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=========================================================================
== NOTICE file corresponding to the section 4 d of ==
== the Apache License, Version 2.0, ==
== in this case for the ImageJ HDF Plugin distribution. ==
=========================================================================
ImageJ HDF Plugin
Copyright 2011 Matthias Schlachter
This product includes software developed by Matthias Schlachter.
The initial release of this software was developed by Matthias Schlachter
at the Chair of Pattern Recognition and Image Processing, University of
Freiburg, Germany.

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/* =========================================================================
*
* Copyright 2011 Matthias Schlachter
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
import ij.*;
import ij.io.*;
import ij.plugin.*;
import ij.plugin.filter.PlugInFilter;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import java.lang.Math;
import java.io.IOException;
import java.io.File;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import javax.swing.tree.DefaultMutableTreeNode;
import ncsa.hdf.object.*; // the common object package
import ncsa.hdf.object.h5.*; // the HDF5 implementation
import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
import ncsa.hdf.hdflib.HDFException;
public class HDF5_Batch_
{
public static void run(String arg)
{
parseArgs(arg);
System.out.println("filename");
System.out.println(_filename);
System.out.println("varnames");
for(int i=0; i<_varnames.length; i++)
System.out.println(_varnames[i]);
HDF5_Writer_ w = new HDF5_Writer_();
w.setToBatchMode(_filename,_varnames);
w.run(null);
}
private static void parseArgs(String arg)
{
String[] result = arg.split("]\\s");
_filename = result[0].replaceAll("file=\\[","");
String[] splitVars = result[1].split("\\s");
_varnames = new String[splitVars.length];
for (int x=0; x<splitVars.length; x++)
_varnames[x] = splitVars[x];
}
static private String _filename = null;
static private String[] _varnames = null;
// end of class
}

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/* =========================================================================
*
* Copyright 2011 Matthias Schlachter
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
import ij.IJ;
import ij.Prefs;
import ij.gui.GenericDialog;
import ij.plugin.PlugIn;
import java.util.regex.*;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.lang.String;
public class HDF5_Config implements PlugIn
{
public void run(String arg)
{
// set default values
setDefaultsIfNoValueExists();
// read ImageJ Preferences
boolean groupVarsByName =
Boolean.getBoolean(getDefaultValue("HDF5.groupVarsByName"));
groupVarsByName = Prefs.get("HDF5.groupVarsByName", groupVarsByName);
boolean showUnmatchedDataSetNames =
Boolean.getBoolean(getDefaultValue("HDF5.showUnmatchedDataSetNames"));
showUnmatchedDataSetNames = Prefs.get("HDF5.showUnmatchedDataSetNames",
showUnmatchedDataSetNames);
String groupVarsByNameFormatGroup =
getDefaultValue("HDF5.groupVarsByNameFormatGroup");
groupVarsByNameFormatGroup
= Prefs.get("HDF5.groupVarsByNameFormatGroup",
groupVarsByNameFormatGroup);
String groupVarsByNameFormat =
getDefaultValue("HDF5.groupVarsByNameFormat");
groupVarsByNameFormat = Prefs.get("HDF5.groupVarsByNameFormat",
groupVarsByNameFormat);
String dollarRegexpForGrouping =
getDefaultValue("HDF5.dollarRegexpForGrouping");
dollarRegexpForGrouping = Prefs.get("HDF5.dollarRegexpForGrouping",
dollarRegexpForGrouping);
GenericDialog configDiag =
new GenericDialog("HDF5 Preferences");
configDiag.addMessage("Reader:");
configDiag.addCheckbox("Group data set names instead of showing a list " +
"of data set names.",
groupVarsByName);
configDiag.addCheckbox("Show unmatched data set names in a separate list",
showUnmatchedDataSetNames);
configDiag.addStringField("HDF5 group containing pattern " +
"for data set grouping: ",
groupVarsByNameFormatGroup,15);
configDiag.addStringField("Pattern for grouping (if no attributes" +
" are found): ",
groupVarsByNameFormat,15);
// configDiag.addStringField("$ regexp (ignored because only numbers" +
// " work right now): ",
// dollarRegexpForGrouping,15);
configDiag.addMessage("Writer:");
String yesLabel = "Save";
String noLabel = "Reset";
configDiag.enableYesNoCancel(yesLabel,noLabel);
configDiag.showDialog();
if(configDiag.wasCanceled())
{
// do nothing
return;
}
if(!configDiag.wasOKed())
{
// reset button was pressed
System.out.println("reset button was pressed");
// reset all and return a new dialog
configDiag.setVisible(false);
this.run(arg);
return;
}
// get parameters check if they are correct
groupVarsByName = configDiag.getNextBoolean();
System.out.println("groupVarsByName: " +
Boolean.toString(groupVarsByName));
showUnmatchedDataSetNames = configDiag.getNextBoolean();
System.out.println("showUnmatchedDataSetNames: " +
Boolean.toString(showUnmatchedDataSetNames));
groupVarsByNameFormatGroup = configDiag.getNextString();
System.out.println("groupVarsByNameFormatGroup: " +
groupVarsByNameFormatGroup);
groupVarsByNameFormat = configDiag.getNextString();
System.out.println("groupVarsByNameFormat: " +
groupVarsByNameFormat);
// dollarRegexpForGrouping = configDiag.getNextString();
// System.out.println("dollarRegexpForGrouping: " +
// dollarRegexpForGrouping);
try
{
String[] formatTokens
= HDF5_GroupedVarnames.parseFormatString(groupVarsByNameFormat,
dollarRegexpForGrouping);
for(int i=0; i<formatTokens.length; i++)
{
System.out.println("tok " + Integer.toString(i) + " : "
+ formatTokens[i]);
}
}
catch(PatternSyntaxException e)
{
// produce an error dialog an start over
String errMsg = e.getMessage();
System.out.println(errMsg);
// reset all and return a new dialog
configDiag.setVisible(false);
this.run(arg);
return;
}
System.out.println("Saving...");
// all OK and "Save" was pressed, so save it...
Prefs.set("HDF5.groupVarsByName",
groupVarsByName);
Prefs.set("HDF5.showUnmatchedDataSetNames",
showUnmatchedDataSetNames);
Prefs.set("HDF5.groupVarsByNameFormatGroup",
groupVarsByNameFormatGroup);
Prefs.set("HDF5.groupVarsByNameFormat",
groupVarsByNameFormat);
//
// ignore the $ regexp for now, because only numbers work
//
Prefs.set("HDF5.dollarRegexpForGrouping",
dollarRegexpForGrouping);
}
public static void setDefaultsIfNoValueExists()
{
boolean groupVarsByName =
Boolean.getBoolean(getDefaultValue("HDF5.groupVarsByName"));
groupVarsByName = Prefs.get("HDF5.groupVarsByName", groupVarsByName);
Prefs.set("HDF5.groupVarsByName",
groupVarsByName);
boolean showUnmatchedDataSetNames =
Boolean.getBoolean(getDefaultValue("HDF5.showUnmatchedDataSetNames"));
showUnmatchedDataSetNames = Prefs.get("HDF5.showUnmatchedDataSetNames",
showUnmatchedDataSetNames);
Prefs.set("HDF5.showUnmatchedDataSetNames",
showUnmatchedDataSetNames);
String groupVarsByNameFormatGroup =
getDefaultValue("HDF5.groupVarsByNameFormatGroup");
groupVarsByNameFormatGroup
= Prefs.get("HDF5.groupVarsByNameFormatGroup",
groupVarsByNameFormatGroup);
Prefs.set("HDF5.groupVarsByNameFormatGroup",
groupVarsByNameFormatGroup);
String groupVarsByNameFormat =
getDefaultValue("HDF5.groupVarsByNameFormat");
groupVarsByNameFormat = Prefs.get("HDF5.groupVarsByNameFormat",
groupVarsByNameFormat);
Prefs.set("HDF5.groupVarsByNameFormat",
groupVarsByNameFormat);
String dollarRegexpForGrouping =
getDefaultValue("HDF5.dollarRegexpForGrouping");
dollarRegexpForGrouping = Prefs.get("HDF5.dollarRegexpForGrouping",
dollarRegexpForGrouping);
Prefs.set("HDF5.dollarRegexpForGrouping",
dollarRegexpForGrouping);
}
public static String getDefaultValue(String key)
{
if(key.equals("HDF5.groupVarsByName"))
{
boolean groupVarsByName = true; // default
return Boolean.toString(groupVarsByName);
}
else if(key.equals("HDF5.showUnmatchedDataSetNames"))
{
boolean showUnmatchedDataSetNames = true; // default
return Boolean.toString(showUnmatchedDataSetNames);
}
else if(key.equals("HDF5.groupVarsByNameFormatGroup"))
{
String groupVarsByNameFormatGroup = "/hints"; // default
return groupVarsByNameFormatGroup;
}
else if(key.equals("HDF5.groupVarsByNameFormat"))
{
String groupVarsByNameFormat = "/t$T/channel$C"; // default
return groupVarsByNameFormat;
}
else if(key.equals("HDF5.dollarRegexpForGrouping"))
{
String dollarRegexpForGrouping = "[0-9]+"; // default
return dollarRegexpForGrouping;
}
else
{
System.out.println("No default value for key: " + key);
return null;
}
}
}

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/* =========================================================================
*
* Copyright 2011 Matthias Schlachter
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
import ij.IJ;
import ij.Prefs;
import ij.plugin.PlugIn;
import java.util.regex.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
public class HDF5_GroupedVarnames
{
public static String[] parseFormatString(String groupVarsByNameFormat,
String dollarRegexpForGrouping)
throws PatternSyntaxException
{
String[] formatTokens = null;
formatTokens = groupVarsByNameFormat.split("([$]T|[$]C)");
boolean containsFormatVars
= groupVarsByNameFormat.contains("$T") &&
groupVarsByNameFormat.contains("$C");
boolean rightOrderOfFormatVars
= groupVarsByNameFormat.indexOf("$T")
< groupVarsByNameFormat.indexOf("$C");
for(int i=0; i<formatTokens.length; i++)
{
System.out.println("tok " + Integer.toString(i) + " : "
+ formatTokens[i]);
}
if(formatTokens.length < 2 ||
!containsFormatVars ||
!rightOrderOfFormatVars)
{
throw new PatternSyntaxException("Your format string has errors. "+
"You must provide $T and $C and "+
"also in correct order!",
groupVarsByNameFormat,
-1);
}
String regexp = groupVarsByNameFormat;
regexp = regexp.replace("$T",
dollarRegexpForGrouping);
regexp = regexp.replace("$C",
dollarRegexpForGrouping);
System.out.println(regexp);
// check if we have a regexp;
Pattern p = null;
p = Pattern.compile(regexp);
return formatTokens;
}
public void parseVarNames(String[] varNames,
String groupVarsByNameFormat,
String dollarRegexpForGrouping)
{
// save format string
formatString = groupVarsByNameFormat;
try
{
formatTokens = parseFormatString(groupVarsByNameFormat,
dollarRegexpForGrouping);
}
catch(PatternSyntaxException e)
{
// produce an error dialog an start over
String errMsg = e.getMessage();
System.out.println(errMsg);
return;
}
String regexp = groupVarsByNameFormat;
regexp = regexp.replace("$T",
dollarRegexpForGrouping);
regexp = regexp.replace("$C",
dollarRegexpForGrouping);
System.out.println(regexp);
// check if we have a regexp;
Pattern p = null;
p = Pattern.compile(regexp);
/*---------------------------------------------------------------------
* parse var names
*---------------------------------------------------------------------*/
for (int i = 0; i < varNames.length; i++)
{
Matcher m=p.matcher(varNames[i]);
boolean b=m.matches();
if(b)
{
System.out.println(varNames[i]);
matchedVarNames.add(varNames[i]);
}
else
{
unMatchedVarNames.add(varNames[i]);
}
}
splitGroupedVarnames();
// ugly hack for sorting ArrayList
Object[] frameListAsArray = frameList.toArray();
Arrays.sort(frameListAsArray);
for(int i=0;i<frameListAsArray.length;i++)
frameList.set(i,(TimeFrame)frameListAsArray[i]);
}
public TimeFrame getFrame(int i)
{
if(i < frameList.size() && i > -1)
return frameList.get(i);
else
return null;
}
private void splitGroupedVarnames()
{
Iterator<String> vars = matchedVarNames.iterator();
while(vars.hasNext())
{
String varName = vars.next();
String[] tokens = null;
if(formatTokens.length == 2)
{
tokens = varName.split(formatTokens[1]);
}
else if(formatTokens.length == 3)
{
tokens = varName.split(formatTokens[2]);
varName = tokens[0];
tokens = varName.split(formatTokens[1]);
}
if(tokens.length < 2 || tokens.length > 3)
{
System.out.println("Error parsing varname!");
}
else
{
Integer channelIndex = new Integer(tokens[1]);
System.out.println("channelIndex: " + channelIndex.toString());
System.out.println("left token: " + tokens[0]);
tokens = tokens[0].split("/t");
Integer frameIndex = new Integer(tokens[1]);
System.out.println("frameIndex: " + frameIndex.toString());
if(minFrameIndex == -1)
minFrameIndex = frameIndex.intValue();
minFrameIndex = Math.min(minFrameIndex,frameIndex.intValue());
if(maxFrameIndex == -1)
maxFrameIndex = frameIndex.intValue();
maxFrameIndex = Math.max(maxFrameIndex,frameIndex.intValue());
if(minChannelIndex == -1)
minChannelIndex = channelIndex.intValue();
minChannelIndex = Math.min(minChannelIndex,channelIndex.intValue());
if(maxChannelIndex == -1)
maxChannelIndex = channelIndex.intValue();
maxChannelIndex = Math.max(maxChannelIndex,channelIndex.intValue());
TimeFrame frame = new TimeFrame(frameIndex.intValue());
int idx = frameList.indexOf(frame);
if(idx != -1)
{
frame = (TimeFrame) frameList.get(idx);
frame.addChannel(channelIndex.intValue());
}
else
{
frame.addChannel(channelIndex.intValue());
frameList.add(frame);
}
//System.out.println(frame.toString());
}
}
}
public int getMinFrameIndex()
{
return minFrameIndex;
}
public int getMaxFrameIndex()
{
return maxFrameIndex;
}
public int getMinChannelIndex()
{
return minChannelIndex;
}
public int getMaxChannelIndex()
{
return maxChannelIndex;
}
public int getNFrames()
{
return frameList.size();
}
public int getNChannels()
{
// TODO: check all frames for min/max of channels not index
if(nChannels == -1)
return maxChannelIndex-minChannelIndex+1;
else
return nChannels;
}
public boolean hasAllFramesInRange()
{
return frameList.size() == (maxFrameIndex-minFrameIndex+1);
}
public String toString()
{
String s = "Data set statistics\n";
s = s + "----------------------------------\n";
s = s + "nFrames: " + Integer.toString(frameList.size()) + "\n";
s = s + "minFrameIndex: " + Integer.toString(minFrameIndex) + "\n";
s = s + "maxFrameIndex: " + Integer.toString(maxFrameIndex) + "\n";
s = s
+ "hasAllFramesInRange: "
+ Boolean.toString(hasAllFramesInRange()) + "\n";
s = s + "minChannelIndex: " + Integer.toString(minChannelIndex) + "\n";
s = s + "maxChannelIndex: " + Integer.toString(maxChannelIndex) + "\n";
// String[] toks = getFormatTokens();
Iterator<TimeFrame> frames = frameList.iterator();
while(frames.hasNext())
{
TimeFrame f = frames.next();
s = s + f.toString() + "\n";
// s = s + "(" + toks[0] +
// Integer.toString(f.getFrameIndex())
// + toks[1] + "$C";
// if(toks.length>2)
// s = s + toks[2] + "\n";
// else
// s = s + "\n";
}
s = s + "----------------------------------";
return s;
}
public List<String> getUnmatchedVarNames()
{
return unMatchedVarNames;
}
public String[] getFormatTokens()
{
return formatTokens;
}
public String getFormatString()
{
return formatString;
}
public void setFrameAndChannelRange(int minFrame,
int skipFrame,
int maxFrame,
int minChannel,
int skipChannel,
int maxChannel)
{
System.out.println("Setting frame range: " +
Integer.toString(minFrame) + ":" +
Integer.toString(skipFrame) + ":" +
Integer.toString(maxFrame));
System.out.println("Setting channel range: " +
Integer.toString(minChannel) + ":" +
Integer.toString(skipChannel) + ":" +
Integer.toString(maxChannel));
if(hasAllFramesInRange())
{
// copy frames
List<TimeFrame> completeFrameList = new ArrayList<TimeFrame>(frameList);
// clear frames
frameList.clear();
// insert wanted frames and channels
for(int f=minFrame;f<maxFrame+1;f+=skipFrame)
{
TimeFrame frameAllChannels = completeFrameList.get(f);
TimeFrame frame = new TimeFrame(frameAllChannels.getFrameIndex());
// TODO remove unwanted channels
for(int c=minChannel;c<maxChannel+1;c+=skipChannel)
{
//System.out.println("Adding channels: " + Integer.toString(c));
frame.addChannel(c);
}
// if(nChannels == -1)
// nChannels = frame.getNChannels();
frameList.add(frame);
}
// TODO update min/max of frames/channels
nChannels = ((maxChannel-minChannel) / skipChannel)+1;
System.out.println("Adding nChannels: " + Integer.toString(nChannels));
}
else
{
System.out.println("-------------------------\n"+
"hasAllFramesInRange==false\n"+
"-------------------------");
// copy frames
List<TimeFrame> completeFrameList = new ArrayList<TimeFrame>(frameList);
// clear frames
frameList.clear();
// insert wanted frames and channels
for(int f=minFrame;f<maxFrame+1;f+=skipFrame)
{
TimeFrame frame = new TimeFrame(f);
int idx = completeFrameList.indexOf(frame);
// System.out.println("index of frame in list: " +
// Integer.toString(idx));
if(idx != -1)
{
// TODO remove unwanted channels
for(int c=minChannel;c<maxChannel+1;c+=skipChannel)
{
//System.out.println("Adding channels: " + Integer.toString(c));
frame.addChannel(c);
}
// if(nChannels == -1)
// nChannels = frame.getNChannels();
frameList.add(frame);
}
else
{
System.out.println("Timestep "+Integer.toString(f)+
" is missing!");
}
}
// TODO update min/max of frames/channels
nChannels = ((maxChannel-minChannel) / skipChannel)+1;
System.out.println("Adding nChannels: " + Integer.toString(nChannels));
}
}
private final List<String> matchedVarNames = new ArrayList<String>();
private final List<String> unMatchedVarNames = new ArrayList<String>();
private final List<TimeFrame> frameList = new ArrayList<TimeFrame>();
private String[] formatTokens = null;
private String formatString = null;
private int minFrameIndex = -1;
private int maxFrameIndex = -1;
private int minChannelIndex = -1;
private int maxChannelIndex = -1;
private int nChannels = -1;
}

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/* =========================================================================
*
* Copyright 2011 Matthias Schlachter
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
import ij.*;
import ij.io.*;
import ij.plugin.*;
import ij.plugin.filter.PlugInFilter;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import java.lang.Math;
import java.io.IOException;
import java.io.File;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import javax.swing.tree.DefaultMutableTreeNode;
import ncsa.hdf.object.*; // the common object package
import ncsa.hdf.object.h5.*; // the HDF5 implementation
import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
import ncsa.hdf.hdflib.HDFException;
public class HDF5_Writer_ implements PlugInFilter
{
private Boolean _batchMode = false;
private String[] _batchVarNames = null;
private String _batchFileName = null;
public int setup(String arg, ImagePlus imp)
{
if (arg.equals("about"))
{
showAbout();
return DONE;
}
// FIXME: set DOES_xx for image type here:
// currently RGB-Types are still missing
// see
// http://rsb.info.nih.gov/ij/developer/api/ij/plugin/filter/PlugInFilter.html
return DOES_8G + DOES_16 + DOES_32 + DOES_RGB
+ NO_CHANGES;
}
public void setToBatchMode(String filename, String [] varnames)
{
_batchMode = true;
_batchFileName = filename;
_batchVarNames = varnames;
}
public void run(ImageProcessor ip)
{
int[] wList = WindowManager.getIDList();
if (wList == null)
{
IJ.error("No windows are open.");
return;
}
String filename = null;
if(_batchMode)
{
filename = _batchFileName;
}
else
{
SaveDialog sd = new SaveDialog("Save HDF5 ...", "", ".h5");
String directory = sd.getDirectory();
String name = sd.getFileName();
filename = directory + name;
if (name == null)
return;
if (name == "")
return;
}
// Retrieve an instance of the implementing class for the HDF5 format
FileFormat fileFormat =
FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
// If the implementing class wasn't found, it's an error.
if (fileFormat == null)
{
System.err.println("Cannot find HDF5 FileFormat.");
return;
}
String[] varNames = null;
if(_batchMode)
{
varNames = _batchVarNames;
}
ImagePlus imp = WindowManager.getCurrentImage();
GenericDialog gd = null;
gd = new GenericDialog("Variable Name Selection");
// check for hyperstack
if(imp.getOpenAsHyperStack() || imp.isHyperStack())
{
System.out.println("This is a hyperstack");
boolean splitChannels = true;
gd.addCheckbox("Split frames and channels",splitChannels);
gd.addStringField(imp.getTitle(), "/t$T/channel$C");
String title = imp.getTitle();
int nDims = imp.getNDimensions();
int nFrames = imp.getNFrames();
int nChannels = imp.getNChannels();
int nLevs = imp.getNSlices();
int nRows = imp.getHeight();
int nCols = imp.getWidth();
boolean isComposite = imp.isComposite() ;
System.out.println("isComposite: "+Boolean.toString(isComposite));
System.out.println("Saving image \""+title+"\"");
System.out.println("nDims: "+Integer.toString(nDims));
System.out.println("nFrames: "+Integer.toString(nFrames));
System.out.println("nChannels: "+Integer.toString(nChannels));
System.out.println("nSlices: "+Integer.toString(nLevs));
System.out.println("nRows: "+Integer.toString(nRows));
System.out.println("nCols: "+Integer.toString(nCols));
gd.showDialog();
if (gd.wasCanceled())
{
IJ.error("Plugin canceled!");
return;
}
splitChannels = gd.getNextBoolean();
String formatString = gd.getNextString();
System.out.println("formatString: "+formatString);
System.out.println("Bitdepth: "+ imp.getBitDepth());
System.out.println("Saving HDF5 File: " + filename);
int imgColorDepth = imp.getBitDepth();
int imgColorType = imp.getType();
Datatype type = null;
if (imgColorType == ImagePlus.GRAY8)
{
System.out.println(" bit depth: " + imgColorDepth
+ ", type: GRAY8");
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE,
Datatype.NATIVE, Datatype.SIGN_NONE);
}
else if (imgColorType == ImagePlus.GRAY16)
{
System.out.println(" bit depth: " + imgColorDepth
+ ", type: GRAY16");
int typeSizeInByte = 2;
type = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte,
Datatype.NATIVE, Datatype.SIGN_NONE);
}
else if (imgColorType == ImagePlus.GRAY32)
{
System.out.println(" bit depth: " + imgColorDepth
+ ", type: GRAY32");
int typeSizeInByte = 4;
type = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE,
Datatype.NATIVE, -1);
}
// open the outfile
H5File outFile = null;
try
{
outFile = (H5File) fileFormat.createFile(filename,
FileFormat.FILE_CREATE_OPEN);
if (!outFile.canWrite())
{
IJ.error("File `" + filename + "`is readonly!");
return;
}
// open the file
outFile.open();
if(splitChannels)
{
// parse format string
String[] formatTokens =
HDF5_GroupedVarnames.
parseFormatString(formatString,
"[0-9]+"); // dummy regexp
long[] channelDims = null;
if(nLevs>1)
{
channelDims = new long[3];
channelDims[0] = nLevs;
channelDims[1] = nRows;
channelDims[2] = nCols;
}
else
{
channelDims = new long[2];
channelDims[0] = nRows;
channelDims[1] = nCols;
}
// iterate over frames and channels
ImageStack stack = imp.getStack();
for(int f=0;f<nFrames;f++)
{
IJ.showProgress(f, nFrames);
for(int c=0;c<nChannels;c++)
{
String fullName = makeDataSetName(formatTokens,
f,c);
String dataSetName = getDataSetDescriptor(fullName);
System.out.println("dataset name: " + dataSetName);
String groupName = getGroupDescriptor(fullName);
System.out.println("group name: " + groupName);
// ensure group exists
Group group = createGroupRecursive(groupName, null, outFile);
// create data set
Dataset dataset = null;
// select hyperslabs
long[] maxdims = channelDims;
long[] chunks = null;
int gzip = 0; // no compression
try
{
dataset = (Dataset) outFile.get(groupName + "/" + dataSetName);
}
catch( Exception e)
{
dataset = null;
}
if(dataset == null)
{
try
{
dataset = outFile.createScalarDS(dataSetName, group, type,
channelDims,
maxdims, chunks, gzip,
null);
}
catch (Exception err)
{
IJ.error(err.getMessage());
return;
}
}
dataset.init();
long[] selected = dataset.getSelectedDims(); // the
// selected
// size of
// the
// dataet
// write levels
System.out.println("selected.length: "+
Integer.toString(selected.length));
System.out.println("channelDims.length: "+
Integer.toString(channelDims.length));
if(nLevs == 1)
{
for (int d = 0; d < selected.length; d++)
{
selected[d] = channelDims[d];
}
int stackIndex = imp.getStackIndex(c+1,1,f+1);
System.out.println("Stackindex: "+
Integer.toString(stackIndex));
// get raw data
Object slice = stack.getPixels(stackIndex);
assert(slice != null);
// write data
try
{
dataset.write(slice);
}
catch(Exception e)
{
IJ.showStatus("Error writing data to file.");
}
}
else
{
selected[0] = 1;
for (int d = 1; d < selected.length; d++)
{
selected[d] = channelDims[d];
}
long[] start = dataset.getStartDims(); // the off set of
// the selection
for (int lvl = 0; lvl < nLevs; ++lvl)
{
// select hyperslab
start[0] = lvl;
int stackIndex = imp.getStackIndex(c+1,lvl+1,f+1);
// get raw data
Object slice = stack.getPixels(stackIndex);
// write data
try
{
dataset.write(slice);
}
catch(Exception e)
{
IJ.showStatus("Error writing data to file.");
}
}
}
}
}
}
else
{
// write one big array
}
outFile.close();
}
catch (HDF5Exception err)
{
IJ.error(err.getMessage());
return;
}
catch (Exception err)
{
IJ.error(err.getMessage());
return;
}
}
else
{
System.out.println("This is NO hyperstack");
// String title = imp.getTitle();
// int nDims = imp.getNDimensions();
// int nFrames = imp.getNFrames();
// int nChannels = imp.getNChannels();
// int nLevs = imp.getNSlices();
// int nRows = imp.getHeight();
// int nCols = imp.getWidth();
// boolean isComposite = imp.isComposite() ;
// System.out.println("isComposite: "+Boolean.toString(isComposite));
// System.out.println("Saving image \""+title+"\"");
// System.out.println("nDims: "+Integer.toString(nDims));
// System.out.println("nFrames: "+Integer.toString(nFrames));
// System.out.println("nChannels: "+Integer.toString(nChannels));
// System.out.println("nSlices: "+Integer.toString(nLevs));
// System.out.println("nRows: "+Integer.toString(nRows));
// System.out.println("nCols: "+Integer.toString(nCols));
gd.addStringField(imp.getTitle(), "");
gd.showDialog();
if (gd.wasCanceled())
{
IJ.error("Plugin canceled!");
return;
}
String varName = gd.getNextString();
if(varName == "")
{
IJ.error("No data set name given. Plugin canceled!");
return;
}
// write data set
try
{
H5File outFile = null;
try
{
outFile = (H5File) fileFormat.createFile(filename,
FileFormat.FILE_CREATE_OPEN);
if (!outFile.canWrite())
{
IJ.error("File `" + filename + "`is readonly!");
return;
}
}
catch (HDF5Exception err)
{
IJ.error(err.getMessage());
return;
}
outFile.open();
// first create all dimensions and variables
// Image color depth and color type
int imgColorDepth;
int imgColorType;
System.out.println("writing data to variable: " + varName);
String dataSetName = getDataSetDescriptor(varName);
System.out.println("dataset name: " + dataSetName);
String groupName = getGroupDescriptor(varName);
System.out.println("group name: " + groupName);
// ensure group exists
Group group = createGroupRecursive(groupName, null, outFile);
int nLevels = imp.getStackSize();
int nRows = imp.getHeight();
int nCols = imp.getWidth();
// get image type (bit depth)
imgColorDepth = imp.getBitDepth();
imgColorType = imp.getType();
long[] dims;
if (imgColorType == ImagePlus.COLOR_RGB ||
imgColorType == ImagePlus.COLOR_256)
{
if(nLevels == 1)
{
// color image
dims = new long[3];
dims[0] = nRows;
dims[1] = nCols;
dims[2] = 3;
}
else
{
// color images have 4 dimensions, grey value images
// have 3.
System.out.println("adding 4 dimensions");
dims = new long[4];
dims[0] = nLevels;
dims[1] = nRows;
dims[2] = nCols;
dims[3] = 3;
}
}
else
{
if(nLevels == 1)
{
// color image
dims = new long[2];
dims[0] = nRows;
dims[1] = nCols;
}
else
{
System.out.println("adding 3 dimensions");
dims = new long[3];
dims[0] = nLevels;
dims[1] = nRows;
dims[2] = nCols;
}
}
// The following is a list of a few example of H5Datatype.
//
// 1. to create unsigned native integer
// H5Datatype type = new H5Dataype(CLASS_INTEGER, NATIVE,
// NATIVE, SIGN_NONE);
// 2. to create 16-bit signed integer with big endian
// H5Datatype type = new H5Dataype(CLASS_INTEGER, 2,
// ORDER_BE, NATIVE);
// 3. to create native float
// H5Datatype type = new H5Dataype(CLASS_FLOAT, NATIVE,
// NATIVE, -1);
// 4. to create 64-bit double
// H5Datatype type = new H5Dataype(CLASS_FLOAT, 8, NATIVE,
// -1);
// H5Datatype type = new
// H5Datatype(H5Datatype.CLASS_INTEGER,
// H5Datatype.NATIVE, H5Datatype.NATIVE,
// H5Datatype.SIGN_NONE);
Datatype type = null;
// supported data types
// FIXME: set the right signed and precision stuff
if (imgColorType == ImagePlus.GRAY8)
{
System.out.println(" bit depth: " + imgColorDepth
+ ", type: GRAY8");
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE,
Datatype.NATIVE, Datatype.SIGN_NONE);
}
else if (imgColorType == ImagePlus.GRAY16)
{
System.out.println(" bit depth: " + imgColorDepth
+ ", type: GRAY16");
int typeSizeInByte = 2;
type = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte,
Datatype.NATIVE, Datatype.SIGN_NONE);
}
else if (imgColorType == ImagePlus.GRAY32)
{
System.out.println(" bit depth: " + imgColorDepth
+ ", type: GRAY32");
int typeSizeInByte = 4;
type = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE,
Datatype.NATIVE, -1);
}
else if (imgColorType == ImagePlus.COLOR_RGB)
{
System.out.println(" bit depth: " + imgColorDepth
+ ", type: COLOR_RGB");
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE,
Datatype.NATIVE, Datatype.SIGN_NONE);
}
else if (imgColorType == ImagePlus.COLOR_256)
{
// FIXME: not supported yet
System.out.println(" bit depth: " + imgColorDepth
+ ", type: COLOR_256");
System.out.println(" ERROR: untested, this might fail.");
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE,
Datatype.NATIVE, Datatype.SIGN_NONE);
}
// select hyperslabs
long[] maxdims = dims;
int nDims = dims.length;
// long[] chunks = findOptimalChunksize( nDims,
// dims);
long[] chunks = null;
int gzip = 0; // no compression
// create dataset
Dataset dataset = null;
try
{
dataset = (Dataset) outFile.get(groupName + "/" + dataSetName);
}
catch( Exception e)
{
dataset = null;
}
if(dataset == null)
{
dataset = outFile.createScalarDS(dataSetName, group, type,
dims, maxdims, chunks, gzip,
null);
}
dataset.init();
long[] selected = dataset.getSelectedDims(); // the
// selected
// size of
// the
// dataet
ImageStack stack = imp.getStack();
if(nLevels == 1)
{
for (int d = 0; d < selected.length; d++)
{
selected[d] = dims[d];
}
// get raw data
Object slice = stack.getPixels(nLevels);
if(imgColorType == ImagePlus.COLOR_RGB)
slice = computeRgbSlice(stack.getPixels(nLevels));
// write data
dataset.write(slice);
}
else
{
selected[0] = 1;
for (int d = 1; d < selected.length; d++)
{
selected[d] = dims[d];
}
long[] start = dataset.getStartDims(); // the off set of
// the selection
for (int lvl = 0; lvl < nLevels; ++lvl)
{
IJ.showProgress(lvl, nLevels);
// select hyperslab
start[0] = lvl;
// get raw data
Object slice = stack.getPixels(lvl + 1);
if(imgColorType == ImagePlus.COLOR_RGB)
slice = computeRgbSlice(stack.getPixels(lvl + 1));
// write data
dataset.write(slice);
}
}
// get pixel sizes
ij.measure.Calibration cal = imp.getCalibration();
System.out.println(" Element-Size in um (level,row,col): "
+ cal.pixelDepth + ", " + cal.pixelHeight + ", "
+ cal.pixelWidth);
float[] element_sizes = new float[3];
element_sizes[0] = (float) cal.pixelDepth;
element_sizes[1] = (float) cal.pixelHeight;
element_sizes[2] = (float) cal.pixelWidth;
Datatype attrType = new H5Datatype(Datatype.CLASS_FLOAT,
Datatype.NATIVE, Datatype.NATIVE,
-1);
long[] attrDims = { 3 };
Attribute element_size_um = null;
try
{
element_size_um = getAttribute(dataset, "element_size_um");
}
catch(Exception e)
{
element_size_um = null;
}
if(element_size_um == null)
{
element_size_um = new Attribute("element_size_um",
attrType, attrDims);
}
element_size_um.setValue(element_sizes);
// write element_size_um
dataset.writeMetadata(element_size_um);
outFile.close();
}
catch (HDF5Exception err)
{
System.err.println("Caught HDF5Exception");
err.printStackTrace();
}
catch (java.io.IOException err)
{
System.err.println("IO Error while writing '" + filename + "': "
+ err);
}
catch (Exception err)
{
System.err.println("Range Error while writing '" + filename
+ "': " + err);
}
}
}
int byteToUnsignedByte(int n)
{
if (n < 0)
return (256 + n);
return n;
}
void showAbout()
{
IJ.showMessage("About HDF5 Writer:", "Written by Matthias Schlachter\n"
+ "University of Freiburg, 2010");
}
private static Group createGroupRecursive(String groupRelativName,
Group group, FileFormat file)
{
if (groupRelativName == null || file == null)
return null;
if (group == null)
group = (Group) ((DefaultMutableTreeNode) file.getRootNode())
.getUserObject();
while (groupRelativName.charAt(0) == '/')
{
// trim leading slash
groupRelativName = groupRelativName.substring(1);
}
while (groupRelativName.charAt(groupRelativName.length() - 1) == '/')
{
// trim last slash
groupRelativName = groupRelativName.substring(0, groupRelativName
.length() - 2);
}
int posOfSlash = groupRelativName.indexOf('/');
if (posOfSlash == -1)
{
try
{
Group newGroup;
String newGroupName;
if (group.isRoot())
newGroupName = "/" + groupRelativName;
else
newGroupName = group.getFullName() + "/" + groupRelativName;
newGroup = (Group) file.get(newGroupName);
if (newGroup == null)
newGroup = file.createGroup(newGroupName, group);
return newGroup;
}
catch (Exception e)
{
return null;
}
}
else
{
String subgroupRelativName = groupRelativName.substring(posOfSlash);
String currentGroup = groupRelativName.substring(0, posOfSlash);
System.out.println("Create: " + currentGroup);
System.out.println("Call back for: " + subgroupRelativName);
try
{
Group newGroup;
String newGroupName;
if (group.isRoot())
newGroupName = "/" + currentGroup;
else
newGroupName = group.getFullName() + "/" + currentGroup;
System.out.println("try opening: "+newGroupName);
newGroup = (Group) file.get(newGroupName);
if (newGroup == null)
newGroup = file.createGroup(newGroupName, group);
return createGroupRecursive(subgroupRelativName, newGroup, file);
}
catch (Exception e)
{
return null;
}
}
// never come here
}
private static String getGroupDescriptor(String absName)
{
String groupName = absName;
while (groupName.charAt(0) == '/')
{
// trim leading slash
groupName = groupName.substring(1);
}
while (groupName.charAt(groupName.length() - 1) == '/')
{
// trim last slash
groupName = groupName.substring(0, groupName.length() - 2);
}
int posOfLastSlash = groupName.lastIndexOf('/');
if (posOfLastSlash == -1)
return null;
else
return groupName.substring(0, posOfLastSlash);
}
private static String getDataSetDescriptor(String absName)
{
String dataSetName = absName;
while (dataSetName.charAt(0) == '/')
{
// trim leading slash
dataSetName = dataSetName.substring(1);
}
while (dataSetName.charAt(dataSetName.length() - 1) == '/')
{
// trim last slash
dataSetName = dataSetName.substring(0, dataSetName.length() - 2);
}
int posOfLastSlash = dataSetName.lastIndexOf('/');
if (posOfLastSlash == -1)
return dataSetName;
else
return dataSetName.substring(posOfLastSlash + 1);
}
long[] findOptimalChunksize( int Rank,
long[] dataDims)
{
long[] best_chunksize = new long[Rank];
int maxChunkVol = 262144;
// small sanity check first:
int data_volume = 1;
for( int d = 0; d < Rank; ++d)
data_volume *= dataDims[d];
if( data_volume < maxChunkVol) {
for( int d = 0; d < Rank; ++d)
best_chunksize[d] = dataDims[d];
return best_chunksize;
}
else return null;
}
private static List<Attribute> getAttrList(Dataset ds) throws Exception
{
if (ds == null)
return null;
List<Attribute> attributes = new ArrayList<Attribute>();
List members = ds.getMetadata();
int n = members.size();
Metadata obj = null;
for (int i = 0; i < n; i++)
{
obj = (Metadata) members.get(i);
if (obj instanceof Attribute)
{
try
{
System.out.println(((Attribute) obj).getName());
attributes.add((Attribute) obj);
}
catch (java.lang.UnsupportedOperationException e)
{
System.out
.println("Caught UnsupportedOperationException datasets2.add((Dataset) obj)");
System.out.println(e.getMessage());
}
}
}
return attributes;
}
private static Attribute
getAttribute(Dataset ds, String attrName) throws Exception
{
List<Attribute> attrList = getAttrList(ds);
Iterator<Attribute> attrIter = attrList.iterator();
while (attrIter.hasNext())
{
Attribute attr = attrIter.next();
if (attr.getName().equals(attrName))
{
return attr;
}
}
return null;
}
private Object computeRgbSlice(Object pixels)
{
byte rgbslice[];
int size = ((int[])pixels).length;
rgbslice = new byte[size*3];
for(int i=0;i<size;i++)
{
int red= (((int[]) pixels)[i] & 0xff0000) >> 16;
int green= (((int[]) pixels)[i] & 0x00ff00) >> 8;
int blue= ((int[]) pixels)[i] & 0x0000ff;
rgbslice[3*i + 0] = (byte) red;
rgbslice[3*i + 1] = (byte) green;
rgbslice[3*i + 2] =(byte) blue;
}
return rgbslice;
}
private String makeDataSetName(String[] toks,int frame,int channel)
{
String dName =
toks[0] +
Integer.toString(frame) +
toks[1] +
Integer.toString(channel);
if(toks.length>2)
dName = dName + toks[2];
return dName;
}
// end of class
}

104
src/TimeFrame.java Normal file
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@ -0,0 +1,104 @@
/* =========================================================================
*
* Copyright 2011 Matthias Schlachter
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
import java.util.ArrayList;
import java.util.Arrays;
//import java.util.Iterator;
//import java.util.List;
public class TimeFrame implements Comparable
{
public TimeFrame(int index)
{
frameIndex = index;
}
public TimeFrame(String index)
{
frameIndex = Integer.parseInt(index);
}
public void addChannel(int index)
{
Integer channelIndex = new Integer(index);
if(!channels.contains(channelIndex))
channels.add(new Integer(index));
else
System.out.println("channel" + channelIndex.toString()
+ " already in list!");
}
public void addChannel(String index)
{
addChannel(Integer.parseInt(index));
}
public boolean equals(Object obj)
{
TimeFrame f = (TimeFrame) obj;
if(f.frameIndex == frameIndex)
return true;
return false;
}
public String toString()
{
String s = "FrameIdx: " + Integer.toString(frameIndex) + "; ";
s = s + "nChannels: " + Integer.toString(channels.size()) + "; ";
s = s + "channels: ";
for(int i=0;i<channels.size();i++)
s = s + Integer.toString(channels.get(i)) + ";";
return s;
}
public int getNChannels()
{
return channels.size();
}
public int getFrameIndex()
{
return frameIndex;
}
public int[] getChannelIndices()
{
Object[] channelsAsArray = channels.toArray();
Arrays.sort(channelsAsArray);
int[] channelsIdx = new int[channelsAsArray.length];
for(int i=0;i<channelsAsArray.length;i++)
channelsIdx[i] = ((Integer) channelsAsArray[i]).intValue();
return channelsIdx;
}
public int compareTo(Object obj)
{
TimeFrame f = (TimeFrame) obj;
if(frameIndex<f.frameIndex)
return -1;
else if(frameIndex>f.frameIndex)
return 1;
else
return 0;
}
private final int frameIndex;
private final ArrayList<Integer> channels = new ArrayList<Integer>();
}