//TODO! implement mgrid that takes (string lhs, string rhs) and (Slice lhs, Slice rhs) fallbacking to each other. /// <summary> /// nd_grid instance which returns a dense multi-dimensional “meshgrid”. /// An instance of numpy.lib.index_tricks.nd_grid which returns an dense (or fleshed out) mesh-grid when indexed, so that each returned argument has the same shape. /// The dimensions and number of the output arrays are equal to the number of indexing dimensions.If the step length is not a complex number, then the stop is not inclusive. /// </summary> /// <param name="lhs"></param> /// <param name="rhs"></param> /// <returns>mesh-grid `ndarrays` all of the same dimensions</returns> /// <remarks>https://docs.scipy.org/doc/numpy/reference/generated/numpy.mgrid.html</remarks> public static (NDArray, NDArray) mgrid(NDArray lhs, NDArray rhs) { if (!(lhs.ndim == 1 || rhs.ndim == 1)) { throw new IncorrectShapeException(); } IArraySlice nd1Data = lhs.Storage.GetData(); IArraySlice nd2Data = rhs.Storage.GetData(); int[] resultDims = new int[] { lhs.Storage.Shape.Dimensions[0], rhs.Storage.Shape.Dimensions[0] }; NDArray res1 = new NDArray(lhs.dtype, resultDims); NDArray res2 = new NDArray(lhs.dtype, resultDims); IArraySlice res1Arr = res1.Storage.GetData(); IArraySlice res2Arr = res2.Storage.GetData(); int counter = 0; for (int row = 0; row < nd1Data.Count; row++) { for (int col = 0; col < nd2Data.Count; col++) { res1Arr[counter] = nd1Data[row]; res2Arr[counter] = nd2Data[col]; counter++; } } return(res1, res2); }
/// <summary> /// Convert an array of size 1 to its scalar equivalent. /// </summary> /// <param name="arr">Input array of size 1.</param> /// <returns></returns> /// <remarks>https://docs.scipy.org/doc/numpy-1.16.0/reference/generated/numpy.asscalar.html</remarks> public static T asscalar <T>(IArraySlice arr) where T : unmanaged { if (arr.Count != 1) { throw new IncorrectSizeException("Unable to convert NDArray to scalar because size is not 1."); } return((T)Convert.ChangeType(arr[0], typeof(T))); }
/// <summary> /// Constructor which takes .NET array /// dtype and shape is determined from array /// </summary> /// <param name="values"></param> /// <param name="shape"></param> /// <param name="order"></param> /// <returns>Array with values</returns> /// <remarks>This constructor calls <see cref="IStorage.Allocate(NumSharp.Shape,System.Type)"/></remarks> public NDArray(IArraySlice values, Shape shape = default, char order = 'C') : base(values, shape, order) { var underlying = values.GetType().GenericTypeArguments[0]; if (underlying != typeof(T)) { throw new ArgumentException($"Array type must be the same as T. {underlying.Name} != {typeof(T).Name}", nameof(values)); } }
/* sort all type LMS suffixes */ private static void LMSsort(IArraySlice T, int[] SA, IArraySlice C, IArraySlice B, int n, int k) { int b, i, j; int c0, c1; /* compute SAl */ if (C == B) { GetCounts(T, C, n, k); } GetBuckets(C, B, k, false); /* find starts of buckets */ j = n - 1; c1 = T[j]; b = B[c1]; --j; SA[b++] = (T[j] < c1) ? ~j : j; for (i = 0; i < n; ++i) { if (0 < (j = SA[i])) { c0 = T[j]; if (c0 != c1) { B[c1] = b; c1 = c0; b = B[c1]; } --j; SA[b++] = (T[j] < c1) ? ~j : j; SA[i] = 0; } else if (j < 0) { SA[i] = ~j; } } /* compute SAs */ if (C == B) { GetCounts(T, C, n, k); } GetBuckets(C, B, k, true); /* find ends of buckets */ c1 = 0; for (i = n - 1, b = B[c1]; 0 <= i; --i) { if (0 < (j = SA[i])) { if ((c0 = T[j]) != c1) { B[c1] = b; b = B[c1 = c0]; } --j; SA[--b] = (T[j] > c1) ? ~(j + 1) : j; SA[i] = 0; } } }
/// <summary> /// Constructor which takes .NET array /// dtype and shape is determined from array /// </summary> /// <param name="values"></param> /// <param name="shape"></param> /// <param name="order"></param> /// <returns>Array with values</returns> /// <remarks>This constructor calls <see cref="IStorage.Allocate(NumSharp.Shape,System.Type)"/></remarks> public NDArray(IArraySlice values, Shape shape = default, char order = 'C') : this(values.TypeCode) { if (order != 'C') shape.ChangeTensorLayout(order); if (shape.IsEmpty) shape = Shape.Vector((int) values.Count); //TODO! when long index, remove cast int Storage.Allocate(values, shape); }
/// <summary> /// Constructor which takes .NET array /// dtype and shape is determined from array /// </summary> /// <param name="values"></param> /// <param name="shape"></param> /// <param name="order"></param> /// <returns>Array with values</returns> /// <remarks>This constructor calls <see cref="IStorage.Allocate(NumSharp.Shape,System.Type)"/></remarks> public NDArray(IArraySlice values, Shape shape = default, char order = 'C') : this(values.TypeCode) { if (order != 'C') shape.ChangeTensorLayout(order); if (shape.IsEmpty) shape = Shape.Vector(values.Count); Storage.Allocate(values, shape); }
/* compute SA and BWT */ private static void InduceSA(IArraySlice T, int[] SA, IArraySlice C, IArraySlice B, int n, int k) { int b, i, j; int c0, c1; /* compute SAl */ if (C == B) { GetCounts(T, C, n, k); } GetBuckets(C, B, k, false); /* find starts of buckets */ j = n - 1; b = B[c1 = T[j]]; SA[b++] = ((0 < j) && (T[j - 1] < c1)) ? ~j : j; for (i = 0; i < n; ++i) { j = SA[i]; SA[i] = ~j; if (0 < j) { if ((c0 = T[--j]) != c1) { B[c1] = b; c1 = c0; b = B[c1]; } SA[b++] = ((0 < j) && (T[j - 1] < c1)) ? ~j : j; } } /* compute SAs */ if (C == B) { GetCounts(T, C, n, k); } GetBuckets(C, B, k, true); /* find ends of buckets */ for (i = n - 1, b = B[c1 = 0]; 0 <= i; --i) { if (0 < (j = SA[i])) { if ((c0 = T[--j]) != c1) { B[c1] = b; c1 = c0; b = B[c1]; } SA[--b] = ((j == 0) || (T[j - 1] > c1)) ? ~j : j; } else { SA[i] = ~j; } } }
private static void GetCounts(IArraySlice T, IArraySlice C, int n, int k) { for (int i = 0; i < k; ++i) { C[i] = 0; } for (int i = 0; i < n; ++i) { var ti = T[i]; C[ti] = C[ti] + 1; } }
private static void GetBuckets(IArraySlice C, IArraySlice B, int k, bool end) { int i, sum = 0; if (end) { for (i = 0; i < k; ++i) { sum += C[i]; B[i] = sum; } } else { for (i = 0; i < k; ++i) { sum += C[i]; B[i] = sum - C[i]; } } }
public NDIterator(IArraySlice slice, Shape shape, Shape?broadcastedShape, bool autoReset = false) : this((IMemoryBlock)slice, shape, broadcastedShape, autoReset) { }
private NDArray(IArraySlice array, Shape shape) : this(array.TypeCode) { Storage.Allocate(array, shape); }
/* find the suffix array SA of T[0..n-1] in {0..k-1}^n * use a working space (excluding T and SA) of at most 2n+O(1) for a constant alphabet */ private static int SaisMain(IArraySlice T, int[] SA, int fs, int n, int k, bool isbwt) { IArraySlice C, B, RA; int i, j, b, m, p, q, name, pidx = 0, newfs; int c0, c1; uint flags = 0; if (k <= MINBUCKETSIZE) { C = new IntArraySlice(new int[k], 0); if (k <= fs) { B = new IntArraySlice(SA, n + fs - k); flags = 1; } else { B = new IntArraySlice(new int[k], 0); flags = 3; } } else if (k <= fs) { C = new IntArraySlice(SA, n + fs - k); if (k <= (fs - k)) { B = new IntArraySlice(SA, n + fs - k * 2); flags = 0; } else if (k <= (MINBUCKETSIZE * 4)) { B = new IntArraySlice(new int[k], 0); flags = 2; } else { B = C; flags = 8; } } else { C = B = new IntArraySlice(new int[k], 0); flags = 4 | 8; } /* stage 1: reduce the problem by at least 1/2 * sort all the LMS-substrings */ GetCounts(T, C, n, k); GetBuckets(C, B, k, true); /* find ends of buckets */ for (i = 0; i < n; ++i) { SA[i] = 0; } b = -1; i = n - 1; j = n; m = 0; c0 = T[n - 1]; do { c1 = c0; } while ((0 <= --i) && ((c0 = T[i]) >= c1)); for (; 0 <= i;) { do { c1 = c0; } while ((0 <= --i) && ((c0 = T[i]) <= c1)); if (0 <= i) { if (0 <= b) { SA[b] = j; } b = --B[c1]; j = i; ++m; do { c1 = c0; } while ((0 <= --i) && ((c0 = T[i]) >= c1)); } } if (1 < m) { LMSsort(T, SA, C, B, n, k); name = LMSpostproc(T, SA, n, m); } else if (m == 1) { SA[b] = j + 1; name = 1; } else { name = 0; } /* stage 2: solve the reduced problem * recurse if names are not yet unique */ if (name < m) { if ((flags & 4) != 0) { C = null; B = null; } if ((flags & 2) != 0) { B = null; } newfs = (n + fs) - (m * 2); if ((flags & (1 | 4 | 8)) == 0) { if ((k + name) <= newfs) { newfs -= k; } else { flags |= 8; } } for (i = m + (n >> 1) - 1, j = m * 2 + newfs - 1; m <= i; --i) { if (SA[i] != 0) { SA[j--] = SA[i] - 1; } } RA = new IntArraySlice(SA, m + newfs); SaisMain(RA, SA, newfs, m, name, false); RA = null; i = n - 1; j = m * 2 - 1; c0 = T[n - 1]; do { c1 = c0; } while ((0 <= --i) && ((c0 = T[i]) >= c1)); for (; 0 <= i;) { do { c1 = c0; } while ((0 <= --i) && ((c0 = T[i]) <= c1)); if (0 <= i) { SA[j--] = i + 1; do { c1 = c0; } while ((0 <= --i) && ((c0 = T[i]) >= c1)); } } for (i = 0; i < m; ++i) { SA[i] = SA[m + SA[i]]; } if ((flags & 4) != 0) { C = B = new IntArraySlice(new int[k], 0); } if ((flags & 2) != 0) { B = new IntArraySlice(new int[k], 0); } } /* stage 3: induce the result for the original problem */ if ((flags & 8) != 0) { GetCounts(T, C, n, k); } /* put all left-most S characters into their buckets */ if (1 < m) { GetBuckets(C, B, k, true); /* find ends of buckets */ i = m - 1; j = n; p = SA[m - 1]; c1 = T[p]; do { q = B[c0 = c1]; while (q < j) { SA[--j] = 0; } do { SA[--j] = p; if (--i < 0) { break; } p = SA[i]; } while ((c1 = T[p]) == c0); } while (0 <= i); while (0 < j) { SA[--j] = 0; } } if (!isbwt) { InduceSA(T, SA, C, B, n, k); } else { pidx = ComputeBwt(T, SA, C, B, n, k); } C = null; B = null; return(pidx); }
private static int ComputeBwt(IArraySlice T, int[] SA, IArraySlice C, IArraySlice B, int n, int k) { int b, i, j, pidx = -1; int c0, c1; /* compute SAl */ if (C == B) { GetCounts(T, C, n, k); } GetBuckets(C, B, k, false); /* find starts of buckets */ j = n - 1; c1 = T[j]; b = B[c1]; SA[b++] = ((0 < j) && (T[j - 1] < c1)) ? ~j : j; for (i = 0; i < n; ++i) { if (0 < (j = SA[i])) { SA[i] = ~(c0 = T[--j]); if (c0 != c1) { B[c1] = b; b = B[c1 = c0]; } SA[b++] = ((0 < j) && (T[j - 1] < c1)) ? ~j : j; } else if (j != 0) { SA[i] = ~j; } } /* compute SAs */ if (C == B) { GetCounts(T, C, n, k); } GetBuckets(C, B, k, true); /* find ends of buckets */ for (i = n - 1, b = B[c1 = 0]; 0 <= i; --i) { if (0 < (j = SA[i])) { SA[i] = (c0 = T[--j]); if (c0 != c1) { B[c1] = b; c1 = c0; b = B[c1]; } SA[--b] = ((0 < j) && (T[j - 1] > c1)) ? ~((int)T[j - 1]) : j; } else if (j != 0) { SA[i] = ~j; } else { pidx = i; } } return(pidx); }
private static int LMSpostproc(IArraySlice T, int[] SA, int n, int m) { int i, j, p, q, plen, qlen, name; int c0, c1; bool diff; /* compact all the sorted substrings into the first m items of SA * 2*m must be not larger than n (proveable) */ for (i = 0; (p = SA[i]) < 0; ++i) { SA[i] = ~p; } if (i < m) { for (j = i, ++i; ; ++i) { if ((p = SA[i]) < 0) { SA[j++] = ~p; SA[i] = 0; if (j == m) { break; } } } } /* store the length of all substrings */ i = n - 1; j = n - 1; c0 = T[n - 1]; do { c1 = c0; } while ((0 <= --i) && ((c0 = T[i]) >= c1)); for (; 0 <= i;) { do { c1 = c0; } while ((0 <= --i) && ((c0 = T[i]) <= c1)); if (0 <= i) { SA[m + ((i + 1) >> 1)] = j - i; j = i + 1; do { c1 = c0; } while ((0 <= --i) && ((c0 = T[i]) >= c1)); } } /* find the lexicographic names of all substrings */ for (i = 0, name = 0, q = n, qlen = 0; i < m; ++i) { p = SA[i]; plen = SA[m + (p >> 1)]; diff = true; if ((plen == qlen) && ((q + plen) < n)) { for (j = 0; (j < plen) && (T[p + j] == T[q + j]); ++j) { } if (j == plen) { diff = false; } } if (diff != false) { ++name; q = p; qlen = plen; } SA[m + (p >> 1)] = name; } return(name); }