/**
* 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);
}
}
/** Restores original disk or network version of image. */
public void revertToSaved(ImagePlus imp) {
Image img;
ProgressBar pb = IJ.getInstance().getProgressBar();
ImageProcessor ip;
String path = fi.directory + fi.fileName;
if (fi.fileFormat == fi.GIF_OR_JPG) {
// restore gif or jpg
img = Toolkit.getDefaultToolkit().createImage(path);
imp.setImage(img);
if (imp.getType() == ImagePlus.COLOR_RGB) Opener.convertGrayJpegTo8Bits(imp);
return;
}
if (fi.fileFormat == fi.DICOM) {
// restore DICOM
ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.DICOM", path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.fileFormat == fi.BMP) {
// restore BMP
ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.BMP_Reader", path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.fileFormat == fi.PGM) {
// restore PGM
ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.PGM_Reader", path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.fileFormat == fi.ZIP_ARCHIVE) {
// restore ".zip" file
ImagePlus imp2 = (new Opener()).openZip(path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
// restore PNG or another image opened using ImageIO
if (fi.fileFormat == fi.IMAGEIO) {
ImagePlus imp2 = (new Opener()).openUsingImageIO(path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.nImages > 1) return;
ColorModel cm;
if (fi.url == null || fi.url.equals("")) IJ.showStatus("Loading: " + path);
else IJ.showStatus("Loading: " + fi.url + fi.fileName);
Object pixels = readPixels(fi);
if (pixels == null) return;
cm = createColorModel(fi);
switch (fi.fileType) {
case FileInfo.GRAY8:
case FileInfo.COLOR8:
case FileInfo.BITMAP:
ip = new ByteProcessor(width, height, (byte[]) pixels, cm);
imp.setProcessor(null, ip);
break;
case FileInfo.GRAY16_SIGNED:
case FileInfo.GRAY16_UNSIGNED:
case FileInfo.GRAY12_UNSIGNED:
ip = new ShortProcessor(width, height, (short[]) pixels, cm);
imp.setProcessor(null, ip);
break;
case FileInfo.GRAY32_INT:
case FileInfo.GRAY32_FLOAT:
ip = new FloatProcessor(width, height, (float[]) pixels, cm);
imp.setProcessor(null, ip);
break;
case FileInfo.RGB:
case FileInfo.BGR:
case FileInfo.ARGB:
case FileInfo.ABGR:
case FileInfo.RGB_PLANAR:
img =
Toolkit.getDefaultToolkit()
.createImage(new MemoryImageSource(width, height, (int[]) pixels, 0, width));
imp.setImage(img);
break;
}
}
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;
}
public boolean install(String path) {
boolean isURL = path.contains("://");
String lcPath = path.toLowerCase();
if (isURL) path = Opener.updateUrl(path);
boolean isTool =
lcPath.endsWith("tool.ijm")
|| lcPath.endsWith("tool.txt")
|| lcPath.endsWith("tool.class")
|| lcPath.endsWith("tool.jar");
boolean isMacro = lcPath.endsWith(".txt") || lcPath.endsWith(".ijm");
byte[] data = null;
String name = path;
if (isURL) {
int index = path.lastIndexOf("/");
if (index != -1 && index <= path.length() - 1) name = path.substring(index + 1);
data = download(path, name);
} else {
File f = new File(path);
name = f.getName();
data = download(f);
}
if (data == null) return false;
if (name.endsWith(".txt") && !name.contains("_"))
name = name.substring(0, name.length() - 4) + ".ijm";
if (name.endsWith(".zip")) {
if (!name.contains("_")) {
IJ.error("Plugin Installer", "No underscore in file name:\n \n " + name);
return false;
}
name = name.substring(0, name.length() - 4) + ".jar";
}
String dir = null;
boolean isLibrary = name.endsWith(".jar") && !name.contains("_");
if (isLibrary) {
dir = Menus.getPlugInsPath() + "jars";
File f = new File(dir);
if (!f.exists()) {
boolean ok = f.mkdir();
if (!ok) dir = Menus.getPlugInsPath();
}
}
if (isTool) {
dir = Menus.getPlugInsPath() + "Tools" + File.separator;
File f = new File(dir);
if (!f.exists()) {
boolean ok = f.mkdir();
if (!ok) dir = null;
}
if (dir != null && isMacro) {
String name2 = getToolName(data);
if (name2 != null) name = name2;
}
}
if (dir == null) {
SaveDialog sd =
new SaveDialog("Save Plugin, Macro or Script...", Menus.getPlugInsPath(), name, null);
String name2 = sd.getFileName();
if (name2 == null) return false;
dir = sd.getDirectory();
}
// IJ.log(dir+" "+Menus.getPlugInsPath());
if (!savePlugin(new File(dir, name), data)) return false;
if (name.endsWith(".java")) IJ.runPlugIn("ij.plugin.Compiler", dir + name);
Menus.updateImageJMenus();
if (isTool) {
if (isMacro) IJ.runPlugIn("ij.plugin.Macro_Runner", "Tools/" + name);
else if (name.endsWith(".class")) {
name = name.replaceAll("_", " ");
name = name.substring(0, name.length() - 6);
IJ.run(name);
}
}
return true;
}