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ENH: Support for binary point file (.bin) reading and writing #943

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ENH: Support for binary point file (.bin) reading and writing #943

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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -38,3 +38,5 @@ CMakeFiles/
CTestTestfile.cmake
.idea/
.githooks/clangFormatMac
/cmake-build-debug/
/build/
Comment on lines +41 to +42
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I would like to see this as a separate commit. (Following the principle of "One Commit. One Change.") Why do those directories appear in your source tree? Are they specific to a particular tool or platform? I'm fine with the change itself, but I would like some clarification!

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Hi, sorry for the late reply due to other obligations.
This can be safely ignored, i did not realize this change in .gitignore

6 changes: 6 additions & 0 deletions Common/itkTransformixInputPointFileReader.h
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Expand Up @@ -83,6 +83,11 @@ class ITK_TEMPLATE_EXPORT TransformixInputPointFileReader : public MeshFileReade
*/
itkGetConstMacro(NumberOfPoints, unsigned long);

/** Get and set whether to read the points from a binary file.
*/
itkGetConstMacro(Binary, bool);
itkSetMacro(Binary, bool);

/** Prepare the allocation of the output mesh during the first back
* propagation of the pipeline. Updates the PointsAreIndices and NumberOfPoints.
*/
Expand All @@ -100,6 +105,7 @@ class ITK_TEMPLATE_EXPORT TransformixInputPointFileReader : public MeshFileReade
private:
unsigned long m_NumberOfPoints{ 0 };
bool m_PointsAreIndices{ false };
bool m_Binary{ false };

std::ifstream m_Reader{};
};
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91 changes: 71 additions & 20 deletions Common/itkTransformixInputPointFileReader.hxx
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Expand Up @@ -40,30 +40,60 @@ TransformixInputPointFileReader<TOutputMesh>::GenerateOutputInformation()
{
this->m_Reader.close();
}
this->m_Reader.open(this->m_FileName);

/** Read the first entry */
std::string indexOrPoint;
this->m_Reader >> indexOrPoint;
if( this->m_Binary ) {
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We use automatic code formatting by clang-format. It looks like this code still needs to be formatted that way, as I would expect it to place the { on the next line. (We use a specific (old) version of clang-format: 8.0.1) No problem, of course, we can fix that later.

this->m_Reader.open(this->m_FileName, std::ios::binary);

/** Read index flag */
unsigned long isindex;
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I'm sorry to say the use of (signed or unsigned) long is problematic, because its size differs between currently supported platforms and compilers. On Linux/GCC it's typically 64 bits, whereas on Windows/MSVC, it's 32 bits. If you want to write unsigned integers on one platform and read them back on another, better use either uint32_t or uint64_t. (In general use cases, unsigned int is usually fine, as it is the "default" unsigned type, and it's 32-bits on all supported platforms.)

this->m_Reader.read((char*) &isindex, sizeof(isindex));
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Instead of C-style (char*) cast, please use reinterpret_cast<const char *>. C-style casts are generally considered unsafe.


if( isindex == 0 )
{
/** Input points are specified in world coordinates. */
this->m_PointsAreIndices = false;
}
else //if( indexOrPoint == 1 )
{
/** Input points are specified as image indices. */
this->m_PointsAreIndices = true;
}

/** Read number of points */
unsigned long nrofpoints;
this->m_Reader.read((char*) &nrofpoints, sizeof(nrofpoints));
this->m_NumberOfPoints = nrofpoints;

/** Leave the file open for the generate data method */

/** Set the IsIndex bool and the number of points.*/
if (indexOrPoint == "point")
{
/** Input points are specified in world coordinates. */
this->m_PointsAreIndices = false;
this->m_Reader >> this->m_NumberOfPoints;
}
else if (indexOrPoint == "index")
{
/** Input points are specified as image indices. */
this->m_PointsAreIndices = true;
this->m_Reader >> this->m_NumberOfPoints;
}
else
else //if( this->m_Binary )
{
/** Input points are assumed to be specified as image indices. */
this->m_PointsAreIndices = true;
this->m_NumberOfPoints = atoi(indexOrPoint.c_str());
this->m_Reader.open(this->m_FileName);

/** Read the first entry */
std::string indexOrPoint;
this->m_Reader >> indexOrPoint;

/** Set the IsIndex bool and the number of points.*/
if (indexOrPoint == "point")
{
/** Input points are specified in world coordinates. */
this->m_PointsAreIndices = false;
this->m_Reader >> this->m_NumberOfPoints;
}
else if (indexOrPoint == "index")
{
/** Input points are specified as image indices. */
this->m_PointsAreIndices = true;
this->m_Reader >> this->m_NumberOfPoints;
}
else
{
/** Input points are assumed to be specified as image indices. */
this->m_PointsAreIndices = true;
this->m_NumberOfPoints = atoi(indexOrPoint.c_str());
}
}

/** Leave the file open for the generate data method */
Expand All @@ -90,6 +120,27 @@ TransformixInputPointFileReader<TOutputMesh>::GenerateData()
/** Read the file */
if (this->m_Reader.is_open())
{
if( this->m_Binary ){
for( unsigned long i = 0; i < this->m_NumberOfPoints; ++i )
{
// read point from binary file
PointType point;

if( !this->m_Reader.eof() )
{
this->m_Reader.read((char*) &point, sizeof(point));
} else {
std::ostringstream msg;
msg << "The file is not large enough. "
<< std::endl << "Filename: " << this->m_FileName
<< std::endl;
MeshFileReaderException e( __FILE__, __LINE__, msg.str().c_str(), ITK_LOCATION );
throw e;
}
points->push_back( point );
}
}
else //if( this->m_Binary ){
for (unsigned int i = 0; i < this->m_NumberOfPoints; ++i)
{
// read point from textfile
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2 changes: 1 addition & 1 deletion Core/ComponentBaseClasses/elxTransformBase.h
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Expand Up @@ -399,7 +399,7 @@ class ITK_TEMPLATE_EXPORT TransformBase : public BaseComponentSE<TElastix>

/** Function to transform coordinates from fixed to moving image. */
void
TransformPointsSomePoints(const std::string & filename) const;
TransformPointsSomePoints(const std::string & filename, const bool binary = false) const;

/** Function to transform coordinates from fixed to moving image, given as VTK file. */
void
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125 changes: 83 additions & 42 deletions Core/ComponentBaseClasses/elxTransformBase.hxx
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Expand Up @@ -686,6 +686,11 @@ TransformBase<TElastix>::TransformPoints() const
log::info(" The transform is evaluated on some points, specified in a VTK input point file.");
this->TransformPointsSomePointsVTK(def);
}
else if (itksys::SystemTools::StringEndsWith(def, ".bin") || itksys::SystemTools::StringEndsWith(def, ".BIN"))
{
log::info(" The transform is evaluated on some points, specified in a binary input point file.");
this->TransformPointsSomePoints(def, true);
}
else
{
log::info(" The transform is evaluated on some points, specified in the input point file.");
Expand Down Expand Up @@ -721,7 +726,7 @@ TransformBase<TElastix>::TransformPoints() const

template <class TElastix>
void
TransformBase<TElastix>::TransformPointsSomePoints(const std::string & filename) const
TransformBase<TElastix>::TransformPointsSomePoints(const std::string & filename, const bool binary) const
{
/** Typedef's. */
using FixedImageRegionType = typename FixedImageType::RegionType;
Expand All @@ -739,6 +744,7 @@ TransformBase<TElastix>::TransformPointsSomePoints(const std::string & filename)
/** Construct an ipp-file reader. */
const auto ippReader = itk::TransformixInputPointFileReader<PointSetType>::New();
ippReader->SetFileName(filename);
ippReader->SetBinary(binary);

/** Read the input points. */
log::info(std::ostringstream{} << " Reading input point file: " << filename);
Expand All @@ -760,7 +766,7 @@ TransformBase<TElastix>::TransformPointsSomePoints(const std::string & filename)
{
log::info(" Input points are specified in world coordinates.");
}
const unsigned int nrofpoints = ippReader->GetNumberOfPoints();
const unsigned long nrofpoints = ippReader->GetNumberOfPoints();
log::info(std::ostringstream{} << " Number of specified input points: " << nrofpoints);

/** Get the set of input points. */
Expand Down Expand Up @@ -794,7 +800,7 @@ TransformBase<TElastix>::TransformPointsSomePoints(const std::string & filename)
/** Read the input points, as index or as point. */
if (ippReader->GetPointsAreIndices())
{
for (unsigned int j = 0; j < nrofpoints; ++j)
for (unsigned long j = 0; j < nrofpoints; ++j)
{
/** The read point from the inutPointSet is actually an index
* Cast to the proper type.
Expand All @@ -811,7 +817,7 @@ TransformBase<TElastix>::TransformPointsSomePoints(const std::string & filename)
}
else
{
for (unsigned int j = 0; j < nrofpoints; ++j)
for (unsigned long j = 0; j < nrofpoints; ++j)
{
/** Compute index of nearest voxel in fixed image. */
InputPointType point{};
Expand All @@ -827,7 +833,7 @@ TransformBase<TElastix>::TransformPointsSomePoints(const std::string & filename)

/** Apply the transform. */
log::info(" The input points are transformed.");
for (unsigned int j = 0; j < nrofpoints; ++j)
for (unsigned long j = 0; j < nrofpoints; ++j)
{
/** Call TransformPoint. */
outputpointvec[j] = this->GetAsITKBaseType()->TransformPoint(inputpointvec[j]);
Expand Down Expand Up @@ -860,50 +866,85 @@ TransformBase<TElastix>::TransformPointsSomePoints(const std::string & filename)
!outputDirectoryPath.empty())
{
/** Create filename and file stream. */
const std::string outputPointsFileName = outputDirectoryPath + "outputpoints.txt";
std::ofstream outputPointsFile(outputPointsFileName);
const std::string extension = binary ? "bin" : "txt";
const std::string outputPointsFileName = outputDirectoryPath + "outputpoints." + extension;

std::ofstream outputPointsFile(outputPointsFileName, binary ? std::ios_base::binary : std::ios_base::out );
outputPointsFile << std::showpoint << std::fixed;
log::info(std::ostringstream{} << " The transformed points are saved in: " << outputPointsFileName);

const auto writeToFile = [&outputPointsFile](const auto & rangeOfElements) {
for (const auto element : rangeOfElements)
{
outputPointsFile << element << ' ';
}
};

/** Print the results. */
for (unsigned int j = 0; j < nrofpoints; ++j)
{
/** The input index. */
outputPointsFile << "Point\t" << j << "\t; InputIndex = [ ";
writeToFile(inputindexvec[j]);

/** The input point. */
outputPointsFile << "]\t; InputPoint = [ ";
writeToFile(inputpointvec[j]);

/** The output index in fixed image. */
outputPointsFile << "]\t; OutputIndexFixed = [ ";
writeToFile(outputindexfixedvec[j]);
/** Write the results. */

/** The output point. */
outputPointsFile << "]\t; OutputPoint = [ ";
writeToFile(outputpointvec[j]);
if (binary) { //Note: for speed, write the transformed points only
unsigned long isindex = ippReader->GetPointsAreIndices() ? 1 : 0;
outputPointsFile.write((char*) &isindex, sizeof(isindex));

/** The output point minus the input point. */
outputPointsFile << "]\t; Deformation = [ ";
writeToFile(deformationvec[j]);
unsigned long numberOfPoints = nrofpoints;
outputPointsFile.write((char*) &numberOfPoints, sizeof(numberOfPoints));

if (alsoMovingIndices)
for( unsigned int j = 0; j < nrofpoints; j++ )
{
/** The output index in moving image. */
outputPointsFile << "]\t; OutputIndexMoving = [ ";
writeToFile(outputindexmovingvec[j]);
}

outputPointsFile << "]" << std::endl;
} // end for nrofpoints
if ( ippReader->GetPointsAreIndices() )
{
/** The output index in fixed image. */
for( unsigned int i = 0; i < FixedImageDimension; i++ )
{
outputPointsFile.write((char*) &outputindexfixedvec[ j ][ i ], sizeof(outputindexfixedvec[ j ][ i ]) );
}
}
else
{
/** The output point. */
for( unsigned int i = 0; i < FixedImageDimension; i++ )
{
outputPointsFile.write((char*) &outputpointvec[ j ][ i ], sizeof(outputpointvec[ j ][ i ]) );
}
}
} // end for nrofpoints

outputPointsFile.close();
}
else //if (binary)
{
const auto writeToFile = [&outputPointsFile](const auto & rangeOfElements) {
for (const auto element : rangeOfElements)
{
outputPointsFile << element << ' ';
}
};

for (unsigned int j = 0; j < nrofpoints; ++j)
{
/** The input index. */
outputPointsFile << "Point\t" << j << "\t; InputIndex = [ ";
writeToFile(inputindexvec[j]);

/** The input point. */
outputPointsFile << "]\t; InputPoint = [ ";
writeToFile(inputpointvec[j]);

/** The output index in fixed image. */
outputPointsFile << "]\t; OutputIndexFixed = [ ";
writeToFile(outputindexfixedvec[j]);

/** The output point. */
outputPointsFile << "]\t; OutputPoint = [ ";
writeToFile(outputpointvec[j]);

/** The output point minus the input point. */
outputPointsFile << "]\t; Deformation = [ ";
writeToFile(deformationvec[j]);

if (alsoMovingIndices)
{
/** The output index in moving image. */
outputPointsFile << "]\t; OutputIndexMoving = [ ";
writeToFile(outputindexmovingvec[j]);
}

outputPointsFile << "]" << std::endl;
} // end for nrofpoints
}
}

} // end TransformPointsSomePoints()
Expand Down