user can specify desired roi. compiles. records. tested.

MyLibs/Talk2FrameGrabber.cpp

@@ -73,11 +73,12 @@ FrameGrabber* CreateFrameGrabberObject(){
  * and prepares the FrameGrabber for Acuisiation
  *
  */
-FrameGrabber* TurnOnFrameGrabber(){
+FrameGrabber* TurnOnFrameGrabber(int desiredWidth, int desiredHeight){
 	FrameGrabber* fg= CreateFrameGrabberObject();
 	InitializeFrameGrabber(fg);
 	//FrameGrabberSetRegionOfInterest(fg,0,127,1024,768);
-	//FrameGrabberSetRegionOfInterest(fg,0,0,1024,768);
+
+	FrameGrabberSetRegionOfInterest(fg,0,0,desiredWidth,desiredHeight);
 	PrepareFrameGrabberForAcquire(fg);
 	return fg;
 }

MyLibs/Talk2FrameGrabber.h

@@ -94,7 +94,7 @@ FrameGrabber* CreateFrameGrabberObject();
  * and prepares the FrameGrabber for Acuisiation
  *
  */
-FrameGrabber* TurnOnFrameGrabber();
+FrameGrabber* TurnOnFrameGrabber(int desiredWidth, int desiredHeight);
 
 /*
  * Initializes the frame grabber with a fg object

MyLibs/WormAnalysis.c

@@ -1091,12 +1091,17 @@ int CreateWormHUDS(IplImage* TempImage, WormAnalysisData* Worm, WormAnalysisPara
 	//cvDrawContours(TempImage, Worm->Boundary, cvScalar(255,0,0),cvScalar(0,255,0),100);
 
 	DrawSequence(&TempImage,Worm->Boundary);
-
+	
 //	DrawSequence(&TempImage,Worm->Segmented->LeftBound);
 //	DrawSequence(&TempImage,Worm->Segmented->RightBound);
 
+	if (!(Worm->Tail==NULL) && !(Worm->Head==NULL)) {
+
+
 	cvCircle(TempImage,*(Worm->Tail),CircleDiameterSize,cvScalar(255,255,255),1,CV_AA,0);
 	cvCircle(TempImage,*(Worm->Head),CircleDiameterSize/2,cvScalar(255,255,255),1,CV_AA,0);
+
+	}
 
 	/** Prepare Text **/
 	CvFont font;

MyLibs/experiment.c

@@ -119,6 +119,9 @@ Experiment* CreateExperimentStruct() {
 	/** Input Dimensions **/
 	exp->inputWidth=0;
 	exp->inputHeight=0;
+	exp->desiredInputSizeProvided=0; // 1 means the user provided only a width or height, 2 means the user provided both a width and a height
+	exp->desiredInputWidth=0;
+	exp->desiredInputHeight=0;
 
 	/** FrameGrabber Input **/
 	exp->fg = NULL;
@@ -234,6 +237,9 @@ void displayHelp() {
 	printf("\t-t\n\t\tUse USB stage tracker.\n\n");
 	printf("\t-x\n\tx 512\t Target x position  of worm for stage feedback loop. 0 is left.\n\n");
 	printf("\t-y\n\ty 384\t Target y position of worm for stage feedback loop. 0 is top.\n\n");
+	printf("\t-w 1088 \n\t\t Set the desired camera ROI width to 1088 (note this only works for the framegrabber) and must be consistent with pylon.\n\n");
+	printf("\t-h 1088 \n\t\t Set the desired camera ROI height to 1088 (note this only works for the framegrabber) and must be consistent with pylon.\n\n");
+
 	printf(
 			"\t-p  protocol.yml\n\t\tIlluminate according to a YAML protocol file.\n\n");
 	printf("\t-?\n\t\tDisplay this help.\n\n");
@@ -251,7 +257,7 @@ int HandleCommandLineArguments(Experiment* exp) {
 	opterr = 0;
 
 	int c;
-	while ((c = getopt(exp->argc, exp->argv, "sri:d:o:p:gtx:y:?")) != -1) {
+	while ((c = getopt(exp->argc, exp->argv, "sri:d:o:p:gtx:y:w:h:?")) != -1) {
 		switch (c) {
 		case 'i': /** specify input video file **/
 			exp->VidFromFile = 1;
@@ -327,6 +333,20 @@ int HandleCommandLineArguments(Experiment* exp) {
 				}
 				printf("Stage feedback target y= %d pixels.\n",exp->stageFeedbackTarget.y );
 		break;
+
+		case 'w': /** Pass in a desired camera input width **/
+				if (optarg != NULL) {
+					exp->desiredInputWidth = atoi(optarg);
+					exp->desiredInputSizeProvided=exp->desiredInputSizeProvided + 1;
+				}
+		break;
+
+		case 'h': /** Pass in a desired camera input width **/
+				if (optarg != NULL) {
+					exp->desiredInputHeight = atoi(optarg);
+					exp->desiredInputSizeProvided=exp->desiredInputSizeProvided + 1;
+				}
+		break;
 
 
 		case '?':
@@ -1046,12 +1066,24 @@ void RollVideoInput(Experiment* exp) {
 		/** Use source from camera **/
 		if (exp->UseFrameGrabber) {
 			/**Use Frame Grabber **/
-			exp->fg = TurnOnFrameGrabber();
+
+			if (exp->desiredInputSizeProvided==2){ 
+				// if the user provided a desired width and hegiht
+				exp->inputWidth=exp->desiredInputWidth;
+				exp->inputHeight=exp->desiredInputHeight;
+
+			}else{
+
+				exp->inputWidth=exp->fg->xsize;
+				exp->inputHeight=exp->fg->ysize;
+			}
+
+
+			exp->fg = TurnOnFrameGrabber(exp->inputWidth, exp->inputHeight);
 
 			printf("Query frame grabber for size of images..\n");
 
-			exp->inputWidth=exp->fg->xsize;
-			exp->inputHeight=exp->fg->ysize;
+
 
 
 

MyLibs/experiment.h

@@ -113,6 +113,9 @@ typedef struct ExperimentStruct{
 	/** Input Dimensions **/
 	int inputWidth;
 	int inputHeight;
+	int desiredInputSizeProvided; // 1 means the user provided only a width or height, 2 means the user provided both a width and a height
+	int desiredInputWidth;
+	int desiredInputHeight;
 
 	/** MostRecently Observed CameraFrameNumber **/
 	unsigned long lastFrameSeenOutside;

calibrateFG.cpp

@@ -522,7 +522,7 @@ int main (int argc, char** argv){
 	c->LoopsPerPt=20; // Number of frames we use to calibrate a given point
 
 	/** Start Camera **/
-	c->fg= TurnOnFrameGrabber();
+	c->fg= TurnOnFrameGrabber(NSIZEX,NSIZEY);
 
 	/** Set the acquisition timeout to be very long to give the camera time to take long exposures, as is typical with calibration **/
 	setAcquisitionTimeout(c->fg,200);

main.cpp

@@ -223,7 +223,6 @@ int main (int argc, char** argv){
 			/** Handle head-tail illumination sweep **/
 			HandleIlluminationSweep(exp);
 
-
 
 			/** Load Image into Our Worm Objects **/
 
@@ -232,44 +231,45 @@ int main (int argc, char** argv){
 
 			/** Apply Levels**/  //Note this is slightly redundant with LoadWormImg
 			if (exp->e == 0) exp->e=simpleAdjustLevels(exp->fromCCD->iplimg, exp->Worm->ImgOrig, exp->Params->LevelsMin, exp->Params->LevelsMax);
-
+			
 
 			TICTOC::timer().tic("EntireSegmentation");
 			/** Do Segmentation **/
-			DoSegmentation(exp);
+			if (exp->RecordOnly==0) DoSegmentation(exp);
 			TICTOC::timer().toc("EntireSegmentation");
 
 
-
 			/** Real-Time Curvature Phase Analysis, and phase induced illumination **/
 		    HandleCurvaturePhaseAnalysis(exp);
 
+
 			/** If the DLP is not displaying right now, than turn off the mirrors */
 			ClearDLPifNotDisplayingNow(exp);
 
 
+
 			/* Transform the segmented worm coordinates into DLP space */
 			/* Note that this is much more computationally efficient than to transform the original image 
 			or to transform the resulting illumination pattern                                           */ 
-
+						
 			TICTOC::timer().tic("TransformSegWormCam2DLP");
-			if (exp->e == 0 && exp->RecordOnly!=0){
+			if (exp->e == 0 && exp->RecordOnly==0){
 				TransformSegWormCam2DLP(exp->Worm->Segmented, exp->segWormDLP,exp->Calib);
 			}
 			TICTOC::timer().toc("TransformSegWormCam2DLP");
 
 			/** Handle the Choise of Illumination Protocol Here**/
 			/** ANDY: write this here **/
-			if (exp->RecordOnly!=0) HandleTimedSecondaryProtocolStep(exp->p,exp->Params);
-
+			if (exp->RecordOnly==0) HandleTimedSecondaryProtocolStep(exp->p,exp->Params);
+	
 
 			/*** Do Some Illumination ***/
 
 			/** Clear the illumination pattern **/
 			SetFrame(exp->forDLP,0);
 			SetFrame(exp->IlluminationFrame,0);
 
-			if (exp->e == 0 && exp->RecordOnly!=0) {
+			if (exp->e == 0 && exp->RecordOnly==0) {
 				if (exp->Params->IllumFloodEverything) {
 					SetFrame(exp->IlluminationFrame,128); // Turn all of the pixels on
 					SetFrame(exp->forDLP,128); // Turn all of the pixels o
@@ -301,16 +301,20 @@ int main (int argc, char** argv){
 			}
 
 
+
 			TICTOC::timer().tic("SendFrameToDLP");
 			if (exp->e == 0 && exp->Params->DLPOn && !(exp->SimDLP)) T2DLP_SendFrame((unsigned char *) exp->forDLP->binary, exp->myDLP); // Send image to DLP
 			TICTOC::timer().toc("SendFrameToDLP");
 
 
 			/*** DIsplay Some Monitoring Output ***/
 			if (exp->e == 0) CreateWormHUDS(exp->HUDS,exp->Worm,exp->Params,exp->IlluminationFrame);
+
+
 			if (exp->e==0 && exp->stageIsPresent==1) MarkRecenteringTarget(exp);
 
 
+
 			if (exp->e == 0 &&  EverySoOften(exp->Worm->frameNum,exp->Params->DispRate) ){
 				TICTOC::timer().tic("DisplayOnScreen");
 				/** Setup Display but don't actually send to screen **/