test.c

/*
 * Copyright 2010 Andrew Leifer et al <leifer@fas.harvard.edu>
 * This file is part of MindControl.
 *
 * MindControl is free software: you can redistribute it and/or modify
 * it under the terms of the GNU  General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * MindControl s distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with MindControl. If not, see <http://www.gnu.org/licenses/>.
 *
 * For the most up to date version of this software, see:
 * https://github.com/samuellab/mindcontrol
 *
 *
 *
 * NOTE: If you use any portion of this code in your research, kindly cite:
 * Leifer, A.M., Fang-Yen, C., Gershow, M., Alkema, M., and Samuel A. D.T.,
 * 	"Optogenetic manipulation of neural activity with high spatial resolution in
 *	freely moving Caenorhabditis elegans," Nature Methods, Submitted (2010).
 */

/*
 * This is a test program that performs some basic tests of the mindcontrol software.
 * It is mostly useful for debugging.
 */

//Standard C headers
#include <stdio.h>
#include <ctime>
#include <time.h>
#include <conio.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>


//C++ header
#include <iostream>
#include <limits>

using namespace std;

//OpenCV Headers
#include <highgui.h>
#include <cv.h>
#include <cxcore.h>



//Andy's Headers
#include "MyLibs/AndysOpenCvLib.h"
#include "MyLibs/WormAnalysis.h"
#include "MyLibs/IllumWormProtocol.h"
#include "MyLibs/version.h"

//3rd Party Libraries
#include "3rdPartyLibs/tictoc.h"

Protocol* CreateTestProtocol(char* name){

	Protocol* myP=CreateProtocolObject();
	myP->Description="A test protocol.";
	myP->Filename=name;

	myP->GridSize=cvSize(21,99);
	/** Create the Steps Object and Load it into the Protocol **/
	myP->Steps=CreateStepsObject(myP->memory);


	/** Create Some Polygons **/
	WormPolygon* Head = CreateWormPolygon(myP->memory,myP->GridSize);
	WormPolygon* Left = CreateWormPolygon(myP->memory,myP->GridSize);
	WormPolygon* Right = CreateWormPolygon(myP->memory,myP->GridSize);
	WormPolygon* Tail = CreateWormPolygon(myP->memory,myP->GridSize);
	WormPolygon* Everything = CreateWormPolygon(myP->memory,myP->GridSize);

	//(length along centerline,radius from centerline)
	cvSeqPush(Head->Points,&cvPoint(-10,0));
	cvSeqPush(Head->Points,&cvPoint(10,0));
	cvSeqPush(Head->Points,&cvPoint(10,20));
	cvSeqPush(Head->Points,&cvPoint(-10,20));

	cvSeqPush(Left->Points,&cvPoint(0,30));
	cvSeqPush(Left->Points,&cvPoint(-10,30));
	cvSeqPush(Left->Points,&cvPoint(-10,70));
	cvSeqPush(Left->Points,&cvPoint(0,70));

	cvSeqPush(Right->Points,&cvPoint(0,30));
	cvSeqPush(Right->Points,&cvPoint(10,30));
	cvSeqPush(Right->Points,&cvPoint(10,70));
	cvSeqPush(Right->Points,&cvPoint(0,70));

	cvSeqPush(Tail->Points,&cvPoint(-10,80));
	cvSeqPush(Tail->Points,&cvPoint(0,80));
	cvSeqPush(Tail->Points,&cvPoint(0,99));
	cvSeqPush(Tail->Points,&cvPoint(-10,99));

	cvSeqPush(Everything->Points,&cvPoint(-10,0));
	cvSeqPush(Everything->Points,&cvPoint(10,0));
	cvSeqPush(Everything->Points,&cvPoint(10,99));
	cvSeqPush(Everything->Points,&cvPoint(-10,99));

	/** Create an Illumination Montage**/
	CvSeq* FirstIllum=CreateIlluminationMontage(myP->memory);
	CvSeq* SecondIllum=CreateIlluminationMontage(myP->memory);
	CvSeq* ThirdIllum=CreateIlluminationMontage(myP->memory);
	CvSeq* FourthIllum=CreateIlluminationMontage(myP->memory);


	/** Let's load up the illumination montages with polygons**/
	cvSeqPush(FirstIllum,&Head);
	cvSeqPush(FirstIllum,&Tail);
	cvSeqPush(FirstIllum,&Left);
	cvSeqPush(FirstIllum,&Right);

	printf("FirstIllum->total=%d\n",FirstIllum->total);

	cvSeqPush(SecondIllum,&Head);
	cvSeqPush(SecondIllum,&Right);


	cvSeqPush(ThirdIllum,&Tail);
	cvSeqPush(ThirdIllum,&Left);

    cvSeqPush(FourthIllum,&Everything);



	/** Let's Load the montages into a series of steps **/
	cvSeqPush(myP->Steps,&FirstIllum);
	cvSeqPush(myP->Steps,&SecondIllum);
	cvSeqPush(myP->Steps,&ThirdIllum);
	cvSeqPush(myP->Steps,&FourthIllum);


	printf("Writing test protocol in file: %s\n",myP->Filename);
	WriteProtocolToYAML(myP);

	printf("Head->points->total=%d\n",Head->Points->total);
	DestroyWormPolygon(&Head);
	DestroyWormPolygon(&Tail);
	DestroyWormPolygon(&Left);
	DestroyWormPolygon(&Right);
	return myP;

}




int main(){

	//char* name = (char*) malloc(sizeof(char)*50);



	printf(copyString("Hello you World\n"));

	printf("Points between line test\n");
	CvMemStorage* mem= cvCreateMemStorage();
	CvSeq* test=cvCreateSeq(CV_SEQ_ELTYPE_POINT, sizeof(CvSeq), sizeof(CvPoint),mem);
	GetLineFromEndPts(cvPoint(0,0),cvPoint(10,15),test);
	return 0;

	CvMemStorage* MyMem= cvCreateMemStorage();
	CvFileStorage* fs=cvOpenFileStorage("appendTest.yaml",MyMem,CV_STORAGE_APPEND);
	cvStartWriteStruct(fs,"Experiment",CV_NODE_MAP,NULL);
		cvWriteInt(fs,"x",10);
		cvWriteString(fs,"string","calvin And Hobbes");
	cvEndWriteStruct(fs);
	cvReleaseFileStorage(&fs);

	return 0;


	Protocol* myP=CreateTestProtocol("protocol.yml");
	VerifyProtocol(myP);

	WriteProtocolToYAML(myP);
	DestroyProtocolObject(&myP);

	printf("Done writing...\n\n");
	Protocol* protocol2 = LoadProtocolFromFile("protocol.yml");
	VerifyProtocol(protocol2);
	protocol2->Filename="protoco2.yml";

	printf("protocol2->Steps->total=%d\n",protocol2->Steps->total);
	WriteProtocolToYAML(protocol2);








	printf("GenerateRectangleWorm\n");



	IplImage* rectWorm= GenerateRectangleWorm(protocol2->GridSize);
	printf("ShowImage\n");
	cvNamedWindow("RectWorm");
	cvShowImage("RectWorm",rectWorm);
	int k;
	for (k = 0; k < protocol2->Steps->total; ++k) {
		printf("====Step Number %d====\n",k);
		cvZero(rectWorm);
		TICTOC::timer().tic("IllumRectWorm()");
		IllumRectWorm(rectWorm,protocol2,k,0);
		TICTOC::timer().toc("IllumRectWorm()");
		cvShowImage("RectWorm",rectWorm);
		cvWaitKey(0);

	}

	printf("%s",TICTOC::timer().generateReportCstr());
	return 0;
}