public void encodeInt()
{
byte[] res = new byte[10];
int l;
l = MSNumpress.encodeInt(0L, res, 0);
Assert.AreEqual(1, l);
Assert.AreEqual(8, res[0] & 0xf);
l = MSNumpress.encodeInt(-1L, res, 0);
Assert.AreEqual(2, l);
Assert.AreEqual(0xf, res[0] & 0xf);
Assert.AreEqual(0xf, res[1] & 0xf);
l = MSNumpress.encodeInt(35L, res, 0);
Assert.AreEqual(3, l);
Assert.AreEqual(6, res[0] & 0xf);
Assert.AreEqual(0x3, res[1] & 0xf);
Assert.AreEqual(0x2, res[2] & 0xf);
l = MSNumpress.encodeInt(370000000L, res, 0);
Assert.AreEqual(9, l);
Assert.AreEqual(0, res[0] & 0xf);
Assert.AreEqual(0x0, res[1] & 0xf);
Assert.AreEqual(0x8, res[2] & 0xf);
Assert.AreEqual(0x0, res[3] & 0xf);
Assert.AreEqual(0xc, res[4] & 0xf);
Assert.AreEqual(0xd, res[5] & 0xf);
Assert.AreEqual(0x0, res[6] & 0xf);
Assert.AreEqual(0x6, res[7] & 0xf);
Assert.AreEqual(0x1, res[8] & 0xf);
}
public void encodeDecodeSlof()
{
Random random = new Random();
int n = 1000;
double[] ics = new double[n];
for (int i = 0; i < n; i++)
{
ics[i] = Math.Pow(10, 6 * random.NextDouble());
}
byte[] encoded = new byte[n * 2 + 8];
double fixedPoint = MSNumpress.optimalSlofFixedPoint(ics, n);
int encodedBytes = MSNumpress.encodeSlof(ics, n, encoded, fixedPoint);
double[] decoded = new double[n];
int decodedDoubles = MSNumpress.decodeSlof(encoded, encodedBytes, decoded);
Assert.AreEqual(n, decodedDoubles);
for (int i = 0; i < n; i++)
{
Assert.AreEqual(0.0, (ics[i] - decoded[i]) / ((ics[i] + decoded[i]) / 2), 0.0005);
}
}
public void encodeDecodeLinear()
{
Random random = new Random();
int n = 1000;
double[] mzs = new double[n];
mzs[0] = 300 + random.NextDouble();
for (int i = 1; i < n; i++)
{
mzs[i] = mzs[i - 1] + random.NextDouble();
}
byte[] encoded = new byte[n * 5];
double fixedPoint = MSNumpress.optimalLinearFixedPoint(mzs, n);
int encodedBytes = MSNumpress.encodeLinear(mzs, n, encoded, fixedPoint);
double[] decoded = new double[n];
int decodedDoubles = MSNumpress.decodeLinear(encoded, encodedBytes, decoded);
Assert.AreEqual(n, decodedDoubles);
var list = Enumerable.Range(0, 1000).Select(i => decoded[i] / mzs[i]).ToList();
for (int i = 0; i < n; i++)
{
Assert.AreEqual(mzs[i], decoded[i], 0.000005);
}
}
public void encodeDecodeLinearEmpty()
{
byte[] encoded = new byte[8];
int encodedBytes = MSNumpress.encodeLinear(new double[0], 0, encoded, 100000.0);
double[] decoded = new double[0];
int decodedBytes = MSNumpress.decodeLinear(encoded, 8, decoded);
Assert.AreEqual(0, decodedBytes);
}
public void encodeDecodeFixedPoint()
{
double fp = 300.21941382293625;
byte[] encoded = new byte[8];
MSNumpress.encodeFixedPoint(fp, encoded);
double decoded = MSNumpress.decodeFixedPoint(encoded);
Assert.AreEqual(fp, decoded, 0);
}
public void LargeNegativesTest()
{
Random random = new Random();
int n = 5;
double[] ics = new double[] { -1000, 1000, -2000, 2000, -3000 };
double fixedPoint = MSNumpress.optimalSlofFixedPoint(ics, n);
Assert.AreNotEqual(fixedPoint, Double.NaN);
}
public void DecodeShotPicManuallyAndAutomatically()
{
var bytes = new byte[] { 106, 40, 134, 162 };
var manual = new double[4];
var numberOfDoubles = MSNumpress.decodePic(bytes, bytes.Length, manual);
Assert.AreEqual(4, numberOfDoubles);
var automatic = MSNumpress.decode(MSNumpress.ACC_NUMPRESS_PIC, bytes, bytes.Length);
CollectionAssert.AreEqual(manual, automatic);
}
public void encodeFixedPoint()
{
byte[] encoded = new byte[8];
MSNumpress.encodeFixedPoint(1.00, encoded);
Assert.AreEqual(0x3f, 0xff & encoded[0]);
Assert.AreEqual(0xf0, 0xff & encoded[1]);
Assert.AreEqual(0x0, 0xff & encoded[2]);
Assert.AreEqual(0x0, 0xff & encoded[3]);
Assert.AreEqual(0x0, 0xff & encoded[4]);
Assert.AreEqual(0x0, 0xff & encoded[5]);
Assert.AreEqual(0x0, 0xff & encoded[6]);
Assert.AreEqual(0x0, 0xff & encoded[7]);
}
/// <summary>
/// Convenience function for decoding binary data encoded by MSNumpress.
/// </summary>
/// <param name="cvAccession">The PSI-MS obo CV accession of the encoded data.</param>
/// <param name="data">array of double to be encoded.</param>
/// <param name="dataSize">number of doubles from data to encode.</param>
/// <returns>The decoded doubles</returns>
/// <exception cref="ArgumentException">
/// Cannot decode numLin data, need at least 8 initial bytes for fixed point.
/// or
/// Corrupt numLin data!
/// or
/// Cannot decode numPic data, need at least 8 initial bytes for fixed point.
/// or
/// Corrupt numPic data!
/// or
/// '" + cvAccession + "' is not a numpress compression term
/// </exception>
/// <remarks>
/// If the passed cvAccession is one of
///
/// ACC_NUMPRESS_LINEAR = "MS:1002312"
/// ACC_NUMPRESS_PIC = "MS:1002313"
/// ACC_NUMPRESS_SLOF = "MS:1002314"
///
/// the corresponding decode function will be called.
/// </remarks>
public static double[] decode(string cvAccession, byte[] data, int dataSize)
{
if (cvAccession == ACC_NUMPRESS_LINEAR)
{
if (dataSize < 8 || data.Length < 8)
{
throw new ArgumentException("Cannot decode numLin data, need at least 8 initial bytes for fixed point.");
}
double[] buffer = new double[dataSize * 2];
int nbrOfDoubles = MSNumpress.decodeLinear(data, dataSize, buffer);
if (nbrOfDoubles < 0)
{
throw new ArgumentException("Corrupt numLin data!");
}
double[] result = new double[nbrOfDoubles];
Array.Copy(buffer, 0, result, 0, nbrOfDoubles);
return(result);
}
if (cvAccession == ACC_NUMPRESS_SLOF)
{
double[] result = new double[(dataSize - 8) / 2];
MSNumpress.decodeSlof(data, dataSize, result);
return(result);
}
if (cvAccession == ACC_NUMPRESS_PIC)
{
if (dataSize < 8 || data.Length < 8)
{
throw new ArgumentException("Cannot decode numPic data, need at least 8 initial bytes for fixed point.");
}
double[] buffer = new double[dataSize * 2];
int nbrOfDoubles = MSNumpress.decodePic(data, dataSize, buffer);
if (nbrOfDoubles < 0)
{
throw new ArgumentException("Corrupt numPic data!");
}
double[] result = new double[nbrOfDoubles];
Array.Copy(buffer, 0, result, 0, nbrOfDoubles);
return(result);
}
throw new ArgumentException("'" + cvAccession + "' is not a numpress compression term");
}
public void encodeLinear()
{
double[] mzs = { 100.0, 200.0, 300.00005, 400.00010 };
byte[] encoded = new byte[40];
int encodedBytes = MSNumpress.encodeLinear(mzs, 4, encoded, 100000.0);
Assert.AreEqual(18, encodedBytes);
Assert.AreEqual(0x80, 0xff & encoded[8]);
Assert.AreEqual(0x96, 0xff & encoded[9]);
Assert.AreEqual(0x98, 0xff & encoded[10]);
Assert.AreEqual(0x00, 0xff & encoded[11]);
Assert.AreEqual(0x75, 0xff & encoded[16]);
Assert.AreEqual(0x80, 0xf0 & encoded[17]);
}
public void decodeLinearNice()
{
double[] mzs = { 100.0, 200.0, 300.00005, 400.00010 };
byte[] encoded = new byte[28];
int encodedBytes = MSNumpress.encodeLinear(mzs, 4, encoded, 100000.0);
double[] decoded = new double[4];
int numDecoded = MSNumpress.decodeLinear(encoded, encodedBytes, decoded);
Assert.AreEqual(4, numDecoded);
Assert.AreEqual(100.0, decoded[0], 0.000005);
Assert.AreEqual(200.0, decoded[1], 0.000005);
Assert.AreEqual(300.00005, decoded[2], 0.000005);
Assert.AreEqual(400.00010, decoded[3], 0.000005);
}
public void decodeLinearWierd()
{
double[] mzs = { 100.0, 200.0, 4000.00005, 0.00010 };
byte[] encoded = new byte[28];
double fixedPoint = MSNumpress.optimalLinearFixedPoint(mzs, 4);
int encodedBytes = MSNumpress.encodeLinear(mzs, 4, encoded, fixedPoint);
double[] decoded = new double[4];
int numDecoded = MSNumpress.decodeLinear(encoded, encodedBytes, decoded);
Assert.AreEqual(100.0, decoded[0], 0.000005);
Assert.AreEqual(200.0, decoded[1], 0.000005);
Assert.AreEqual(4000.00005, decoded[2], 0.000005);
Assert.AreEqual(0.00010, decoded[3], 0.000005);
}
public void NegativesOneTest()
{
Random random = new Random();
int n = 5;
double[] ics = new double[] { -1, 1, -2, 2, -3 };
double fixedPoint = MSNumpress.optimalSlofFixedPoint(ics, n);
Assert.AreNotEqual(fixedPoint, Double.NaN);
ics = new double[] { -1.001, 1.001, -2.001, 2.001, -3.001 };
fixedPoint = MSNumpress.optimalSlofFixedPoint(ics, n);
Assert.AreNotEqual(fixedPoint, Double.NaN);
ics = new double[] { -.99, .99, -1.99, 1.99, -2.99 };
fixedPoint = MSNumpress.optimalSlofFixedPoint(ics, n);
Assert.AreNotEqual(fixedPoint, Double.NaN);
}
public void encodeDecodeLinear5()
{
Random random = new Random();
int n = 1000;
double[] mzs = new double[n];
mzs[0] = 300 + random.NextDouble();
for (int i = 1; i < n; i++)
{
mzs[i] = mzs[i - 1] + random.NextDouble();
}
byte[] encoded = new byte[n * 5];
double[] decoded = new double[n];
double[] firstDecoded = new double[n];
double fixedPoint = MSNumpress.optimalLinearFixedPoint(mzs, n);
int encodedBytes = MSNumpress.encodeLinear(mzs, n, encoded, fixedPoint);
int decodedDoubles = MSNumpress.decodeLinear(encoded, encodedBytes, decoded);
for (int i = 0; i < n; i++)
{
firstDecoded[i] = decoded[i];
}
for (int i = 0; i < 5; i++)
{
MSNumpress.encodeLinear(decoded, n, encoded, fixedPoint);
MSNumpress.decodeLinear(encoded, encodedBytes, decoded);
}
Assert.AreEqual(n, decodedDoubles);
for (int i = 0; i < n; i++)
{
Assert.AreEqual(firstDecoded[i], decoded[i], double.Epsilon);
}
}
public void encodeDecodeSlof5()
{
Random random = new Random();
int n = 1000;
double[] ics = new double[n];
for (int i = 0; i < n; i++)
{
ics[i] = Math.Pow(10, 6 * random.NextDouble());
}
byte[] encoded = new byte[n * 2 + 8];
double[] decoded = new double[n];
double[] firstDecoded = new double[n];
double fixedPoint = MSNumpress.optimalSlofFixedPoint(ics, n);
int encodedBytes = MSNumpress.encodeSlof(ics, n, encoded, fixedPoint);
int decodedDoubles = MSNumpress.decodeSlof(encoded, encodedBytes, decoded);
for (int i = 0; i < n; i++)
{
firstDecoded[i] = decoded[i];
}
for (int i = 0; i < 5; i++)
{
MSNumpress.encodeSlof(decoded, n, encoded, fixedPoint);
MSNumpress.decodeSlof(encoded, encodedBytes, decoded);
}
Assert.AreEqual(n, decodedDoubles);
for (int i = 0; i < n; i++)
{
Assert.AreEqual(firstDecoded[i], decoded[i], double.Epsilon);
}
}
public void TestEncodeDecodePic5()
{
Random random = new Random();
int n = 1000;
double[] ics = new double[n];
for (int i = 0; i < n; i++)
{
ics[i] = Math.Pow(10, 6 * random.NextDouble());
}
byte[] encoded = new byte[n * 5];
double[] decoded = new double[n];
double[] firstDecoded = new double[n];
int encodedBytes = MSNumpress.encodePic(ics, n, encoded);
int decodedDoubles = MSNumpress.decodePic(encoded, encodedBytes, decoded);
for (int i = 0; i < n; i++)
{
firstDecoded[i] = decoded[i];
}
for (int i = 0; i < 5; i++)
{
MSNumpress.encodePic(decoded, n, encoded);
MSNumpress.decodePic(encoded, encodedBytes, decoded);
}
Assert.AreEqual(n, decodedDoubles);
for (int i = 0; i < n; i++)
{
Assert.AreEqual(firstDecoded[i], decoded[i], double.Epsilon);
}
}
public void encodeDecodePic()
{
Random random = new Random();
int n = 1000;
double[] ics = new double[n];
for (int i = 0; i < n; i++)
{
ics[i] = Math.Pow(10, 6 * random.NextDouble());
}
byte[] encoded = new byte[n * 5];
int encodedBytes = MSNumpress.encodePic(ics, n, encoded);
double[] decoded = new double[n];
int decodedDoubles = MSNumpress.decodePic(encoded, encodedBytes, decoded);
Assert.AreEqual(n, decodedDoubles);
for (int i = 0; i < n; i++)
{
Assert.AreEqual(ics[i], decoded[i], 0.5);
}
}