import org.micromanager.MMAcquisitionEngineMT;
import org.micromanager.utils.MMException;
import org.micromanager.metadata.MMAcqDataException;
import org.micromanager.AcqControlDlg;
import org.micromanager.image5d.Image5DWindow;
import java.util.ArrayList;


public class MMAcquisitionEngineMTMosaic extends MMAcquisitionEngineMT {
	
	ArrayList contigSetup = new ArrayList();
	ArrayList img5dList = new ArrayList();
	AffineTransform offScreenToStageTransformOld_;
	double magOld_;
	Point2D.Double originOld_;

	private int getContigIndex(positionIndex) {
		contig = getContig(posList_.getPosition(positionIndex));
		return conIdx = contigs.indexOf(contig);
	}

	protected void setupImage5DArray() {
	   img5d_ = new Image5D[contigs.size()]; 
	   i5dWin_ = new Image5DWindow[contigs.size()];
   }

	protected void fullSetup(int posIdx) throws MMException, IOException, MMAcqDataException {
		contigCount = contigs.size();
		conIdx = getContigIndex(posIdx);
		setupImage5d(conIdx);
		contigSetup.add(conIdx);
	   acquisitionDirectorySetup(posIdx);
	}

   protected void insertPixelsIntoImage5D(int sliceIdx, int channelIdx, int actualFrameCount,
		   int posIndexNormalized, Object img) {
		conIdx = getContigIndex(posIndexNormalized);
		pos = posList_.getPosition(posIndexNormalized);
		rect = getContigBoundsOffScreen(getContig(pos));
		moveOriginTo(new Point((int)rect.x, (int)rect.y));
		stagePos = new Point2D.Double(pos.getX(),pos.getY());
		pixel = stageToOffScreen(gui.getXYStagePosition());
		placePatchInImage5D(img5d_[conIdx], channelIdx+1, sliceIdx+1, actualFrameCount+1, (int) pixel.x, (int) pixel.y, img, 512, 512);
		img5d_[conIdx].updateAndDraw();
		//gui.displayImage(img);
		if (!i5dWin_[conIdx].isPlaybackRunning())
		{
		   img5d_[conIdx].setCurrentPosition(0, 0, channelIdx, sliceIdx, actualFrameCount);
		}

		/*print("conIdex:  "+conIdx);
		print("posIndex: "+posIndexNormalized);
		print("frame:    "+actualFrameCount);
	   print("slice:    "+sliceIdx);
		print("channel:  "+channelIdx);
		print("pixel:    "+pixel.x+","+pixel.y);
		print("");
		*/
   }

	protected int getAvailablePosIndex(int posIndexNormalized) {
		conIdx = getContigIndex(posIndexNormalized);
		int index=(null!=img5d_[conIdx])
			?conIdx
			:0;
		return index;
	}

	protected void setupImage5DWindowCountdown(GregorianCalendar cldStart,
			int posIndexNormalized) {
		conIdx = getContigIndex(posIndexNormalized);
		if (i5dWin_ != null)
			if (i5dWin_[conIdx] != null) {
	    	   i5dWin_[conIdx].startCountdown((long)frameIntervalMs_ - (GregorianCalendar.getInstance().getTimeInMillis() - cldStart.getTimeInMillis()), numFrames_ - frameCount_);
	      }
	}

   protected Image5D createImage5D(int posIdx, int type, int numSlices, int actualFrames) {
		print("createImage5D");
		rect = getContigBoundsOffScreen(contigs.get(posIdx));
		return new Image5D(acqName_, type, (int) rect.getWidth(), (int) rect.getHeight(), channels_.size(), numSlices, actualFrames, true);
   }

	protected void generateMetaData(double zCur, int sliceIdx, int channelIdx, int posIdx, int posIndexNormalized, double exposureMs, Object img) {
	// Do nothing for now.
		;
	}

	protected void cleanup() {
		offScreenToStageTranform = offScreenToStageTransformOld_;
		setMag(magOld_);
		setOrigin(originOld_);
		super.cleanup();
		contigSetup.clear();
		img5dList.clear();
	}

	public void acquire() {
		posList_ = convertRoiManagerToPositionList(rm);
		offScreenToStageTransformOld_ = offScreenToStageTransform;
		magOld_ = surveyorMagnification;
		originOld_ = getOrigin();
		setupContigs(posList_);
		setMag(1.0);
		super.acquire();
	}
}

MMAcquisitionEngineMTMosaic newMosaicEngine() {
	eng = new MMAcquisitionEngineMTMosaic();
	eng.setCore(mmc, gui.afMgr_);
	eng.enableMultiPosition(true);
	return eng;
}

void createMosaicAcqDialog(MMAcquisitionEngineMTMosaic eng) {
	acq = new AcqControlDlg(eng, gui.mainPrefs_, gui);
	acq.multiPosCheckBox_.setVisible(false);
	acq.multiPosCheckBox_.setSelected(true);
	acq.listButton.setVisible(false);
	surveyorRoiLabel = new JLabel("(Each Surveyor ROI makes one mosaic.)");
	surveyorRoiLabel.setFont(new Font("Arial", Font.PLAIN, 10));
	surveyorRoiLabel.setBounds(15, 18, 200, 19);
	acq.positionsPanel_.add(surveyorRoiLabel);
	acq.Title = acq.Title + " (Surveyor Mosaics)";
	acq.posModeCombo_.SelectedIndex = 1;
	acq.show();
}


void setupContigs(PositionList posList) {
	frameWidth = getROI()[2];
	frameHeight = getROI()[3];
	pixelSize = mmc.getPixelSizeUm();
	findContigs(posList);
}