public static void doFor(File comparisonFile, String base) {
System.out.println("profile ------------------------- " + comparisonFile);
// Load similarities
final Map<Tuple<File, File>, ColocCoefficients> comparison;
comparison = CompareAll.loadCache(null, comparisonFile);
// comparison=CompareAll.loadCache(datas, CompareAll.cachedValuesFileT);
// Find out which files there are
Set<File> datas = IntExpFileUtil.getAnnotated(); // new TreeSet<File>();//.getAnnotated();
/*
for(Tuple<File,File> t:comparison.keySet())
IntExpFileUtil.getAnnotated()
if(t.fst().exists())
datas.add(t.fst());*/
// Only keep those actually calculated
Set<File> found = new TreeSet<File>();
for (Tuple<File, File> a : comparison.keySet()) found.add(a.fst());
datas.retainAll(found);
System.out.println(datas);
Map<File, String> nameMap = new HashMap<File, String>();
int countName = 0;
StringBuffer sbSed = new StringBuffer();
for (File fa : datas) {
// Similarity -> disimilarity, just a change of sign
String tempName = ("n" + countName + "nnnnnnnnnn").substring(0, 10);
nameMap.put(fa, tempName);
countName++;
String newName = IntExpFileUtil.getGeneName(fa) + " " + fa.getName();
sbSed.append(" | sed 's/" + tempName + "/" + newName + "/'");
}
System.out.println("# recordings: " + datas.size());
HashSet<String> strainNames = new HashSet<String>();
for (File fa : datas) {
String name = fa.getName();
name = name.substring(0, name.indexOf('_'));
strainNames.add(name);
}
System.out.println("# strains: " + strainNames.size());
for (String type : new String[] {"l2", "pearson"}) {
StringBuffer sb = new StringBuffer();
sb.append("" + datas.size() + "\n");
for (File fa : datas) {
// Similarity -> disimilarity, just a change of sign
String name = nameMap.get(fa); // (fa.getName()+" ").substring(0,10);
sb.append(name);
for (File fb : datas) {
ColocCoefficients coef = comparison.get(Tuple.make(fa, fb));
if (coef == null) System.out.println("-----------------Null for " + fa + " " + fb);
Double v = null;
if (type.equals("pearson")) {
v = 1.0 - Math.abs(coef.getPearson());
if (fa.equals(fb)) System.out.println("should be 0: " + v); // may need to force 0
if (v == null || Double.isInfinite(v) || Double.isNaN(v)) v = 0.0;
} else if (type.equals("l2")) {
v = coef.getL2();
if (v == null || Double.isInfinite(v) || Double.isNaN(v))
v = 0.5 * 0.5; // doubtful? but probably not further away
if (fa.equals(fb)) v = 0.0;
}
sb.append(" " + v);
}
sb.append("\n");
}
try {
File basedir = new File(new File(CompareAll.outputBaseDir, "phylip"), base + "-" + type);
basedir.mkdirs();
EvFileUtil.writeFile(new File(basedir, "infile"), sb.toString());
String fSed =
"cat outfile" + sbSed + " > outfile2\n" + "cat outtree" + sbSed + " > outtree2\n";
EvFileUtil.writeFile(new File(basedir, "fix.sh"), fSed);
} catch (IOException e) {
e.printStackTrace();
}
}
}
public static EvStack apply(EvStack in, double sigmaX, double sigmaY, double sigmaZ) {
int w = in.getWidth();
int h = in.getHeight();
int d = in.getDepth();
/*
*
System.out.println("incoming stack "+in);
System.out.println("Generating kernel");
EvStack kernel=GenerateSpecialImage.genGaussian3D(sigmaX, sigmaY, sigmaZ, w, h, d);
System.out.println(kernel);
kernel.forceEvaluation();
System.gc();
System.out.println("Rotating");
kernel=EvOpRotateImage3D.apply(kernel, null,null, null); //old kernel is collected here
System.out.println(kernel);
kernel.forceEvaluation();
System.gc();
System.out.println("fft kernel");
EvStack[] ckernel=new EvOpFourierRealForwardFull3D().exec(kernel);
ckernel[0].forceEvaluation();
ckernel[1].forceEvaluation();
System.out.println(ckernel[0]);
System.out.println(ckernel[1]);
System.gc();
System.out.println("fft im");
EvStack[] cin=new EvOpFourierRealForwardFull3D().exec(in);
cin[0].forceEvaluation();
cin[1].forceEvaluation();
System.out.println(cin[0]);
System.out.println(cin[1]);
System.gc();
System.out.println("mul");
cin=new EvOpImageComplexMulImage().exec(cin[0],cin[1],ckernel[0],ckernel[1]);
// EvStack[] mul=new EvOpImageComplexMulImage().exec(cin[0],cin[1],ckernel[0],ckernel[1]);
cin[0].forceEvaluation();
cin[1].forceEvaluation();
System.out.println(cin[0]);
System.out.println(cin[1]);
System.gc();
return EvOpFourierComplexInverse3D.transform(cin[0], cin[1],true).fst();
*/
System.out.println("Generating kernel");
EvStack kernel = GenerateSpecialImage.genGaussian3D(sigmaX, sigmaY, sigmaZ, w, h, d);
System.gc();
System.out.println("Rotating");
kernel = EvOpWrapImage3D.apply(kernel, null, null, null); // old kernel is collected here
System.gc();
System.out.println("fft kernel");
Tuple<EvStack, EvStack> ckernel = EvOpFourierRealForwardFull3D.transform(kernel);
System.gc();
System.out.println("fft im");
Tuple<EvStack, EvStack> cin = EvOpFourierRealForwardFull3D.transform(in);
System.gc();
/*
System.out.println("mul");
EvStack[] mul=new EvOpImageComplexMulImage().exec(cin.fst(),cin.snd(),ckernel.fst(),ckernel.snd());
System.gc();
return EvOpFourierComplexInverse3D.transform(mul[0], mul[1],true).fst();
*/
System.out.println("mul");
EvOpImageComplexMulImage.timesInPlaceDouble(cin.fst(), cin.snd(), ckernel.fst(), ckernel.snd());
System.gc();
return EvOpFourierComplexInverse3D.transform(cin.fst(), cin.snd(), true).fst();
}