lineage/Identify.java

   1 package lineage;
   2
   3 import ij.gui.GenericDialog;
   4 import ini.trakem2.display.Line3D;
   5 import ini.trakem2.plugin.TPlugIn;
   6 import ini.trakem2.utils.Bureaucrat;
   7 import ini.trakem2.utils.IJError;
   8 import ini.trakem2.utils.Utils;
   9 import ini.trakem2.utils.Worker;
  10
  11 import java.io.InputStreamReader;
  12 import java.io.Reader;
  13 import java.lang.reflect.Method;
  14
  15 public class Identify implements TPlugIn {
  16
  17         public Identify() {}
  18
  19         static {
  20                 try {
  21                         Thread.currentThread().setContextClassLoader(ij.IJ.getClassLoader());
  22                         Class<?> c = Class.forName("clojure.lang.Compiler");
  23                         Method load = c.getDeclaredMethod("load", new Class[]{Reader.class});
  24                         load.invoke(null, new Object[]{new InputStreamReader(Identify.class.getResourceAsStream("/lineage/identify.clj"))});
  25                         // As a side effect, inits clojure runtime
  26                 } catch (Throwable t) {
  27                         IJError.print(t);
  28                 }
  29         }
  30
  31         /**
  32          * Takes 2 arg (the Pipe or Polyline and the lib-name)
  33          * or 5 args: Line3D pipe, String lib-name, double delta, boolean direct and boolean substring
  34          */
  35         static public Object identify(Object... args) {
  36                 try {
  37                         Class<?> RT = Class.forName("clojure.lang.RT");
  38                         Method var = RT.getDeclaredMethod("var", new Class[]{String.class, String.class});
  39                         Object fn = var.invoke(null, new Object[]{"lineage.identify", "identify"});
  40                         Class<?>[] cc = new Class[args.length];
  41                         for (int i=0; i<cc.length; i++) cc[i] = Object.class;
  42                         Method invoke = Class.forName("clojure.lang.Var").getDeclaredMethod("invoke", cc);
  43                         return invoke.invoke(fn, args);
  44                 } catch (Throwable e) {
  45                         IJError.print(e);
  46                 }
  47                 return null;
  48         }
  49
  50         static private class Params {
  51
  52                 private final String[] libs = {"Drosophila-3rd-instar"};
  53
  54                 private double delta = 1.0;
  55                 private int lib_index = 0;
  56                 private boolean direct = true;
  57                 private boolean substring = false;
  58
  59                 synchronized public Params clone() {
  60                         Params p = new Params();
  61                         p.delta = delta;
  62                         p.lib_index = lib_index;
  63                         p.direct = direct;
  64                         p.substring = substring;
  65                         return p;
  66                 }
  67
  68                 synchronized private boolean setup() {
  69                         GenericDialog gd = new GenericDialog("Setup NIT");
  70                         gd.addNumericField("delta:", delta, 2);
  71                         gd.addCheckbox("direct", direct);
  72                         gd.addCheckbox("substring", substring);
  73                         gd.addChoice("Library: ", libs, libs[0]);
  74                         gd.showDialog();
  75                         if (gd.wasCanceled()) return false;
  76                         double d = gd.getNextNumber();
  77                         if (Double.isNaN(d)) {
  78                                 Utils.log("Invalid delta value!");
  79                                 return false;
  80                         }
  81                         if (d < 0) d = 1.0;
  82                         delta = d;
  83                         lib_index = gd.getNextChoiceIndex();
  84                         direct = gd.getNextBoolean();
  85                         substring = gd.getNextBoolean();
  86                         return true;
  87                 }
  88         }
  89
  90         /** Store start up values. New instances take the current values. */
  91         static private Params PARAMS = new Params();
  92
  93         private Params params = PARAMS.clone();
  94
  95         public boolean setup(Object... args) {
  96                 return params.setup();
  97         }
  98
  99         public Bureaucrat identify(final Line3D pipe) {
 100                 return Bureaucrat.createAndStart(new Worker.Task("Identifying " + pipe) {
 101                         public void exec() {
 102                                 if (null == pipe) return;
 103                                 Params p = params.clone();
 104                                 identify(pipe, p.libs[p.lib_index], p.delta, p.direct, p.substring);
 105                         }
 106                 }, pipe.getProject());
 107         }
 108
 109         public Object invoke(Object... args) {
 110                 if (null == args || args.length < 1 || null == args[0] || !(args[0] instanceof Line3D)) return null;
 111                 Line3D pipe = (Line3D) args[0];
 112                 Params p = params.clone();
 113                 return identify(pipe, p.libs[p.lib_index], p.delta, p.direct, p.substring);
 114         }
 115
 116         public boolean applies(final Object ob) {
 117                 return null != ob && ob instanceof Line3D;
 118         }
 119 }