/**
 Polargraph controller
 Copyright Sandy Noble 2012.
 
 This file is part of Polargraph Controller.
 
 Polargraph Controller 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.
 
 Polargraph Controller is 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 Polargraph Controller.  If not, see <http://www.gnu.org/licenses/>.
 
 Requires the excellent ControlP5 GUI library available from http://www.sojamo.de/libraries/controlP5/.
 Requires the excellent Geomerative library available from http://www.ricardmarxer.com/geomerative/.
 
 This is an application for controlling a polargraph machine, communicating using ASCII command language over a serial link.
 
 sandy.noble@gmail.com
 http://www.polargraph.co.uk/
 http://code.google.com/p/polargraph/
 */

class DisplayMachine extends Machine
{
  private Rectangle outline = null;
  private float scaling = 1.0;
  private Scaler scaler = null;
  private PVector offset = null;
  private float imageTransparency = 1.0;

  private Set<PVector> extractedPixels = new HashSet<PVector>(0);

  PImage scaledImage = null;
  
  private PVector currentPixel = null;

  public DisplayMachine(Machine m, PVector offset, float scaling)
  {
    // construct
    super(m.getWidth(), m.getHeight(), m.getMMPerRev(), m.getStepsPerRev());

    super.machineSize = m.machineSize;

    super.page = m.page;
    super.imageFrame = m.imageFrame;
    super.pictureFrame = m.pictureFrame;

    super.imageBitmap = m.imageBitmap;
    super.imageFilename = m.imageFilename;

    super.stepsPerRev = m.stepsPerRev;
    super.mmPerRev = m.mmPerRev;

    super.mmPerStep = m.mmPerStep;
    super.stepsPerMM = m.stepsPerMM;
    super.maxLength = m.maxLength;
    super.gridSize = m.gridSize;

    this.offset = offset;
    this.scaling = scaling;
    this.scaler = new Scaler(scaling, 100.0);

    this.outline = null;
  }

  public Rectangle getOutline()
  {
    outline = new Rectangle(offset, new PVector(sc(super.getWidth()), sc(super.getHeight())));
    return this.outline;
  }

  private Scaler getScaler()
  {
    if (scaler == null)
      this.scaler = new Scaler(getScaling(), getMMPerStep());
    return scaler;
  }

  public void setScale(float scale)
  {
    this.scaling = scale;
    this.scaler = new Scaler(scale, getMMPerStep());
  }
  public float getScaling()
  {
    return this.scaling;
  }
  public float sc(float val)
  {
    return getScaler().scale(val);
  }
  public void setOffset(PVector offset)
  {
    this.offset = offset;
  }
  public PVector getOffset()
  {
    return this.offset;
  }
  public void setImageTransparency(float trans)
  {
    this.imageTransparency = trans;
  }
  public int getImageTransparency()
  {
    float f = 255.0 * this.imageTransparency;
    f += 0.5;
    int result = (int) f;
    return result;
  }
  
  public PVector getCurrentPixel()
  {
    return this.currentPixel;
  }
  public void setCurrentPixel(PVector p)
  {
    this.currentPixel = p;
  }

  public void loadNewImageFromFilename(String filename)
  {
    super.loadImageFromFilename(filename);
    super.sizeImageFrameToImageAspectRatio();
    this.setExtractedPixels(new HashSet<PVector>(0));
  }

  public final int DROP_SHADOW_DISTANCE = 4;
  public String getZoomText()
  {
    NumberFormat nf = NumberFormat.getNumberInstance(Locale.UK);
    DecimalFormat df = (DecimalFormat)nf;  
    df.applyPattern("###");
    String zoom = df.format(scaling * 100) + "% zoom";
    return zoom;
  }

  public String getDimensionsAsText(Rectangle r)
  {
    return getDimensionsAsText(r.getSize());
  }
  public String getDimensionsAsText(PVector p)
  {
    String dim = inMM(p.x) + " x " + inMM(p.y) + "mm";
    return dim;
  }

  public void drawForSetup()
  {
    // work out the scaling factor.
    noStroke();
    // draw machine outline

    // drop shadow
    fill(80);
    rect(getOutline().getLeft()+DROP_SHADOW_DISTANCE, getOutline().getTop()+DROP_SHADOW_DISTANCE, getOutline().getWidth(), getOutline().getHeight());

    fill(getMachineColour());
    rect(getOutline().getLeft(), getOutline().getTop(), getOutline().getWidth(), getOutline().getHeight());
    text("machine " + getDimensionsAsText(getSize()) + " " + getZoomText(), getOutline().getLeft(), getOutline().getTop());

    if (displayingGuides)
    {
      // draw some guides
      stroke(getGuideColour());
      strokeWeight(1);
      // centre line
      line(getOutline().getLeft()+(getOutline().getWidth()/2), getOutline().getTop(), 
      getOutline().getLeft()+(getOutline().getWidth()/2), getOutline().getBottom());

      // page top line
      line(getOutline().getLeft(), getOutline().getTop()+sc(getHomePoint().y), 
      getOutline().getRight(), getOutline().getTop()+sc(getHomePoint().y));
    }

    // draw page
    fill(getPageColour());
    rect(getOutline().getLeft()+sc(getPage().getLeft()), 
    getOutline().getTop()+sc(getPage().getTop()), 
    sc(getPage().getWidth()), 
    sc(getPage().getHeight()));
    text("page " + getDimensionsAsText(getPage()), getOutline().getLeft()+sc(getPage().getLeft()), 
    getOutline().getTop()+sc(getPage().getTop()));
    fill(0);
    text("offset " + getDimensionsAsText(getPage().getPosition()), 
    getOutline().getLeft()+sc(getPage().getLeft()), 
    getOutline().getTop()+sc(getPage().getTop())+10);
    noFill();

    // draw home point
    noFill();
    strokeWeight(5);
    stroke(0, 128);
    PVector onScreen = scaleToScreen(inMM(getHomePoint()));
    ellipse(onScreen.x, onScreen.y, 15, 15);
    strokeWeight(2);
    stroke(255);
    ellipse(onScreen.x, onScreen.y, 15, 15);
    
    text("Home point", onScreen.x+ 15, onScreen.y-5);
    text(int(inMM(getHomePoint().x)+0.5) + ", " + int(inMM(getHomePoint().y)+0.5), onScreen.x+ 15, onScreen.y+15);


    if (displayingGuides 
      && getOutline().surrounds(getMouseVector())
      && currentMode != MODE_MOVE_IMAGE
      && mouseOverControls().isEmpty()
      )
    {  
      drawHangingStrings();
      drawLineLengthTexts();
      cursor(CROSS);
    }
    else
    {
      cursor(ARROW);
    }
  }

  public void drawLineLengthTexts()
  {
    PVector actual = inMM(asNativeCoords(inSteps(scaleToDisplayMachine(getMouseVector()))));
    PVector cart = scaleToDisplayMachine(getMouseVector());
    NumberFormat nf = NumberFormat.getNumberInstance(Locale.UK);
    DecimalFormat df = (DecimalFormat)nf;  
    df.applyPattern("###.#");

    text("Line 1: " + df.format(actual.x) + "mm", getDisplayMachine().getOutline().getLeft()+10, getDisplayMachine().getOutline().getTop()+18);
    text("Line 2: " + df.format(actual.y) + "mm", getDisplayMachine().getOutline().getLeft()+10, getDisplayMachine().getOutline().getTop()+28);

    text("X Position: " + df.format(cart.x) + "mm", getDisplayMachine().getOutline().getLeft()+10, getDisplayMachine().getOutline().getTop()+42);
    text("Y Position: " + df.format(cart.y) + "mm", getDisplayMachine().getOutline().getLeft()+10, getDisplayMachine().getOutline().getTop()+52);
  }

  public void draw()
  {
    // work out the scaling factor.
    noStroke();
    // draw machine outline

//    fill(80);
//    rect(getOutline().getLeft()+DROP_SHADOW_DISTANCE, getOutline().getTop()+DROP_SHADOW_DISTANCE, getOutline().getWidth(), getOutline().getHeight());

    fill(getMachineColour());
    rect(getOutline().getLeft(), getOutline().getTop(), getOutline().getWidth(), getOutline().getHeight());



    if (displayingGuides)
    {
      // draw some guides
      stroke(getGuideColour());
      strokeWeight(1);
      // centre line
      line(getOutline().getLeft()+(getOutline().getWidth()/2), getOutline().getTop(), 
      getOutline().getLeft()+(getOutline().getWidth()/2), getOutline().getBottom());

      // page top line
      line(getOutline().getLeft(), getOutline().getTop()+sc(getHomePoint().y), 
      getOutline().getRight(), getOutline().getTop()+sc(getHomePoint().y));
    }

    // draw page
    fill(getPageColour());
    rect(getOutline().getLeft()+sc(getPage().getLeft()), 
    getOutline().getTop()+sc(getPage().getTop()), 
    sc(getPage().getWidth()), 
    sc(getPage().getHeight()));
    text("page " + getDimensionsAsText(getPage()), getOutline().getLeft()+sc(getPage().getLeft()), 
    getOutline().getTop()+sc(getPage().getTop())-3);
    noFill();



    // draw actual image
    if (displayingImage && imageIsReady())
    {
      float ox = getOutline().getLeft()+sc(getImageFrame().getLeft());
      float oy = getOutline().getTop()+sc(getImageFrame().getTop());
      float w = sc(getImageFrame().getWidth());
      float h = sc(getImageFrame().getHeight());
      tint(255, getImageTransparency());
      image(getImage(), ox, oy, w, h);
      noTint();
      strokeWeight(1);
      stroke(150, 150, 150, 40);
      rect(ox, oy, w-1, h-1);
      fill(150, 150, 150, 40);
      text("image", ox, oy-3);
      noFill();
    }
    
    stroke(getBackgroundColour(),150);
    strokeWeight(3);
    noFill();
    rect(getOutline().getLeft()-2, getOutline().getTop()-2, getOutline().getWidth()+3, getOutline().getHeight()+3);

    stroke(getMachineColour(),150);
    strokeWeight(3);
    noFill();
    rect(getOutline().getLeft()+sc(getPage().getLeft())-2, 
    getOutline().getTop()+sc(getPage().getTop())-2, 
    sc(getPage().getWidth())+4, 
    sc(getPage().getHeight())+4);



    if (displayingSelectedCentres)
    {
      drawExtractedPixelCentres();
    }
    if (displayingDensityPreview)
    {
      drawExtractedPixelDensities();
    }
    if (displayingGuides)
    {
      drawPictureFrame();
    }

    if (displayingVector && getVectorShape() != null)
    {
      displayVectorImage();
    }

    if (displayingGuides 
      && getOutline().surrounds(getMouseVector())
      && currentMode != MODE_MOVE_IMAGE
      && mouseOverControls().isEmpty()
      )
    {
      drawHangingStrings();
      drawRows();
      cursor(CROSS);
    }
    else
    {
      cursor(ARROW);
    }
  }
  
  public void drawForTrace()
  {
    // work out the scaling factor.
    noStroke();
    // draw machine outline
    
//    liveImage = trace_buildLiveImage();
    // draw actual image

//    if (drawingLiveVideo)
//    {
//      displayLiveVideo();
//    }
    
    if (drawingTraceShape && traceShape != null)
    {
      displaytraceShape();
    }
    else
    {
      
    }
  }
  
//  public void displayLiveVideo()
//  {
//    // draw actual image, maximum size
//    if (processedLiveImage != null)
//    {
//      // origin - top left of the corner
//      float ox = getPanel(PANEL_NAME_WEBCAM).getOutline().getRight()+7;
//      float oy = getPanel(PANEL_NAME_GENERAL).getOutline().getTop();
//      
//      // calculate size to display at.
//      float aspectRatio = (rotateWebcamImage) ? 480.0/640.0 : 640.0/480.0; // rotated, remember
//      float h = height - getPanel(PANEL_NAME_GENERAL).getOutline().getTop() -10;
//      float w = h * (480.0/640.0);
////      println("height: " + h + ", width: " + w);
////      println("origin x: " + ox + ", y: " + oy);
//      
//      if (rotateWebcamImage) 
//      {
//        float t = h;
//        h = w;
//        w = t;
//      }
//      
//      //stroke(255);
//      rect(ox,oy,w,h);
//
//      tint(255, getImageTransparency());
//      if (rotateWebcamImage)
//      {
//        translate(ox, oy);
//        rotate(radians(270));
//        image(processedLiveImage, -w, 0, w, h);
//        image(liveImage, -w, (w-(w/4))+10, w/4, h/4);
////        stroke(0,255,0);
////        ellipse(0,0,80,40);
////        stroke(0,0,255);
////        ellipse(-w,0,80,40);
//        rotate(radians(-270));
//        translate(-ox, -oy);
//      }
//      else
//      {
//        translate(ox, oy);
//        image(processedLiveImage, 0, 0, h, w);
//        image(liveImage, h-(h/4), w+10, h/4, w/4);
//        translate(-ox, -oy);
//      }
//      noTint();
//      noFill();
//    }
//  }
  
  public void displaytraceShape()
  {
    strokeWeight(1);
    
    if (captureShape != null)
    {
      //displaytraceShapeAtFullSize(traceShape, false, color(150,150,150));
      displaytraceShapeAtFullSize(captureShape, true, color(0,0,0));
    }
    else
    {
      displaytraceShapeAtFullSize(traceShape, false, color(255,255,255));
    }
  }
  
  public void displaytraceShapeAtFullSize(RShape vec, boolean illustrateSequence, Integer colour)
  {
    RG.ignoreStyles();
    // work out scaling to make it full size on the screen
    float aspectRatio = vec.getWidth()/vec.getHeight(); // rotated, remember
    float h = height - getPanel(PANEL_NAME_GENERAL).getOutline().getTop() -10;
    float w = h * aspectRatio;
    float scaler = h / vec.getWidth();
    if (rotateWebcamImage)
      scaler =  h / vec.getHeight();
    PVector position = new PVector(getPanel(PANEL_NAME_TRACE).getOutline().getRight()+7, getPanel(PANEL_NAME_GENERAL).getOutline().getTop());

    noFill();
    RPoint[][] pointPaths = vec.getPointsInPaths();
    if (illustrateSequence)
      pointPaths = sortPathsCentreFirst(vec, pathLengthHighPassCutoff);
    
    if (pointPaths != null)
    {
      float incPerPath = 0.0;
      if (illustrateSequence)
        incPerPath = 255.0 / (float) pointPaths.length;

      for(int i = 0; i<pointPaths.length; i++)
      {
        float col = (float)i * incPerPath;
//        if (pointPaths[i].length >= pathLengthHighPassCutoff)
//        {
          if (pointPaths[i] != null) 
          {
            if (illustrateSequence)
              stroke((int)col, (int)col, (int)col, 128);
            else
              stroke(colour);
              
            beginShape();
            for (int j = 0; j<pointPaths[i].length; j++)
            {
              PVector p = new PVector(pointPaths[i][j].x, pointPaths[i][j].y);
              p = PVector.mult(p, scaler);
              p = PVector.add(p, position);
              vertex(p.x, p.y);
            }
            endShape();
//          }
        }
      }
    }
    noFill();
  }
  
  public void displayVectorImage()
  {
    displayVectorImage(getVectorShape(), vectorScaling/100, getVectorPosition(), color(0,0,0), true);
    
    if (captureShape != null)
    {
      float scaling = inMM(getPictureFrame().getWidth()) / captureShape.getWidth();
      PVector position = new PVector(inMM(getPictureFrame().getPosition().x), inMM(getPictureFrame().getPosition().y) + (captureShape.getHeight() * scaling));
      displayVectorImage(captureShape, 
        scaling, 
        position, 
        color(0,200,0), true);
    }
  }
  
  public void displayVectorImage(RShape vec, float scaling, PVector position, int strokeColour, boolean drawCentroid)
  {
    PVector centroid = new PVector(vec.width/2, vec.height/2);
    centroid = PVector.mult(centroid, (vectorScaling/100));
    centroid = PVector.add(centroid, getVectorPosition());
    centroid = scaleToScreen(centroid);

    RPoint[][] pointPaths = vec.getPointsInPaths();
    RG.ignoreStyles();
    strokeWeight(1);
    if (pointPaths != null)
    {
      for(int i = 0; i<pointPaths.length; i++)
      {
        if (pointPaths[i] != null) 
        {
          beginShape();
          for (int j = 0; j<pointPaths[i].length; j++)
          {
            PVector p = new PVector(pointPaths[i][j].x, pointPaths[i][j].y);
            p = PVector.mult(p, scaling);
            p = PVector.add(p, position);
            if (getPage().surrounds(inSteps(p)))
            {
              p = scaleToScreen(p);
              stroke(strokeColour);
              vertex(p.x, p.y);
              //ellipse(p.x, p.y, 3, 3);
            }
          }
          endShape();
        }
      }
      if (drawCentroid)
      {
        // draw spot at centre
        fill(255,0,0,128);
        ellipse(centroid.x, centroid.y, 20,20);
        noFill();
      }
    }
  }


  // this scales a value from the screen to be a position on the machine
  /**  Given a point on-screen, this works out where on the 
   actual machine it refers to.
   */
  public PVector scaleToDisplayMachine(PVector screen)
  {
    // offset
    float x = screen.x - getOffset().x;
    float y = screen.y - getOffset().y;

    // transform
    float scalingFactor = 1.0/getScaling();
    x = scalingFactor * x;
    y = scalingFactor * y;

    // and out
    PVector mach = new PVector(x, y);
    return mach;
  }

  /** This works out the position, on-screen of a specific point on the machine.
   Both values are cartesian coordinates.
   */
  public PVector scaleToScreen(PVector mach)
  {
    // transform
    float x = mach.x * scaling;
    float y = mach.y * scaling;

    // offset
    x = x + getOffset().x;
    y = y + getOffset().y;

    // and out!
    PVector screen = new PVector(x, y);
    return screen;
  }

  // converts a cartesian coord into a native one
  public PVector convertToNative(PVector cart)
  {
    // width of machine in mm
    float width = inMM(super.getWidth());

    // work out distances
    float a = dist(0, 0, cart.x, cart.y);
    float b = dist(width, 0, cart.x, cart.y);

    // and out
    PVector nativeMM = new PVector(a, b);
    return nativeMM;
  }

  void drawPictureFrame()
  {
    strokeWeight(1);

    PVector topLeft = scaleToScreen(inMM(getPictureFrame().getTopLeft()));
    PVector botRight = scaleToScreen(inMM(getPictureFrame().getBotRight()));

    stroke (getFrameColour());

    // top left    
    line(topLeft.x-4, topLeft.y, topLeft.x-10, topLeft.y);
    line(topLeft.x, topLeft.y-4, topLeft.x, topLeft.y-10);

    // top right
    line(botRight.x+4, topLeft.y, botRight.x+10, topLeft.y);
    line(botRight.x, topLeft.y-4, botRight.x, topLeft.y-10);

    // bot right
    line(botRight.x+4, botRight.y, botRight.x+10, botRight.y);
    line(botRight.x, botRight.y+4, botRight.x, botRight.y+10);

    // bot left
    line(topLeft.x-4, botRight.y, topLeft.x-10, botRight.y);
    line(topLeft.x, botRight.y+4, topLeft.x, botRight.y+10);

    stroke(255);


    //    float width = inMM(getPictureFrame().getBotRight().x - getPictureFrame().getTopLeft().x);
    //    println("width: "+ width);
  }


  public void drawHangingStrings()
  {
    // hanging strings
    strokeWeight(4);
    stroke(255, 255, 255, 64);
    line(getOutline().getLeft(), getOutline().getTop(), mouseX, mouseY);
    line(getOutline().getRight(), getOutline().getTop(), mouseX, mouseY);
  }

  /**  This draws on screen, showing an arc highlighting the row that the mouse
   is on.
   */
  public void drawRows()
  {
    PVector mVect = getMouseVector();

    // scale it to  find out the coordinates on the machine that the mouse is pointing at.
    mVect = scaleToDisplayMachine(mVect);
    // convert it to the native coordinates system
    mVect = convertToNative(mVect);
    // snap it to the grid
    mVect = snapToGrid(mVect, getGridSize());
    // scale it back to find out how to represent this on-screen
    mVect = scaleToScreen(mVect);

    // and finally, because scaleToScreen also allows for the machine position (offset), subtract it.
    mVect.sub(getOffset());

    float rowThickness = inMM(getGridSize()) * getScaling();
    rowThickness = (rowThickness < 1.0) ? 1.0 : rowThickness;
    strokeWeight(rowThickness);
    stroke(150, 200, 255, 50);
    strokeCap(SQUARE);

    float dia = mVect.x*2;
    arc(getOutline().getLeft(), getOutline().getTop(), dia, dia, 0, 1.57079633);

    dia = mVect.y*2;
    arc(getOutline().getRight(), getOutline().getTop(), dia, dia, 1.57079633, 3.14159266);
    
  }

  void drawExtractedPixelCentres()
  {
    for (PVector cartesianPos : getExtractedPixels())
    {
      // scale em, danno.
      PVector scaledPos = scaleToScreen(cartesianPos);
      strokeWeight(1);
      stroke(255, 0, 0, 128);
      noFill();
      line(scaledPos.x-1, scaledPos.y-1, scaledPos.x+1, scaledPos.y+1);
      line(scaledPos.x-1, scaledPos.y+1, scaledPos.x+1, scaledPos.y-1);
    }
  }

  void drawExtractedPixelDensities()
  {

    float pixelSize = inMM(getGridSize()) * getScaling();
    pixelSize = (pixelSize < 1.0) ? 1.0 : pixelSize;

    pixelSize = pixelSize * getPixelScalingOverGridSize();

    if (getExtractedPixels() != null)
    {
      for (PVector cartesianPos : getExtractedPixels())
      {
        if ((cartesianPos.z <= pixelExtractBrightThreshold) && (cartesianPos.z >= pixelExtractDarkThreshold))
        {
          // scale em, danno.
          PVector scaledPos = scaleToScreen(cartesianPos);
          noStroke();
          fill(cartesianPos.z);
          switch (getDensityPreviewStyle())
          {
            case DENSITY_PREVIEW_ROUND: 
              previewRoundPixel(scaledPos, pixelSize, pixelSize);
              break;
            case DENSITY_PREVIEW_DIAMOND:
              previewDiamondPixel(scaledPos, pixelSize, pixelSize, cartesianPos.z);
              break;
            default:
              previewRoundPixel(scaledPos, pixelSize, pixelSize);
              break;
          }
        }
      }
    }
    noFill();
  }
  
  void previewDiamondPixel(PVector pos, float wide, float high, float brightness)
  {
    wide*=1.4;
    high*=1.4;
    // shall I try and draw a diamond here instead? OK! I'll do it! Ha!
    float halfWidth = wide / 2.0;
    float halfHeight = high / 2.0;
    fill(0,0,0, 255-brightness);
    quad(pos.x, pos.y-halfHeight, pos.x+halfWidth, pos.y, pos.x, pos.y+halfHeight, pos.x-halfWidth, pos.y);
    
  }
  void previewNativePixel(PVector pos, float wide, float high)
  {
    // shall I try and draw a diamond here instead? OK! I'll do it! Ha!
    float halfWidth = wide / 2.0;
    float halfHeight = high / 2.0;
    quad(pos.x, pos.y-halfHeight, pos.x+halfWidth, pos.y, pos.x, pos.y+halfHeight, pos.x-halfWidth, pos.y);
    
  }
  void previewRoundPixel(PVector pos, float wide, float high)
  {
     ellipse(pos.x, pos.y, wide*1.1, high*1.1);
  }
  
  color getPixelAtScreenCoords(PVector pos)
  {
    pos = scaleToDisplayMachine(pos);
    pos = inSteps(pos);
    float scalingFactor = getImage().width / getImageFrame().getWidth();
    color col = super.getPixelAtMachineCoords(pos, scalingFactor);
    return col;
  }

  Set<PVector> getExtractedPixels()
  {
    return this.extractedPixels;
  }
  void setExtractedPixels(Set<PVector> p)
  {
    this.extractedPixels = p;
  }

  /* This will return a list of pixels that are included in the area in the 
   parameter.  All coordinates are for the screen.
   */
  Set<PVector> getPixelsPositionsFromArea(PVector p, PVector s, float rowSize)
  {
    extractPixelsFromArea(p, s, rowSize, 0.0);
    return getExtractedPixels();
  }

  public void extractPixelsFromArea(PVector p, PVector s, float rowSize, float sampleSize)
  {
    // get the native positions from the superclass
    Set<PVector> nativePositions = super.getPixelsPositionsFromArea(inSteps(p), inSteps(s), rowSize, sampleSize);

    // work out the cartesian positions
    Set<PVector> cartesianPositions = new HashSet<PVector>(nativePositions.size());
    for (PVector nativePos : nativePositions)
    {
      // convert to cartesian
      PVector displayPos = super.asCartesianCoords(nativePos);
      displayPos = inMM(displayPos);
      displayPos.z = nativePos.z;
      cartesianPositions.add(displayPos);
    }
    setExtractedPixels(cartesianPositions);
  }


  public Set<PVector> extractNativePixelsFromArea(PVector p, PVector s, float rowSize, float sampleSize)
  {
    // get the native positions from the superclass
    Set<PVector> nativePositions = super.getPixelsPositionsFromArea(inSteps(p), inSteps(s), rowSize, sampleSize);
    return nativePositions;
  }

  protected PVector snapToGrid(PVector loose, float rowSize)
  {
    PVector snapped = inSteps(loose);
    snapped = super.snapToGrid(snapped, rowSize);
    snapped = inMM(snapped);
    return snapped;
  }
  
  public boolean pixelsCanBeExtracted()
  {
    if (super.getImage() == null)
      return false;
    else
      return true;
  }
}