/*
* Smooths, thresholds and finds the worms contour.
* The original image must already be loaded into Worm.ImgOrig
* The Smoothed image is deposited into Worm.ImgSmooth
* The thresholded image is deposited into Worm.ImgThresh
* The Boundary is placed in Worm.Boundary
*
*/
void FindWormBoundary(WormAnalysisData* Worm, WormAnalysisParam* Params){
/** This function currently takes around 5-7 ms **/
/**
* Before I forget.. plan to make this faster by:
* a) using region of interest
* b) decimating to make it smaller (maybe?)
* c) resize
* d) not using CV_GAUSSIAN for smoothing
*/
TICTOC::timer().tic("cvSmooth");
cvSmooth(Worm->ImgOrig,Worm->ImgSmooth,CV_GAUSSIAN,Params->GaussSize*2+1);
//cvSmooth(Worm->ImgOrig,Worm->ImgSmooth,CV_MEDIAN,Params->GaussSize*2+1);
//cvSmooth(Worm->ImgOrig,Worm->ImgSmooth,CV_BLUR,Params->GaussSize*2+1,Params->GaussSize*2+1);
TICTOC::timer().toc("cvSmooth");
TICTOC::timer().tic("cvThreshold");
cvThreshold(Worm->ImgSmooth,Worm->ImgThresh,Params->BinThresh,255,CV_THRESH_BINARY );
TICTOC::timer().toc("cvThreshold");
CvSeq* contours;
IplImage* TempImage=cvCreateImage(cvGetSize(Worm->ImgThresh),IPL_DEPTH_8U,1);
cvCopy(Worm->ImgThresh,TempImage);
TICTOC::timer().tic("cvFindContours");
cvFindContours(TempImage,Worm->MemStorage, &contours,sizeof(CvContour),CV_RETR_EXTERNAL,CV_CHAIN_APPROX_NONE,cvPoint(0,0));
TICTOC::timer().toc("cvFindContours");
TICTOC::timer().tic("cvLongestContour");
if (contours) LongestContour(contours,&(Worm->Boundary));
TICTOC::timer().toc("cvLongestContour");
cvReleaseImage(&TempImage);
}
/*
* Smooths, thresholds and finds the worms contour.
* The original image must already be loaded into Worm.ImgOrig
* The Smoothed image is deposited into Worm.ImgSmooth
* The thresholded image is deposited into Worm.ImgThresh
* The Boundary is placed in Worm.Boundary
*
*/
void FindWormBoundary(WormAnalysisData* Worm, WormAnalysisParam* Params){
/** This function currently takes around 5-7 ms **/
/**
* Before I forget.. plan to make this faster by:
* a) using region of interest
* b) decimating to make it smaller (maybe?)
* c) resize
* d) not using CV_GAUSSIAN for smoothing
*/
/** Smooth the Image **/
TICTOC::timer().tic("cvSmooth");
cvSmooth(Worm->ImgOrig,Worm->ImgSmooth,CV_GAUSSIAN,Params->GaussSize*2+1);
TICTOC::timer().toc("cvSmooth");
/** Dilate and Erode **/
// cvDilate(Worm->ImgSmooth, Worm->ImgSmooth,NULL,3);
// cvErode(Worm->ImgSmooth, Worm->ImgSmooth,NULL,2);
/** Threshold the Image **/
TICTOC::timer().tic("cvThreshold");
cvThreshold(Worm->ImgSmooth,Worm->ImgThresh,Params->BinThresh,255,CV_THRESH_BINARY );
TICTOC::timer().toc("cvThreshold");
/** Dilate and Erode **/
if (Params->DilateErode==1){
TICTOC::timer().tic("DilateAndErode");
cvDilate(Worm->ImgThresh, Worm->ImgThresh,NULL,3);
cvErode(Worm->ImgThresh, Worm->ImgThresh,NULL,2);
TICTOC::timer().toc("DilateAndErode");
}
/** Find Contours **/
CvSeq* contours;
IplImage* TempImage=cvCreateImage(cvGetSize(Worm->ImgThresh),IPL_DEPTH_8U,1);
cvCopy(Worm->ImgThresh,TempImage);
TICTOC::timer().tic("cvFindContours");
cvFindContours(TempImage,Worm->MemStorage, &contours,sizeof(CvContour),CV_RETR_EXTERNAL,CV_CHAIN_APPROX_NONE,cvPoint(0,0));
TICTOC::timer().toc("cvFindContours");
CvSeq* rough;
/** Find Longest Contour **/
TICTOC::timer().tic("cvLongestContour");
if (contours) LongestContour(contours,&rough);
TICTOC::timer().toc("cvLongestContour");
cvReleaseImage(&TempImage);
/** Smooth the Boundary **/
if (Params->BoundSmoothSize>0){
TICTOC::timer().tic("SmoothBoundary");
CvSeq* smooth=smoothPtSequence(rough,Params->BoundSmoothSize,Worm->MemStorage);
Worm->Boundary=cvCloneSeq(smooth);
TICTOC::timer().toc("SmoothBoundary");
} else {
Worm->Boundary=cvCloneSeq(rough);
}
}
