diff -u -r1.8 -r1.9
--- Stitcher.java	7 Aug 2010 18:29:20 -0000	1.8
+++ Stitcher.java	9 Sep 2010 16:11:11 -0000	1.9
@@ -36,7 +36,6 @@

     	String savePath = "/"+getArg(inFile, "save_path");
     	String autorunFile = getArg(inFile, "autorun_file");
     	String imageFileName = "/"+getArg(inFile, "image_name");

-    	double theta = 0; try {theta = Double.parseDouble(getArg(inFile,"theta")); } catch (Exception e) {}

     	double pxSize = 0.001397; try {pxSize = Double.parseDouble(getArg(inFile,"pixel_size")); } catch (Exception e) {}
     	String[] blanksList = getArg(inFile, "blanks").split(",");
     	int[] blanks = new int[blanksList.length];

@@ -45,7 +44,9 @@

     	}
     	int tileW = 2048; try{tileW = Integer.parseInt(getArg(inFile, "tile_width"));} catch (Exception e) {}
     	int tileH = 2048; try{tileH = Integer.parseInt(getArg(inFile, "tile_height"));} catch (Exception e) {}

-

+    	
+    	String outFile = "";
+    	

 		//read in the file and create a list of command lines (split by SET_PART_REPEAT)(dont use arg 0)
 		String[] lines = getLines(imagePath+"/"+autorunFile,"SET_PART_REPEAT");
 	    

@@ -77,8 +78,8 @@

         double dX = moveX.get(0)/pxSize;
         double dY = (ymins.get(0)-ymins.get(1))/pxSize;
         //find size of total stitched image

-	    double totalW = (maxCols-1)*dX + imgW*Math.cos(theta) + imgH*Math.sin(theta);
-	    double totalH = (lines.length-1)*dX + imgW*Math.sin(theta) + imgH*Math.cos(theta);

+	    double totalW = (maxCols-1)*dX + imgW;
+	    double totalH = (lines.length-1)*dX + imgH;

 	    /*********************/
 	    
 	    //make flat field matrix averaging matrix

@@ -131,6 +132,9 @@

         		int[][] layers = new int[tileW][tileH];
         		int lastImage = 0;
         		boolean draw = false;

+        		boolean foundCenter = false;
+        		String centerX = "n/a";
+        		String centerY = "n/a";

         		//loop through all images using cols and rows from the autorun file
         		for (int r=0; r<lines.length-1; r++) {
         	    	int nCols = cols.get(r)+1;

@@ -140,13 +144,20 @@

         	    		double maxTileRenderX = (col+1)*tileW+imgW;
         	    		double minTileRenderY = row*tileW-imgH;
         	    		double maxTileRenderY = (row+1)*tileW+imgH;

-        	    		double drawX = c*dX*Math.cos(theta)+(xmins.get(r)-xMin)/pxSize;
-        	    		double drawY = r*dY+c*dX*Math.sin(theta);

+        	    		double drawX = c*dX+(xmins.get(r)-xMin)/pxSize;
+        	    		double drawY = r*dY;

         	    		lastImage++;
         	    		//if it is in the tile, make a square with the image tilted appropriately
         	        	if (drawX>minTileRenderX && drawX<maxTileRenderX && drawY>minTileRenderY && drawY<maxTileRenderY) {
     	        			image = ImageIO.read(new File(imagePath+"/"+imageFileName.replace("%",""+lastImage)));
             	            WritableRaster imgRaster = image.getRaster();

+            	            
+            	            //find coordinates of center of tile
+            	            if (foundCenter == false) {
+	            	            centerX = ""+( (xmins.get(r)/pxSize+c*dX) - (drawX-col*tileW) + tileW/2 );
+	            	            centerY = ""+( ymins.get(r) - (drawY-row*tileH) +tileH/2 );
+	            	            foundCenter = true;
+            	            }

 	            	        
             	            //write the image to toStore, averaging with any values already there (for each cell write to pixel)
             	            for (int y=0; y < imgH; ++y) {

@@ -174,6 +185,7 @@

         	        }
         	    }
         		if (draw==true) ImageIO.write(toStore, "PNG", new File(savePath+"/stitched_images/"+row+"_"+col+".png"));

+        		outFile += (""+row+"_"+col+"\t"+centerX+"\t"+centerY+"\n");

         	}
         }
 

@@ -181,6 +193,11 @@

     	System.out.println("\nRuntime: "+(endDate.getTime()-startDate.getTime())/1000/60);
     	//writes data needed for Tiler.java to info.txt
     	try {

+    	    BufferedWriter outprint = new BufferedWriter(new FileWriter(savePath+"/out.txt"));
+    	    outprint.write(outFile);
+    	    outprint.close();
+    	} catch (IOException e) {System.out.println("Could not create out.txt:\n"+e);}//writes stats about each tile to out.txt
+    	try {

     	    BufferedWriter outprint = new BufferedWriter(new FileWriter(savePath+"/info.txt"));
     	    outprint.write(Math.ceil(totalW/tileW)+"\n"+Math.ceil(totalH/tileH)+"\n"+tileW+"\n"+tileH+"\n"+savePath);
     	    outprint.close();