use of ini.trakem2.tree.TemplateThing in project TrakEM2 by trakem2.
the class ProjectTiler method createRetiledSibling.
/**
* Take a {@link Project}, a size for the image tiles, and a target directory,
* and create a new copy of the current project in that folder but with the underlying
* images converted to tiles with a translation-only transform (saved as zipped TIFFs,
* with extension ".tif.zip").
* The new, returned {@link Project} represents the given project but with much
* simpler transformations (just translation) for the images and a defined size for
* the latter, which helps a lot regarding storage space of the XML (and parsing and
* saving time) and performance when browsing layers (keep in mind that, for a 32k x 32k image,
* at 100% zoom one would have to load a 32k x 32k image and render just a tiny bit
* of it). The copied Project preserves the ID of the {@link Layer}s of the original
* {@link Project}, as well as the dimensions; this means the copy is a sibling of
* the original, and it is possible to send segmentations from one to the other "as is"
* (directly, without having to transform along with the images which would not be possible).
*
* Image files are stored as
*
* The non-image objects of the given project are copied into the new project as well.
*
* @param srcProject The project to create a sibling of.
* @param targetDirectory The directory in which to create all the necessary data and mipmap folders for the new Project.
* @param tileWidth The width of the tiles to create for the data of the new project.
* @param tileHeight The height of the tiles.
* @param exportImageType Any of {@link ImagePlus#GRAY8}, {@link ImagePlus#GRAY16} or {@link ImagePlus#COLOR_RGB}, otherwise an {@link IllegalArgumentException} is thrown.
* @param onlyVisibleImages Whether to consider visible images only.
* @param nExportThreads Number of layers to export in parallel. Use a small number when original images are huge (such as larger than 4096 x 4096 pixels).
* @param createMipMaps Whether to generate the mipmaps when done or not.
*
* @throws Exception IllegalArgumentException When {@code exportImageType} is not {@link ImagePlus#GRAY16} or {@link ImagePlus#COLOR_RGB}, or when the directory exists and cannot be written to.
*/
public static final Project createRetiledSibling(final Project srcProject, final String targetDirectory, final int tileWidth, final int tileHeight, final int exportImageType, final boolean onlyVisibleImages, final int nExportThreads, final boolean createMipMaps) throws Exception {
// Validate exportImageType
switch(exportImageType) {
case ImagePlus.GRAY8:
case ImagePlus.GRAY16:
case ImagePlus.COLOR_RGB:
break;
default:
throw new IllegalArgumentException("Can only accept GRAY8, GRAY16 or COLOR_RGB as values for 'exportImageType'!");
}
// Validate targetDirectory
final File fdir = new File(targetDirectory);
if (fdir.exists()) {
if (!fdir.isDirectory() || !fdir.canWrite())
throw new IllegalArgumentException("Invalid directory: not a directory or cannot write to: " + targetDirectory);
} else {
if (!fdir.mkdirs()) {
throw new IllegalArgumentException("Cannot create directory at: " + targetDirectory);
}
}
final String targetDir = Utils.fixDir(targetDirectory);
// Create "data" directory
final String dataDir = new StringBuilder(targetDir).append("data/").toString();
final File fDataDir = new File(dataDir);
if (fDataDir.exists() && (!fDataDir.isDirectory() || !fDataDir.canWrite())) {
throw new IllegalArgumentException("Cannot create or write to 'data' directory in the targetDirectory at: " + targetDir);
} else {
fDataDir.mkdir();
}
// Create new Project, plain, without any automatic creation of a Layer or a Display
final Project newProject = Project.newFSProject("blank", null, targetDir, false);
final LayerSet newLayerSet = newProject.getRootLayerSet();
newLayerSet.setCalibration(srcProject.getRootLayerSet().getCalibrationCopy());
if (!createMipMaps) {
Utils.log("MipMaps are DISABLED:\n --> When done, right-click and choose 'Display - Properties...' and enable mipmaps,\n and then run 'Project - Regenerate all mipmaps'\n");
newProject.getLoader().setMipMapsRegeneration(false);
Utils.log("mipmaps enabled? " + newProject.getLoader().isMipMapsRegenerationEnabled());
}
// Copy the Template Tree of types
newProject.resetRootTemplateThing(srcProject.getRootTemplateThing().clone(newProject, true), null);
for (final TemplateThing tt : newProject.getRootTemplateThing().getUniqueTypes(new HashMap<String, TemplateThing>()).values()) {
newProject.addUniqueType(tt);
}
// Clone layers with the exact same IDs, so that the two projects are siblings at the layer-level:
// (Being siblings allows for treelines, arealists, etc. to be transferred from one to another "as is").
final List<Layer> srcLayers = srcProject.getRootLayerSet().getLayers();
final List<Layer> newLayers = new ArrayList<Layer>();
for (final Layer srcLayer : srcLayers) {
final Layer newLayer = new Layer(newProject, srcLayer.getId(), srcLayer.getZ(), srcLayer.getThickness());
// to update the ID generator in FSLoader
newLayer.addToDatabase();
newLayerSet.add(newLayer);
newLayers.add(newLayer);
newProject.getRootLayerThing().addChild(new LayerThing(newProject.getRootLayerThing().getChildTemplate("layer"), newProject, newLayer));
}
newProject.getLayerTree().rebuild();
// Update the LayerSet
newLayerSet.setDimensions(srcProject.getRootLayerSet().getLayerWidth(), srcProject.getRootLayerSet().getLayerHeight(), LayerSet.NORTHWEST);
Display.updateLayerScroller(newLayerSet);
Display.update(newLayerSet);
// Copy template from the src Project
// (It's done after creating layers so the IDs will not collide with those of the Layers)
newProject.resetRootTemplateThing(srcProject.getRootTemplateThing().clone(newProject, false), null);
// Export tiles as new Patch instances, creating new image files in disk
final int numThreads = Math.max(1, Math.min(nExportThreads, Runtime.getRuntime().availableProcessors()));
int i = 0;
for (final Layer srcLayer : srcLayers) {
Utils.log("Processing layer " + (i + 1) + "/" + srcLayers.size() + " -- " + new Date());
final int layerIndex = i++;
// Create subDirectory
final String dir = dataDir + "/" + layerIndex + "/";
new File(dir).mkdir();
// Create a new Layer with the same Z and thickness
final Layer newLayer = newLayers.get(layerIndex);
// Export layer tiles
final ArrayList<Patch> patches = new ArrayList<Patch>();
if (ImagePlus.GRAY16 == exportImageType) {
Process.progressive(ExportUnsignedShort.exportTiles(srcLayer, tileWidth, tileHeight, onlyVisibleImages), new CountingTaskFactory<Callable<ExportedTile>, Patch>() {
public Patch process(final Callable<ExportedTile> c, final int index) {
try {
// Create the tile
final ExportedTile t = c.call();
// Store the file
final String title = layerIndex + "-" + index;
final String path = dir + title + ".tif.zip";
final ImagePlus imp = new ImagePlus(title, t.sp);
if (!new FileSaver(imp).saveAsZip(path)) {
throw new Exception("Could not save tile: " + path);
}
// Create a Patch
final Patch patch = new Patch(newProject, title, t.x, t.y, imp);
patch.setLocked(true);
newProject.getLoader().addedPatchFrom(path, patch);
return patch;
} catch (Exception e) {
IJError.print(e);
return null;
}
}
}, patches, numThreads);
} else {
// GRAY8 or COLOR_RGB: created from mipmaps
Process.progressive(tileSequence(srcLayer, tileWidth, tileHeight, onlyVisibleImages), new CountingTaskFactory<Rectangle, Patch>() {
@Override
public Patch process(final Rectangle bounds, final int index) {
try {
// Create the tile
final ImagePlus imp = srcLayer.getProject().getLoader().getFlatImage(srcLayer, bounds, 1.0, -1, exportImageType, Patch.class, null, false, Color.black);
final String title = layerIndex + "-" + index;
imp.setTitle(title);
final String path = dir + title + ".tif.zip";
if (!new FileSaver(imp).saveAsZip(path)) {
throw new Exception("Could not save tile: " + path);
}
// Create a Patch
final Patch patch = new Patch(newProject, title, bounds.x, bounds.y, imp);
patch.setLocked(true);
newProject.getLoader().addedPatchFrom(path, patch);
return patch;
} catch (Exception e) {
IJError.print(e);
return null;
}
}
}, patches, numThreads);
}
// Add all Patches to the new Layer
for (final Patch p : patches) {
newLayer.add(p);
}
}
// Copy all segmentations "As is"
final ProjectThing root = srcProject.getRootProjectThing();
if (null != root.getChildren() && !root.getChildren().isEmpty()) {
final ProjectThing source_pt = srcProject.getRootProjectThing().getChildren().get(0);
// "As is"
final int transfer_mode = 0;
final ProjectThing landing_parent = newProject.getRootProjectThing();
srcProject.getProjectTree().rawSendToSiblingProject(source_pt, transfer_mode, newProject, landing_parent);
}
// Copy all floating text labels
i = 0;
for (final Layer srcLayer : srcLayers) {
for (final DLabel srcLabel : srcLayer.getAll(DLabel.class)) {
newLayers.get(i++).add(srcLabel.clone(newProject, false));
}
}
if (createMipMaps) {
final LinkedList<Future<?>> fus = new LinkedList<Future<?>>();
final int batch = Runtime.getRuntime().availableProcessors();
for (final Layer newLayer : newLayers) {
for (final Patch p : newLayer.getAll(Patch.class)) {
fus.add(p.updateMipMaps());
// Don't build-up too much
if (fus.size() > batch * 3) {
while (fus.size() > batch) {
try {
fus.removeFirst().get();
} catch (Exception e) {
IJError.print(e);
}
}
}
}
}
Utils.wait(fus);
}
// Save:
newProject.saveAs(targetDir + "exported.xml", false);
return newProject;
}
use of ini.trakem2.tree.TemplateThing in project TrakEM2 by trakem2.
the class TMLHandler method startElement.
public void startElement(String namespace_URI, String local_name, String qualified_name, Attributes attributes) throws SAXException {
if (null == loader)
return;
// Utils.log2("startElement: " + qualified_name);
this.counter++;
if (0 == counter % 100) {
// davi-experimenting: don't talk so much when you have > 600,000 patches to load!
Utils.showStatus("Loading " + counter, false);
}
try {
// failsafe:
qualified_name = qualified_name.toLowerCase();
final HashMap<String, String> ht_attributes = new HashMap<String, String>();
for (int i = attributes.getLength() - 1; i > -1; i--) {
ht_attributes.put(attributes.getQName(i).toLowerCase(), attributes.getValue(i));
}
// get the id, which whenever possible it's the id of the encapsulating Thing object. The encapsulated object id is the oid
// The type is specified by the qualified_name
Thing thing = null;
if (0 == qualified_name.indexOf("t2_")) {
if (qualified_name.equals("t2_display")) {
// store for later, until the layers exist
if (open_displays)
al_displays.add(ht_attributes);
} else {
// a Layer, LayerSet or Displayable object
thing = makeLayerThing(qualified_name, ht_attributes);
if (null != thing) {
if (null == root_lt && thing.getObject() instanceof LayerSet) {
root_lt = (LayerThing) thing;
}
}
}
} else if (qualified_name.equals("project")) {
if (null != this.root_pt) {
Utils.log("WARNING: more than one project definitions.");
return;
}
// Create the project
this.project = new Project(Long.parseLong(ht_attributes.remove("id")), ht_attributes.remove("title"));
// temp, but will be the same anyway
this.project.setTempLoader(this.loader);
this.project.parseXMLOptions(ht_attributes);
// register id
this.project.addToDatabase();
String title = ht_attributes.get("title");
if (null != title)
this.project.setTitle(title);
// Add all unique TemplateThing types to the project
for (Iterator<TemplateThing> it = root_tt.getUniqueTypes(new HashMap<String, TemplateThing>()).values().iterator(); it.hasNext(); ) {
this.project.addUniqueType(it.next());
}
this.project.addUniqueType(this.project_tt);
this.root_pt = new ProjectThing(this.project_tt, this.project, this.project);
// Add a project pointer to all template things
this.root_tt.addToDatabase(this.project);
thing = root_pt;
} else if (qualified_name.startsWith("ict_transform") || qualified_name.startsWith("iict_transform")) {
makeCoordinateTransform(qualified_name, ht_attributes);
} else if (!qualified_name.equals("trakem2")) {
// Any abstract object
thing = makeProjectThing(qualified_name, ht_attributes);
}
if (null != thing) {
// get the previously open thing and add this new_thing to it as a child
int size = al_open.size();
if (size > 0) {
Thing parent = al_open.get(size - 1);
parent.addChild(thing);
// Utils.log2("Adding child " + thing + " to parent " + parent);
}
// add the new thing as open
al_open.add(thing);
}
} catch (Exception e) {
IJError.print(e);
skip = true;
}
}
use of ini.trakem2.tree.TemplateThing in project TrakEM2 by trakem2.
the class LayerThing method getPopupItems.
public JMenuItem[] getPopupItems(ActionListener listener) {
JMenuItem item;
ArrayList<JMenuItem> al_items = new ArrayList<JMenuItem>();
JMenu menu = new JMenu("Add...");
ArrayList<TemplateThing> tc = template.getChildren();
if (null != tc) {
for (Iterator<TemplateThing> it = tc.iterator(); it.hasNext(); ) {
// changing underscores for spaces, for the 'layer_set' type to read nice
item = new JMenuItem("new " + it.next().getType().replace('_', ' '));
item.addActionListener(listener);
menu.add(item);
}
if (template.getType().replaceAll("_", " ").equals("layer set")) {
item = new JMenuItem("many new layers...");
item.addActionListener(listener);
menu.add(item);
}
}
if (0 != menu.getItemCount()) {
al_items.add(menu);
}
// Add a "Show" for all except the root LayerSet
if (null != parent) {
item = new JMenuItem("Show");
item.addActionListener(listener);
al_items.add(item);
}
if (template.getType().equals("layer")) {
// adjust z and thickness
item = new JMenuItem("Adjust...");
item.addActionListener(listener);
al_items.add(item);
}
item = new JMenuItem("Rename...");
item.addActionListener(listener);
al_items.add(item);
if (template.getType().replaceAll("_", " ").equals("layer set")) {
if (null != parent) {
item = new JMenuItem("Show centered in Display");
item.addActionListener(listener);
al_items.add(item);
}
item = new JMenuItem("Resize LayerSet...");
item.addActionListener(listener);
al_items.add(item);
LayerSet layer_set = (LayerSet) object;
final boolean empty = 0 == layer_set.getLayers().size();
item = new JMenuItem("Autoresize LayerSet");
item.addActionListener(listener);
al_items.add(item);
if (empty)
item.setEnabled(false);
item = new JMenuItem("Translate layers in Z...");
item.addActionListener(listener);
al_items.add(item);
if (empty)
item.setEnabled(false);
item = new JMenuItem("Reverse layer Z coords...");
item.addActionListener(listener);
al_items.add(item);
if (empty)
item.setEnabled(false);
item = new JMenuItem("Reset layer Z and thickness");
item.addActionListener(listener);
al_items.add(item);
if (empty)
item.setEnabled(false);
item = new JMenuItem("Search...");
item.addActionListener(listener);
al_items.add(item);
if (empty)
item.setEnabled(false);
}
item = new JMenuItem("Import stack...");
// contains layers already, wouldn't know where to put it!
if (template.getType().replaceAll("_", " ").equals("layer set") && 0 != ((LayerSet) object).getLayers().size())
item.setEnabled(false);
item.addActionListener(listener);
al_items.add(item);
if (template.getType().equals("layer")) {
item = new JMenuItem("Import grid...");
item.addActionListener(listener);
al_items.add(item);
item = new JMenuItem("Import sequence as grid...");
item.addActionListener(listener);
al_items.add(item);
item = new JMenuItem("Import from text file...");
item.addActionListener(listener);
al_items.add(item);
}
// add a delete to all except the root LayerSet
if (null != parent) {
al_items.add(new JMenuItem(""));
item = new JMenuItem("Delete...");
item.addActionListener(listener);
al_items.add(item);
}
JMenuItem[] items = new JMenuItem[al_items.size()];
al_items.toArray(items);
return items;
}
use of ini.trakem2.tree.TemplateThing in project TrakEM2 by trakem2.
the class LayerTree method addLayer.
/**
* Used by the Loader.importStack and the "many new layers" command.
*/
public void addLayer(LayerSet layer_set, Layer layer) {
if (null == layer_set || null == layer)
return;
try {
// find the node that contains the LayerSet
DefaultMutableTreeNode root_node = (DefaultMutableTreeNode) this.getModel().getRoot();
LayerThing root_lt = (LayerThing) root_node.getUserObject();
Thing thing = null;
if (root_lt.getObject().equals(layer_set))
thing = root_lt;
else
thing = root_lt.findChild(layer_set);
DefaultMutableTreeNode parent_node = DNDTree.findNode(thing, this);
if (null == parent_node) {
Utils.log("LayerTree: LayerSet not found.");
return;
}
LayerThing parent_thing = (LayerThing) parent_node.getUserObject();
double z = layer.getZ();
// find the node whose 'z' is larger than z, and add the Layer before that.
int n = parent_node.getChildCount();
int i = 0;
for (; i < n; i++) {
DefaultMutableTreeNode child_node = (DefaultMutableTreeNode) parent_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 the 'i' layer which has a larger z
break;
}
TemplateThing tt = parent_thing.getChildTemplate("layer");
if (null == tt) {
Utils.log("LayerTree: Null template Thing!");
return;
}
LayerThing new_thing = new LayerThing(tt, layer.getProject(), layer);
// Add the new_thing to the tree
if (null != new_thing) {
parent_thing.addChild(new_thing);
DefaultMutableTreeNode new_node = new DefaultMutableTreeNode(new_thing);
// TODO when changing the Z of a layer, the insertion is proper but an empty space is left //Utils.log("LayerTree: inserting at: " + i);
((DefaultTreeModel) this.getModel()).insertNodeInto(new_node, parent_node, i);
TreePath treePath = new TreePath(new_node.getPath());
this.scrollPathToVisible(treePath);
this.setSelectionPath(treePath);
}
} catch (Exception e) {
IJError.print(e);
}
}
use of ini.trakem2.tree.TemplateThing 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);
}
}
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