//
// DisplayHandler.java
//
/*
LOCI Plugins for ImageJ: a collection of ImageJ plugins including the
Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions,
Data Browser and Stack Slicer. Copyright (C) 2005-@year@ Melissa Linkert,
Curtis Rueden and Christopher Peterson.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.plugins.in;
import ij.ImagePlus;
import ij.WindowManager;
import java.io.IOException;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import javax.xml.parsers.ParserConfigurationException;
import loci.common.ReflectException;
import loci.common.ReflectedUniverse;
import loci.common.StatusEvent;
import loci.common.StatusListener;
import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.FormatException;
import loci.formats.IFormatReader;
import loci.formats.gui.XMLWindow;
import loci.formats.services.OMEXMLService;
import loci.plugins.BF;
import loci.plugins.util.DataBrowser;
import loci.plugins.util.ROIHandler;
import loci.plugins.util.SearchableWindow;
import loci.plugins.util.WindowTools;
import org.xml.sax.SAXException;
/**
* Logic for displaying images and metadata onscreen using ImageJ.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/loci-plugins/src/loci/plugins/in/DisplayHandler.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/loci-plugins/src/loci/plugins/in/DisplayHandler.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Curtis Rueden ctrueden at wisc.edu
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class DisplayHandler implements StatusListener {
// -- Fields --
protected ImportProcess process;
protected ImporterOptions options;
protected XMLWindow xmlWindow;
// -- Constructor --
public DisplayHandler(ImportProcess process) {
this.process = process;
options = process.getOptions();
}
// -- DisplayHandler API methods --
/** Displays standard metadata in a table in its own window. */
public SearchableWindow displayOriginalMetadata() {
if (!options.isShowMetadata()) return null;
String name = process.getIdName();
ImporterMetadata meta = process.getOriginalMetadata();
String metaString = meta.getMetadataString("\t");
SearchableWindow metaWindow = new SearchableWindow(
"Original Metadata - " + name, "Key\tValue", metaString, 400, 400);
metaWindow.setVisible(true);
return metaWindow;
}
/** Displays OME-XML metadata in a tree in its own window. */
public XMLWindow displayOMEXML() throws FormatException, IOException {
if (!options.isShowOMEXML()) return null;
XMLWindow metaWindow = null;
metaWindow = new XMLWindow("OME Metadata - " + process.getIdName());
Exception exc = null;
try {
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
metaWindow.setXML(service.getOMEXML(process.getOMEMetadata()));
WindowTools.placeWindow(metaWindow);
metaWindow.setVisible(true);
}
catch (DependencyException e) { exc = e; }
catch (ServiceException e) { exc = e; }
catch (ParserConfigurationException e) { exc = e; }
catch (SAXException e) { exc = e; }
if (exc != null) throw new FormatException(exc);
xmlWindow = metaWindow; // save reference to OME-XML window
return metaWindow;
}
/** Displays the given images according to the configured options. */
public void displayImages(ImagePlus[] imps) {
if (imps != null) {
for (ImagePlus imp : imps) displayImage(imp);
}
}
/** Displays the given image according to the configured options. */
public void displayImage(ImagePlus imp) {
if (options.isViewNone()) return;
else if (options.isViewStandard()) displayNormal(imp);
else if (options.isViewHyperstack()) displayNormal(imp);
else if (options.isViewBrowser()) displayDataBrowser(imp);
else if (options.isViewImage5D()) displayImage5D(imp);
else if (options.isViewView5D()) displayView5D(imp);
else throw new IllegalStateException("Unknown display mode");
}
/**
* Displays in a normal ImageJ window.
* ImageJ will show the image as either a standard 2D image window
* or as a hyperstack (up to 5D, with ZCT sliders) depending on whether
* imp.setOpenAsHyperStack(true) has been called.
*/
public void displayNormal(ImagePlus imp) {
imp.show();
}
public void displayDataBrowser(ImagePlus imp) {
IFormatReader r = process.getReader();
String[] dimTypes = r.getChannelDimTypes();
int[] dimLengths = r.getChannelDimLengths();
new DataBrowser(imp, null, dimTypes, dimLengths, xmlWindow);
}
public void displayImage5D(ImagePlus imp) {
WindowManager.setTempCurrentImage(imp);
IFormatReader r = process.getReader();
ReflectedUniverse ru = new ReflectedUniverse();
try {
ru.exec("import i5d.Image5D");
ru.setVar("title", imp.getTitle());
ru.setVar("stack", imp.getStack());
ru.setVar("sizeC", imp.getNChannels());
ru.setVar("sizeZ", imp.getNSlices());
ru.setVar("sizeT", imp.getNFrames());
ru.exec("i5d = new Image5D(title, stack, sizeC, sizeZ, sizeT)");
ru.setVar("cal", imp.getCalibration());
ru.setVar("fi", imp.getOriginalFileInfo());
ru.exec("i5d.setCalibration(cal)");
ru.exec("i5d.setFileInfo(fi)");
//ru.exec("i5d.setDimensions(sizeC, sizeZ, sizeT)");
ru.exec("i5d.show()");
}
catch (ReflectException exc) {
WindowTools.reportException(exc, options.isQuiet(),
"Sorry, there was a problem interfacing with Image5D");
}
}
public void displayView5D(ImagePlus imp) {
WindowManager.setTempCurrentImage(imp);
//new view5d.View5D_("");
Exception exc = null;
try {
Class<?> c = Class.forName("view5d.View5D_");
Constructor<?> con = c.getConstructor();
con.newInstance();
}
catch (ClassNotFoundException e) { exc = e; }
catch (SecurityException e) { exc = e; }
catch (NoSuchMethodException e) { exc = e; }
catch (IllegalArgumentException e) { exc = e; }
catch (InstantiationException e) { exc = e; }
catch (IllegalAccessException e) { exc = e; }
catch (InvocationTargetException e) { exc = e; }
if (exc != null) {
WindowTools.reportException(exc, options.isQuiet(),
"Sorry, there was a problem interfacing with View5D");
}
}
public void displayROIs(ImagePlus[] imps) {
if (!options.showROIs()) return;
ROIHandler.openROIs(process.getOMEMetadata(), imps);
}
// -- StatusListener methods --
/** Reports status updates via ImageJ's status bar mechanism. */
public void statusUpdated(StatusEvent e) {
String msg = e.getStatusMessage();
if (msg != null) BF.status(options.isQuiet(), msg);
int value = e.getProgressValue();
int max = e.getProgressMaximum();
if (value >= 0 && max >= 0) BF.progress(options.isQuiet(), value, max);
}
}