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Orbit, a versatile image analysis software for biological image-based quantification
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2018 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see externalRepositoryComputers;
private final static List temporaryUsers; // e.g. annotations of those can be modified by others
private static IImageProvider remoteImageProvider = null; // just for remembering when switching to local filesystem provider
private static IImageProvider localImageProvider = new ImageProviderLocal();
private static ICustomMenu customMenu = null;
private static boolean showLIMSMetas = false;
private static boolean checkVersion = true;
private static String explicitLibDir = null;
private static String localDBFile;
private static boolean localImageCache = true;
static {
try {
Properties props = new Properties();
// defaults
props.put("ImageProvider", "com.actelion.research.orbit.imageprovider.ImageProviderOmero");
props.put("ScaleOut", "com.actelion.research.orbit.imageAnalysis.dal.ScaleoutNoop");
// read properties
readConfigProperties(props);
logger.info("Configured image provider: " + props.getProperty("ImageProvider"));
logger.info("Different image providers can be configured in resources/config.properties or resources/config_custom.properties (priority).");
try {
imageProvider = (IImageProvider) Class.forName(props.getProperty("ImageProvider")).newInstance();
} catch (IllegalStateException e) {
final String m = e.getMessage() + "\n\nOrbit will continue with the fallback local filesystem image provider.";
logger.warn(m);
if (!GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadlessInstance() && !ScaleoutMode.SCALEOUTMODE.get()) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
Object[] options = new Object[]{"Continue", "More Information"};
if (JOptionPane.showOptionDialog(null, m, "Image provider not available, using local filesystem fallback", JOptionPane.YES_NO_OPTION, JOptionPane.INFORMATION_MESSAGE, null, options, options[0]) == JOptionPane.NO_OPTION) {
if (Desktop.isDesktopSupported()) {
try {
Desktop.getDesktop().browse(new URI(OrbitUtils.orbitImageProviderURL));
} catch (Exception e1) {
e1.printStackTrace();
}
}
}
}
});
}
imageProvider = localImageProvider;
}
logger.info("scaleout mode: "+ScaleoutMode.SCALEOUTMODE.get());
// if (localImageCache && ScaleoutMode.SCALEOUTMODE.get()) {
// File tempDir = new File(OrbitUtils.getCurrentDir()+File.separator+"tempimages");
// tempDir.deleteOnExit();
// logger.info("local file cache temp dir: "+tempDir.getAbsolutePath());
// ((ImageProviderOrbit) imageProvider).setLocalImageProvider(new ImageProviderLocalCached(tempDir.getAbsolutePath(), imageProvider));
// }
scaleOut = (IScaleout) Class.forName(props.getProperty("ScaleOut")).newInstance();
String sparkMaster = props.getProperty("SparkMaster", "local[*]");
String strTempUsers = props.getProperty("TemporaryUsers");
temporaryUsers = parseString(strTempUsers);
String strExtRepComp = props.getProperty("ExternalRepositoryComputers");
externalRepositoryComputers = parseString(strExtRepComp);
String strCustomMenu = props.getProperty("CustomMenu");
if (strCustomMenu != null && strCustomMenu.length() > 0) {
customMenu = (ICustomMenu) Class.forName(strCustomMenu).newInstance();
logger.info("Custom Menu: " + customMenu);
}
String strLIMSMetas = props.getProperty("ShowLIMSMetas");
if (strLIMSMetas != null && strLIMSMetas.length() > 0) {
try {
showLIMSMetas = Boolean.parseBoolean(strLIMSMetas);
} catch (Exception e) {
logger.error("cannot parse ShowLIMSMetas value. Should be 'true' or 'false' but is " + strLIMSMetas);
}
logger.info("Show LIMS Metadata: " + showLIMSMetas);
}
String strCheckVersion = props.getProperty("CheckVersion");
if (strCheckVersion != null && strCheckVersion.length() > 0) {
try {
checkVersion = Boolean.parseBoolean(strCheckVersion);
} catch (Exception e) {
logger.error("cannot parse CheckVersion value. Should be 'true' or 'false' but is " + strCheckVersion);
}
logger.debug("CheckVersion: " + strCheckVersion);
}
String explicitLibDirStr = props.getProperty("explicitLibDir");
if (explicitLibDirStr != null && explicitLibDirStr.length() > 0) {
explicitLibDir = explicitLibDirStr;
}
logger.info("image provider: " + imageProvider);
logger.info("scaleOut: " + scaleOut);
if (scaleOut.toString().endsWith("ScaleoutSpark")) {
Class[] paramString = new Class[]{String.class};
scaleOut.getClass().getDeclaredMethod("setMaster", paramString).invoke(scaleOut, new String(sparkMaster));
logger.info("SparkMaster: " + sparkMaster);
}
logger.debug("temporary users: " + temporaryUsers);
logger.debug("external repository computers: " + externalRepositoryComputers);
try {
localDBFile = System.getProperty("user.home") + File.separator + "orbit.db";
String userLocalDB = props.getProperty("localDBFile");
if (userLocalDB != null && userLocalDB.length() > 0) {
localDBFile = userLocalDB;
}
logger.info("local db file: " + localDBFile);
if (!ScaleoutMode.SCALEOUTMODE.get()) {
File dbFile = new File(localDBFile);
if (!dbFile.exists()) {
DAODataFileSQLite.createTable();
DAORawAnnotationSQLite.createTable();
}
// check for column raw_data_dile.series
if (!DAODataFileSQLite.ColumnSeriesExist()) {
DAODataFileSQLite.createColumnSeries();
}
}
} catch (Exception ex) {
logger.error("Could not create the local database file: "+localDBFile, ex);
}
// channelNames -> hue values
String channelHues = props.getProperty("channelHues"); // e.g. channelHues=dapi:203,tritc=50
if (channelHues!=null) {
String[] hues= channelHues.split(",");
if (hues!=null && hues.length>0) {
for (String chanHue: hues) {
String[] nameHue = chanHue.split(":");
if (nameHue!=null && nameHue.length==2) {
try {
float f = Float.parseFloat(nameHue[1].trim());
ChannelToHue.userHueMap.put(nameHue[0].trim().toLowerCase(), f/360f);
logger.info("setting custom channel hue: "+nameHue[0]+": "+nameHue[1]);
} catch (Exception e) {
logger.warn("error parsing hue value "+nameHue[1]+" for channel name "+nameHue[0]);
}
}
}
}
}
// read user channel2hues from preferences
if (!ScaleoutMode.SCALEOUTMODE.get()) {
Preferences channelPrefs = Preferences.userNodeForPackage(ChannelToHue.class);
for (String key: channelPrefs.keys()) {
if (key.startsWith(OrbitUtils.CHANNEL_NAME2HUE)) {
String channelName = key.replaceFirst(OrbitUtils.CHANNEL_NAME2HUE,"").toLowerCase();
float hue = channelPrefs.getFloat(key,-1f);
if (hue>=0f) {
ChannelToHue.userHueMap.put(channelName, hue);
logger.info("setting custom channel hue (preferences): "+channelName+": "+hue);
}
}
}
}
} catch (Exception e) {
throw new RuntimeException(e);
}
}
public static void readConfigProperties(Properties props) throws IOException {
InputStream propsStream;
propsStream = DALConfig.class.getResourceAsStream("/config_custom.properties");
if (propsStream == null) {
propsStream = DALConfig.class.getResourceAsStream("/config.properties");
logger.info("using config file: resources/config.properties ");
} else {
logger.info("using config file: resources/config_custom.properties ");
}
props.load(propsStream);
try {
if (propsStream != null) propsStream.close();
} catch (Exception e) {
logger.warn("cannot close properties stream");
}
}
public static String getLibDir() throws URISyntaxException, UnsupportedEncodingException {
if (explicitLibDir != null) {
logger.info("using explicit lib dir: " + explicitLibDir);
return explicitLibDir;
}
CodeSource codeSource = OrbitUtils.class.getProtectionDomain().getCodeSource();
File jarFile;
if (codeSource.getLocation() != null) {
jarFile = new File(codeSource.getLocation().toURI());
} else {
String path = OrbitUtils.class.getResource(OrbitUtils.class.getSimpleName() + ".class").getPath();
String jarFilePath = path.substring(path.indexOf(":") + 1, path.indexOf("!"));
jarFilePath = URLDecoder.decode(jarFilePath, "UTF-8");
jarFile = new File(jarFilePath);
}
String jarDir = jarFile.getParentFile().getAbsolutePath();
logger.debug("libDir: " + jarDir);
return jarDir;
}
public static IImageProvider getImageProvider() {
return imageProvider;
}
public static void setImageProvider(IImageProvider imageProvider) {
DALConfig.imageProvider = imageProvider;
}
public static IScaleout getScaleOut() {
return scaleOut;
}
public static void setScaleOut(IScaleout scaleOut) {
DALConfig.scaleOut = scaleOut;
}
public static List getExternalRepositoryComputers() {
return externalRepositoryComputers;
}
public static List getTemporaryUsers() {
return temporaryUsers;
}
public static boolean isShowLIMSMetas() {
return showLIMSMetas;
}
public static void setShowLIMSMetas(boolean showLIMSMetas) {
DALConfig.showLIMSMetas = showLIMSMetas;
}
public static boolean isCheckVersion() {
return checkVersion;
}
public static void setCheckVersion(boolean checkVersion) {
DALConfig.checkVersion = checkVersion;
}
public static String getLocalDBFile() {
return localDBFile;
}
/**
* can be null
*/
public static ICustomMenu getCustomMenu() {
return customMenu;
}
private static List parseString(String s) {
List list = new ArrayList<>();
if (s != null && s.length() > 0) {
String[] arr = s.split(",");
if (arr != null && arr.length > 0) {
for (String s1 : arr) {
list.add(s1);
}
}
}
return list;
}
public static boolean isLocalImageProvider() {
return getImageProvider() instanceof ImageProviderLocal;
}
public static boolean onlyLocalImageProviderAvailable() {
return remoteImageProvider == localImageProvider;
}
public static void switchLocalRemoteImageProvider() {
if (isLocalImageProvider()) {
setImageProvider(remoteImageProvider);
} else {
remoteImageProvider = getImageProvider(); // remember
setImageProvider(localImageProvider);
}
logger.info("image provider switched to " + getImageProvider() + " isLocal: " + isLocalImageProvider());
if (OrbitTiledImage2.tileCache!=null) {
OrbitTiledImage2.tileCache.invalidateAll();
}
}
}