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.*;
public class FileSaver {
public static final int DEFAULT_JPEG_QUALITY = 85;
private static int jpegQuality;
private static int bsize = 32768;
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;
public FileSaver(ImagePlus imp) {
this.imp = imp;
fi = imp.getFileInfo();
}
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;
}
public boolean saveAsTiff() {
String path = getPath("TIFF", ".tif");
if (path==null)
return false;
if (fi.nImages>1)
return saveAsTiffStack(path);
else
return saveAsTiff(path);
}
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();
String label = imp.isStack()?imp.getStack().getSliceLabel(1):null;
if (label!=null) {
fi.sliceLabels = new String[1];
fi.sliceLabels[0] = 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(); 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;
}
public boolean saveAsTiffStack(String path) {
if (fi.nImages==1) {
error("This is not a stack");
return false;
}
boolean virtualStack = imp.getStack().isVirtual();
if (virtualStack)
fi.virtualStack = (VirtualStack)imp.getStack();
fi.info = imp.getInfoProperty();
fi.description = getDescriptionString();
if (virtualStack) {
FileInfo ofi = imp.getOriginalFileInfo();
if (path!=null && ofi!=null && path.equals(ofi.directory+ofi.fileName)) {
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++) {
String label = vs.getSliceLabel(i);
if (i==1 && label==null)
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);
fi.properties = imp.getPropertiesAsArray();
if (imp.isComposite()) saveDisplayRangesAndLuts(imp, fi);
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("saveAsTiffStack", path, e);
return false;
} finally {
if (out!=null)
try {out.close();} catch (IOException e) {}
}
updateImp(fi, FileInfo.TIFF);
return true;
}
public byte[] serialize() {
if (imp.getStack().isVirtual())
return null;
fi.info = imp.getInfoProperty();
saveName = true;
fi.description = getDescriptionString();
saveName = false;
fi.sliceLabels = imp.getStack().getSliceLabels();
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);
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;
} finally {
if (out!=null)
try {out.close();} catch (IOException e) {}
}
return out.toByteArray();
}
public 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;
}
}
}
public boolean saveAsZip() {
String path = getPath("TIFF/ZIP", ".zip");
if (path==null)
return false;
else
return saveAsZip(path);
}
public boolean saveAsZip(String path) {
if (imp.getProperty("FHT")!=null && path.contains("FFT of "))
setupFFTSave();
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();
fi.info = imp.getInfoProperty();
fi.properties = imp.getPropertiesAsArray();
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.sliceLabels = imp.getStack().getSliceLabels();
if (imp.isComposite()) saveDisplayRangesAndLuts(imp, fi);
if (fi.nImages>1 && 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;
}
public boolean saveAsGif() {
String path = getPath("GIF", ".gif");
if (path==null)
return false;
else
return saveAsGif(path);
}
public boolean saveAsGif(String path) {
IJ.runPlugIn(imp, "ij.plugin.GifWriter", path);
updateImp(fi, FileInfo.GIF_OR_JPG);
return true;
}
public static boolean okForJpeg(ImagePlus imp) {
return true;
}
public boolean saveAsJpeg() {
String type = "JPEG ("+getJpegQuality()+")";
String path = getPath(type, ".jpg");
if (path==null)
return false;
else
return saveAsJpeg(path);
}
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;
}
public boolean saveAsBmp() {
String path = getPath("BMP", ".bmp");
if (path==null)
return false;
else
return saveAsBmp(path);
}
public boolean saveAsBmp(String path) {
IJ.runPlugIn(imp, "ij.plugin.BMP_Writer", path);
updateImp(fi, FileInfo.BMP);
return true;
}
public boolean saveAsPgm() {
String extension = imp.getBitDepth()==24?".pnm":".pgm";
String path = getPath("PGM", extension);
if (path==null)
return false;
else
return saveAsPgm(path);
}
public boolean saveAsPgm(String path) {
IJ.runPlugIn(imp, "ij.plugin.PNM_Writer", path);
updateImp(fi, FileInfo.PGM);
return true;
}
public boolean saveAsPng() {
String path = getPath("PNG", ".png");
if (path==null)
return false;
else
return saveAsPng(path);
}
public boolean saveAsPng(String path) {
IJ.runPlugIn(imp, "ij.plugin.PNG_Writer", path);
updateImp(fi, FileInfo.IMAGEIO);
return true;
}
public boolean saveAsFits() {
if (!okForFits(imp)) return false;
String path = getPath("FITS", ".fits");
if (path==null)
return false;
else
return saveAsFits(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;
}
public boolean saveAsRaw() {
String path = getPath("Raw", ".raw");
if (path==null)
return false;
if (imp.getStackSize()==1)
return saveAsRaw(path);
else
return saveAsRawStack(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; i<n; i++)
pixels[i] = (short)(pixels[i]-32768);
}
ImageWriter file = new ImageWriter(fi);
out = new BufferedOutputStream(new FileOutputStream(path),bsize);
file.write(out);
out.close();
}
catch (IOException e) {
showErrorMessage("saveAsRaw", path, e);
return false;
} finally {
if (out!=null)
try {out.close();} catch (IOException e) {}
}
if (signed16Bit) {
for (int i=0; i<n; i++)
pixels[i] = (short)(pixels[i]+32768);
}
updateImp(fi, fi.RAW);
return true;
}
public boolean saveAsRawStack(String path) {
if (fi.nImages==1)
{IJ.log("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";
}
OutputStream out = null;
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);
out = new BufferedOutputStream(new FileOutputStream(path),bsize);
file.write(out);
out.close();
} catch (IOException e) {
showErrorMessage("saveAsRawStack", path, e);
return false;
} finally {
if (out!=null)
try {out.close();} catch (IOException e) {}
}
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;
}
public boolean saveAsText() {
String path = getPath("Text", ".txt");
if (path==null)
return false;
return saveAsText(path);
}
public boolean saveAsText(String path) {
DataOutputStream out = null;
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);
out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(path)));
file.write(out);
out.close();
} catch (IOException e) {
showErrorMessage("saveAsText", path, e);
return false;
} finally {
if (out!=null)
try {out.close();} catch (IOException e) {}
}
return true;
}
public boolean saveAsLut() {
if (imp.getType()==ImagePlus.COLOR_RGB) {
error("RGB Images do not have a LUT.");
return false;
}
String path = getPath("LUT", ".lut");
if (path==null)
return false;
return saveAsLut(path);
}
public boolean saveAsLut(String path) {
LookUpTable lut = imp.createLut();
int mapSize = lut.getMapSize();
if (mapSize==0) {
error("RGB Images do not have a LUT.");
return false;
}
if (mapSize<256) {
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;
OutputStream out = null;
try {
ImageWriter file = new ImageWriter(fi);
out = new FileOutputStream(path);
file.write(out);
out.close();
}
catch (IOException e) {
showErrorMessage("saveAsLut", path, e);
return false;
} finally {
if (out!=null)
try {out.close();} catch (IOException e) {}
}
return true;
}
public void updateImagePlus(String path, int fileFormat) {
if (imp==null || fi==null)
return;
if (name==null && path!=null) {
File f = new File(path);
directory = f.getParent() + File.separator;
name = f.getName();
}
updateImp(fi, fileFormat);
}
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;
fi.description = null;
imp.setTitle(name);
fi.imageSaved = true;
imp.setFileInfo(fi);
}
}
private void showErrorMessage(String title, String path, IOException e) {
String msg = e.getMessage();
if (msg.length()>100)
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);
}
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<fi.coefficients.length; i++)
sb.append("c"+i+"="+fi.coefficients[i]+"\n");
}
}
appendEscapedLine(sb, "vunit="+fi.valueUnit);
if (cal.zeroClip() && bitDepth!=32)
sb.append("zeroclip=true\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"))
appendEscapedLine(sb, "tunit="+cal.getTimeUnit());
if (!cal.getYUnit().equals(cal.getUnit()))
appendEscapedLine(sb, "yunit="+cal.getYUnit());
if (!cal.getZUnit().equals(cal.getUnit()))
appendEscapedLine(sb, "zunit="+cal.getZUnit());
if (fi.nImages>1) {
if (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");
}
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");
}
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)
appendEscapedLine(sb, "info="+cal.info);
if (cal.getInvertY())
sb.append("inverty=true\n");
if (saveName)
appendEscapedLine(sb, "name="+imp.getTitle());
if (imp.getType()==ImagePlus.COLOR_256)
sb.append("8bitcolor=true\n");
sb.append((char)0);
return new String(sb);
}
void appendEscapedLine(StringBuffer sb, String str) {
for (int i=0; i<str.length(); i++) {
char c = str.charAt(i);
if (c>=0x20 && c<0x7f && c!='\\')
sb.append(c);
else if (c<=0xffff) { sb.append("\\u");
sb.append(Tools.int2hex(c, 4));
}
}
sb.append('\n');
}
public static void setJpegQuality(int quality) {
jpegQuality = quality;
if (jpegQuality<0) jpegQuality = 0;
if (jpegQuality>100) jpegQuality = 100;
}
public static int getJpegQuality() {
return jpegQuality;
}
public static void setBufferSize(int bufferSize) {
bsize = bufferSize;
if (bsize<2048) bsize = 2048;
}
}