resolved trivial merge conflicts

MyLibs/IllumWormProtocol.c

@@ -49,6 +49,7 @@
 //OpenCV Headers
 //#include <cxcore.h>
 #include "opencv2/highgui/highgui_c.h"
+#include "opencv2/imgproc/imgproc_c.h"
 //#include <cv.h>
 
 // Andy's Libraries

MyLibs/Talk2FrameGrabber.cpp

@@ -229,7 +229,7 @@ int PrepareFrameGrabberForAcquire(FrameGrabber* fg){
 
 		// Set the timout to be very short
 		printf("Setting acquisition timeout time.\n");
-		setAcquisitionTimeout(fg, 10); //in Aravis lab this was 4
+		setAcquisitionTimeout(fg, 100); //in Aravis lab this was 4
 
 
 		printf("Prepare frame grabber for acquire completed.");

MyLibs/Talk2Stage.c

@@ -103,7 +103,7 @@ HANDLE InitializeUsbStage(){
 
 		/** Open the Serial Port **/
 		HANDLE hSerial;
-		hSerial = CreateFile("COM3", GENERIC_READ | GENERIC_WRITE, FILE_SHARE_WRITE | FILE_SHARE_READ, NULL, OPEN_EXISTING, 0, NULL);
+		hSerial = CreateFile("COM4", GENERIC_READ | GENERIC_WRITE, FILE_SHARE_WRITE | FILE_SHARE_READ, NULL, OPEN_EXISTING, 0, NULL);
 		if(hSerial==INVALID_HANDLE_VALUE){
 			if(GetLastError()==ERROR_FILE_NOT_FOUND){
 				//serial port does not exist.
@@ -156,6 +156,24 @@ HANDLE InitializeUsbStage(){
 
 }
 
+
+/*
+ *
+ *  SendCommandToStage This is a wrapper of the Windows function WriteFile()
+ *  See, e.g.  https://msdn.microsoft.com/en-us/library/windows/desktop/aa365747%28v=vs.85%29.aspx
+ *
+ */
+
+BOOL SendCommandToStage(HANDLE hfile, LPCVOID lpBuffer, DWORD nNumberOfBytesToWrite, LPDWORD      lpNumberOfBytesWritten, LPOVERLAPPED lpOverlapped){
+	BOOL bErrorFlag;
+	bErrorFlag=WriteFile(hfile, lpBuffer, nNumberOfBytesToWrite, lpNumberOfBytesWritten, lpOverlapped);
+	printf(" [SENT STAGE] `%s` \n",lpBuffer);
+	return bErrorFlag;
+
+}
+
+
+
 /*
  If you don't clear some buffer and you are using the virtual com port driver, then 
  the stage stops responding to commands after around the 3300th command. By running this function
@@ -172,13 +190,14 @@ void clearStageBuffer(HANDLE s){
 
         COMSTAT Status; 
 
-        ClearCommError( s, &dwErrors, &Status); 
+        ClearCommError( s, &dwErrors, &Status);  // Windows function to clear a devices error flag
         Length = Status.cbInQue;        // get the rx data length in buffer 
-        // Get data and put it in to iBuffer 
+        // Get data and put it in to pText 
         DWORD nRead; 
         char * pText; 
         pText = (char *)malloc(sizeof(char)*(Length + 2)); 
         ReadFile(s,pText, Length, &nRead,NULL); 
+		printf(" [STAGE REPLY] `%s`\n",pText); // Display to console
         free(pText); 
  		return;
 
@@ -201,8 +220,8 @@ int spinStage(HANDLE s, int xspeed,int yspeed){
 
 
 	char* buff=(char*) malloc(sizeof(char)*1024);
-	sprintf(buff,"SPIN X=%d Y=%d\r",xspeed,yspeed);
-	bErrorFlag=WriteFile(s, buff, strlen(buff), &Length, NULL);
+	sprintf(buff,"SPIN X=%d Y=%d\r",-yspeed,-xspeed);
+	bErrorFlag=SendCommandToStage(s, buff, strlen(buff), &Length, NULL);
 	free(buff);
 
 	if (FALSE == bErrorFlag)
@@ -219,8 +238,16 @@ int spinStage(HANDLE s, int xspeed,int yspeed){
 
 int haltStage(HANDLE s){
 		DWORD Length;
-		WriteFile(s, "HALT\r", strlen("HALT\r"), &Length, NULL);
+		BOOL bErrorFlag = FALSE;
+		printf("About to tell stage to halt, but first pausing execution for 5 ms\n");
+		 _sleep(5);
+		bErrorFlag=SendCommandToStage(s, "HALT\r", strlen("HALT\r"), &Length, NULL);
+		if (FALSE == bErrorFlag){
+			printf("Failure: Unable to write to serial port.\n");
+		}
 		clearStageBuffer(s);
+		printf("Continuing to pause execution for 5 ms\n");
+		_sleep(5);
 		return 0;
 
 }
@@ -229,7 +256,7 @@ int moveStageRel(HANDLE s, int xpos, int ypos){
 	DWORD Length;
 	char* buff=(char*) malloc(sizeof(char)*1024);
 	sprintf(buff,"MOVEI X=%d Y=%d\r",xpos,ypos);
-	WriteFile(s, buff, strlen(buff), &Length, NULL);
+	SendCommandToStage(s, buff, strlen(buff), &Length, NULL);
 	free(buff);
 	clearStageBuffer(s);
 	return 0;
@@ -238,15 +265,15 @@ int moveStageRel(HANDLE s, int xpos, int ypos){
 
 int zeroStage(HANDLE s){
 	DWORD Length;
-	WriteFile(s, "HERE X=0 Y=0\r", strlen("HERE X=0 Y=0\r"), &Length, NULL);
+	SendCommandToStage(s, "HERE X=0 Y=0\r", strlen("HERE X=0 Y=0\r"), &Length, NULL);
 	clearStageBuffer(s);
 	return 0;
 
 }
 
 int centerStage(HANDLE s){
 	DWORD Length;
-	WriteFile(s, "CENTER X=30000 Y=30000\r", strlen("CENTER X=30000 Y=30000\r"), &Length, NULL);
+	SendCommandToStage(s, "CENTER X=30000 Y=30000\r", strlen("CENTER X=30000 Y=30000\r"), &Length, NULL);
 	printf("Centering stage.\n This takes a really really long time.\n");
 	printf("Hit enter when done. This will zero the stage.\n");
 	scanf("");

MyLibs/TransformLib.c

@@ -28,9 +28,8 @@
 
 
 //OpenCV Headers
-//#include <cxcore.h>
 #include "opencv2/highgui/highgui_c.h"
-//#include <cv.h>
+#include "opencv2/imgproc/imgproc_c.h"
 
 #include <stdio.h>
 #include <stdbool.h>