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 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;
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;
}
/** Save the image or stack in TIFF format using a save file
dialog. Returns false if the user selects cancel. */
public boolean saveAsTiff() {
String path = getPath("TIFF", ".tif");
if (path==null)
return false;
if (fi.nImages>1)
return saveAsTiffStack(path);
else
return saveAsTiff(path);
}
/** Save the image in TIFF format using the specified path. */
public boolean saveAsTiff(String path) {
fi.nImages = 1;
Object info = imp.getProperty("Info");
if (info!=null && (info instanceof String))
fi.info = (String)info;
Object label = imp.getProperty("Label");
if (label!=null && (label instanceof String)) {
fi.sliceLabels = new String[1];
fi.sliceLabels[0] = (String)label;
}
fi.description = getDescriptionString();
fi.roi = RoiEncoder.saveAsByteArray(imp.getRoi());
fi.overlay = getOverlay(imp);
try {
TiffEncoder file = new TiffEncoder(fi);
DataOutputStream out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(path)));
file.write(out);
out.close();
} catch (IOException e) {
showErrorMessage(e);
return false;
}
updateImp(fi, FileInfo.TIFF);
return true;
}
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; i<overlay.size(); i++) {
Roi roi = overlay.get(i);
if (i==0)
roi.setPrototypeOverlay(overlay);
array[i] = RoiEncoder.saveAsByteArray(roi);
}
return array;
}
/** Save the stack as a multi-image TIFF using the specified path. */
public boolean saveAsTiffStack(String path) {
if (fi.nImages==1)
{IJ.error("This is not a stack"); return false;}
boolean virtualStack = imp.getStack().isVirtual();
if (virtualStack)
fi.virtualStack = (VirtualStack)imp.getStack();
Object info = imp.getProperty("Info");
if (info!=null && (info instanceof String))
fi.info = (String)info;
fi.description = getDescriptionString();
if (virtualStack) {
FileInfo fi = imp.getOriginalFileInfo();
if (path!=null && path.equals(fi.directory+fi.fileName)) {
IJ.error("TIFF virtual stacks cannot be saved in place.");
return false;
}
String[] labels = null;
ImageStack vs = imp.getStack();
for (int i=1; i<=vs.getSize(); i++) {
ImageProcessor ip = vs.getProcessor(i);
String label = vs.getSliceLabel(i);
if (i==1 && (label==null||label.length()<200)) break;
if (labels==null) labels = new String[vs.getSize()];
labels[i-1] = label;
}
fi.sliceLabels = labels;
} else
fi.sliceLabels = imp.getStack().getSliceLabels();
fi.roi = RoiEncoder.saveAsByteArray(imp.getRoi());
fi.overlay = getOverlay(imp);
if (imp.isComposite()) saveDisplayRangesAndLuts(imp, fi);
try {
TiffEncoder file = new TiffEncoder(fi);
DataOutputStream out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(path)));
file.write(out);
out.close();
}
catch (IOException e) {
showErrorMessage(e);
return false;
}
updateImp(fi, FileInfo.TIFF);
return true;
}
/** Converts this image to a TIFF encoded array of bytes,
which can be decoded using Opener.deserialize(). */
public byte[] serialize() {
if (imp.getStack().isVirtual())
return null;
Object info = imp.getProperty("Info");
if (info!=null && (info instanceof String))
fi.info = (String)info;
saveName = true;
fi.description = getDescriptionString();
saveName = false;
fi.sliceLabels = imp.getStack().getSliceLabels();
fi.roi = RoiEncoder.saveAsByteArray(imp.getRoi());
fi.overlay = getOverlay(imp);
if (imp.isComposite()) saveDisplayRangesAndLuts(imp, fi);
ByteArrayOutputStream out = null;
try {
TiffEncoder encoder = new TiffEncoder(fi);
out = new ByteArrayOutputStream();
encoder.write(out);
out.close();
} catch (IOException e) {
return null;
}
return out.toByteArray();
}
void saveDisplayRangesAndLuts(ImagePlus imp, FileInfo fi) {
CompositeImage ci = (CompositeImage)imp;
int channels = imp.getNChannels();
fi.displayRanges = new double[channels*2];
for (int i=1; i<=channels; i++) {
LUT lut = ci.getChannelLut(i);
fi.displayRanges[(i-1)*2] = lut.min;
fi.displayRanges[(i-1)*2+1] = lut.max;
}
if (ci.hasCustomLuts()) {
fi.channelLuts = new byte[channels][];
for (int i=0; i<channels; i++) {
LUT lut = ci.getChannelLut(i+1);
byte[] bytes = lut.getBytes();
if (bytes==null)
{fi.channelLuts=null; break;}
fi.channelLuts[i] = bytes;
}
}
}
/** Uses a save file dialog to save the image or stack as a TIFF
in a ZIP archive. Returns false if the user selects cancel. */
public boolean saveAsZip() {
String path = getPath("TIFF/ZIP", ".zip");
if (path==null)
return false;
else
return saveAsZip(path);
}
/** Save the image or stack in TIFF/ZIP format using the specified path. */
public boolean saveAsZip(String path) {
//fi.nImages = 1;
if (!path.endsWith(".zip"))
path = path+".zip";
if (name==null)
name = imp.getTitle();
if (name.endsWith(".zip"))
name = name.substring(0,name.length()-4);
if (!name.endsWith(".tif"))
name = name+".tif";
fi.description = getDescriptionString();
Object info = imp.getProperty("Info");
if (info!=null && (info instanceof String))
fi.info = (String)info;
fi.roi = RoiEncoder.saveAsByteArray(imp.getRoi());
fi.overlay = getOverlay(imp);
fi.sliceLabels = imp.getStack().getSliceLabels();
if (imp.isComposite()) saveDisplayRangesAndLuts(imp, fi);
if (fi.nImages>1 && imp.getStack().isVirtual())
fi.virtualStack = (VirtualStack)imp.getStack();
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) {
showErrorMessage(e);
return false;
}
updateImp(fi, FileInfo.TIFF);
return true;
}
public static boolean okForGif(ImagePlus imp) {
int type = imp.getType();
if (type==ImagePlus.COLOR_RGB) {
IJ.error("To save as Gif, the image must be converted to \"8-bit Color\".");
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() {
if (!okForGif(imp))
return false;
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) {
if (!okForGif(imp)) return false;
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. */
/** 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;
try {
signed16Bit = imp.getCalibration().isSigned16Bit();
if (signed16Bit) {
pixels = (short[])imp.getProcessor().getPixels();
n = imp.getWidth()*imp.getHeight();
for (int i=0; i<n; i++)
pixels[i] = (short)(pixels[i]-32768);
}
ImageWriter file = new ImageWriter(fi);
OutputStream out = new BufferedOutputStream(new FileOutputStream(path));
file.write(out);
out.close();
}
catch (IOException e) {
showErrorMessage(e);
return false;
}
if (signed16Bit) {
for (int i=0; i<n; i++)
pixels[i] = (short)(pixels[i]+32768);
}
updateImp(fi, fi.RAW);
return true;
}
/** Save the stack as raw data using the specified path. */
public boolean saveAsRawStack(String path) {
if (fi.nImages==1)
{IJ.write("This is not a stack"); return false;}
fi.intelByteOrder = Prefs.intelByteOrder;
boolean signed16Bit = false;
Object[] stack = null;
int n = 0;
boolean virtualStack = imp.getStackSize()>1 && imp.getStack().isVirtual();
if (virtualStack) {
fi.virtualStack = (VirtualStack)imp.getStack();
if (imp.getProperty("AnalyzeFormat")!=null) fi.fileName="FlipTheseImages";
}
try {
signed16Bit = imp.getCalibration().isSigned16Bit();
if (signed16Bit && !virtualStack) {
stack = (Object[])fi.pixels;
n = imp.getWidth()*imp.getHeight();
for (int slice=0; slice<fi.nImages; slice++) {
short[] pixels = (short[])stack[slice];
for (int i=0; i<n; i++)
pixels[i] = (short)(pixels[i]-32768);
}
}
ImageWriter file = new ImageWriter(fi);
OutputStream out = new BufferedOutputStream(new FileOutputStream(path));
file.write(out);
out.close();
}
catch (IOException e) {
showErrorMessage(e);
return false;
}
if (signed16Bit) {
for (int slice=0; slice<fi.nImages; slice++) {
short[] pixels = (short[])stack[slice];
for (int i=0; i<n; i++)
pixels[i] = (short)(pixels[i]+32768);
}
}
updateImp(fi, fi.RAW);
return true;
}
/** Save the image as tab-delimited text using a save file
dialog. Returns false if the user selects cancel. */
public boolean saveAsText() {
String path = getPath("Text", ".txt");
if (path==null)
return false;
return saveAsText(path);
}
/** Save the image as tab-delimited text using the specified path. */
public boolean saveAsText(String path) {
try {
Calibration cal = imp.getCalibration();
int precision = Analyzer.getPrecision();
int measurements = Analyzer.getMeasurements();
boolean scientificNotation = (measurements&Measurements.SCIENTIFIC_NOTATION)!=0;
if (scientificNotation)
precision = -precision;
TextEncoder file = new TextEncoder(imp.getProcessor(), cal, precision);
DataOutputStream out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(path)));
file.write(out);
out.close();
}
catch (IOException e) {
showErrorMessage(e);
return false;
}
return true;
}
/** Save the current LUT using a save file
dialog. Returns false if the user selects cancel. */
public boolean saveAsLut() {
if (imp.getType()==ImagePlus.COLOR_RGB) {
IJ.error("RGB Images do not have a LUT.");
return false;
}
String path = getPath("LUT", ".lut");
if (path==null)
return false;
return saveAsLut(path);
}
/** Save the current LUT using the specified path. */
public boolean saveAsLut(String path) {
LookUpTable lut = imp.createLut();
int mapSize = lut.getMapSize();
if (mapSize==0) {
IJ.error("RGB Images do not have a LUT.");
return false;
}
if (mapSize<256) {
IJ.error("Cannot save LUTs with less than 256 entries.");
return false;
}
byte[] reds = lut.getReds();
byte[] greens = lut.getGreens();
byte[] blues = lut.getBlues();
byte[] pixels = new byte[768];
for (int i=0; i<256; i++) {
pixels[i] = reds[i];
pixels[i+256] = greens[i];
pixels[i+512] = blues[i];
}
FileInfo fi = new FileInfo();
fi.width = 768;
fi.height = 1;
fi.pixels = pixels;
try {
ImageWriter file = new ImageWriter(fi);
OutputStream out = new FileOutputStream(path);
file.write(out);
out.close();
}
catch (IOException e) {
showErrorMessage(e);
return false;
}
return true;
}
private void updateImp(FileInfo fi, int fileFormat) {
imp.changes = false;
if (name!=null) {
fi.fileFormat = fileFormat;
FileInfo ofi = imp.getOriginalFileInfo();
if (ofi!=null) {
if (ofi.openNextName==null) {
fi.openNextName = ofi.fileName;
fi.openNextDir = ofi.directory;
} else {
fi.openNextName = ofi.openNextName;
fi.openNextDir = ofi.openNextDir ;
}
}
fi.fileName = name;
fi.directory = directory;
//if (fileFormat==fi.TIFF)
// fi.offset = TiffEncoder.IMAGE_START;
fi.description = null;
imp.setTitle(name);
imp.setFileInfo(fi);
}
}
void showErrorMessage(IOException e) {
String msg = e.getMessage();
if (msg.length()>100)
msg = msg.substring(0, 100);
IJ.error("FileSaver", "An error occured writing the file.\n \n" + 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)
sb.append("unit="+(fi.unit.equals("\u00B5m")?"um":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 (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");
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");
}
// get min and max display values
ImageProcessor ip = imp.getProcessor();
double min = ip.getMin();
double max = ip.getMax();
int type = imp.getType();
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");
if (saveName)
sb.append("name="+imp.getTitle()+"\n");
sb.append((char)0);
return new String(sb);
}
/** 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;
}
}