##    readroi.R - Read ImageJ files in to R
##    Copyright (C) 2011 David C. Sterratt <david.c.sterratt@ed.ac.uk>

##    This program 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.

##    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.

##  ImageJ/NIH Image 64 byte ROI outline header
##     2 byte numbers are big-endian signed shorts
##     0-3     "Iout"
##     4-5     version (>=217)
##     6-7     roi type
##     8-9     top
##     10-11   left
##     12-13   bottom
##     14-15   right
##     16-17   NCoordinates
##     18-33   x1,y1,x2,y2 (straight line)
##     34-35   stroke width (v1.43i or later)
##     36-39   ShapeRoi size (type must be 1 if this value>0)
##     40-43   stroke color (v1.43i or later)
##     44-47   fill color (v1.43i or later)
##     48-49   subtype (v1.43k or later)
##     50-51   options (v1.43k or later)
##     52-52   arrow style or aspect ratio (v1.43p or later)
##     53-53   arrow head size (v1.43p or later)
##     54-55   rounded rect arc size (v1.43p or later)
##     56-59   position
##     60-63   reserved (zeros)
##     64-       x-coordinates (short), followed by y-coordinates
##

##' Read an ImageJ ROI file. This returns a structure containing the
##' ImageJ data. 
##'
##' @title Read an ImageJ ROI file
##' @param file Name of ImageJ ROI file to read
##' @param verbose Whether to report information
##' @return A structure of class IJROI containing the ROI information
##' @author David Sterratt
##' @examples
##' path <- file.path(system.file(package = "retistruct"), "extdata", "ijroi")
##' im <- as.raster(readPNG(file.path(path, "imagej-logo.png")))
##' plot(NA, NA, xlim=c(0, ncol(im)), ylim=c(nrow(im), 0), asp=1) 
##' rasterImage(im, 0,  nrow(im), ncol(im), 0, interpolate=FALSE)
##' r <- read.ijroi(file.path(path, "rect.roi"))
##' plot(r, TRUE)
##' r <- read.ijroi(file.path(path, "polygon.roi"))
##' plot(r, TRUE)
##' r <- read.ijroi(file.path(path, "oval.roi"))
##' plot(r, TRUE)
##' 
read.ijroi <- function(file, verbose=FALSE) {
  ## Define internal helper functions
  getByte <- function(con) {
    pos <- seek(con) 
    n <- readBin(con, raw(0), 1, size=1)
    if (verbose)
      message(paste("Pos ", pos , ": Byte ", n, sep=""))
    return(as.integer(n))
  }

  getShort <- function(con) {
    pos <- seek(con) 
    n <- readBin(con, integer(0), 1, size=2, signed=TRUE, endian="big")
    if (n < -5000) {
      seek(con, -2, origin="current")
      n <- readBin(con, integer(0), 1, size=2, signed=FALSE, endian="big")
    }
    if (verbose)
      message(paste("Pos ", pos , ": Short ", n, sep=""))
    return(n)
  }
  
  getInt <- function(con)  {
    pos <- seek(con) 
    n <- readBin(con, integer(0), 1, size=4, signed=TRUE, endian="little")
    if (verbose)
      message(paste("Pos ", pos , ": Integer ", n, sep=""))
    return (n);
  }

  getFloat <- function(con)  {
    pos <- seek(con) 
    n <- readBin(con, double(0), 1, size=4, signed=TRUE, endian="big")
    if (verbose)
      message(paste("Pos ", pos , ": Float ", n, sep=""))
    return (n);
  }
  
  ## subtypes
  subtypes <- list(TEXT    = 1,
                   ARROW   = 2,
                   ELLIPSE = 3)

  ## options
  opts <- list(SPLINE_FIT    = as.raw(1),
               DOUBLE_HEADED = as.raw(2),
               OUTLINE       = as.raw(4))
  
  ## types
  types <- list(polygon  = 0,
                rect     = 1,
                oval     = 2,
                line     = 3,
                freeline = 4,
                polyline = 5,
                noRoi    = 6,
                freehand = 7,
                traced   = 8,
                angle    = 9,
                point    = 10)

  ## Main code
  name <- NULL
  if (!is.null(file)) {
    size <- file.info(file)$size
    if (!grepl(".roi$", file) && size>5242880)
      stop("This is not an ROI or file size>5MB)")
    name <- basename(file)
  }
  
  ## Open the connection
  con <- file(file, "rb")

  ## Test that it's the right kind of file
  if (getByte(con) != 73 || getByte(con) != 111) {  ## "Iout"
    stop("This is not an ImageJ ROI");
  }

  if (verbose)
    message("Reading format data")
  
  ## Create place to store data
  r <- list()

  ## Get the data. This all has to be in the order corresponding to the
  ## positions mentioned at the top of the file
  getShort(con)                         # Unused
  r$version <-      getShort(con)
  r$type <-         getByte(con)
  getByte(con)                          # Unused
  r$top <-          getShort(con)       # TOP
  r$left <-         getShort(con)       # LEFT
  r$bottom <-       getShort(con)       # Bottom
  r$right <-        getShort(con)       # RIGHT
  r$width <-    with(r, right-left)
  r$height <-   with(r, bottom-top)
  r$n <-            getShort(con)       # N_COORDINATES
  r$x1 <-           getFloat(con)     
  r$y1 <-           getFloat(con)     
  r$x2 <-           getFloat(con)     
  r$y2 <-           getFloat(con)
  r$strokeWidth <-  getShort(con)       # STROKE_WIDTH
  r$shapeRoiSize <- getInt(con)         # SHAPE_ROI_SIZE
  r$strokeColor <-  getInt(con)
  r$fillColor <-    getInt(con)
  r$subtype <-      getShort(con)       # SUBTYPE
  r$options < as.raw(getShort(con))     # OPTIONS
  if (r$type == "oval") {
    r$aspectRatio <- getFloat(con)      # ELLIPSE_ASPECT_RATIO
  } else {
    r$style <-      getByte(con)        # ARROW_STYLE
    r$headSize <-   getByte(con)        # ARROW_HEAD_SIZE    
    r$arcSize <-    getShort(con)       # ROUNDED_RECT_ARC_SIZE
  }
  r$position <-     getInt(con)         # POSITION
  getShort(con)                         # Unused
  getShort(con)                         # Unused

  if (verbose)
    message("Reading coordinate data")
  
  if (!is.null(name) && (grepl(".roi$", name)))
    r$name <- substring(name, 1, nchar(name) - 4)
    
  isComposite <- (r$shapeRoiSize >0);
  if (isComposite) {
    stop("Composite ROIs not supported")
    ## roi = getShapeRoi();
    ## if (version>=218) getStrokeWidthAndColor(roi);
    ##          roi.setPosition(position);
    ## return roi;
  }
  ## if (r$type %in% types[c("rect")]) {

  ## if (r$type %in% types[c("oval")]) {

  if (r$type %in% types["line"]) {
    if (r$subtype %in% types("ARROW")) {
      r$doubleHeaded <- (r$options & opts$DOUBLE_HEADED) !=0
      r$outline <- (r$options & opts$OUTLINE) !=0
      ##                     if (style>=Arrow.FILLED && style<=Arrow.OPEN)
      ##                         ((Arrow)roi).setStyle(style);

      ##                     if (headSize>=0 && style<=30)
      ##                         ((Arrow)roi).setHeadSize(headSize);
      ##                 } else
      ##                     roi = new Line(x1, y1, x2, y2);
    }
  }

  ## Read in coordinates
  if (r$type %in% types[c("polygon", "freehand", "traced", "polyline", "freeline", "angle", "point")]) {
    r$coords <- matrix(NA, r$n, 2)
    if (r$n > 0) {
      for (i in 1:r$n) {
        r$coords[i, 1] <- getShort(con)
      }
      for (i in 1:r$n) {
        r$coords[i, 2] <- getShort(con)
      }
      r$coords[r$coords<0] <- 0
      r$coords[,1] <- r$coords[,1] + r$left
      r$coords[,2] <- r$coords[,2] + r$top
    }
  } 

  r$strType <- names(types)[which(types==r$type)]
  r$types <- types
  close(con)
  class(r) <- "IJROI"
  return(r)
}

plot.IJROI <- function(x, add=FALSE, ...) {
  with(x, {
    if (!add) 
      plot(NA, NA, xlim=range(coords[,1]), ylim=range(coords[,2]))

    if (type == types["rect"]) {
      rect(left, bottom, right, top, ...)
    }
    if (type == types["oval"]) {
      theta <- seq(0, 2*pi, len=360)
      polygon(left + width/2*(1 + sin(theta)),
              top + height/2*(1 + cos(theta)), ...)
    }
    if (type == types["line"]) {
      warning("Plotting line not yet supported")
    }
    if (type %in% types[c("polygon", "freehand", "traced")]) {
      coords <- rbind(coords, coords[1,])
      lines(coords, ...)
    }
    if (type %in% types[c("polyline", "freeline", "angle")]) {
      lines(coords, ...)
    }
    if (type %in% types[c("point")]) {
      points(coords, ...)
    }
    
    
  })
}

## Demo
## demo.roi <- function() {
##   im <- as.raster(readPNG("~/image.png"))
##   plot(NA, NA, xlim=c(0, ncol(im)), ylim=c(nrow(im), 0), asp=1) 
##   rasterImage(im, 0,  nrow(im), ncol(im), 0)
##   r <- read.roi("~/image.roi")
##   plot(r, TRUE, col="cyan")
##   return(r)
## }

## ##                         if (subtype==ELLIPSE) {
## ##                             double ex1 = getFloat(X1);      
## ##                             double ey1 = getFloat(Y1);      
## ##                             double ex2 = getFloat(X2);      
## ##                             double ey2 = getFloat(Y2);

## ##                             roi = new EllipseRoi(ex1,ey1,ex2,ey2,aspectRatio);
## ##                             break;
## ##                         }
## ##             default:
## ##                 throw new IOException("Unrecognized ROI type: "+type);
## ##         }
## ##         if (name!=null) roi.setName(name);
        
## ##         // read stroke width, stroke color and fill color (1.43i or later)
## ##         if (version>=218) {
## ##             getStrokeWidthAndColor(roi);
## ##             boolean splineFit = (options&SPLINE_FIT)!=0;
## ##             if (splineFit && roi instanceof PolygonRoi)
## ##                 ((PolygonRoi)roi).fitSpline();
## ##         }
        
## ##         if (version>=218 && subtype==TEXT)
## ##             roi = getTextRoi(roi);

## ##         roi.setPosition(position);
## ##         return roi;
## ##     }

## ## }

## ##     void getStrokeWidthAndColor(Roi roi) {
## ##         if (strokeWidth>0)
## ##             roi.setStrokeWidth(strokeWidth);
## ##         if (strokeColor!=0) {
## ##             int alpha = (strokeColor>>24)&0xff;
## ##             roi.setStrokeColor(new Color(strokeColor, alpha!=255));
## ##         }

## ##         if (fillColor!=0) {
## ##             int alpha = (fillColor>>24)&0xff;
## ##             roi.setFillColor(new Color(fillColor, alpha!=255));
## ##         }
## ##     }
    
## ##     Roi getTextRoi(Roi roi) {
## ##         Rectangle r = roi.getBounds();
## ##         int hdrSize = RoiEncoder.HEADER_SIZE;
## ##         int size = getInt(hdrSize);
## ##         int style = getInt(hdrSize+4);
## ##         int nameLength = getInt(hdrSize+8);
## ##         int textLength = getInt(hdrSize+12);
## ##         char[] name = new char[nameLength];
## ##         char[] text = new char[textLength];
## ##         for (int i=0; i<nameLength; i++)
## ##             name[i] = (char)getShort(hdrSize+16+i*2);
## ##         for (int i=0; i<textLength; i++)
## ##             text[i] = (char)getShort(hdrSize+16+nameLength*2+i*2);
## ##         Font font = new Font(new String(name), style, size);
## ##         Roi roi2 = new TextRoi(r.x, r.y, new String(text), font);
## ##         roi2.setStrokeColor(roi.getStrokeColor());
## ##         roi2.setFillColor(roi.getFillColor());
## ##         return roi2;
## ##     }