30 #include "DGtal/base/Common.h" 31 #include "DGtal/base/BasicFunctors.h" 32 #include "DGtal/helpers/StdDefs.h" 33 #include "DGtal/io/readers/GenericReader.h" 34 #include "DGtal/io/viewers/Viewer3D.h" 35 #include "DGtal/io/DrawWithDisplay3DModifier.h" 36 #include "DGtal/io/readers/PointListReader.h" 37 #include "DGtal/io/readers/MeshReader.h" 39 #include "DGtal/io/Color.h" 40 #include "DGtal/io/colormaps/GradientColorMap.h" 41 #include "DGtal/images/ImageSelector.h" 46 using namespace DGtal;
103 template <
typename Space = DGtal::Z3i::Space,
typename KSpace = DGtal::Z3i::KSpace>
114 QObject::connect(
this, SIGNAL(drawFinished(
bool)),
this, SLOT(saveSnapshot(
bool)));
120 typedef ViewerSnap<>
Viewer;
125 template<
typename TImage>
127 displayCoordsCallBack(
void* viewer,
int name,
void* data )
129 TImage *image = (TImage *) data;
130 std::stringstream ss;
133 if (image->domain().isInside(p)){
134 ss <<
"Selected intensity: " << (*image)(p) <<
"p " << p[0] <<
" "<< p[1] <<
" " << p[2] ;
135 ((
Viewer *) viewer)->displayMessage(QString(ss.str().c_str()), 100000);
141 template <
typename TImage>
143 processDisplay(ViewerSnap<> &viewer, TImage &image,
144 const typename TImage::Value &thresholdMin,
145 const typename TImage::Value &thresholdMax,
146 unsigned int numDisplayedMax,
147 unsigned int transparency,
148 bool interDisplay=
false)
150 Domain domain = image.domain();
152 unsigned int numDisplayed = 0;
153 gradient.addColor(Color::Blue);
154 gradient.addColor(Color::Green);
155 gradient.addColor(Color::Yellow);
156 gradient.addColor(Color::Red);
158 typename TImage::Value val= image( (*it) );
159 if(numDisplayed > numDisplayedMax)
161 Color c= gradient(val);
162 if(val<=thresholdMax && val >=thresholdMin)
177 viewer << SetSelectCallback3D(displayCoordsCallBack<TImage>,
185 int main(
int argc,
char** argv )
189 app.description(
"Display volume file as a voxel set by using QGLviewer. \n Example: \n \t 3dVolViewer $DGtal/examples/samples/lobster.vol -m 60 -t 10");
190 std::string inputFileName;
193 double thresholdMin {0};
194 double thresholdMax {255};
195 unsigned int transparency {255};
196 unsigned int numDisplayedMax {500000};
197 std::string displayMesh;
198 std::string snapShotFile;
199 std::vector<unsigned int> colorMesh;
200 string inputType {
""};
201 bool interactiveDisplayVoxCoords {
false};
203 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." )
205 ->check(CLI::ExistingFile);
207 app.add_option(
"--inputType", inputType,
"to specify the input image type (int or double).")
208 -> check(CLI::IsMember({
"int",
"double"}));
210 app.add_option(
"--thresholdMin,-m", thresholdMin,
"threshold min (excluded) to define binary shape.",
true);
211 app.add_option(
"--thresholdMax,-M", thresholdMax,
"threshold max (included) to define binary shape.",
true);
212 app.add_option(
"--rescaleInputMin", rescaleInputMin,
"min value used to rescale the input intensity (to avoid basic cast into 8 bits image).",
true);
213 app.add_option(
"--rescaleInputMax", rescaleInputMax,
"max value used to rescale the input intensity (to avoid basic cast into 8 bits image).",
true);
214 app.add_option(
"--numMaxVoxel,-n", numDisplayedMax,
"set the maximal voxel number to be displayed.");
215 app.add_option(
"--displayMesh", displayMesh,
"display a Mesh given in OFF or OFS format.");
216 app.add_option(
"--colorMesh", colorMesh,
"set the color of Mesh (given from displayMesh option) : r g b a ")
218 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." );
219 app.add_option(
"--transparency,-t", transparency,
"change the defaukt transparency",
true);
220 app.add_flag(
"--interactiveDisplayVoxCoords,-c", interactiveDisplayVoxCoords,
" by using this option the coordinates can be displayed after selection (shift+left click on voxel).");
221 app.get_formatter()->column_width(40);
222 CLI11_PARSE(app, argc, argv);
225 QApplication application(argc,argv);
227 Viewer viewer(snapShotFile !=
"");
228 if(snapShotFile !=
""){
229 viewer.setSnapshotFileName(QString(snapShotFile.c_str()));
231 viewer.setWindowTitle(
"simple Volume Viewer");
237 string extension = inputFileName.substr(inputFileName.find_last_of(
".") + 1);
239 std::vector<double> vectValD;
240 std::vector<int> vectValI;
241 std::vector<unsigned char> vectValUC;
245 Image3D_D imageD = Image3D_D(d);
246 Image3D_I imageI = Image3D_I(d);
249 if(extension !=
"sdp")
251 unsigned int numDisplayed=0;
254 if (inputType==
"double")
258 trace.
info() <<
"Image loaded: D "<<imageD<< std::endl;
259 processDisplay(viewer, imageD, thresholdMin, thresholdMax, numDisplayedMax, transparency,
260 interactiveDisplayVoxCoords);
262 else if (inputType==
"int")
265 trace.
info() <<
"Image loaded: "<<image<< std::endl;
266 processDisplay(viewer, imageI, (
int)thresholdMin, (
int)thresholdMax, numDisplayedMax, transparency,
267 interactiveDisplayVoxCoords);
273 trace.
info() <<
"Image loaded: "<<image<< std::endl;
274 processDisplay(viewer, image, thresholdMin, thresholdMax, numDisplayedMax, transparency,
275 interactiveDisplayVoxCoords);
282 trace.
info() <<
"Image loaded: "<<image<< std::endl;
283 processDisplay(viewer, image, thresholdMin, thresholdMax, numDisplayedMax, transparency,
284 interactiveDisplayVoxCoords);
287 else if(extension==
"sdp")
290 for(
unsigned int i=0;i< vectVoxels.size(); i++){
291 viewer <<
Z3i::Point(vectVoxels.at(i), functors::Round<>());
294 if(displayMesh !=
"")
296 if(colorMesh.size() != 0)
298 Color c(colorMesh[0], colorMesh[1], colorMesh[2], colorMesh[3]);
299 viewer.setFillColor(c);
307 viewer << Viewer3D<>::updateDisplay;
308 if(snapShotFile !=
"")
311 if(!viewer.restoreStateFromFile())
315 std::string extension = snapShotFile.substr(snapShotFile.find_last_of(
".") + 1);
316 std::string basename = snapShotFile.substr(0, snapShotFile.find_last_of(
"."));
317 for(
int i=0; i< viewer.snapshotCounter()-1; i++){
319 s << basename <<
"-"<< setfill(
'0') << setw(4)<< i <<
"." << extension;
320 trace.
info() <<
"erase temp file: " << s.str() << std::endl;
321 remove(s.str().c_str());
324 s << basename <<
"-"<< setfill(
'0') << setw(4)<< viewer.snapshotCounter()-1 <<
"." << extension;
325 rename(s.str().c_str(), snapShotFile.c_str());
328 return application.exec();
int main(int argc, char **argv)
static TContainer import(const std::string &filename, std::vector< unsigned int > dimSpace=std::vector< unsigned int >())
Trace trace(traceWriterTerm)
void green(const unsigned char aGreenValue)
void red(const unsigned char aRedValue)
typename Self::Domain Domain
void blue(const unsigned char aBlueValue)