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vtkTIFFReader.cxx
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/*=========================================================================
Program: Visualization Toolkit
Module: vtkTIFFReader.cxx,v
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notice for more information.
=========================================================================*/
#include "vtkTIFFReader.h"
#include "vtkDataArray.h"
#include "vtkImageData.h"
#include "vtkPointData.h"
#include "vtkErrorCode.h"
#include "vtkObjectFactory.h"
#include <sys/stat.h>
#include <vtkstd/string>
extern "C" {
#include "vtk_tiff.h"
}
//-------------------------------------------------------------------------
vtkStandardNewMacro(vtkTIFFReader);
class vtkTIFFReaderInternal
{
public:
vtkTIFFReaderInternal();
int Initialize();
void Clean();
int CanRead();
int Open( const char *filename );
TIFF *Image;
bool IsOpen;
unsigned int Width;
unsigned int Height;
unsigned short NumberOfPages;
unsigned short CurrentPage;
unsigned short SamplesPerPixel;
unsigned short Compression;
unsigned short BitsPerSample;
unsigned short Photometrics;
bool HasValidPhotometricInterpretation;
unsigned short PlanarConfig;
unsigned short Orientation;
unsigned long int TileDepth;
unsigned int TileRows;
unsigned int TileColumns;
unsigned int TileWidth;
unsigned int TileHeight;
unsigned short NumberOfTiles;
unsigned int SubFiles;
unsigned int ResolutionUnit;
float XResolution;
float YResolution;
short SampleFormat;
static void ErrorHandler(const char* module, const char* fmt, va_list ap);
};
extern "C" {
void vtkTIFFReaderInternalErrorHandler(const char* vtkNotUsed(module),
const char* vtkNotUsed(fmt),
va_list vtkNotUsed(ap))
{
// Do nothing
// Ignore errors
}
}
//-------------------------------------------------------------------------
int vtkTIFFReaderInternal::Open( const char *filename )
{
this->Clean();
struct stat fs;
if ( stat(filename, &fs) )
{
return 0;
}
this->Image = TIFFOpen(filename, "r");
if ( !this->Image)
{
this->Clean();
return 0;
}
if ( !this->Initialize() )
{
this->Clean();
return 0;
}
this->IsOpen = true;
return 1;
}
//-------------------------------------------------------------------------
void vtkTIFFReaderInternal::Clean()
{
if ( this->Image )
{
TIFFClose(this->Image);
}
this->Image=NULL;
this->Width = 0;
this->Height = 0;
this->SamplesPerPixel = 0;
this->Compression = 0;
this->BitsPerSample = 0;
this->Photometrics = 0;
this->HasValidPhotometricInterpretation = false;
this->PlanarConfig = 0;
this->TileDepth = 0;
this->CurrentPage = 0;
this->NumberOfPages = 0;
this->NumberOfTiles = 0;
this->TileRows = 0;
this->TileColumns = 0;
this->TileWidth = 0;
this->TileHeight = 0;
this->XResolution = 1;
this->YResolution = 1;
this->SubFiles = 0;
this->SampleFormat = 1;
this->ResolutionUnit = 1; // none
this->IsOpen = false;
}
//-------------------------------------------------------------------------
vtkTIFFReaderInternal::vtkTIFFReaderInternal()
{
this->Image = NULL;
TIFFSetErrorHandler(&vtkTIFFReaderInternalErrorHandler);
TIFFSetWarningHandler(&vtkTIFFReaderInternalErrorHandler);
this->Clean();
}
//-------------------------------------------------------------------------
int vtkTIFFReaderInternal::Initialize()
{
if ( this->Image )
{
if ( !TIFFGetField(this->Image, TIFFTAG_IMAGEWIDTH, &this->Width) ||
!TIFFGetField(this->Image, TIFFTAG_IMAGELENGTH, &this->Height) )
{
return 0;
}
// Get the resolution in each direction
TIFFGetField(this->Image, TIFFTAG_XRESOLUTION, &this->XResolution);
TIFFGetField(this->Image, TIFFTAG_YRESOLUTION, &this->YResolution);
TIFFGetField(this->Image, TIFFTAG_RESOLUTIONUNIT, &this->ResolutionUnit);
// Check the number of pages. First by looking at the number of directories
this->NumberOfPages = TIFFNumberOfDirectories(this->Image);
if(this->NumberOfPages == 0)
{
if ( !TIFFGetField(this->Image,TIFFTAG_PAGENUMBER,&this->CurrentPage,
&this->NumberOfPages))
{
// Check the Image Description tag to know the number of images
// This is used by ImageJ
char** description = new char*[255];
if (TIFFGetField(this->Image,TIFFTAG_IMAGEDESCRIPTION,description))
{
// look for the number of images
vtkstd::string desc = description[0];
int pos = desc.find("images=");
int pos2 = desc.find("\n");
if( (pos != -1) && (pos2 != -1))
{
this->NumberOfPages = atoi(desc.substr(pos+7,pos2-pos-7).c_str());
}
}
}
}
// If the number of pages is still zero we look if the image is tiled
if(this->NumberOfPages == 0 && TIFFIsTiled(this->Image))
{
this->NumberOfTiles = TIFFNumberOfTiles(this->Image);
if ( !TIFFGetField(this->Image,TIFFTAG_TILEWIDTH,&this->TileWidth)
|| !TIFFGetField(this->Image,TIFFTAG_TILELENGTH,&this->TileHeight)
)
{
cerr << "Cannot read tile width and tile length from file" << endl;
}
else
{
TileRows = this->Height/this->TileHeight;
TileColumns = this->Width/this->TileWidth;
}
}
// Checking if the TIFF contains subfiles
if(this->NumberOfPages > 1)
{
this->SubFiles = 0;
for(unsigned int page = 0;page<this->NumberOfPages;page++)
{
long subfiletype = 6;
if(TIFFGetField(this->Image, TIFFTAG_SUBFILETYPE, &subfiletype))
{
if(subfiletype == 0)
{
this->SubFiles+=1;
}
}
TIFFReadDirectory(this->Image);
}
// Set the directory to the first image
TIFFSetDirectory(this->Image,0);
}
// TIFFTAG_ORIENTATION tag from the image
// data and use it if available. If the tag is not found in the image data,
// use ORIENTATION_BOTLEFT by default.
int status = TIFFGetField(this->Image, TIFFTAG_ORIENTATION,
&this->Orientation);
if( ! status )
{
this->Orientation = ORIENTATION_BOTLEFT;
}
TIFFGetFieldDefaulted(this->Image, TIFFTAG_SAMPLESPERPIXEL,
&this->SamplesPerPixel);
TIFFGetFieldDefaulted(this->Image, TIFFTAG_COMPRESSION, &this->Compression);
TIFFGetFieldDefaulted(this->Image, TIFFTAG_BITSPERSAMPLE,
&this->BitsPerSample);
TIFFGetFieldDefaulted(this->Image, TIFFTAG_PLANARCONFIG, &this->PlanarConfig);
TIFFGetFieldDefaulted(this->Image, TIFFTAG_SAMPLEFORMAT, &this->SampleFormat);
// If TIFFGetField returns false, there's no Photometric Interpretation
// set for this image, but that's a required field so we set a warning flag.
// (Because the "Photometrics" field is an enum, we can't rely on setting
// this->Photometrics to some signal value.)
if (TIFFGetField(this->Image, TIFFTAG_PHOTOMETRIC, &this->Photometrics))
{
this->HasValidPhotometricInterpretation = true;
}
else
{
this->HasValidPhotometricInterpretation = false;
}
if ( !TIFFGetField(this->Image, TIFFTAG_TILEDEPTH, &this->TileDepth) )
{
this->TileDepth = 0;
}
}
return 1;
}
//-------------------------------------------------------------------------
int vtkTIFFReaderInternal::CanRead()
{
return ( this->Image && ( this->Width > 0 ) && ( this->Height > 0 ) &&
( this->SamplesPerPixel > 0 ) &&
( this->Compression == COMPRESSION_NONE ||
this->Compression == COMPRESSION_PACKBITS ||
this->Compression == COMPRESSION_LZW
) &&
( this->HasValidPhotometricInterpretation ) &&
( this->Photometrics == PHOTOMETRIC_RGB ||
this->Photometrics == PHOTOMETRIC_MINISWHITE ||
this->Photometrics == PHOTOMETRIC_MINISBLACK ||
this->Photometrics == PHOTOMETRIC_PALETTE ) &&
( this->PlanarConfig == PLANARCONFIG_CONTIG ) &&
( !this->TileDepth ) &&
( this->BitsPerSample == 8 || this->BitsPerSample == 16 ) );
}
//-------------------------------------------------------------------------
vtkTIFFReader::vtkTIFFReader()
{
this->InitializeColors();
this->InternalImage = new vtkTIFFReaderInternal;
this->OutputExtent = 0;
this->OutputIncrements = 0;
this->OrientationTypeSpecifiedFlag = false;
this->OriginSpecifiedFlag = false;
this->SpacingSpecifiedFlag = false;
//Make the default orientation type to be ORIENTATION_BOTLEFT
this->OrientationType = 4;
}
//-------------------------------------------------------------------------
vtkTIFFReader::~vtkTIFFReader()
{
delete this->InternalImage;
}
//-------------------------------------------------------------------------
void vtkTIFFReader::ExecuteInformation()
{
this->InitializeColors();
this->ComputeInternalFileName(this->DataExtent[4]);
if (this->InternalFileName == NULL)
{
vtkErrorMacro( "Need to specify a filename" );
this->SetErrorCode( vtkErrorCode::NoFileNameError );
return;
}
if ( !this->InternalImage->Open(this->InternalFileName) )
{
vtkErrorMacro("Unable to open file " << this->InternalFileName );
this->SetErrorCode( vtkErrorCode::CannotOpenFileError );
this->DataExtent[0] = 0;
this->DataExtent[1] = 0;
this->DataExtent[2] = 0;
this->DataExtent[3] = 0;
this->DataExtent[4] = 0;
this->DataExtent[5] = 0;
this->SetNumberOfScalarComponents(1);
this->vtkImageReader2::ExecuteInformation();
return;
}
// if orientation information is provided, overwrite the value
// read from the tiff image
if( this->OrientationTypeSpecifiedFlag )
{
this->GetInternalImage()->Orientation = OrientationType;
}
if( !SpacingSpecifiedFlag )
{
this->DataSpacing[0] = 1.0;
this->DataSpacing[1] = 1.0;
// If we have some spacing information we use it
if(this->GetInternalImage()->ResolutionUnit>0
&& this->GetInternalImage()->XResolution>0
&& this->GetInternalImage()->YResolution>0
)
{
if(this->GetInternalImage()->ResolutionUnit == 2) // inches
{
this->DataSpacing[0] = 25.4/this->GetInternalImage()->XResolution;
this->DataSpacing[1] = 25.4/this->GetInternalImage()->YResolution;
}
else if(this->GetInternalImage()->ResolutionUnit == 3) // cm
{
this->DataSpacing[0] = 10.0/this->GetInternalImage()->XResolution;
this->DataSpacing[1] = 10.0/this->GetInternalImage()->YResolution;
}
}
}
if( !OriginSpecifiedFlag )
{
this->DataOrigin[0] = 0.0;
this->DataOrigin[1] = 0.0;
}
// pull out the width/height, etc.
this->DataExtent[0] = 0;
this->DataExtent[1] = this->GetInternalImage()->Width - 1;
this->DataExtent[2] = 0;
this->DataExtent[3] = this->GetInternalImage()->Height - 1;
switch ( this->GetFormat() )
{
case vtkTIFFReader::GRAYSCALE:
case vtkTIFFReader::PALETTE_GRAYSCALE:
this->SetNumberOfScalarComponents( 1 );
break;
case vtkTIFFReader::RGB:
this->SetNumberOfScalarComponents(
this->GetInternalImage()->SamplesPerPixel );
break;
case vtkTIFFReader::PALETTE_RGB:
this->SetNumberOfScalarComponents( 3 );
break;
default:
this->SetNumberOfScalarComponents( 4 );
}
if ( !this->GetInternalImage()->CanRead() )
{
this->SetNumberOfScalarComponents( 4 );
}
if (this->GetInternalImage()->BitsPerSample <= 8)
{
if(this->GetInternalImage()->SampleFormat == 2)
{
this->SetDataScalarType( VTK_CHAR );
}
else
{
this->SetDataScalarTypeToUnsignedChar();
}
}
else if (this->GetInternalImage()->BitsPerSample <= 16)
{
if(this->GetInternalImage()->SampleFormat == 2)
{
this->SetDataScalarType( VTK_SHORT );
}
else
{
this->SetDataScalarTypeToUnsignedShort();
}
}
else if (this->GetInternalImage()->BitsPerSample <= 32)
{
if(this->GetInternalImage()->SampleFormat == 2)
{
this->SetDataScalarType( VTK_INT );
}
else
{
this->SetDataScalarTypeToUnsignedInt();
}
}
else
{
vtkErrorMacro( "Unhandled Bit Per Sample: " << this->GetInternalImage()->BitsPerSample );
return;
}
// We check if we have a Zeiss image.
// Meaning that the SamplesPerPixel is 2 but the image should be treated as
// an RGB image.
if(this->GetInternalImage()->SamplesPerPixel == 2)
{
this->SetNumberOfScalarComponents(3);
}
// if the tiff file is multi-pages
// series of tiff images ( 3D volume )
if(this->GetInternalImage()->NumberOfPages>1)
{
if(this->GetInternalImage()->SubFiles>0)
{
this->DataExtent[5] = this->GetInternalImage()->SubFiles;
}
else
{
this->DataExtent[5] = this->GetInternalImage()->NumberOfPages;
}
if( !SpacingSpecifiedFlag )
{
this->DataSpacing[2] = 1.0;
}
if( !OriginSpecifiedFlag )
{
this->DataOrigin[2] = 0.0;
}
}
// if the tiff is tiled
if(this->GetInternalImage()->NumberOfTiles>1)
{
this->DataExtent[1] = this->GetInternalImage()->TileWidth;
this->DataExtent[3] = this->GetInternalImage()->TileHeight;
this->DataExtent[5] = this->GetInternalImage()->NumberOfTiles;
if( !SpacingSpecifiedFlag )
{
this->DataSpacing[2] = 1.0;
}
if( !OriginSpecifiedFlag )
{
this->DataOrigin[2] = 0.0;
}
}
this->vtkImageReader2::ExecuteInformation();
// Don't close the file yet, since we need the image internal
// parameters such as NumberOfPages, NumberOfTiles to decide
// how to read in the image
}
// Set orientation type
//
//ORIENTATION_TOPLEFT 1 (row 0 top, col 0 lhs)
//ORIENTATION_TOPRIGHT 2 (row 0 top, col 0 rhs)
//ORIENTATION_BOTRIGHT 3 (row 0 bottom, col 0 rhs)
//ORIENTATION_BOTLEFT 4 (row 0 bottom, col 0 lhs)
//ORIENTATION_LEFTTOP 5 (row 0 lhs, col 0 top)
//ORIENTATION_RIGHTTOP 6 (row 0 rhs, col 0 top)
//ORIENTATION_RIGHTBOT 7 (row 0 rhs, col 0 bottom)
//ORIENTATION_LEFTBOT 8 (row 0 lhs, col 0 bottom) */
void vtkTIFFReader::SetOrientationType( unsigned int orientationType )
{
if ( orientationType < 1 || orientationType > 8 )
{
vtkErrorMacro( "Invalid Orientation type specified" );
return;
}
if( this->OrientationType != orientationType )
{
this->OrientationType = orientationType;
this->Modified();
}
if( !this->OrientationTypeSpecifiedFlag )
{
this->Modified();
}
// To preserve backward compatibility OrientationTypeSpecifiedFlag would
// always be set to true whatever user input...
this->OrientationTypeSpecifiedFlag = true;
}
//-------------------------------------------------------------------------
template <class OT>
void vtkTIFFReaderUpdate2(vtkTIFFReader *self, OT *outPtr,
int *outExt, vtkIdType* vtkNotUsed(outInc), long)
{
if ( !self->GetInternalImage()->Open(self->GetInternalFileName()) )
{
return;
}
// if orientation information is provided, overwrite the value
// read from the tiff image
if( self->GetOrientationTypeSpecifiedFlag())
{
self->GetInternalImage()->Orientation = self->GetOrientationType();
}
self->InitializeColors();
self->ReadImageInternal(self->GetInternalImage()->Image,
outPtr, outExt, sizeof(OT) );
// close the file
self->GetInternalImage()->Clean();
}
//----------------------------------------------------------------------------
// This function reads in one data of data.
// templated to handle different data types.
template <class OT>
void vtkTIFFReaderUpdate(vtkTIFFReader *self, vtkImageData *data, OT *outPtr)
{
vtkIdType outIncr[3];
int outExtent[6];
OT *outPtr2;
data->GetExtent(outExtent);
data->GetIncrements(outIncr);
long pixSize = data->GetNumberOfScalarComponents()*sizeof(OT);
// multiple number of pages
if(self->GetInternalImage()->NumberOfPages>1 )
{
self->ReadVolume( outPtr );
return;
}
// tiled image
if(self->GetInternalImage()->NumberOfTiles>0 )
{
self->ReadTiles( outPtr );
return;
}
//The input tiff dataset is neither multiple pages and nor
//tiled. Hence close the image and start reading each TIFF
//file
self->GetInternalImage()->Clean();
outPtr2 = outPtr;
int idx2;
for (idx2 = outExtent[4]; idx2 <= outExtent[5]; ++idx2)
{
self->ComputeInternalFileName(idx2);
// read in a TIFF file
vtkTIFFReaderUpdate2(self, outPtr2, outExtent, outIncr, pixSize);
self->UpdateProgress((idx2 - outExtent[4])/
(outExtent[5] - outExtent[4] + 1.0));
outPtr2 += outIncr[2];
}
}
//----------------------------------------------------------------------------
// This function reads a data from a file. The datas extent/axes
// are assumed to be the same as the file extent/order.
void vtkTIFFReader::ExecuteData(vtkDataObject *output)
{
vtkImageData *data = this->AllocateOutputData(output);
if (this->InternalFileName == NULL)
{
vtkErrorMacro("Either a FileName or FilePrefix must be specified.");
return;
}
this->ComputeDataIncrements();
// Call the correct templated function for the output
void *outPtr;
// Call the correct templated function for the input
outPtr = data->GetScalarPointer();
// Needed deep in reading for finding the correct starting location.
this->OutputIncrements = data->GetIncrements();
switch (data->GetScalarType())
{
vtkTemplateMacro(vtkTIFFReaderUpdate(this, data, (VTK_TT *)(outPtr)));
default:
vtkErrorMacro("UpdateFromFile: Unknown data type");
}
data->GetPointData()->GetScalars()->SetName("Tiff Scalars");
}
//----------------------------------------------------------------------------
unsigned int vtkTIFFReader::GetFormat()
{
unsigned int cc;
if ( this->ImageFormat != vtkTIFFReader::NOFORMAT )
{
return this->ImageFormat;
}
switch ( this->GetInternalImage()->Photometrics )
{
case PHOTOMETRIC_RGB:
case PHOTOMETRIC_YCBCR:
this->ImageFormat = vtkTIFFReader::RGB;
return this->ImageFormat;
case PHOTOMETRIC_MINISWHITE:
case PHOTOMETRIC_MINISBLACK:
this->ImageFormat = vtkTIFFReader::GRAYSCALE;
return this->ImageFormat;
case PHOTOMETRIC_PALETTE:
for( cc=0; cc<256; cc++ )
{
unsigned short red, green, blue;
this->GetColor( cc, &red, &green, &blue );
if ( red != green || red != blue )
{
this->ImageFormat = vtkTIFFReader::PALETTE_RGB;
return this->ImageFormat;
}
}
this->ImageFormat = vtkTIFFReader::PALETTE_GRAYSCALE;
return this->ImageFormat;
}
this->ImageFormat = vtkTIFFReader::OTHER;
return this->ImageFormat;
}
//----------------------------------------------------------------------------
void vtkTIFFReader::GetColor( int index, unsigned short *red,
unsigned short *green, unsigned short *blue )
{
*red = 0;
*green = 0;
*blue = 0;
if ( index < 0 )
{
vtkErrorMacro("Color index has to be greater than 0");
return;
}
if ( this->TotalColors > 0 &&
this->ColorRed && this->ColorGreen && this->ColorBlue )
{
if ( index >= this->TotalColors )
{
vtkErrorMacro("Color index has to be less than number of colors ("
<< this->TotalColors << ")");
return;
}
*red = *(this->ColorRed + index);
*green = *(this->ColorGreen + index);
*blue = *(this->ColorBlue + index);
return;
}
unsigned short photometric;
if (!TIFFGetField(this->GetInternalImage()->Image, TIFFTAG_PHOTOMETRIC, &photometric))
{
if ( this->GetInternalImage()->Photometrics != PHOTOMETRIC_PALETTE )
{
vtkErrorMacro("You can only access colors for palette images");
return;
}
}
unsigned short *red_orig, *green_orig, *blue_orig;
switch (this->GetInternalImage()->BitsPerSample)
{
case 1: case 2: case 4:
case 8: case 16:
break;
default:
vtkErrorMacro( "Sorry, can not image with "
<< this->GetInternalImage()->BitsPerSample
<< "-bit samples" );
return;
}
if (!TIFFGetField(this->GetInternalImage()->Image, TIFFTAG_COLORMAP,
&red_orig, &green_orig, &blue_orig))
{
vtkErrorMacro("Missing required \"Colormap\" tag");
return;
}
this->TotalColors = (1L << this->GetInternalImage()->BitsPerSample);
if ( index >= this->TotalColors )
{
vtkErrorMacro("Color index has to be less than number of colors ("
<< this->TotalColors << ")");
return;
}
this->ColorRed = red_orig;
this->ColorGreen = green_orig;
this->ColorBlue = blue_orig;
*red = *(red_orig + index);
*green = *(green_orig + index);
*blue = *(blue_orig + index);
}
//-------------------------------------------------------------------------
void vtkTIFFReader::InitializeColors()
{
this->ColorRed = 0;
this->ColorGreen = 0;
this->ColorBlue = 0;
this->TotalColors = -1;
this->ImageFormat = vtkTIFFReader::NOFORMAT;
}
//-------------------------------------------------------------------------
template <typename T>
void ReadTiledImage(vtkTIFFReader *self, void *out,
unsigned int width,
unsigned int height,
unsigned int vtkNotUsed(size),
int *internalExtents)
{
TIFF *tiff;
uint32 tileWidth, tileLength, x, y, yi, rows, cols, tileSize;
int xx,yy;
int pixelDepth = self->GetInternalImage()->SamplesPerPixel;
T *image;
uint32 imagepos;
image = (T*)out;
tiff = self->GetInternalImage()->Image;
TIFFGetField(tiff, TIFFTAG_TILEWIDTH, &tileWidth);
TIFFGetField(tiff, TIFFTAG_TILELENGTH, &tileLength);
tileSize = TIFFTileSize(tiff);
tdata_t buffer = _TIFFmalloc(tileSize);
for(yi=0;yi<height;yi+=tileLength)
{
for(x=0;x<width;x+=tileWidth)
{
y = yi;
TIFFReadTile(tiff, buffer, x,y,0,0);
if (tileWidth > width - x)
{
cols = width-x;
}
else
{
cols = tileWidth;
}
if(tileLength > height - y)
{
rows = height - y;
}
else
{
rows = tileLength;
}
for(uint32 j = 0;j< rows;j++)
{
for(uint32 i=0;i<cols;i++)
{
uint32 tilepos = (i+j*cols)*pixelDepth;
imagepos = (((height -1) - y)*width+(x) + i - (j)*width)*pixelDepth;
xx = x + i;
yy = (height-1-y-j);
if ( xx >= internalExtents[0] &&
xx <= internalExtents[1] &&
yy >= internalExtents[2] &&
yy <= internalExtents[3] )
{
imagepos = (xx + width*yy)*pixelDepth;
self->EvaluateImageAt(image+imagepos, static_cast<T*>(buffer)+tilepos);
}
}
}
}
}
_TIFFfree(buffer);
}
//-------------------------------------------------------------------------
template<typename T>
void ReadScanlineImage(vtkTIFFReader *self, void *out,
unsigned int vtkNotUsed(width),
unsigned height,
unsigned int vtkNotUsed(size),
int *internalExtents)
{
unsigned int isize = TIFFScanlineSize(self->GetInternalImage()->Image);
unsigned int cc;
int row, inc;
int xx=0, yy=0;
tdata_t buf = _TIFFmalloc(isize);
T *image = (T *)out;
unsigned int c_inc =
self->GetInternalImage()->SamplesPerPixel; // * self->GetInternalImage()->BitsPerSample;
if ( self->GetInternalImage()->PlanarConfig == PLANARCONFIG_CONTIG )
{
for ( row = height-1; row >= 0; row -- )
{
if (TIFFReadScanline(self->GetInternalImage()->Image, buf, row, 0) <= 0)
{
cerr << "Problem reading the row in ReadScalineImage method:" << endl;
break;
}
for (cc = 0; cc < isize; cc += c_inc )
{
if ( xx >= internalExtents[0] &&
xx <= internalExtents[1] &&
yy >= internalExtents[2] &&
yy <= internalExtents[3] )
{
//unsigned char *c = static_cast<unsigned char *>(buf)+cc;
inc = self->EvaluateImageAt( image,
static_cast<T*>(buf) + cc
);
image += inc;
}
xx++;
}
xx=0;
yy++;
}
}
else
{
cerr << "This TIFF reader can only do PLANARCONFIG_CONTIG" << endl;
}
_TIFFfree(buf);
}
//-------------------------------------------------------------------------
void vtkTIFFReader::ReadVolume(void* buffer)
{
if ( this->GetInternalImage()->Compression == COMPRESSION_OJPEG )
{
vtkErrorMacro("This reader cannot read old JPEG compression");
return;
}
int width = this->GetInternalImage()->Width;
int height = this->GetInternalImage()->Height;
for(unsigned int page = 0;page<this->GetInternalImage()->NumberOfPages;page++)
{
if(this->GetInternalImage()->SubFiles>0)
{
long subfiletype = 6;
if(TIFFGetField(this->GetInternalImage()->Image, TIFFTAG_SUBFILETYPE, &subfiletype))
{
if(subfiletype != 0)
{
TIFFReadDirectory(this->GetInternalImage()->Image);
continue;
}
}
}
// if we have a Zeiss image meaning that the SamplesPerPixel is 2
if(this->GetInternalImage()->SamplesPerPixel == 2)
{
if(this->GetDataScalarType() == VTK_UNSIGNED_SHORT)
{
unsigned short* volume = reinterpret_cast<unsigned short*>(buffer);
volume += width*height*this->GetInternalImage()->SamplesPerPixel*page;
this->ReadTwoSamplesPerPixelImage( volume, width, height );
}
else if(this->GetDataScalarType() == VTK_SHORT)
{
short* volume = reinterpret_cast<short*>(buffer);
volume += width*height*this->GetInternalImage()->SamplesPerPixel*page;
this->ReadTwoSamplesPerPixelImage( volume, width, height );
}
else if(this->GetDataScalarType() == VTK_CHAR)
{
char* volume = reinterpret_cast<char*>(buffer);
volume += width*height*this->GetInternalImage()->SamplesPerPixel*page;
this->ReadTwoSamplesPerPixelImage( volume, width, height );
}
else
{
unsigned char* volume = reinterpret_cast<unsigned char*>(buffer);
volume += width*height*this->GetInternalImage()->SamplesPerPixel*page;
this->ReadTwoSamplesPerPixelImage( volume, width, height );
}
break;
}
else if ( !this->GetInternalImage()->CanRead() )
{
uint32 *tempImage;
tempImage = new uint32[ width * height ];
if ( !TIFFReadRGBAImage(this->GetInternalImage()->Image,
width, height,
tempImage, 1 ) )
{
vtkErrorMacro( << "Cannot read TIFF image or as a TIFF RGBA image" );
if ( tempImage != buffer )
{
delete [] tempImage;
}
return;
}
int xx, yy;
uint32* ssimage;
if(this->GetDataScalarType() == VTK_UNSIGNED_SHORT)
{
unsigned short *fimage = (unsigned short *)buffer;
fimage += width*height*4*page;
for ( yy = 0; yy < height; yy ++ )
{
ssimage = tempImage + (height - yy - 1) * width;
for ( xx = 0; xx < width; xx++ )
{
unsigned short red = static_cast<unsigned short>(TIFFGetR(*ssimage));
unsigned short green = static_cast<unsigned short>(TIFFGetG(*ssimage));
unsigned short blue = static_cast<unsigned short>(TIFFGetB(*ssimage));
unsigned short alpha = static_cast<unsigned short>(TIFFGetA(*ssimage));
*(fimage ) = red;
*(fimage+1) = green;
*(fimage+2) = blue;
*(fimage+3) = alpha;
fimage += 4;
ssimage ++;
}
}
}
else if(this->GetDataScalarType() == VTK_SHORT)
{
short *fimage = (short *)buffer;
fimage += width*height*4*page;
for ( yy = 0; yy < height; yy ++ )
{
ssimage = tempImage + (height - yy - 1) * width;
for ( xx = 0; xx < width; xx++ )
{
short red = static_cast<short>(TIFFGetR(*ssimage));
short green = static_cast<short>(TIFFGetG(*ssimage));
short blue = static_cast<short>(TIFFGetB(*ssimage));
short alpha = static_cast<short>(TIFFGetA(*ssimage));
*(fimage ) = red;
*(fimage+1) = green;
*(fimage+2) = blue;
*(fimage+3) = alpha;
fimage += 4;
ssimage ++;
}
}
}
else if(this->GetDataScalarType() == VTK_CHAR)