sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
c34925769c957c11a158dfaf97cfa035b01539d4ef9c23f15cf40f7f1a86856a | C++ | 14,008 | 388 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/native/Copy.h>
#include <ATen/core/Tensor.h>
#include <ATen/Dispatch.h>
#include <ATen/Dispatch_v2.h>
#include <ATen/ExpandUtils.h>
#include <ATen/FunctionalTensorWrapper.h>
#include <ATen/TensorIterator.h>
#include <ATen/native/quantized/Copy.h>
#include <ATen... |
37b59c4f94406e53b89da2dd60ede826daf39d98ae910d491255f72cd45537c5 | C++ | 14,013 | 446 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Dispatch.h>
#include <ATen/Parallel.h>
#include <c10/util/irange.h>
#include <ATen/native/AdaptivePooling.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/NativeFunctions.h>
#else
#include <ATen/ops/adaptive_max_pool3d_backward_n... |
8dac65508ebfe86e828e9389122515893f3f4aaffa0d9a3849f720e5de3e6fa6 | C++ | 14,063 | 428 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Dispatch.h>
#include <ATen/Parallel.h>
#include <ATen/TensorMeta.h>
#include <ATen/native/FractionalMaxPooling.h>
#include <c10/util/irange.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#include <ATen/NativeFuncti... |
e7496821f96228b55edd49feefba1b4cc0c37396ed3e4217c57a1c27c527c929 | C++ | 14,074 | 334 | // 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 Foundation; either version 2
// of the License, or (at your option) any later version.
// This program is distributed in the hope that it will be use... |
032058478db2f38ada36a49c6a0ac83eef05bcb0e26a5385dda7f048eef14cd5 | C++ | 14,082 | 357 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/cpu/StatelessPhilox4x32.h>
#include <ATen/Dispatch.h>
#include <ATen/Dispatch_v2.h>
#include <ATen/ExpandUtils.h>
#include <ATen/core/TransformationHelper.h>
#include <ATen/native/PhiloxStatelessRNG.h>
#ifndef AT_PER_OPERATOR_HEAD... |
5791cf4d429bcbda8ceecb8b4091c7b6528de3da7100e2e2f092a8c1e06deea5 | C++ | 14,095 | 325 | #include <ATen/native/nested/NestedTensorUtils.h>
#include <ATen/Functions.h>
#include <ATen/NativeFunctions.h>
#include <ATen/NestedTensorImpl.h>
#include <ATen/TensorIndexing.h>
#include <ATen/TensorUtils.h>
#include <ATen/core/Tensor.h>
#include <ATen/core/grad_mode.h>
namespace at::native {
Tensor bmm_nested(con... |
5781f732797d1cf7e2d935875b942cf78df9510c0cb5eef1e1e4da045fc188d2 | C++ | 14,108 | 401 | #include "../dep/laynii_lib.h"
#include <sstream>
int show_help(void) {
printf(
"LN2_ZERO_CROSSING: Find zero crossing voxels in a scalar field.\n"
"Usage:\n"
" LN2_ZERO_CROSSING -values equidist_metric.nii.gz -domain mask.nii.gz \n"
"\n"
"Options:\n"
" -help : Show this help.\n"
... |
fd73a6a80cef379be440ff4f453a43170bbd39f780440ab33bb08f1e65059014 | C++ | 14,191 | 343 |
#include "../dep/laynii_lib.h"
#include <sstream>
int show_help(void) {
printf(
"LN2_CONNECTED_CLUSTERS: Find connected clusters in a binary image.\n"
"\n"
"Usage:\n"
" LN2_CONNECTED_CLUSTERS -input input.nii\n"
" ../LN2_CONNECTED_CLUSTERS -input input.nii\n"
"\n"
"Options:\n"
... |
33cc86b6612b3e0ea1923f284330c1937fb0b7afdbcd5307bb100863e6d56972 | C++ | 14,238 | 382 | // Copyright 2008, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
a23e87ab917257f297a1fbff7f4b8f174731ea355905d5da92f75b1eee8ea679 | C++ | 14,380 | 498 | /***************************************************************************
*
* 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
* ... |
992109fb7a26e32d341309d5900708132f1b1cd245e381b1565705c0ec7e30a9 | C++ | 14,382 | 505 | #include "polish.h"
#include <src/ctf.h>
#include <src/jaz/tomography/tomogram.h>
#include <src/jaz/tomography/motion/motion_fit.h>
#include <src/jaz/tomography/motion/trajectory_set.h>
#include <src/jaz/tomography/projection_IO.h>
#include <src/jaz/tomography/prediction.h>
#include <src/jaz/tomography/extraction.h>
#i... |
b39e5b0e926a966329ce9f900f9f37511fafe8cbcef38ce5a9c190abd75a5c24 | C++ | 14,408 | 451 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/cuda/CUDAConfig.h>
#ifdef __HIP_PLATFORM_AMD__
#include <ATen/native/cudnn/hip/BatchNorm.h>
#else
#include <ATen/native/cudnn/BatchNorm.h>
#endif
#if !AT_CUDNN_ENABLED()
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/NativeFuncti... |
5a868d7ad8e7b54374ec7841829b0e6c78b50eb810198d6ebcaab3c7dda8708a | C++ | 14,450 | 375 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/native/layer_norm.h>
#include <ATen/core/Tensor.h>
#include <ATen/Dispatch.h>
#include <ATen/native/cpu/mixed_data_type.h>
#include <c10/util/irange.h>
#include <ATen/OpMathType.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#include <ATen/Nati... |
a0d7baca088e35ff3ec7bcc1562a27b6034d8e7e6e9477a21f4674c3a8db4bdd | C++ | 14,492 | 368 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Parallel.h>
#include <ATen/OpMathType.h>
#include <ATen/native/DispatchStub.h>
#include <ATen/native/FusedAdam.h>
#include <ATen/Dispatch.h>
#include <ATen/cpu/vec/vec.h>
#include <ATen/cpu/vec/functional.h>
namespace at::native {
... |
cbd33004b6886b24c8edcb8aac2249c139ee1f51ccaa13fe93e6366eb063eb8f | C++ | 14,614 | 565 | #include "tomo_mag_fit.h"
#include <src/jaz/tomography/extraction.h>
#include <src/jaz/tomography/prediction.h>
#include <src/jaz/tomography/projection/fwd_projection.h>
#include <omp.h>
using namespace gravis;
TomoMagFit::TomoMagFit(
const std::vector<ParticleIndex>& particle_indices,
const Tomogram& tomogram,
... |
c14e723b7ed5a58180633fdb373372bfa13a32bcf6c34d040130acaca36fe24f | C++ | 14,635 | 496 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Parallel.h>
#include <torch/library.h>
#include <ATen/native/quantized/cpu/QuantizedOps.h>
#include <c10/util/irange.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#include <ATen/NativeFunctions.h>
#else
#include <A... |
02e8f1d4d42765e9e107bdf3ee85ec6e98f40ffc4ef0595db3f388092f818475 | C++ | 14,700 | 491 | /***************************************************************************
*
* 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... |
63b74fa5f15c8b603bc8674c184895a954e962d4c92da392593d6e834bd23dc6 | C++ | 14,712 | 360 | #include "../dep/laynii_lib.h"
int show_help(void) {
printf(
"LN_BOCO: This program does BOLD correction in SS-SI VASO. It does\n"
" the division of nulled and BOLD (not nulled) images.\n"
"\n"
"Usage:\n"
" LN_BOCO -Nulled Nulled_intemp.nii -BOLD BOLD_intemp.nii\n"
" LN_BOCO ... |
164b74a3c0ae27a388a40724487387d867d6dd90d0182ea8e0cf83674f697c56 | C++ | 14,785 | 559 | #include "backproject_2d.h"
#include <src/args.h>
#include <src/metadata_table.h>
#include <src/ctf.h>
#include <src/jaz/util/zio.h>
#include <src/jaz/util/log.h>
#include <src/jaz/single_particle/obs_model.h>
#include <src/jaz/image/interpolation.h>
#include <src/jaz/image/translation.h>
#include <src/jaz/image/taperi... |
c7123fb395048252ac96c750c30528ffde56bb7a3f36bd09b6d546f511c25577 | C++ | 14,835 | 375 | #include "wx/wxprec.h"
#ifndef WX_PRECOMP
#include "wx/wx.h"
#endif
#include "./../app.h"
#include "./../doc.h"
#include "./../view.h"
#include "./../graph.h"
#include "./fitseldlg.h"
#define wxID_LIST 1001
#define wxID_PREVIEW 1002
BEGIN_EVENT_TABLE( wxStfFitSelDlg, wxDialog )
EVT_LIST_ITEM_SELECTED( wxID_LIST,... |
f5ef91ed44aaa3af18c4cfbdc0a33a520497f5f5338d711fc7dca795341d404c | C++ | 14,908 | 702 | /***************************************************************************
*
* 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... |
4c161d9d0e1354675be09577c90e02f4532226997314d3bd62ab46c7ab997956 | C++ | 14,932 | 434 | #include <ATen/TensorUtils.h>
#include <c10/util/accumulate.h>
#include <ostream>
#include <sstream>
namespace at {
std::ostream& operator<<(std::ostream & out, const TensorGeometryArg& t) {
if (t.pos == 0) {
// 0 is distinguished; it usually indicates 'self' or the return
// tensor
out << '\'' << t.na... |
9d607ccbae8e3867c36252b9eb70b7d9e3f1511072c2c580fdb4d4683c59e703 | C++ | 14,952 | 474 | #include <ATen/core/jit_type.h>
#include <c10/core/GradMode.h>
#include <utility>
namespace c10 {
namespace {
// The idea is to only mark possible overlap across dimensions. We want to
// return false for expanded tensors and permuted tensors, for which dimensional
// collapsing is safe.
bool possible_cross_dimensi... |
22f4ba4501727b64535f2a6ac7f638c7148379469d1522e5bab2dfd7722f2425 | C++ | 14,982 | 318 | #include "../dep/laynii_lib.h"
#include <sstream>
int show_help(void) {
printf(
"LN3_NOLAD: Nonlinear anisotropic diffusion filter.\n"
"\n"
"Usage:\n"
" LN3_NOLAD -input input.nii\n"
" ../LN3_NOLAD -input input.nii\n"
"\n"
"Options:\n"
" -help : Show this help.\n"
" ... |
16639df559357ffce81c1dfc7bf4044feca959ad11319196b98f61103bc3145d | C++ | 14,995 | 343 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/native/CPUFallback.h>
#include <ATen/core/ivalue.h>
#include <ATen/core/stack.h>
#include <ATen/core/dispatch/Dispatcher.h>
#include <sstream>
#include <vector>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#else
#include <ATen/ops/_copy_from_a... |
40eef89b08dc2798b2884c67116bcb58565ea26095d74972c3b7b7655a3a44d9 | C++ | 15,000 | 448 | #include <ATen/core/Tensor.h>
#include <ATen/ops/empty.h>
#include <ATen/native/mkldnn/xpu/detail/Attr.h>
#include <ATen/native/mkldnn/xpu/detail/Utils.h>
#include <ATen/native/mkldnn/xpu/detail/oneDNNContext.h>
#include <oneapi/dnnl/dnnl.hpp>
namespace at::native::onednn {
static inline dnnl::memory::dims deconv_co... |
03b71f7d610357e2fdf47570c6c17011ced61fce5852e115c7a95f8823f5260b | C++ | 15,051 | 463 | #define TORCH_ASSERT_NO_OPERATORS
#include <ATen/core/TensorBase.h>
#include <ATen/Dispatch.h>
#include <ATen/EmptyTensor.h>
#include <ATen/Parallel.h>
#include <ATen/OpMathType.h>
#include <ATen/native/cpu/WeightNormKernel.h>
#include <ATen/cpu/vec/functional.h>
#include <ATen/cpu/vec/vec.h>
#include <c10/util/irange... |
7312f27493f9b15d1c1b174caa10fa476e3d20199b8d9a0806dca7b36070c962 | C++ | 15,063 | 445 | #define TORCH_ASSERT_NO_OPERATORS
#include <ATen/Dispatch.h>
#include <ATen/Parallel.h>
#include <ATen/cpu/vec/vec.h>
#include <ATen/native/Unfold2d.h>
#include <ATen/native/cpu/Loops.h>
#include <c10/util/irange.h>
#include <ATen/native/cpu/utils.h>
#include <cmath>
namespace at::native {
namespace {
template <type... |
241d35be8cf749d68c55bc7afd9b414a3395fa13de553558dfc8ee9a31367da2 | C++ | 15,288 | 414 | // WORK in PROGRESS
// TODO(Renzo): Think about what to do with time series data.
// E.g. carpet plot: https://github.com/layerfMRI/repository/tree/master/Layer_me
#include <fstream>
#include <iomanip>
#include "../dep/laynii_lib.h"
int show_help(void) {
printf(
"LN2_PROFILE: Generates layer profiles from 3D... |
8df513f04c3510d957a9f693b00ae687c9843fc6566f626a764407e6bae1a3f5 | C++ | 15,288 | 548 | /*
* iaf_bw_2003.cpp
*
* This file is part of NEST.
*
* Copyright (C) 2004 The NEST Initiative
*
* NEST 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
* (a... |
a7544dfe75a3ae7bbb7e081bd5ef0811310ba34ce443e579a9a46257091c9d66 | C++ | 15,342 | 593 | #include <ATen/cuda/detail/CUDAHooks.h>
#include <ATen/cuda/CUDAGeneratorImpl.h>
#include <ATen/Context.h>
#include <ATen/DynamicLibrary.h>
#include <ATen/cuda/CUDAConfig.h>
#include <ATen/cuda/CUDADevice.h>
#include <ATen/cuda/Exceptions.h>
#include <ATen/cuda/PeerToPeerAccess.h>
#include <ATen/cuda/PinnedMemoryAlloc... |
8c567ee2001b1a3e0fad960be323d1c4cd5bc14f1aae4d43aff31c5d55c361ce | C++ | 15,516 | 582 | #include "src/acc/sycl/device_stubs.h"
#include "src/acc/acc_ptr.h"
#include "src/acc/acc_projector.h"
#include "src/acc/acc_backprojector.h"
#include "src/acc/acc_projector_plan.h"
#include "src/acc/sycl/sycl_benchmark_utils.h"
#include "src/acc/sycl/sycl_helper_functions.h"
#include "src/acc/sycl/sycl_kernels/helper... |
6929cb0f478277aeff0ef17a9465dfe2dfae741a2688fa6d8239ca723644baf1 | C++ | 15,563 | 340 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/core/grad_mode.h>
#include <ATen/ExpandUtils.h>
#include <ATen/TensorOperators.h>
#include <ATen/native/Distance.h>
#include <c10/util/accumulate.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#include <ATen/NativeF... |
2270f5b61c3de21ab228a36e2a9d700a22bb808f0b24a835ddae14ed2f31f66e | C++ | 15,712 | 521 | /*
* assembly.cpp
*
* Created on: Apr 16, 2013
* Author: "Sjors H.W. Scheres"
*/
#include "src/assembly.h"
void Atom::clear()
{
name = "";
occupancy = bfactor = 0.;
coords.clear();
}
Matrix1D<RFLOAT> Atom::getCoordinates()
{
return coords;
}
void Residue::clear()
{
number = -1;
name = "";
... |
9ff9c332c39b19278b45ecc5939c5f1904026b749aaa6daa9a1fd198e0980d22 | C++ | 16,104 | 657 | /***************************************************************************
*
* 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... |
cb22a85fe73932bb8ab66e1f5f5220de83456494102049e7bdacc1f7c2252171 | C++ | 16,125 | 490 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Dispatch.h>
#include <ATen/Parallel.h>
#include <ATen/native/cpu/utils.h>
#include <ATen/native/Resize.h>
#include <c10/util/irange.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#include <ATen/NativeFunctions.h>
#e... |
fa58bf31d8cce2fb4760a3e1f0b24b91428236718a8137a15b688bc614aca8a4 | C++ | 16,154 | 364 |
// TODO(Faruk): Seems there might be an issue with the gaussian kernel's
// symmetry and size corresponding to what is written in CLI
// TODO(Renzo): make the vicinity direction specific vinc_x, vinc_y, vinc_z
#include "../dep/laynii_lib.h"
int show_help(void) {
printf(
"LN2_LAYER_SMOOTH : Layering algorith... |
6670c74ed509a6e8d088f8c2ea8cf34b46384f83ec3da3447af5913ec7c976f3 | C++ | 16,183 | 387 | #include "../dep/laynii_lib.h"
int show_help(void){
printf(
"LN_GRADSMOOTH : Local gradient based smoothing.\n"
"\n"
"Usage:\n"
" LN_GRADSMOOTH -input lo_VASO_act.nii -gradfile lo_gradT1.nii -FWHM 1 -within -selectivity 0.1 \n"
" ../LN_GRADSMOOTH -input lo_VASO_act.nii -gradfile lo_gradT... |
af9e6fba31c6fed95dcc60d63bbb8f4b42d537769d590eec6b75707ba88bf9a7 | C++ | 16,217 | 674 | #include "bfactor_refiner.h"
#include "ctf_refiner.h"
#include <omp.h>
#include <src/ctf.h>
#include <src/time.h>
#include <src/jaz/single_particle/obs_model.h>
#include <src/jaz/single_particle/reference_map.h>
#include <src/jaz/single_particle/fftw_helper.h>
#include <src/jaz/single_particle/image_log.h>
#include ... |
0d27b11a548287dd844778389d5ea4a4c83293440671b7dd0df47a362159b40d | C++ | 16,224 | 417 |
#include "../dep/laynii_lib.h"
#include <sstream>
#include <iostream>
#include <fstream>
#include <algorithm>
#include <set>
#include <vector>
#include <string>
int show_help(void) {
printf(
"LN2_NEIGHBORS: Find first order neighbors of each label, export a text or a nifti file.\n"
"\n"
"Usage:\n"
... |
465a7124a9adab61a28d999958587e0dda5ffe988bb09edba81b674f85bda053 | C++ | 16,268 | 571 | /***************************************************************************
*
* 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... |
76ab314aa8838130884a802678b9050fad9617d4f659cbd8deb60c91d76f60c7 | C++ | 16,274 | 575 | /***************************************************************************
*
* 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... |
0a5fbd22138b4fffa9d2c03c70efd07e752ad9ed5af351229d66e9e4fd6b30a2 | C++ | 16,328 | 483 | #define TORCH_ASSERT_NO_OPERATORS
#include <ATen/EmptyTensor.h>
#include <ATen/Context.h>
#include <c10/core/CPUAllocator.h>
#include <c10/util/safe_numerics.h>
#include <limits>
namespace at::detail {
namespace {
c10::Allocator* GetCPUAllocatorMaybePinned(bool pin_memory) {
if (pin_memory) {
// NB: This is not... |
072681ccb23097ef555fdaf7a14c2bd051ac2fcf9838520e4b7b4a60a0f66900 | C++ | 16,385 | 464 | #include <ATen/core/Dict.h>
#include <ATen/core/jit_type.h>
#include <c10/macros/Macros.h>
#include <c10/util/irange.h>
#include <ostream>
#include <sstream>
#include <utility>
namespace c10 {
OptionalTypePtr OptionalType::create(const TypePtr& contained) {
return OptionalTypePtr(new OptionalType(contained));
}
Ty... |
6a5e6080a23aba470bda5647a45226a43d05edc589f76e8a25793e6850d3cc2e | C++ | 16,386 | 738 | #include "Zernike_helper.h"
#include <src/jaz/optimization/nelder_mead.h>
#include <src/ctf.h>
#include <src/jaz/util/zio.h>
using namespace gravis;
BufferedImage<double> ZernikeHelper::computeEvenZernike(
int s, double pixelSize, const d2Matrix& mag, int n_max)
{
const int cc = Zernike::numberOfEvenCoeffs(n_max)... |
1644c693099ed58da94445a8baa89cedd8b7d700654f9d7cffbb3e78ed4efb0b | C++ | 16,457 | 434 | // 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 Foundation; either version 2
// of the License, or (at your option) any later version.
// This program is distributed in the hope that it will be use... |
31909c97baca204eabff930baff7f3d8c81bbfb4a878a3c2412a56294d3e4828 | C++ | 16,538 | 474 | /***************************************************************************
*
* 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... |
06e690d99dbb6385ea3229739465cb4d942b01d31b7351828a822d07977ab1f9 | C++ | 16,695 | 670 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres", "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
* ... |
610563dc439436e6ecfc16a8da97af4e14a2e68e63c5db78800c63cc00991026 | C++ | 16,712 | 483 | #include <ATen/native/kleidiai/kai_kernels.h>
#include <ATen/native/kleidiai/kai_pack.h>
#include <ATen/native/kleidiai/kai_ukernel_interface.h>
#include <ATen/Parallel.h>
#include <algorithm>
#include <cfloat>
#include <cmath>
#include <unordered_map>
#if AT_KLEIDIAI_ENABLED()
#include <cpuinfo.h>
namespace at::nat... |
742b1702840290b1bcce0ba46351c76a8a463e6332acc8947945357b3034a6bb | C++ | 16,753 | 467 | #include <c10/core/ScalarType.h>
#define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/native/ReduceOps.h>
#include <ATen/native/TensorCompare.h>
#include <numeric>
#include <iterator>
#include <algorithm>
#include <utility>
#include <vector>
#include <ATen/Dispatch.h>
#include <ATen... |
fb351b05e98b01d10959fb15d8a7eb8351db96afd5f419cdd7a22810c074cf99 | C++ | 16,772 | 455 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Dispatch.h>
#include <ATen/ExpandUtils.h>
#include <torch/library.h>
#include <ATen/native/TensorIterator.h>
#include <ATen/native/cpu/Loops.h>
#include <ATen/native/quantized/cpu/OnednnUtils.h>
#include <ATen/native/quantized/cpu/Q... |
04ce43b01d181eaf67176d5d316a18111d116101a54c861c0ca3d4d271fe7a68 | C++ | 16,788 | 545 | // Routines for measuring basic event properties
// last revision: 24-Jan-2011
// C. Schmidt-Hieber, christsc@gmx.de
// 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 Foundation; either version 2
/... |
d78e0afc2b81e0b720498c139dbf8e8cc96a8d5371d4134b4a5b9bea2d34d5e6 | C++ | 16,807 | 551 | /***************************************************************************
*
* 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... |
c2e97f83336e9ee9ebf840048bc7955359ae6e2668435385b16c39141f811b21 | C++ | 16,850 | 645 | #include "modular_ctf_optimisation.h"
#include <src/jaz/optics/magnification_helper.h>
#include <src/ctf.h>
#include <omp.h>
using namespace gravis;
#define DATA_PAD 512
ModularCtfOptimisation::ModularCtfOptimisation(
MetaDataTable &mdt,
ObservationModel* obsModel,
const std::vector<Image<Complex>>& obs,
co... |
5f55b3a7c17c724e1b5e963f37f248fff1857867faff36d58d3b24da9cdc8363 | C++ | 16,897 | 561 | #define TORCH_ASSERT_NO_OPERATORS
#include <ATen/Dispatch.h>
#include <ATen/Parallel.h>
#include <ATen/native/CPUBlas.h>
#include <ATen/native/cpu/zmath.h>
#include <ATen/native/cpu/ReducedPrecisionFloatGemvFastPathKernel.h>
#include <c10/util/irange.h>
#include <c10/util/Unroll.h>
#if !defined(C10_MOBILE)
namespace a... |
886cb8a158a7d6fc172a30124a39fc3c4222270b10490ac9b7dd77d891df25c4 | C++ | 16,914 | 467 | #include <c10/util/Exception.h>
#include <ATen/ATen.h>
#include <ATen/NestedTensorImpl.h>
#include <ATen/native/NonSymbolicBC.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/NativeFunctions.h>
#else
#include <ATen/ops/_nested_from_padded_native.h>
#include <ATen/ops/narrow_native.h>
#endif
#include <ATen/native/ne... |
14f049c6c81c66d976b15202e3564f3f64d225af50364f1153b7d0d0a8afe112 | C++ | 16,953 | 599 | #include "local_particle_refinement.h"
#include <src/jaz/tomography/extraction.h>
#include <src/jaz/tomography/prediction.h>
#include <src/jaz/tomography/projection/fwd_projection.h>
#include <src/jaz/math/Tait_Bryan_angles.h>
#include <src/jaz/math/Euler_angles_relion.h>
#include <src/jaz/optics/damage.h>
using names... |
f2e506b54a723df6b415cf226305ea278b98d061150751372399e101ff4ac692 | C++ | 17,162 | 536 | /***************************************************************************
*
* 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... |
d087ce995a7ddcea7096f3ff85503028f7e29709024a25990c2207612097fbc2 | C++ | 17,241 | 395 | // 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 <ATen/functorch/BatchRulesHelper.h>
#include <ATen/DTensorState.h>
#include <utility>
namespace a... |
9b94353bf9fea4365222447bd468e25fbecd94b5c16c68798fa998126e72b7e9 | C++ | 17,300 | 470 | //********************************************************************************************************************
// FileDataBucket.cpp
//********************************************************************************************************************
#include "FileDataBucket.h"
#include <algorithm>
//********... |
4a63b99e33fc7ea9cc3723b23a6252028ba88d0f8ba3275796778c3ea3f57cfa | C++ | 17,380 | 776 | #include "log.h"
#include "ansi_codes.h"
#include <src/time.h>
#include <src/args.h>
#include <iomanip>
Logger* Log::logger = new FancyLogger();
long int Log::lastItemsDone_global = -1;
long int Log::totalItems_global = 0;
#define MAX_UPDATES_PER_BAR 200
void Log::print(std::string s)
{
logger->print(s);
}
void L... |
c4c85fd160a63634d5585d377a6be1efcac88d988d5a2bbdf528df8ea54cfa21 | C++ | 17,434 | 688 | /***************************************************************************
*
* 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... |
b532de76e03a93629b12e4146a8aaf2d92d17e1a2fe43cce5f7de86e17ee92e9 | C++ | 17,661 | 536 | /***************************************************************************
*
* 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... |
74dd43549b902499d008a05eaf001352b6d0970bc7e8c8ac40680755201cb002 | C++ | 17,694 | 504 | // Returns unique elements of input tensor.
#define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Dispatch_v2.h>
#include <ATen/Parallel.h>
#include <ATen/native/TensorIterator.h>
#include <c10/util/irange.h>
#include <c10/util/Load.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/F... |
bc9ccc23d8d7cb01437e48229478c649fb47cc41022c468125f71a40366c1791 | C++ | 17,770 | 470 | //********************************************************************************************************************
// FileDataBucket.cpp
//********************************************************************************************************************
#include "FileDataBucket.h"
#include <algorithm>
//**... |
86eba21a5381617343313b1b7411ffcecb1c2d54559d77ceb38a5c3cf5f9695c | C++ | 17,805 | 808 | #include "damage.h"
#include <src/jaz/image/power_spectrum.h>
using namespace gravis;
void Damage::applyWeight(
RawImage<float>& stack,
double pixelSize,
const std::vector<double>& doses,
int num_threads, double BfactorPerElectronDose)
{
const int w = stack.xdim;
const int h = stack.ydim;
const int fc =... |
322fb6e79ec232124caeb97ee46b5721defd7924cfaffeef2b8777b745eb2800 | C++ | 17,910 | 434 |
#include "../dep/laynii_lib.h"
int show_help(void) {
printf(
"LN_GRADSMOOTH_ITER : Local gradient based smoothing.\n"
"\n"
" This program is designed smooth to data within layer or columns ,\n"
" In order to avoid smoothing across masks a crawler smoothed only across connected voxels ,\n"
... |
8adf53351f18d2540b7b1d0cebf9d036320904901bfc3396d46239cf63599066 | C++ | 17,912 | 378 | #include <ATen/Context.h>
#include <ATen/LegacyBatchedFallback.h>
#include <ATen/MatrixRef.h>
#include <ATen/LegacyVmapTransforms.h>
#include <ATen/core/dispatch/Dispatcher.h>
#include <c10/util/accumulate.h>
#include <c10/util/irange.h>
#include <bit>
namespace at {
// Given a linear index, return the actual index.
... |
73969b48d7e0422ce31e8ef5d8e5116f1d196e713b83f41625ab9d7626b2ace5 | C++ | 17,988 | 451 | //******************************************************************************************************************************************************
// GeneralOperations.cpp
// Author: Kevin Iamiceli
// Modified March 9, 2003
// Version 3.00
//************************************************************************... |
417350d19d4b4dee31dd722ff4f8bbea2c5006e8ec8be6928d29cccf03efc68b | C++ | 18,094 | 574 | //***********************************************************************************************
//
// Copyright (c) 1993-1997 Axon Instruments.
// All rights reserved.
// Permission is granted to freely to use, modify and copy the code in this file.
//
//************************************************... |
252a6a7f5cbb794e51cd024e2b886acf57457873027c792a177b1f99f2fe58c7 | C++ | 18,100 | 421 | #include "../dep/laynii_lib.h"
int show_help( void )
{
printf(
"LN_LOITUMA : Generates equi-volume layers based on Leaky layers and\n"
" equi-dist layers. This program does not necessarily\n"
" assume any curvature smoothness.\n"
"\n"
"Usage:\n"
" LN_LOITUMA -equid... |
4af82d7e04585ccef37bfcfd4960c5d59c0d3a0b2e470d5cdb2fd15ce6a731e8 | C++ | 18,105 | 723 | /***************************************************************************
*
* 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... |
25f7125543f5fad0cf0a798a9c539c23c942ac7382edc7948e1cdc9fdd77be37 | C++ | 18,131 | 885 | /*
Provides the implementations of cuSPARSE function templates.
*/
#include <ATen/cuda/CUDASparseBlas.h>
namespace at::cuda::sparse {
template <>
void csrgeam2_bufferSizeExt<float>(
CUSPARSE_CSRGEAM2_BUFFERSIZE_ARGTYPES(float)) {
TORCH_CUDASPARSE_CHECK(cusparseScsrgeam2_bufferSizeExt(
handle,
m,
... |
646b05b33c4196f49d3dcb6f1fe65f546ddc3e30e13ae356d42e5747861e1632 | C++ | 18,185 | 659 | /***************************************************************************
*
* 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... |
37010ba8ec3fb7af23ce65550fb08619378c527c777cb1b4633e6598aa308077 | C++ | 18,250 | 511 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/core/Tensor.h>
#include <ATen/Dispatch.h>
#include <ATen/Parallel.h>
#include <ATen/native/Pool.h>
#include <c10/util/irange.h>
#ifndef AT_PER_OPERATOR_HEADERS
#include <ATen/Functions.h>
#include <ATen/NativeFunctions.h>
#else
#include <ATen/ops/avg_pool3d_bac... |
9ae9ccd39b484778e50c85dbfac481ca831057c44768b165eb165f4cbcec73e6 | C++ | 18,300 | 426 | #include<RcppArmadillo.h>
#include<Rcpp.h>
// [[Rcpp::depends(RcppArmadillo)]]
#include "paramEst.h"
#include "computeMatrices.h"
#include "invertPseudoVar.h"
#include "pseudovarPartial.h"
#include "multiP.h"
#include "inference.h"
#include "utils.h"
using namespace Rcpp;
//' GLMM parameter estimation using pseudo-lik... |
437a3346b7b47f398fe105347c1e9dc75f322e7a250b6c6317c0405639c49be1 | C++ | 18,439 | 451 | //******************************************************************************************************************************************************
// GeneralOperations.cpp
// Author: Kevin Iamiceli
// Modified March 9, 2003
// Version 3.00
//*******************************************************************... |
c796591af42880586a7800ba4bd8367791b0a361177a75c2ff3c2240ab48537e | C++ | 18,481 | 462 | #include "../dep/laynii_lib.h"
#include <sstream>
#include <vector>
#include <algorithm>
#include <unordered_set>
int show_help(void) {
printf(
"LN2_UVD_FILTER: Filter using flat coordinates (UV) and depth (D). This program:\n"
" 1. Evaluates voxels within a cylindrical window centered\n"
... |
75e4d94e3f5769c0b811bb65ac661a32fe71ab9a8b07aa73afd46c1b3e21957a | C++ | 18,522 | 567 | #include <ATen/DLConvertor.h>
#include <memory>
using namespace std;
namespace at {
DLDataType getDLDataType(const Tensor& t) {
DLDataType dtype;
dtype.lanes = 1;
dtype.bits = t.element_size() * 8;
switch (t.scalar_type()) {
case ScalarType::UInt1:
case ScalarType::UInt2:
case ScalarType::UInt3:
... |
f08044ed9dd2e79162aebd5fcc6c584e91e2df01aa9bd8669de6acae9e2677d7 | C++ | 18,610 | 451 | #include "../dep/laynii_lib.h"
int show_help(void) {
printf(
"LN2_DEVEIN : Mitigates venous signal in one of three different ways.\n"
"\n"
" 1. Estimates microvascular component in layer-fMRI GE-BOLD. It does so by using an estimate\n"
" of the local macrovascular blood volume amplitude o... |
ddd384a53a5c4bfaee9538f246d6327a7962281954924912b1cc7c9de0df1602 | C++ | 18,612 | 688 | /***************************************************************************
*
* 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... |
fcd543c189fc3c5775c791f47cbd59a47303a06502b2398c5fb7f7e95277cf51 | C++ | 18,645 | 574 | #include "align.h"
#include <src/ctf.h>
#include <src/jaz/tomography/tomogram.h>
#include <src/jaz/tomography/motion/motion_fit.h>
#include <src/jaz/tomography/motion/proto_alignment.h>
#include <src/jaz/tomography/motion/trajectory_set.h>
#include <src/jaz/tomography/motion/shift_alignment.h>
#include <src/jaz/tomogra... |
ba5cff937b7ffd1b619711817f7aeade365397c80dfe1b6eb4d3ba7d7c0afde4 | C++ | 18,648 | 495 | // 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 <ATen/functorch/DynamicLayer.h>
#include <ATen/functorch/TensorWrapper.h>
#include <ATen/functorch/... |
62bf3c3c48d95ed252e3b549a6ad2a27b6cae1744d9798da3e6adc843ba22224 | C++ | 18,690 | 511 | // 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 Foundation; either version 2
// of the License, or (at your option) any later version.
// This program is distributed in the hope that it will be useful,
... |
6509bdc10551eb480c4957bfb3fc58a393ec11d51124789d092b31b931c922a7 | C++ | 18,745 | 652 | #include "reconstruct_particle.h"
#include <src/jaz/tomography/projection/projection.h>
#include <src/jaz/tomography/projection/Fourier_backprojection.h>
#include <src/jaz/tomography/reconstruction.h>
#include <src/jaz/image/centering.h>
#include <src/jaz/image/padding.h>
#include <src/jaz/image/power_spectrum.h>
#incl... |
8ecd6b271c6607d8e12b96c94867cb04ed392cccd686387d680869c887c96f88 | C++ | 18,756 | 748 | /***************************************************************************
*
* 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... |
f82318772abf70696776d76cfdc08175c2a999aaa45586e7ddb0b654e668c325 | C++ | 18,758 | 450 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/native/Distance.h>
#include <algorithm>
#include <ATen/core/Tensor.h>
#include <ATen/Dispatch.h>
#include <ATen/Parallel.h>
#include <ATen/TensorIterator.h>
#include <ATen/cpu/vec/functional.h>
#include <c10/util/irange.h>
namespace at::native {
namespace {
... |
5552433494cc030c36e513b202cde278431fb9300d7d8248dce9332235491607 | C++ | 18,796 | 657 | /*
* 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 <algorithm>
#include <cfloat>
#include <chrono>
#include <cmath>
#include <functional>
#incl... |
40420b9eb08009cf6c70c756bac03c4643b64ee382eb6f5d0bea1890da934760 | C++ | 18,863 | 636 | //#include <afxwin.h> // MFC core and standard components
//#include <afxdisp.h> // MFC Automation classes
#include "Nlx_Error.h"
#include "Nlx_DataTypes.h"
#include "Nlx_Code.h"
#include <fstream>
#include <mex.h>
// Checks for NT Header -- Note: does NOT check for Sun header
BOOL HasHeader(std::fstrea... |
f6b1379a6619aef914a0b7ea352c73f3907b334e06d4707c3c0f4dcb9b8d3dc0 | C++ | 18,875 | 525 | #include <gtest/gtest.h>
#include <ATen/ATen.h>
#include <ATen/core/boxing/KernelFunction.h>
#include <ATen/core/boxing/impl/test_helpers.h>
#include <ATen/core/op_registration/op_registration.h>
using std::vector;
using std::tuple;
using std::optional;
using c10::IValue;
using c10::OperatorKernel;
using c10::Operator... |
a1fc42f191d4eeb5487b3191a5d2ce394e26259a9f3cf5cf20f76b28f092620d | C++ | 18,906 | 425 | #include <ATen/FunctionalizeFallbackKernel.h>
#include <ATen/core/dispatch/Dispatcher.h>
#include <ATen/core/LegacyTypeDispatch.h>
#include <ATen/EmptyTensor.h>
#include <ATen/FunctionalTensorWrapper.h>
#include <ATen/InferSize.h>
#include <ATen/TensorUtils.h>
#include <torch/library.h>
#include <c10/util/irange.h>
#i... |
3a44fd7215ed7e5c20de6f410f98147ec85cadca84710b65c41509fd18257c7e | C++ | 18,960 | 482 | #include "spike_detector.h"
// Constructor
SpikeDetector::SpikeDetector(uint8_t chunk_id)
: raw_data(BUFFER_LENGTH * CHUNKED_CHANNELS, 0.0f),
movavg_data(BUFFER_LENGTH * CHUNKED_CHANNELS, 0.0f),
filtered_out(BUFFER_LENGTH * CHUNKED_CHANNELS, 0.0f),
filtered_hp(BUFFER_LENGTH * CHUNKED_CHANNELS, ... |
5d35b12650595d18eaade387cea9631b76f866ed1e10f4004eb579a9c07ee758 | C++ | 19,045 | 444 | #include<RcppArmadillo.h>
#include<string>
// [[Rcpp::depends(RcppArmadillo)]]
#include "paramEst.h"
#include "computeMatrices.h"
#include "invertPseudoVar.h"
#include "pseudovarPartial.h"
#include "multiP.h"
#include "inference.h"
#include "utils.h"
using namespace Rcpp;
//' GLMM parameter estimation using pseudo-li... |
12c292aeee2f757014e16f575b7830998382c02a4a3a6e42de073052573b25bc | C++ | 19,080 | 700 | /*
* 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 "fully-connected-operator-tester.h"
TEST(FULLY_CONNECTED_OP, inte... |
26bed681dba23e6bcc8b541958dcf51c355c0bfc6b46684868ca34e66a431f89 | C++ | 19,276 | 591 | #include <ATen/Context.h>
#include <ATen/ExpandUtils.h>
#include <ATen/native/ConvUtils.h>
#include <ATen/native/mkldnn/xpu/detail/Utils.h>
#include <oneapi/dnnl/dnnl.hpp>
#include <oneapi/dnnl/dnnl_common.hpp>
namespace at::native::onednn {
dnnl::memory make_onednn_memory(
dnnl::memory::desc md,
dnnl::engin... |
715eca0479c32ecf60fccd50117cab03f267aef5751c22f7503c3de3e995c7e2 | C++ | 19,348 | 468 | // 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 Foundation; either version 2
// of the License, or (at your option) any later version.
// This program is distributed in the hope that it will be use... |
ed44dfa02d90f0d2bfea2d0d22840810ba7017972bc03eb0ddb3d028b616617c | C++ | 19,499 | 636 | //#include <afxwin.h> // MFC core and standard components
//#include <afxdisp.h> // MFC Automation classes
#include "Nlx_Error.h"
#include "Nlx_DataTypes.h"
#include "Nlx_Code.h"
#include <fstream>
#include <mex.h>
// Checks for NT Header -- Note: does NOT check for Sun header
BOOL HasHeader(st... |
e0054f7b812a31c3171c695791e365f89f94edf4c922d2f76ddd2b9c2da24e90 | C++ | 19,685 | 462 |
#include "../dep/laynii_lib.h"
int shoq_help(void) {
printf(
"LN2_DIFFUSE: WORK IN PROGRESS... EXTREMELY EXPERIMENTAL!\n"
"\n"
"Usage:\n"
" LN2_DIFFUSE -input data.nii -nr_steps 5\n"
"\n"
"Options:\n"
" -help : Show this help.\n"
" -input : Input image.\n"
" ... |
13400b10c04b1a3c872b35a33e2b522aab0e61f489b11a61ea802935d80e7c7c | C++ | 19,766 | 612 | /***************************************************************************
*
* 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... |
0ddd13b6696bae6fed99c50e62af6b872039e3e7716d798c02f925d141e842ed | C++ | 19,773 | 554 | #define TORCH_ASSERT_ONLY_METHOD_OPERATORS
#include <ATen/Context.h>
#include <ATen/Dispatch.h>
#include <ATen/Utils.h>
#include <ATen/core/TensorBody.h>
#include <ATen/core/ivalue.h>
#include <ATen/core/jit_type_base.h>
#include <ATen/native/quantized/PackedParams.h>
#include <ATen/native/quantized/cpu/conv_serializat... |
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