Example usage for com.mongodb BasicDBList get

Introduction

In this page you can find the example usage for com.mongodb BasicDBList get.

Prototype

public Object get(final String key) 

Source Link

Document

Gets a value at an index.

Usage

From source file:tango.gui.MeasurementDisplayer.java

License:Open Source License

public void setObjects(List selectedObjects) {
    eraseText();//from   ww  w  .  j a v  a 2  s. c o m
    if (currentStructures == null) {
        refreshText();
        return;
    }
    if (selectedObjects == null || selectedObjects.size() == 0) { //display misc & number
        if (currentDBOs != null)
            for (BasicDBObject o : currentDBOs)
                append(o);
        label.setText("structures");
    } else if (selectedObjects.size() == 1) { //display o
        Object3DGui o = (Object3DGui) selectedObjects.get(0);
        append(Core.getExperiment().getConnector().getObject(nucId, o.getChannel().getIdx(), o.getLabel(),
                null));
        label.setText("object");
    } else if (selectedObjects.size() == 2) { //display o2o

        BasicDBObject disp = new BasicDBObject();
        Object3DGui o1 = (Object3DGui) selectedObjects.get(0);
        Object3DGui o2 = (Object3DGui) selectedObjects.get(1);
        int[] selStruct = new int[] { o1.getChannel().getIdx(), o2.getChannel().getIdx() };
        MeasurementKey key = new MeasurementKey(selStruct, MeasurementStructure.ArrayO2O); //currentStructures
        int size;
        int idx1 = 0;
        int idx2 = 0;
        for (int i = 0; i < currentStructures.length; i++) {
            if (currentStructures[i] == o1.getChannel().getIdx())
                idx1 = i;
            if (currentStructures[i] == o2.getChannel().getIdx())
                idx2 = i;
        }
        int idx, idxInv;
        if (idx1 != idx2) {
            idx = (o1.getLabel() - 1) * getCount(o2.getChannel().getIdx()) + o2.getLabel() - 1;
            idxInv = (o2.getLabel() - 1) * getCount(o1.getChannel().getIdx()) + o1.getLabel() - 1;
            size = getCount(o1.getChannel().getIdx()) * getCount(o2.getChannel().getIdx());
        } else {
            idx = (o1.getLabel() - 1) * getCount(o1.getChannel().getIdx())
                    - ((o1.getLabel() - 1) * o1.getLabel()) / 2 + o2.getLabel() - o1.getLabel() - 1;
            idxInv = idx;
            size = getCount(o1.getChannel().getIdx());
            size = size * (size - 1) / 2;
        }
        //System.out.println("idx"+idx+ " idx1:"+o1.getLabel()+ " idx2:"+o2.getLabel()+ " count1:"+getCount(o1.getChannel().getIdx())+ " count2:"+getCount(o2.getChannel().getIdx()));
        for (Map.Entry<MeasurementKey, ArrayList<String>> entry : Core.getExperiment().getKeys().entrySet()) {
            if (entry.getKey().includeO2O(key)) {
                BasicDBObject dbo = o2o.get(entry.getKey());
                if (dbo == null) {
                    dbo = Core.getExperiment().getConnector().getMeasurementStructure(nucId,
                            entry.getKey().getStructures(), entry.getValue(), true)[0];
                    o2o.put(entry.getKey(), dbo);
                }
                for (String k : entry.getValue()) {
                    Object o = dbo.get(k);
                    if (o != null) {
                        if (o instanceof BasicDBList) {
                            BasicDBList list = (BasicDBList) o;
                            if (list.size() == size) {
                                if (entry.getKey().invertedOrder(o1.getChannel().getIdx(),
                                        o2.getChannel().getIdx()))
                                    disp.append(k, list.get(idxInv));
                                else
                                    disp.append(k, list.get(idx));
                            }
                        } else if (size == 1 && o instanceof Number) {
                            disp.append(k, o);
                        }
                        //else disp.append(k, "Wrong Array Size");
                    } else
                        disp.append(k, null);
                }
            }
        }
        append(disp);
        label.setText("object to object");
    } else
        label.setText("");
    refreshText();
}

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From source file:tango.gui.parameterPanel.MultiParameterPanel.java

License:Open Source License

public MultiParameterPanel(Core core, DBObject data, int minNb, int maxNb, Dimension minimumSize,
        PanelDisplayer panelDisplayer, boolean enableTest, Class<T> clazz) {
    this.core = core;
    this.enableTest = enableTest;
    this.minNbRows = maxNb == 1 ? 1 : Math.max(2, minimumSize.height / 40);
    this.maxNb = maxNb;
    this.minNb = minNb;
    this.panelDisplayer = panelDisplayer;
    this.clazz = clazz;
    this.data = data;
    this.panelElements = new ArrayList<PanelElementAbstract>();
    listLayout = new GridLayout(0, 1, 5, 0);
    this.listPanel = new JPanel(listLayout);
    this.listPanel.setMinimumSize(minimumSize);
    this.add = new JButton("Add");
    if (maxNb > 1) {
        Box addJP = Box.createHorizontalBox();
        addJP.add(Box.createHorizontalStrut(5));
        addJP.add(add);/*w w w .  ja  va2s.  c o m*/
        addJP.add(Box.createHorizontalGlue());
        listPanel.add(addJP);
        add.addActionListener(this);
    }
    if (this.data != null && maxNb > 1) {
        BasicDBList list = (BasicDBList) data;
        for (int i = 0; i < list.size(); i++) {
            addElement((BasicDBObject) list.get(i), i);
        }
    } else if (maxNb == 1) {
        if (this.data != null)
            addElement((BasicDBObject) data, 0);
        else
            addElement(null, 0);
    } else if (minNb > 0) {
        for (int i = 0; i < minNb; i++) {
            addElement(null, i);
        }
    }
}

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From source file:tango.mongo.MongoConnector.java

License:Open Source License

public synchronized ImageHandler getInputImage(ObjectId field_id, int idx) {
    BasicDBObject query = new BasicDBObject("field_id", field_id).append("fileRank", idx);
    GridFSDBFile f = this.gfsField.findOne(query);
    if (f != null) {
        ImageHandler res = createImage(f);
        if (res != null) {
            return res;
        }/*ww w.  jav  a 2  s  .  c  om*/
    }
    // open from directory
    BasicDBObject field = this.getField(field_id);
    String error = "could'nt open file:" + idx + " from field:" + field.getString("name")
            + " please relink files by launching the command \"import files\"";
    if (field.containsField("files")) {
        BasicDBList files = (BasicDBList) field.get("files");
        if (files.size() > 1) { // separated files
            if (idx >= files.size()) {
                IJ.log(error);
            } else {
                BasicDBObject fileObj = (BasicDBObject) files.get(idx);
                File file = new File(fileObj.getString("path"));
                if (file.exists()) {
                    return ImageOpener.OpenChannel(file, 0, 0, 0);
                }

            }
        } else {
            BasicDBObject fileObj = (BasicDBObject) files.get(0);
            File file = new File(fileObj.getString("path"));
            if (file.exists()) {
                return ImageOpener.OpenChannel(file, idx, fileObj.getInt("series"),
                        fileObj.getInt("timePoint"));
            }
        }
    } else {
        IJ.log(error);
    }

    return null;
}

---

From source file:tango.mongo.MongoConnector.java

License:Open Source License

public synchronized byte[] createInputImageThumbnail(ObjectId field_id, int idx) {
    BasicDBObject query = new BasicDBObject("field_id", field_id).append("fileRank", idx);
    GridFSDBFile f = this.gfsField.findOne(query);
    if (f != null) {
        ImageHandler res = createImage(f);
        if (res != null) {
            return res.getThumbNail(Field.tmbSize, Field.tmbSize);
        }/* w  w w  . j a va2 s.  c o m*/
    }
    // open from directory
    BasicDBObject field = this.getField(field_id);
    String error = "could'nt open file:" + idx + " from field:" + field.getString("name")
            + " please relink files by launching the command \"import files\"";
    if (field.containsField("files")) {
        BasicDBList files = (BasicDBList) field.get("files");
        if (files.size() > 1) { // separated files
            if (idx >= files.size()) {
                IJ.log(error);
            } else {
                BasicDBObject fileObj = (BasicDBObject) files.get(idx);
                File file = new File(fileObj.getString("path"));
                if (file.exists()) {
                    return ImageOpener.openThumbnail(file, 0, 0, 0, Field.tmbSize, Field.tmbSize);
                }

            }
        } else {
            BasicDBObject fileObj = (BasicDBObject) files.get(0);
            File file = new File(fileObj.getString("path"));
            if (file.exists()) {
                return ImageOpener.openThumbnail(file, idx, fileObj.getInt("series"),
                        fileObj.getInt("timePoint"), Field.tmbSize, Field.tmbSize);
            }
        }
    } else {
        IJ.log(error);
    }
    return null;
}

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From source file:tango.mongo.MongoUtils.java

License:Open Source License

public static int[] getIntArray(DBObject dbo, String key) {
    //IJ.log("mongoutils:"+dbo.get(key));
    if (!dbo.containsField(key))
        return null;
    Object o = dbo.get(key);//from  w w  w.  j  av a 2s . co m
    if (o instanceof BasicDBList) {
        BasicDBList list = ((BasicDBList) dbo.get(key));
        int[] res = new int[list.size()];
        for (int i = 0; i < list.size(); i++) {
            res[i] = (Integer) (list.get("" + i));
        }
        return res;
    } else if (o instanceof int[])
        return (int[]) o;
    else
        return new int[] { (Integer) o };
}

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From source file:tango.mongo.MongoUtils.java

License:Open Source License

public static double[] getDoubleArray(DBObject dbo, String key) {
    if (!dbo.containsField(key))
        return null;
    BasicDBList list = ((BasicDBList) dbo.get(key));
    double[] res = new double[list.size()];
    for (int i = 0; i < list.size(); i++) {
        res[i] = (Double) (list.get("" + i));
    }/*from  ww w. j  a v a 2s.  c o m*/
    return res;
}

---

From source file:tango.mongo.MongoUtils.java

License:Open Source License

public static float[] getFloatArray(BasicDBList list, String key) {
    float[] res = new float[list.size()];
    boolean field = false;
    for (int i = 0; i < list.size(); i++) {
        BasicDBObject o = ((BasicDBObject) list.get(i));
        if (o.containsField(key)) {
            field = true;//from   w  w  w  . j ava  2s .c  o  m
            res[i] = (float) o.getDouble(key);
        }
    }
    return field ? res : null;
}

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From source file:tango.parameter.MultiParameter.java

License:Open Source License

@Override
public void dbGet(BasicDBObject dbo) {
    BasicDBObject subDBO = (BasicDBObject) dbo.get(id);
    if (subDBO == null)
        return;/*from www .j ava2s  . c o  m*/
    nb.dbGet(subDBO);
    majParameters(nb.getValue());
    Object o = subDBO.get("parameters");
    if (o != null) {
        BasicDBList list = (BasicDBList) o;
        int size = Math.min(parameters.size(), list.size()); // case of invalid parametrization 
        for (int i = 0; i < size; i++) {
            Parameter[] ps = parameters.get(i);
            BasicDBObject subSubDBO = (BasicDBObject) list.get(i);
            for (Parameter p : ps)
                p.dbGet(subSubDBO);
        }
    }
    toggleVisibility(!subDBO.getBoolean("isCollapsed", false));
    majPanel();
}

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From source file:tango.plugin.filter.PostFilterSequence.java

License:Open Source License

public PostFilterSequence(BasicDBObject type, int nbCPUs, boolean verbose) {
    if (type == null || !type.containsField("postFilters"))
        return;/*from  ww w.ja v a  2s  .  c om*/
    BasicDBList prefilters = (BasicDBList) type.get("postFilters");
    filters = new ArrayList<PostFilter>(prefilters.size());
    for (int i = 0; i < prefilters.size(); i++) {
        Object o = prefilters.get(i);
        if (o != null) {
            BasicDBObject data = (BasicDBObject) o;
            if (!data.getBoolean("isActivated", true)) {
                filters.add(new DummyPostFilter());
                continue;
            }
            PostFilter f = PluginFactory.getPostFilter(data.getString("method"));
            if (f != null) {
                Parameter[] parameters = f.getParameters();
                for (Parameter p : parameters)
                    p.dbGet(data);
                filters.add(f);
                f.setMultithread(nbCPUs);
                f.setVerbose(verbose);
            }
        }
    }
}

---

From source file:tango.plugin.filter.PreFilterSequence.java

License:Open Source License

public PreFilterSequence(BasicDBObject settings, int nbCPUs, boolean verbose) {
    if (settings == null || !settings.containsField("preFilters"))
        return;//from  www.ja  v a 2s  .c o  m
    BasicDBList prefilters = (BasicDBList) settings.get("preFilters");
    filters = new ArrayList<PreFilter>(prefilters.size());
    for (int i = 0; i < prefilters.size(); i++) {
        //IJ.log(i+"");
        Object o = prefilters.get(i);
        if (o != null) {
            BasicDBObject data = (BasicDBObject) o;
            //IJ.log("preFilter:"+data);
            if (!data.getBoolean("isActivated", true)) {
                filters.add(new DummyPreFilter());
                continue;
            }
            PreFilter f = PluginFactory.getPreFilter(data.getString("method"));
            if (f != null) {
                //IJ.log("preFilter loaded:"+f.getId());
                Parameter[] parameters = f.getParameters();
                for (Parameter p : parameters)
                    p.dbGet(data);
                filters.add(f);
                f.setMultithread(nbCPUs);
                f.setVerbose(verbose);
            }
        }
    }
}

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