ij.io.FileInfo Java Examples

/** Returns the path where the imp is saved to: the storage folder plus a name. */
public String handlePathlessImage(final ImagePlus imp) {
	FileInfo fi = imp.getOriginalFileInfo();
	if (null == fi) fi = imp.getFileInfo();
	if (null == fi.fileName || fi.fileName.equals("")) {
		fi.fileName = "img_" + System.currentTimeMillis() + ".tif";
	}
	if (!fi.fileName.endsWith(".tif")) fi.fileName += ".tif";
	fi.directory = dir_storage;
	if (imp.getNSlices() > 1) {
		new FileSaver(imp).saveAsTiffStack(dir_storage + fi.fileName);
	} else {
		new FileSaver(imp).saveAsTiff(dir_storage + fi.fileName);
	}
	Utils.log2("Saved a copy into the storage folder:\n" + dir_storage + fi.fileName);
	return dir_storage + fi.fileName;
}
 

private ImagePlus extractChannel(ImagePlus imp, int channel) {

        int width = imp.getWidth();
        int height = imp.getHeight();
        int zslices = imp.getNSlices();
        int frames = imp.getNFrames();

        FileInfo fileInfo = imp.getOriginalFileInfo();

        // create empty stack
        ImageStack stack2 = new ImageStack(width, height);
        // create new ImagePlus for selected channel
        ImagePlus imp2 = new ImagePlus();
        imp2.setTitle("C" + channel + "-" + imp.getTitle());

        // copy slices
        for (int t = 1; t <= frames; t++)
            for (int z = 1; z <= zslices; z++) {
                int slice = imp.getStackIndex(channel, z, t);
                stack2.addSlice("", imp.getStack().getProcessor(slice));
            }

        imp2.setStack(stack2);
        imp2.setDimensions(1, zslices, frames);
        if (zslices * frames > 1)
            imp2.setOpenAsHyperStack(true);
        imp2.setFileInfo(fileInfo);

        return imp2;
    }
 

private ImagePlus extractZSlice(ImagePlus imp, int zslice) {

        int width = imp.getWidth();
        int height = imp.getHeight();
        int channels = imp.getNChannels();
        int frames = imp.getNFrames();

        FileInfo fileInfo = imp.getOriginalFileInfo();

        // create empty stack
        ImageStack stack2 = new ImageStack(width, height);
        // create new ImagePlus for selected frame
        ImagePlus imp2 = new ImagePlus();
        imp2.setTitle("Z" + zslice + "-" + imp.getTitle());

        // copy slices
        for (int f = 1; f <= frames; f++)
            for (int c = 1; c <= channels; c++) {
                int slice = imp.getStackIndex(c, zslice, f);
                stack2.addSlice("", imp.getStack().getProcessor(slice));
            }

        imp2.setStack(stack2);
        imp2.setDimensions(channels, 1, frames);
        if (channels * frames > 1)
            imp2.setOpenAsHyperStack(true);
        imp2.setFileInfo(fileInfo);

        return imp2;
    }
 

public String getOriginalFilename() {
	final FileInfo originalFileInfo = originalImage.getOriginalFileInfo();
	if (originalFileInfo.directory == null)
		return "[unknown]";
	else
		return new File(originalFileInfo.directory, originalFileInfo.fileName).getAbsolutePath();

}
 

/**
 * @return the path to save current profile
 */
private String getExportPath() {
	if (this.exportPath == null && originalImage != null) {
		final FileInfo fi = originalImage.getOriginalFileInfo();
		if (fi != null && fi.directory != null)
			this.exportPath = fi.directory;
	}
	return this.exportPath;
}
 

/** Returns null if the ImagePlus was preprocessed or doesn't have an original FileInfo
 * (which means the image does not come from a file). */
static public final String getPath(final ImagePlus imp) {
	final FileInfo fi = imp.getOriginalFileInfo();
	if (null == fi || Loader.PREPROCESSED == fi.fileFormat) return null;
	final String dir = fi.directory;
	if (null == dir) {
		return fi.url;
	}
	return dir + fi.fileName;
}
 

/** Returns true on success.
 * <p>
 *  Core functionality adapted from {@code ij.io.FileSaver} class by Wayne Rasband.
 *  </p>
 */
static public final boolean saveAsZip(final ImagePlus imp, String path) {
	// safety checks
	if (null == imp) {
		Utils.log("Null imp, can't saveAsZip");
		return false;
	}
	if (!checkPath(path)) return false;
	// ok, onward:
	FileInfo fi = imp.getFileInfo();
	if (!path.endsWith(".zip")) path = path+".zip";
	String name = imp.getTitle();
	if (name.endsWith(".zip")) name = name.substring(0,name.length()-4);
	if (!name.endsWith(".tif")) name = name+".tif";
	fi.description = ImageSaver.getDescriptionString(imp, fi);
	Object info = imp.getProperty("Info");
	if (info!=null && (info instanceof String))
		fi.info = (String)info;
	fi.sliceLabels = imp.getStack().getSliceLabels();
	try {
		ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(path));
		DataOutputStream out = new DataOutputStream(new BufferedOutputStream(zos));
       	zos.putNextEntry(new ZipEntry(name));
		TiffEncoder te = new TiffEncoder(fi);
		te.write(out);
		out.close();
	}
	catch (IOException e) {
		IJError.print(e);
		return false;
	}
	return true;
}
 

/** Returns the array of AreaList or null if the file dialog is canceled. The xo,yo is the pivot of reference. */
static public Collection<AreaList> importAmiraLabels(Layer first_layer, double xo, double yo, final String default_dir) {
	// open file
	OpenDialog od = new OpenDialog("Choose Amira Labels File", default_dir, "");
	String filename = od.getFileName();
	if (null == filename || 0 == filename.length()) return null;
	String dir = od.getDirectory();
	if (IJ.isWindows()) dir = dir.replace('\\', '/');
	if (!dir.endsWith("/")) dir += "/";
	String path =  dir + filename;
	AmiraMeshDecoder dec = new AmiraMeshDecoder();
	if (!dec.open(path)) {
		YesNoDialog yn = new YesNoDialog("Error", "File was not an Amira labels file.\nChoose another one?");
		if (yn.yesPressed()) return importAmiraLabels(first_layer, xo, yo, default_dir);
		return null;
	}
	ImagePlus imp = null;
	if (dec.isTable()) {
		Utils.showMessage("Select the other file (the labels)!");
		return null;
	} else {
		FileInfo fi = new FileInfo();
		fi.fileName = filename;
		fi.directory = dir;
		imp = new ImagePlus("Amira", dec.getStack());
		dec.parameters.setParameters(imp);
	}
	return extractAmiraLabels(imp, dec.parameters, first_layer, xo, yo);
}
 

public void setFileInfo(FileInfo fi) {
	Utils.log("PatchStack: can't setFileInfo");
}
 

public FileInfo getFileInfo() {
	ImagePlus imp = patch[currentSlice-1].getProject().getLoader().fetchImagePlus(patch[currentSlice-1]);
	return imp.getFileInfo();
}
 

protected final ImagePlus preProcess(final Patch p, ImagePlus imp, final long image_n_bytes) {
	if (null == p) return imp;
	try {
		final String path = preprocessors.get(p);
		boolean update = false;
		if (null != path) {
			final File f = new File(path);
			if (!f.exists()) {
				Utils.log("ERROR: preprocessor script file does NOT exist: " + path);
				return imp;
			} else if (!f.canRead()) {
				Utils.log("ERROR: can NOT read preprocessor script file at: " + path);
				return imp;
			}
			if (null == imp) {
				imp = new ImagePlus(); // uninitialized: the script may generate its data
			} else {
				// Prepare image for pre-processing
				imp.getProcessor().setMinAndMax(p.getMin(), p.getMax()); // for 8-bit and RGB images, your problem: setting min and max will expand the range.
			}
			// Free 10 times the memory taken by the image, as a gross estimate of memory consumption by the script
			releaseToFit(Math.min(10 * image_n_bytes, MAX_MEMORY / 4));
			// Run the script
			ini.trakem2.scripting.PatchScript.run(p, imp, path);
			// Update Patch image properties:
			if (null != imp.getProcessor() && null != imp.getProcessor().getPixels() && imp.getWidth() > 0 && imp.getHeight() > 0) {
				update = true;
			} else {
				Utils.log("ERROR: preprocessor script failed to create a valid image:"
						+ "\n  ImageProcessor: " + imp.getProcessor()
						+ "\n  pixel array: " + (null == imp.getProcessor() ? null : imp.getProcessor().getPixels())
						+ "\n  width: " + imp.getWidth()
						+ "\n  height: " + imp.getHeight());
			}
		}
		// Now apply the Patch filters, if any
		final IFilter[] fs = p.getFilters();
		if (null != fs && fs.length > 0) {
			ImageProcessor ip = imp.getProcessor();
			for (final IFilter filter : fs) {
				ip = filter.process(ip);
			}
			if (ip != imp.getProcessor()) {
				imp.setProcessor(ip);
			}
			update = true;
		}
		// Now apply intensity correction if available
		update |= mapIntensities(p, imp);
		if (update) {
			// 1: Tag the ImagePlus as altered (misuses fileFormat field, which is unused in any case)
			final FileInfo fi = imp.getOriginalFileInfo();
			if (null != fi) fi.fileFormat = Loader.PREPROCESSED; // otherwise, the null original FileInfo is a valid tag by itself in the persistence.Cache
			// 2: cache
			cache(p, imp);
			// 3: update properties of the Patch
			p.updatePixelProperties(imp);
		}
	} catch (final Exception e) {
		IJError.print(e);
	}
	return imp;
}
 

/** Returns a string containing information about the specified  image. */
static public final String getDescriptionString(final ImagePlus imp, final FileInfo fi) {
	final Calibration cal = imp.getCalibration();
	final StringBuilder sb = new StringBuilder(100);
	sb.append("ImageJ="+ImageJ.VERSION+"\n");
	if (fi.nImages>1 && fi.fileType!=FileInfo.RGB48)
		sb.append("images="+fi.nImages+"\n");
	int channels = imp.getNChannels();
	if (channels>1)
		sb.append("channels="+channels+"\n");
	int slices = imp.getNSlices();
	if (slices>1)
		sb.append("slices="+slices+"\n");
	int frames = imp.getNFrames();
	if (frames>1)
		sb.append("frames="+frames+"\n");
	if (fi.unit!=null)
		sb.append("unit="+fi.unit+"\n");
	if (fi.valueUnit!=null && fi.calibrationFunction!=Calibration.CUSTOM) {
		sb.append("cf="+fi.calibrationFunction+"\n");
		if (fi.coefficients!=null) {
			for (int i=0; i<fi.coefficients.length; i++)
				sb.append("c"+i+"="+fi.coefficients[i]+"\n");
		}
		sb.append("vunit="+fi.valueUnit+"\n");
		if (cal.zeroClip()) sb.append("zeroclip=true\n");
	}
	
	// get stack z-spacing and fps
	if (fi.nImages>1) {
		if (fi.pixelDepth!=0.0 && fi.pixelDepth!=1.0)
			sb.append("spacing="+fi.pixelDepth+"\n");
		if (cal.fps!=0.0) {
			if ((int)cal.fps==cal.fps)
				sb.append("fps="+(int)cal.fps+"\n");
			else
				sb.append("fps="+cal.fps+"\n");
		}
		sb.append("loop="+(cal.loop?"true":"false")+"\n");
		if (cal.frameInterval!=0.0) {
			if ((int)cal.frameInterval==cal.frameInterval)
				sb.append("finterval="+(int)cal.frameInterval+"\n");
			else
				sb.append("finterval="+cal.frameInterval+"\n");
		}
		if (!cal.getTimeUnit().equals("sec"))
			sb.append("tunit="+cal.getTimeUnit()+"\n");
	}
	
	// get min and max display values
	final ImageProcessor ip = imp.getProcessor();
	final double min = ip.getMin();
	final double max = ip.getMax();
	final int type = imp.getType();
	final boolean enhancedLut = (type==ImagePlus.GRAY8 || type==ImagePlus.COLOR_256) && (min!=0.0 || max !=255.0);
	if (enhancedLut || type==ImagePlus.GRAY16 || type==ImagePlus.GRAY32) {
		sb.append("min="+min+"\n");
		sb.append("max="+max+"\n");
	}
	
	// get non-zero origins
	if (cal.xOrigin!=0.0)
		sb.append("xorigin="+cal.xOrigin+"\n");
	if (cal.yOrigin!=0.0)
		sb.append("yorigin="+cal.yOrigin+"\n");
	if (cal.zOrigin!=0.0)
		sb.append("zorigin="+cal.zOrigin+"\n");
	if (cal.info!=null && cal.info.length()<=64 && cal.info.indexOf('=')==-1 && cal.info.indexOf('\n')==-1)
		sb.append("info="+cal.info+"\n");			
	sb.append((char)0);
	return new String(sb);
}
 

/**
 * Writes a {@link BufferedImage} to the specified {@link OutputStream} using ImageJ's {@link TiffEncoder}.
 *
 * @param  bufferedImage     image to write.
 * @param  outputStream      target stream.
 *
 * @throws IOException
 *   if any errors occur.
 */
public static void writeTiffImage(final BufferedImage bufferedImage,
                                  final OutputStream outputStream)
        throws IOException {
    final ImagePlus ip = new ImagePlus("", bufferedImage);
    final FileInfo fileInfo = ip.getFileInfo();
    final TiffEncoder tiffEncoder = new TiffEncoder(fileInfo);
    tiffEncoder.write(outputStream);
}