com.github.celldynamics.quimp.utils.QuimpToolsCollection Maven / Gradle / Ivy
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QuimP software, a set of plugins for ImageJ to quantify spatio-temporal patterns of fluorescently labeled proteins in the cortex of moving cells.
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package com.github.celldynamics.quimp.utils;
import java.io.IOException;
import java.net.URL;
import java.text.SimpleDateFormat;
import java.time.Instant;
import java.time.format.DateTimeFormatter;
import java.time.temporal.TemporalAccessor;
import java.util.Arrays;
import java.util.Date;
import java.util.Enumeration;
import java.util.jar.Attributes;
import java.util.jar.Manifest;
import org.apache.commons.lang3.text.WordUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.github.celldynamics.quimp.Outline;
import com.github.celldynamics.quimp.PropertyReader;
import com.github.celldynamics.quimp.QuimP;
import com.github.celldynamics.quimp.QuimpVersion;
import com.github.celldynamics.quimp.Vert;
/**
* Collection of tools used across QuimP.
*
* @author Richard
* @author p.baniukiewicz
*/
public class QuimpToolsCollection {
/**
* The Constant LOGGER.
*/
static final Logger LOGGER = LoggerFactory.getLogger(QuimpToolsCollection.class.getName());
/**
* Message returned by {@link #getQuimPBuildInfo()} if info is not found in jar.
*/
public static final String defNote = "0.0.0";
/**
* Prepare info plate for QuimP.
*
* @return QuimP version
*
* @see #getFormattedQuimPversion(QuimpVersion)
*/
public String getQuimPversion() {
QuimpVersion quimpBuildInfo = getQuimPBuildInfo();
return getFormattedQuimPversion(quimpBuildInfo);
}
/**
* Prepare info plate for QuimP.
*
* It contains version, names, etc. By general QuimpToolsCollection class is static. These
* methods can not be so they must be called:
*
*
* LOGGER.debug(new Tool().getQuimPversion());
*
*
* @param quimpBuildInfo info read from jar
* @return Formatted string with QuimP version and authors
* @see #getQuimPBuildInfo()
*/
public static String getFormattedQuimPversion(QuimpVersion quimpBuildInfo) {
//!>
String infoPlate = "---------------------------------------------------------\n"
+ "| QuimP, by |\n"
+ "| Richard Tyson ([email protected]) |\n"
+ "| Till Bretschneider ([email protected]) |\n"
+ "| Piotr Baniukiewicz ([email protected]) |\n"
+ "| Web page: "
+ new PropertyReader().readProperty("quimpconfig.properties", "webPage")
+ " |\n"
+ "---------------------------------------------------------\n";
//!<
infoPlate = infoPlate.concat("\n");
infoPlate = infoPlate.concat("QuimP version: " + quimpBuildInfo.getVersion());
infoPlate = infoPlate.concat("\n");
infoPlate = infoPlate.concat("Build by: " + quimpBuildInfo.getBuildstamp());
infoPlate = infoPlate.concat("\n");
infoPlate = infoPlate.concat("Internal name: " + quimpBuildInfo.getName());
infoPlate = infoPlate.concat("\n");
return infoPlate;
}
/**
* Get build info read from jar file.
*
* @return Formatted strings with build info and version.
*/
public QuimpVersion getQuimPBuildInfo() {
String[] ret = new String[3];
try {
Enumeration resources = getClass().getClassLoader().getResources("META-INF/MANIFEST.MF");
// get internal name - jar name
String iname = new PropertyReader().readProperty("quimpconfig.properties", "internalName");
while (resources.hasMoreElements()) {
URL reselement = resources.nextElement();
if (!reselement.toString().contains("/" + iname)) {
continue;
}
Manifest manifest = new Manifest(reselement.openStream());
Attributes attributes = manifest.getMainAttributes();
try {
String date = attributes.getValue("Implementation-Date");
ret[1] = attributes.getValue("Built-By") + " on: " + implementationDateConverter(date);
ret[0] = attributes.getValue("Implementation-Version");
ret[2] = attributes.getValue("Implementation-Title");
LOGGER.trace(Arrays.toString(ret));
} catch (Exception e) {
; // do not care about problems - just use defaults defined on beginning
}
}
} catch (IOException e) {
; // do not care about problems - just use defaults defined on beginning
}
// replace possible nulls with default text
ret[0] = ret[0] == null ? defNote : ret[0];
ret[1] = ret[1] == null ? defNote : ret[1];
ret[2] = ret[2] == null ? defNote : ret[2];
// prepare output
QuimpVersion retmap = new QuimpVersion(ret[0], ret[1], ret[2]);
return retmap;
}
/**
* Reformat date from jar (put there by Maven).
*
* @param dateString string in format "2017-02-24T08:55:44+0000"
* @return String in format "yyyy-MM-dd hh:mm:ss"
*/
public static String implementationDateConverter(String dateString) {
DateTimeFormatter timeFormatter = DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ssZ");
TemporalAccessor accessor = timeFormatter.parse(dateString);
Date date = Date.from(Instant.from(accessor));
SimpleDateFormat dt = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
return dt.format(date);
}
/**
* S 2 d.
*
* @param s the s
* @return the double
*/
public static double s2d(String s) {
Double d;
try {
d = new Double(s);
} catch (NumberFormatException e) {
d = null;
}
if (d != null) {
return (d.doubleValue());
} else {
return (0.0);
}
}
/**
* Get file name without extension.
*
* @param filename name of the file
* @return file (with path) without extension
*/
public static String removeExtension(String filename) {
// extract fileName without extension
int dotI = filename.lastIndexOf(".");
if (dotI > 0 && filename.length() - dotI <= 6) { // assume extension of length max 5+dot
filename = filename.substring(0, dotI);
}
return filename;
}
/**
* Get file extension.
*
* @param filename Name of file
* @return extension without dot
*/
public static String getFileExtension(String filename) {
// extract fileName without extension
int dotI = filename.lastIndexOf(".");
if (dotI > 0) {
filename = filename.substring(dotI + 1, filename.length());
}
return filename;
}
/**
* Closest floor.
*
* @param o the o
* @param target the target
* @return the vert
*/
public static Vert closestFloor(Outline o, double target) {
// find the vert with coor closest (floored) to target coordinate
Vert v = o.getHead();
double coordA;
double coordB;
do {
// coordA = v.fCoord;
// coordB = v.getNext().fCoord;
coordA = v.coord;
coordB = v.getNext().coord;
// System.out.println("A: " + coordA + ", B: "+ coordB);
if ((coordA > coordB)) {
if (coordA <= target && coordB + 1 > target) {
break;
}
if (coordA - 1 <= target && coordB > target) {
break;
}
} else {
if (coordA <= target && coordB > target) {
break;
}
}
v = v.getNext();
} while (!v.isHead());
return v;
}
/**
* Distance to scale.
*
* @param value the value
* @param scale the scale
* @return the double
*/
public static double distanceToScale(double value, double scale) {
// assums pixelwidth is in micro meters
return value * scale;
}
/**
* Distance to scale.
*
* @param value the value
* @param scale the scale
* @return the double
*/
public static double distanceToScale(int value, double scale) {
return value * scale;
}
/**
* Area to scale.
*
* @param value the value
* @param scale the scale
* @return the double
*/
public static double areaToScale(double value, double scale) {
// assums pixelwidth is in micro meters
return value * (scale * scale);
}
/**
* Speed to scale.
*
* @param value the value
* @param scale the scale
* @param frameInterval the frame interval
* @return the double
*/
public static double speedToScale(double value, double scale, double frameInterval) {
return (value * scale) / frameInterval;
}
/**
* Speed to scale.
*
* @param value the value
* @param scale the scale
* @param frameInterval the frame interval
* @return the double
*/
public static double speedToScale(int value, double scale, double frameInterval) {
return (value * scale) / frameInterval;
}
/**
* Distance from scale.
*
* @param value the value
* @param scale the scale
* @return the double
*/
public static double distanceFromScale(double value, double scale) {
return value / scale;
}
/**
* Date as string.
*
* @return the string
*/
public static String dateAsString() {
SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
Date date = new Date();
return formatter.format(date);
}
/**
* Sets the limits equal.
*
* @param migLimits the mig limits
* @return the double[]
*/
public static double[] setLimitsEqual(double[] migLimits) { // min and max
if (migLimits.length < 2) {
LOGGER.warn("Array to short. Needs a min and max");
return migLimits;
}
// Set limits to equal positive and negative
if (migLimits[1] < 0) {
migLimits[1] = -migLimits[0];
}
if (migLimits[0] > 0) {
migLimits[0] = -migLimits[1];
}
// Make min and max equal for mig and conv
if (migLimits[0] < -migLimits[1]) {
migLimits[1] = -migLimits[0];
} else {
migLimits[0] = -migLimits[1];
}
return migLimits;
}
/**
* Insert \n character after given number of chars trying to not break words.
*
* @param in Input string
* @param len line length
* @return Wrapped string
* @see http://stackoverflow.com/questions/8314566/splitting-a-string-on-to-several-different-lines-in-java
*/
public static String stringWrap(String in, int len) {
return stringWrap(in, len, "\n");
}
/**
* Insert \n character after default number of chars trying to not break words.
*
* @param in Input string
* @return Wrapped string
* @see http://stackoverflow.com/questions/8314566/splitting-a-string-on-to-several-different-lines-in-java
*/
public static String stringWrap(String in) {
return stringWrap(in, QuimP.LINE_WRAP, "\n");
}
/**
* Insert any symbol after given number of chars trying to not break words.
*
* It preserve position of new line symbol if present in text.
*
* @param in Input string
* @param len line length
* @param brek symbol to insert on line break
* @return Wrapped string
* @see http://stackoverflow.com/questions/8314566/splitting-a-string-on-to-several-different-lines-in-java
*/
public static String stringWrap(String in, int len, String brek) {
String[] sp = in.split("\n");
String str = "";
for (String s : sp) {
s = s.concat("\n");
str = str.concat(WordUtils.wrap(s, len, brek, false, "( |/|\\\\)"));
}
str = str.trim();
// String str = WordUtils.wrap(in, len, brek, false, "( |/|\\\\)");
return str;
}
}
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