commit 3c12bbe8a8162ac2ddc0f23083044ff8280a8567 parent 2816588db7ff2c82c7441f7485221ac22abcbbb1 Author: [email protected] <[email protected]> Date: Thu, 21 Dec 2023 13:10:18 +0000 .npy reading/writing Diffstat:
316 files changed, 625 insertions(+), 0 deletions(-)
diff --git a/include/kfr/base/npy.hpp b/include/kfr/base/npy.hpp @@ -0,0 +1,494 @@ +/** @addtogroup tensor + * @{ + */ +/* + Copyright (C) 2016-2023 Dan Cazarin (https://www.kfrlib.com) + This file is part of KFR + + KFR is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 2 of the License, or + (at your option) any later version. + + KFR is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with KFR. + + If GPL is not suitable for your project, you must purchase a commercial license to use KFR. + Buying a commercial license is mandatory as soon as you develop commercial activities without + disclosing the source code of your own applications. + See https://www.kfrlib.com for details. + */ +#pragma once + +#include "tensor.hpp" +#include <complex> +#include <kfr/base/endianness.hpp> +#include <kfr/simd/complex.hpp> + +namespace kfr +{ + +namespace internal_generic +{ +template <typename T> +std::string_view npy_format() +{ + using namespace cometa; + static_assert(is_poweroftwo(sizeof(T)) && is_between(sizeof(T), 1, 16)); + if constexpr (std::is_floating_point_v<T>) + { + const std::string_view fmts[] = { "|f1", "<f2", "<f4", "<f8" }; + static_assert(sizeof(T) <= 8); + return fmts[ilog2(sizeof(T))]; + } + else if constexpr (std::is_integral_v<T> && std::is_unsigned_v<T>) + { + const std::string_view fmts[] = { "|u1", "<u2", "<u4", "<u8" }; + static_assert(sizeof(T) <= 8); + return fmts[ilog2(sizeof(T))]; + } + else if constexpr (std::is_integral_v<T> && std::is_signed_v<T>) + { + const std::string_view fmts[] = { "|i1", "<i2", "<i4", "<i8" }; + static_assert(sizeof(T) <= 8); + return fmts[ilog2(sizeof(T))]; + } + else if constexpr (is_complex<T>) + { + const std::string_view fmts[] = { "|c1", "<c2", "<c4", "<c8", "<c16" }; + static_assert(sizeof(T) <= 16); + return fmts[ilog2(sizeof(T))]; + } + else if constexpr (std::is_same_v<T, bool>) + { + return "|b1"; + } + else + { + static_assert("Cannot save type to python"); + return ""; + } +} +template <index_t Dim> +std::string npy_shape(shape<Dim> sh) +{ + std::string result = "("; + for (index_t i : sh) + { + if (result.size() > 1) + result += ", "; + result += std::to_string(i); + } + if (Dim == 1) + result += ","; + return result + ")"; +} + +template <typename Fn> +struct npy_writer +{ + Fn&& fn; + size_t written = 0; + + void operator()(const void* d, size_t size) + { + fn(d, size); + written += size; + } + void operator()(std::string_view s) { operator()(s.data(), s.size()); } + void operator()(std::initializer_list<uint8_t> b) { operator()(&*b.begin(), b.size()); } + + template <typename Num> + void operator()(cometa::ctype_t<Num>, cometa::identity<Num> n) + { + operator()(&n, sizeof(Num)); + } + template <typename Num> + void operator()(cometa::ctype_t<Num>, const Num* n, size_t count) + { + operator()(n, sizeof(Num) * count); + } +}; + +template <typename Fn> +struct npy_reader +{ + Fn&& fn; + + bool operator()(void* d, size_t size) { return fn(d, size); } + + template <typename Num> + Num operator()(cometa::ctype_t<Num>) + { + Num result; + if (!operator()(&result, sizeof(Num))) + return {}; + return result; + } + template <typename Num> + bool operator()(cometa::ctype_t<Num>, Num& n) + { + return operator()(&n, sizeof(Num)); + } + template <typename Num> + bool operator()(cometa::ctype_t<Num>, Num* n, size_t count) + { + return operator()(n, sizeof(Num) * count); + } + + std::string operator()(cometa::ctype_t<char>, size_t count) + { + std::string result(count, ' '); + if (!operator()(cometa::ctype<char>, result.data(), count)) + return {}; + return result; + } +}; + +struct npy_header +{ + std::string descr; + bool fortran_order = false; + std::vector<index_t> shape; +}; + +inline bool npy_skip_whitespace(std::string_view& data) +{ + while (!data.empty() && uint8_t(data[0]) <= uint8_t(' ')) + data = data.substr(1); + return !data.empty(); +} +inline bool npy_parse_string(std::string_view& data, std::string& content, char q = '\'') +{ + if (data.empty() || data[0] != q) + return false; + data = data.substr(1); + while (!data.empty() && data[0] != q) + { + if (data[0] == '\\') + { + data = data.substr(1); + if (data.empty()) + return false; + } + content += data[0]; + data = data.substr(1); + } + if (data.empty()) + return false; + data = data.substr(1); + return true; +} + +inline bool npy_skip_value(std::string_view& data, char close = '}', std::string context = {}) +{ + std::string dummy; + while (!data.empty()) + { + switch (data[0]) + { + case '\'': + case '"': + if (!npy_parse_string(data, dummy, data[0])) + return false; + break; + case '(': + case '[': + case '{': + context += data[0]; + break; + case ')': + case ']': + case '}': + if (context.empty()) + return data[0] == close; + if (context.back() == data[0]) + context.pop_back(); + break; + case ',': + if (context.empty()) + return true; + else + data = data.substr(1); + break; + default: + data = data.substr(1); + break; + } + } + return false; +} + +inline bool npy_parse_bool(std::string_view& data, bool& content) +{ + if (data.size() >= 5 && data.substr(0, 5) == "False") + { + content = false; + data = data.substr(5); + return true; + } + if (data.size() >= 4 && data.substr(0, 4) == "True") + { + content = true; + data = data.substr(4); + return true; + } + return false; +} +inline bool npy_parse_integer(std::string_view& data, index_t& content) +{ + const char* orig = data.data(); + if (data[0] < '0' || data[0] > '9') + return false; + + while (data[0] >= '0' && data[0] <= '9') + data = data.substr(1); + content = std::stoll(std::string(orig, data.data() - orig)); + return true; +} +inline bool npy_parse_shape(std::string_view& data, std::vector<index_t>& content) +{ + if (data[0] != '(') + return false; + data = data.substr(1); + if (!npy_skip_whitespace(data)) + return false; + for (;;) + { + index_t num; + if (!npy_parse_integer(data, num)) + return false; + content.push_back(num); + if (!npy_skip_whitespace(data)) + return false; + if (data[0] == ')') + { + data = data.substr(1); + return true; + } + if (data[0] != ',') + return false; + data = data.substr(1); + if (!npy_skip_whitespace(data)) + return false; + if (data[0] == ')') + { + data = data.substr(1); + return true; + } + } +} + +inline bool npy_decode_field(std::string_view& data, npy_header& hdr) +{ + if (!npy_skip_whitespace(data)) + return false; + std::string name; + if (!npy_parse_string(data, name)) + return false; + if (!npy_skip_whitespace(data)) + return false; + if (data.empty() || data[0] != ':') + return false; + data = data.substr(1); + if (!npy_skip_whitespace(data)) + return false; + if (data.empty()) + return false; + + if (name == "descr") + { + return npy_parse_string(data, hdr.descr); + } + else if (name == "fortran_order") + { + return npy_parse_bool(data, hdr.fortran_order); + } + else if (name == "shape") + { + return npy_parse_shape(data, hdr.shape); + } + else + { + return npy_skip_value(data); + } + + if (!npy_skip_whitespace(data)) + return false; + if (data.empty() || data[0] != ',') + return false; + data = data.substr(1); + return true; +} + +inline bool npy_decode_dict(std::string_view data, npy_header& hdr) +{ + if (data.size() < 10 || data[0] != '{') + return false; + data = data.substr(1); + while (!data.empty() && data[0] != '}') + { + if (!npy_decode_field(data, hdr)) + { + return false; + } + if (data[0] == '}') + return true; + if (data.empty() || data[0] != ',') + return false; + data = data.substr(1); + if (!npy_skip_whitespace(data)) + return false; + } + return !data.empty() && data[0] == '}'; +} + +inline std::string_view npy_magic = "\x93NUMPY"; + +} // namespace internal_generic + +template <typename T, index_t Dims, typename Fn> +void save_to_npy(const tensor<T, Dims>& t, Fn&& write_callback) +{ + using namespace internal_generic; + + npy_writer<Fn&> wr{ write_callback }; + wr(internal_generic::npy_magic); + wr(ctype<uint16_t>, 0x0001); + + std::string header = std::string("{'descr': '") + std::string(npy_format<T>()) + + "', 'fortran_order': False, 'shape': " + npy_shape(t.shape()) + ", }"; + + std::string_view padding = " "; + + size_t total_header = cometa::align_up(wr.written + 2 + header.size() + 1, 64); + header += padding.substr(0, total_header - (wr.written + 2 + header.size() + 1)); + header += '\n'; + uint16_t header_len = header.size(); + wr(cometa::ctype<uint16_t>, header_len); + wr(header); + if (t.is_contiguous()) + { + wr(cometa::ctype<T>, t.data(), t.size()); + } + else + { + tensor<T, Dims> copy = t.copy(); + wr(cometa::ctype<T>, copy.data(), copy.size()); + } +} + +enum class npy_decode_result +{ + ok, + cannot_read, + invalid_header, + invalid_type, + invalid_shape, +}; + +template <typename T, index_t Dims, typename Fn> +npy_decode_result load_from_npy(tensor<T, Dims>& result, Fn&& read_callback) +{ + using namespace internal_generic; + + npy_reader<Fn&> rd{ read_callback }; + + if (std::string s = rd(ctype<char>, internal_generic::npy_magic.size()); s != internal_generic::npy_magic) + return npy_decode_result::cannot_read; + uint16_t v; + if (v = rd(ctype<uint16_t>); v != 1 && v != 2 && v != 3) + return npy_decode_result::cannot_read; + uint32_t header_len; + if (v >= 2) + { + if (!rd(ctype<uint32_t>, header_len)) + return npy_decode_result::cannot_read; + } + else + { + uint16_t header_len16; + if (!rd(ctype<uint16_t>, header_len16)) + return npy_decode_result::cannot_read; + header_len = header_len16; + } + std::string header = rd(ctype<char>, header_len); + + npy_header hdr; + if (!npy_decode_dict(header, hdr)) + return npy_decode_result::invalid_header; + + std::string_view tfmt = npy_format<T>(); + bool convert_endianness = false; + if (hdr.descr != tfmt) + { + if (hdr.descr.size() > 1 && hdr.descr[0] != tfmt[0] && hdr.descr.substr(1) == tfmt.substr(1)) + { + convert_endianness = hdr.descr[0] == '>'; + } + else + { + return npy_decode_result::invalid_type; + } + } + if (hdr.shape.size() != Dims) + return npy_decode_result::invalid_shape; + + shape<Dims> sh; + std::copy(hdr.shape.begin(), hdr.shape.end(), sh.begin()); + if (sh.product() == 0) + return npy_decode_result::invalid_shape; + + tensor<T, 1> buffer(shape<1>{ sh.product() }); + + rd(ctype<T>, buffer.data(), buffer.size()); + if (convert_endianness) + { + convert_endianess(buffer.data(), buffer.size()); + } + if (hdr.fortran_order) + { + result = tensor<T, Dims>(buffer.data(), sh, internal_generic::strides_for_shape<Dims, true>(sh), + buffer.finalizer()); + } + else + { + result = tensor<T, Dims>(buffer.data(), sh, internal_generic::strides_for_shape<Dims, false>(sh), + buffer.finalizer()); + } + + return npy_decode_result::ok; +} +} // namespace kfr + +namespace cometa +{ +template <> +struct representation<kfr::npy_decode_result> +{ + using type = std::string; + static std::string get(kfr::npy_decode_result value) + { + switch (value) + { + case kfr::npy_decode_result::ok: + return "ok"; + case kfr::npy_decode_result::cannot_read: + return "cannot_read"; + case kfr::npy_decode_result::invalid_header: + return "invalid_header"; + case kfr::npy_decode_result::invalid_type: + return "invalid_type"; + case kfr::npy_decode_result::invalid_shape: + return "invalid_shape"; + default: + return "(unknown)"; + } + } +}; +} // namespace cometa diff --git a/sources.cmake b/sources.cmake @@ -31,6 +31,7 @@ set( ${PROJECT_SOURCE_DIR}/include/kfr/base/handle.hpp ${PROJECT_SOURCE_DIR}/include/kfr/base/math_expressions.hpp ${PROJECT_SOURCE_DIR}/include/kfr/base/memory.hpp + ${PROJECT_SOURCE_DIR}/include/kfr/base/npy.hpp ${PROJECT_SOURCE_DIR}/include/kfr/base/random.hpp ${PROJECT_SOURCE_DIR}/include/kfr/base/random_bits.hpp ${PROJECT_SOURCE_DIR}/include/kfr/base/reduce.hpp @@ -238,6 +239,7 @@ set( ${PROJECT_SOURCE_DIR}/include/kfr/base/handle.hpp ${PROJECT_SOURCE_DIR}/include/kfr/base/math_expressions.hpp ${PROJECT_SOURCE_DIR}/include/kfr/base/memory.hpp + ${PROJECT_SOURCE_DIR}/include/kfr/base/npy.hpp ${PROJECT_SOURCE_DIR}/include/kfr/base/random.hpp ${PROJECT_SOURCE_DIR}/include/kfr/base/random_bits.hpp ${PROJECT_SOURCE_DIR}/include/kfr/base/reduce.hpp @@ -328,6 +330,7 @@ set( ${PROJECT_SOURCE_DIR}/include/kfr/base/handle.hpp 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b/tests/unit/base/npy.cpp @@ -0,0 +1,126 @@ +/** + * KFR (https://www.kfrlib.com) + * Copyright (C) 2016-2023 Dan Cazarin + * See LICENSE.txt for details + */ + +#include <kfr/base.hpp> +#include <kfr/base/npy.hpp> +#include <kfr/io/file.hpp> +#include <kfr/io/tostring.hpp> + +namespace kfr +{ +inline namespace CMT_ARCH_NAME +{ + +template <index_t Dims> +static std::string shape_str(shape<Dims> size) +{ + if constexpr (Dims == 1) + return std::to_string(size.back()); + else + return shape_str(size.remove_back()) + "x" + std::to_string(size.back()); +} + +template <typename T> +static std::string py_type() +{ + if constexpr (std::is_same_v<T, bool>) + return "bool"; + else if constexpr (std::is_floating_point_v<T>) + return "float" + std::to_string(sizeof(T) * 8); + else if constexpr (is_complex<T>) + return "complex" + std::to_string(sizeof(T) * 8); + else if constexpr (std::is_unsigned_v<T>) + return "uint" + std::to_string(sizeof(T) * 8); + else if constexpr (std::is_signed_v<T>) + return "int" + std::to_string(sizeof(T) * 8); + else + return "?"; +} + +template <typename T, index_t Dims> +static std::string filename(shape<Dims> size, int ver, char order, char endianness) +{ + return shape_str(size) + "-" + py_type<T>() + "-v" + std::to_string(ver) + "-" + order + "-" + + endianness + "e.npy"; +} + +template <typename T, index_t Dims> +static void test_npy_t(shape<Dims> size) +{ + for (int ver : { 1, 2 }) + { + for (char order : { 'c', 'f' }) + { + for (char endianness : { 'l', 'b' }) + { + std::string filepath = + KFR_SRC_DIR "/tests/npy/" + filename<T, Dims>(size, ver, order, endianness); + testo::scope s(filepath); + std::shared_ptr<file_reader<void>> f = open_file_for_reading(filepath); + CHECK(f != nullptr); + if (!f) + continue; + + tensor<T, Dims> data; + tensor<T, Dims> reference(size); + reference.flatten() = counter<subtype<T>>(); + npy_decode_result result = + load_from_npy(data, [f](void* d, size_t size) { return f->read(d, size) == size; }); + CHECK(result == npy_decode_result::ok); + CHECK(data.shape() == size); + CHECK(data == reference); + + if (endianness == 'l' && order == 'c' && ver == 1) + { + f->seek(0, seek_origin::end); + std::vector<uint8_t> reference_binary; + reference_binary.resize(f->tell()); + f->seek(0, seek_origin::begin); + f->read(reference_binary.data(), reference_binary.size()); + + std::vector<uint8_t> binary; + save_to_npy(reference, + [&](const void* d, size_t sz) + { + binary.insert(binary.end(), reinterpret_cast<const uint8_t*>(d), + reinterpret_cast<const uint8_t*>(d) + sz); + }); + CHECK(binary.size() == reference_binary.size()); + CHECK(std::equal(binary.begin(), binary.end(), reference_binary.begin(), + reference_binary.end())); + } + } + } + } +} + +template <index_t Dims> +static void test_npy(shape<Dims> size) +{ + test_npy_t<u8>(size); + test_npy_t<u16>(size); + test_npy_t<u32>(size); + test_npy_t<u64>(size); + test_npy_t<i8>(size); + test_npy_t<i16>(size); + test_npy_t<i32>(size); + test_npy_t<i64>(size); + test_npy_t<f32>(size); + test_npy_t<f64>(size); + test_npy_t<c32>(size); + test_npy_t<c64>(size); + // test_npy_t<bool>(size); +} + +TEST(npy_all) +{ + test_npy(shape{ 110 }); + test_npy(shape{ 10, 11 }); + test_npy(shape{ 2, 5, 11 }); +} + +} // namespace CMT_ARCH_NAME +} // namespace kfr diff --git a/tests/unit/base/tensor.cpp b/tests/unit/base/tensor.cpp @@ -6,6 +6,7 @@ #include <kfr/base/basic_expressions.hpp> #include <kfr/base/math_expressions.hpp> +#include <kfr/base/npy.hpp> #include <kfr/base/reduce.hpp> #include <kfr/base/simd_expressions.hpp> #include <kfr/base/tensor.hpp>