Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
- ======================================================================-====*/
+ ===========================================================================**/
#include "vvLandmarks.h"
#include <ios>
#include <string>
#include <locale.h>
+#include <vtkVersion.h>
#include "vtkPolyData.h"
#include "vtkPoints.h"
#include "vtkFloatArray.h"
#include "vtkPointData.h"
#include "clitkCommon.h"
+#include <itksys/SystemTools.hxx>
//--------------------------------------------------------------------
vvLandmarks::vvLandmarks(int size)
{
- mLandmarks.resize(0);
- mFilename = "";
+ mLandmarks.resize(size);
+ mLandmarksInitial.resize(size);
+ mFilenames.resize(0);
+ mTime = 0;
for (int i = 0; i < size; i++) {
+ mLandmarks[i].resize(0);
+ mLandmarksInitial[i].resize(0);
vtkPoints *points = vtkPoints::New();
mPoints.push_back(points);
+ mIds.push_back(vtkFloatArray::New());
+ mLabels.push_back(vtkStringArray::New());
+ mLabels.back()->SetName("labels");
}
mPolyData = vtkPolyData::New();
- mIds = vtkFloatArray::New();
}
//--------------------------------------------------------------------
{
for (unsigned int i = 0; i < mPoints.size(); i++) {
mPoints[i]->Delete();
+ mIds[i]->Delete();
+ mLabels[i]->Delete();
}
/*for(unsigned int i = 0; i < mText.size(); i++) {
mText[i]->Delete();
}*/
- if (mIds)
- mIds->Delete();
if (mPolyData)
mPolyData->Delete();
}
void vvLandmarks::AddLandmark(float x,float y,float z,float t,double value)
{
vvLandmark point;
+ vtkIdType idPoint;
point.coordinates[0] = x;
point.coordinates[1] = y;
point.coordinates[2] = z;
point.coordinates[3] = t;
point.pixel_value=value;
- mLandmarks.push_back(point);
- mPoints[int(t)]->InsertNextPoint(x,y,z);
-
+ mLandmarks[mTime].push_back(point);
+ mLandmarksInitial[mTime].push_back(point);
+
+ idPoint = mPoints[int(t)]->InsertNextPoint(x,y,z);
+ std::string str_vtkIdType; // string which will contain the result
+ std::ostringstream convert; // stream used for the conversion
+ convert << idPoint; // insert the textual representation of 'idPoint' in the characters in the stream
+ str_vtkIdType = convert.str(); // set 'str_vtkIdType' to the contents of the stream
+ mLabels[mTime]->InsertNextValue(str_vtkIdType.c_str());
+
std::stringstream numberVal;
numberVal << (mLandmarks.size()-1);
/*
mText.push_back(number);
*/
- mIds->InsertNextTuple1(0.55);
+ mIds[mTime]->InsertNextTuple1(0.55);
//mIds->InsertTuple1(mLandmarks.size(),mLandmarks.size());
SetTime(int(t));
}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+void vvLandmarks::TransformUpdate(vtkAbstractTransform* transform)
+{
+ //For all Time, For all landmarks, I apply the transform
+ for(int time=0; time<mLandmarks.size(); ++time)
+ {
+ for(int landmark=0; landmark<mLandmarks[time].size(); ++landmark)
+ {
+ double ptBeforeTransform[3], ptAfterTransform[3];
+ ptBeforeTransform[0]= mLandmarksInitial[time][landmark].coordinates[0];
+ ptBeforeTransform[1]= mLandmarksInitial[time][landmark].coordinates[1];
+ ptBeforeTransform[2]= mLandmarksInitial[time][landmark].coordinates[2];
+ transform->TransformPoint(ptBeforeTransform, ptAfterTransform);
+
+ mLandmarks[time][landmark].coordinates[0]= ptAfterTransform[0];
+ mLandmarks[time][landmark].coordinates[1]= ptAfterTransform[1];
+ mLandmarks[time][landmark].coordinates[2]= ptAfterTransform[2];
+ }
+ }
+}
+//--------------------------------------------------------------------
//--------------------------------------------------------------------
void vvLandmarks::RemoveLastLandmark()
{
- mPoints[mLandmarks.back().coordinates[3]]->SetNumberOfPoints(
- mPoints[mLandmarks.back().coordinates[3]]->GetNumberOfPoints()-1);
- mPolyData->Modified();
+ mPoints[mTime]->SetNumberOfPoints(mPoints[mTime]->GetNumberOfPoints()-1);
// mText.pop_back();
- mLandmarks.pop_back();
- mIds->RemoveLastTuple();
+ mLandmarks[mTime].pop_back();
+ mLandmarksInitial[mTime].pop_back();
+ mIds[mTime]->RemoveLastTuple();
+ mLabels[mTime]->SetNumberOfValues(mLabels[mTime]->GetNumberOfValues()-1);
+ mLabels[mTime]->Modified();
+ mPolyData->Modified();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void vvLandmarks::RemoveLandmarkWithLabel(vtkStdString label, int time)
+{
+ if (label != "P1" && label != "P2")
+ return;
+ // erase a vtkPoint by shifiting the array .
+ // not a problem here because there are no
+ // pologyons linking the points
+ int t = time;//mLandmarks[index].coordinates[3];
+ int npoints = mPoints[t]->GetNumberOfPoints();
+
+ //search of the index corresponding to the label
+ int index(0);
+ while (mLabels[t]->GetValue(index) != label)
+ ++index;
+
+ for (int i = index; i < npoints - 1; i++) {
+ mPoints[t]->InsertPoint(i, mPoints[t]->GetPoint(i+1));
+ std::string str_i; // string which will contain the result
+ std::ostringstream convert; // stream used for the conversion
+ convert << i; // insert the textual representation of 'i' in the characters in the stream
+ str_i = convert.str(); // set 'str_i' to the contents of the stream
+ mLabels[t]->SetValue(i,mLabels[t]->GetValue(i+1));
+ }
+ mPoints[t]->SetNumberOfPoints(npoints-1);
+ mLabels[t]->SetNumberOfValues(npoints-1);
+ mLabels[t]->Modified();
+ mPolyData->Modified();
+
+ mLandmarks[t].erase(mLandmarks[t].begin() + index);
+ mLandmarksInitial[t].erase(mLandmarksInitial[t].begin() + index);
+ mIds[t]->RemoveLastTuple();
}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+void vvLandmarks::RemoveLandmark(int index)
+{
+ // erase a vtkPoint by shifiting the array .
+ // not a problem here because there are no
+ // pologyons linking the points
+ int t = mTime;//mLandmarks[index].coordinates[3];
+ int npoints = mPoints[t]->GetNumberOfPoints();
+ for (int i = index; i < npoints - 1; i++) {
+ mPoints[t]->InsertPoint(i, mPoints[t]->GetPoint(i+1));
+ std::string str_i; // string which will contain the result
+ std::ostringstream convert; // stream used for the conversion
+ convert << i; // insert the textual representation of 'i' in the characters in the stream
+ str_i = convert.str(); // set 'str_i' to the contents of the stream
+ mLabels[t]->SetValue(i,str_i.c_str());
+ }
+ mPoints[t]->SetNumberOfPoints(npoints-1);
+ mLabels[t]->SetNumberOfValues(npoints-1);
+ mLabels[t]->Modified();
+ mPolyData->Modified();
+
+ mLandmarks[t].erase(mLandmarks[t].begin() + index);
+ mLandmarksInitial[t].erase(mLandmarksInitial[t].begin() + index);
+ mIds[t]->RemoveLastTuple();
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+void vvLandmarks::RemoveAll()
+{
+ for (unsigned int i = 0; i < mLandmarks.size(); i++) {
+ mLandmarks[i].clear();
+ mLandmarksInitial[i].clear();
+ mPoints[i]->SetNumberOfPoints(0);
+ mLabels[i]->SetNumberOfValues(0);
+ mIds[i]->SetNumberOfValues(0);
+ }
+}
+//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
void vvLandmarks::ChangeComments(int index, std::string comments)
{
- mLandmarks[index].comments = comments;
+ mLandmarks[mTime][index].comments = comments;
+ mLandmarksInitial[mTime][index].comments = comments;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
double vvLandmarks::GetPixelValue(int index)
{
- return mLandmarks[index].pixel_value;
+ return mLandmarks[mTime][index].pixel_value;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
float* vvLandmarks::GetCoordinates(int index)
{
- return mLandmarks[index].coordinates;
+ return mLandmarks[mTime][index].coordinates;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
std::string vvLandmarks::GetComments(int index)
{
- return mLandmarks[index].comments;
+ return mLandmarks[mTime][index].comments;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-void vvLandmarks::LoadFile(std::string filename)
+bool vvLandmarks::LoadFile(std::vector<std::string> filenames)
{
- std::ifstream fp(filename.c_str(), std::ios::in|std::ios::binary);
- if (!fp.is_open()) {
- std::cerr <<"Unable to open file " << filename << std::endl;
- return;
- }
- mFilename = filename;
- mLandmarks.clear();
- char line[255];
- for (unsigned int i = 0; i < mPoints.size(); i++)
+ // all files in the sequence must be of the same type
+ std::string extension = itksys::SystemTools::GetFilenameExtension(filenames[0]);
+ if (extension == ".txt")
+ return LoadTxtFile(filenames);
+ else if (extension == ".pts")
+ return LoadPtsFile(filenames);
+
+ return false;
+}
+
+//--------------------------------------------------------------------
+bool vvLandmarks::LoadTxtFile(std::vector<std::string> filenames)
+{
+ mFilenames = filenames;
+ for (unsigned int i = 0; i < mPoints.size(); i++) {
+ mLandmarks[i].clear();
+ mLandmarksInitial[i].clear();
mPoints[i]->SetNumberOfPoints(0);
- bool first_line=true;
- while (fp.getline(line,255)) {
- // DD(line);
- std::string stringline = line;
- if (first_line) {
- first_line=false;
- ///New landmark format: first line is "LANDMARKSXX", where XX is the version number
- if (stringline.size() >= 10 && stringline.compare(0,9,"LANDMARKS")==0) {
- std::istringstream ss(stringline.c_str()+9);
- ss >> mFormatVersion;
- continue; //skip first line
- } else
- mFormatVersion=0;
+ }
+
+ int err = 0;
+ for (unsigned int f = 0; f < filenames.size(); f++) {
+ std::ifstream fp(filenames[f].c_str(), std::ios::in|std::ios::binary);
+ if (!fp.is_open()) {
+ std::cerr <<"Unable to open file " << filenames[f] << std::endl;
+ err++;
}
- if (stringline.size() > 1) {
- vvLandmark point;
- int previousSpace = 0;
- int space=0;
- if (mFormatVersion>0) {
+ vtkIdType idPoint;
+ char line[255];
+ bool first_line=true;
+ while (fp.getline(line,255)) {
+ // DD(line);
+ std::string stringline = line;
+ stringline += "\n";
+
+ if (first_line) {
+ first_line=false;
+ ///New landmark format: first line is "LANDMARKSXX", where XX is the version number
+ if (stringline.size() >= 10 && stringline.compare(0,9,"LANDMARKS")==0) {
+ std::istringstream ss(stringline.c_str()+9);
+ ss >> mFormatVersion;
+ continue; //skip first line
+ } else
+ mFormatVersion=0;
+ }
+ if (stringline.size() > 1) {
+ vvLandmark point;
+ int previousSpace = 0;
+ int space=0;
+ if (mFormatVersion>0) {
+ space = stringline.find(" ", previousSpace+1);
+ if (space < -1 || space > (int)stringline.size()) {
+ ErrorMsg(mLandmarks.size(),"index");
+ continue;
+ }
+ //int index = atoi(stringline.substr(previousSpace,space - previousSpace).c_str());
+ previousSpace = space;
+ }
space = stringline.find(" ", previousSpace+1);
if (space < -1 || space > (int)stringline.size()) {
- ErrorMsg(mLandmarks.size(),"index");
+ ErrorMsg(mLandmarks.size(),"x position");
continue;
}
- //int index = atoi(stringline.substr(previousSpace,space - previousSpace).c_str());
+ point.coordinates[0] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
+ // DD(point.coordinates[0]);
previousSpace = space;
- }
- space = stringline.find(" ", previousSpace+1);
- if (space < -1 || space > (int)stringline.size()) {
- ErrorMsg(mLandmarks.size(),"x position");
- continue;
- }
- point.coordinates[0] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
- // DD(point.coordinates[0]);
- previousSpace = space;
- space = stringline.find(" ", previousSpace+1);
- if (space < -1 || space > (int)stringline.size()) {
- ErrorMsg(mLandmarks.size(),"y position");
- continue;
- }
- point.coordinates[1] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
- // DD(point.coordinates[1]);
- previousSpace = space;
- space = stringline.find(" ", previousSpace+1);
- if (space < -1 || space > (int)stringline.size()) {
- ErrorMsg(mLandmarks.size(),"z position");
- continue;
- }
- point.coordinates[2] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
- previousSpace = space;
- if (mFormatVersion>0) {
space = stringline.find(" ", previousSpace+1);
if (space < -1 || space > (int)stringline.size()) {
- ErrorMsg(mLandmarks.size(),"t position");
+ ErrorMsg(mLandmarks.size(),"y position");
continue;
}
- point.coordinates[3] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
+ point.coordinates[1] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
+ // DD(point.coordinates[1]);
previousSpace = space;
space = stringline.find(" ", previousSpace+1);
if (space < -1 || space > (int)stringline.size()) {
- ErrorMsg(mLandmarks.size(),"pixel value");
+ ErrorMsg(mLandmarks.size(),"z position");
continue;
}
- point.pixel_value = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
- // DD(point.pixel_value);
- } else {
- point.pixel_value=0.; //Not in file
- point.coordinates[3]=0.;
- }
- previousSpace = space;
- //this is the maximum size of comments
- space = (stringline.find("\n", previousSpace+1) < 254 ? stringline.find("\n", previousSpace+1) : 254);
- if (previousSpace != -1) {
- point.comments = stringline.substr(previousSpace,space - (previousSpace)).c_str();
+ point.coordinates[2] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
+ previousSpace = space;
+ if (mFormatVersion>0) {
+ space = stringline.find(" ", previousSpace+1);
+ if (space < -1 || space > (int)stringline.size()) {
+ ErrorMsg(mLandmarks.size(),"t position");
+ continue;
+ }
+ point.coordinates[3] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
+ previousSpace = space;
+ space = stringline.find(" ", previousSpace+1);
+ if (space < -1 || space > (int)stringline.size()) {
+ ErrorMsg(mLandmarks.size(),"pixel value");
+ continue;
+ }
+ point.pixel_value = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
+ // DD(point.pixel_value);
+ } else {
+ point.pixel_value=0.; //Not in file
+ point.coordinates[3]=(float)f;
+ }
+ previousSpace = space;
+ //this is the maximum size of comments
+ space = (stringline.find("\n", previousSpace+1) < 254 ? stringline.find("\n", previousSpace+1) : 254);
+ if (previousSpace != -1) {
+ point.comments = stringline.substr(previousSpace,space - (previousSpace)).c_str();
+ }
+ // DD(point.comments);
+ mLandmarks[int(point.coordinates[3])].push_back(point);
+ mLandmarksInitial[int(point.coordinates[3])].push_back(point);
+ mIds[int(point.coordinates[3])]->InsertNextTuple1(0.55);
+ idPoint = mPoints[int(point.coordinates[3])]->InsertNextPoint(
+ point.coordinates[0],point.coordinates[1],point.coordinates[2]);
+ std::string str_vtkIdType; // string which will contain the result
+ std::ostringstream convert; // stream used for the conversion
+ convert << idPoint; // insert the textual representation of 'idPoint' in the characters in the stream
+ str_vtkIdType = convert.str(); // set 'str_vtkIdType' to the contents of the stream
+ mLabels[int(point.coordinates[3])]->InsertNextValue(str_vtkIdType.c_str());
}
- // DD(point.comments);
- mLandmarks.push_back(point);
- mIds->InsertNextTuple1(0.55);
- mPoints[int(point.coordinates[3])]->InsertNextPoint(
- point.coordinates[0],point.coordinates[1],point.coordinates[2]);
}
}
+
+ if (err > 0 && err == filenames.size())
+ return false;
+
SetTime(0);
+
+ return true;
}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+bool vvLandmarks::LoadPtsFile(std::vector<std::string> filenames)
+{
+ mFilenames = filenames;
+ for (unsigned int i = 0; i < mPoints.size(); i++) {
+ mPoints[i]->SetNumberOfPoints(0);
+ mLandmarks[i].clear();
+ mLandmarksInitial[i].clear();
+ }
+
+ int err = 0;
+ for (unsigned int f = 0; f < filenames.size(); f++) {
+ std::ifstream fp(filenames[f].c_str(), std::ios::in|std::ios::binary);
+ if (!fp.is_open()) {
+ std::cerr <<"Unable to open file " << filenames[f] << std::endl;
+ err++;
+ }
+ vtkIdType idPoint;
+ char line[255];
+ bool first_line=true;
+ while (fp.getline(line,255)) {
+ std::string stringline = line;
+ stringline += "\n";
+
+ std::string separators = "\t\n\r ";
+ if (stringline.size() > 1) {
+ vvLandmark point;
+ int previousSpace = 0;
+ int space=0;
+
+ if (stringline[0] == '#') // comments
+ continue;
+
+ space = stringline.find_first_of(separators, previousSpace+1);
+ if (space == std::string::npos) {
+ ErrorMsg(mLandmarks.size(),"x position");
+ continue;
+ }
+ point.coordinates[0] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
+ // DD(point.coordinates[0]);
+ previousSpace = space;
+ space = stringline.find_first_of(separators, previousSpace+1);
+ if (space == std::string::npos) {
+ ErrorMsg(mLandmarks.size(),"y position");
+ continue;
+ }
+ point.coordinates[1] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
+ // DD(point.coordinates[1]);
+ previousSpace = space;
+ space = stringline.find_first_of(separators, previousSpace+1);
+ if (space == std::string::npos) {
+ ErrorMsg(mLandmarks.size(),"z position");
+ continue;
+ }
+ point.coordinates[2] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
+ previousSpace = space;
+ point.pixel_value=0.; //Not in file
+ point.coordinates[3]=(float)f; //Not in file
+ point.comments = ""; //Not in file
+
+ // DD(point.comments);
+ mLandmarks[int(point.coordinates[3])].push_back(point);
+ mLandmarksInitial[int(point.coordinates[3])].push_back(point);
+ mIds[int(point.coordinates[3])]->InsertNextTuple1(0.55);
+ idPoint = mPoints[int(point.coordinates[3])]->InsertNextPoint(
+ point.coordinates[0],point.coordinates[1],point.coordinates[2]);
+ std::string str_vtkIdType; // string which will contain the result
+ std::ostringstream convert; // stream used for the conversion
+ convert << idPoint; // insert the textual representation of 'idPoint' in the characters in the stream
+ str_vtkIdType = convert.str(); // set 'str_vtkIdType' to the contents of the stream
+ mLabels[int(point.coordinates[3])]->InsertNextValue(str_vtkIdType.c_str());
+ }
+ }
+ }
+
+ SetTime(0);
+ DD("vvLandmarks::LoadPtsFile")
+ if (err > 0 && err == filenames.size())
+ return false;
+
+
+ return true;
+}
+//--------------------------------------------------------------------
//--------------------------------------------------------------------
bool vvLandmarks::ErrorMsg(int num,const char * text)
void vvLandmarks::SaveFile(std::string filename)
{
std::string fileContent = "LANDMARKS1\n"; //File format version identification
- for (unsigned int i = 0; i < mLandmarks.size(); i++) {
- std::stringstream out;
- out.imbue(std::locale("C")); //This is to specify that the dot is to be used as the decimal separator
- out << i << " "
- << mLandmarks[i].coordinates[0] << " "
- << mLandmarks[i].coordinates[1] << " "
- << mLandmarks[i].coordinates[2] << " "
- << mLandmarks[i].coordinates[3] << " "
- << mLandmarks[i].pixel_value << " ";
- fileContent += out.str();
- if (mLandmarks[i].comments.size() == 0)
- fileContent += " ";
- else
- fileContent += mLandmarks[i].comments;
- fileContent += "\n";
+ for (unsigned int t = 0; t < mLandmarks.size(); t++) {
+ for (unsigned int i = 0; i < mLandmarks[t].size(); i++) {
+ std::stringstream out;
+ out.imbue(std::locale("C")); //This is to specify that the dot is to be used as the decimal separator
+ out << i << " "
+ << mLandmarksInitial[t][i].coordinates[0] << " "
+ << mLandmarksInitial[t][i].coordinates[1] << " "
+ << mLandmarksInitial[t][i].coordinates[2] << " "
+ << mLandmarksInitial[t][i].coordinates[3] << " "
+ << mLandmarksInitial[t][i].pixel_value << " ";
+ fileContent += out.str();
+ if (mLandmarksInitial[t][i].comments.size() == 0)
+ fileContent += " ";
+ else
+ fileContent += mLandmarksInitial[t][i].comments;
+ fileContent += "\n";
+ }
}
std::ofstream fp(filename.c_str(), std::ios::trunc);
if ( !fp ) {
{
if (time >= 0 && time <= ((int)mPoints.size() -1)) {
mPolyData->SetPoints(mPoints[time]);
- mPolyData->GetPointData()->SetScalars(mIds);
+ mPolyData->GetPointData()->SetScalars(mIds[time]);
+ mPolyData->GetPointData()->AddArray(mLabels[time]);
mPolyData->Modified();
+#if VTK_MAJOR_VERSION <= 5
mPolyData->Update();
+#else
+ //mPolyData->Update();
+#endif
+ mTime = time;
}
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff