private static Dictionary <string, ulong[]> GetFingerprints(string path)
{
var files = Directory.EnumerateFiles(path, "*.mp3", SearchOption.AllDirectories);
var fingerprints = new Dictionary <string, ulong[]>();
foreach (var file in files)
{
var fileName = Path.GetFileName(file);
if (fingerprints.ContainsKey(fileName))
{
continue;
}
Write($"Fingerprinting {fileName}... ");
var stopwatch = new Stopwatch();
stopwatch.Start();
var fingerprint = Fingerprinter.GetFingerprint(file);
stopwatch.Stop();
WriteLine($"{stopwatch.ElapsedMilliseconds:##0,000}ms");
fingerprints.Add(Path.GetFileName(file), fingerprint);
}
return(fingerprints);
}
public ChromaContext(int algorithm)
{
this.algorithm = algorithm;
var config = FingerprinterConfiguration.CreateConfiguration(algorithm);
this.fingerprinter = new Fingerprinter(config);
}
public void TestCalculate_BitFingerprint()
{
IAtomContainer mol1 = TestMoleculeFactory.MakeIndole();
IAtomContainer mol2 = TestMoleculeFactory.MakePyrrole();
Fingerprinter fp = new Fingerprinter(1024, 8);
double similarity = Tanimoto.Calculate(fp.GetBitFingerprint(mol1), fp.GetBitFingerprint(mol2));
Assert.AreEqual(0.3939, similarity, 0.01 * 2);
}
/// <summary>
/// Initializes a new instance of the <see cref="ChromaContext" /> class.
/// </summary>
/// <param name="algorithm">The algorithm to use, see <see cref="ChromaprintAlgorithm" /> (default = TEST2)</param>
/// <param name="fftService">The FFT service.</param>
public ChromaContext(ChromaprintAlgorithm algorithm, IFFTService fftService)
{
this.Algorithm = (int)algorithm;
this.fftService = fftService;
var config = FingerprinterConfiguration.CreateConfiguration(algorithm);
this.fingerprinter = new Fingerprinter(config, fftService);
}
void Main()
{
IAtomContainer molecule1 = null;
IAtomContainer molecule2 = null;
Fingerprinter fingerprinter = null;
#region 1
BitArray fingerprint1 = fingerprinter.GetBitFingerprint(molecule1).AsBitSet();
BitArray fingerprint2 = fingerprinter.GetBitFingerprint(molecule2).AsBitSet();
double tanimoto_coefficient = Tanimoto.Calculate(fingerprint1, fingerprint2);
#endregion
}
public void TestTanimoto2()
{
IAtomContainer mol1 = TestMoleculeFactory.MakeIndole();
IAtomContainer mol2 = TestMoleculeFactory.MakeIndole();
Fingerprinter fingerprinter = new Fingerprinter();
BitArray bs1 = fingerprinter.GetBitFingerprint(mol1).AsBitSet();
BitArray bs2 = fingerprinter.GetBitFingerprint(mol2).AsBitSet();
var tanimoto = Tanimoto.Calculate(bs1, bs2);
if (standAlone)
{
System.Console.Out.WriteLine("Tanimoto: " + tanimoto);
}
if (!standAlone)
{
Assert.AreEqual(1.0, tanimoto, 0.001);
}
}
public void TestCompareBitSetandBitFingerprintTanimoto()
{
IAtomContainer mol1 = TestMoleculeFactory.Make123Triazole();
IAtomContainer mol2 = TestMoleculeFactory.MakeImidazole();
Fingerprinter fingerprinter = new Fingerprinter(1024, 8);
BitArray bs1 = fingerprinter.GetBitFingerprint(mol1).AsBitSet();
BitArray bs2 = fingerprinter.GetBitFingerprint(mol2).AsBitSet();
var tanimoto = Tanimoto.Calculate(bs1, bs2);
BitSetFingerprint fp1 = new BitSetFingerprint(bs1);
BitSetFingerprint fp2 = new BitSetFingerprint(bs2);
double tanimoto2 = Tanimoto.Calculate(fp1, fp2);
Assert.AreEqual(tanimoto, tanimoto2, 0.01);
IntArrayFingerprint ifp1 = new IntArrayFingerprint(fp1);
IntArrayFingerprint ifp2 = new IntArrayFingerprint(fp2);
tanimoto2 = Tanimoto.Calculate(ifp1, ifp2);
Assert.AreEqual(tanimoto, tanimoto2, 0.01);
}
public void KeggR00258()
{
var sp = CDK.SmilesParser;
string smiles1 = "O=C(O)CCC(=O)C(=O)O";
string smiles2 = "O=C(O)C(N)CCC(=O)O";
string smiles3 = "O=C(O)C(N)C";
string smiles4 = "CC(=O)C(=O)O";
var molecule1 = sp.ParseSmiles(smiles1);
var molecule2 = sp.ParseSmiles(smiles2);
var molecule3 = sp.ParseSmiles(smiles3);
var molecule4 = sp.ParseSmiles(smiles4);
Fingerprinter fingerprinter = new Fingerprinter(1024, 6);
BitArray bs1 = fingerprinter.GetBitFingerprint(molecule1).AsBitSet();
BitArray bs2 = fingerprinter.GetBitFingerprint(molecule2).AsBitSet();
BitArray bs3 = fingerprinter.GetBitFingerprint(molecule3).AsBitSet();
BitArray bs4 = fingerprinter.GetBitFingerprint(molecule4).AsBitSet();
Assert.AreEqual(0.75, (double)Tanimoto.Calculate(bs1, bs2), 0.1);
Assert.AreEqual(0.46, (double)Tanimoto.Calculate(bs1, bs3), 0.1);
Assert.AreEqual(0.52, (double)Tanimoto.Calculate(bs1, bs4), 0.1);
Assert.AreEqual(0.53, (double)Tanimoto.Calculate(bs2, bs3), 0.1);
Assert.AreEqual(0.42, (double)Tanimoto.Calculate(bs2, bs4), 0.1);
Assert.AreEqual(0.8, (double)Tanimoto.Calculate(bs3, bs4), 0.1);
}
public void Test()
{
Fingerprinter.GetFingerprint("C:\\Users\\Stevo\\Music\\Iron Maiden\\Seventh Son of a Seventh Son\\02 Infinite Dreams.mp3");
}
/// <summary>
/// Build fingerprint
/// </summary>
/// <param name="mol"></param>
public static BitSetFingerprint BuildBitSetFingerprint(
IAtomContainer mol,
FingerprintType fpType,
int fpSubtype = -1,
int fpLen = -1)
{
// Data for Tanimoto similarity using various fingerprint types for CorpId 123456 query.
// Cart - Standard MDL Oracle Cartridge scores
//
// Similarity Score
// ------------------------------------------------
// Size -> 192 896 1024 1024 128 1024 320
// CorpId Cart MACCS PbChm ECFP4 EXT EState Basic Sbstr
// ------ ---- ---- ---- ---- ---- ---- ---- ----
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 0.98 0.96 0.77 0.95 1.00 0.95 1.00
// 123456 0.99 0.98 0.96 0.77 0.95 1.00 0.94 1.00
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 0.91 1.00 0.81 1.00 1.00 1.00 1.00
// 123456 0.98 0.95 1.00 0.74 0.92 1.00 0.93 0.94
// 123456 0.98 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.98 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.98 1.00 0.83 0.76 0.77 0.90 0.76 0.94
// LSH Bin Count - The number of LSH bins (of 25) that match the query bin values
//--------------
// CorpId MAC PbC ECFP EX
// ------ --- --- --- ---
// 123456 25 25 25 25
// 123456 25 20 7 16
// 123456 25 20 9 19
// 123456 25 25 25 25
// 123456 25 25 25 25
// 123456 20 25 9 25
// 123456 21 25 11 17
// 123456 25 25 25 25
// 123456 25 25 25 25
// 123456 25 9 6 11
// Data for Tanimoto similarity using various Circular fingerprint types.
// Using 2 molecules where the 2nd just has an added methyl group.
//
// Measure Score
// -------- -----
// ECFP0 1.00
// ECFP2 .88
// ECFP4 .75
// ECFP6 .64
// FCFP0 1.00
// FCFP2 .92
// FCFP4 .84
// FCFP6 .74
IFingerprinter ifptr = null;
IBitFingerprint ibfp = null;
BitSetFingerprint bfp = null;
IAtomContainer mol2;
string s = "";
DateTime t0 = DateTime.Now;
double getFptrTime = 0, buildFpTime = 0;
if (fpType == FingerprintType.Basic) // size = 1024
{
ifptr = new Fingerprinter();
}
else if (fpType == FingerprintType.Circular) // size variable
{
CircularFingerprinterClass cfpClass = (CircularFingerprinterClass)fpSubtype;
if (cfpClass < CircularFingerprinterClass.ECFP0 || cfpClass > CircularFingerprinterClass.ECFP6)
{
cfpClass = (CircularFingerprinterClass)CircularFingerprintType.DefaultCircularClass; // default class
}
if (fpLen < 0)
{
fpLen = CircularFingerprintType.DefaultCircularLength; // default length
}
ifptr = new CircularFingerprinter(cfpClass, fpLen);
//CircularFingerprinter cfp = (CircularFingerprinter)ifptr;
//ICountFingerprint cntFp = cfp.getCountFingerprint(mol); // debug
//s = CircularFpToString(cfp); // debug
}
else if (fpType == FingerprintType.Extended) // size = 1024
{
ifptr = new ExtendedFingerprinter(); // use DEFAULT_SIZE and DEFAULT_SEARCH_DEPTH
}
else if (fpType == FingerprintType.EState) // size = 128
{
ifptr = new EStateFingerprinter(); // use DEFAULT_SIZE and DEFAULT_SEARCH_DEPTH
}
else if (fpType == FingerprintType.MACCS) // size = 192
{
if (MACCSFp == null)
{
MACCSFp = new MACCSFingerprinter();
}
ifptr = MACCSFp;
}
else if (fpType == FingerprintType.PubChem) // size = 896
{
//IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
ifptr = new PubchemFingerprinter();
}
else if (fpType == FingerprintType.ShortestPath) // size =
{
ifptr = new ShortestPathFingerprinter(); // fails with atom type issue for many structures (e.g. 123456)
}
else if (fpType == FingerprintType.Signature) // size =
{
ifptr = new SignatureFingerprinter(); // can't convert array fingerprint to bitsetfingerprint
}
else if (fpType == FingerprintType.Substructure) // size = 320
{
ifptr = new SubstructureFingerprinter();
}
else
{
throw new Exception("Invalid CdkFingerprintType: " + fpType);
}
getFptrTime = TimeOfDay.Delta(ref t0);
ibfp = ifptr.GetBitFingerprint(mol);
bfp = (BitSetFingerprint)ibfp;
buildFpTime = TimeOfDay.Delta(ref t0);
//long size = bfp.size();
//int card = bfp.Cardinality;
return(bfp);
}
public static void Main()
{
const string path = "C:\\Users\\Stevo\\Music\\Iron Maiden";
Dictionary <string, ulong[]> fingerprints;
if (!File.Exists("cache.json"))
{
var stopwatch = new Stopwatch();
stopwatch.Start();
WriteLine("Cache not found, generating fingerprints.");
fingerprints = GetFingerprints(path);
stopwatch.Stop();
WriteLine($"{fingerprints.Count} fingerprints generated in {(int) stopwatch.Elapsed.TotalSeconds}s");
File.WriteAllText("cache.json", JsonConvert.SerializeObject(fingerprints));
}
else
{
WriteLine("Cache found.");
fingerprints = JsonConvert.DeserializeObject <Dictionary <string, ulong[]> >(File.ReadAllText("cache.json"));
}
if (!File.Exists("temp.wav"))
{
WriteLine("Press enter to start listening...");
ReadLine();
using var source = new WaveInEvent();
var buffer = new byte[source.WaveFormat.AverageBytesPerSecond * 20];
var stream = new WaveFileWriter("temp.wav", source.WaveFormat);
source.DataAvailable += (s, a) =>
{
if (stream.Position + a.BytesRecorded > buffer.Length)
{
return;
}
stream.Write(a.Buffer, 0, a.BytesRecorded);
};
source.StartRecording();
for (var i = 0; i < 20; i++)
{
WriteLine(i);
Thread.Sleep(1000);
}
source.StopRecording();
stream.Close();
stream.Dispose();
}
//var fingerprint = Fingerprinter.GetFingerprint("temp.wav");
var fingerprint = Fingerprinter.GetFingerprint("04 Blood Brothers.m4a");
var results = new List <Tuple <int, string> >();
foreach (var print in fingerprints)
{
var matches = 0;
foreach (var key in print.Value)
{
foreach (var subKey in fingerprint)
{
if (key == subKey)
{
matches++;
}
}
}
WriteLine($"{print.Key} gets {matches} matches.");
results.Add(new Tuple <int, string>(matches, print.Key));
}
WriteLine("\n\n\n");
results.OrderBy(t => t.Item1).ToList().ForEach(t =>
{
if (t.Item2 == "04 Blood Brothers.mp3")
{
ForegroundColor = ConsoleColor.Cyan;
}
WriteLine($"{t.Item1,5} : {t.Item2}");
ForegroundColor = ConsoleColor.Green;
});
}
