sequenzo 0.1.18__cp39-cp39-macosx_10_9_universal2.whl → 0.1.20__cp39-cp39-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h

@@ -1,264 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_CXX11_TENSOR_TENSOR_TRAITS_H
-#define EIGEN_CXX11_TENSOR_TENSOR_TRAITS_H
-
-namespace Eigen {
-namespace internal {
-
-
-template<typename Scalar, int Options>
-class compute_tensor_flags
-{
-  enum {
-    is_dynamic_size_storage = 1,
-
-    is_aligned =
-    (
-        ((Options&DontAlign)==0) && (
-#if EIGEN_MAX_STATIC_ALIGN_BYTES>0
-            (!is_dynamic_size_storage)
-#else
-            0
-#endif
-            |
-#if EIGEN_MAX_ALIGN_BYTES>0
-            is_dynamic_size_storage
-#else
-            0
-#endif
-      )
-     ),
-    packet_access_bit = packet_traits<Scalar>::Vectorizable && is_aligned ? PacketAccessBit : 0
-  };
-
-  public:
-    enum { ret = packet_access_bit };
-};
-
-
-template<typename Scalar_, int NumIndices_, int Options_, typename IndexType_>
-struct traits<Tensor<Scalar_, NumIndices_, Options_, IndexType_> >
-{
-  typedef Scalar_ Scalar;
-  typedef Dense StorageKind;
-  typedef IndexType_ Index;
-  static const int NumDimensions = NumIndices_;
-  static const int Layout = Options_ & RowMajor ? RowMajor : ColMajor;
-  enum {
-    Options = Options_,
-    Flags = compute_tensor_flags<Scalar_, Options_>::ret | (is_const<Scalar_>::value ? 0 : LvalueBit)
-  };
-  template <typename T> struct MakePointer {
-    typedef T* Type;
-  };
-  typedef typename MakePointer<Scalar>::Type PointerType;
-};
-
-
-template<typename Scalar_, typename Dimensions, int Options_, typename IndexType_>
-struct traits<TensorFixedSize<Scalar_, Dimensions, Options_, IndexType_> >
-{
-  typedef Scalar_ Scalar;
-  typedef Dense StorageKind;
-  typedef IndexType_ Index;
-  static const int NumDimensions = array_size<Dimensions>::value;
-  static const int Layout = Options_ & RowMajor ? RowMajor : ColMajor;
-  enum {
-    Options = Options_,
-    Flags = compute_tensor_flags<Scalar_, Options_>::ret | (is_const<Scalar_>::value ? 0: LvalueBit)
-  };
-  template <typename T> struct MakePointer {
-    typedef T* Type;
-  };
-  typedef typename MakePointer<Scalar>::Type PointerType;
-};
-
-
-template<typename PlainObjectType, int Options_, template <class> class MakePointer_>
-struct traits<TensorMap<PlainObjectType, Options_, MakePointer_> >
-  : public traits<PlainObjectType>
-{
-  typedef traits<PlainObjectType> BaseTraits;
-  typedef typename BaseTraits::Scalar Scalar;
-  typedef typename BaseTraits::StorageKind StorageKind;
-  typedef typename BaseTraits::Index Index;
-  static const int NumDimensions = BaseTraits::NumDimensions;
-  static const int Layout = BaseTraits::Layout;
-  enum {
-    Options = Options_,
-    Flags = BaseTraits::Flags
-  };
-  template <class T> struct MakePointer {
-    // Intermediate typedef to workaround MSVC issue.
-    typedef MakePointer_<T> MakePointerT;
-    typedef typename MakePointerT::Type Type;
-  };
-  typedef typename MakePointer<Scalar>::Type PointerType;
-};
-
-template<typename PlainObjectType>
-struct traits<TensorRef<PlainObjectType> >
-  : public traits<PlainObjectType>
-{
-  typedef traits<PlainObjectType> BaseTraits;
-  typedef typename BaseTraits::Scalar Scalar;
-  typedef typename BaseTraits::StorageKind StorageKind;
-  typedef typename BaseTraits::Index Index;
-  static const int NumDimensions = BaseTraits::NumDimensions;
-  static const int Layout = BaseTraits::Layout;
-  enum {
-    Options = BaseTraits::Options,
-    Flags = BaseTraits::Flags
-  };
-  typedef typename BaseTraits::PointerType PointerType;
-};
-
-
-template<typename _Scalar, int NumIndices_, int Options, typename IndexType_>
-struct eval<Tensor<_Scalar, NumIndices_, Options, IndexType_>, Eigen::Dense>
-{
-  typedef const Tensor<_Scalar, NumIndices_, Options, IndexType_>EIGEN_DEVICE_REF type;
-};
-
-template<typename _Scalar, int NumIndices_, int Options, typename IndexType_>
-struct eval<const Tensor<_Scalar, NumIndices_, Options, IndexType_>, Eigen::Dense>
-{
-  typedef const Tensor<_Scalar, NumIndices_, Options, IndexType_>EIGEN_DEVICE_REF type;
-};
-
-template<typename Scalar_, typename Dimensions, int Options, typename IndexType_>
-struct eval<TensorFixedSize<Scalar_, Dimensions, Options, IndexType_>, Eigen::Dense>
-{
-  typedef const TensorFixedSize<Scalar_, Dimensions, Options, IndexType_>EIGEN_DEVICE_REF type;
-};
-
-template<typename Scalar_, typename Dimensions, int Options, typename IndexType_>
-struct eval<const TensorFixedSize<Scalar_, Dimensions, Options, IndexType_>, Eigen::Dense>
-{
-  typedef const TensorFixedSize<Scalar_, Dimensions, Options, IndexType_>EIGEN_DEVICE_REF type;
-};
-
-template<typename PlainObjectType, int Options, template <class> class MakePointer>
-struct eval<TensorMap<PlainObjectType, Options, MakePointer>, Eigen::Dense>
-{
-  typedef const TensorMap<PlainObjectType, Options, MakePointer>EIGEN_DEVICE_REF type;
-};
-
-template<typename PlainObjectType, int Options, template <class> class MakePointer>
-struct eval<const TensorMap<PlainObjectType, Options, MakePointer>, Eigen::Dense>
-{
-  typedef const TensorMap<PlainObjectType, Options, MakePointer>EIGEN_DEVICE_REF type;
-};
-
-template<typename PlainObjectType>
-struct eval<TensorRef<PlainObjectType>, Eigen::Dense>
-{
-  typedef const TensorRef<PlainObjectType>EIGEN_DEVICE_REF type;
-};
-
-template<typename PlainObjectType>
-struct eval<const TensorRef<PlainObjectType>, Eigen::Dense>
-{
-  typedef const TensorRef<PlainObjectType>EIGEN_DEVICE_REF type;
-};
-
-// TODO nested<> does not exist anymore in Eigen/Core, and it thus has to be removed in favor of ref_selector.
-template<typename T, int n=1, typename PlainObject = void> struct nested
-{
-  typedef typename ref_selector<T>::type type;
-};
-
-template <typename Scalar_, int NumIndices_, int Options_, typename IndexType_>
-struct nested<Tensor<Scalar_, NumIndices_, Options_, IndexType_> >
-{
-  typedef const Tensor<Scalar_, NumIndices_, Options_, IndexType_>EIGEN_DEVICE_REF type;
-};
-
-template <typename Scalar_, int NumIndices_, int Options_, typename IndexType_>
-struct nested<const Tensor<Scalar_, NumIndices_, Options_, IndexType_> >
-{
-  typedef const Tensor<Scalar_, NumIndices_, Options_, IndexType_>EIGEN_DEVICE_REF type;
-};
-
-template <typename Scalar_, typename Dimensions, int Options, typename IndexType_>
-struct nested<TensorFixedSize<Scalar_, Dimensions, Options, IndexType_> >
-{
-  typedef const TensorFixedSize<Scalar_, Dimensions, Options, IndexType_>EIGEN_DEVICE_REF type;
-};
-
-template <typename Scalar_, typename Dimensions, int Options, typename IndexType_>
-struct nested<const TensorFixedSize<Scalar_, Dimensions, Options, IndexType_> >
-{
-  typedef const TensorFixedSize<Scalar_, Dimensions, Options, IndexType_>EIGEN_DEVICE_REF type;
-};
-
-
-template <typename PlainObjectType>
-struct nested<TensorRef<PlainObjectType> >
-{
-  typedef const TensorRef<PlainObjectType>EIGEN_DEVICE_REF type;
-};
-
-template <typename PlainObjectType>
-struct nested<const TensorRef<PlainObjectType> >
-{
-  typedef const TensorRef<PlainObjectType>EIGEN_DEVICE_REF type;
-};
-
-}  // end namespace internal
-
-// Convolutional layers take in an input tensor of shape (D, R, C, B), or (D, C,
-// R, B), and convolve it with a set of filters, which can also be presented as
-// a tensor (D, K, K, M), where M is the number of filters, K is the filter
-// size, and each 3-dimensional tensor of size (D, K, K) is a filter. For
-// simplicity we assume that we always use square filters (which is usually the
-// case in images), hence the two Ks in the tensor dimension.  It also takes in
-// a few additional parameters:
-// Stride (S): The convolution stride is the offset between locations where we
-//             apply the filters.  A larger stride means that the output will be
-//             spatially smaller.
-// Padding (P): The padding we apply to the input tensor along the R and C
-//              dimensions.  This is usually used to make sure that the spatial
-//              dimensions of the output matches our intention.
-//
-// Two types of padding are often used:
-//   SAME: The pad value is computed so that the output will have size
-//         R/S and C/S.
-//   VALID: no padding is carried out.
-// When we do padding, the padded values at the padded locations are usually
-// zero.
-//
-// The output dimensions for convolution, when given all the parameters above,
-// are as follows:
-// When Padding = SAME: the output size is (B, R', C', M), where
-//   R' = ceil(float(R) / float(S))
-//   C' = ceil(float(C) / float(S))
-// where ceil is the ceiling function.  The input tensor is padded with 0 as
-// needed.  The number of padded rows and columns are computed as:
-//   Pr = ((R' - 1) * S + K - R) / 2
-//   Pc = ((C' - 1) * S + K - C) / 2
-// when the stride is 1, we have the simplified case R'=R, C'=C, Pr=Pc=(K-1)/2.
-// This is where SAME comes from - the output has the same size as the input has.
-// When Padding = VALID: the output size is computed as
-//   R' = ceil(float(R - K + 1) / float(S))
-//   C' = ceil(float(C - K + 1) / float(S))
-// and the number of padded rows and columns are computed in the same way as in
-// the SAME case.
-// When the stride is 1, we have the simplified case R'=R-K+1, C'=C-K+1, Pr=0,
-// Pc=0.
-typedef enum {
-  PADDING_VALID = 1,
-  PADDING_SAME = 2
-} PaddingType;
-
-}  // end namespace Eigen
-
-#endif // EIGEN_CXX11_TENSOR_TENSOR_TRAITS_H

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorUInt128.h

@@ -1,249 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2015 Benoit Steiner <benoit.steiner.goog@gmail.com>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_CXX11_TENSOR_TENSOR_UINT128_H
-#define EIGEN_CXX11_TENSOR_TENSOR_UINT128_H
-
-namespace Eigen {
-namespace internal {
-
-
-template <uint64_t n>
-struct static_val {
-  static const uint64_t value = n;
-  EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE operator uint64_t() const { return n; }
-
-  EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE static_val() { }
-
-  template <typename T>
-  EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE static_val(const T& v) {
-    EIGEN_UNUSED_VARIABLE(v);
-    eigen_assert(v == n);
-  }
-};
-
-
-template <typename HIGH = uint64_t, typename LOW = uint64_t>
-struct TensorUInt128
-{
-  HIGH high;
-  LOW low;
-
-  template<typename OTHER_HIGH, typename OTHER_LOW>
-  EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-  TensorUInt128(const TensorUInt128<OTHER_HIGH, OTHER_LOW>& other) : high(other.high), low(other.low) {
-    EIGEN_STATIC_ASSERT(sizeof(OTHER_HIGH) <= sizeof(HIGH), YOU_MADE_A_PROGRAMMING_MISTAKE);
-    EIGEN_STATIC_ASSERT(sizeof(OTHER_LOW) <= sizeof(LOW), YOU_MADE_A_PROGRAMMING_MISTAKE);
-  }
-
-  template<typename OTHER_HIGH, typename OTHER_LOW>
-  EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-  TensorUInt128& operator = (const TensorUInt128<OTHER_HIGH, OTHER_LOW>& other) {
-    EIGEN_STATIC_ASSERT(sizeof(OTHER_HIGH) <= sizeof(HIGH), YOU_MADE_A_PROGRAMMING_MISTAKE);
-    EIGEN_STATIC_ASSERT(sizeof(OTHER_LOW) <= sizeof(LOW), YOU_MADE_A_PROGRAMMING_MISTAKE);
-    high = other.high;
-    low = other.low;
-    return *this;
-  }
-
-  template<typename T>
-  EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-  explicit TensorUInt128(const T& x) : high(0), low(x) {
-    eigen_assert((static_cast<typename conditional<sizeof(T) == 8, uint64_t, uint32_t>::type>(x) <= NumTraits<uint64_t>::highest()));
-    eigen_assert(x >= 0);
-  }
-
-  EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-  TensorUInt128(HIGH y, LOW x) : high(y), low(x) { }
-
-  EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE operator LOW() const {
-    return low;
-  }
-  EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE LOW lower() const {
-    return low;
-  }
-  EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE HIGH upper() const {
-    return high;
-  }
-};
-
-
-template <typename HL, typename LL, typename HR, typename LR>
-EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-bool operator == (const TensorUInt128<HL, LL>& lhs, const TensorUInt128<HR, LR>& rhs)
-{
-  return (lhs.high == rhs.high) & (lhs.low == rhs.low);
-}
-
-template <typename HL, typename LL, typename HR, typename LR>
-EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-bool operator != (const TensorUInt128<HL, LL>& lhs, const TensorUInt128<HR, LR>& rhs)
-{
-  return (lhs.high != rhs.high) | (lhs.low != rhs.low);
-}
-
-template <typename HL, typename LL, typename HR, typename LR>
-EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-bool operator >= (const TensorUInt128<HL, LL>& lhs, const TensorUInt128<HR, LR>& rhs)
-{
-  if (lhs.high != rhs.high) {
-    return lhs.high > rhs.high;
-  }
-  return lhs.low >= rhs.low;
-}
-
-template <typename HL, typename LL, typename HR, typename LR>
-EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-bool operator < (const TensorUInt128<HL, LL>& lhs, const TensorUInt128<HR, LR>& rhs)
-{
-  if (lhs.high != rhs.high) {
-    return lhs.high < rhs.high;
-  }
-  return lhs.low < rhs.low;
-}
-
-template <typename HL, typename LL, typename HR, typename LR>
-EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-TensorUInt128<uint64_t, uint64_t> operator + (const TensorUInt128<HL, LL>& lhs, const TensorUInt128<HR, LR>& rhs)
-{
-  TensorUInt128<uint64_t, uint64_t> result(lhs.high + rhs.high, lhs.low + rhs.low);
-  if (result.low < rhs.low) {
-    result.high += 1;
-  }
-  return result;
-}
-
-template <typename HL, typename LL, typename HR, typename LR>
-EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-TensorUInt128<uint64_t, uint64_t> operator - (const TensorUInt128<HL, LL>& lhs, const TensorUInt128<HR, LR>& rhs)
-{
-  TensorUInt128<uint64_t, uint64_t> result(lhs.high - rhs.high, lhs.low - rhs.low);
-  if (result.low > lhs.low) {
-    result.high -= 1;
-  }
-  return result;
-}
-
-
-template <typename HL, typename LL, typename HR, typename LR>
-static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
-TensorUInt128<uint64_t, uint64_t> operator * (const TensorUInt128<HL, LL>& lhs, const TensorUInt128<HR, LR>& rhs)
-{
-  // Split each 128-bit integer into 4 32-bit integers, and then do the
-  // multiplications by hand as follow:
-  //   lhs      a  b  c  d
-  //   rhs      e  f  g  h
-  //           -----------
-  //           ah bh ch dh
-  //           bg cg dg
-  //           cf df
-  //           de
-  // The result is stored in 2 64bit integers, high and low.
-
-  const uint64_t LOW = 0x00000000FFFFFFFFLL;
-  const uint64_t HIGH = 0xFFFFFFFF00000000LL;
-
-  uint64_t d = lhs.low & LOW;
-  uint64_t c = (lhs.low & HIGH) >> 32LL;
-  uint64_t b = lhs.high & LOW;
-  uint64_t a = (lhs.high & HIGH) >> 32LL;
-
-  uint64_t h = rhs.low & LOW;
-  uint64_t g = (rhs.low & HIGH) >> 32LL;
-  uint64_t f = rhs.high & LOW;
-  uint64_t e = (rhs.high & HIGH) >> 32LL;
-
-  // Compute the low 32 bits of low
-  uint64_t acc = d * h;
-  uint64_t low = acc & LOW;
-  //  Compute the high 32 bits of low. Add a carry every time we wrap around
-  acc >>= 32LL;
-  uint64_t carry = 0;
-  uint64_t acc2 = acc + c * h;
-  if (acc2 < acc) {
-    carry++;
-  }
-  acc = acc2 + d * g;
-  if (acc < acc2) {
-    carry++;
-  }
-  low |= (acc << 32LL);
-
-  // Carry forward the high bits of acc to initiate the computation of the
-  // low 32 bits of high
-  acc2 = (acc >> 32LL) | (carry << 32LL);
-  carry = 0;
-
-  acc = acc2 + b * h;
-  if (acc < acc2) {
-    carry++;
-  }
-  acc2 = acc + c * g;
-  if (acc2 < acc) {
-    carry++;
-  }
-  acc = acc2 + d * f;
-  if (acc < acc2) {
-    carry++;
-  }
-  uint64_t high = acc & LOW;
-
-  // Start to compute the high 32 bits of high.
-  acc2 = (acc >> 32LL) | (carry << 32LL);
-
-  acc = acc2 + a * h;
-  acc2 = acc + b * g;
-  acc = acc2 + c * f;
-  acc2 = acc + d * e;
-  high |= (acc2 << 32LL);
-
-  return TensorUInt128<uint64_t, uint64_t>(high, low);
-}
-
-template <typename HL, typename LL, typename HR, typename LR>
-static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
-TensorUInt128<uint64_t, uint64_t> operator / (const TensorUInt128<HL, LL>& lhs, const TensorUInt128<HR, LR>& rhs)
-{
-  if (rhs == TensorUInt128<static_val<0>, static_val<1> >(1)) {
-    return TensorUInt128<uint64_t, uint64_t>(lhs.high, lhs.low);
-  } else if (lhs < rhs) {
-    return TensorUInt128<uint64_t, uint64_t>(0);
-  } else {
-    // calculate the biggest power of 2 times rhs that's less than or equal to lhs
-    TensorUInt128<uint64_t, uint64_t> power2(1);
-    TensorUInt128<uint64_t, uint64_t> d(rhs);
-    TensorUInt128<uint64_t, uint64_t> tmp(lhs - d);
-    while (lhs >= d) {
-      tmp = tmp - d;
-      d = d + d;
-      power2 = power2 + power2;
-    }
-
-    tmp = TensorUInt128<uint64_t, uint64_t>(lhs.high, lhs.low);
-    TensorUInt128<uint64_t, uint64_t> result(0);
-    while (power2 != TensorUInt128<static_val<0>, static_val<0> >(0)) {
-      if (tmp >= d) {
-        tmp = tmp - d;
-        result = result + power2;
-      }
-      // Shift right
-      power2 = TensorUInt128<uint64_t, uint64_t>(power2.high >> 1, (power2.low >> 1) | (power2.high << 63));
-      d = TensorUInt128<uint64_t, uint64_t>(d.high >> 1, (d.low >> 1) | (d.high << 63));
-    }
-
-    return result;
-  }
-}
-
-
-}  // namespace internal
-}  // namespace Eigen
-
-
-#endif  // EIGEN_CXX11_TENSOR_TENSOR_UINT128_H