use of ini.trakem2.display.Display3D in project TrakEM2 by trakem2.
the class Display3D method show.
/**
* Scan the {@link ProjectThing} children and assign the renderable ones to an existing {@link Display3D} for their {@link LayerSet}, or open a new one. If {@code true == wait && -1 != resample}, then the method returns only when the mesh/es have been added.
*/
public static Future<Vector<Future<Content>>> show(final ProjectThing pt, final boolean wait, final int resample) {
if (null == pt)
return null;
final Future<Vector<Future<Content>>> fu = launchers.submit(new Callable<Vector<Future<Content>>>() {
@Override
public Vector<Future<Content>> call() {
// Scan the given ProjectThing for 3D-viewable items
// So: find arealist, pipe, ball, and profile_list types
final HashSet<ProjectThing> hs = pt.findBasicTypeChildren();
if (null == hs || 0 == hs.size()) {
Utils.logAll("Node " + pt + " does not contain any 3D-displayable children");
return null;
}
// Remove profile if it lives under a profile_list
for (final Iterator<ProjectThing> it = hs.iterator(); it.hasNext(); ) {
final ProjectThing pt = it.next();
if (null != pt.getObject() && pt.getObject().getClass() == Profile.class && pt.getParent().getType().equals("profile_list")) {
it.remove();
}
}
setWaitingCursor();
// Start new scheduler to publish/add meshes to the 3D Viewer every 5 seconds and when done.
final Hashtable<Display3D, Vector<Content>> contents = new Hashtable<Display3D, Vector<Content>>();
final ScheduledExecutorService updater = Executors.newScheduledThreadPool(1);
final AtomicInteger counter = new AtomicInteger();
updater.scheduleWithFixedDelay(new Runnable() {
@Override
public void run() {
// Obtain a copy of the contents queue
final HashMap<Display3D, Vector<Content>> m = new HashMap<Display3D, Vector<Content>>();
synchronized (contents) {
m.putAll(contents);
contents.clear();
}
if (m.isEmpty())
return;
// Add all to the corresponding Display3D
for (final Map.Entry<Display3D, Vector<Content>> e : m.entrySet()) {
e.getKey().universe.addContentLater(e.getValue());
counter.getAndAdd(e.getValue().size());
}
Utils.showStatus(new StringBuilder("Rendered ").append(counter.get()).append('/').append(hs.size()).toString());
}
}, 100, 4000, TimeUnit.MILLISECONDS);
// A list of all generated Content objects
final Vector<Future<Content>> list = new Vector<Future<Content>>();
for (final Iterator<ProjectThing> it = hs.iterator(); it.hasNext(); ) {
// obtain the Displayable object under the node
final ProjectThing child = it.next();
final Object obc = child.getObject();
final Displayable displ = obc.getClass().equals(String.class) ? null : (Displayable) obc;
if (null != displ) {
if (displ.getClass().equals(Profile.class)) {
// handled by profile_list Thing
continue;
}
if (!displ.isVisible()) {
Utils.log("Skipping non-visible node " + displ);
continue;
}
}
// obtain the containing LayerSet
final Display3D d3d;
if (null != displ)
d3d = Display3D.get(displ.getLayerSet());
else if (child.getType().equals("profile_list")) {
final ArrayList<ProjectThing> al_children = child.getChildren();
if (null == al_children || 0 == al_children.size())
continue;
// else, get the first Profile and get its LayerSet
d3d = Display3D.get(((Displayable) ((ProjectThing) al_children.get(0)).getObject()).getLayerSet());
} else {
Utils.log("Don't know what to do with node " + child);
d3d = null;
}
if (null == d3d) {
Utils.log("Could not get a proper 3D display for node " + displ);
// java3D not installed most likely
return null;
}
boolean already;
synchronized (d3d.ht_pt_meshes) {
already = d3d.ht_pt_meshes.containsKey(child);
}
if (already) {
if (child.getObject() instanceof ZDisplayable) {
Utils.log("Updating 3D view of " + child.getObject());
} else {
Utils.log("Updating 3D view of " + child);
}
}
list.add(d3d.executors.submit(new Callable<Content>() {
@Override
public Content call() {
Content c = null;
try {
c = d3d.createMesh(child, displ, resample).call();
Vector<Content> vc;
synchronized (contents) {
vc = contents.get(d3d);
if (null == vc)
vc = new Vector<Content>();
contents.put(d3d, vc);
}
vc.add(c);
} catch (final Exception e) {
IJError.print(e);
}
return c;
}
}));
// If it's the last one:
if (!it.hasNext()) {
// Add the concluding task, that waits on all and shuts down the scheduler
d3d.executors.submit(new Runnable() {
@Override
public void run() {
// Wait until all are done
for (final Future<Content> c : list) {
try {
c.get();
} catch (final Throwable t) {
IJError.print(t);
}
}
try {
// Shutdown scheduler and execute remaining tasks
for (final Runnable r : updater.shutdownNow()) {
r.run();
}
} catch (final Throwable e) {
IJError.print(e);
}
// Reset cursor
doneWaiting();
Utils.showStatus(new StringBuilder("Done rendering ").append(counter.get()).append('/').append(hs.size()).toString());
}
});
}
}
return list;
}
});
if (wait && -1 != resample) {
try {
fu.get();
} catch (final Throwable t) {
IJError.print(t);
}
}
return fu;
}
use of ini.trakem2.display.Display3D in project TrakEM2 by trakem2.
the class Display3D method showVolume.
public static void showVolume(final Patch p) {
final Display3D d3d = get(p.getLayerSet());
d3d.adjustResampling();
// d3d.universe.resetView();
final String title = makeTitle(p) + " volume";
// remove if present
d3d.universe.removeContent(title);
final PatchStack ps = p.makePatchStack();
final ImagePlus imp = get8BitStack(ps);
final Content ct = d3d.universe.addVoltex(imp, null, title, 0, new boolean[] { true, true, true }, d3d.resample);
setTransform(ct, ps.getPatch(0));
// locks the added content
ct.setLocked(true);
}
use of ini.trakem2.display.Display3D in project TrakEM2 by trakem2.
the class Display3D method removeFrom3D.
/**
* Remove all basic type children contained in {@code pt} and its children, recursively.
*
* @param pt
*/
public static void removeFrom3D(final ProjectThing pt) {
final HashSet<ProjectThing> hs = pt.findBasicTypeChildren();
if (null == hs || 0 == hs.size()) {
Utils.logAll("Nothing to remove from 3D.");
return;
}
// Ignore Profile instances ("profile_list" takes care of them)
for (final ProjectThing child : hs) {
if (child.getByType().equals("profile"))
continue;
// Find the LayerSet
LayerSet lset = null;
if (child.getType().equals("profile_list")) {
if (!child.hasChildren())
continue;
for (final ProjectThing p : child.getChildren()) {
if (null != p.getObject() && p.getObject() instanceof Profile) {
lset = ((Displayable) p.getObject()).getLayerSet();
break;
}
}
if (null == lset)
continue;
} else if (child.getType().equals("profile")) {
// Taken care of by "profile list"
continue;
} else {
final Displayable d = (Displayable) child.getObject();
if (null == d) {
Utils.log("Null object for ProjectThing " + child);
continue;
}
lset = d.getLayerSet();
}
if (null == lset) {
Utils.log("No LayerSet found for " + child);
continue;
}
final Display3D d3d = getDisplay(lset);
if (null == d3d) {
Utils.log("No Display 3D found for " + child);
// no Display3D window open
continue;
}
final String oldTitle = d3d.ht_pt_meshes.remove(child);
if (null == oldTitle) {
Utils.log("Could not find a title for " + child);
continue;
}
Utils.log("Removed from 3D view: " + oldTitle);
d3d.getUniverse().removeContent(oldTitle);
}
}
use of ini.trakem2.display.Display3D in project TrakEM2 by trakem2.
the class Display3D method showOrthoslices.
public static void showOrthoslices(final Patch p) {
final Display3D d3d = get(p.getLayerSet());
d3d.adjustResampling();
// d3d.universe.resetView();
final String title = makeTitle(p) + " orthoslices";
// remove if present
d3d.universe.removeContent(title);
final PatchStack ps = p.makePatchStack();
final ImagePlus imp = get8BitStack(ps);
final Content ct = d3d.universe.addOrthoslice(imp, null, title, 0, new boolean[] { true, true, true }, d3d.resample);
setTransform(ct, ps.getPatch(0));
// locks the added content
ct.setLocked(true);
}
use of ini.trakem2.display.Display3D in project TrakEM2 by trakem2.
the class Compare method variabilityAnalysis.
/**
* @param reference_project If null, then the first one found in the Project.getProjects() lists is used.
* @param regex A String (can be null) to filter objects by, to limit what gets processed.
* If regex is not null, then only ProjectThing nodes with the matching regex are analyzed (shallow: none of their children are questioned, but pipes will be built from them all).
* @param generate_plots Whether to generate the variability plots at all.
* @param show_plots If generate_plots, whether to show the plots in a stack image window or to save them.
* @param show_3D Whether to show any 3D data.
* @param show_condensed_3D If show_3D, whether to show the condensed vector strings, i.e. the "average" pipes.
* @param show_sources_3D If show_3D, whether to show the source pipes from which the condensed vector string was generated.
* @param sources_color_table Which colors to give to the pipes of which Project.
* @param show_envelope_3D If show_3D, whether to generate the variability envelope.
* @param envelope_alpha If show_envelope_3D, the envelope takes an alpha value between 0 (total transparency) and 1 (total opacity)
* @param delta_envelope The delta to resample the envelope to. When smaller than or equal to 1, no envelope resampling occurs.
* @param show_axes_3D If show_3D, whether to display the reference axes as well.
* @param heat_map If show_3D, whether to color the variability with a Fire LUT.
* If not show_condensed_3D, then the variability is shown in color-coded 3D spheres placed at the entry point to the neuropile.
* @param map_condensed If not null, all VectorString3D are put into this map.
* @param projects The projects to use.
*/
public static Bureaucrat variabilityAnalysis(final Project reference_project, final String regex, final String[] ignore, final boolean show_cata_dialog, final boolean generate_plots, final boolean show_plots, final String plot_dir_, final boolean show_3D, final boolean show_condensed_3D, final boolean show_sources_3D, final Map<Project, Color> sources_color_table, final boolean show_envelope_3D, final float envelope_alpha, final double delta_envelope, final int envelope_type, final boolean show_axes_3D, final boolean heat_map, final Map<String, VectorString3D> map_condensed, final Project[] projects) {
// gather all open projects
final Project[] p = null == projects ? Project.getProjects().toArray(new Project[0]) : projects;
// make the reference_project be the first in the array
if (null != reference_project && reference_project != p[0]) {
for (int i = 0; i < p.length; i++) {
if (reference_project == p[i]) {
p[i] = p[0];
p[0] = reference_project;
break;
}
}
}
final Worker worker = new Worker("Comparing all to all") {
@Override
public void run() {
startedWorking();
try {
Utils.log2("Asking for CATAParameters...");
final CATAParameters cp = new CATAParameters();
cp.regex = regex;
cp.delta_envelope = delta_envelope;
cp.envelope_type = envelope_type;
if (show_cata_dialog && !cp.setup(false, regex, true, true)) {
finishedWorking();
return;
}
// so source points are stored in VectorString3D for each resampled and interpolated point
cp.with_source = true;
// Store a series of results, depending on options
final HashMap<String, Display3D> results = new HashMap<String, Display3D>();
String plot_dir = plot_dir_;
if (generate_plots && !show_plots) {
// Save plots
if (null == plot_dir) {
final DirectoryChooser dc = new DirectoryChooser("Choose plots directory");
plot_dir = dc.getDirectory();
if (null == plot_dir) {
finishedWorking();
return;
}
}
if (IJ.isWindows())
plot_dir = plot_dir.replace('\\', '/');
if (!plot_dir.endsWith("/"))
plot_dir += "/";
}
Utils.log2("Gathering chains...");
// Gather chains that do not match the ignore regexes
// will transform them as well to the reference found in the first project in the p array
Object[] ob = gatherChains(p, cp, ignore);
ArrayList<Chain> chains = (ArrayList<Chain>) ob[0];
// to keep track of each project's chains
final ArrayList[] p_chains = (ArrayList[]) ob[1];
ob = null;
if (null == chains) {
finishedWorking();
return;
}
Utils.log2("Collecting bundles...");
final HashMap<Project, HashMap<String, VectorString3D>> axes = new HashMap<Project, HashMap<String, VectorString3D>>();
// Sort out into groups by unique names of lineage bundles
final HashMap<String, ArrayList<Chain>> bundles = new HashMap<String, ArrayList<Chain>>();
for (final Chain chain : chains) {
String title = chain.getCellTitle();
final String t = title.toLowerCase();
// unnamed
if (0 == t.indexOf('[') || 0 == t.indexOf('#'))
continue;
Utils.log("Accepting " + title);
title = title.substring(0, title.indexOf(' '));
// lineage bundle instance chains
ArrayList<Chain> bc = bundles.get(title);
if (null == bc) {
bc = new ArrayList<Chain>();
bundles.put(title, bc);
}
bc.add(chain);
}
Utils.log2("Found " + bundles.size() + " bundles.");
chains = null;
if (null != cp.regex && show_axes_3D && axes.size() < 3) {
// Must find the Mushroom Body lobes separately
final String cp_regex = cp.regex;
cp.regex = "mb";
final Object[] o = gatherChains(p, cp, ignore);
final ArrayList<Chain> lobes = (ArrayList<Chain>) o[0];
Utils.logAll("Found " + lobes.size() + " chains for lobes");
for (final Chain chain : lobes) {
final String t = chain.getCellTitle().toLowerCase();
if (-1 != t.indexOf("peduncle") || -1 != t.indexOf("medial lobe") || -1 != t.indexOf("dorsal lobe")) {
Utils.logAll("adding " + t);
final Project pr = chain.pipes.get(0).getProject();
HashMap<String, VectorString3D> m = axes.get(pr);
if (null == m) {
m = new HashMap<String, VectorString3D>();
axes.put(pr, m);
}
m.put(t, chain.vs);
continue;
}
}
cp.regex = cp_regex;
} else {
Utils.logAll("Not: cp.regex = " + cp.regex + " show_axes_3D = " + show_axes_3D + " axes.size() = " + axes.size());
}
final HashMap<String, VectorString3D> condensed = new HashMap<String, VectorString3D>();
Utils.log2("Condensing each bundle...");
// Condense each into a single VectorString3D
for (final Map.Entry<String, ArrayList<Chain>> entry : bundles.entrySet()) {
final ArrayList<Chain> bc = entry.getValue();
if (bc.size() < 2) {
Utils.log2("Skipping single: " + entry.getKey());
continue;
}
final VectorString3D[] vs = new VectorString3D[bc.size()];
for (int i = 0; i < vs.length; i++) vs[i] = bc.get(i).vs;
final VectorString3D c = condense(cp, vs, this);
c.setCalibration(p[0].getRootLayerSet().getCalibrationCopy());
condensed.put(entry.getKey(), c);
if (this.hasQuitted())
return;
}
// Store:
if (null != map_condensed) {
map_condensed.putAll(condensed);
}
if (generate_plots) {
Utils.log2("Plotting stdDev for each condensed bundle...");
// Y axis: the stdDev at each point, computed from the group of points that contribute to each
for (final Map.Entry<String, VectorString3D> e : condensed.entrySet()) {
final String name = e.getKey();
final VectorString3D c = e.getValue();
final Plot plot = makePlot(cp, name, c);
// FAILS//plot.addLabel(10, cp.plot_height-5, name); // must be added after setting size
if (show_plots)
plot.show();
else if (null != plot_dir)
new FileSaver(plot.getImagePlus()).saveAsPng(plot_dir + name.replace('/', '-') + ".png");
}
}
if (show_3D) {
final HashMap<String, Color> heat_table = new HashMap<String, Color>();
if (heat_map || show_envelope_3D) {
// Create a Fire LUT
final ImagePlus lutimp = new ImagePlus("lut", new ByteProcessor(4, 4));
IJ.run(lutimp, "Fire", "");
final IndexColorModel icm = (IndexColorModel) lutimp.getProcessor().getColorModel();
final byte[] reds = new byte[256];
final byte[] greens = new byte[256];
final byte[] blues = new byte[256];
icm.getReds(reds);
icm.getGreens(greens);
icm.getBlues(blues);
final List<String> names = new ArrayList<String>(bundles.keySet());
Collections.sort(names);
// find max stdDev
double max = 0;
final HashMap<String, Double> heats = new HashMap<String, Double>();
for (final String name : names) {
final VectorString3D vs_merged = condensed.get(name);
if (null == vs_merged) {
Utils.logAll("WARNING could not find a condensed pipe for " + name);
continue;
}
final double[] stdDev = vs_merged.getStdDevAtEachPoint();
// double avg = 0;
// for (int i=0; i<stdDev.length; i++) avg += stdDev[i];
// avg = avg/stdDev.length;
Arrays.sort(stdDev);
// median is more representative than average
final double median = stdDev[stdDev.length / 2];
if (max < median)
max = median;
heats.put(name, median);
}
for (final Map.Entry<String, Double> e : heats.entrySet()) {
final String name = e.getKey();
final double median = e.getValue();
// scale between 0 and max to get a Fire LUT color:
int index = (int) ((median / max) * 255);
if (index > 255)
index = 255;
final Color color = new Color(0xff & reds[index], 0xff & greens[index], 0xff & blues[index]);
Utils.log2(new StringBuilder(name).append('\t').append(median).append('\t').append(reds[index]).append('\t').append(greens[index]).append('\t').append(blues[index]).toString());
heat_table.put(name, color);
}
}
final LayerSet common_ls = new LayerSet(p[0], -1, "Common", 10, 10, 0, 0, 0, 512, 512, false, 2, new AffineTransform());
final Display3D d3d = Display3D.get(common_ls);
float env_alpha = envelope_alpha;
if (env_alpha < 0) {
Utils.log2("WARNING envelope_alpha is invalid: " + envelope_alpha + "\n Using 0.4f instead");
env_alpha = 0.4f;
} else if (env_alpha > 1)
env_alpha = 1.0f;
for (final String name : bundles.keySet()) {
final ArrayList<Chain> bc = bundles.get(name);
final VectorString3D vs_merged = condensed.get(name);
if (null == vs_merged) {
Utils.logAll("WARNING: could not find a condensed vs for " + name);
continue;
}
if (show_sources_3D) {
if (null != sources_color_table) {
final HashSet<String> titles = new HashSet<String>();
for (final Chain chain : bc) {
final Color c = sources_color_table.get(chain.getRoot().getProject());
final String title = chain.getCellTitle();
String t = title;
int i = 2;
while (titles.contains(t)) {
t = title + "-" + i;
i += 1;
}
titles.add(t);
Display3D.addMesh(common_ls, chain.vs, t, null != c ? c : Color.gray);
}
} else {
for (final Chain chain : bc) Display3D.addMesh(common_ls, chain.vs, chain.getCellTitle(), Color.gray);
}
}
if (show_condensed_3D) {
Display3D.addMesh(common_ls, vs_merged, name + "-condensed", heat_map ? heat_table.get(name) : Color.red);
}
if (show_envelope_3D) {
double[] widths = makeEnvelope(cp, vs_merged);
if (cp.delta_envelope > 1) {
vs_merged.addDependent(widths);
vs_merged.resample(cp.delta_envelope);
widths = vs_merged.getDependent(0);
}
Display3D.addMesh(common_ls, vs_merged, name + "-envelope", heat_map ? heat_table.get(name) : Color.red, widths, env_alpha);
} else if (heat_map) {
// Show spheres in place of envelopes, at the starting tip (neuropile entry point)
final double x = vs_merged.getPoints(0)[0];
final double y = vs_merged.getPoints(1)[0];
final double z = vs_merged.getPoints(2)[0];
final double r = 10;
final Color color = heat_table.get(name);
if (null == color) {
Utils.logAll("WARNING: heat table does not have a color for " + name);
continue;
}
final Content sphere = d3d.getUniverse().addMesh(ij3d.Mesh_Maker.createSphere(x, y, z, r), new Color3f(heat_table.get(name)), name + "-sphere", 1);
}
}
if (show_axes_3D) {
for (int i = 0; i < p.length; i++) {
final Map<String, VectorString3D> m = axes.get(p[i]);
if (null == m) {
Utils.log2("No axes found for project " + p[i]);
continue;
}
for (final Map.Entry<String, VectorString3D> e : m.entrySet()) {
Display3D.addMesh(common_ls, e.getValue(), e.getKey() + "-" + i, Color.gray);
}
}
}
results.put("d3d", Display3D.get(common_ls));
}
this.result = results;
Utils.log2("Done.");
} catch (final Exception e) {
IJError.print(e);
} finally {
finishedWorking();
}
}
};
return Bureaucrat.createAndStart(worker, p[0]);
}
Aggregations