Examples with Loader ini.trakem2.persistence.Loader used on opensource projects

Example 1 with Loader

use of ini.trakem2.persistence.Loader in project TrakEM2 by trakem2.

the class DBLoader method getRootLayerThing.

/**
 * Fetches the root LayerSet, fills it with children (recursively) and uses the profiles, pipes, etc., from the project_thing. Will reconnect the links and open Displays for the layers that have one.
 */
public LayerThing getRootLayerThing(Project project, ProjectThing project_thing, TemplateThing layer_set_tt, TemplateThing layer_tt) {
    synchronized (db_lock) {
        // connect if disconnected
        if (!connectToDatabase()) {
            return null;
        }
        HashMap hs_pt = new HashMap();
        unpack(project_thing, hs_pt);
        LayerThing root = null;
        try {
            // -1 signals root
            ResultSet r = connection.prepareStatement("SELECT * FROM ab_things WHERE project_id=" + project.getId() + " AND type='layer_set' AND parent_id=-1").executeQuery();
            if (r.next()) {
                root = getLayerThing(r, project, hs_pt, layer_set_tt, layer_tt);
            }
            r.close();
            if (null == root) {
                Utils.log("Loader.getRootLayerThing: can't find it for project id=" + project.getId());
                return null;
            }
            // Redo the links! hs_pt contains now all Displayable objects.
            ResultSet rl = connection.prepareStatement("SELECT * FROM ab_links WHERE project_id=" + project.getId()).executeQuery();
            while (rl.next()) {
                Long id1 = new Long(rl.getLong("id1"));
                Long id2 = new Long(rl.getLong("id2"));
                Object ob1 = hs_pt.get(id1);
                Object ob2 = hs_pt.get(id2);
                if (null != ob1 && null != ob2) {
                    Displayable d = (Displayable) ob1;
                    d.link((Displayable) ob2, false);
                } else {
                    Utils.log("Loader: broken link between " + id1 + " and " + id2);
                }
            }
            rl.close();
        } catch (Exception e) {
            IJError.print(e);
            return null;
        }
        return root;
    }
}

Example 2 with Loader

use of ini.trakem2.persistence.Loader in project TrakEM2 by trakem2.

the class PatchStack method decacheAll.

/**
 * Remove all awts and snaps from the loader's cache, and repaint (which will remake as many as needed)
 */
public void decacheAll() {
    // record already flushed imps, since there can be shared imps among Patch instances (for example in stacks)
    final HashSet<ImagePlus> hs = new HashSet<ImagePlus>();
    final Loader loader = patch[currentSlice - 1].getProject().getLoader();
    for (int i = 0; i < patch.length; i++) {
        ImagePlus imp = loader.fetchImagePlus(patch[i]);
        if (hs.contains(imp))
            continue;
        else if (null != imp)
            hs.add(imp);
        loader.decache(imp);
        loader.flushMipMaps(patch[i].getId());
        Display.repaint(patch[i].getLayer(), patch[i], 0);
    }
}

Example 3 with Loader

use of ini.trakem2.persistence.Loader in project TrakEM2 by trakem2.

the class PatchStack method invertLookupTable.

public void invertLookupTable() {
    Loader loader = patch[currentSlice - 1].getProject().getLoader();
    ImagePlus imp = loader.fetchImagePlus(patch[currentSlice - 1]);
    imp.getProcessor().invert();
    Display.repaint(patch[currentSlice - 1].getLayer(), patch[currentSlice - 1], 0);
    // TODO if the database updates are too much, then one could put a "save" button somewhere that shows as "unsaved" (red?) when there are unsaved changes.
    patch[currentSlice - 1].updateInDatabase("tiff_working");
    // just saved
    imp.changes = false;
}

Example 4 with Loader

use of ini.trakem2.persistence.Loader in project TrakEM2 by trakem2.

the class PatchStack method createColor256Copy.

// WARNING This method will fail if the stack has slices of different dimensions
/**
 * Does not respect local transform of the patches, this is intended for confocal stacks.
 */
public ImagePlus createColor256Copy() {
    final Rectangle box = patch[0].getBoundingBox();
    final int width = box.width;
    final int height = box.height;
    Loader loader = patch[0].getProject().getLoader();
    // the montage, in RGB
    patch[0].getProject().getLoader().releaseToFit(4 * patch.length * width * height);
    final ColorProcessor montage = new ColorProcessor(width * patch.length, height);
    for (int i = 0; i < patch.length; i++) {
        montage.insert(this.stack.getProcessor(i + 1), i * width, 0);
    }
    final MedianCut mc = new MedianCut(montage);
    loader.releaseToFit(patch.length * width * height);
    ImageProcessor m2 = mc.convertToByte(256);
    final ImageStack st = new ImageStack(width, height);
    for (int i = 0; i < patch.length; i++) {
        m2.setRoi(i * width, 0, width, height);
        loader.releaseToFit(width * height);
        st.addSlice(null, m2.crop());
    }
    ImagePlus imp = new ImagePlus("color256", st);
    imp.setCalibration(patch[0].getLayer().getParent().getCalibrationCopy());
    // imp.getCalibration().pixelDepth = patch[0].getLayer().getThickness();
    return imp;
}

Example 5 with Loader

use of ini.trakem2.persistence.Loader in project TrakEM2 by trakem2.

the class PatchStack method createGray8Copy.

// WARNING This method will fail if the stack has slices of different dimensions
/**
 * Does not respect local transform of the patches, this is intended for confocal stacks.
 */
public ImagePlus createGray8Copy() {
    final Rectangle box = patch[0].getBoundingBox();
    final int width = box.width;
    final int height = box.height;
    // compute minimum bounding box
    ImageStack st = new ImageStack(width, height);
    Loader loader = patch[0].getProject().getLoader();
    for (int i = 1; i < patch.length; i++) {
        loader.releaseToFit(width * height);
        st.addSlice(Integer.toString(i), this.stack.getProcessor(i).convertToByte(true));
    }
    ImagePlus imp = new ImagePlus("byte", st);
    imp.setCalibration(patch[0].getLayer().getParent().getCalibrationCopy());
    // imp.getCalibration().pixelDepth = patch[0].getLayer().getThickness();
    return imp;
}