use of ini.trakem2.tree.LayerThing in project TrakEM2 by trakem2.
the class Project method createNewProject.
private static Project createNewProject(Loader loader, boolean ask_for_template, TemplateThing template_root, boolean clone_ids) {
Project project = new Project(loader);
// Utils.log2("ask_for_template: " + ask_for_template);
if (ask_for_template)
template_root = project.loader.askForXMLTemplate(project);
if (null == template_root) {
template_root = new TemplateThing("anything");
} else if (clone_ids) {
// the given template_root belongs to another project from which we are cloning
template_root = template_root.clone(project, true);
}
// else, use the given template_root as is.
// create tree
project.template_tree = new TemplateTree(project, template_root);
project.root_tt = template_root;
// collect unique TemplateThing instances
synchronized (project.ht_unique_tt) {
project.ht_unique_tt.clear();
project.ht_unique_tt.putAll(template_root.getUniqueTypes(new HashMap<String, TemplateThing>()));
}
// add all TemplateThing objects to the database, recursively
if (!clone_ids)
template_root.addToDatabase(project);
// else already done when cloning the root_tt
// create a non-database bound template for the project Thing
TemplateThing project_template = new TemplateThing("project");
project.ht_unique_tt.put("project", project_template);
project_template.addChild(template_root);
// create the project Thing, to be root of the whole project thing tree
try {
project.root_pt = new ProjectThing(project_template, project, project);
} catch (Exception e) {
IJError.print(e);
}
// create the user objects tree
project.project_tree = new ProjectTree(project, project.root_pt);
// create the layer's tree
project.createLayerTemplates();
// initialized with default values, and null parent to signal 'root'
project.layer_set = new LayerSet(project, "Top Level", 0, 0, null, 2048, 2048);
try {
project.root_lt = new LayerThing(Project.layer_set_template, project, project.layer_set);
project.layer_tree = new LayerTree(project, project.root_lt);
} catch (Exception e) {
project.remove();
IJError.print(e);
}
// create the project control window, containing the trees in a double JSplitPane
// beware that this call is asynchronous, dispatched by the SwingUtilities.invokeLater to avoid havok with Swing components.
ControlWindow.add(project, project.template_tree, project.project_tree, project.layer_tree);
// register
al_open_projects.add(project);
return project;
}
use of ini.trakem2.tree.LayerThing in project TrakEM2 by trakem2.
the class Layer method exportXML.
@Override
public void exportXML(final StringBuilder sb_body, final String indent, final XMLOptions options) {
final String in = indent + "\t";
// 1 - open tag
sb_body.append(indent).append("<t2_layer oid=\"").append(id).append("\"\n").append(in).append(" thickness=\"").append(thickness).append("\"\n").append(in).append(" z=\"").append(z).append("\"\n");
// TODO this search is linear!
final LayerThing lt = project.findLayerThing(this);
String title;
if (null == lt)
title = null;
else
title = lt.getTitle();
if (null == title)
title = "";
// TODO 'title' should be a property of the Layer, not the LayerThing. Also, the LayerThing should not exist: LayerSet and Layer should be directly presentable in a tree. They are not Things as in "objects of the sample", but rather, structural necessities such as Patch.
sb_body.append(in).append(" title=\"").append(title).append("\"\n");
sb_body.append(indent).append(">\n");
// 2 - export children
if (null != al_displayables) {
for (final Displayable d : al_displayables) {
d.exportXML(sb_body, in, options);
}
}
// 3 - close tag
sb_body.append(indent).append("</t2_layer>\n");
}
use of ini.trakem2.tree.LayerThing in project TrakEM2 by trakem2.
the class Layer method getPrintableTitle.
/**
* Returns a title such as 018__4-K4_2__z1.67 , which is [layer_set index]__[title]__[z coord] . The ordinal number starts at 1 and finishes at parent's length, inclusive.
*/
public String getPrintableTitle() {
final LayerThing lt = project.findLayerThing(this);
if (null == lt)
return toString();
String title = lt.getTitle();
if (null == title)
title = "";
else
title = title.replace(' ', '_');
final StringBuilder sb = new StringBuilder().append(parent.indexOf(this) + 1);
final int s_size = Integer.toString(parent.size()).length();
while (sb.length() < s_size) {
sb.insert(0, '0');
}
sb.append('_').append('_').append(title).append('_').append('_').append('z').append(Utils.cutNumber(this.z, 3, true));
return sb.toString();
}
use of ini.trakem2.tree.LayerThing in project TrakEM2 by trakem2.
the class Project method openDBProject.
/**
* Open a TrakEM2 project from the database. Queries the database for existing projects and if more than one, asks which one to open.
*/
public static Project openDBProject() {
if (Utils.wrongImageJVersion())
return null;
DBLoader loader = new DBLoader();
if (!loader.isReady())
return null;
// check connection
if (!loader.isConnected()) {
Utils.showMessage("Can't talk to database.");
loader.destroy();
return null;
}
// query the database for existing projects
Project[] projects = loader.getProjects();
if (null == projects) {
Utils.showMessage("Can't talk to database (null list of projects).");
loader.destroy();
return null;
}
Project project = null;
if (0 == projects.length) {
Utils.showMessage("No projects in this database.");
loader.destroy();
return null;
} else if (1 == projects.length) {
project = projects[0];
} else {
// ask to choose one
String[] titles = new String[projects.length];
for (int i = 0; i < projects.length; i++) {
titles[i] = projects[i].title;
}
GenericDialog gd = new GenericDialog("Choose");
gd.addMessage("Choose project to open:");
gd.addChoice("project: ", titles, titles[titles.length - 1]);
gd.showDialog();
if (gd.wasCanceled()) {
loader.destroy();
return null;
}
project = projects[gd.getNextChoiceIndex()];
}
// check if the selected project is open already
for (final Project p : al_open_projects) {
if (loader.isIdenticalProjectSource(p.loader) && p.id == project.id && p.title.equals(project.title)) {
Utils.showMessage("A project with title " + p.title + " and id " + p.id + " from the same database is already open.");
loader.destroy();
return null;
}
}
// now, open the selected project
// assign loader
project.loader = loader;
// grab the XML template
TemplateThing template_root = loader.getTemplateRoot(project);
if (null == template_root) {
Utils.showMessage("Failed to retrieve the template tree.");
project.destroy();
return null;
}
project.template_tree = new TemplateTree(project, template_root);
synchronized (project.ht_unique_tt) {
project.ht_unique_tt.clear();
project.ht_unique_tt.putAll(template_root.getUniqueTypes(new HashMap<String, TemplateThing>()));
}
// create the project Thing, to be root of the whole user Thing tree (and load all its objects)
// to collect all created displayables, and then reassign to the proper layers.
HashMap<Long, Displayable> hs_d = new HashMap<Long, Displayable>();
try {
// create a template for the project Thing
TemplateThing project_template = new TemplateThing("project");
project.ht_unique_tt.put("project", project_template);
project_template.addChild(template_root);
project.root_pt = loader.getRootProjectThing(project, template_root, project_template, hs_d);
// restore parent/child and attribute ownership and values (now that all Things exist)
project.root_pt.setup();
} catch (Exception e) {
Utils.showMessage("Failed to retrieve the Thing tree for the project.");
IJError.print(e);
project.destroy();
return null;
}
// create the user objects tree
project.project_tree = new ProjectTree(project, project.root_pt);
// restore the expanded state of each node
loader.restoreNodesExpandedState(project);
// create the layers templates
project.createLayerTemplates();
// fetch the root layer thing and the root layer set (will load all layers and layer sets, with minimal contents of patches; gets the basic objects -profile, pipe, etc.- from the project.root_pt). Will open all existing displays for each layer.
LayerThing root_layer_thing = null;
try {
root_layer_thing = loader.getRootLayerThing(project, project.root_pt, Project.layer_set_template, Project.layer_template);
if (null == root_layer_thing) {
project.destroy();
Utils.showMessage("Could not retrieve the root layer thing.");
return null;
}
// set the child/parent relationships now that everything exists
root_layer_thing.setup();
project.layer_set = (LayerSet) root_layer_thing.getObject();
if (null == project.layer_set) {
project.destroy();
Utils.showMessage("Could not retrieve the root layer set.");
return null;
}
// set the active layer to each ZDisplayable
project.layer_set.setup();
// debug:
// Utils.log2("$$$ root_lt: " + root_layer_thing + " ob: " + root_layer_thing.getObject().getClass().getName() + "\n children: " + ((LayerSet)root_layer_thing.getObject()).getLayers().size());
project.layer_tree = new LayerTree(project, root_layer_thing);
project.root_lt = root_layer_thing;
} catch (Exception e) {
Utils.showMessage("Failed to retrieve the Layer tree for the project.");
IJError.print(e);
project.destroy();
return null;
}
// if all when well, register as open:
al_open_projects.add(project);
// create the project control window, containing the trees in a double JSplitPane
ControlWindow.add(project, project.template_tree, project.project_tree, project.layer_tree);
// now open the displays that were stored for later, if any:
Display.openLater();
return project;
}
use of ini.trakem2.tree.LayerThing in project TrakEM2 by trakem2.
the class Project method createSubproject.
/**
* Create a new subproject for the given layer range and ROI.
* Create a new Project using the given project as template. This means the DTD of the given project is copied, as well as the storage and mipmaps folders; everything else is empty in the new project.
*/
public Project createSubproject(final Rectangle roi, final Layer first, final Layer last, final boolean ignore_hidden_patches) {
try {
// The order matters.
final Project pr = new Project(new FSLoader(this.getLoader().getStorageFolder()));
pr.id = this.id;
// copy properties
pr.title = this.title;
pr.ht_props.putAll(this.ht_props);
// copy template
pr.root_tt = this.root_tt.clone(pr, true);
pr.template_tree = new TemplateTree(pr, pr.root_tt);
synchronized (pr.ht_unique_tt) {
pr.ht_unique_tt.clear();
pr.ht_unique_tt.putAll(root_tt.getUniqueTypes(new HashMap<String, TemplateThing>()));
}
TemplateThing project_template = new TemplateThing("project");
project_template.addChild(pr.root_tt);
pr.ht_unique_tt.put("project", project_template);
// create the layers templates
pr.createLayerTemplates();
// copy LayerSet and all involved Displayable objects
// (A two-step process to provide the layer_set pointer and all Layer pointers to the ZDisplayable to copy and crop.)
pr.layer_set = (LayerSet) this.layer_set.clone(pr, first, last, roi, false, true, ignore_hidden_patches);
LayerSet.cloneInto(this.layer_set, first, last, pr, pr.layer_set, roi, true);
// create layer tree
pr.root_lt = new LayerThing(Project.layer_set_template, pr, pr.layer_set);
pr.layer_tree = new LayerTree(pr, pr.root_lt);
// add layer nodes to the layer tree (solving chicken-and-egg problem)
pr.layer_set.updateLayerTree();
// copy project tree
pr.root_pt = this.root_pt.subclone(pr);
pr.project_tree = new ProjectTree(pr, pr.root_pt);
// not copying node expanded state.
// register
al_open_projects.add(pr);
// add to gui:
ControlWindow.add(pr, pr.template_tree, pr.project_tree, pr.layer_tree);
// Above, the id of each object is preserved from this project into the subproject.
// The abstract structure should be copied in full regardless, without the basic objects
// included if they intersect the roi.
// Regenerate mipmaps (blocks GUI from interaction other than navigation)
pr.loader.regenerateMipMaps(pr.layer_set.getDisplayables(Patch.class));
pr.restartAutosaving();
return pr;
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
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