/
RoiManager.java
2379 lines (2259 loc) · 68.2 KB
/
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.Colors;
import ij.plugin.OverlayLabels;
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 {
public static final String LOC_KEY = "manager.loc";
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 IGNORE_POSITION=-999;
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 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 int[] selectedIndexes;
private boolean appendResults;
private ResultsTable mmResults;
private int imageID;
private boolean allowRecording;
private boolean recordShowAll = true;
/** Opens the "ROI Manager" window, or activates it if it is already open.
* @see #getRoiManager
*/
public RoiManager() {
super("ROI Manager");
if (instance!=null) {
WindowManager.toFront(instance);
return;
}
if (IJ.isMacro() && Interpreter.getBatchModeRoiManager()!=null)
return;
instance = this;
list = new JList();
showWindow();
}
/* Constructs an ROIManager without displaying it. */
public RoiManager(boolean b) {
super("ROI Manager");
list = new JList();
listModel = new DefaultListModel();
list.setModel(listModel);
}
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);
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();
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.center(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();
//addPopupItem("Select All");
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("Sort");
addPopupItem("Specify...");
addPopupItem("Remove Positions...");
addPopupItem("Labels...");
addPopupItem("List");
addPopupItem("Interpolate ROIs");
addPopupItem("Translate...");
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(MENU);
else if (command.equals("Open..."))
open(null);
else if (command.equals("Save...")) {
Thread t1 = new Thread(new Runnable() {
public void run() {save();}
});
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)"))
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("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("Translate..."))
translate();
else if (command.equals("Help"))
help();
else if (command.equals("Options..."))
options();
else if (command.equals("\"Show All\" Color..."))
setShowAllColor();
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());
}
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) {
addRoi(roi, false, null, -1);
}
boolean addRoi(boolean promptForName) {
return addRoi(null, promptForName, null, IGNORE_POSITION);
}
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;
boolean ignorePosition = false;
if (lineWidth==IGNORE_POSITION) {
ignorePosition = true;
lineWidth = -1;
}
if (lineWidth<0) {
int sw = (int)roi.getStrokeWidth();
lineWidth = sw>1?sw:defaultLineWidth;
}
if (lineWidth>100) lineWidth = 1;
int n = getCount();
int position = imp!=null&&!ignorePosition?roi.getPosition():0;
int saveCurrentSlice = imp!=null?imp.getCurrentSlice():0;
if (position>0 && position!=saveCurrentSlice)
imp.setSliceWithoutUpdate(position);
else
position = 0;
if (n>0 && !IJ.isMacro() && imp!=null) {
// 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()) {
if (position>0)
imp.setSliceWithoutUpdate(saveCurrentSlice);
return 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) {
if (position>0)
imp.setSliceWithoutUpdate(saveCurrentSlice);
return false;
}
listModel.addElement(label);
roi.setName(label);
Roi roiCopy = (Roi)roi.clone();
setRoiPosition(imp, roiCopy);
if (lineWidth>1)
roiCopy.setStrokeWidth(lineWidth);
if (color!=null)
roiCopy.setStrokeColor(color);
rois.add(roiCopy);
updateShowAll();
if (record())
recordAdd(defaultColor, defaultLineWidth);
if (position>0)
imp.setSliceWithoutUpdate(saveCurrentSlice);
return true;
}
void recordAdd(Color color, int lineWidth) {
if (Recorder.scriptMode())
Recorder.recordCall("rm.addRoi(imp.getRoi());");
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 third argument ('n') will
be used to form the first part of the ROI label if it is >= 0. */
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
label = label+"-"+n;
if (label==null)
return;
listModel.addElement(label);
if (label2!=null)
roi.setName(label2);
else
roi.setName(label);
rois.add((Roi)roi.clone());
}
boolean isStandardName(String name) {
if (name==null) return false;
boolean isStandard = false;
int len = name.length();
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)=='-')
isStandard = true;
else if (len>=11 && name.charAt(5)=='-')
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) 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 list 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) {
rois.remove(i);
listModel.remove(i);
}
}
}
ImagePlus imp = WindowManager.getCurrentImage();
if (count>1 && index.length==1 && imp!=null)
imp.deleteRoi();
updateShowAll();
if (record()) Recorder.record("roiManager", "Delete");
return true;
}
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();
setRoiPosition(imp, roi2);
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.getCPosition()==0 && roi.getZPosition()==0 && roi.getTPosition()==0)
roi.setPosition(position);
rois.set(index, roi);
listModel.setElementAt(name2, index);
list.setSelectedIndex(index);
if (Prefs.useNamesAsLabels && labelsCheckbox.getState()) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp!=null) imp.draw();
}
if (record())
Recorder.record("roiManager", "Rename", name2);
return true;
}
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) {
Roi roi = (Roi)rois.get(index);
if (imp==null || roi==null)
return false;
if (setSlice) {
int c = roi.getCPosition();
int z = roi.getZPosition();
int t = roi.getTPosition();
boolean hyperstack = imp.isHyperStack();
//IJ.log("restore: "+hyperstack+" "+c+" "+z+" "+t);
if (hyperstack && (c>0||z>0||t>0))
imp.setPosition(c, z, t);
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)
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;
}
void 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;
path = directory + name;
}
if (Recorder.record && !Recorder.scriptMode())
Recorder.record("roiManager", "Open", path);
if (path.endsWith(".zip")) {
openZip(path);
return;
}
Opener o = new Opener();
if (name==null) name = o.getName(path);
Roi roi = o.openRoi(path);
if (roi!=null) {
if (name.endsWith(".roi"))
name = name.substring(0, name.length()-4);
listModel.addElement(name);
rois.add(roi);
}
updateShowAll();
}
// Modified on 2005/11/15 by Ulrik Stervbo to only read .roi files and to not empty the current list
void openZip(String path) {
ZipInputStream in = null;
ByteArrayOutputStream out = null;
int nRois = 0;
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) {
error(e.toString());
} finally {
if (in!=null)
try {in.close();} catch (IOException e) {}
if (out!=null)
try {out.close();} catch (IOException e) {}
}
if(nRois==0)
error("This ZIP archive does not appear to contain \".roi\" files");
updateShowAll();
}
boolean save() {
if (getCount()==0)
return error("The selection list is empty.");
int[] indexes = getIndexes();
if (indexes.length>1)
return saveMultiple(indexes, null);
String name = (String) listModel.getElementAt(indexes[0]);
Macro.setOptions(null);
SaveDialog sd = new SaveDialog("Save Selection...", name, ".roi");
String name2 = sd.getFileName();
if (name2 == null)
return false;
String dir = sd.getDirectory();
Roi roi = (Roi)rois.get(indexes[0]);
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]);
RoiEncoder re = new RoiEncoder(dir+name2);
try {
re.write(roi);
} catch (IOException e) {
IJ.error("ROI Manager", e.getMessage());
}
if (record()) {
String path = dir+name2;
if (Recorder.scriptMode())
Recorder.recordCall("IJ.saveAs(imp, \"Selection\", \""+path+"\");");
else
Recorder.record("saveAs", "Selection", path);
}
return true;
}
boolean saveMultiple(int[] indexes, String path) {
Macro.setOptions(null);
if (path==null) {
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();
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);
String label = (String) listModel.getElementAt(indexes[i]);
Roi roi = (Roi)rois.get(indexes[i]);
if (IJ.debugMode) IJ.log("saveMultiple: "+i+" "+label+" "+roi);
if (roi==null) continue;
if (!label.endsWith(".roi")) label += ".roi";
zos.putNextEntry(new ZipEntry(label));
re.write(roi);
out.flush();
}
out.close();
} catch (IOException e) {
error(""+e);
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())
Recorder.record("roiManager", "Save", path);
return true;
}
private void listRois() {
Roi[] list = getRoisAsArray();
OverlayCommands.listRois(list);
if (record())
Recorder.record("roiManager", "List");
}
boolean measure(int mode) {
ImagePlus imp = getImage();
if (imp==null)
return false;
int[] indexes = getIndexes();
if (indexes.length==0) return false;
boolean allSliceOne = true;
for (int i=0; i<indexes.length; i++) {
Roi roi = (Roi)rois.get(indexes[i]);
String label = (String) listModel.getElementAt(indexes[i]);
if (getSliceNumber(roi,label)>1) allSliceOne=false;
}
int measurements = Analyzer.getMeasurements();
if (imp.getStackSize()>1)
Analyzer.setMeasurements(measurements|Measurements.SLICE);
int currentSlice = imp.getCurrentSlice();
Analyzer.setMeasurements(measurements&(~Measurements.ADD_TO_OVERLAY));
for (int i=0; i<indexes.length; i++) {
if (restore(getImage(), indexes[i], !allSliceOne))
IJ.run("Measure");
else
break;
}
Analyzer.setMeasurements(measurements);
imp.setSlice(currentSlice);
if (indexes.length>1)
IJ.run("Select None");
if (record()) Recorder.record("roiManager", "Measure");
return true;
}
/** This method measures the selected ROIs, or all ROIs if
* none are selected, on all the slices of a stack and returns
* a ResultsTable arranged with one row per slice.
* @see <a href="http://imagej.nih.gov/ij/macros/js/MultiMeasureDemo.js">JavaScript example</a>
*/
public ResultsTable multiMeasure(ImagePlus imp) {
ResultsTable rt = multiMeasure(imp, getIndexes(), imp.getStackSize(), false);
imp.deleteRoi();
return rt;
}
/** This method performs measurements for several ROI's in a stack
and arranges the results with one line per slice. By contrast, the
measure() method produces several lines per slice. The results
from multiMeasure() may be easier to import into a spreadsheet
program for plotting or additional analysis. Based on the multi()
method in Bob Dougherty's Multi_Measure plugin
(http://www.optinav.com/Multi-Measure.htm).
*/
boolean multiMeasure(String cmd) {
ImagePlus imp = getImage();
if (imp==null) return false;
int[] indexes = getIndexes();
if (indexes.length==0)
return false;
int measurements = Analyzer.getMeasurements();
int nSlices = imp.getStackSize();
if (cmd!=null)
appendResults = cmd.contains("append")?true:false;
if (IJ.isMacro()) {
if (cmd.startsWith("multi-measure")) {
measureAll = cmd.contains(" measure") && nSlices>1;
onePerSlice = cmd.contains(" one");
appendResults = cmd.contains(" append");
} else {
if (nSlices>1)
measureAll = true;
onePerSlice = true;
}
} else {
GenericDialog gd = new GenericDialog("Multi Measure");
if (nSlices>1)
gd.addCheckbox("Measure all "+nSlices+" slices", measureAll);
gd.addCheckbox("One row per slice", onePerSlice);
gd.addCheckbox("Append results", appendResults);
int columns = getColumnCount(imp, measurements)*indexes.length;
String str = nSlices==1?"this option":"both options";
gd.setInsets(10, 25, 0);
gd.addMessage(
"Enabling "+str+" will result\n"+
"in a table with "+columns+" columns."
);
gd.showDialog();
if (gd.wasCanceled()) return false;
if (nSlices>1)
measureAll = gd.getNextBoolean();
onePerSlice = gd.getNextBoolean();
appendResults = gd.getNextBoolean();
}
if (!measureAll) nSlices = 1;
int currentSlice = imp.getCurrentSlice();
if (!onePerSlice) {
int measurements2 = nSlices>1?measurements|Measurements.SLICE:measurements;
ResultsTable rt = new ResultsTable();
Analyzer analyzer = new Analyzer(imp, measurements2, rt);
for (int slice=1; slice<=nSlices; slice++) {
if (nSlices>1) imp.setSliceWithoutUpdate(slice);
for (int i=0; i<indexes.length; i++) {
if (restoreWithoutUpdate(imp, indexes[i]))
analyzer.measure();
else
break;
}
}
rt.show("Results");
if (nSlices>1)
imp.setSlice(currentSlice);
} else {
ResultsTable rtMulti = multiMeasure(imp, indexes, nSlices, appendResults);
mmResults = (ResultsTable)rtMulti.clone();
rtMulti.show("Results");
imp.setSlice(currentSlice);
if (indexes.length>1)
IJ.run("Select None");
}
if (record()) {
if (Recorder.scriptMode()) {
Recorder.recordCall("rt = rm.multiMeasure(imp);");
Recorder.recordCall("rt.show(\"Results\");");
} else {
if ((nSlices==1||measureAll) && onePerSlice && !appendResults)
Recorder.record("roiManager", "Multi Measure");
else {
String options = "";
if (measureAll)
options += " measure_all";
if (onePerSlice)
options += " one";
if (appendResults)
options += " append";
Recorder.record("roiManager", "multi-measure"+options);
}
}
}
return true;
}
private ResultsTable multiMeasure(ImagePlus imp, int[] indexes, int nSlices, boolean appendResults) {
Analyzer aSys = new Analyzer(imp); // System Analyzer
ResultsTable rtSys = Analyzer.getResultsTable();
ResultsTable rtMulti = new ResultsTable();