Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 61 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class DBLoader method importStackAsPatches.

/**
 * Returns the last Patch.
 */
protected Patch importStackAsPatches(final Project project, final Layer first_layer, final double x, final double y, final ImagePlus imp_stack, final boolean as_copy, final String filepath) {
    double pos_x = Double.MAX_VALUE != x ? x : first_layer.getLayerWidth() / 2 - imp_stack.getWidth() / 2;
    double pos_y = Double.MAX_VALUE != y ? y : first_layer.getLayerHeight() / 2 - imp_stack.getHeight() / 2;
    final double thickness = first_layer.getThickness();
    final String title = Utils.removeExtension(imp_stack.getTitle()).replace(' ', '_');
    Utils.showProgress(0);
    Patch previous_patch = null;
    final int n = imp_stack.getStackSize();
    for (int i = 1; i <= n; i++) {
        Layer layer = first_layer;
        double z = first_layer.getZ() + (i - 1) * thickness;
        // will create new layer if not found
        if (i > 1)
            layer = first_layer.getParent().getLayer(z, thickness, true);
        if (null == layer) {
            Utils.log("Display.importStack: could not create new layers.");
            return null;
        }
        ImageProcessor ip = imp_stack.getStack().getProcessor(i);
        if (as_copy)
            ip = ip.duplicate();
        ImagePlus imp_patch_i = new ImagePlus(title + "__slice=" + i, ip);
        String label = imp_stack.getStack().getSliceLabel(i);
        if (null == label)
            label = "";
        Patch patch = new Patch(project, label + " " + title + " " + i, pos_x, pos_y, imp_patch_i);
        layer.add(patch);
        if (null != previous_patch)
            patch.link(previous_patch);
        previous_patch = patch;
        Utils.showProgress(i * (1.0 / n));
    }
    Utils.showProgress(1.0);
    // return the last Patch
    return previous_patch;
}

Example 62 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class DBLoader method fetchImagePlus.

public ImagePlus fetchImagePlus(Patch p) {
    synchronized (db_lock) {
        long id = p.getId();
        // see if the ImagePlus is cached:
        ImagePlus imp = mawts.get(id);
        if (null != imp) {
            if (null != imp.getProcessor() && null != imp.getProcessor().getPixels()) {
                // may have been flushed by ImageJ, for example when making images from a stack
                return imp;
            } else {
                // can't hurt
                flush(imp);
            }
        }
        // connect if disconnected
        if (!connectToDatabase()) {
            return null;
        }
        releaseMemory2();
        InputStream i_stream = null;
        try {
            // StopWatch sw = new StopWatch();
            ResultSet r = connection.prepareStatement("SELECT tiff_working FROM ab_patches WHERE tiff_working IS NOT NULL AND id=" + id).executeQuery();
            boolean found = false;
            if (r.next()) {
                found = true;
                // sw.elapsed();
                i_stream = r.getBinaryStream("tiff_working");
                // sw.elapsed();
                imp = unzipTiff(i_stream, p.getTitle());
                // sw.elapsed();
                i_stream.close();
                mawts.put(id, imp, (int) Math.max(p.getWidth(), p.getHeight()));
            }
            r.close();
            // if the working is not there, fetch the original instead
            if (!found) {
                r = connection.prepareStatement("SELECT tiff_original FROM ab_patches WHERE id=" + id).executeQuery();
                if (r.next()) {
                    // sw.elapsed();
                    i_stream = r.getBinaryStream("tiff_original");
                    // sw.elapsed();
                    // will apply the preprocessor plugin to it as well
                    imp = unzipTiff(i_stream, p.getTitle());
                    // sw.elapsed();
                    i_stream.close();
                    mawts.put(id, imp, (int) Math.max(p.getWidth(), p.getHeight()));
                }
                r.close();
            }
            // non-destructive contrast: min and max
            if (null != imp) {
            // OBSOLETE and wrong -- but then this whole class is obsolete// p.putMinAndMax(imp);
            }
        } catch (Exception e) {
            IJError.print(e);
            if (null != i_stream) {
                try {
                    i_stream.close();
                } catch (Exception ie) {
                    IJError.print(ie);
                }
            }
            return null;
        }
        return imp;
    }
}

Example 63 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class DBLoader method updateInDatabase.

/**
 * The ImagePlus, if updated, is saved in the 'tiff_working' column always.
 */
private void updateInDatabase(Patch patch, String key) throws Exception {
    if (key.equals("tiff_snapshot")) {
        /* // DEPRECATED, now using mipmaps
			InputStream i_stream = null;
			try {
				ImagePlus imp = new ImagePlus("s", snaps.get(patch.getId())); // not calling fetchSnapshot because old code could end in a loop.
				if (null == imp) {
					Utils.log2("DBLoader: snapshot ImagePlus is null!");
					stmt_update_snap.setNull(1, java.sql.Types.BINARY);
				} else {
					i_stream = createZippedStream(imp);
					stmt_update_snap.setBinaryStream(1, i_stream, i_stream.available());
					flush(imp);
				}
				stmt_update_snap.setLong(2, patch.getId());
				stmt_update_snap.executeUpdate();
			} catch (Exception e) {
				IJError.print(e);
			} finally {
				if (null != i_stream) try { i_stream.close(); } catch (Exception e1) { IJError.print(e1); }
			}
			*/
        return;
    }
    StringBuffer sb = new StringBuffer("UPDATE ab_patches SET ");
    boolean update_imp = false;
    if (key.equals("tiff_working")) {
        sb.append("imp_type=").append(patch.getType()).append(", tiff_working=?");
        update_imp = true;
    } else if (key.equals("remove_tiff_working")) {
        sb.append("tiff_working=NULL");
    } else if (key.equals("min_and_max")) {
        sb.append("min=").append(patch.getMin()).append(", max=").append(patch.getMax());
    } else {
        // try the Displayable level
        updateInDatabase((Displayable) patch, key);
        return;
    }
    PreparedStatement st = connection.prepareStatement(sb.append(" WHERE id=").append(patch.getId()).toString());
    int i = 1;
    InputStream i_stream2 = null;
    try {
        if (update_imp) {
            // WARNING if the cache is very small relative to the size of the images, this strategy may fail
            ImagePlus imp = mawts.get(patch.getId());
            i_stream2 = createZippedStream(imp);
            st.setBinaryStream(i, i_stream2, i_stream2.available());
            // defensive programming: if later I add any other ..
            i++;
        }
        st.executeUpdate();
        if (null != i_stream2)
            i_stream2.close();
    } catch (Exception e) {
        IJError.print(e);
        if (null != i_stream2)
            try {
                i_stream2.close();
            } catch (Exception e2) {
                IJError.print(e2);
            }
    }
}

Example 64 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class DBLoader method fetchOriginal.

public synchronized ImagePlus fetchOriginal(Patch patch) {
    // connect if disconnected
    if (!connectToDatabase()) {
        return null;
    }
    // assume RGB, thus multiply by 4 (an int has 4 bytes)
    long imp_size = (long) (patch.getWidth() * patch.getHeight() * 4);
    releaseToFit(MIN_FREE_BYTES > imp_size ? MIN_FREE_BYTES : imp_size);
    ImagePlus imp = null;
    InputStream i_stream = null;
    try {
        ResultSet r = connection.prepareStatement("SELECT id, tiff_original FROM ab_patches WHERE id=" + patch.getId()).executeQuery();
        if (r.next()) {
            // fetch stream
            i_stream = r.getBinaryStream("tiff_original");
            imp = unzipTiff(i_stream, patch.getTitle());
            i_stream.close();
        }
        r.close();
    } catch (Exception e) {
        Utils.log("Loader.fetchOriginal: ERROR fetching original ImagePlus for Patch id=" + patch.getId());
        IJError.print(e);
        if (null != i_stream) {
            try {
                i_stream.close();
            } catch (Exception ee) {
                Utils.log("Loader.fetchOriginal: could not close stream.");
            }
        }
        return null;
    }
    if (null == imp)
        Utils.log("WARNING fetching a null original");
    return imp;
}

Example 65 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class AmiraImporter method importAmiraLabels.

/**
 * Returns the array of AreaList or null if the file dialog is canceled. The xo,yo is the pivot of reference.
 */
public static Collection<AreaList> importAmiraLabels(Layer first_layer, double xo, double yo, final String default_dir) {
    // open file
    OpenDialog od = new OpenDialog("Choose Amira Labels File", default_dir, "");
    String filename = od.getFileName();
    if (null == filename || 0 == filename.length())
        return null;
    String dir = od.getDirectory();
    if (IJ.isWindows())
        dir = dir.replace('\\', '/');
    if (!dir.endsWith("/"))
        dir += "/";
    String path = dir + filename;
    AmiraMeshDecoder dec = new AmiraMeshDecoder();
    if (!dec.open(path)) {
        YesNoDialog yn = new YesNoDialog("Error", "File was not an Amira labels file.\nChoose another one?");
        if (yn.yesPressed())
            return importAmiraLabels(first_layer, xo, yo, default_dir);
        return null;
    }
    ImagePlus imp = null;
    if (dec.isTable()) {
        Utils.showMessage("Select the other file (the labels)!");
        return null;
    } else {
        FileInfo fi = new FileInfo();
        fi.fileName = filename;
        fi.directory = dir;
        imp = new ImagePlus("Amira", dec.getStack());
        dec.parameters.setParameters(imp);
    }
    return extractAmiraLabels(imp, dec.parameters, first_layer, xo, yo);
}