Examples with ParameterSettings gdsc.smlm.ij.settings.ParameterSettings used on opensource projects

Example 1 with ParameterSettings

use of gdsc.smlm.ij.settings.ParameterSettings in project GDSC-SMLM by aherbert.

the class BatchPeakFit method setParameters.

/**
	 * Modify the XML document using the specified values for the given parameter. For each value
	 * call the method recursively for the next parameter. If there are no more parameters
	 * then add the XML document to the xmlSettings.
	 * 
	 * @param parameters
	 *            The list of parameters
	 * @param i
	 *            Parameter to process
	 * @param doc
	 *            The XML document containing all the current parameters
	 * @param xmlSettings
	 *            A list of XML parameter settings
	 */
private void setParameters(ArrayList<ParameterSettings> parameters, int i, Document doc, ArrayList<String> xmlSettings) {
    if (i < parameters.size()) {
        ParameterSettings param = parameters.get(i);
        NodeList nodes = doc.getElementsByTagName(param.name);
        if (nodes.getLength() == 1) {
            // For each value, set the parameter and move to the next
            String[] values = param.value.split(",");
            for (String value : values) {
                Node node = nodes.item(0);
                node.setTextContent(value);
                setParameters(parameters, i + 1, doc, xmlSettings);
            }
        } else {
            // Just move to the next parameter
            setParameters(parameters, i + 1, doc, xmlSettings);
        }
    } else {
        // Add the final XML to the parameters to run
        TransformerFactory tf = TransformerFactory.newInstance();
        Transformer transformer;
        try {
            transformer = tf.newTransformer();
            transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
            StringWriter writer = new StringWriter();
            transformer.transform(new DOMSource(doc), new StreamResult(writer));
            xmlSettings.add(writer.getBuffer().toString());
        } catch (TransformerConfigurationException e) {
            e.printStackTrace();
        } catch (TransformerException e) {
            e.printStackTrace();
        }
    }
}

Example 2 with ParameterSettings

use of gdsc.smlm.ij.settings.ParameterSettings in project GDSC-SMLM by aherbert.

the class BatchPeakFit method itemStateChanged.

/*
	 * (non-Javadoc)
	 * 
	 * @see java.awt.event.ItemListener#itemStateChanged(java.awt.event.ItemEvent)
	 */
public void itemStateChanged(ItemEvent e) {
    // When the checkbox is clicked, create a default configuration file and update the
    // GenericDialog with the file location.		
    Checkbox cb = (Checkbox) e.getSource();
    if (cb.getState()) {
        cb.setState(false);
        Document doc = getDefaultSettingsXmlDocument();
        if (doc == null)
            return;
        try {
            // Look for nodes that are part of the fit configuration
            XPathFactory factory = XPathFactory.newInstance();
            XPath xpath = factory.newXPath();
            XPathExpression expr = xpath.compile("//gdsc.smlm.engine.FitEngineConfiguration//*");
            // For each node, add the name and value to the BatchParameters
            BatchSettings batchSettings = new BatchSettings();
            batchSettings.resultsDirectory = System.getProperty("java.io.tmpdir");
            batchSettings.images.add("/path/to/image.tif");
            Object result = expr.evaluate(doc, XPathConstants.NODESET);
            NodeList nodes = (NodeList) result;
            for (int i = 0; i < nodes.getLength(); i++) {
                Node node = nodes.item(i);
                if (// Only nodes with a single text entry
                node.getChildNodes().getLength() == 1) {
                    batchSettings.parameters.add(new ParameterSettings(node.getNodeName(), node.getTextContent()));
                }
            }
            // Save the settings file
            String[] path = Utils.decodePath(configFilenameText.getText());
            OpenDialog chooser = new OpenDialog("Settings_file", path[0], path[1]);
            if (chooser.getFileName() != null) {
                String newFilename = chooser.getDirectory() + chooser.getFileName();
                if (!newFilename.endsWith(".xml"))
                    newFilename += ".xml";
                FileOutputStream fs = null;
                try {
                    fs = new FileOutputStream(newFilename);
                    xs.toXML(batchSettings, fs);
                } finally {
                    if (fs != null) {
                        fs.close();
                    }
                }
                // Update dialog filename
                configFilenameText.setText(newFilename);
            }
        } catch (Exception ex) {
            ex.printStackTrace();
        }
    }
}