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RoiManager.java
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RoiManager.java
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package ij.plugin.frame;
import java.awt.*;
import java.awt.event.*;
import java.io.*;
import java.util.*;
import java.awt.List;
import java.util.zip.*;
import java.awt.geom.*;
import javax.swing.DefaultListModel;
import javax.swing.JList;
import javax.swing.JScrollPane;
import javax.swing.ListSelectionModel;
import javax.swing.ScrollPaneConstants;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.io.*;
import ij.plugin.filter.*;
import ij.plugin.*;
import ij.util.*;
import ij.macro.*;
import ij.measure.*;
import ij.plugin.OverlayCommands;
/** This plugin implements the Analyze/Tools/ROI Manager command. */
public class RoiManager extends PlugInFrame implements ActionListener, ItemListener, MouseListener, MouseWheelListener, ListSelectionListener, Iterable<Roi> {
public static final String LOC_KEY = "manager.loc";
private static final String MULTI_CROP_DIR = "multi-crop.dir";
private static final int BUTTONS = 11;
private static final int DRAW=0, FILL=1, LABEL=2;
private static final int SHOW_ALL=0, SHOW_NONE=1, LABELS=2, NO_LABELS=3;
private static final int MENU=0, COMMAND=1;
private static final int CHANNEL=0, SLICE=1, FRAME=2, SHOW_DIALOG=3;
private static int rows = 15;
private static int lastNonShiftClick = -1;
private static boolean allowMultipleSelections = true;
private static String moreButtonLabel = "More "+'\u00bb';
private Panel panel;
private static Frame instance;
private static int colorIndex = 4;
private JList list;
private DefaultListModel listModel;
private ArrayList rois = new ArrayList();
private boolean canceled;
private boolean macro;
private boolean ignoreInterrupts;
private PopupMenu pm;
private Button moreButton, colorButton;
private Checkbox showAllCheckbox = new Checkbox("Show All", false);
private Checkbox labelsCheckbox = new Checkbox("Labels", false);
private Overlay overlayTemplate;
private static boolean measureAll = true;
private static boolean onePerSlice = true;
private static boolean restoreCentered;
private int prevID;
private boolean noUpdateMode;
private int defaultLineWidth = 1;
private Color defaultColor;
private boolean firstTime = true;
private boolean appendResults;
private static ResultsTable mmResults, mmResults2;
private int imageID;
private boolean allowRecording;
private boolean recordShowAll = true;
private boolean allowDuplicates;
private double translateX = 10.0;
private double translateY = 10.0;
private static String errorMessage;
private boolean multiCropShow = true;
private boolean multiCropSave;
private int multiCropFormatIndex;
private static double angle = 45.0;
private static double xscale = 1.5;
private static double yscale = 1.5;
private static boolean scaleCentered = true;
/** Opens the "ROI Manager" window, or activates it if it is already open.
* @see #RoiManager(boolean)
* @see #getRoiManager
*/
public RoiManager() {
super("ROI Manager");
if (instance!=null) {
WindowManager.toFront(instance);
return;
}
if (IJ.isMacro() && Interpreter.getBatchModeRoiManager()!=null) {
list = new JList();
listModel = new DefaultListModel();
list.setModel(listModel);
return;
}
instance = this;
list = new JList();
errorMessage = null;
showWindow();
}
/** Constructs an ROI Manager without displaying it. The boolean argument is ignored. */
public RoiManager(boolean b) {
super("ROI Manager");
list = new JList();
listModel = new DefaultListModel();
list.setModel(listModel);
errorMessage = null;
}
void showWindow() {
ImageJ ij = IJ.getInstance();
addKeyListener(ij);
addMouseListener(this);
addMouseWheelListener(this);
WindowManager.addWindow(this);
//setLayout(new FlowLayout(FlowLayout.CENTER,5,5));
setLayout(new BorderLayout());
listModel = new DefaultListModel();
list.setModel(listModel);
GUI.scale(list);
list.setPrototypeCellValue("0000-0000-0000 ");
list.addListSelectionListener(this);
list.addKeyListener(ij);
list.addMouseListener(this);
list.addMouseWheelListener(this);
if (IJ.isLinux()) list.setBackground(Color.white);
JScrollPane scrollPane = new JScrollPane(list, ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS, ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
add("Center", scrollPane);
panel = new Panel();
int nButtons = BUTTONS;
panel.setLayout(new GridLayout(nButtons, 1, 5, 0));
addButton("Add [t]");
addButton("Update");
addButton("Delete");
addButton("Rename...");
addButton("Measure");
addButton("Deselect");
addButton("Properties...");
addButton("Flatten [F]");
addButton(moreButtonLabel);
showAllCheckbox.addItemListener(this);
panel.add(showAllCheckbox);
labelsCheckbox.addItemListener(this);
panel.add(labelsCheckbox);
add("East", panel);
addPopupMenu();
GUI.scale(this);
pack();
Dimension size = getSize();
if (size.width>270)
setSize(size.width-40, size.height);
list.remove(0);
Point loc = Prefs.getLocation(LOC_KEY);
if (loc!=null)
setLocation(loc);
else
GUI.centerOnImageJScreen(this);
show();
}
void addButton(String label) {
Button b = new Button(label);
b.addActionListener(this);
b.addKeyListener(IJ.getInstance());
b.addMouseListener(this);
if (label.equals(moreButtonLabel)) moreButton = b;
panel.add(b);
}
void addPopupMenu() {
pm = new PopupMenu();
GUI.scalePopupMenu(pm);
addPopupItem("Open...");
addPopupItem("Save...");
addPopupItem("Fill");
addPopupItem("Draw");
addPopupItem("AND");
addPopupItem("OR (Combine)");
addPopupItem("XOR");
addPopupItem("Split");
addPopupItem("Add Particles");
addPopupItem("Multi Measure");
addPopupItem("Multi Plot");
addPopupItem("Multi Crop");
addPopupItem("Sort");
addPopupItem("Specify...");
addPopupItem("Remove Positions...");
addPopupItem("Labels...");
addPopupItem("List");
addPopupItem("Interpolate ROIs");
addPopupItem("Scale...");
addPopupItem("Rotate...");
addPopupItem("Translate...");
addPopupItem("ROI Manager Action");
addPopupItem("Help");
addPopupItem("Options...");
add(pm);
}
void addPopupItem(String s) {
MenuItem mi=new MenuItem(s);
mi.addActionListener(this);
pm.add(mi);
}
public void actionPerformed(ActionEvent e) {
String label = e.getActionCommand();
if (label==null)
return;
String command = label;
allowRecording = true;
if (command.equals("Add [t]"))
runCommand("add");
else if (command.equals("Update"))
update(true);
else if (command.equals("Delete"))
delete(false);
else if (command.equals("Rename..."))
rename(null);
else if (command.equals("Properties..."))
setProperties(null, -1, null);
else if (command.equals("Flatten [F]"))
flatten();
else if (command.equals("Measure"))
measure(getImage());
else if (command.equals("Open..."))
open(null);
else if (command.equals("Save...")) {
Thread t1 = new Thread(new Runnable() {
public void run() {
save(null);
}
});
t1.start();
} else if (command.equals("Fill"))
drawOrFill(FILL);
else if (command.equals("Draw"))
drawOrFill(DRAW);
else if (command.equals("Deselect"))
deselect();
else if (command.equals(moreButtonLabel)) {
Point ploc = panel.getLocation();
Point bloc = moreButton.getLocation();
pm.show(this, ploc.x, bloc.y);
} else if (command.equals("OR (Combine)")) {
new MacroRunner("roiManager(\"Combine\");");
if (Recorder.record) Recorder.record("roiManager", "Combine");
} else if (command.equals("Split"))
split();
else if (command.equals("AND"))
and();
else if (command.equals("XOR"))
xor();
else if (command.equals("Add Particles"))
addParticles();
else if (command.equals("Multi Measure"))
multiMeasure("");
else if (command.equals("Multi Plot"))
multiPlot();
else if (command.equals("Multi Crop"))
multiCrop();
else if (command.equals("Sort"))
sort();
else if (command.equals("Specify..."))
specify();
else if (command.equals("Remove Positions..."))
removePositions(SHOW_DIALOG);
else if (command.equals("Labels..."))
labels();
else if (command.equals("List"))
listRois();
else if (command.equals("Interpolate ROIs"))
interpolateRois();
else if (command.equals("Scale..."))
scale();
else if (command.equals("Rotate..."))
rotate();
else if (command.equals("Translate..."))
translate();
else if (command.equals("Help"))
help();
else if (command.equals("Options..."))
options();
else if (command.equals("\"Show All\" Color..."))
setShowAllColor();
else if (command.equals("ROI Manager Action"))
IJ.run(command);
allowRecording = false;
}
private void interpolateRois() {
IJ.runPlugIn("ij.plugin.RoiInterpolator", "");
if (record())
Recorder.record("roiManager", "Interpolate ROIs");
}
public void itemStateChanged(ItemEvent e) {
Object source = e.getSource();
boolean showAllMode = showAllCheckbox.getState();
if (source==showAllCheckbox) {
if (firstTime && okToSet())
labelsCheckbox.setState(true);
showAll(showAllCheckbox.getState()?SHOW_ALL:SHOW_NONE);
if (Recorder.record && recordShowAll) {
if (showAllMode)
Recorder.record("roiManager", "Show All");
else
Recorder.record("roiManager", "Show None");
}
recordShowAll = true;
firstTime = false;
return;
}
if (source==labelsCheckbox) {
if (firstTime && okToSet())
showAllCheckbox.setState(true);
boolean editState = labelsCheckbox.getState();
boolean showAllState = showAllCheckbox.getState();
if (!showAllState && !editState)
showAll(SHOW_NONE);
else {
showAll(editState?LABELS:NO_LABELS);
if (Recorder.record) {
if (editState)
Recorder.record("roiManager", "Show All with labels");
else if (showAllState)
Recorder.record("roiManager", "Show All without labels");
}
if (editState && !showAllState && okToSet()) {
showAllCheckbox.setState(true);
recordShowAll = false;
}
}
firstTime = false;
return;
}
}
private boolean okToSet() {
//return !(IJ.isMacOSX()&&IJ.isJava18());
return false;
}
void add(boolean shiftKeyDown, boolean altKeyDown) {
if (shiftKeyDown)
addAndDraw(altKeyDown);
else if (altKeyDown)
addRoi(true);
else
addRoi(false);
}
/** Adds the specified ROI. */
public void addRoi(Roi roi) {
allowDuplicates = true;
addRoi(roi, false, null, -1);
}
boolean addRoi(boolean promptForName) {
return addRoi(null, promptForName, null, -1);
}
boolean addRoi(Roi roi, boolean promptForName, Color color, int lineWidth) {
if (listModel==null)
IJ.log("<<Error: Uninitialized RoiManager>>");
ImagePlus imp = roi==null?getImage():WindowManager.getCurrentImage();
if (roi==null) {
if (imp==null)
return false;
roi = imp.getRoi();
if (roi==null) {
error("The active image does not have a selection.");
return false;
}
}
if ((roi instanceof PolygonRoi) && ((PolygonRoi)roi).getNCoordinates()==0)
return false;
if (color==null && roi.getStrokeColor()!=null)
color = roi.getStrokeColor();
else if (color==null && defaultColor!=null)
color = defaultColor;
if (lineWidth<0) {
int sw = (int)roi.getStrokeWidth();
lineWidth = sw>1?sw:defaultLineWidth;
}
if (lineWidth>100) lineWidth = 1;
int n = getCount();
int saveCurrentSlice = imp!=null?imp.getCurrentSlice():0;
if (n>0 && !IJ.isMacro() && imp!=null && !allowDuplicates) {
// check for duplicate
Roi roi2 = (Roi)rois.get(n-1);
if (roi2!=null) {
String label = (String)listModel.getElementAt(n-1);
int slice2 = getSliceNumber(roi2, label);
if (roi.equals(roi2) && (slice2==-1||slice2==imp.getCurrentSlice()) && imp.getID()==prevID && !Interpreter.isBatchMode())
return false;
}
}
allowDuplicates = false;
prevID = imp!=null?imp.getID():0;
String name = roi.getName();
if (isStandardName(name))
name = null;
String label = name!=null?name:getLabel(imp, roi, -1);
if (promptForName)
label = promptForName(label);
if (label==null)
return false;
listModel.addElement(label);
roi.setName(label);
Roi roiCopy = (Roi)roi.clone();
boolean hasPosition = roiCopy.getPosition()>0 || roiCopy.getPosition()==PointRoi.POINTWISE_POSITION || roiCopy.hasHyperStackPosition();
if (!hasPosition && imp!=null && imp.getStackSize()>1)
roiCopy.setPosition(imp); // set ROI position to current stack position
if (lineWidth>1)
roiCopy.setStrokeWidth(lineWidth);
if (color!=null)
roiCopy.setStrokeColor(color);
rois.add(roiCopy);
updateShowAll();
if (record())
recordAdd(defaultColor, defaultLineWidth);
return true;
}
void recordAdd(Color color, int lineWidth) {
if (Recorder.scriptMode())
Recorder.recordCall("rm.addRoi(roi);");
else if (color!=null && lineWidth==1)
Recorder.recordString("roiManager(\"Add\", \""+getHex(color)+"\");\n");
else if (lineWidth>1)
Recorder.recordString("roiManager(\"Add\", \""+getHex(color)+"\", "+lineWidth+");\n");
else
Recorder.record("roiManager", "Add");
}
String getHex(Color color) {
if (color==null) color = ImageCanvas.getShowAllColor();
String hex = Integer.toHexString(color.getRGB());
if (hex.length()==8) hex = hex.substring(2);
return hex;
}
/** Adds the specified ROI to the list. The second argument ('n') will
* be used to form the first part of the ROI label if it is zero or greater.
* @param roi the Roi to be added
* @param n if zero or greater, will be used to form the first part of the label
*/
public void add(Roi roi, int n) {
add((ImagePlus)null, roi, n);
}
/** Adds the specified ROI to the list. The third argument ('n') will
* be used to form the first part of the ROI label if it is zero or greater.
* @param imp the image associated with the ROI, or null
* @param roi the Roi to be added
* @param n if zero or greater, will be used to form the first part of the label
*/
public void add(ImagePlus imp, Roi roi, int n) {
if (IJ.debugMode && n<3 && roi!=null) IJ.log("RoiManager.add: "+n+" "+roi.getName());
if (roi==null)
return;
String label = roi.getName();
String label2 = label;
if (label==null)
label = getLabel(imp, roi, n);
else {
if (n>=0)
label = n+"-"+label;
}
if (label==null)
return;
listModel.addElement(label);
if (label2!=null)
roi.setName(label2);
else
roi.setName(label);
rois.add((Roi)roi.clone());
}
/** Replaces the ROI at the specified index. */
public void setRoi(Roi roi, int index) {
if (index<0 || index>=rois.size())
throw new IllegalArgumentException("setRoi: Index out of range");
rois.set(index, (Roi)roi.clone());
updateShowAll();
}
boolean isStandardName(String name) {
if (name==null)
return false;
int len = name.length();
if (len<9 || (len>0&&!Character.isDigit(name.charAt(0))))
return false;
boolean isStandard = false;
if (len>=14 && name.charAt(4)=='-' && name.charAt(9)=='-' )
isStandard = true;
else if (len>=17 && name.charAt(5)=='-' && name.charAt(11)=='-' )
isStandard = true;
else if (len>=9 && name.charAt(4)=='-' && Character.isDigit(name.charAt(5)))
isStandard = true;
else if (len>=11 && name.charAt(5)=='-' && Character.isDigit(name.charAt(6)))
isStandard = true;
return isStandard;
}
String getLabel(ImagePlus imp, Roi roi, int n) {
Rectangle r = roi.getBounds();
int xc = r.x + r.width/2;
int yc = r.y + r.height/2;
if (n>=0)
{xc = yc; yc=n;}
if (xc<0) xc = 0;
if (yc<0) yc = 0;
int digits = 4;
String xs = "" + xc;
if (xs.length()>digits) digits = xs.length();
String ys = "" + yc;
if (ys.length()>digits) digits = ys.length();
if (digits==4 && imp!=null && (imp.getStackSize()>=10000||imp.getHeight()>=10000))
digits = 5;
xs = "000000" + xc;
ys = "000000" + yc;
String label = ys.substring(ys.length()-digits) + "-" + xs.substring(xs.length()-digits);
if (imp!=null && imp.getStackSize()>1) {
int slice = imp.getCurrentSlice();
String zs = "000000" + slice;
label = zs.substring(zs.length()-digits) + "-" + label;
}
return label;
}
void addAndDraw(boolean altKeyDown) {
if (altKeyDown) {
if (!addRoi(true)) return;
} else if (!addRoi(false))
return;
ImagePlus imp = WindowManager.getCurrentImage();
if (imp!=null) {
Undo.setup(Undo.COMPOUND_FILTER, imp);
IJ.run(imp, "Draw", "slice");
Undo.setup(Undo.COMPOUND_FILTER_DONE, imp);
}
if (record()) Recorder.record("roiManager", "Add & Draw");
}
boolean delete(boolean replacing) {
int count = getCount();
if (count==0)
return error("The ROI Manager is empty.");
int index[] = getSelectedIndexes();
if (index.length==0 || (replacing&&count>1)) {
String msg = "Delete all items on the list?";
if (replacing)
msg = "Replace items on the list?";
canceled = false;
if (!IJ.isMacro() && !macro) {
YesNoCancelDialog d = new YesNoCancelDialog(this, "ROI Manager", msg);
if (d.cancelPressed())
{canceled = true; return false;}
if (!d.yesPressed()) return false;
}
index = getAllIndexes();
}
if (count==index.length && !replacing) {
rois.clear();
listModel.removeAllElements();
} else {
for (int i=count-1; i>=0; i--) {
boolean delete = false;
for (int j=0; j<index.length; j++) {
if (index[j]==i)
delete = true;
}
if (delete) {
if (EventQueue.isDispatchThread()) {
rois.remove(i);
listModel.remove(i);
} else
deleteOnEDT(i);
}
}
}
ImagePlus imp = WindowManager.getCurrentImage();
//if (count>1 && index.length==1 && imp!=null)
// imp.deleteRoi();
updateShowAll();
if (record())
Recorder.record("roiManager", "Delete");
return true;
}
// Delete ROI on event dispatch thread
private void deleteOnEDT(final int i) {
try {
EventQueue.invokeAndWait(new Runnable() {
public void run() {
rois.remove(i);
listModel.remove(i);
}
});
} catch (
Exception e) {
}
}
boolean update(boolean clone) {
ImagePlus imp = getImage();
if (imp==null)
return false;
ImageCanvas ic = imp.getCanvas();
boolean showingAll = ic!=null && ic.getShowAllROIs();
Roi roi = imp.getRoi();
if (roi==null) {
error("The active image does not have a selection.");
return false;
}
int index = list.getSelectedIndex();
if (index<0 && !showingAll)
return error("Exactly one item in the list must be selected.");
if (index>=0) {
if (clone) {
String name = (String)listModel.getElementAt(index);
Roi roi2 = (Roi)roi.clone();
if (roi2.getPosition() != PointRoi.POINTWISE_POSITION)
roi2.setPosition(imp);
roi.setName(name);
roi2.setName(name);
rois.set(index, roi2);
} else
rois.set(index, roi);
}
if (record()) Recorder.record("roiManager", "Update");
updateShowAll();
return true;
}
boolean rename(String name2) {
int index = list.getSelectedIndex();
if (index<0)
return error("Exactly one item in the list must be selected.");
String name = (String)listModel.getElementAt(index);
if (name2==null)
name2 = promptForName(name);
if (name2==null)
return false;
if (name2.equals(name))
return false;
Roi roi = (Roi)rois.get(index);
roi.setName(name2);
int position = getSliceNumber(name2);
if (position>0 && !roi.hasHyperStackPosition())
roi.setPosition(position);
rois.set(index, roi);
listModel.setElementAt(name2, index);
list.setSelectedIndex(index);
ImagePlus imp = WindowManager.getCurrentImage();
if (imp!=null && imp.getRoi()!=null)
imp.setRoi(roi);
if (Prefs.useNamesAsLabels && labelsCheckbox.getState())
if (imp!=null) imp.draw();
if (record())
Recorder.record("roiManager", "Rename", name2);
return true;
}
public void rename(int index, String newName) {
if (index<0 || index>=getCount())
throw new IllegalArgumentException("Index out of range: "+index);
Roi roi = (Roi)rois.get(index);
roi.setName(newName);
listModel.setElementAt(newName, index);
}
String promptForName(String name) {
GenericDialog gd = new GenericDialog("ROI Manager");
gd.addStringField("Rename As:", name, 20);
gd.showDialog();
if (gd.wasCanceled())
return null;
else
return gd.getNextString();
}
boolean restore(ImagePlus imp, int index, boolean setSlice) {
if (index>=rois.size())
return false;
Roi roi = (Roi)rois.get(index);
if (imp==null || roi==null)
return false;
//IJ.log("restore: "+roi.getPosition()+" "+roi.getZPosition()+" "+imp.getNSlices()+" "+imp.getStackSize());
if (setSlice) {
boolean hyperstack = imp.isHyperStack();
int position = roi.getPosition();
if (hyperstack && roi.hasHyperStackPosition())
imp.setPosition(roi.getCPosition(), roi.getZPosition(), roi.getTPosition());
else if (hyperstack && imp.getNSlices()==1)
imp.setPosition(imp.getChannel(), 1, position);
else if (hyperstack)
imp.setPosition(imp.getChannel(), position, imp.getChannel());
else if (roi.getZPosition()>0 && imp.getNSlices()==imp.getStackSize())
imp.setSlice(roi.getZPosition());
else if (position>0 && position<=imp.getStackSize())
imp.setSlice(position);
else if ((roi instanceof PointRoi) && !Prefs.showAllPoints && !((PointRoi)roi).hasPointPosition(imp.getSlice()))
imp.setSlice(((PointRoi)roi).getPointPosition(0));
else {
String label = (String)listModel.getElementAt(index);
int n = getSliceNumber(roi, label);
if (n>=1 && n<=imp.getStackSize()) {
if (hyperstack) {
if (imp.getNSlices()>1 && n<=imp.getNSlices())
imp.setPosition(imp.getC(),n,imp.getT());
else if (imp.getNFrames()>1 && n<=imp.getNFrames())
imp.setPosition(imp.getC(),imp.getZ(),n);
else
imp.setPosition(n);
} else
imp.setSlice(n);
}
}
}
if (showAllCheckbox.getState() && !restoreCentered && !noUpdateMode) {
roi.setImage(null);
imp.setRoi(roi);
return true;
}
Roi roi2 = (Roi)roi.clone();
Rectangle r = roi2.getBounds();
int width= imp.getWidth(), height=imp.getHeight();
if (restoreCentered) {
ImageCanvas ic = imp.getCanvas();
if (ic!=null) {
Rectangle r1 = ic.getSrcRect();
Rectangle r2 = roi2.getBounds();
roi2.setLocation(r1.x+r1.width/2-r2.width/2, r1.y+r1.height/2-r2.height/2);
}
}
if (r.x>=width || r.y>=height || (r.x+r.width)<0 || (r.y+r.height)<0) {
if (roi2.getType()!=Roi.POINT)
roi2.setLocation((width-r.width)/2, (height-r.height)/2);
}
if (noUpdateMode) {
imp.setRoi(roi2, false);
noUpdateMode = false;
} else
imp.setRoi(roi2, true);
return true;
}
private boolean restoreWithoutUpdate(ImagePlus imp, int index) {
noUpdateMode = true;
if (imp==null)
imp = getImage();
return restore(imp, index, false);
}
/** Returns the slice number associated with the specified name,
or -1 if the name does not include a slice number. */
public int getSliceNumber(String label) {
int slice = -1;
if (label.length()>=14 && label.charAt(4)=='-' && label.charAt(9)=='-')
slice = (int)Tools.parseDouble(label.substring(0,4),-1);
else if (label.length()>=17 && label.charAt(5)=='-' && label.charAt(11)=='-')
slice = (int)Tools.parseDouble(label.substring(0,5),-1);
else if (label.length()>=20 && label.charAt(6)=='-' && label.charAt(13)=='-')
slice = (int)Tools.parseDouble(label.substring(0,6),-1);
return slice;
}
/** Returns the slice number associated with the specified ROI or name,
or -1 if the ROI or name does not include a slice number. */
int getSliceNumber(Roi roi, String label) {
int slice = roi!=null?roi.getPosition():-1;
if (slice==0)
slice=-1;
if (slice==-1)
slice = getSliceNumber(label);
return slice;
}
/** Opens a single .roi file or a ZIP-compressed set of ROIs.
* Returns 'true' if the operation was succesful.
*/
public boolean open(String path) {
Macro.setOptions(null);
String name = null;
if (path==null || path.equals("")) {
OpenDialog od = new OpenDialog("Open Selection(s)...", "");
String directory = od.getDirectory();
name = od.getFileName();
if (name==null)
return false;
path = directory + name;
}
if (Recorder.record && !IJ.macroRunning()) {
if (Recorder.scriptMode())
Recorder.recordCall("rm.open(\""+path+"\");");
else
Recorder.record("roiManager", "Open", path);
}
boolean ok = false;
if (path.endsWith(".zip")) {
Recorder.suspendRecording();
ok = openZip(path);
Recorder.resumeRecording();
return ok;
}
Opener o = new Opener();
if (name==null) name = o.getName(path);
Roi roi = o.openRoi(path);
if (roi!=null) {
if (roi.getName()!=null)
name = roi.getName();
if (name.endsWith(".roi"))
name = name.substring(0, name.length()-4);
listModel.addElement(name);
rois.add(roi);
errorMessage = null;
ok = true;
} else {
errorMessage = "Unable to open ROI at "+path;
ok = false;
}
updateShowAll();
return ok;
}
// Modified on 2005/11/15 by Ulrik Stervbo to only read .roi files and to not empty the current list
boolean openZip(String path) {
ZipInputStream in = null;
ByteArrayOutputStream out = null;
int nRois = 0;
errorMessage = null;
try {
in = new ZipInputStream(new FileInputStream(path));
byte[] buf = new byte[1024];
int len;
ZipEntry entry = in.getNextEntry();
while (entry!=null) {
String name = entry.getName();
if (name.endsWith(".roi")) {
out = new ByteArrayOutputStream();
while ((len = in.read(buf)) > 0)
out.write(buf, 0, len);
out.close();
byte[] bytes = out.toByteArray();
RoiDecoder rd = new RoiDecoder(bytes, name);
Roi roi = rd.getRoi();
if (roi!=null) {
name = name.substring(0, name.length()-4);
listModel.addElement(name);
rois.add(roi);
nRois++;
}
}
entry = in.getNextEntry();
}
in.close();
} catch (IOException e) {
errorMessage = e.toString();
error(errorMessage);
} finally {
if (in!=null)
try {in.close();} catch (IOException e) {}
if (out!=null)
try {out.close();} catch (IOException e) {}
}
if (nRois==0 && errorMessage==null) {
errorMessage = "This ZIP archive does not contain \".roi\" files: " + path;
error(errorMessage);
}
updateShowAll();
return errorMessage==null;
}
/** If one ROI is selected, it is saved as a .roi
* file, if multiple (or no) ROIs are selected,
* they are saved as a .zip ROI set. Returns
* 'true' if the save operation was succesful.
* @see #setSelectedIndexes
*/
public boolean save(String path) {
if (getCount()==0)
return error("The selection list is empty.");
int[] indexes = getIndexes();
if (indexes.length>1)
return saveMultiple(indexes, path);
else
return saveOne(indexes, path);
}
boolean saveOne(int[] indexes, String path) {
if (indexes.length==0)
return error("The list is empty");
Roi roi = (Roi)rois.get(indexes[0]);
if (path==null) {
Macro.setOptions(null);
String name = (String) listModel.getElementAt(indexes[0]);
SaveDialog sd = new SaveDialog("Save Selection...", name, ".roi");
String name2 = sd.getFileName();
if (name2 == null)
return false;
String dir = sd.getDirectory();
if (!name2.endsWith(".roi")) name2 = name2+".roi";
String newName = name2.substring(0, name2.length()-4);
rois.set(indexes[0], roi);
roi.setName(newName);
listModel.setElementAt(newName, indexes[0]);
path = dir+name2;
}
RoiEncoder re = new RoiEncoder(path);
errorMessage = null;
try {
re.write(roi);
} catch (IOException e) {
errorMessage = e.getMessage();
IJ.error("ROI Manager", errorMessage);
}
if (Recorder.record && !IJ.isMacro()) {
if (Recorder.scriptMode())
Recorder.recordCall("rm.save(\""+path+"\");");
else
Recorder.record("roiManager", "Save", path);
}
return true;
}
boolean saveMultiple(int[] indexes, String path) {
Macro.setOptions(null);
if (path==null || path.equals("")) {
SaveDialog sd = new SaveDialog("Save ROIs...", "RoiSet", ".zip");
String name = sd.getFileName();
if (name == null)
return false;
if (!(name.endsWith(".zip") || name.endsWith(".ZIP")))
name = name + ".zip";
String dir = sd.getDirectory();
path = dir+name;
}
DataOutputStream out = null;
IJ.showStatus("Saving "+indexes.length+" ROIs "+" to "+path);
long t0 = System.currentTimeMillis();
String[] names = new String[listModel.size()];
for (int i=0; i<listModel.size(); i++)
names[i] = (String)listModel.getElementAt(i);
errorMessage = null;
try {
ZipOutputStream zos = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(path)));
out = new DataOutputStream(new BufferedOutputStream(zos));
RoiEncoder re = new RoiEncoder(out);
for (int i=0; i<indexes.length; i++) {
IJ.showProgress(i, indexes.length);
Roi roi = (Roi)rois.get(indexes[i]);
String label = (String)listModel.getElementAt(indexes[i]);
if (IJ.debugMode) IJ.log("saveMultiple: "+i+" "+label+" "+roi);
if (roi==null) continue;
if (!label.endsWith(".roi")) label += ".roi";
try {
zos.putNextEntry(new ZipEntry(label));
} catch(ZipException e) {
label = getUniqueName(names, indexes[i]);
if (!label.endsWith(".roi")) label += ".roi";
zos.putNextEntry(new ZipEntry(label));
}
re.write(roi);
out.flush();
}
out.close();
} catch (IOException e) {
errorMessage = ""+e;
error(errorMessage);
return false;
} finally {
if (out!=null)
try {out.close();} catch (IOException e) {}
}
double time = (System.currentTimeMillis()-t0)/1000.0;
IJ.showProgress(1.0);
IJ.showStatus(IJ.d2s(time,3)+" seconds, "+indexes.length+" ROIs, "+path);
if (Recorder.record && !IJ.isMacro()) {
if (Recorder.scriptMode())
Recorder.recordCall("rm.save(\""+path+"\");");
else
Recorder.record("roiManager", "Save", path);
}
return true;
}
String getUniqueName(String[] names, int index) {
String name = names[index];
int n = 1;
int index2 = getIndex(names, index, name);
while (index2!=-1) {
index2 = getIndex(names, index, name);