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Merge pull request #402 from kerautret/Double3dVolViewxer
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@dcoeurjo
dcoeurjo committed May 1, 2021
2 parents 78bf192 + 10ae6dd commit a9c1388
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12 changes: 7 additions & 5 deletions ChangeLog.md
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@@ -1,14 +1,16 @@
# DGtalTools 1.2
- *global*
- Fix itk2vol and fix ITK cmake configuaration that was making issues with the ITK image read.
(Bertrand Kerautret [#393](https://github.com/DGtal-team/DGtalTools/pull/393))
- Travis: Fix old default osx_image with xcode12.2 and remove non used boost
cmake references. (Bertrand Kerautret [#394](https://github.com/DGtal-team/DGtalTools/pull/394))

- *visualisation*
- *visualisation*:
- 3dVolViewer: improvement of the possibility to read input image of type double (with ITK).
New possibility to select the voxel in order to display image intensity.
(Bertrand Kerautret [#402](https://github.com/DGtal-team/DGtalTools/pull/402))
- 3dVolBoundaryViewer: fix compilation issue (related to CLI11 change) when ITK is activated.
(Bertrand Kerautret [#395](https://github.com/DGtal-team/DGtalTools/pull/395))

- Fix itk2vol and fix ITK cmake configuaration that was making wrong the ITK image read.
(Bertrand Kerautret [#393](https://github.com/DGtal-team/DGtalTools/pull/393))
(Bertrand Kerautret [#395](https://github.com/DGtal-team/DGtalTools/pull/395))


# DGtalTools 1.1
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157 changes: 119 additions & 38 deletions visualisation/3dVolViewer.cpp
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Expand Up @@ -100,8 +100,6 @@ using namespace Z3i;
*/




template < typename Space = DGtal::Z3i::Space, typename KSpace = DGtal::Z3i::KSpace>
struct ViewerSnap: DGtal::Viewer3D <Space, KSpace>
{
Expand All @@ -119,30 +117,96 @@ struct ViewerSnap: DGtal::Viewer3D <Space, KSpace>
bool mySaveSnap;
};

typedef ViewerSnap<> Viewer;



// call back function to display voxel coordinates
template<typename TImage>
int
displayCoordsCallBack( void* viewer, int name, void* data )
{
TImage *image = (TImage *) data;
std::stringstream ss;
Z3i::Point p = DGtal::Linearizer<typename TImage::Domain>::getPoint(name, image->domain());
// Check needed since simetimes the point appears outside (only in non debug mode).
if (image->domain().isInside(p)){
ss << "Selected intensity: " << (*image)(p) << "p " << p[0] << " "<< p[1] << " " << p[2] ;
((Viewer *) viewer)->displayMessage(QString(ss.str().c_str()), 100000);
}
return 0;
}


template <typename TImage>
void
processDisplay(ViewerSnap<> &viewer, TImage &image,
const typename TImage::Value &thresholdMin,
const typename TImage::Value &thresholdMax,
unsigned int numDisplayedMax,
unsigned int transparency,
bool interDisplay=false)
{
Domain domain = image.domain();
GradientColorMap<typename TImage::Value> gradient( thresholdMin, thresholdMax);
unsigned int numDisplayed = 0;
gradient.addColor(Color::Blue);
gradient.addColor(Color::Green);
gradient.addColor(Color::Yellow);
gradient.addColor(Color::Red);
for(Domain::ConstIterator it = domain.begin(), itend=domain.end(); it!=itend; ++it){
typename TImage::Value val= image( (*it) );
if(numDisplayed > numDisplayedMax)
break;
Color c= gradient(val);
if(val<=thresholdMax && val >=thresholdMin)
{
viewer << CustomColors3D(Color((float)(c.red()), (float)(c.green()),(float)(c.blue()), transparency),
Color((float)(c.red()), (float)(c.green()),(float)(c.blue()), transparency));
if (interDisplay)
{
auto p = *it;
auto index = DGtal::Linearizer<typename TImage::Domain>::getIndex( p, domain);
viewer << SetName3D( index ) ;
}
viewer << *it;
numDisplayed++;
}
}
if (interDisplay){
viewer << SetSelectCallback3D(displayCoordsCallBack<TImage>,
&image );
}
}




int main( int argc, char** argv )
{

// parse command line using CLI ----------------------------------------------
CLI::App app;
app.description("Display volume file as a voxel set by using QGLviewer. \n Example: \n \t 3dVolViewer -i $DGtal/examples/samples/lobster.vol -m 60 -t 10");
std::string inputFileName;
DGtal::int64_t rescaleInputMin {0};
DGtal::int64_t rescaleInputMax {255};
int thresholdMin {0};
int thresholdMax {255};
double thresholdMin {0};
double thresholdMax {255};
unsigned int transparency {255};
unsigned int numDisplayedMax {500000};
std::string displayMesh;
std::string snapShotFile;
std::vector<unsigned int> colorMesh;
string inputType {""};
bool interactiveDisplayVoxCoords {false};

app.add_option("-i,--input,1", inputFileName, "vol file (.vol, .longvol .p3d, .pgm3d and if WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255." )
->required()
->check(CLI::ExistingFile);

#ifdef WITH_ITK
app.add_option("--inputType", inputType, "to specify the input image type (int or double).")
-> check(CLI::IsMember({"int", "double"}));
#endif
app.add_option("--thresholdMin,-m", thresholdMin, "threshold min (excluded) to define binary shape.", true);
app.add_option("--thresholdMax,-M", thresholdMax, "threshold max (included) to define binary shape.", true);
app.add_option("--rescaleInputMin", rescaleInputMin, "min value used to rescale the input intensity (to avoid basic cast into 8 bits image).", true);
Expand All @@ -152,57 +216,75 @@ int main( int argc, char** argv )
app.add_option("--colorMesh", colorMesh, "set the color of Mesh (given from displayMesh option) : r g b a ")
->expected(4);
app.add_flag("--doSnapShotAndExit,-d",snapShotFile, "save display snapshot into file. Notes that the camera setting is set by default according the last saved configuration (use SHIFT+Key_M to save current camera setting in the Viewer3D). If the camera setting was not saved it will use the default camera setting." );

app.add_option("--transparency,-t", transparency, "change the defaukt transparency", true);

app.add_flag("--interactiveDisplayVoxCoords,-c", interactiveDisplayVoxCoords, " by using this option the coordinates can be displayed after selection (shift+left click on voxel).");
app.get_formatter()->column_width(40);
CLI11_PARSE(app, argc, argv);
// END parse command line using CLI ----------------------------------------------


QApplication application(argc,argv);
typedef ViewerSnap<> Viewer;

Viewer viewer(snapShotFile != "");
if(snapShotFile != ""){
viewer.setSnapshotFileName(QString(snapShotFile.c_str()));
}

viewer.setWindowTitle("simple Volume Viewer");
viewer.show();

typedef ImageContainerBySTLVector < Z3i::Domain, double > Image3D_D;
typedef ImageContainerBySTLVector < Z3i::Domain, int > Image3D_I;
typedef ImageSelector<Domain, unsigned char>::Type Image;

string extension = inputFileName.substr(inputFileName.find_last_of(".") + 1);

std::vector<double> vectValD;
std::vector<int> vectValI;
std::vector<unsigned char> vectValUC;
// Image of different types are pre constructed here else it will be deleted after the type selection
// (and it is used in display callback)
Z3i::Domain d;
Image3D_D imageD = Image3D_D(d);
Image3D_I imageI = Image3D_I(d);
Image image = Image(d);

if(extension != "sdp")
{
unsigned int numDisplayed=0;


#ifdef WITH_ITK
if (inputType=="double")
{
imageD = DGtal::GenericReader<Image3D_D>::import(inputFileName);
trace.info() << "[done]"<< std::endl;
trace.info() << "Image loaded: D "<<imageD<< std::endl;
processDisplay(viewer, imageD, thresholdMin, thresholdMax, numDisplayedMax, transparency,
interactiveDisplayVoxCoords);
}
else if (inputType=="int")
{
imageI= DGtal::GenericReader<Image3D_I>::import(inputFileName);
trace.info() << "Image loaded: "<<image<< std::endl;
processDisplay(viewer, imageI, (int)thresholdMin, (int)thresholdMax, numDisplayedMax, transparency,
interactiveDisplayVoxCoords);
} else {
typedef DGtal::functors::Rescaling<DGtal::int64_t ,unsigned char > RescalFCT;
Image image = GenericReader< Image >::importWithValueFunctor( inputFileName,RescalFCT(rescaleInputMin,
rescaleInputMax,
0, 255) );

image = GenericReader< Image >::importWithValueFunctor( inputFileName,RescalFCT(rescaleInputMin,
rescaleInputMax,
0, 255) );
trace.info() << "Image loaded: "<<image<< std::endl;
Domain domain = image.domain();
GradientColorMap<long> gradient( thresholdMin, thresholdMax);
gradient.addColor(Color::Blue);
gradient.addColor(Color::Green);
gradient.addColor(Color::Yellow);
gradient.addColor(Color::Red);
for(Domain::ConstIterator it = domain.begin(), itend=domain.end(); it!=itend; ++it){
unsigned char val= image( (*it) );
if(numDisplayed > numDisplayedMax)
break;
Color c= gradient(val);
if(val<=thresholdMax && val >=thresholdMin)
{
viewer << CustomColors3D(Color((float)(c.red()), (float)(c.green()),(float)(c.blue()), transparency),
Color((float)(c.red()), (float)(c.green()),(float)(c.blue()), transparency));
viewer << *it;
numDisplayed++;
}
}
}else if(extension=="sdp")
processDisplay(viewer, image, thresholdMin, thresholdMax, numDisplayedMax, transparency,
interactiveDisplayVoxCoords);
}
#else
typedef DGtal::functors::Rescaling<DGtal::int64_t ,unsigned char > RescalFCT;
image = GenericReader< Image >::importWithValueFunctor( inputFileName,RescalFCT(rescaleInputMin,
rescaleInputMax,
0, 255) );
trace.info() << "Image loaded: "<<image<< std::endl;
processDisplay(viewer, image, thresholdMin, thresholdMax, numDisplayedMax, transparency,
interactiveDisplayVoxCoords);
#endif
}
else if(extension=="sdp")
{
vector<Z3i::RealPoint> vectVoxels = PointListReader<Z3i::RealPoint>::getPointsFromFile(inputFileName);
for(unsigned int i=0;i< vectVoxels.size(); i++){
Expand Down Expand Up @@ -243,6 +325,5 @@ int main( int argc, char** argv )
rename(s.str().c_str(), snapShotFile.c_str());
return 0;
}

return application.exec();
}

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