Adding support of Center-X/Y/Z for VolReader/Writer

ChangeLog.md

@@ -35,6 +35,12 @@
  ArithmeticalDSS) (Tristan Roussillon,
  [#819](https:/DGtal-team/DGtal/pull/819))
 
+- *IO Package*
+ - Now VolReader/VolWriter and LongvolReader/LongvolWriter support the 
+ usage of Center-(X,Y,Z) parameters, as described in Vol file 
+ specification. (Jérémy Levallois, 
+ [#879](https:/DGtal-team/DGtal/pull/879))
+
 - *Math Package*
 
  - New classes to compute nD eigen decomposition of symmetric

src/DGtal/io/readers/LongvolReader.ih

@@ -134,6 +134,7 @@ DGtal::LongvolReader<T, TFunctor>::importLongvol( const std::string & filename,
  }
 
  int sx = 0, sy = 0, sz=0;
+ int cx = 0, cy = 0, cz=0;
 
  getHeaderValueAsInt( "X", &sx, header );
  getHeaderValueAsInt( "Y", &sy, header );
@@ -179,19 +180,33 @@ DGtal::LongvolReader<T, TFunctor>::importLongvol( const std::string & filename,
  }
 
  //Raw Data
- long count = 0;
-
- firstPoint = T::Point::zero;
- lastPoint[0] = sx - 1;
- lastPoint[1] = sy - 1;
- lastPoint[2] = sz - 1;
+
+ if( getHeaderValueAsInt( "Center-X", &cx, header ) == 0 )
+ {
+ getHeaderValueAsInt( "Center-Y", &cy, header );
+ getHeaderValueAsInt( "Center-Z", &cz, header );
+
+ firstPoint[0] = cx - (sx - 1)/2;
+ firstPoint[1] = cy - (sy - 1)/2;
+ firstPoint[2] = cz - (sz - 1)/2;
+ lastPoint[0] = cx + sx/2;
+ lastPoint[1] = cy + sy/2;
+ lastPoint[2] = cz + sz/2;
+ }
+ else
+ {
+ firstPoint = T::Point::zero;
+ lastPoint[0] = sx - 1;
+ lastPoint[1] = sy - 1;
+ lastPoint[2] = sz - 1;
+ }
  typename T::Domain domain( firstPoint, lastPoint );
 
  try
  {
  T image( domain);
 
- count = 0;
+ long count = 0;
  DGtal::uint64_t val=0;
 
  typename T::Domain::ConstIterator it = domain.begin();
@@ -274,6 +289,6 @@ DGtal::LongvolReader<T, TFunctor>::getHeaderValueAsInt( const char *type, int *d
  if ( i == -1 )
  return 1;
 
- return sscanf( header[i].value, "%d", dest ) != 0;
+ return sscanf( header[i].value, "%d", dest ) == 0;
 }
 

src/DGtal/io/readers/VolReader.h

@@ -90,7 +90,7 @@ namespace DGtal
  // ----------------------- Standard services ------------------------------
 
  typedef TImageContainer ImageContainer;
- typedef typename TImageContainer::Value Value; 
+ typedef typename TImageContainer::Value Value;
  typedef TFunctor Functor;
 
  BOOST_CONCEPT_ASSERT(( CUnaryFunctor<TFunctor, unsigned char, Value > )) ; 

src/DGtal/io/readers/VolReader.ih

@@ -146,6 +146,7 @@ DGtal::VolReader<T, TFunctor>::importVol( const std::string & filename,
  }
 
  int sx = 0, sy= 0, sz= 0;
+ int cx = 0, cy= 0, cz= 0;
 
  getHeaderValueAsInt( "X", &sx, header );
  getHeaderValueAsInt( "Y", &sy, header );
@@ -191,19 +192,34 @@ DGtal::VolReader<T, TFunctor>::importVol( const std::string & filename,
  }
 
  //Raw Data
- long count = 0;
 
- firstPoint = T::Point::zero;
- lastPoint[0] = sx - 1;
- lastPoint[1] = sy - 1;
- lastPoint[2] = sz - 1;
+ if( getHeaderValueAsInt( "Center-X", &cx, header ) == 0 )
+ {
+ getHeaderValueAsInt( "Center-Y", &cy, header );
+ getHeaderValueAsInt( "Center-Z", &cz, header );
+
+ firstPoint[0] = cx - (sx - 1)/2;
+ firstPoint[1] = cy - (sy - 1)/2;
+ firstPoint[2] = cz - (sz - 1)/2;
+ lastPoint[0] = cx + sx/2;
+ lastPoint[1] = cy + sy/2;
+ lastPoint[2] = cz + sz/2;
+ }
+ else
+ {
+ firstPoint = T::Point::zero;
+ lastPoint[0] = sx - 1;
+ lastPoint[1] = sy - 1;
+ lastPoint[2] = sz - 1;
+ }
+
  typename T::Domain domain( firstPoint, lastPoint );
 
  try
  {
  T image( domain );
 
- count = 0;
+ long count = 0;
  unsigned char val;
  typename T::Domain::ConstIterator it = domain.begin();
  long int total = sx * sy * sz;
@@ -285,6 +301,6 @@ DGtal::VolReader<T, TFunctor>::getHeaderValueAsInt( const char *type, int *dest
  if ( i == -1 )
  return 1;
 
- return sscanf( header[i].value, "%d", dest ) != 0;
+ return sscanf( header[i].value, "%d", dest ) == 0;
 }
 

src/DGtal/io/writers/LongvolWriter.ih

@@ -47,16 +47,22 @@ namespace DGtal {
  DGtal::IOException dgtalio;
 
  std::ofstream out;
- typename I::Domain domain = aImage.domain(); 
+ typename I::Domain domain = aImage.domain(); 
+ const typename I::Domain::Point &upBound = domain.upperBound();
+ const typename I::Domain::Point &lowBound = domain.lowerBound(); 
  typename I::Domain::Point p = I::Domain::Point::diagonal(1);
- typename I::Domain::Vector size = (domain.upperBound() - domain.lowerBound()) + p;
+ typename I::Domain::Vector size = (upBound - lowBound) + p;
+ typename I::Domain::Vector center = lowBound + ((upBound - lowBound)/2);
  typename I::Value val;
 
  try
  {
  out.open(filename.c_str());
 
  //Longvol format
+ out << "Center-X: " << center[0] <<std::endl;
+ out << "Center-Y: " << center[1] <<std::endl;
+ out << "Center-Z: " << center[2] <<std::endl;
  out << "X: "<< size[0]<<std::endl;
  out << "Y: "<< size[1]<<std::endl;
  out << "Z: "<< size[2]<<std::endl;

src/DGtal/io/writers/VolWriter.ih

@@ -47,21 +47,23 @@ namespace DGtal {
  DGtal::IOException dgtalio;
 
  std::ofstream out;
- typename I::Domain::Vector size;
- const typename I::Domain::Point &upBound = aImage.domain().upperBound();
- const typename I::Domain::Point &lowBound = aImage.domain().lowerBound();
- size[0]=upBound[0]-lowBound[0]+1;
- size[1]=upBound[1]-lowBound[1]+1;
- size[2]=upBound[2]-lowBound[2]+1;
-
  typename I::Domain domain = aImage.domain();
+ const typename I::Domain::Point &upBound = domain.upperBound();
+ const typename I::Domain::Point &lowBound = domain.lowerBound();
+ typename I::Domain::Point p = I::Domain::Point::diagonal(1);
+ typename I::Domain::Vector size = (upBound - lowBound) + p;
+ typename I::Domain::Vector center = lowBound + ((upBound - lowBound)/2);
+
  typename I::Value val;
 
  try
  {
  out.open(filename.c_str());
 
  //Vol format
+ out << "Center-X: " << center[0] <<std::endl;
+ out << "Center-Y: " << center[1] <<std::endl;
+ out << "Center-Z: " << center[2] <<std::endl;
  out << "X: "<< size[0]<<std::endl;
  out << "Y: "<< size[1]<<std::endl;
  out << "Z: "<< size[2]<<std::endl;

tests/images/testSliceImageFromFunctor.cpp

@@ -74,15 +74,15 @@ bool testSliceImageFromFunctor()
  projX(image.domain().upperBound()));
 
 
- DGtal::functors::Projector<DGtal::Z3i::Space> aSliceFunctor(20); aSliceFunctor.initAddOneDim(0);
+ DGtal::functors::Projector<DGtal::Z3i::Space> aSliceFunctor(0); aSliceFunctor.initAddOneDim(0);
  MySliceImageAdapter sliceImageX(image, domainX, aSliceFunctor, DGtal::functors::Identity());
  res &= PGMWriter<MySliceImageAdapter>::exportPGM("exportedSlice2DDimX.pgm",sliceImageX);
 
  DGtal::functors::Projector<DGtal::Z2i::Space> projY(0); projY.initRemoveOneDim(1); 
  DGtal::Z2i::Domain domainY(projY(image.domain().lowerBound()), 
  projY(image.domain().upperBound()));
 
- DGtal::functors::Projector<DGtal::Z3i::Space> aSliceFunctor2(20); aSliceFunctor2.initAddOneDim(1);
+ DGtal::functors::Projector<DGtal::Z3i::Space> aSliceFunctor2(0); aSliceFunctor2.initAddOneDim(1);
  MySliceImageAdapter sliceImageY(image, domainY, aSliceFunctor2, DGtal::functors::Identity());
  res &= PGMWriter<MySliceImageAdapter>::exportPGM("exportedSlice2DDimY.pgm",sliceImageY);
 
@@ -92,13 +92,13 @@ bool testSliceImageFromFunctor()
  projZ(image.domain().upperBound()));
 
 
- DGtal::functors::Projector<DGtal::Z3i::Space> aSliceFunctor3(20); aSliceFunctor3.initAddOneDim(2);
+ DGtal::functors::Projector<DGtal::Z3i::Space> aSliceFunctor3(0); aSliceFunctor3.initAddOneDim(2);
  MySliceImageAdapter sliceImageZ(image, domainZ, aSliceFunctor3, DGtal::functors::Identity());
  res &= PGMWriter<MySliceImageAdapter>::exportPGM("exportedSlice2DDimZ.pgm",sliceImageZ);
 
 
  PointVector<3, int> center(0,0,0); 
- DGtal::functors::SliceRotator2D< HyperRectDomain<SpaceND<3, int> >, int> sliceRot(2, image.domain(), 20, 2, 0.5, center);
+ DGtal::functors::SliceRotator2D< HyperRectDomain<SpaceND<3, int> >, int> sliceRot(2, image.domain(), 0, 2, M_PI/4.0, center);
 
 
  MyRotatorSliceImageAdapter sliceRotImageZ(image, domainZ, sliceRot, DGtal::functors::Identity());

tests/io/readers/testVolReader.cpp

@@ -102,7 +102,7 @@ bool testVolReader()
 
 bool testIOException()
 {
-  unsigned int nbok = 0;
+ unsigned int nbok = 0;
  unsigned int nb = 0;
 
  trace.beginBlock ( "Testing VolReader ..." );
@@ -136,21 +136,58 @@ bool testIOException()
  return nbok == nb;
 }
 
+bool testConsistence()
+{
+ trace.beginBlock ( "Testing VolWriter ..." );
+
+ typedef SpaceND<3> Space4Type;
+ typedef HyperRectDomain<Space4Type> TDomain;
+ typedef TDomain::Point Point;
+
+ //Default image selector = STLVector
+ typedef ImageSelector<TDomain, unsigned char>::Type Image;
+ TDomain domain(Point(-17,-14,-13), Point(5,7,11));
+ Image image(domain);
+ trace.info() << image.domain() <<endl;
+
+ VolWriter<Image>::exportVol("testConsistence.vol",image);
+
+ trace.endBlock();
+
+ trace.beginBlock ( "Testing VolReader ..." );
+
+ Image image2 = VolReader<Image>::importVol( "testConsistence.vol" );
+
+ trace.info() << image2.domain() <<endl;
+ trace.endBlock();
+
+ if( image.domain().lowerBound() != image2.domain().lowerBound() 
+ || image.domain().upperBound() != image2.domain().upperBound() )
+ {
+ return false;
+ }
+ return true;
+}
+
 ///////////////////////////////////////////////////////////////////////////////
 // Standard services - public :
 
 int main( int argc, char** argv )
 {
+ int aaaaa = 21/2;
+ std::cout << aaaaa << std::endl;
+
  trace.beginBlock ( "Testing class VolReader" );
  trace.info() << "Args:";
  for ( int i = 0; i < argc; ++i )
  trace.info() << " " << argv[ i ];
  trace.info() << endl;
 
- bool res = testVolReader() && testIOException(); // && ... other tests
+ bool res = testVolReader() && testIOException() && testConsistence(); // && ... other tests
  trace.emphase() << ( res ? "Passed." : "Error." ) << endl;
  trace.endBlock();
  return res ? 0 : 1;
+
 }
 // //
 ///////////////////////////////////////////////////////////////////////////////