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common objects for orbit image analysis
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2016 Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, 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 dateFormat = new ThreadLocal() {
@Override
protected SimpleDateFormat initialValue() {
return new SimpleDateFormat("HH:mm:ss");
}
};
// HCS specific
public final static String PlateFormat_1536 = "1536";
public final static String PlateFormat_384 = "384";
public final static String PlateFormat_96 = "96";
public static int MAX_INTENS_16BIT = 65535;
// LIMS specific
public static List generateBiosampleMetas(LIMSBioSample sample, RawMetaFactoryFile rmff) {
List rmList = new ArrayList();
rmList.add(rmff.createMetaAuto("Name", sample.getSampleId()));
rmList.add(rmff.createMetaAuto("Type", sample.getBiotype()));
rmList.add(rmff.createMetaAuto("Study ID", sample.getStudyId()));
rmList.add(rmff.createMetaAuto("Study IVV", sample.getStudyIVV()));
rmList.add(rmff.createMetaAuto("Study Group", sample.getStudyGroup()));
rmList.add(rmff.createMetaAuto("Study Phase", sample.getStudyPhase()));
rmList.add(rmff.createMetaAuto("Container Type", sample.getContainerType()));
rmList.add(rmff.createMetaAuto("Container Location", sample.getContainerLocation()));
rmList.add(rmff.createMetaAuto("Create User", sample.getCreUser()));
rmList.add(rmff.createMetaDate("Create Date", sample.getCreDate()));
rmList.add(rmff.createMetaAuto("Comment", sample.getComment()));
Map metas = sample.getMetaData();
for (String key : metas.keySet()) {
rmList.add(rmff.createMetaAuto(key, metas.get(key)));
}
Map parentMetas = sample.getParentMetaData();
for (String key : parentMetas.keySet()) {
rmList.add(rmff.createMetaAuto(key, parentMetas.get(key)));
}
return rmList;
}
// other
/**
* returns the ending of the filename (and converts it toLower is toLower = true)
*
* @return
*/
public static String getExtension(String filename, boolean toLower) {
String ext = null;
String s = filename;
int i = s.lastIndexOf('.');
if (i > 0 && i < s.length() - 1) {
ext = s.substring(i + 1);
}
if (ext != null && toLower) ext = ext.toLowerCase();
return ext;
}
/**
* returns the lower case ending of the filename
*
* @return
*/
public static String getExtension(String filename) {
return getExtension(filename, true);
}
/**
* returns the lowercase ending of the filename
*
* @param f
* @return
*/
public static String getExtension(File f) {
return getExtension(f.getName());
}
/**
* Formats fileSize (in byte) in B/KB/MB/GB
*
* @param fileSize
* @return
*/
public static String formatFileSize(long fileSize) {
String unit = "B";
double size = 0;
if (fileSize < 1024) {
unit = "B";
size = (double) fileSize;
} else if (fileSize < (1024 * 1024L)) {
unit = "KB";
size = (double) fileSize / (1024L);
} else if (fileSize < (1024 * 1024 * 1024L)) {
unit = "MB";
size = (double) fileSize / (1024 * 1024L);
} else {
unit = "GB";
size = (double) fileSize / (1024 * 1024 * 1024L);
}
return String.format("%1$.2f", size) + " " + unit;
}
/**
* formats time in seconds.
*
* @param s
* @return
*/
public static String formatTime(double s) {
String d = "";
if (s > 3600 * 24) {
d = Integer.toString((int) (s / (3600 * 24))) + "d +";
s -= 3600 * 24;
}
return d + dateFormat.get().format(new Date((long) s * 1000L - 3600000));
}
/**
* formats a millisec time
*
* @param ms
* @return
*/
public static String formatTime(long ms) {
double s = ms / 1000d;
return formatTime(s);
}
public static void centerComponent(Component comp) {
Toolkit toolkit = comp.getToolkit();
Dimension size = toolkit.getScreenSize();
comp.setLocation((size.width - comp.getWidth()) / 2, (size.height - comp.getHeight()) / 2);
}
/**
* checks if a file ends with tiff or tif
*
* @param filename
* @return
*/
public static boolean isTiffFileStrict(String filename) {
String ext = getExtension(filename);
if (ext != null) {
return ext.equals("tiff") || ext.equals("tif");
}
return false;
}
/**
* checks if a file ends with tiff, tif, svs, ndpi
*
* @param filename
* @return
*/
public static boolean isTiffFile(String filename) {
String ext = getExtension(filename);
if (ext != null) {
return ext.equals("tiff") || ext.equals("tif") || ext.equals("svs") || ext.equals("ndpi");
}
return false;
}
public static boolean isTiffFile(File f) {
if (f == null) return false;
return isTiffFile(f.getName());
}
public static boolean isNDPIFile(File f) {
if (f == null) return false;
return isNDPIFile(f.getName());
}
public static boolean isNDPIFile(String filename) {
if (filename == null) return false;
return filename.toLowerCase().endsWith(".ndpi");
}
public static boolean isSVSFile(String filename) {
if (filename == null) return false;
return filename.toLowerCase().endsWith(".svs");
}
public static boolean isTifFile(String filename) {
if (filename == null) return false;
return filename.toLowerCase().endsWith(".tif") || filename.toLowerCase().endsWith(".tiff");
}
public static boolean isZVIFile(String filename) {
if (filename == null) return false;
return filename.toLowerCase().endsWith(".zvi");
}
public static boolean isLIFFile(String filename) {
if (filename == null) return false;
return filename.toLowerCase().endsWith(".lif");
}
public static boolean isZVIFile(File f) {
if (f == null) return false;
return isZVIFile(f.getName());
}
public static boolean isLIFFile(File f) {
if (f == null) return false;
return isLIFFile(f.getName());
}
public static boolean isImageFile(String filename) {
String extension = getExtension(filename);
if (extension != null) {
return extension.equals("tiff") ||
extension.equals("tif") ||
extension.equals("jpeg") ||
extension.equals("jpg") ||
extension.equals("jp2") ||
extension.equals("j2k") ||
extension.equals("gif") ||
extension.equals("png") ||
extension.equals("bmp") ||
extension.equals("svs") ||
extension.equals("zvi") ||
extension.equals("lif") ||
extension.equals("ndpi") ||
extension.equals("ndpis") ||
extension.equals("dcm") ||
extension.equals("pcx") ||
extension.equals("psd");
}
return false;
}
public static boolean isStandardImageFile(String filename) {
String extension = getExtension(filename);
if (extension != null) {
return extension.equals("jpeg") ||
extension.equals("jpg") ||
extension.equals("gif") ||
extension.equals("png") ||
extension.equals("bmp");
}
return false;
}
public static boolean isImageFile(File f) {
if (f == null) return false;
return isImageFile(f.getName());
}
public static HashMap getHashFromMetaList(List rmList) {
if (rmList == null) return null;
HashMap rmHash = new HashMap(rmList.size());
for (RawMeta rm : rmList) {
if (rm.getValue() == null) continue;
rmHash.put(rm.getName(), rm);
}
return rmHash;
}
public static String getContentStr(URL url) {
StringBuilder sb = new StringBuilder();
BufferedReader in = null;
try {
in = new BufferedReader(
new InputStreamReader(url.openStream()));
String inputLine;
while ((inputLine = in.readLine()) != null) {
sb.append(inputLine + "\n");
}
in.close();
} catch (IOException e) {
e.printStackTrace();
} finally {
try {
if (in != null) in.close();
} catch (Exception e) {
}
}
return sb.toString();
}
public static void getContentToOutputstream(URL url, OutputStream out) {
byte[] bytes = new byte[1024];
InputStream is = null;
try {
is = new BufferedInputStream(url.openStream());
int bytesRead = 0;
while ((bytesRead = is.read(bytes, 0, bytes.length)) > 0) {
out.write(bytes, 0, bytesRead);
}
out.flush();
} catch (IOException e) {
e.printStackTrace();
} finally {
try {
if (is != null) is.close();
} catch (Exception e) {
}
}
}
/**
* Returns the content of the url or of the redirected page (one-time redirection only)
*
* @param url
* @return
*/
public String getRedirectedContentStr(URL url) {
StringBuilder sb = new StringBuilder();
BufferedReader in = null;
try {
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
String newUrl = conn.getHeaderField("Location"); // the random page will redirect us...
conn.disconnect();
URL url2 = newUrl != null ? new URL(newUrl) : url;
in = new BufferedReader(
new InputStreamReader(url2.openStream()));
String inputLine;
while ((inputLine = in.readLine()) != null) {
sb.append(inputLine + "\n");
}
in.close();
} catch (IOException e) {
e.printStackTrace();
} finally {
try {
if (in != null) in.close();
} catch (Exception e) {
}
}
return sb.toString();
}
public static String packStringList(List strList) {
StringBuilder sb = new StringBuilder();
for (int i = 0; i < strList.size(); i++) {
sb.append(strList.get(i));
if (i < strList.size() - 1) {
sb.append(";");
}
}
return sb.toString();
}
public static List unpackStringList(String string) {
List list = new ArrayList();
String[] split = string.split(";");
if (split != null && split.length > 0 && !split[0].isEmpty()) {
for (String s : split) {
list.add(s);
}
}
return list;
}
}