sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
5fb31db6cd05bba8806d274d04bab79ffa09a9170c0fb960d276972e412abafb | C++ | 821 | 33 | #include <src/args.h>
#include <src/jaz/tomography/tomogram.h>
#include <src/jaz/tomography/projection/real_backprojection.h>
#include <src/jaz/tomography/tomogram_set.h>
#include <src/jaz/image/resampling.h>
#include <src/jaz/image/filter.h>
#include <src/jaz/image/detection.h>
#include <src/jaz/image/similarity.h>
#i... |
bef0da37c9e80e5773726d912aeb76a5df6da4f43083076a84d6064cbaf26546 | C++ | 840 | 24 | #define TORCH_ASSERT_NO_OPERATORS
#include <ATen/native/UnaryOps.h>
#include <ATen/Dispatch.h>
#include <ATen/native/Math.h>
#include <ATen/native/TensorIterator.h>
#include <ATen/native/cpu/Loops.h>
namespace at::native {
inline namespace CPU_CAPABILITY {
static void spherical_bessel_j0_kernel(TensorIteratorBas... |
1c16157780a09e1ca5fe717efa9a71390e19fa2a6b2df8b64e9da1d80281bc2b | C++ | 852 | 50 | #include "catalogue.h"
#include <fstream>
Catalogue::Catalogue()
{
}
Catalogue::Catalogue(std::string filename)
{
std::ifstream ifs(filename);
const int maxlen = 4096;
char buffer[maxlen];
while (ifs.getline(buffer, maxlen))
{
particles.push_back(DynamoParticle(buffer));
}
}
std::vector<std::vector<Dynam... |
5b47a8fd29cf42c3dcd21e24be96d87527747d35ce2f985f88b78daa712f8be5 | C++ | 853 | 39 | #include <hip/hip_runtime.h>
#include "test00.h"
#include "kernels/add.h"
#include <iostream>
void HipTest00 :: run()
{
int N = 1<<20; // 1M elements
// Allocate Unified Memory -- accessible from CPU or GPU
float *x, *y;
hipMallocManaged(&x, N*sizeof(float));
hipMallocManaged(&y, N*sizeof(float));
// ini... |
f5268f4d0cb71e10cffabf9192e23cc5a6455e8074073185fe7bd8a60854cc1a | C++ | 853 | 29 | #include <ATen/detail/PrivateUse1HooksInterface.h>
namespace at {
static PrivateUse1HooksInterface* privateuse1_hooks = nullptr;
static std::mutex _hooks_mutex_lock;
TORCH_API void RegisterPrivateUse1HooksInterface(at::PrivateUse1HooksInterface* hook_) {
std::lock_guard<std::mutex> lock(_hooks_mutex_lock);
TORCH... |
7d918dbe2f9663ae93449c6b7bb0dde32cf27e21a3b9c4ba13e893b003b3fb16 | C++ | 861 | 29 | #include <ATen/Config.h>
#if AT_MKL_ENABLED()
#ifdef USE_MIMALLOC_ON_MKL
#include <c10/core/impl/alloc_cpu.h>
#include <mkl.h>
#if INTEL_MKL_VERSION > 20230000L
/*
MKL have a method to register memory allocation APIs via i_malloc.h, High
performance memory allocation APIs will help improve MKL performance.
Please chec... |
a1ed13ad0e2e9aa1d42ff686a5328dbe178ae268ca404bfee95dc74cff00cff5 | C++ | 862 | 40 | #include "Fourier_2D_deformation_model.h"
Fourier2DDeformationModel::Fourier2DDeformationModel()
{
}
Fourier2DDeformationModel::Fourier2DDeformationModel(
const Deformation2D::Parameters& parameters,
const gravis::i2Vector& imageSize)
:
imageSize(imageSize),
gridSize(parameters.grid_width, parameters.gri... |
af63e0ef4e02d8cee297b58f86c113701dc4c310f428b9f8483d38954ba96d90 | C++ | 871 | 41 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/native/UnfoldBackward.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#include <ATen/NativeFunctions.h>
#else
#include <ATen/ops/unfold_backward_native.h>
#include <ATen/ops/zeros.h>
#endif
namespace at::native {
DEFINE_DISPATCH(unfold_backward... |
3bf129d56ae8123c55dc00f1c2364131c01933539c572f2aa1906a9255a0bb51 | C++ | 877 | 24 | #define TORCH_ASSERT_NO_OPERATORS
#include <ATen/native/UnaryOps.h>
#include <ATen/Dispatch.h>
#include <ATen/native/Math.h>
#include <ATen/native/TensorIterator.h>
#include <ATen/native/cpu/Loops.h>
namespace at::native {
inline namespace CPU_CAPABILITY {
static void scaled_modified_bessel_k1_kernel(TensorItera... |
bb7167135f7923a1729d518ae0df48f549f02dede0e96428ddd237756d46acba | C++ | 877 | 24 | #define TORCH_ASSERT_NO_OPERATORS
#include <ATen/native/UnaryOps.h>
#include <ATen/Dispatch.h>
#include <ATen/native/Math.h>
#include <ATen/native/TensorIterator.h>
#include <ATen/native/cpu/Loops.h>
namespace at::native {
inline namespace CPU_CAPABILITY {
static void scaled_modified_bessel_k0_kernel(TensorItera... |
17dc02d78421a885d70ae2fb281dbd25c94948693dff45fb67b8c1bf29bd67ae | C++ | 883 | 30 | #include <src/args.h>
#include <src/jaz/tomography/programs/powspec.h>
int main(int argc, char *argv[])
{
IOParser parser;
PowspecProgram pp;
parser.setCommandLine(argc, argv);
int gen_section = parser.addSection("General options");
pp.stackFn = parser.getOption("--ts", "Tilt stack(s) (e.g. 'a.mrc,b.mrc')");... |
5df20fe03b4cceeabfc82a7ee2543700a796c2bdba906799e10db495ddf9a074 | C++ | 886 | 41 |
#include <unistd.h>
#include <string.h>
#include <fstream>
#include <src/args.h>
#include <src/image.h>
#include <src/fftw.h>
#include <src/complex.h>
#include <src/metadata_table.h>
#include <src/jaz/single_particle/slice_helper.h>
#include <src/jaz/single_particle/img_proc/filter_helper.h>
#include <src/jaz/single_... |
a05de4e580166bbaa2f34d2808de9147116464c1474b40abeb5f877accad1630 | C++ | 887 | 33 | #include <ATen/core/CachingHostAllocator.h>
#include <array>
namespace at {
namespace {
std::array<HostAllocator*, at::COMPILE_TIME_MAX_DEVICE_TYPES>
allocator_array{};
std::array<uint8_t, at::COMPILE_TIME_MAX_DEVICE_TYPES>
allocator_priority{};
} // anonymous namespace
void setHostAllocator(
at::Devi... |
16754f831c724b80e6080743cc1dd63ae66b2d42cae417c240e990e97977a56c | C++ | 890 | 19 | #include <gtest/gtest.h>
#include <ATen/core/op_registration/op_allowlist.h>
namespace allowlist_contains_test {
static_assert(c10::impl::allowlist_contains("", ""), "");
static_assert(!c10::impl::allowlist_contains("", "a"), "");
static_assert(!c10::impl::allowlist_contains("a", ""), "");
static_assert(!c10::... |
c0a316e826e0819862f1bb6b87941b3ef4e233353d980c517f99a59c2abedd17 | C++ | 897 | 32 | /* Portions of this code are under:
Copyright (c) 2022 Advanced Micro Devices, Inc. All rights reserved.
*/
#undef ALTCPU
#include <hip/hip_runtime.h>
#include "src/ml_optimiser.h"
#include "src/acc/acc_ptr.h"
#include "src/acc/acc_projector.h"
#include "src/acc/acc_projector_plan.h"
#include "src/acc/acc_backprojec... |
a5b2d8e580735882b3f3bf554fd8721f9c70f7905ee97030592cee54ddcf2f22 | C++ | 899 | 40 | #include "filament_model.h"
#include "coordinate_conventions.h"
#include <omp.h>
using namespace gravis;
void DummyFilamentModel::apply(
const std::vector<double>& params,
const std::vector<std::vector<float>>& encodedCoords,
std::vector<std::vector<float>>& signedDist_out,
int num_threads) const
{
const... |
0ff520e89d00e2bf59f1f06a83a969242e1bb1059778fa851f3dc9d9df05f785 | C++ | 903 | 49 | #include "recursive_line_search.h"
#include <limits>
#include <iostream>
double RecursiveLineSearch::optimize(
const Optimization &opt, double x0, double x1, int steps, int recursions, bool verbose)
{
double bestX = x0;
double minCost = std::numeric_limits<double>::max();
const double step = (x1 - x0) / (steps... |
a130ab2ad83a2f33fe4f9823fa206ef95dc662c68cb40b8897eff56a29466f35 | C++ | 929 | 20 | /***************************************************************************
*
* Author: "Jasenko Zivanov"
* MRC Laboratory of Molecular Biology
*
* This program 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 Foun... |
ca3f1a783db90b71c0fe56d8a816da205a8f613935da90b3ad9107ccc45eb3a8 | C++ | 941 | 21 | #include "gcmi_mex_adapter_utils.hpp"
#include <omp.h>
class MexFunction : public gcmi::MexAdapterBase {
public:
void operator()(matlab::mex::ArgumentList outputs, matlab::mex::ArgumentList inputs) override {
if (inputs.size() != 2 || outputs.size() > 1) {
fail("gcmi_cpp_omp_probe:usage", "gcm... |
559c399f26de7847cceb54732846c111e2d2acb3e3a64de4f8b88f9206a3f142 | C++ | 948 | 34 | #include <src/args.h>
#include <src/jaz/tomography/programs/tomo_ctf.h>
int main(int argc, char *argv[])
{
IOParser parser;
TomoCtfProgram tcp;
parser.setCommandLine(argc, argv);
int gen_section = parser.addSection("General options");
tcp.stackFn = parser.getOption("--ts", "Tilt sequence image stack (e.g. ... |
33919eccc284861bd1796b4fd2a9f6f8073e360977b1bd3800f99c8d5c76ae31 | C++ | 953 | 37 | #include <ATen/ThreadLocalPythonObjects.h>
#include <c10/util/Exception.h>
#include <utility>
namespace at::impl {
static thread_local ThreadLocalPythonObjects py_objects;
void ThreadLocalPythonObjects::set(const std::string& key, std::shared_ptr<SafePyObject> value) {
py_objects.obj_dict_[key] = std::move(value... |
f444dd0c45e1bd94277c8d4e51a09662951c3231ad6b6939309d592fd80d7528 | C++ | 954 | 22 | /***************************************************************************
*
* Author: "Jasenko Zivanov"
* MRC Laboratory of Molecular Biology
*
* This program 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 Foun... |
fecbe03590c5b4329e26366a337ead06ce9a794d31b736b955542d1da7160a8a | C++ | 955 | 32 | #include <ATen/core/Generator.h>
#include <ATen/core/Tensor.h>
#include <c10/util/Exception.h>
namespace at {
void Generator::set_state(const at::Tensor& new_state) {
TORCH_CHECK(new_state.defined(), "Undefined tensor is not allowed");
this->impl_->set_state(*new_state.unsafeGetTensorImpl());
}
at::Tensor Genera... |
13644d92d7f508261245ded145b69f3347bdcd86c57e173c7afbf76d29fba7c6 | C++ | 957 | 38 | #include <ATen/cudnn/Types.h>
#include <c10/util/Exception.h>
namespace at::native {
cudnnDataType_t getCudnnDataTypeFromScalarType(const at::ScalarType dtype) {
if (dtype == c10::kQInt8 || dtype == at::kChar) {
return CUDNN_DATA_INT8;
} else if (dtype == at::kFloat) {
return CUDNN_DATA_FLOAT;
} else ... |
e1c05840a96542dbd6a637bfc9ee11a07ffc815000cd68247ccd5c530217122f | C++ | 962 | 43 | // Copyright (C) 1996,2018,2026 Bernd Feige
// This file is part of avg_q and released under the GPL v3 (see avg_q/COPYING).
#include "LinkedObject.hh"
#include "Point.hh"
#include "Points.hh"
#include "TPoints.hh"
#include "Triangle.hh"
#include "Triangls.hh"
#include "ConvexMesh.hh"
extern "C" {
#include "bf.h"
#in... |
844d94c661dcfcd460885e127c50f0b638a96b832f0492fbb1a8c25cfc303602 | C++ | 967 | 21 | /***************************************************************************
*
* Author: "Jasenko Zivanov"
* MRC Laboratory of Molecular Biology
*
* This program 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 Foun... |
d838f54dbc9013ee194421a6d215d893c03277cffe2f6b52612fc4076e69d474 | C++ | 967 | 21 | /***************************************************************************
*
* Author: "Jasenko Zivanov"
* MRC Laboratory of Molecular Biology
*
* This program 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 Foun... |
702abe02a0ff8f5316653a7d6204ee38bfd2ab45f76dc54a501f07f0b706010a | C++ | 970 | 36 | #include "gcmi_kernels.hpp"
#include <cstddef>
#include <exception>
#include <string>
extern "C" void gcmi_info_cc_slice_bridge(
const double* x,
std::size_t ntrl,
std::size_t xdim,
std::size_t npage,
const double* y,
std::size_t ydim,
std::size_t threads,
double* output,
const cha... |
da67ce2f6d550d20d02d112ba29b05384f6fe37a7156fd4b1f9788b05d8d1ba3 | C++ | 970 | 37 | #include "structure_tensor.h"
#include <src/jaz/segmentation/diffusion.h>
#include <src/jaz/segmentation/diffusion_tensors.h>
BufferedImage<Tensor3x3<float>> StructureTensor :: computeNonLinear(
const RawImage<float>& src,
double rho,
double sigma0,
double taper,
int diffusion_iterations,
int outer_iterations... |
3748c8da20b7b80d52e970aee7164694e84cfa5084c86af77044930ba56dc931 | C++ | 976 | 41 | // Copyright (C) 1996 Bernd Feige
// This file is part of avg_q and released under the GPL v3 (see avg_q/COPYING).
#include "Array.hh"
Array::Array(int nr_of_vectors, int nr_of_elements, int element_skip) {
thisarray.nr_of_vectors=nr_of_vectors;
thisarray.nr_of_elements=nr_of_elements;
thisarray.element_skip=eleme... |
34781871abdbccbfab9b083fa359ac08c6d5636d2088c5dadebd0b220229f1c4 | C++ | 987 | 37 | #include <ATen/cuda/CUDAContext.h>
#include <ATen/detail/CUDAHooksInterface.h>
#include <ATen/native/cuda/ScaledBlasDeviceUtils.h>
#include <string>
#include <vector>
namespace at::native::scaled {
#ifdef USE_ROCM
// On ROCm, sm90_only/sm100_only are ignored.
bool scaled_mm_arch_allowed(bool /*sm90_only*/, bool /*sm... |
c345ca600d61a41336639f53c5496e5576115a3132524bf528310b3cc81f2706 | C++ | 1,003 | 25 | #include "gcmi_mex_adapter_utils.hpp"
#include "gcmi_kernels.hpp"
class MexFunction : public gcmi::MexAdapterBase {
public:
void operator()(matlab::mex::ArgumentList outputs, matlab::mex::ArgumentList inputs) override {
if (inputs.size() != 2 || outputs.size() > 1) {
fail("copnorm_slice_cpp:us... |
5e7754689df6cb1df681dead17196f55eacc4ffc6dd3a79735bb901984581a99 | C++ | 1,011 | 33 | #include <src/args.h>
#include <src/jaz/tomography/programs/substack.h>
int main(int argc, char *argv[])
{
IOParser parser;
SubstackProgram sp;
parser.setCommandLine(argc, argv);
int gen_section = parser.addSection("General options");
sp.particlesFn = parser.getOption("--i", "Input particle set");
sp.tomoLis... |
0f942c3cf218e6cde136008f79edee4e166a7e71f657355c7a438ef8df6cf71f | C++ | 1,013 | 27 | #include <ATen/core/dispatch/Dispatcher.h>
#include <c10/core/impl/PyInterpreter.h>
#include <torch/library.h>
namespace at::impl {
static void metaFallback(
const c10::OperatorHandle& op,
c10::DispatchKeySet dispatch_keys,
torch::jit::Stack* stack) {
c10::Dispatcher::singleton().throwIfHasPythonModule(... |
adf40bdb8fedf14950d610e2989d9e8a0a60f16a44ee01895e914bbed98b0431 | C++ | 1,016 | 34 | #include <src/args.h>
#include <src/jaz/tomography/programs/dark_erase.h>
int main(int argc, char *argv[])
{
IOParser parser;
DarkEraseProgram dep;
parser.setCommandLine(argc, argv);
int gen_section = parser.addSection("General options");
dep.stackFn = parser.getOption("--ts", "Tilt sequence image stack (e... |
af09c32f833a1a170043f22f79b22d2140ea8992b6251aaa63371d055ee19561 | C++ | 1,023 | 33 | #ifdef USE_RUY_QMATMUL
#include <ATen/ATen.h>
#include <ATen/native/quantized/cpu/RuyUtils.h>
namespace at::native::ruy_utils {
static thread_local ruy::Context context;
ruy::Context* get_ruy_context() {
return &context;
}
// Adopted from Ruy:
// https://github.com/google/ruy/blob/2d950b3bfa7ebfbe7a97ecb44b1cc4d... |
32a05b35e3a555f066bd25a12d18f1f26045b0cf39a56e1a8fda06de56848ae6 | C++ | 1,028 | 38 | #include <ATen/TensorGeometry.h>
#include <c10/util/overflows.h>
namespace at {
// See TensorGeometry.h on why this is useful now that we cache is_contiguous.
template <typename T>
static bool _geometry_is_contiguous(ArrayRef<T> sizes, ArrayRef<T> strides) {
assert(!overflows<std::int64_t>(sizes.size()));
auto di... |
214baa609742365c275daed8f2a6c06717bf1e488eba2cf90cb683f9a01a6643 | C++ | 1,037 | 23 | /***************************************************************************
*
* Author: "Jasenko Zivanov"
* MRC Laboratory of Molecular Biology
*
* This program 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 Foun... |
346c94433c7868bd94eaccf9bdd00f3c0b2ee6a2949f4bb59e1458ee683adce5 | C++ | 1,044 | 24 | /***************************************************************************
*
* Author: "Jasenko Zivanov"
* MRC Laboratory of Molecular Biology
*
* This program 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 Foun... |
748eba2c786039f6d83ac77aab8e5287b6a54e78e85418419dd22e45b30605e8 | C++ | 1,046 | 63 | #include "topaz_helper.h"
#include <src/macros.h>
using namespace gravis;
std::map<std::string, std::vector<TopazHelper::Particle>> TopazHelper::read(
std::string fileName, double minScore)
{
std::ifstream file(fileName);
if (!file)
{
REPORT_ERROR("Unable to read: " + fileName);
}
std::map< std::st... |
f38219a1d7880b298f833ffc950a784029434d0e552ebf54473cd1b068cddfaa | C++ | 1,066 | 44 | #include <src/jaz/tomography/projection/projection.h>
#include <src/jaz/tomography/extraction.h>
#include <src/jaz/image/normalization.h>
#include <src/jaz/image/centering.h>
#include <src/jaz/tomography/reconstruction.h>
#include <src/args.h>
#include <src/jaz/gravis/t4Matrix.h>
#include <omp.h>
using namespace grav... |
3eccd27a9e67ff0f7bbbc202233a56ae08554f5e7f8b0073270d209c54dde49b | C++ | 1,070 | 53 | #include "motif_detection.h"
#include <src/jaz/math/Euler_angles_dynamo.h>
using namespace gravis;
MotifDetection::MotifDetection()
{
}
MotifDetection::MotifDetection(d4Matrix alignment, int centerIndex, int tomoIndex, double score)
: alignment(alignment),
centerIndex(centerIndex),
tomoIndex(tomoIndex),
score(sc... |
75e3d74b6848e3aaf2e46296742a1ebdcf8db2352f077fb0ef6cfa3e44f5815b | C++ | 1,074 | 54 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Config.h>
#include <ATen/Parallel.h>
#include <ATen/cpu/vec/functional.h>
#include <ATen/cpu/vec/vec.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/NativeFunctions.h>
#else
#include <ATen/ops/zero_native.h>
#endif
#if !AT_MKLDN... |
e2f6526acd7b040496e80c3c92e674aefa7177df5c61824de5faecd88fd0232d | C++ | 1,088 | 49 | #include <src/args.h>
#include <src/jaz/tomography/tomolist.h>
#include <src/jaz/tomography/tomogram.h>
#include <src/jaz/mesh/mesh_builder.h>
#include <src/jaz/util/zio.h>
#include <src/jaz/util/log.h>
#include <src/jaz/tomography/tomogram_set.h>
#include <src/jaz/tomography/particle_set.h>
#include <src/jaz/tomograph... |
1c3de877bd6555aee92780f97d32fe48359642730b966575e73f5227048e743c | C++ | 1,109 | 34 | #include <ATen/core/DeprecatedTypePropertiesRegistry.h>
#include <ATen/core/DeprecatedTypeProperties.h>
#include <c10/util/irange.h>
namespace at {
void DeprecatedTypePropertiesDeleter::operator()(DeprecatedTypeProperties * ptr) {
delete ptr;
}
DeprecatedTypePropertiesRegistry::DeprecatedTypePropertiesRegistry() ... |
7ea555696f34bec38c1c395d8c4178e9af326bbc58413b6e3b831ec0bca320ab | C++ | 1,135 | 58 |
#include <src/args.h>
#include <src/metadata_table.h>
#include <src/jaz/single_particle/stack_helper.h>
using namespace gravis;
int main(int argc, char *argv[])
{
IOParser parser;
std::string starFn;
parser.setCommandLine(argc, argv);
parser.addSection("General options");
starFn = parser.getOption("--i", "Inpu... |
5a3eb9f3fa0d766736bd96488b7795393bf8279ba9211677652b7002ace9a4f1 | C++ | 1,138 | 51 | #include "tomo_ctf.h"
#include <src/jaz/tomography/projection/projection.h>
#include <src/jaz/tomography/extraction.h>
#include <src/jaz/image/normalization.h>
#include <src/jaz/image/centering.h>
#include <src/args.h>
#include <src/jaz/gravis/t4Matrix.h>
#include <src/jaz/tomography/tomo_ctf_find.h>
#include <omp.h>... |
b8ba79264c8773d9413a831cbfb38973d1d157095e8a8f392e2f055afd70e6aa | C++ | 1,153 | 36 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/Dispatch.h>
#include <ATen/OpMathType.h>
#include <ATen/native/TensorFactories.h>
#include <ATen/native/TensorIterator.h>
#include <ATen/native/cpu/Loops.h>
namespace at::native {
namespace {
void complex_kernel(TensorIterator& iter) {
AT_DISPATCH_FLOATING_T... |
52bf6c4898e28c5f10cd8a2a63f964a53fecd55b01a16f9f8ec267e2994619d8 | C++ | 1,154 | 47 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Config.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/NativeFunctions.h>
#else
#include <ATen/ops/copy_native.h>
#endif
#if !AT_MKLDNN_ENABLED()
namespace at::native {
Tensor& copy_mkldnn_(Tensor& self, const Tensor& src, bo... |
f94b892e5d86924d474039e22a09a652a88ae9b569188255b15b969f42a077d8 | C++ | 1,157 | 53 | #include "class_helper.h"
#include <src/jaz/util/index_sort.h>
int ClassHelper::countClasses(const MetaDataTable &particles_table)
{
int max_class = -1;
for (long int p = 0; p < particles_table.numberOfObjects(); p++)
{
const int class_id = particles_table.getIntMinusOne(EMDL_PARTICLE_CLASS, p);
if (class_id... |
b4649dbd20629135ee2a7b365230b1161078b790b18c4a9c58e62c1c9df0fe52 | C++ | 1,160 | 49 | #include "stack_helper.h"
void NewStackHelper::FourierTransformStack_fast(
const RawImage<float>& stack,
RawImage<fComplex>& stackOut,
bool center,
int num_threads,
FFT::Normalization normalization)
{
const int w = stack.xdim;
const int h = stack.ydim;
const int fc = stack.zdim;
const int wh = w/... |
fdc4330b8bc4b8bd1ecd1cd57b81b32b154f6ed6e5e3a5db5280c1ae5d421416 | C++ | 1,161 | 45 | /*
* Copyright (c) Facebook, Inc. and its affiliates.
* All rights reserved.
*
* This source code is licensed under the BSD-style license found in the
* LICENSE file in the root directory of this source tree.
*/
#include <gtest/gtest.h>
#include <qnnpack/x8lut.h>
#include "lut-microkernel-tester.h"
TEST(X8LUT... |
a54c9f1fd19d39d8490c2d1c59d77ee013c53e61ed8e53613e7eecb02a6e6894 | C++ | 1,174 | 38 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/native/AmpKernels.h>
#include <ATen/core/Tensor.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#include <ATen/NativeFunctions.h>
#else
#include <ATen/ops/_amp_foreach_non_finite_check_and_unscale_native.h>
#include <ATen/ops/_amp_update_scale_na... |
e81497db971e6fb040f0061aea9bd94651c59f795e7b52a260ea41f28c624e9d | C++ | 1,177 | 25 | //******************************************************************************************************************************************************
// Nlx2MatEV.cpp
// Author: Kevin Iamiceli
// Created March 15, 2003
// Version 3.00
//********************************************************************************... |
bbf466f6e9dd5df1b77326d41defdc8da509f1276dee4f519409756dceb139ed | C++ | 1,178 | 25 | //******************************************************************************************************************************************************
// Nlx2MatCSC.cpp
// Author: Kevin Iamiceli
// Created March 15, 2003
// Version 3.00
//*******************************************************************************... |
ee463f48c55b602aa823dc3be45430a59ef70f65022e4259d8978a9320f90f58 | C++ | 1,179 | 39 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
0d1933fb8c10fa75e5d50477cbbc74f5e47b208ca24653562882f478afbb3efe | C++ | 1,195 | 38 | #define TORCH_ASSERT_NO_OPERATORS
#include <ATen/native/Normalization.h>
#include <ATen/TensorIterator.h>
#include <ATen/native/cpu/Loops.h>
#include <ATen/cpu/vec/vec.h>
#include <ATen/Dispatch.h>
namespace at::native {
namespace {
void renorm_scale_factor_impl(TensorIteratorBase& iter, double maxnorm) {
AT_DISP... |
20e69fed4f603dc34c6803f22d2a21e849bd921bf497cc4c9ef8c99f484c04db | C++ | 1,196 | 40 | /***************************************************************************
*
* Author: "Takanori Nakane"
* MRC Laboratory of Molecular Biology
*
* This program 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 Foun... |
3f20c0b323ead886007c52eccab172e41e3cb9c72df749769fc5d4c531f6086b | C++ | 1,196 | 24 | //******************************************************************************************************************************************************
// Nlx2MatSpike.cpp
// Author: Kevin Iamiceli
// Modified March 9, 2003
// Version 3.00
//*****************************************************************************... |
fdccd6207cc7089d518c72097201983d162d4273eb26d1de0fa987737fe35064 | C++ | 1,202 | 25 | //******************************************************************************************************************************************************
// Nlx2MatEV.cpp
// Author: Kevin Iamiceli
// Created March 15, 2003
// Version 3.00
//***************************************************************************... |
c2a56dd0ff629280c2b016cf659a2394b885b97c8b9cea2203376a348809751e | C++ | 1,203 | 25 | //******************************************************************************************************************************************************
// Nlx2MatCSC.cpp
// Author: Kevin Iamiceli
// Created March 15, 2003
// Version 3.00
//**************************************************************************... |
9069936c8321364f94abfa7b195db68e595bf5dad639fec1fbbcf74c4a1aaeb6 | C++ | 1,207 | 40 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
7e74444fe5ee420c54367bc2b67d8ce871b77ed077801b46d5ac49bf36374783 | C++ | 1,210 | 40 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/native/TensorIterator.h>
#include <ATen/native/cpu/Loops.h>
#include <ATen/core/Tensor.h>
#include <ATen/Dispatch.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#else
#include <ATen/ops/_empty_affine_quantized.h>
#include <ATen/ops/_make_per_ten... |
59895015c652be54ecbe707fc7298b82f8d16f696bb05812f241006e50817c7d | C++ | 1,211 | 36 | #ifndef __AXI_DMA_PKG_PKG__
#define __AXI_DMA_PKG_PKG__
#include "stdio.h"
#include "string.h"
#include "cstdint"
#include "inttypes.h"
#include <cmath>
namespace axi_parameters {
// static const uint8_t BURST_SIZE = 61;
// static const uint32_t BURST_VALUE_MASK = (uint32_t) ((uint32_t) (std::pow(2, BURST_SIZE)... |
86d1d87c5346c476d385a5a385542720d845e2a6b3404725d93713c7363356b8 | C++ | 1,211 | 60 |
#include "stringUtils.h"
// In place string converstion functions
void PascalToCString( axgchar *string )
{
// First byte of pascal string contains string length
short stringLength = string[0];
// Shift string left
for ( short i = 0; i < stringLength; i++ )
string[i] = string[i+1];
// Append null byte
st... |
bf9e3e7f029d669b9f3cd9ca46864ba76fadc4a8c08e404b4ac0d221b5ecaf70 | C++ | 1,211 | 40 | /***************************************************************************
*
* Author: "Jasenko Zivanov"
* MRC Laboratory of Molecular Biology
*
* This program 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 Foun... |
a44056450d3fbd8740618dcf6d6db9da30faccaa53fc63dc1d3f5a1c2366ec19 | C++ | 1,216 | 41 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
c73006d06973648109a99ab68378b8a22a1d459c265fbba7a8b1b1a6a5417067 | C++ | 1,216 | 43 | #include <ATen/native/mkldnn/OpContext.h>
#if AT_MKLDNN_ENABLED()
#include <ATen/native/mkldnn/ConvPrepack.h>
namespace at::native::mkldnn {
c10::intrusive_ptr<ConvOpContext> MkldnnConvOpContext::create_context(
at::Tensor&& weight,
std::optional<at::Tensor>&& bias,
std::vector<int64_t>&& padding,
st... |
22ad228a03fcd196b5d384918160ea0f83442be258cb2e8e7dda689c160af505 | C++ | 1,217 | 47 |
/***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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... |
7359246fc0cdf73f122d4c00d75f702977ae6010e4f45b8afd1fb93e0c4c8b4f | C++ | 1,217 | 41 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
6651889b650ed8b43386753f74a79ed947d3fc75566850242071fccc675cbf09 | C++ | 1,219 | 49 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Config.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/NativeFunctions.h>
#else
#include <ATen/ops/_softmax_native.h> // for mkldnn_softmax
#endif
#if !AT_MKLDNN_ENABLED()
namespace at::native {
Tensor mkldnn_softmax(... |
f833b666917c81122055e51cd1d31c2b3bd1c49cea3883e22d0d0b3fc6cb609d | C++ | 1,219 | 58 | #include "symmetry.h"
std::vector<gravis::d4Matrix> Symmetry::getPointGroupMatrices(
std::string symmGroup)
{
SymList SL;
SL.read_sym_file(symmGroup);
const int sc = SL.SymsNo();
std::vector<gravis::d4Matrix> R(sc);
for (int isym = 0; isym < sc; isym++)
{
Matrix2D<RFLOAT> L0, R0;
SL.get_matrices(is... |
03f74d9351df40e5b388395f1f224508bae9a7e9b037a021aeedc2881a2be1b3 | C++ | 1,220 | 42 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
fd3ea1586e135574b8ce2ea6df22dbbe19ba0a5d9435d7cfb8465e50af0dd423 | C++ | 1,220 | 24 | //******************************************************************************************************************************************************
// Nlx2MatSpike.cpp
// Author: Kevin Iamiceli
// Modified March 9, 2003
// Version 3.00
//************************************************************************... |
105c87905718bd7d6c33f6e3749a6c4e2495246e1372fa7bf6f2e7b92329dbaf | C++ | 1,221 | 62 | #include "closest_spline_point_problem.h"
using namespace gravis;
ClosestSplinePointProblem::ClosestSplinePointProblem(
const Spline<d2Vector,double> &spline2D, d2Vector pos
)
: spline2D(spline2D),
pos(pos)
{}
double ClosestSplinePointProblem::f(const std::vector<double> &x, void *tempStorage) const
{
return ... |
61ad95ba9b8303a78c9cee2279c0e903dc384a266a5b779002936d1c916599a5 | C++ | 1,223 | 41 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
28db6a255076ac7f17c7fb58d9936689640de94d015ddcbebabb90a6add5ddb4 | C++ | 1,225 | 43 |
/***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 ... |
100cd3b48bf36832c6318ad12d6e0e040872befe8b7574454108192024c20f56 | C++ | 1,226 | 29 | //******************************************************************************************************************************************************
// Nlx2MatVT.cpp
// Author: Kevin Iamiceli
// Created Sept 15, 2003
// Version 2.00
//*********************************************************************************... |
44192fb8034f225167acc9afe27cb4d022d6e66687ce6b9122c4a59486d3c093 | C++ | 1,231 | 43 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/EmptyTensor.h>
#include <ATen/core/Tensor.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/NativeFunctions.h>
#else
#include <ATen/ops/empty_native.h>
#include <ATen/ops/empty_strided_native.h>
#endif
namespace at::native {
Tensor empty_meta_symint(
SymInt... |
f3c80e61a5c1d1b81169f084b2635b3f24e5871d7e6880ff5494af28283edf2f | C++ | 1,234 | 41 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
3e7faea6d224636552b3915206ca80833d9501070f7e2ee836a01c1d00d008e7 | C++ | 1,240 | 40 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/NativeFunctions.h>
#include <ATen/CUDAFunctions.h>
#else
#include <ATen/ops/eq_cuda_dispatch.h>
#include <ATen/ops/equal_native.h>
#endif
namespace at::native {
bool cuda_equal(const Tensor& self, ... |
30e7f5a26ed4c1e7be92f6a652ea712999596c3b808d15017eed8cd45524faeb | C++ | 1,249 | 42 | /***************************************************************************
*
* Authors: "Jasenko Zivanov & Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
b5034a76365068e5012353bd9205898b8c293399539faa6c034d834b92a26ff8 | C++ | 1,250 | 45 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
ca13e4503dfd298d9695507a90240569bedc84c629aa1c3b3734ed777d0e97d2 | C++ | 1,255 | 29 | //******************************************************************************************************************************************************
// Nlx2MatVT.cpp
// Author: Kevin Iamiceli
// Created Sept 15, 2003
// Version 2.00
//****************************************************************************... |
a62b58d49a2bc2b1d7a784edce405f7dfa5d0a49bede3a309b828af06f77ef20 | C++ | 1,261 | 45 | /***************************************************************************
*
* Authors: "Jasenko Zivanov & Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
a643038f8e03069d284bd8ccaef12d2a546e1f834cc31070a6316853c09ad65b | C++ | 1,261 | 42 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
7e50e3edcca2ad37a6ca8c407eb3f36258a7302ddfc07799e1385585990602f3 | C++ | 1,272 | 59 | #include "membrane_template.h"
#include <src/jaz/image/interpolation.h>
MembraneTemplate::MembraneTemplate(
double spacing,
double inside_level,
double inside_halo_level,
double membrane_level,
double centre_level,
double outside_halo_level,
double outside_level )
: d(spacing/2.0),
spacing(spacin... |
275f572c4dda8ed448a09c1f2b2829caeb8f0ba1f10fcc61cb8e2ca4804d9548 | C++ | 1,285 | 36 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/core/ivalue.h>
#include <torch/library.h>
#include <ATen/native/quantized/cpu/QuantizedOps.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#else
#include <ATen/ops/_empty_affine_quantized.h>
#endif
namespace at::nat... |
fd1ec924bd305256bc6f2c2b1d85adda95be34afedc2c1968cee60047e12eebc | C++ | 1,285 | 46 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
333ba7c765c27f2f3609f6535571e11d153a56a40ae708f9d69e253d2afe5ac8 | C++ | 1,293 | 48 | /*
* Copyright (c) Facebook, Inc. and its affiliates.
* All rights reserved.
*
* This source code is licensed under the BSD-style license found in the
* LICENSE file in the root directory of this source tree.
*/
#include <gtest/gtest.h>
#include <qnnpack/u8lut32norm.h>
#include "lut-norm-microkernel-tester.h"
... |
c0867d1adbfc7b0924c6ddea929b888a78836927c5fc5be116a6a2bee57a7101 | C++ | 1,295 | 70 | #include "zs_axi_dma_lib.hpp"
#include <vector>
#include "stdio.h"
#define TEST_SIZE 1023
#define NUM_TESTS 1
#define NUMCONV 64
#define KERNEL_SIZE 7
int file2array(const char * filename, int32_t * kernel_weights);
int file2array(const char * filename, int32_t * kernel_weights) {
FILE* file = fopen(filename, "r... |
aacd852ae0341a1408a7dbed5643819837c4627727ce70a609dcb0a7d378bb37 | C++ | 1,305 | 46 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
53b0b4f16723ab06bb7cda18284737b209651fd336f94f2b3e68c83c1d8b1d7d | C++ | 1,309 | 36 | #include <src/args.h>
#include <src/jaz/tomography/programs/find_lattice.h>
int main(int argc, char *argv[])
{
IOParser parser;
FindLatticeProgram flp;
parser.setCommandLine(argc, argv);
int gen_section = parser.addSection("General options");
flp.tomoFn = parser.getOption("--t", "Tomogram");
flp.spacing_ang... |
d630cfe2b1655e444c8d0c1d176149c3b1875642f52afbad75e51fd965208cc9 | C++ | 1,311 | 32 | #include "gcmi_mex_adapter_utils.hpp"
#include <vector>
class MexFunction : public gcmi::MexAdapterBase {
public:
void operator()(matlab::mex::ArgumentList outputs, matlab::mex::ArgumentList inputs) override {
if (inputs.size() != 1 || outputs.size() > 1) {
fail("gcmi_cpp_blas_probe:usage", "g... |
e9c90bc83cdcd8cf413b6747fe587a8b68d6aee97d5166019426defc422f365e | C++ | 1,311 | 45 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
fd9a7bb7ad57c01c9678e8a382b8307c79fd69216439c1850aed55ee0416991f | C++ | 1,323 | 42 | #include "../libstfio/channel.h"
#include <gtest/gtest.h>
TEST(Channel_test, constructors)
{
Channel ch0;
EXPECT_EQ( ch0.size(), 0 );
Section sec(32768);
Channel ch1(sec);
EXPECT_EQ( ch1.size(), 1 );
EXPECT_EQ( ch1[0].size(), 32768 );
std::deque<Section> sec_list(16, Section(32768));
... |
bded598128f4f4b609a8ee8089ec4337252d4f1f7c70a3dee7986586a17bb922 | C++ | 1,330 | 51 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
a6012d5b75059fba8cd7d561a04d3139ef131a644a4f9813effa95b0fbf82b23 | C++ | 1,348 | 47 | /***************************************************************************
*
* Authors: "Jasenko Zivanov & Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
d85740fef45d59930e530025fe7e97b8c1707f3f6a4a5420b041422ea926c3fd | C++ | 1,348 | 29 | #include "gcmi_mex_adapter_utils.hpp"
#include "gcmi_kernels.hpp"
class MexFunction : public gcmi::MexAdapterBase {
public:
void operator()(matlab::mex::ArgumentList outputs, matlab::mex::ArgumentList inputs) override {
if (inputs.size() != 6 || outputs.size() > 1) {
fail("info_cd_slice_cpp:us... |
7640b631ce242f354c8ceb4e90863e516a5a507c44cd4f3329a02707bd122ff6 | C++ | 1,351 | 53 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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 F... |
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