CDMS/src/CDMS/ImageNavigatorII
diff -u -r1.6 -r1.7
--- Stitcher.java 3 Aug 2010 19:32:05 -0000 1.6
+++ Stitcher.java 3 Aug 2010 22:18:16 -0000 1.7
@@ -1,7 +1,5 @@
package CDMS.ImageNavigatorII;
-import java.awt.Graphics2D;
-import java.awt.geom.AffineTransform;
import java.awt.image.*;
import java.io.*;
import javax.imageio.ImageIO;
@@ -18,6 +16,7 @@
*
* File Structure:
* >Image Set Folder
+ * >info.txt [file created by Stitcher to transfer data to Tiler]
* >gmapviewer.htm [the website navigator file!]
* >resources [do not touch these files, they are used by the Google API for the navigator]
* >stitched_images [stitched images will be saved here]
@@ -30,12 +29,13 @@
public static void main(String[] args) throws IOException {
Date startDate = new Date();
//read in the file and create a list of command lines (split by SET_PART_REPEAT)(dont use arg 0)
- String imagePath = "/nfs/farm/g/ee/u15/cdms/CDMS_ImageNavigator/IZipG47_Side2_Al/";
- String savePath = "/nfs/farm/g/ee/u15/cdms/CDMS_ImageNavigatorII/IZipG47_Side2_Al/";
- String autorunFile = "Autorun_IZipG47_Side2_Al_23July10.txt";
- String imageFileName = "/"+"IZipG47_Side2_Al-#.png";
+ String imagePath = "/nfs/farm/g/ee/u15/cdms/CDMS_ImageNavigator/IZipG47_Side1_TES/";
+ String savePath = "/nfs/farm/g/ee/u15/cdms/CDMS_ImageNavigatorII/IZipG47_Side1_TES/";
+ String autorunFile = "Autorun_IZipG47_Side1_TES_29July10.txt";
+ String imageFileName = "/"+"IZipG47_Side1_TES-#.png";
double theta = Math.atan(2/640);
double pxSize = 1.397/1000; //x75.3 magnification: 5.452um | x293 magnification: 1.397um
+ int[] blanks = {4032,4040,7852,895,8313};
String[] lines = getLines(imagePath+"/"+autorunFile);
@@ -68,15 +68,37 @@
int tileH = 2048;
double dX = moveX.get(0)/pxSize;
double dY = (ymins.get(0)-ymins.get(1))/pxSize;
- //find size of image holder and make holder
- int holderW = (int)Math.ceil(imgW*Math.cos(theta)+imgH*Math.sin(theta));
- int holderH = (int)Math.ceil(imgW*Math.sin(theta)+imgH*Math.cos(theta));
- BufferedImage holder = new BufferedImage(holderW, holderH, image.getType());
//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);
- AffineTransform at;
/*********************/
+
+ //make flat field matrix averaging matrix
+ int[][][] ff = new int[imgW][imgH][3];
+ int rTot=0, gTot=0, bTot=0;
+ for (int x=0; x<imgW; x++) {
+ for (int y=0; y<imgW; y++) {
+ int r=0, g=0, b=0;
+ for (int i=0;i<blanks.length; i++) {
+ image = ImageIO.read(new File(imagePath+"/"+imageFileName.replace("#",""+blanks[i])));
+ WritableRaster raster = image.getRaster();
+ r += raster.getSample(x, y, 0);
+ g += raster.getSample(x, y, 1);
+ b += raster.getSample(x, y, 2);
+ }
+ rTot += r;
+ gTot += g;
+ bTot += b;
+ ff[x][y][0] = Math.round(r/blanks.length);
+ ff[x][y][1] = Math.round(g/blanks.length);
+ ff[x][y][2] = Math.round(b/blanks.length);
+ }
+ }
+ double rAvg = rTot/(imgW*imgH*blanks.length);
+ double gAvg = gTot/(imgW*imgH*blanks.length);
+ double bAvg = bTot/(imgW*imgH*blanks.length);
+
+ //loop through all large tiles of stitched images
for (int row=0;row<Math.ceil(totalH/tileH); row++) {
for (int col=0;col<Math.ceil(totalW/tileW); col++) {
System.out.println("new tile("+row+","+col+")");
@@ -86,9 +108,9 @@
BufferedImage toStore = new BufferedImage(tileW, tileH, image.getType());
WritableRaster toStoreRaster = toStore.getRaster().createCompatibleWritableRaster();
int[][] layers = new int[tileW][tileH];
- Graphics2D g2 = holder.createGraphics();
int lastImage = 0;
boolean draw = false;
+ //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;
for (int c=0; c<nCols; c++) {
@@ -103,14 +125,12 @@
//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)));
- at = AffineTransform.getTranslateInstance(0, 0);
- g2.drawRenderedImage(image, at);
- WritableRaster holderRaster = holder.getRaster();
+ WritableRaster imgRaster = image.getRaster();
- //write the square with the tilted image to toStore, averaging with any values already there
- for (int y=0; y < holderH; ++y) {
- for (int x=0; x < holderW; ++x) {
+ //write the image to toStore, averaging with any values already there (for each cell write to pixel)
+ for (int y=0; y < imgH; ++y) {
+ for (int x=0; x < imgW; ++x) {
int drawXtoStore = (int)Math.round(drawX-col*tileW+x);
int drawYtoStore = (int)Math.round(drawY-row*tileH+y);
if (drawXtoStore > 0 && drawXtoStore < tileW && drawYtoStore > 0 && drawYtoStore < tileH) {
@@ -118,14 +138,14 @@
double sumG = toStoreRaster.getSample(drawXtoStore, drawYtoStore, 1);
double sumB = toStoreRaster.getSample(drawXtoStore, drawYtoStore, 2);
int z = layers[drawXtoStore][drawYtoStore];
- sumR = (z*sumR + holderRaster.getSample(x, y, 0))/(z+1);
- sumG = (z*sumG + holderRaster.getSample(x, y, 1))/(z+1);
- sumB = (z*sumB + holderRaster.getSample(x, y, 2))/(z+1);
+ sumR = (z*sumR + imgRaster.getSample(x, y, 0))/(z+1);
+ sumG = (z*sumG + imgRaster.getSample(x, y, 1))/(z+1);
+ sumB = (z*sumB + imgRaster.getSample(x, y, 2))/(z+1);
layers[drawXtoStore][drawYtoStore]++;
if(sumR!=0 || sumG!=0 || sumB!=0) draw=true;
- toStoreRaster.setSample(drawXtoStore, drawYtoStore, 0, sumR);
- toStoreRaster.setSample(drawXtoStore, drawYtoStore, 1, sumG);
- toStoreRaster.setSample(drawXtoStore, drawYtoStore, 2, sumB);
+ toStoreRaster.setSample(drawXtoStore, drawYtoStore, 0, sumR*rAvg/ff[x][y][0]);
+ toStoreRaster.setSample(drawXtoStore, drawYtoStore, 1, sumG*gAvg/ff[x][y][1]);
+ toStoreRaster.setSample(drawXtoStore, drawYtoStore, 2, sumB*bAvg/ff[x][y][2]);
}
}
}
@@ -134,7 +154,6 @@
}
}
if (draw==true) ImageIO.write(toStore, "PNG", new File(savePath+"/stitched_images/"+row+"_"+col+".png"));
- g2.dispose();
}
}
