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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2012 SRI International
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit is free software: you can
// redistribute it and/or modify it under the terms of the GNU General Public
// License as published by the Free Software Foundation, either version 3 of
// the License, or (at your option) any later version.
//
// The Computational Morphometry Toolkit is distributed in the hope that it
// will be useful, but WITHOUT ANY WARRANTY; without even the implied
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License along
// with the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include "cmtkVolumeFromFile.h"
#include <System/cmtkConsole.h>
#include <System/cmtkCompressedStream.h>
#include <Base/cmtkTypes.h>
#include <stdio.h>
namespace
cmtk
{
/** \addtogroup IO */
//@{
/// BioRad microscopy image file header
typedef struct
{
unsigned short nx, ny; // 0 2*2 image width and height in pixels
short npic; // 4 2 number of images in file
short ramp1_min; // 6 2*2 LUT1 ramp min. and max.
short ramp1_max;
int notes; // 10 4 no notes=0; has notes=non zero
short byte_format; // 14 2 bytes=TRUE(1); words=FALSE(0)
unsigned short n; // 16 2 image number within file
char name[32]; // 18 32 file name
short merged; // 50 2 merged format
unsigned short color1; // 52 2 LUT1 color status
unsigned short file_id; // 54 2 valid .PIC file=12345
short ramp2_min; // 56 2*2 LUT2 ramp min. and max.
short ramp2_max;
unsigned short color2; // 60 2 LUT2 color status
short edited; // 62 2 image has been edited=TRUE(1)
short lens; // 64 2 Integer part of lens magnification
float mag_factor; // 66 4 4 byte real mag. factor (old ver.)
unsigned short dummy[3]; // 70 6 NOT USED (old ver.=real lens mag.)
} FileHeaderBioRad;
const UniformVolume::SmartPtr
VolumeFromFile::ReadBioRad( const std::string& path )
{
CompressedStream stream( path );
// Biorad header is 76 bytes
char buffer[76];
if ( 1 != stream.Read( &buffer, sizeof(buffer), 1 ) )
{
StdErr << "ERROR: cannot read header from BioRad file " << path << ". Bailing out.\n";
return UniformVolume::SmartPtr( NULL );
}
FileHeaderBioRad header;
memcpy( &header.nx, buffer+0, sizeof( header.nx ) );
memcpy( &header.ny, buffer+2, sizeof( header.ny ) );
memcpy( &header.npic, buffer+4, sizeof( header.npic ) );
memcpy( &header.notes, buffer+10, sizeof( header.notes ) );
memcpy( &header.byte_format, buffer+14, sizeof( header.byte_format ) );
memcpy( &header.file_id, buffer+54, sizeof( header.file_id ) );
// check MagicNumber
#ifdef WORDS_BIGENDIAN
if ( Memory::ByteSwap( header.file_id ) != 12345 )
{
StdErr << "ERROR: BioRad file " << path << " has invalid magic number. Bailing out.\n";
return UniformVolume::SmartPtr( NULL );
}
#else
if ( header.file_id != 12345 )
{
StdErr << "ERROR: BioRad file " << path << " has invalid magic number. Bailing out.\n";
return UniformVolume::SmartPtr( NULL );
}
#endif
#ifdef WORDS_BIGENDIAN
int dims[3] = { Memory::ByteSwap( header.nx ), Memory::ByteSwap( header.ny ), Memory::ByteSwap( header.npic ) };
#else
int dims[3] = { header.nx, header.ny, header.npic };
#endif
int numPixels = dims[0] * dims[1] * dims[2];
TypedArray::SmartPtr dataArray;
if ( header.byte_format )
{
dataArray = TypedArray::SmartPtr( TypedArray::Create( TYPE_BYTE, numPixels ) );
}
else
{
dataArray = TypedArray::SmartPtr( TypedArray::Create( TYPE_USHORT, numPixels ) );
}
stream.Read( dataArray->GetDataPtr(), dataArray->GetItemSize(), dataArray->GetDataSize() );
double pixelsizeX = 1, pixelsizeY = 1, pixelsizeZ = 1;
bool flipX = false, flipY = false, flipZ = false;;
while ( ! stream.Feof() )
{
char lineheader[16], line[80];
stream.Read( lineheader, sizeof( lineheader ), 1 );
stream.Read( line, sizeof( line ), 1 );
// StdErr.printf( "%s\n->%s\n", lineheader, line );
double d1, d2, d3;
if ( 3 == sscanf( line, "AXIS_2 %20lf %20lf %20lf", &d1, &d2, &d3 ) )
{
pixelsizeX = fabs( d3 );
flipX = (d3 < 0 );
}
if ( 3 == sscanf( line, "AXIS_3 %20lf %20lf %20lf", &d1, &d2, &d3 ) )
{
pixelsizeY = fabs( d3 );
flipY = (d3 < 0 );
}
if ( 3 == sscanf( line, "AXIS_4 %20lf %20lf %20lf", &d1, &d2, &d3 ) )
{
pixelsizeZ = fabs( d3 );
flipZ = (d3 < 0 );
}
}
#ifdef WORDS_BIGENDIAN
Types::Coordinate lensScale = 1; //Memory::ByteSwap( header.lens );
#else
Types::Coordinate lensScale = 1; //header.lens;
#endif
// GJ I think this was backwards - want to swap if we ARE on big endian
// since Biorad is always little endian
//#ifndef WORDS_BIGENDIAN
#ifdef WORDS_BIGENDIAN
// change endianness from Sun to whatever we're currently on.
dataArray->ChangeEndianness();
#endif
UniformVolume::SmartPtr volume( new UniformVolume( DataGrid::IndexType::FromPointer( dims ), lensScale * pixelsizeX, lensScale * pixelsizeY, lensScale * pixelsizeZ, dataArray ) );
if ( flipX )
{
StdErr << "WARNING: x pixel spacing is negative. Resulting volume will be mirrored accordingly.\n";
volume->ApplyMirrorPlane( AXIS_X );
}
if ( flipY )
{
StdErr << "WARNING: y pixel spacing is negative. Resulting volume will be mirrored accordingly.\n";
volume->ApplyMirrorPlane( AXIS_Y );
}
if ( flipZ )
{
StdErr << "WARNING: z pixel spacing is negative. Resulting volume will be mirrored accordingly.\n";
volume->ApplyMirrorPlane( AXIS_Z );
}
return volume;
}
} // namespace cmtk
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