/*=========================================================================

  Program:   Visualization Toolkit
  Module:    vtkImageReader.cxx
  Language:  C++
  Date:      $Date$
  Version:   $Revision$

  Copyright (c) 1993-2002 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 "vtkImageReader.h"

#include "vtkByteSwap.h"
#include "vtkImageData.h"
#include "vtkObjectFactory.h"
#include "vtkTransform.h"

vtkCxxRevisionMacro(vtkImageReader, "1.107");
vtkStandardNewMacro(vtkImageReader);

vtkCxxSetObjectMacro(vtkImageReader,Transform,vtkTransform);

#ifdef read
#undef read
#endif

#ifdef close
#undef close
#endif

//----------------------------------------------------------------------------
vtkImageReader::vtkImageReader()
{
  int idx;
  
  for (idx = 0; idx < 3; ++idx)
    {
    this->DataVOI[idx*2] = this->DataVOI[idx*2 + 1] = 0;
    }
  
  // Left over from short reader
  this->DataMask = 0xffff;
  this->Transform = NULL;
}

//----------------------------------------------------------------------------
vtkImageReader::~vtkImageReader()
{ 
  this->SetTransform(NULL);
}





//----------------------------------------------------------------------------
void vtkImageReader::PrintSelf(ostream& os, vtkIndent indent)
{
  int idx;
  
  this->Superclass::PrintSelf(os,indent);

  os << indent << "Data Mask: " << this->DataMask << "\n";
  os << indent << "DataVOI: (" << this->DataVOI[0];
  for (idx = 1; idx < 6; ++idx)
    {
    os << ", " << this->DataVOI[idx];
    }
  os << ")\n";
  if ( this->Transform )
    {
    os << indent << "Transform: " << this->Transform << "\n";
    }
  else
    {
    os << indent << "Transform: (none)\n";
    }
}


//----------------------------------------------------------------------------
// This method returns the largest data that can be generated.
void vtkImageReader::ExecuteInformation()
{
  vtkImageData *output = this->GetOutput();
  float spacing[3];
  int extent[6];
  float origin[3];
  
  
  // set the extent, if the VOI has not been set then default to
  // the DataExtent
  if (this->DataVOI[0] || this->DataVOI[1] || 
      this->DataVOI[2] || this->DataVOI[3] || 
      this->DataVOI[4] || this->DataVOI[5])
    {
    this->ComputeTransformedExtent(this->DataVOI,extent);
    output->SetWholeExtent(extent);
    }
  else
    {
    this->ComputeTransformedExtent(this->DataExtent,extent);
    output->SetWholeExtent(extent);
    }
    
  // set the spacing
  this->ComputeTransformedSpacing(spacing);
  output->SetSpacing(spacing);

  // set the origin.
  this->ComputeTransformedOrigin(origin);
  output->SetOrigin(origin);

  output->SetScalarType(this->DataScalarType);
  output->SetNumberOfScalarComponents(this->NumberOfScalarComponents);
}



int vtkImageReader::OpenAndSeekFile(int dataExtent[6], int idx)
{
  unsigned long streamStart;

  if (!this->FileName && !this->FilePattern)
    {
    vtkErrorMacro(<<"Either a FileName or FilePattern must be specified.");
    return 0;
    }
  this->ComputeInternalFileName(idx);
  this->OpenFile();
  if ( !this->File )
    {
    return 0;
    }
  // convert data extent into constants that can be used to seek.
  streamStart = 
    (dataExtent[0] - this->DataExtent[0]) * this->DataIncrements[0];
  
  if (this->FileLowerLeft)
    {
    streamStart = streamStart + 
      (dataExtent[2] - this->DataExtent[2]) * this->DataIncrements[1];
    }
  else
    {
    streamStart = streamStart + 
      (this->DataExtent[3] - this->DataExtent[2] - dataExtent[2]) * 
      this->DataIncrements[1];
    }
  
  // handle three and four dimensional files
  if (this->GetFileDimensionality() >= 3)
    {
    streamStart = streamStart + 
      (dataExtent[4] - this->DataExtent[4]) * this->DataIncrements[2];
    }
  
  streamStart += this->GetHeaderSize(idx);
  
  // error checking
  this->File->seekg((long)streamStart, ios::beg);
  if (this->File->fail())
    {
    vtkErrorMacro(<< "File operation failed: " << streamStart << ", ext: "
                  << dataExtent[0] << ", " << dataExtent[1] << ", "
                  << dataExtent[2] << ", " << dataExtent[3] << ", "
                  << dataExtent[4] << ", " << dataExtent[5]);
    vtkErrorMacro(<< "Header size: " << this->GetHeaderSize(idx) << ", file ext: "
                  << this->DataExtent[0] << ", " << this->DataExtent[1] << ", "
                  << this->DataExtent[2] << ", " << this->DataExtent[3] << ", "
                  << this->DataExtent[4] << ", " << this->DataExtent[5]);
    return 0;
    }
  return 1;        
}

//----------------------------------------------------------------------------
// This function reads in one data of data.
// templated to handle different data types.
template <class IT, class OT>
void vtkImageReaderUpdate2(vtkImageReader *self, vtkImageData *data,
                           IT *inPtr, OT *outPtr)
{
  int inIncr[3], outIncr[3];
  OT *outPtr0, *outPtr1, *outPtr2;
  long streamSkip0, streamSkip1;
  unsigned long streamRead;
  int idx0, idx1, idx2, pixelRead;
  unsigned char *buf;
  int inExtent[6];
  int dataExtent[6];
  int comp, pixelSkip;
  long filePos, correction = 0;
  unsigned long count = 0;
  unsigned short DataMask;
  unsigned long target;
  
  // Get the requested extents.
  data->GetExtent(inExtent);
  // Convert them into to the extent needed from the file. 
  self->ComputeInverseTransformedExtent(inExtent,dataExtent);
  
  // get and transform the increments
  data->GetIncrements(inIncr);
  self->ComputeInverseTransformedIncrements(inIncr,outIncr);

  DataMask = self->GetDataMask();

  // compute outPtr2 
  outPtr2 = outPtr;
  if (outIncr[0] < 0) 
    {
    outPtr2 = outPtr2 - outIncr[0]*(dataExtent[1] - dataExtent[0]);
    }
  if (outIncr[1] < 0) 
    {
    outPtr2 = outPtr2 - outIncr[1]*(dataExtent[3] - dataExtent[2]);
    }
  if (outIncr[2] < 0) 
    {
    outPtr2 = outPtr2 - outIncr[2]*(dataExtent[5] - dataExtent[4]);
    }

  // length of a row, num pixels read at a time
  pixelRead = dataExtent[1] - dataExtent[0] + 1; 
  streamRead = static_cast<unsigned long>(pixelRead * 
                                          self->GetDataIncrements()[0]);  
  streamSkip0 = (long)(self->GetDataIncrements()[1] - streamRead);
  streamSkip1 = (long)(self->GetDataIncrements()[2] - 
    (dataExtent[3] - dataExtent[2] + 1)* self->GetDataIncrements()[1]);
  pixelSkip = data->GetNumberOfScalarComponents();
    
  // read from the bottom up
  if (!self->GetFileLowerLeft()) 
    {
    streamSkip0 = (long)(-static_cast<long>(streamRead) 
                         - self->GetDataIncrements()[1]);
    streamSkip1 = (long)(self->GetDataIncrements()[2] + 
      (dataExtent[3] - dataExtent[2] + 1)* self->GetDataIncrements()[1]);
    }
  
    
  // create a buffer to hold a row of the data
  buf = new unsigned char[streamRead];
  
  target = (unsigned long)((dataExtent[5]-dataExtent[4]+1)*
                           (dataExtent[3]-dataExtent[2]+1)/50.0);
  target++;

  // read the data row by row
  if (self->GetFileDimensionality() == 3)
    {
    if ( !self->OpenAndSeekFile(dataExtent,0) )
      {
      delete [] buf;
      return;
      }
    }
  for (idx2 = dataExtent[4]; idx2 <= dataExtent[5]; ++idx2)
    {
    if (self->GetFileDimensionality() == 2)
      {
      if ( !self->OpenAndSeekFile(dataExtent,idx2) )
        {
        delete [] buf;
        return;
        }
      }
    outPtr1 = outPtr2;
    for (idx1 = dataExtent[2]; 
         !self->AbortExecute && idx1 <= dataExtent[3]; ++idx1)
      {
      if (!(count%target))
        {
        self->UpdateProgress(count/(50.0*target));
        }
      count++;
      outPtr0 = outPtr1;

      // read the row.
      self->GetFile()->read((char *)buf, streamRead);
#ifdef __APPLE_CC__
      if (static_cast<unsigned long>(self->GetFile()->gcount()) != streamRead)
      // Apple's gcc3 returns fail when reading _to_ eof
#else
      if ( static_cast<unsigned long>(self->GetFile()->gcount()) != 
           streamRead || self->GetFile()->fail())
#endif
        {
        vtkGenericWarningMacro("File operation failed. row = " << idx1
                               << ", Tried to Read = " << streamRead
                               << ", Read = " << self->GetFile()->gcount()
                               << ", Skip0 = " << streamSkip0
                               << ", Skip1 = " << streamSkip1
                               << ", FilePos = " << self->GetFile()->tellg());
        delete [] buf;
        return;
        }
      // handle swapping
      if (self->GetSwapBytes())
        {
        // pixelSkip is the number of components in data
        vtkByteSwap::SwapVoidRange(buf, pixelRead*pixelSkip, sizeof(IT));
        }
      
      // copy the bytes into the typed data
      inPtr = (IT *)(buf);
      for (idx0 = dataExtent[0]; idx0 <= dataExtent[1]; ++idx0)
        {
        // Copy pixel into the output.
        if (DataMask == 0xffff)
          {
          for (comp = 0; comp < pixelSkip; comp++)
            {
            outPtr0[comp] = (OT)(inPtr[comp]);
            }
          }
        else
          {
          // left over from short reader (what about other types.
          for (comp = 0; comp < pixelSkip; comp++)
            {
            outPtr0[comp] = (OT)((short)(inPtr[comp]) & DataMask);
            }
          }
        // move to next pixel
        inPtr += pixelSkip;
        outPtr0 += outIncr[0];
        }

      // move to the next row in the file and data
      filePos = self->GetFile()->tellg();

/* Unfortunately this doesn't work as a fix, but I'll leave it here for a bit
   to provoke ideas.
      if (filePos == -1)
        {
        self->GetFile()->clear(self->GetFile()->rdstate() & ~ios::eofbit);
        self->GetFile()->clear(self->GetFile()->rdstate() & ~ios::failbit);
        filePos = self->GetFile()->tellg();
        }
*/
#if defined(VTK_USE_ANSI_STDLIB ) && ((defined(__sgi) && !defined(__GNUC__)) \
    || (__BORLANDC__>=0x0560) || defined (__APPLE_CC__))
      // this check is required for SGI's when vtk is build with VTK_USE_ANSI_STDLIB
      // seems that after a read that just reaches EOF, tellg reports a -1.
      // clear() does not work, so we have to reopen the file.
      // NB: Also Borland CBuilder 6 suffers from same trouble
      // As does Apple's gcc3
      if (filePos == -1)
        {
        self->OpenFile();
        self->GetFile()->seekg(0,ios::end);
        filePos = self->GetFile()->tellg();
        }
#endif
      // watch for case where we might rewind too much
      // if that happens, store the value in correction and apply later
      if (filePos + streamSkip0 >= 0)
        {
        self->GetFile()->seekg(self->GetFile()->tellg() + streamSkip0, ios::beg);
        correction = 0;
        }
      else
        {
        correction = streamSkip0;
        }
      outPtr1 += outIncr[1];
      }
    // move to the next image in the file and data
    self->GetFile()->seekg(self->GetFile()->tellg() + streamSkip1 + correction, 
                      ios::beg);
    outPtr2 += outIncr[2];
    }

  // delete the temporary buffer
  delete [] buf;
}


//----------------------------------------------------------------------------
// This function reads in one data of one slice.
// templated to handle different data types.
template <class T>
void vtkImageReaderUpdate1(vtkImageReader *self, vtkImageData *data, T *inPtr)
{
  void *outPtr;

  // Call the correct templated function for the input
  outPtr = data->GetScalarPointer();
  switch (data->GetScalarType())
    {
    vtkTemplateMacro4(vtkImageReaderUpdate2, self, data, inPtr, 
                      (VTK_TT *)(outPtr));
    default:
      vtkGenericWarningMacro("Update1: Unknown data type\n");
    }  
}
//----------------------------------------------------------------------------
// This function reads a data from a file.  The datas extent/axes
// are assumed to be the same as the file extent/order.
void vtkImageReader::ExecuteData(vtkDataObject *output)
{
  vtkImageData *data = this->AllocateOutputData(output);
  
  void *ptr = NULL;
  int *ext;

  if (!this->FileName && !this->FilePattern)
    {
    vtkErrorMacro("Either a valid FileName or FilePattern must be specified.");
    return;
    }

  ext = data->GetExtent();

  data->GetPointData()->GetScalars()->SetName("ImageFile");

  vtkDebugMacro("Reading extent: " << ext[0] << ", " << ext[1] << ", " 
        << ext[2] << ", " << ext[3] << ", " << ext[4] << ", " << ext[5]);
  
  this->ComputeDataIncrements();
  
  // Call the correct templated function for the output
  switch (this->GetDataScalarType())
    {
    vtkTemplateMacro3(vtkImageReaderUpdate1, this, data, (VTK_TT *)(ptr));
    default:
      vtkErrorMacro(<< "UpdateFromFile: Unknown data type");
    }   
}





void vtkImageReader::ComputeTransformedSpacing (float Spacing[3])
{
  if (!this->Transform)
    {
    memcpy (Spacing, this->DataSpacing, 3 * sizeof (float));
    }
  else
    {
    float transformedSpacing[3];
    memcpy (transformedSpacing, this->DataSpacing, 3 * sizeof (float));
    this->Transform->TransformVector(transformedSpacing, transformedSpacing);

    for (int i = 0; i < 3; i++)
      {
      Spacing[i] = fabs(transformedSpacing[i]);
      }
    vtkDebugMacro("Transformed Spacing " << Spacing[0] << ", " << Spacing[1] << ", " << Spacing[2]);
    }
}

// if the spacing is negative we need to tranlate the origin
// basically O' = O + spacing*(dim-1) for any axis that would
// have a negative spaing
void vtkImageReader::ComputeTransformedOrigin (float origin[3])
{
  if (!this->Transform)
    {
    memcpy (origin, this->DataOrigin, 3 * sizeof (float));
    }
  else
    {
    float transformedOrigin[3];
    float transformedSpacing[3];
    int transformedExtent[6];
    
    memcpy (transformedSpacing, this->DataSpacing, 3 * sizeof (float));
    this->Transform->TransformVector(transformedSpacing, transformedSpacing);

    memcpy (transformedOrigin, this->DataOrigin, 3 * sizeof (float));
    this->Transform->TransformPoint(transformedOrigin, transformedOrigin);

    this->ComputeTransformedExtent(this->DataExtent,transformedExtent);
    
    for (int i = 0; i < 3; i++) 
      {
      if (transformedSpacing[i] < 0)
        {
        origin[i] = transformedOrigin[i] + transformedSpacing[i]*
          (transformedExtent[i*2+1] -  transformedExtent[i*2] + 1);
        }
      else
        {
        origin[i] = transformedOrigin[i];
        }
      }
    vtkDebugMacro("Transformed Origin " << origin[0] << ", " << origin[1] << ", " << origin[2]);
    }
}

void vtkImageReader::ComputeTransformedExtent(int inExtent[6],
                                              int outExtent[6])
{
  float transformedExtent[3];
  int temp;
  int idx;
  int dataExtent[6];
  
  if (!this->Transform)
    {
    memcpy (outExtent, inExtent, 6 * sizeof (int));
    memcpy (dataExtent, this->DataExtent, 6 * sizeof(int));
    }
  else
    {
    // need to know how far to translate to start at 000
    // first transform the data extent
    transformedExtent[0] = this->DataExtent[0];
    transformedExtent[1] = this->DataExtent[2];
    transformedExtent[2] = this->DataExtent[4];
    this->Transform->TransformPoint(transformedExtent, transformedExtent);
    dataExtent[0] = (int) transformedExtent[0];
    dataExtent[2] = (int) transformedExtent[1];
    dataExtent[4] = (int) transformedExtent[2];
    
    transformedExtent[0] = this->DataExtent[1];
    transformedExtent[1] = this->DataExtent[3];
    transformedExtent[2] = this->DataExtent[5];
    this->Transform->TransformPoint(transformedExtent, transformedExtent);
    dataExtent[1] = (int) transformedExtent[0];
    dataExtent[3] = (int) transformedExtent[1];
    dataExtent[5] = (int) transformedExtent[2];

    for (idx = 0; idx < 6; idx += 2)
      {
      if (dataExtent[idx] > dataExtent[idx+1]) 
        {
        temp = dataExtent[idx];
        dataExtent[idx] = dataExtent[idx+1];
        dataExtent[idx+1] = temp;
        }
      }

    // now transform the inExtent
    transformedExtent[0] = inExtent[0];
    transformedExtent[1] = inExtent[2];
    transformedExtent[2] = inExtent[4];
    this->Transform->TransformPoint(transformedExtent, transformedExtent);
    outExtent[0] = (int) transformedExtent[0];
    outExtent[2] = (int) transformedExtent[1];
    outExtent[4] = (int) transformedExtent[2];
    
    transformedExtent[0] = inExtent[1];
    transformedExtent[1] = inExtent[3];
    transformedExtent[2] = inExtent[5];
    this->Transform->TransformPoint(transformedExtent, transformedExtent);
    outExtent[1] = (int) transformedExtent[0];
    outExtent[3] = (int) transformedExtent[1];
    outExtent[5] = (int) transformedExtent[2];
    }

  for (idx = 0; idx < 6; idx += 2)
    {
    if (outExtent[idx] > outExtent[idx+1]) 
      {
      temp = outExtent[idx];
      outExtent[idx] = outExtent[idx+1];
      outExtent[idx+1] = temp;
      }
    // do the slide to 000 origin by subtracting the minimum extent
    outExtent[idx] -= dataExtent[idx];
    outExtent[idx+1] -= dataExtent[idx];
    }
  
  vtkDebugMacro(<< "Transformed extent are:" 
  << outExtent[0] << ", " << outExtent[1] << ", "
  << outExtent[2] << ", " << outExtent[3] << ", "
  << outExtent[4] << ", " << outExtent[5]);
}

void vtkImageReader::ComputeInverseTransformedExtent(int inExtent[6],
                                                     int outExtent[6])
{
  float transformedExtent[3];
  int temp;
  int idx;
  
  if (!this->Transform)
    {
    memcpy (outExtent, inExtent, 6 * sizeof (int));
    for (idx = 0; idx < 6; idx += 2)
      {
      // do the slide to 000 origin by subtracting the minimum extent
      outExtent[idx] += this->DataExtent[idx];
      outExtent[idx+1] += this->DataExtent[idx];
      }
    }
  else
    {
    // need to know how far to translate to start at 000
    int dataExtent[6];
    // first transform the data extent
    transformedExtent[0] = this->DataExtent[0];
    transformedExtent[1] = this->DataExtent[2];
    transformedExtent[2] = this->DataExtent[4];
    this->Transform->TransformPoint(transformedExtent, transformedExtent);
    dataExtent[0] = (int) transformedExtent[0];
    dataExtent[2] = (int) transformedExtent[1];
    dataExtent[4] = (int) transformedExtent[2];
    
    transformedExtent[0] = this->DataExtent[1];
    transformedExtent[1] = this->DataExtent[3];
    transformedExtent[2] = this->DataExtent[5];
    this->Transform->TransformPoint(transformedExtent, transformedExtent);
    dataExtent[1] = (int) transformedExtent[0];
    dataExtent[3] = (int) transformedExtent[1];
    dataExtent[5] = (int) transformedExtent[2];

    for (idx = 0; idx < 6; idx += 2)
      {
      if (dataExtent[idx] > dataExtent[idx+1]) 
        {
        temp = dataExtent[idx];
        dataExtent[idx] = dataExtent[idx+1];
        dataExtent[idx+1] = temp;
        }
      }

    for (idx = 0; idx < 6; idx += 2)
      {
      // do the slide to 000 origin by subtracting the minimum extent
      inExtent[idx] += dataExtent[idx];
      inExtent[idx+1] += dataExtent[idx];
      }

    transformedExtent[0] = inExtent[0];
    transformedExtent[1] = inExtent[2];
    transformedExtent[2] = inExtent[4];
    this->Transform->GetLinearInverse()->TransformPoint(transformedExtent, 
                                                        transformedExtent);
    outExtent[0] = (int) transformedExtent[0];
    outExtent[2] = (int) transformedExtent[1];
    outExtent[4] = (int) transformedExtent[2];
    
    transformedExtent[0] = inExtent[1];
    transformedExtent[1] = inExtent[3];
    transformedExtent[2] = inExtent[5];
    this->Transform->GetLinearInverse()->TransformPoint(transformedExtent,
                                                        transformedExtent);
    outExtent[1] = (int) transformedExtent[0];
    outExtent[3] = (int) transformedExtent[1];
    outExtent[5] = (int) transformedExtent[2];

    for (idx = 0; idx < 6; idx += 2)
      {
      if (outExtent[idx] > outExtent[idx+1]) 
        {
        temp = outExtent[idx];
        outExtent[idx] = outExtent[idx+1];
        outExtent[idx+1] = temp;
        }
      }
    }
    
    vtkDebugMacro(<< "Inverse Transformed extent are:" 
    << outExtent[0] << ", " << outExtent[1] << ", "
    << outExtent[2] << ", " << outExtent[3] << ", "
    << outExtent[4] << ", " << outExtent[5]);
}

void vtkImageReader::ComputeTransformedIncrements(int inIncr[3],
                                                  int outIncr[3])
{
  float transformedIncr[3];
  
  if (!this->Transform)
    {
    memcpy (outIncr, inIncr, 3 * sizeof (int));
    }
  else
    {
    transformedIncr[0] = inIncr[0];
    transformedIncr[1] = inIncr[1];
    transformedIncr[2] = inIncr[2];
    this->Transform->TransformVector(transformedIncr, transformedIncr);
    outIncr[0] = (int) transformedIncr[0];
    outIncr[1] = (int) transformedIncr[1];
    outIncr[2] = (int) transformedIncr[2];
    vtkDebugMacro(<< "Transformed Incr are:" 
    << outIncr[0] << ", " << outIncr[1] << ", " << outIncr[2]);
    }
}


void vtkImageReader::ComputeInverseTransformedIncrements(int inIncr[3],
                                                         int outIncr[3])
{
  float transformedIncr[3];
  
  if (!this->Transform)
    {
    memcpy (outIncr, inIncr, 3 * sizeof (int));
    }
  else
    {
    transformedIncr[0] = inIncr[0];
    transformedIncr[1] = inIncr[1];
    transformedIncr[2] = inIncr[2];
    this->Transform->GetLinearInverse()->TransformVector(transformedIncr,
                                                         transformedIncr);
    outIncr[0] = (int) transformedIncr[0];
    outIncr[1] = (int) transformedIncr[1];
    outIncr[2] = (int) transformedIncr[2];
    vtkDebugMacro(<< "Inverse Transformed Incr are:" 
    << outIncr[0] << ", " << outIncr[1] << ", " << outIncr[2]);
    }
}
