Example 26 with Display
use of ini.trakem2.display.Display in project TrakEM2 by trakem2.
the class LayerTree method actionPerformed.
public void actionPerformed(ActionEvent ae) {
try {
String command = ae.getActionCommand();
// commands for multiple selections:
TreePath[] paths = this.getSelectionPaths();
if (null != paths && paths.length > 1) {
if (command.equals("Reverse layer Z coords")) {
// check that all layers belong to the same layer set
// just do it
Layer[] layer = new Layer[paths.length];
LayerSet ls = null;
for (int i = 0; i < paths.length; i++) {
layer[i] = (Layer) ((LayerThing) ((DefaultMutableTreeNode) paths[i].getLastPathComponent()).getUserObject()).getObject();
if (null == ls)
ls = layer[i].getParent();
else if (!ls.equals(layer[i].getParent())) {
Utils.showMessage("To reverse, all layers must belong to the same layer set");
return;
}
}
final ArrayList<Layer> al = new ArrayList<Layer>();
for (int i = 0; i < layer.length; i++) al.add(layer[i]);
ls.addLayerEditedStep(al);
// ASSSUMING layers are already Z ordered! CHECK
for (int i = 0, j = layer.length - 1; i < layer.length / 2; i++, j--) {
double z = layer[i].getZ();
layer[i].setZ(layer[j].getZ());
layer[j].setZ(z);
}
updateList(ls);
ls.addLayerEditedStep(al);
Display.updateLayerScroller(ls);
} else if (command.equals("Translate layers in Z...")) {
GenericDialog gd = ControlWindow.makeGenericDialog("Range");
gd.addMessage("Translate selected range in the Z axis:");
gd.addNumericField("by: ", 0, 4);
gd.showDialog();
if (gd.wasCanceled())
return;
// else, displace
double dz = gd.getNextNumber();
if (Double.isNaN(dz)) {
Utils.showMessage("Invalid number");
return;
}
HashSet<LayerSet> hs_parents = new HashSet<LayerSet>();
for (int i = 0; i < paths.length; i++) {
Layer layer = (Layer) ((LayerThing) ((DefaultMutableTreeNode) paths[i].getLastPathComponent()).getUserObject()).getObject();
layer.setZ(layer.getZ() + dz);
hs_parents.add(layer.getParent());
}
for (LayerSet ls : hs_parents) {
updateList(ls);
}
// now update all profile's Z ordering in the ProjectTree
ProjectThing root_pt = project.getRootProjectThing();
for (final ProjectThing pt : root_pt.findChildrenOfType("profile_list")) {
pt.fixZOrdering();
project.getProjectTree().updateList(pt);
}
project.getProjectTree().updateUILater();
// Display.updateLayerScroller((LayerSet)((DefaultMutableTreeNode)getModel().getRoot()).getUserObject());
} else if (command.equals("Delete...")) {
if (!Utils.check("Really remove all selected layers?"))
return;
for (int i = 0; i < paths.length; i++) {
DefaultMutableTreeNode lnode = (DefaultMutableTreeNode) paths[i].getLastPathComponent();
LayerThing lt = (LayerThing) lnode.getUserObject();
Layer layer = (Layer) lt.getObject();
if (!layer.remove(false)) {
Utils.showMessage("Could not delete layer " + layer);
this.updateUILater();
return;
}
if (lt.remove(false)) {
((DefaultTreeModel) this.getModel()).removeNodeFromParent(lnode);
}
}
this.updateUILater();
} else if (command.equals("Scale Z and thickness...")) {
GenericDialog gd = new GenericDialog("Scale Z");
gd.addNumericField("scale: ", 1.0, 2);
gd.showDialog();
double scale = gd.getNextNumber();
if (Double.isNaN(scale) || 0 == scale) {
Utils.showMessage("Imvalid scaling factor: " + scale);
return;
}
for (int i = 0; i < paths.length; i++) {
DefaultMutableTreeNode lnode = (DefaultMutableTreeNode) paths[i].getLastPathComponent();
LayerThing lt = (LayerThing) lnode.getUserObject();
Layer layer = (Layer) lt.getObject();
layer.setZ(layer.getZ() * scale);
layer.setThickness(layer.getThickness() * scale);
}
this.updateUILater();
} else {
Utils.showMessage("Don't know what to do with command " + command + " for multiple selected nodes");
}
return;
}
// commands for single selection:
if (null == selected_node)
return;
LayerThing thing = (LayerThing) selected_node.getUserObject();
LayerThing new_thing = null;
TemplateThing tt = null;
Object ob = null;
int i_position = -1;
if (command.startsWith("new ")) {
String name = command.substring(4).toLowerCase();
if (name.equals("layer")) {
// Create new Layer and add it to the selected node
LayerSet set = (LayerSet) thing.getObject();
Layer new_layer = Layer.create(thing.getProject(), set);
if (null == new_layer)
return;
tt = thing.getChildTemplate("layer");
ob = new_layer;
Display.updateTitle(set);
} else if (name.equals("layer set")) {
// with space in the middle
// Create a new LayerSet and add it in the middle
Layer layer = (Layer) thing.getObject();
LayerSet new_set = layer.getParent().create(layer);
if (null == new_set)
return;
layer.add(new_set);
// add it at the end of the list
// with space, not underscore
tt = thing.getChildTemplate("layer set");
ob = new_set;
i_position = selected_node.getChildCount();
Display.update(layer);
} else {
Utils.log("LayerTree.actionPerformed: don't know what to do with the command: " + command);
return;
}
} else if (command.equals("many new layers...")) {
LayerSet set = (LayerSet) thing.getObject();
List<Layer> layers = Layer.createMany(set.getProject(), set);
// add them to the tree as LayerThing
if (null == layers)
return;
for (Layer la : layers) {
// null layers will be skipped
addLayer(set, la);
}
Display.updateTitle(set);
return;
} else if (command.equals("Show")) {
// create a new Display
DBObject dbo = (DBObject) thing.getObject();
// the top level LayerSet
if (thing.getType().equals("layer_set") && null == ((LayerSet) dbo).getParent())
return;
Display.createDisplay(dbo.getProject(), thing.getType().equals("layer") ? (Layer) dbo : ((LayerSet) dbo).getParent());
return;
} else if (command.equals("Show centered in Display")) {
LayerSet ls = (LayerSet) thing.getObject();
Display.showCentered(ls.getParent(), ls, false, false);
} else if (command.equals("Delete...")) {
remove(true, thing, selected_node);
return;
} else if (command.equals("Import stack...")) {
if (thing.getObject() instanceof LayerSet) {
LayerSet set = (LayerSet) thing.getObject();
Layer layer = null;
if (0 == set.getLayers().size()) {
layer = Layer.create(set.getProject(), set);
if (null == layer)
return;
tt = thing.getChildTemplate("Layer");
ob = layer;
} else
// click on a desired, existing layer.
return;
layer.getProject().getLoader().importStack(layer, null, true);
} else if (thing.getObject() instanceof Layer) {
Layer layer = (Layer) thing.getObject();
layer.getProject().getLoader().importStack(layer, null, true);
return;
}
} else if (command.equals("Import grid...")) {
if (thing.getObject() instanceof Layer) {
Layer layer = (Layer) thing.getObject();
layer.getProject().getLoader().importGrid(layer);
}
} else if (command.equals("Import sequence as grid...")) {
if (thing.getObject() instanceof Layer) {
Layer layer = (Layer) thing.getObject();
layer.getProject().getLoader().importSequenceAsGrid(layer);
}
} else if (command.equals("Import from text file...")) {
if (thing.getObject() instanceof Layer) {
Layer layer = (Layer) thing.getObject();
layer.getProject().getLoader().importImages(layer);
}
} else if (command.equals("Resize LayerSet...")) {
if (thing.getObject() instanceof LayerSet) {
LayerSet ls = (LayerSet) thing.getObject();
ij.gui.GenericDialog gd = ControlWindow.makeGenericDialog("Resize LayerSet");
gd.addNumericField("new width: ", ls.getLayerWidth(), 3);
gd.addNumericField("new height: ", ls.getLayerHeight(), 3);
gd.addChoice("Anchor: ", LayerSet.ANCHORS, LayerSet.ANCHORS[0]);
gd.showDialog();
if (gd.wasCanceled())
return;
float new_width = (float) gd.getNextNumber(), new_height = (float) gd.getNextNumber();
// will complain and prevent cropping existing Displayable objects
ls.setDimensions(new_width, new_height, gd.getNextChoiceIndex());
}
} else if (command.equals("Autoresize LayerSet")) {
if (thing.getObject() instanceof LayerSet) {
LayerSet ls = (LayerSet) thing.getObject();
ls.setMinimumDimensions();
}
} else if (command.equals("Adjust...")) {
if (thing.getObject() instanceof Layer) {
Layer layer = (Layer) thing.getObject();
ij.gui.GenericDialog gd = ControlWindow.makeGenericDialog("Adjust Layer");
gd.addNumericField("new z: ", layer.getZ(), 4);
gd.addNumericField("new thickness: ", layer.getThickness(), 4);
gd.showDialog();
if (gd.wasCanceled())
return;
double new_z = gd.getNextNumber();
layer.setThickness(gd.getNextNumber());
if (new_z != layer.getZ()) {
layer.setZ(new_z);
// move in the tree
/*
DefaultMutableTreeNode child = findNode(thing, this);
DefaultMutableTreeNode parent = (DefaultMutableTreeNode)child.getParent();
parent.remove(child);
// reinsert
int n = parent.getChildCount();
int i = 0;
for (; i < n; i++) {
DefaultMutableTreeNode child_node = (DefaultMutableTreeNode)parent.getChildAt(i);
LayerThing child_thing = (LayerThing)child_node.getUserObject();
if (!child_thing.getType().equals("Layer")) continue;
double iz = ((Layer)child_thing.getObject()).getZ();
if (iz < new_z) continue;
// else, add the layer here, after this one
break;
}
((DefaultTreeModel)this.getModel()).insertNodeInto(child, parent, i);
*/
// fix tree crappiness (empty slot ?!?)
/* // the fix doesn't work. ARGH TODO
Enumeration e = parent.children();
parent.removeAllChildren();
i = 0;
while (e.hasMoreElements()) {
//parent.add((DefaultMutableTreeNode)e.nextElement());
((DefaultTreeModel)this.getModel()).insertNodeInto(child, parent, i);
i++;
}*/
// easier and correct: overkill
updateList(layer.getParent());
// set selected
DefaultMutableTreeNode child = findNode(thing, this);
TreePath treePath = new TreePath(child.getPath());
this.scrollPathToVisible(treePath);
this.setSelectionPath(treePath);
}
}
return;
} else if (command.equals("Rename...")) {
GenericDialog gd = ControlWindow.makeGenericDialog("Rename");
gd.addStringField("new name: ", thing.getTitle());
gd.showDialog();
if (gd.wasCanceled())
return;
project.getRootLayerSet().addUndoStep(new RenameThingStep(thing));
thing.setTitle(gd.getNextString());
project.getRootLayerSet().addUndoStep(new RenameThingStep(thing));
} else if (command.equals("Translate layers in Z...")) {
// / TODO: this method should use multiple selections directly on the tree
if (thing.getObject() instanceof LayerSet) {
LayerSet ls = (LayerSet) thing.getObject();
ArrayList<Layer> al_layers = ls.getLayers();
String[] layer_names = new String[al_layers.size()];
for (int i = 0; i < layer_names.length; i++) {
layer_names[i] = ls.getProject().findLayerThing(al_layers.get(i)).toString();
}
GenericDialog gd = ControlWindow.makeGenericDialog("Range");
gd.addMessage("Translate selected range in the Z axis:");
gd.addChoice("from: ", layer_names, layer_names[0]);
gd.addChoice("to: ", layer_names, layer_names[layer_names.length - 1]);
gd.addNumericField("by: ", 0, 4);
gd.showDialog();
if (gd.wasCanceled())
return;
// else, displace
double dz = gd.getNextNumber();
if (Double.isNaN(dz)) {
Utils.showMessage("Invalid number");
return;
}
int i_start = gd.getNextChoiceIndex();
int i_end = gd.getNextChoiceIndex();
for (int i = i_start; i <= i_end; i++) {
Layer layer = (Layer) al_layers.get(i);
layer.setZ(layer.getZ() + dz);
}
// update node labels and position
updateList(ls);
}
} else if (command.equals("Reverse layer Z coords...")) {
// / TODO: this method should use multiple selections directly on the tree
if (thing.getObject() instanceof LayerSet) {
LayerSet ls = (LayerSet) thing.getObject();
ArrayList<Layer> al_layers = ls.getLayers();
String[] layer_names = new String[al_layers.size()];
for (int i = 0; i < layer_names.length; i++) {
layer_names[i] = ls.getProject().findLayerThing(al_layers.get(i)).toString();
}
GenericDialog gd = ControlWindow.makeGenericDialog("Range");
gd.addMessage("Reverse Z coordinates of selected range:");
gd.addChoice("from: ", layer_names, layer_names[0]);
gd.addChoice("to: ", layer_names, layer_names[layer_names.length - 1]);
gd.showDialog();
if (gd.wasCanceled())
return;
int i_start = gd.getNextChoiceIndex();
int i_end = gd.getNextChoiceIndex();
for (int i = i_start, j = i_end; i < i_end / 2; i++, j--) {
Layer layer1 = (Layer) al_layers.get(i);
double z1 = layer1.getZ();
Layer layer2 = (Layer) al_layers.get(j);
layer1.setZ(layer2.getZ());
layer2.setZ(z1);
}
// update node labels and position
updateList(ls);
}
} else if (command.equals("Search...")) {
Search.showWindow();
} else if (command.equals("Reset layer Z and thickness")) {
LayerSet ls = ((LayerSet) thing.getObject());
List<Layer> layers = ls.getLayers();
ls.addLayerEditedStep(layers);
int i = 0;
for (final Layer la : ls.getLayers()) {
la.setZ(i++);
la.setThickness(1);
}
ls.addLayerEditedStep(layers);
} else {
Utils.log("LayerTree.actionPerformed: don't know what to do with the command: " + command);
return;
}
if (null == tt)
return;
new_thing = new LayerThing(tt, thing.getProject(), ob);
if (-1 == i_position && new_thing.getType().equals("layer")) {
// find the node whose 'z' is larger than z, and add the Layer before that.
// (just because there could be objects other than LayerThing with a Layer in it in the future, so set.getLayers().indexOf(layer) may not be useful)
double z = ((Layer) ob).getZ();
int n = selected_node.getChildCount();
int i = 0;
for (; i < n; i++) {
DefaultMutableTreeNode child_node = (DefaultMutableTreeNode) selected_node.getChildAt(i);
LayerThing child_thing = (LayerThing) child_node.getUserObject();
if (!child_thing.getType().equals("layer")) {
continue;
}
double iz = ((Layer) child_thing.getObject()).getZ();
if (iz < z) {
continue;
}
// else, add the layer here, after this one
break;
}
i_position = i;
}
thing.addChild(new_thing);
DefaultMutableTreeNode new_node = new DefaultMutableTreeNode(new_thing);
((DefaultTreeModel) this.getModel()).insertNodeInto(new_node, selected_node, i_position);
TreePath treePath = new TreePath(new_node.getPath());
this.scrollPathToVisible(treePath);
this.setSelectionPath(treePath);
if (new_thing.getType().equals("layer set")) {
// add the first layer to it, and open it in a Display
LayerSet newls = (LayerSet) new_thing.getObject();
Layer la = new Layer(newls.getProject(), 0, 1, newls);
addLayer(newls, la);
new Display(newls.getProject(), la);
}
} catch (Exception e) {
IJError.print(e);
}
}
Also used :
DefaultMutableTreeNode(javax.swing.tree.DefaultMutableTreeNode)
ArrayList(java.util.ArrayList)
DBObject(ini.trakem2.persistence.DBObject)
GenericDialog(ij.gui.GenericDialog)
ArrayList(java.util.ArrayList)
List(java.util.List)
HashSet(java.util.HashSet)
LayerSet(ini.trakem2.display.LayerSet)
DefaultTreeModel(javax.swing.tree.DefaultTreeModel)
Layer(ini.trakem2.display.Layer)
TreePath(javax.swing.tree.TreePath)
DBObject(ini.trakem2.persistence.DBObject)
Display(ini.trakem2.display.Display)
Example 27 with Display
use of ini.trakem2.display.Display in project TrakEM2 by trakem2.
the class ProjectThing method getPopupItems.
public JMenuItem[] getPopupItems(final ActionListener listener) {
JMenuItem item = null;
ArrayList<JMenuItem> al_items = new ArrayList<JMenuItem>();
JMenu menu = new JMenu("Add...");
// call the project unique type
final ArrayList<TemplateThing> tc = project.getTemplateThing(template.getType()).getChildren();
if (null != tc) {
for (final TemplateThing tt : tc) {
item = new JMenuItem("new " + tt.getType());
item.addActionListener(listener);
menu.add(item);
}
item = new JMenuItem("many...");
item.addActionListener(listener);
menu.add(item);
}
if (0 != menu.getItemCount()) {
if (template.getType().equals("profile_list") && null != al_children && al_children.size() > 0) {
// can't add a new profile unless linked to another one.
item.setEnabled(false);
}
al_items.add(menu);
}
// generic for all:
// a 'Show' command on a non-basic type is a render preview.
addPopupItem("Unhide", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, Event.ALT_MASK, true));
addPopupItem("Hide", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, 0, true));
addPopupItem("Info", listener, al_items);
addPopupItem("Rename...", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F2, 0, true));
// enable duplicating for basic types only
if (Project.isBasicType(getType())) {
addPopupItem("Duplicate", listener, al_items);
}
addPopupItem("Select in display", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_A, 0, true));
if (null != object && object instanceof Displayable) {
addPopupItem("Show centered in Display", listener, al_items);
}
if (null != object && object instanceof Tree<?>) {
addPopupItem("Show tabular view", listener, al_items);
}
// plugins
JMenuItem plugin_menu = Utils.addPlugIns("Project Tree", project, new Callable<Displayable>() {
public Displayable call() {
if (object instanceof Displayable)
return (Displayable) object;
return null;
}
});
if (null != plugin_menu)
al_items.add(plugin_menu);
addPopupItem("Measure", listener, al_items);
addPopupItem("Show in 3D", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_3, 0, true));
addPopupItem("Remove from 3D view", listener, al_items);
if (template.getType().equals("project")) {
if (project.getLoader() instanceof DBLoader) {
addPopupItem("Export project...", listener, al_items);
} else if (project.getLoader() instanceof FSLoader) {
addPopupItem("Save", listener, al_items).setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, 0, true));
addPopupItem("Save as...", listener, al_items);
}
}
if (!(template.getType().equals("project") && project.getLoader() instanceof FSLoader)) {
addPopupItem("Delete...", listener, al_items);
}
JMenuItem[] items = new JMenuItem[al_items.size()];
al_items.toArray(items);
return items;
}
Also used :
FSLoader(ini.trakem2.persistence.FSLoader)
ZDisplayable(ini.trakem2.display.ZDisplayable)
Displayable(ini.trakem2.display.Displayable)
DBLoader(ini.trakem2.persistence.DBLoader)
ArrayList(java.util.ArrayList)
JMenuItem(javax.swing.JMenuItem)
JMenu(javax.swing.JMenu)
Example 28 with Display
use of ini.trakem2.display.Display in project TrakEM2 by trakem2.
the class ProjectTree method actionPerformed.
public void actionPerformed(final ActionEvent ae) {
if (!project.isInputEnabled())
return;
super.dispatcher.exec(new Runnable() {
public void run() {
try {
if (null == selected_node)
return;
final Object ob = selected_node.getUserObject();
if (!(ob instanceof ProjectThing))
return;
final ProjectThing thing = (ProjectThing) ob;
int i_position = 0;
String command = ae.getActionCommand();
final Object obd = thing.getObject();
if (command.startsWith("new ") || command.equals("Duplicate")) {
ProjectThing new_thing = null;
if (command.startsWith("new ")) {
// if it's a Displayable, it will be added to whatever layer is in the front Display
new_thing = thing.createChild(command.substring(4));
} else if (command.equals("Duplicate")) {
// just to keep myself from screwing in the future
if (Project.isBasicType(thing.getType()) && null != thing.getParent()) {
new_thing = ((ProjectThing) thing.getParent()).createClonedChild(thing);
}
// adjust parent
selected_node = (DefaultMutableTreeNode) selected_node.getParent();
}
// add it to the tree
if (null != new_thing) {
DefaultMutableTreeNode new_node = new DefaultMutableTreeNode(new_thing);
((DefaultTreeModel) ProjectTree.this.getModel()).insertNodeInto(new_node, selected_node, i_position);
TreePath treePath = new TreePath(new_node.getPath());
ProjectTree.this.scrollPathToVisible(treePath);
ProjectTree.this.setSelectionPath(treePath);
}
// bring the display to front
if (new_thing.getObject() instanceof Displayable) {
Display.getFront().getFrame().toFront();
}
} else if (command.equals("many...")) {
ArrayList<TemplateThing> children = thing.getTemplate().getChildren();
if (null == children || 0 == children.size())
return;
String[] cn = new String[children.size()];
int i = 0;
for (final TemplateThing child : children) {
cn[i] = child.getType();
i++;
}
GenericDialog gd = new GenericDialog("Add many children");
gd.addNumericField("Amount: ", 1, 0);
gd.addChoice("New child: ", cn, cn[0]);
gd.addCheckbox("Recursive", true);
gd.showDialog();
if (gd.wasCanceled())
return;
int amount = (int) gd.getNextNumber();
if (amount < 1) {
Utils.showMessage("Makes no sense to create less than 1 child!");
return;
}
project.getRootLayerSet().addChangeTreesStep();
final ArrayList<ProjectThing> nc = thing.createChildren(cn[gd.getNextChoiceIndex()], amount, gd.getNextBoolean());
addLeafs(nc, new Runnable() {
public void run() {
project.getRootLayerSet().addChangeTreesStep();
}
});
} else if (command.equals("Unhide")) {
thing.setVisible(true);
} else if (command.equals("Select in display")) {
boolean shift_down = 0 != (ae.getModifiers() & ActionEvent.SHIFT_MASK);
selectInDisplay(thing, shift_down);
} else if (command.equals("Show centered in Display")) {
if (obd instanceof Displayable) {
Displayable displ = (Displayable) obd;
Display.showCentered(displ.getLayer(), displ, true, 0 != (ae.getModifiers() & ActionEvent.SHIFT_MASK));
}
} else if (command.equals("Show tabular view")) {
((Tree<?>) obd).createMultiTableView();
} else if (command.equals("Show in 3D")) {
Display3D.showAndResetView(thing);
} else if (command.equals("Remove from 3D view")) {
Display3D.removeFrom3D(thing);
} else if (command.equals("Hide")) {
// find all Thing objects in this subtree starting at Thing and hide their Displayable objects.
thing.setVisible(false);
} else if (command.equals("Delete...")) {
// store old state
project.getRootLayerSet().addChangeTreesStep();
remove(true, thing, selected_node);
// store new state
project.getRootLayerSet().addChangeTreesStep();
return;
} else if (command.equals("Rename...")) {
// if (!Project.isBasicType(thing.getType())) {
rename(thing);
// }
} else if (command.equals("Measure")) {
// block displays while measuring
Bureaucrat.createAndStart(new Worker("Measuring") {
public void run() {
startedWorking();
try {
thing.measure();
} catch (Throwable e) {
IJError.print(e);
} finally {
finishedWorking();
}
}
}, thing.getProject());
} else /* else if (command.equals("Export 3D...")) {
GenericDialog gd = ControlWindow.makeGenericDialog("Export 3D");
String[] choice = new String[]{".svg [preserves links and hierarchical grouping]", ".shapes [limited to one profile per layer per profile_list]"};
gd.addChoice("Export to: ", choice, choice[0]);
gd.addNumericField("Z scaling: ", 1, 2);
gd.showDialog();
if (gd.wasCanceled()) return;
double z_scale = gd.getNextNumber();
switch (gd.getNextChoiceIndex()) {
case 0:
Render.exportSVG(thing, z_scale);
break;
case 1:
new Render(thing).save(z_scale);
break;
}
}*/
if (command.equals("Export project...") || command.equals("Save as...")) {
// "Save as..." is for a FS project
Utils.log2("Calling export project at " + System.currentTimeMillis());
thing.getProject().getLoader().saveTask(thing.getProject(), "Save as...");
} else if (command.equals("Save")) {
// overwrite the xml file of a FSProject
// Just do the same as in "Save as..." but without saving the images and overwritting the XML file without asking.
thing.getProject().getLoader().saveTask(thing.getProject(), "Save");
} else if (command.equals("Info")) {
showInfo(thing);
return;
} else if (command.equals("Move up")) {
move(selected_node, -1);
} else if (command.equals("Move down")) {
move(selected_node, 1);
} else if (command.equals("Collapse nodes of children nodes")) {
if (null == selected_node)
return;
Enumeration<?> c = selected_node.children();
while (c.hasMoreElements()) {
DefaultMutableTreeNode child = (DefaultMutableTreeNode) c.nextElement();
if (child.isLeaf())
continue;
collapsePath(new TreePath(child.getPath()));
}
} else if (command.equals("Sibling project")) {
sendToSiblingProjectTask(selected_node);
} else {
Utils.log("ProjectTree.actionPerformed: don't know what to do with the command: " + command);
return;
}
} catch (Exception e) {
IJError.print(e);
}
}
});
}
Also used :
Displayable(ini.trakem2.display.Displayable)
ZDisplayable(ini.trakem2.display.ZDisplayable)
DefaultMutableTreeNode(javax.swing.tree.DefaultMutableTreeNode)
TreePath(javax.swing.tree.TreePath)
GenericDialog(ij.gui.GenericDialog)
AreaTree(ini.trakem2.display.AreaTree)
Tree(ini.trakem2.display.Tree)
JTree(javax.swing.JTree)
Worker(ini.trakem2.utils.Worker)
DBObject(ini.trakem2.persistence.DBObject)
Example 29 with Display
use of ini.trakem2.display.Display in project TrakEM2 by trakem2.
the class Search method makeGUI.
private void makeGUI() {
// create GUI if not there
if (null == search_frame) {
search_frame = ControlWindow.createJFrame("Search Regular Expressions");
search_frame.addWindowListener(new WindowAdapter() {
public void windowClosing(WindowEvent we) {
instance.destroy();
}
});
search_tabs = new JTabbedPane(JTabbedPane.TOP);
kl = new KeyAdapter() {
public void keyPressed(KeyEvent ke) {
tryCloseTab(ke);
}
};
search_tabs.addKeyListener(kl);
search_field = new JTextField(14);
search_field.addKeyListener(new VKEnterListener());
GridBagLayout gb = new GridBagLayout();
GridBagConstraints c = new GridBagConstraints();
JPanel all = new JPanel();
all.setLayout(gb);
all.setPreferredSize(new Dimension(600, 400));
JButton b = new JButton("Search");
b.addActionListener(new ButtonListener());
pulldown = new JComboBox(new String[] { "All", "All displayables", "Labels", "Images", "Area Lists", "Profiles", "Pipes", "Balls", "Layers", "Dissectors", "Polylines", "Treelines", "AreaTrees", "Connectors" });
List<Project> ps = Project.getProjects();
String[] sps = new String[ps.size()];
int k = 0;
for (final Project p : ps) sps[k++] = p.getTitle();
this.projects = new JComboBox(sps);
Display front = Display.getFront();
if (null != front)
this.projects.setSelectedIndex(ps.indexOf(front.getProject()));
c.gridx = 0;
c.gridy = 0;
c.fill = GridBagConstraints.HORIZONTAL;
c.weightx = 1;
c.insets = new Insets(4, 10, 5, 2);
gb.setConstraints(search_field, c);
all.add(search_field);
c.gridx = 1;
c.weightx = 0;
c.insets = new Insets(4, 2, 5, 10);
gb.setConstraints(b, c);
all.add(b);
c.gridx = 2;
gb.setConstraints(pulldown, c);
all.add(pulldown);
c.gridx = 3;
gb.setConstraints(projects, c);
all.add(projects);
c.gridx = 0;
c.gridy = 1;
c.gridwidth = 4;
c.weightx = 1;
c.weighty = 1;
c.fill = GridBagConstraints.BOTH;
c.insets = new Insets(0, 0, 0, 0);
gb.setConstraints(search_tabs, c);
all.add(search_tabs);
search_frame.getContentPane().add(all);
search_frame.pack();
javax.swing.SwingUtilities.invokeLater(new Runnable() {
public void run() {
ij.gui.GUI.center(search_frame);
search_frame.setVisible(true);
}
});
} else {
search_frame.toFront();
}
}
Also used :
JPanel(javax.swing.JPanel)
GridBagConstraints(java.awt.GridBagConstraints)
Insets(java.awt.Insets)
GridBagLayout(java.awt.GridBagLayout)
JComboBox(javax.swing.JComboBox)
JTabbedPane(javax.swing.JTabbedPane)
KeyAdapter(java.awt.event.KeyAdapter)
JButton(javax.swing.JButton)
WindowAdapter(java.awt.event.WindowAdapter)
Dimension(java.awt.Dimension)
JTextField(javax.swing.JTextField)
KeyEvent(java.awt.event.KeyEvent)
Project(ini.trakem2.Project)
WindowEvent(java.awt.event.WindowEvent)
Display(ini.trakem2.display.Display)
Example 30 with Display
use of ini.trakem2.display.Display in project TrakEM2 by trakem2.
the class Polyline method mousePressed.
@Override
public void mousePressed(final MouseEvent me, final Layer layer, int x_p, int y_p, final double mag) {
// transform the x_p, y_p to the local coordinates
final int x_pd = x_p;
final int y_pd = y_p;
if (!this.at.isIdentity()) {
final Point2D.Double po = inverseTransformPoint(x_p, y_p);
x_p = (int) po.x;
y_p = (int) po.y;
}
final int tool = ProjectToolbar.getToolId();
final Display display = ((DisplayCanvas) me.getSource()).getDisplay();
final long layer_id = layer.getId();
index = findPoint(x_p, y_p, layer_id, mag);
if (ProjectToolbar.PENCIL == tool && n_points > 0 && -1 == index && !me.isShiftDown() && !Utils.isControlDown(me)) {
// Check that there are any images -- otherwise may hang. TODO
if (layer_set.getDisplayables(Patch.class).isEmpty()) {
Utils.log("No images are present!");
return;
}
final double scale = layer_set.getVirtualizationScale();
// Ok now with all found images, create a virtual stack that provides access to them all, with caching.
final Worker[] worker = new Worker[2];
final TraceParameters tr_ = tr_map.get(layer_set);
final TraceParameters tr = null == tr_ ? new TraceParameters() : tr_;
if (null == tr_) {
synchronized (tr_map) {
tr_map.put(layer_set, tr);
}
}
if (tr.update) {
worker[0] = new Worker("Preparing Hessian...") {
@Override
public void run() {
startedWorking();
try {
Utils.log("Push ESCAPE key to cancel autotrace anytime.");
final ImagePlus virtual = new LayerStack(layer_set, scale, ImagePlus.GRAY8, Patch.class, display.getDisplayChannelAlphas(), Segmentation.fmp.SNT_invert_image).getImagePlus();
// virtual.show();
final Calibration cal = virtual.getCalibration();
double minimumSeparation = 1;
if (cal != null)
minimumSeparation = Math.min(cal.pixelWidth, Math.min(cal.pixelHeight, cal.pixelDepth));
final ComputeCurvatures hessian = new ComputeCurvatures(virtual, minimumSeparation, null, cal != null);
hessian.run();
tr.virtual = virtual;
// tr.scale = scale;
tr.hessian = hessian;
tr.update = false;
} catch (final Exception e) {
IJError.print(e);
}
finishedWorking();
}
};
Bureaucrat.createAndStart(worker[0], project);
}
final Point2D.Double po = transformPoint(p[0][n_points - 1], p[1][n_points - 1]);
final int start_x = (int) po.x;
final int start_y = (int) po.y;
// 0-based
final int start_z = layer_set.indexOf(layer_set.getLayer(p_layer[n_points - 1]));
// must transform into virtual space
final int goal_x = (int) (x_pd * scale);
final int goal_y = (int) (y_pd * scale);
final int goal_z = layer_set.indexOf(layer);
/*
Utils.log2("x_pd, y_pd : " + x_pd + ", " + y_pd);
Utils.log2("scale: " + scale);
Utils.log2("start: " + start_x + "," + start_y + ", " + start_z);
Utils.log2("goal: " + goal_x + "," + goal_y + ", " + goal_z);
Utils.log2("virtual: " + tr.virtual);
*/
final boolean simplify = me.isAltDown();
worker[1] = new Worker("Tracer - waiting on hessian") {
@Override
public void run() {
startedWorking();
try {
if (null != worker[0]) {
// Wait until hessian is ready
worker[0].join();
}
setTaskName("Tracing path");
final int reportEveryMilliseconds = 2000;
tr.tracer = new TracerThread(tr.virtual, 0, 255, // timeout seconds
120, reportEveryMilliseconds, start_x, start_y, start_z, goal_x, goal_y, goal_z, // reciproal pix values at start and goal
true, tr.virtual.getStackSize() == 1, tr.hessian, null == tr.hessian ? 1 : 4, null, null != tr.hessian);
tr.tracer.addProgressListener(new SearchProgressCallback() {
@Override
public void pointsInSearch(final SearchInterface source, final int inOpen, final int inClosed) {
worker[1].setTaskName("Tracing path: open=" + inOpen + " closed=" + inClosed);
}
@Override
public void finished(final SearchInterface source, final boolean success) {
if (!success) {
Utils.logAll("Could NOT trace a path");
}
}
@Override
public void threadStatus(final SearchInterface source, final int currentStatus) {
// This method gets called every reportEveryMilliseconds
if (worker[1].hasQuitted()) {
source.requestStop();
}
}
});
tr.tracer.run();
final Path result = tr.tracer.getResult();
tr.tracer = null;
if (null == result) {
// : "+
Utils.log("Finding a path failed");
// not public //SearchThread.exitReasonStrings[tracer.getExitReason()]);
return;
}
// TODO: precise_x_positions etc are likely to be broken (calibrated or something)
// Remove bogus points: those at the end with 0,0 coords
int len = result.points;
final double[][] pos = result.getXYZUnscaled();
for (int i = len - 1; i > -1; i--) {
if (0 == pos[0][i] && 0 == pos[1][i]) {
len--;
} else
break;
}
// Transform points: undo scale, and bring to this Polyline AffineTransform:
final AffineTransform aff = new AffineTransform();
/* Inverse order: */
/* 2 */
aff.concatenate(Polyline.this.at.createInverse());
/* 1 */
aff.scale(1 / scale, 1 / scale);
final double[] po = new double[len * 2];
for (int i = 0, j = 0; i < len; i++, j += 2) {
po[j] = pos[0][i];
po[j + 1] = pos[1][i];
}
final double[] po2 = new double[len * 2];
// what a stupid format: consecutive x,y pairs
aff.transform(po, 0, po2, 0, len);
long[] p_layer_ids = new long[len];
double[] pox = new double[len];
double[] poy = new double[len];
for (int i = 0, j = 0; i < len; i++, j += 2) {
// z_positions in 0-(N-1), not in 1-N like slices!
p_layer_ids[i] = layer_set.getLayer((int) pos[2][i]).getId();
pox[i] = po2[j];
poy[i] = po2[j + 1];
}
// Simplify path: to steps of 5 calibration units, or 5 pixels when not calibrated.
if (simplify) {
setTaskName("Simplifying path");
final Object[] ob = Polyline.simplify(pox, poy, p_layer_ids, 10000, layer_set);
pox = (double[]) ob[0];
poy = (double[]) ob[1];
p_layer_ids = (long[]) ob[2];
len = pox.length;
}
// Record the first newly-added autotraced point index:
last_autotrace_start = Polyline.this.n_points;
Polyline.this.appendPoints(pox, poy, p_layer_ids, len);
Polyline.this.repaint(true, null);
Utils.logAll("Added " + len + " new points.");
} catch (final Exception e) {
IJError.print(e);
}
finishedWorking();
}
};
Bureaucrat.createAndStart(worker[1], project);
index = -1;
return;
}
if (ProjectToolbar.PEN == tool || ProjectToolbar.PENCIL == tool) {
if (Utils.isControlDown(me) && me.isShiftDown()) {
final long lid = Display.getFrontLayer(this.project).getId();
if (-1 == index || lid != p_layer[index]) {
index = findNearestPoint(x_p, y_p, layer_id);
}
if (-1 != index) {
// delete point
removePoint(index);
index = -1;
repaint(false, null);
}
// In any case, terminate
return;
}
if (// disable!
-1 != index && layer_id != p_layer[index])
// disable!
index = -1;
else // if no conditions are met, attempt to add point
if (-1 == index && !me.isShiftDown() && !me.isAltDown()) {
// add a new point
index = addPoint(x_p, y_p, layer_id, mag);
is_new_point = true;
repaint(false, null);
return;
}
}
}
Also used :
Path(tracing.Path)
SearchInterface(tracing.SearchInterface)
ComputeCurvatures(features.ComputeCurvatures)
Calibration(ij.measure.Calibration)
ImagePlus(ij.ImagePlus)
NoninvertibleTransformException(java.awt.geom.NoninvertibleTransformException)
Point2D(java.awt.geom.Point2D)
LayerStack(ini.trakem2.imaging.LayerStack)
TracerThread(tracing.TracerThread)
Worker(ini.trakem2.utils.Worker)
AffineTransform(java.awt.geom.AffineTransform)
SearchProgressCallback(tracing.SearchProgressCallback)
Aggregations
ArrayList (java.util.ArrayList)11
Layer (ini.trakem2.display.Layer)10
Worker (ini.trakem2.utils.Worker)10
LayerSet (ini.trakem2.display.LayerSet)9
ZDisplayable (ini.trakem2.display.ZDisplayable)9
DBObject (ini.trakem2.persistence.DBObject)9
ImagePlus (ij.ImagePlus)8
Display (ini.trakem2.display.Display)8
Displayable (ini.trakem2.display.Displayable)8
HashSet (java.util.HashSet)8
Project (ini.trakem2.Project)7
GenericDialog (ij.gui.GenericDialog)6
Roi (ij.gui.Roi)6
ProjectThing (ini.trakem2.tree.ProjectThing)6
Rectangle (java.awt.Rectangle)6
File (java.io.File)6
DirectoryChooser (ij.io.DirectoryChooser)5
Calibration (ij.measure.Calibration)5
Future (java.util.concurrent.Future)5
JPopupMenu (javax.swing.JPopupMenu)5
