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ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.
package ij.io;
import java.awt.*;
import java.io.*;
import java.util.zip.*;
import ij.*;
import ij.process.*;
import ij.measure.Calibration;
import ij.plugin.filter.Analyzer;
import ij.plugin.frame.Recorder;
import ij.plugin.JpegWriter;
import ij.plugin.Orthogonal_Views;
import ij.gui.*;
import ij.measure.Measurements;
import ij.util.Tools;
import javax.imageio.*;
/** Saves images in tiff, gif, jpeg, raw, zip and text format. */
public class FileSaver {
public static final int DEFAULT_JPEG_QUALITY = 85;
private static int jpegQuality;
private static int bsize = 32768; // 32K default buffer size
static {setJpegQuality(ij.Prefs.getInt(ij.Prefs.JPEG, DEFAULT_JPEG_QUALITY));}
private static String defaultDirectory = null;
private ImagePlus imp;
private FileInfo fi;
private String name;
private String directory;
private boolean saveName;
/** Constructs a FileSaver from an ImagePlus. */
public FileSaver(ImagePlus imp) {
this.imp = imp;
fi = imp.getFileInfo();
}
/** Resaves the image. Calls saveAsTiff() if this is a new image, not a TIFF,
or if the image was loaded using a URL. Returns false if saveAsTiff() is
called and the user selects cancel in the file save dialog box. */
public boolean save() {
FileInfo ofi = null;
if (imp!=null) ofi = imp.getOriginalFileInfo();
boolean validName = ofi!=null && imp.getTitle().equals(ofi.fileName);
if (validName && ofi.fileFormat==FileInfo.TIFF && ofi.directory!=null && !ofi.directory.equals("") && (ofi.url==null||ofi.url.equals(""))) {
name = imp.getTitle();
directory = ofi.directory;
String path = directory+name;
File f = new File(path);
if (f==null || !f.exists())
return saveAsTiff();
if (!IJ.isMacro()) {
GenericDialog gd = new GenericDialog("Save as TIFF");
gd.addMessage("\""+ofi.fileName+"\" already exists.\nDo you want to replace it?");
gd.setOKLabel("Replace");
gd.showDialog();
if (gd.wasCanceled())
return false;
}
IJ.showStatus("Saving "+path);
if (imp.getStackSize()>1) {
IJ.saveAs(imp, "tif", path);
return true;
} else
return saveAsTiff(path);
} else
return saveAsTiff();
}
String getPath(String type, String extension) {
name = imp.getTitle();
SaveDialog sd = new SaveDialog("Save as "+type, name, extension);
name = sd.getFileName();
if (name==null)
return null;
directory = sd.getDirectory();
imp.startTiming();
String path = directory+name;
return path;
}
/** Saves the image or stack in TIFF format using a save file
dialog. Returns false if the user selects cancel. Equivalent to
IJ.saveAsTiff(imp,""), which is more convenient. */
public boolean saveAsTiff() {
String path = getPath("TIFF", ".tif");
if (path==null)
return false;
if (fi.nImages>1)
return saveAsTiffStack(path);
else
return saveAsTiff(path);
}
/** Saves the image in TIFF format using the specified path. Equivalent to
IJ.saveAsTiff(imp,path), which is more convenient. */
public boolean saveAsTiff(String path) {
if (fi.nImages>1)
return saveAsTiffStack(path);
if (imp.getProperty("FHT")!=null && path.contains("FFT of "))
setupFFTSave();
fi.info = imp.getInfoProperty();
Object label = imp.getProperty("Label");
if (label!=null && (label instanceof String)) {
fi.sliceLabels = new String[1];
fi.sliceLabels[0] = (String)label;
}
fi.description = getDescriptionString();
if (imp.getProperty(Plot.PROPERTY_KEY) != null) {
Plot plot = (Plot)(imp.getProperty(Plot.PROPERTY_KEY));
fi.plot = plot.toByteArray();
}
fi.roi = RoiEncoder.saveAsByteArray(imp.getRoi());
fi.overlay = getOverlay(imp);
fi.properties = imp.getPropertiesAsArray();
DataOutputStream out = null;
try {
TiffEncoder file = new TiffEncoder(fi);
out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(path),bsize));
file.write(out);
out.close();
} catch (IOException e) {
showErrorMessage("saveAsTiff", path, e);
return false;
} finally {
if (out!=null)
try {out.close();} catch (IOException e) {}
}
updateImp(fi, FileInfo.TIFF);
return true;
}
private void setupFFTSave() {
Object obj = imp.getProperty("FHT");
if (obj==null) return;
FHT fht = (obj instanceof FHT)?(FHT)obj:null;
if (fht==null) return;
if (fht.originalColorModel!=null && fht.originalBitDepth!=24)
fht.setColorModel(fht.originalColorModel);
ImagePlus imp2 = new ImagePlus(imp.getTitle(), fht);
imp2.setProperty("Info", imp.getProperty("Info"));
imp2.setProperties(imp.getPropertiesAsArray());
imp2.setCalibration(imp.getCalibration());
imp = imp2;
fi = imp.getFileInfo();
}
public static byte[][] getOverlay(ImagePlus imp) {
if (imp.getHideOverlay())
return null;
Overlay overlay = imp.getOverlay();
if (overlay==null) {
ImageCanvas ic = imp.getCanvas();
if (ic==null) return null;
overlay = ic.getShowAllList(); // ROI Manager "Show All" list
if (overlay==null) return null;
}
int n = overlay.size();
if (n==0)
return null;
if (Orthogonal_Views.isOrthoViewsImage(imp))
return null;
byte[][] array = new byte[n][];
for (int i=0; i1 && imp.getStack().isVirtual())
fi.virtualStack = (VirtualStack)imp.getStack();
DataOutputStream out = null;
try {
ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(path));
out = new DataOutputStream(new BufferedOutputStream(zos,bsize));
zos.putNextEntry(new ZipEntry(name));
TiffEncoder te = new TiffEncoder(fi);
te.write(out);
out.close();
}
catch (IOException e) {
showErrorMessage("saveAsZip", path, e);
return false;
} finally {
if (out!=null)
try {out.close();} catch (IOException e) {}
}
updateImp(fi, FileInfo.TIFF);
return true;
}
public static boolean okForGif(ImagePlus imp) {
if (imp.getType()==ImagePlus.COLOR_RGB)
return false;
else
return true;
}
/** Save the image in GIF format using a save file
dialog. Returns false if the user selects cancel
or the image is not 8-bits. */
public boolean saveAsGif() {
String path = getPath("GIF", ".gif");
if (path==null)
return false;
else
return saveAsGif(path);
}
/** Save the image in Gif format using the specified path. Returns
false if the image is not 8-bits or there is an I/O error. */
public boolean saveAsGif(String path) {
IJ.runPlugIn(imp, "ij.plugin.GifWriter", path);
updateImp(fi, FileInfo.GIF_OR_JPG);
return true;
}
/** Always returns true. */
public static boolean okForJpeg(ImagePlus imp) {
return true;
}
/** Save the image in JPEG format using a save file
dialog. Returns false if the user selects cancel.
@see #setJpegQuality
@see #getJpegQuality
*/
public boolean saveAsJpeg() {
String type = "JPEG ("+getJpegQuality()+")";
String path = getPath(type, ".jpg");
if (path==null)
return false;
else
return saveAsJpeg(path);
}
/** Save the image in JPEG format using the specified path.
@see #setJpegQuality
@see #getJpegQuality
*/
public boolean saveAsJpeg(String path) {
String err = JpegWriter.save(imp, path, jpegQuality);
if (err==null && !(imp.getType()==ImagePlus.GRAY16 || imp.getType()==ImagePlus.GRAY32))
updateImp(fi, FileInfo.GIF_OR_JPG);
return true;
}
/** Save the image in BMP format using a save file dialog.
Returns false if the user selects cancel. */
public boolean saveAsBmp() {
String path = getPath("BMP", ".bmp");
if (path==null)
return false;
else
return saveAsBmp(path);
}
/** Save the image in BMP format using the specified path. */
public boolean saveAsBmp(String path) {
IJ.runPlugIn(imp, "ij.plugin.BMP_Writer", path);
updateImp(fi, FileInfo.BMP);
return true;
}
/** Saves grayscale images in PGM (portable graymap) format
and RGB images in PPM (portable pixmap) format,
using a save file dialog.
Returns false if the user selects cancel.
*/
public boolean saveAsPgm() {
String extension = imp.getBitDepth()==24?".pnm":".pgm";
String path = getPath("PGM", extension);
if (path==null)
return false;
else
return saveAsPgm(path);
}
/** Saves grayscale images in PGM (portable graymap) format
and RGB images in PPM (portable pixmap) format,
using the specified path. */
public boolean saveAsPgm(String path) {
IJ.runPlugIn(imp, "ij.plugin.PNM_Writer", path);
updateImp(fi, FileInfo.PGM);
return true;
}
/** Save the image in PNG format using a save file dialog.
Returns false if the user selects cancel. */
public boolean saveAsPng() {
String path = getPath("PNG", ".png");
if (path==null)
return false;
else
return saveAsPng(path);
}
/** Save the image in PNG format using the specified path. */
public boolean saveAsPng(String path) {
IJ.runPlugIn(imp, "ij.plugin.PNG_Writer", path);
updateImp(fi, FileInfo.IMAGEIO);
return true;
}
/** Save the image in FITS format using a save file dialog.
Returns false if the user selects cancel. */
public boolean saveAsFits() {
if (!okForFits(imp)) return false;
String path = getPath("FITS", ".fits");
if (path==null)
return false;
else
return saveAsFits(path);
}
/** Save the image in FITS format using the specified path. */
public boolean saveAsFits(String path) {
if (!okForFits(imp)) return false;
IJ.runPlugIn(imp, "ij.plugin.FITS_Writer", path);
updateImp(fi, FileInfo.FITS);
return true;
}
public static boolean okForFits(ImagePlus imp) {
if (imp.getBitDepth()==24) {
IJ.error("FITS Writer", "Grayscale image required");
return false;
} else
return true;
}
/** Save the image or stack as raw data using a save file
dialog. Returns false if the user selects cancel. */
public boolean saveAsRaw() {
String path = getPath("Raw", ".raw");
if (path==null)
return false;
if (imp.getStackSize()==1)
return saveAsRaw(path);
else
return saveAsRawStack(path);
}
/** Save the image as raw data using the specified path. */
public boolean saveAsRaw(String path) {
fi.nImages = 1;
fi.intelByteOrder = Prefs.intelByteOrder;
boolean signed16Bit = false;
short[] pixels = null;
int n = 0;
OutputStream out = null;
try {
signed16Bit = imp.getCalibration().isSigned16Bit();
if (signed16Bit) {
pixels = (short[])imp.getProcessor().getPixels();
n = imp.getWidth()*imp.getHeight();
for (int i=0; i1 && imp.getStack().isVirtual();
if (virtualStack) {
fi.virtualStack = (VirtualStack)imp.getStack();
if (imp.getProperty("AnalyzeFormat")!=null) fi.fileName="FlipTheseImages";
}
OutputStream out = null;
try {
signed16Bit = imp.getCalibration().isSigned16Bit();
if (signed16Bit && !virtualStack) {
stack = (Object[])fi.pixels;
n = imp.getWidth()*imp.getHeight();
for (int slice=0; slice100)
msg = msg.substring(0, 100);
msg = "File saving error (IOException):\n \"" + msg + "\"";
IJ.error("FileSaver."+title, msg+" \n "+path);
IJ.showProgress(1.0);
}
private void error(String msg) {
IJ.error("FileSaver", msg);
}
/** Returns a string containing information about the specified image. */
public String getDescriptionString() {
Calibration cal = imp.getCalibration();
StringBuffer sb = new StringBuffer(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 (imp.isHyperStack()) sb.append("hyperstack=true\n");
if (imp.isComposite()) {
String mode = ((CompositeImage)imp).getModeAsString();
sb.append("mode="+mode+"\n");
}
if (fi.unit!=null)
appendEscapedLine(sb, "unit="+fi.unit);
int bitDepth = imp.getBitDepth();
if (fi.valueUnit!=null && (fi.calibrationFunction!=Calibration.CUSTOM||bitDepth==32)) {
if (bitDepth!=32) {
sb.append("cf="+fi.calibrationFunction+"\n");
if (fi.coefficients!=null) {
for (int i=0; i=0x20 && c<0x7f && c!='\\')
sb.append(c);
else if (c<=0xffff) { //(supplementary unicode characters >0xffff unsupported)
sb.append("\\u");
sb.append(Tools.int2hex(c, 4));
}
}
sb.append('\n');
}
/** Specifies the image quality (0-100). 0 is poorest image quality,
highest compression, and 100 is best image quality, lowest compression. */
public static void setJpegQuality(int quality) {
jpegQuality = quality;
if (jpegQuality<0) jpegQuality = 0;
if (jpegQuality>100) jpegQuality = 100;
}
/** Returns the current JPEG quality setting (0-100). */
public static int getJpegQuality() {
return jpegQuality;
}
/** Sets the BufferedOutputStream buffer size in bytes (default is 32K). */
public static void setBufferSize(int bufferSize) {
bsize = bufferSize;
if (bsize<2048) bsize = 2048;
}
}
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