com.actelion.research.orbit.utils.ChannelToHue Maven / Gradle / Ivy
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common objects for orbit image analysis
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2017 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 hueMap = new ConcurrentHashMap<>(mappings.length);
public final static Map userHueMap = new ConcurrentHashMap<>();
static {
for (ChannelHue channelHue: mappings) {
hueMap.put(channelHue.getChannel(), channelHue.getHue());
}
}
public static float getHue(String channel) {
if (channel==null) return HueDAPI;
String channelName = channel.trim().toLowerCase();
if (userHueMap.containsKey(channelName)) return userHueMap.get(channelName);
if (hueMap.containsKey(channelName)) return hueMap.get(channelName);
if (channelName.contains("dapi")) return HueDAPI;
if (channelName.contains("fitc")) return HueFITC;
if (channelName.contains("tritc")) return HueTRITC;
if (channelName.contains("cy5")) return HueCy5;
if (channelName.contains("cy3")) return HueCy3;
if (channelName.contains("gfp")) return HueEGFP;
if (channelName.contains("alexa") || channelName.contains("af")) {
if (channelName.contains("350")) return HueAlexa350;
if (channelName.contains("388")) return HueAlexa388;
if (channelName.contains("405")) return HueAlexa405;
if (channelName.contains("430")) return HueAlexa430;
if (channelName.contains("488")) return HueAlexa488;
if (channelName.contains("500")) return HueAlexa500;
if (channelName.contains("514")) return HueAlexa514;
if (channelName.contains("532")) return HueAlexa532;
if (channelName.contains("546")) return HueAlexa546;
if (channelName.contains("550")) return HueAlexa550;
if (channelName.contains("555")) return HueAlexa555;
if (channelName.contains("568")) return HueAlexa568;
if (channelName.contains("594")) return HueAlexa594;
if (channelName.contains("610")) return HueAlexa610;
if (channelName.contains("633")) return HueAlexa633;
if (channelName.contains("635")) return HueAlexa635;
if (channelName.contains("647")) return HueAlexa647;
if (channelName.contains("650")) return HueAlexa650;
if (channelName.contains("660")) return HueAlexa660;
if (channelName.contains("680")) return HueAlexa680;
if (channelName.contains("700")) return HueAlexa700;
if (channelName.contains("750")) return HueAlexa750;
if (channelName.contains("790")) return HueAlexa790;
}
if (channelName.contains("violet")) return 264f / 360f;
if (channelName.contains("red")) return 0f / 360f;
if (channelName.contains("green")) return 102f / 360f;
if (channelName.contains("blue")) return 231f / 360f;
for (String name: hueMap.keySet()) {
if (channelName.contains(name)) return hueMap.get(name);
}
System.out.println("Channel-color unknown. Please define a color for channel: "+channel);
return HueDAPI;
}
public static class ChannelHue {
String channel;
float hue;
public ChannelHue(String channel, float hue) {
this.channel = channel;
this.hue = hue;
}
public String getChannel() {
return channel;
}
public void setChannel(String channel) {
this.channel = channel;
}
public float getHue() {
return hue;
}
public void setHue(float hue) {
this.hue = hue;
}
}
}