageIO;
using Superclass = ImageIOBase;
using Pointer = SmartPointer<Self>;
using U8 = unsigned char;
using S8 = signed char;
using U16 = unsigned short;
using S16 = short;
using U32 = unsigned int;
using S32 = int;
using U64 = uint64_t;
using S64 = int64_t;
using F32 = float;
using F64 = double;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** \see LightObject::GetNameOfClass() */
itkOverrideGetNameOfClassMacro(IPLCommonImageIO);
/*-------- This part of the interfaces deals with reading data. ----- */
/** Determine if the file can be read with this ImageIO implementation.
* \author Hans J Johnson
* \param FileNameToRead The name of the file to test for reading.
* \post Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
* \return Returns true if this ImageIO can read the file specified.
*/
bool
CanReadFile(const char * FileNameToRead) override;
/** Set the spacing and dimension information for the set filename. */
void
ReadImageInformation() override;
/** Optionally, modify spacing, origin and direction */
virtual void
ModifyImageInformation()
{}
/** Reads the data from disk into the memory buffer provided. */
void
Read(void * buffer) override;
/** Compute the size (in bytes) of the components of a pixel. For
* example, and RGB pixel of unsigned char would have a
* component size of 1 byte. */
unsigned int
GetComponentSize() const override;
/*-------- This part of the interfaces deals with writing data. ----- */
/** Determine if the file can be written with this ImageIO implementation.
* \param FileNameToWrite The name of the file to test for writing.
* \author Hans J. Johnson
* \post Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
* \return Returns true if this ImageIO can write the file specified.
*/
bool
CanWriteFile(const char * FileNameToWrite) override;
/** Set the spacing and dimension information for the set filename. */
void
WriteImageInformation() override;
/** Writes the data to disk from the memory buffer provided. Make sure
* that the IORegions has been set properly. */
void
Write(const void * buffer) override;
/** Set sorting method by name ascending. */
virtual void
SortImageListByNameAscend();
/** Set sorting method by name descending. */
virtual void
SortImageListByNameDescend();
protected:
IPLCommonImageIO();
~IPLCommonImageIO() override;
void
PrintSelf(std::ostream & os, Indent indent) const override;
int
AddElementToList(char const * const filename,
const float sliceLocation,
const int offset,
const int XDim,
const int YDim,
const float XRes,
const float YRes,
const int Key1,
const int Key2);
void
sortImageListAscend();
void
sortImageListDescend();
int
statTimeToAscii(void * clock, char * timeString, int len);
virtual GEImageHeader *
ReadHeader(const char * FileNameToRead);
//
// data members
GEImageHeader * m_ImageHeader{};
IOByteOrderEnum m_SystemByteOrder{};
IPLFileNameList * m_FilenameList{};
//
// return 0 on success, -1 on failure
int
GetStringAt(std::ifstream & f, std::streamoff Offset, char * buf, size_t amount, bool throw_exception = true);
int
GetIntAt(std::ifstream & f, std::streamoff Offset, int * ip, bool throw_exception = true);
int
GetShortAt(std::ifstream & f, std::streamoff Offset, short * ip, bool throw_exception = true);
int
GetFloatAt(std::ifstream & f, std::streamoff Offset, float * ip, bool throw_exception = true);
int
GetDoubleAt(std::ifstream & f, std::streamoff Offset, double * ip, bool throw_exception = true);
short
hdr2Short(char * hdr);
int
hdr2Int(char * hdr);
float
hdr2Float(char * hdr);
double
hdr2Double(char * hdr);
};
} // end namespace itk
#define RAISE_EXCEPTION() \
{ \
ExceptionObject exception(__FILE__, __LINE__); \
exception.SetDescription("File cannot be read"); \
throw exception; \
} \
ITK_MACROEND_NOOP_STATEMENT
#define IOCHECK() \
if (f.fail()) \
{ \
if (f.is_open()) \
{ \
f.close(); \
} \
RAISE_EXCEPTION(); \
} \
ITK_MACROEND_NOOP_STATEMENT
#endif // itkIPLCommonImageIO_h
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