void Calculate(const ProtectedRoutePlanner *route_planner,
const PolarSettings &polar_settings,
const TaskBehaviour &task_behaviour,
const DerivedInfo &calculated) {
if (route_planner != nullptr && !route_planner->IsTerrainReachEmpty())
CalculateRoute(*route_planner);
else
CalculateDirect(polar_settings, task_behaviour, calculated);
}
ImagePlus* CaptureManager::Access(int p, int z, bool fluorescence, bool noImage, int preload)
{
if (p < 0 || p >= frameCount || z < 0 || z >= slideCount)
return NULL;
// preload next three pictures
if (preload)
{
for (int i = 1; i <= 3; i++)
{
int newpos = i + p;
int newZPos = z + newpos/frameCount;
if (preload == 1) // all
{
if (newZPos <= slideCount)
{
if (newpos >= frameCount)
newpos = newpos % frameCount;
Preload(CalculateDirect(newpos, newZPos, fluorescence));
}
}
else if (preload == 2) // t-direction
{
if (newpos < frameCount)
Preload(CalculateDirect(newpos, z, fluorescence));
}
else // z-direction
{
newZPos = z + i;
if (newZPos < slideCount)
Preload(CalculateDirect(p, newZPos, fluorescence));
}
}
}
int direct = CalculateDirect(p, z, fluorescence);
ImagePlus* temp = book[direct];
if (!temp->orig && !noImage)
temp->orig = cvLoadImage(m_capture->getFilename(direct).mb_str());
return temp;
}
void CaptureManager::Release(int p, int z, bool fluorescence)
{
// unload previous loaded image
if (!IsInNeighborhood(p, z))
{
int direct = CalculateDirect(p, z, fluorescence);
if (book[direct]->isLoading)
book[direct]->isLoading = false;
else
m_queue->AddJob(Job(Job::thread_delete, direct, book[direct]->orig), 1);
book[direct]->orig = NULL;
}
}
bool CaptureManager::SaveContours(const char* file)
{
std::ofstream outfile;
outfile.open(file, std::ofstream::out);
if (!outfile)
{
wxLogError(_T("Unable to open file %s"), file);
return false;
}
//int numContours=book[0]->contourArray.size();
outfile << "#width: " << size.width << ", height: " << size.height << ", frameCount: " << frameCount << ", slideCount: " << slideCount << ", fluorescence: " << (hasFluorescence?"yes":"no") << ", fps: " << fps << std::endl;
for (int frame=0; frame < frameCount; frame++)
{
for (int slide=0; slide < slideCount; slide++)
{
for (int fluor=0; fluor < (hasFluorescence?2:1); fluor++)
{
int direct = CalculateDirect(frame, slide, (fluor==0?true:false));
int numContours = book[direct]->contourArray.size();
outfile << "#Frame: " << frame << ", Slide: " << slide << ", Fluorescence: " << (hasFluorescence&&fluor==0?"yes":"no") << ", Cell count: " << numContours << std::endl;
for (int cell = 0; cell < numContours; cell++)
{
CvSeq *seq = book[direct]->contourArray[cell];
int numPoints = seq->total;
outfile << "#Cell: " << cell+1 << ", Point Count: " << numPoints << std::endl;
for (int i=0; i<numPoints; i++)
{
CvPoint* point = (CvPoint*) cvGetSeqElem(seq, i);
outfile << point->x << " " << point->y << " ";
}
outfile << std::endl;
}
}
}
}
outfile.flush();
outfile.close();
return true;
}
bool CaptureManager::ImportContours(const char* file)
{
std::ifstream infile;
//std::cout << "opening: " << file << std::endl;
infile.open(file, std::ifstream::in);
if (!infile)
{
wxLogError(_T("Unable to open file %s"), file);
return false;
}
//check if there's already some detected cells.
bool hasCells = false;
for( int j=0; j<slideCount; j++)
{
for( int i=0; i<frameCount; i++ )
{
for( int k=0; k<2; k++ )
{
if (book[CalculateDirect(i,j,(k==0?false:true))]->contourArray.size())
{
hasCells = true;
break;
}
}
}
}
if (hasCells)
{
int reply = wxMessageBox(_T("There are already detected cells. Do you want to remove existing cells before importing tracking data?"), _T("Remove existing cells?"), wxYES_NO | wxCANCEL, NULL);
if (reply == wxCANCEL)
return false;
else if(reply == wxYES)
{
for( int j=0; j<slideCount; j++)
for( int i=0; i<frameCount; i++ )
for( int k=0; k<2; k++ )
book[CalculateDirect(i,j,(k==0?false:true))]->RemoveAllContours();
}
}
//TODO: give notice if the movie info of the track-data does not match with current movie.
int NumCells;
int Width, Height, FrameCount, SlideCount, FPS;
std::string ignStr, flString;
infile >> ignStr >> Width >> ignStr >> ignStr >> Height >> ignStr >> ignStr >> FrameCount >> ignStr >> ignStr >> SlideCount >> ignStr >> ignStr >> flString >> ignStr >> FPS;
//std::cout << Width << " " << Height << " " << FrameCount << " " << SlideCount << " " << flString << " " << FPS << std::endl;
bool fluor = (flString.compare("yes,") == 0);
if (Width != size.width || Height != size.height || FrameCount != frameCount || SlideCount != slideCount || fluor != hasFluorescence || FPS != fps)
{
int reply = wxMessageBox(_T("The contours to be loaded do not fit the current image series. Proceed?"), _T("Proceed?"), wxYES_NO | wxCANCEL, NULL);
if (reply == wxCANCEL)
return false;
}
int frame = -1, slide = -1, numContours = -1;
bool noErrors = true;
while (noErrors && !infile.eof())
{
flString.clear();
infile >> ignStr >> frame >> ignStr >> ignStr >> slide >> ignStr >> ignStr >> flString >> ignStr >> ignStr >> numContours;
//std::cout << frame << " " << slide << " " << flString << " " << numContours << " " << std::endl;
if (frame >= 0 && frame < frameCount && slide >= 0 && slide < slideCount && noErrors)
{
for (int cell=0; cell<numContours && noErrors; cell++)
{
int cellid,numPoints;
/*if(cell >= 1)
{
char* buffer = (char*) malloc (sizeof(char)*1);
fread (buffer,1,1,fp);
std::cout << cell << " -- " << buffer << std::endl;
}*/
infile >> ignStr >> cellid >> ignStr >> ignStr >> ignStr >> numPoints;
std::vector<wxPoint> roi(numPoints);
for (int i=0; i<numPoints && noErrors; i++)
{
infile >> roi[i].x >> roi[i].y;
//std::cout << roi[i].x << " " << roi[i].y << std::endl;
}
if (noErrors)
book[CalculateDirect(frame, slide, (flString.compare("yes,") == 0))]->AddRoi(roi);
}
}
}
infile.close();
this->ReloadCurrentFrameContours();
return true;
}
int CaptureManager::GetTotalPos()
{
return CalculateDirect(pos, zPos, viewFluorescence);
}
