/**
* Return an ImageRecord containing the images pixel dimensions.
*
* @param file absolute file path to image
* @return ImageRecord containing the images pixel dimensions
*/
public static ImageRecord getImageDimensions(final String file) {
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("Getting image dimensions from: {}", file);
}
final ImageRecord dim = new ImageRecord(file);
final Opener o = new Opener();
final ImagePlus imp = o.openImage(file);
if (imp == null) {
return null;
}
ImageProcessor ip = imp.getProcessor();
final int width = ip.getWidth();
final int height = ip.getHeight();
if (LOGGER.isDebugEnabled()) {
LOGGER.debug(
"{} (width: {} | height: {})", file, Integer.toString(width), Integer.toString(height));
}
dim.setWidth(width);
dim.setHeight(height);
ip = null;
return dim;
}
public static void main(String[] args) throws IOException, WriteException {
// TODO code application logic here
int cellNum = 0;
double[] cTCF = new double[30];
ImagePlus img = null;
Opener op = new Opener();
for (int i = 0; i < 30; i++) {
String num = Integer.toString(i);
img = op.openImage("E:/Photobleaching/Target/1/" + num + ".tif");
ImageProcessor im = img.getProcessor().duplicate();
// set region of interest for target cell
im.setRoi(342, 668, 36, 36);
double cellMean = im.getStatistics().mean;
double cellArea = im.getStatistics().area;
double cellIntensity = cellMean * cellArea;
// --------------------------------------------------------------------------
// calculate Integrated Density of background for target cell area
// --------------------------------------------------------------------------
ImageProcessor background1 = img.getProcessor().duplicate();
// set region of interest for background
background1.setRoi(341, 591, 21, 20);
double backgroundMean1 = background1.getStatistics().mean;
double backgroundIntensity1 = backgroundMean1 * cellArea;
ImageProcessor background2 = img.getProcessor().duplicate();
// set region of interest for background
background2.setRoi(383, 641, 20, 20);
double backgroundMean2 = background2.getStatistics().mean;
double backgroundIntensity2 = backgroundMean2 * cellArea;
double backgroundIntensity = (backgroundIntensity1 + backgroundIntensity2) / 2;
// calculate corrected total cell fluorescence (CTCF)
cTCF[cellNum] = cellIntensity - backgroundIntensity;
cellNum = cellNum + 1;
}
WriteToExcel write = new WriteToExcel();
write.write(1, cellNum, cTCF);
}
public Image getImage(JCRNodeWrapper node) throws IOException, RepositoryException {
File tmp = null;
OutputStream os = null;
try {
tmp = File.createTempFile("image", null);
Node contentNode = node.getNode(Constants.JCR_CONTENT);
os = new BufferedOutputStream(new FileOutputStream(tmp));
InputStream is = contentNode.getProperty(Constants.JCR_DATA).getBinary().getStream();
try {
IOUtils.copy(is, os);
} finally {
IOUtils.closeQuietly(os);
IOUtils.closeQuietly(is);
}
Opener op = new Opener();
ImagePlus ip = op.openImage(tmp.getPath());
return new ImageJImage(node.getPath(), ip, op.getFileType(tmp.getPath()));
} finally {
IOUtils.closeQuietly(os);
FileUtils.deleteQuietly(tmp);
}
}
public static String createThumbImage(String fileAbsolutePath, String fileSaveAsNameSuffix) {
try {
Opener opener = new Opener();
ImagePlus imp = opener.openImage(fileAbsolutePath);
ImageProcessor ip = imp.getProcessor();
StackProcessor sp = new StackProcessor(imp.getStack(), ip);
int width = imp.getWidth();
int height = imp.getHeight();
int cropWidth = 0;
int cropHeight = 0;
if (width > height) {
cropWidth = height;
cropHeight = height;
} else {
cropWidth = width;
cropHeight = width;
}
int x = -1;
int y = -1;
if (width == height) {
x = 0;
y = 0;
} else if (width > height) {
x = (width - height) / 2;
y = 0;
} else if (width < height) {
x = 0;
y = (height - width) / 2;
}
ImageStack croppedStack = sp.crop(x, y, cropWidth, cropHeight);
imp.setStack(null, croppedStack);
sp = new StackProcessor(imp.getStack(), imp.getProcessor());
ImageStack resizedStack = sp.resize(100, 100, true);
imp.setStack(null, resizedStack);
File generateSourcePath = new File(fileAbsolutePath);
StringBuffer filePath =
new StringBuffer(generateSourcePath.getParentFile().getParentFile().getAbsolutePath());
File generatePath = new File(filePath.toString() + File.separator + "generate");
if (!generatePath.exists()) {
generatePath.mkdirs();
}
filePath = new StringBuffer(generateSourcePath.getName());
filePath.replace(filePath.lastIndexOf("."), filePath.lastIndexOf("."), fileSaveAsNameSuffix);
String saveAsFilePath = generatePath.getAbsolutePath() + File.separator + filePath.toString();
IJ.save(imp, saveAsFilePath);
return saveAsFilePath;
} catch (Exception e) {
e.printStackTrace();
}
return null;
}