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biom.cpp
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biom.cpp
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/*
* BSD 3-Clause License
*
* Copyright (c) 2016-2021, UniFrac development team.
* All rights reserved.
*
* See LICENSE file for more details
*/
#include <cstdlib>
#include <iostream>
#include <stdio.h>
#include "biom.hpp"
using namespace H5;
using namespace su;
/* datasets defined by the BIOM 2.x spec */
const std::string OBS_INDPTR = std::string("/observation/matrix/indptr");
const std::string OBS_INDICES = std::string("/observation/matrix/indices");
const std::string OBS_DATA = std::string("/observation/matrix/data");
const std::string OBS_IDS = std::string("/observation/ids");
const std::string SAMPLE_INDPTR = std::string("/sample/matrix/indptr");
const std::string SAMPLE_INDICES = std::string("/sample/matrix/indices");
const std::string SAMPLE_DATA = std::string("/sample/matrix/data");
const std::string SAMPLE_IDS = std::string("/sample/ids");
biom::biom(std::string filename) {
file = H5File(filename.c_str(), H5F_ACC_RDONLY);
/* establish the datasets */
obs_indices = file.openDataSet(OBS_INDICES.c_str());
obs_data = file.openDataSet(OBS_DATA.c_str());
sample_indices = file.openDataSet(SAMPLE_INDICES.c_str());
sample_data = file.openDataSet(SAMPLE_DATA.c_str());
/* cache IDs and indptr */
sample_ids = std::vector<std::string>();
obs_ids = std::vector<std::string>();
sample_indptr = std::vector<uint32_t>();
obs_indptr = std::vector<uint32_t>();
load_ids(OBS_IDS.c_str(), obs_ids);
load_ids(SAMPLE_IDS.c_str(), sample_ids);
load_indptr(OBS_INDPTR.c_str(), obs_indptr);
load_indptr(SAMPLE_INDPTR.c_str(), sample_indptr);
/* cache shape and nnz info */
n_samples = sample_ids.size();
n_obs = obs_ids.size();
set_nnz();
/* define a mapping between an ID and its corresponding offset */
obs_id_index = std::unordered_map<std::string, uint32_t>();
sample_id_index = std::unordered_map<std::string, uint32_t>();
create_id_index(obs_ids, obs_id_index);
create_id_index(sample_ids, sample_id_index);
/* load obs sparse data */
obs_indices_resident = (uint32_t**)malloc(sizeof(uint32_t**) * n_obs);
if(obs_indices_resident == NULL) {
fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n",
sizeof(uint32_t**) * n_obs, __FILE__, __LINE__);
exit(EXIT_FAILURE);
}
obs_data_resident = (double**)malloc(sizeof(double**) * n_obs);
if(obs_data_resident == NULL) {
fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n",
sizeof(double**) * n_obs, __FILE__, __LINE__);
exit(EXIT_FAILURE);
}
obs_counts_resident = (unsigned int*)malloc(sizeof(unsigned int) * n_obs);
if(obs_counts_resident == NULL) {
fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n",
sizeof(unsigned int) * n_obs, __FILE__, __LINE__);
exit(EXIT_FAILURE);
}
uint32_t *current_indices = NULL;
double *current_data = NULL;
for(unsigned int i = 0; i < obs_ids.size(); i++) {
std::string id_ = obs_ids[i];
unsigned int n = get_obs_data_direct(id_, current_indices, current_data);
obs_counts_resident[i] = n;
obs_indices_resident[i] = current_indices;
obs_data_resident[i] = current_data;
}
sample_counts = get_sample_counts();
}
biom::~biom() {
for(unsigned int i = 0; i < n_obs; i++) {
free(obs_indices_resident[i]);
free(obs_data_resident[i]);
}
free(obs_indices_resident);
free(obs_data_resident);
free(obs_counts_resident);
}
void biom::set_nnz() {
// should these be cached?
DataType dtype = obs_data.getDataType();
DataSpace dataspace = obs_data.getSpace();
hsize_t dims[1];
dataspace.getSimpleExtentDims(dims, NULL);
nnz = dims[0];
}
void biom::load_ids(const char *path, std::vector<std::string> &ids) {
DataSet ds_ids = file.openDataSet(path);
DataType dtype = ds_ids.getDataType();
DataSpace dataspace = ds_ids.getSpace();
hsize_t dims[1];
dataspace.getSimpleExtentDims(dims, NULL);
/* the IDs are a dataset of variable length strings */
char **dataout = (char**)malloc(sizeof(char*) * dims[0]);
if(dataout == NULL) {
fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n",
sizeof(char*) * dims[0], __FILE__, __LINE__);
exit(EXIT_FAILURE);
}
ds_ids.read((void*)dataout, dtype);
ids.reserve(dims[0]);
for(unsigned int i = 0; i < dims[0]; i++) {
ids.push_back(dataout[i]);
}
for(unsigned int i = 0; i < dims[0]; i++)
free(dataout[i]);
free(dataout);
}
void biom::load_indptr(const char *path, std::vector<uint32_t> &indptr) {
DataSet ds = file.openDataSet(path);
DataType dtype = ds.getDataType();
DataSpace dataspace = ds.getSpace();
hsize_t dims[1];
dataspace.getSimpleExtentDims(dims, NULL);
uint32_t *dataout = (uint32_t*)malloc(sizeof(uint32_t) * dims[0]);
if(dataout == NULL) {
fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n",
sizeof(uint32_t) * dims[0], __FILE__, __LINE__);
exit(EXIT_FAILURE);
}
ds.read((void*)dataout, dtype);
indptr.reserve(dims[0]);
for(unsigned int i = 0; i < dims[0]; i++)
indptr.push_back(dataout[i]);
free(dataout);
}
void biom::create_id_index(std::vector<std::string> &ids,
std::unordered_map<std::string, uint32_t> &map) {
uint32_t count = 0;
map.reserve(ids.size());
for(auto i = ids.begin(); i != ids.end(); i++, count++) {
map[*i] = count;
}
}
unsigned int biom::get_obs_data_direct(const std::string &id, uint32_t *& current_indices_out, double *& current_data_out) {
uint32_t idx = obs_id_index.at(id);
uint32_t start = obs_indptr[idx];
uint32_t end = obs_indptr[idx + 1];
hsize_t count[1] = {end - start};
hsize_t offset[1] = {start};
DataType indices_dtype = obs_indices.getDataType();
DataType data_dtype = obs_data.getDataType();
DataSpace indices_dataspace = obs_indices.getSpace();
DataSpace data_dataspace = obs_data.getSpace();
DataSpace indices_memspace(1, count, NULL);
DataSpace data_memspace(1, count, NULL);
indices_dataspace.selectHyperslab(H5S_SELECT_SET, count, offset);
data_dataspace.selectHyperslab(H5S_SELECT_SET, count, offset);
current_indices_out = (uint32_t*)malloc(sizeof(uint32_t) * count[0]);
if(current_indices_out == NULL) {
fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n",
sizeof(uint32_t) * count[0], __FILE__, __LINE__);
exit(EXIT_FAILURE);
}
current_data_out = (double*)malloc(sizeof(double) * count[0]);
if(current_data_out == NULL) {
fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n",
sizeof(double) * count[0], __FILE__, __LINE__);
exit(EXIT_FAILURE);
}
obs_indices.read((void*)current_indices_out, indices_dtype, indices_memspace, indices_dataspace);
obs_data.read((void*)current_data_out, data_dtype, data_memspace, data_dataspace);
return count[0];
}
template<class TFloat>
void biom::get_obs_data_TT(const std::string &id, TFloat* out) const {
uint32_t idx = obs_id_index.at(id);
unsigned int count = obs_counts_resident[idx];
const uint32_t * const indices = obs_indices_resident[idx];
const double * const data = obs_data_resident[idx];
// reset our output buffer
for(unsigned int i = 0; i < n_samples; i++)
out[i] = 0.0;
for(unsigned int i = 0; i < count; i++) {
out[indices[i]] = data[i];
}
}
void biom::get_obs_data(const std::string &id, double* out) const {
biom::get_obs_data_TT(id,out);
}
void biom::get_obs_data(const std::string &id, float* out) const {
biom::get_obs_data_TT(id,out);
}
// note: out is supposed to be fully filled, i.e. out[start:end]
template<class TFloat>
void biom::get_obs_data_range_TT(const std::string &id, unsigned int start, unsigned int end, bool normalize, TFloat* out) const {
uint32_t idx = obs_id_index.at(id);
unsigned int count = obs_counts_resident[idx];
const uint32_t * const indices = obs_indices_resident[idx];
const double * const data = obs_data_resident[idx];
// reset our output buffer
for(unsigned int i = start; i < end; i++)
out[i-start] = 0.0;
if (normalize) {
for(unsigned int i = 0; i < count; i++) {
const int32_t j = indices[i];
if ((j>=start)&&(j<end)) {
out[j-start] = data[i]/sample_counts[j];
}
}
} else {
for(unsigned int i = 0; i < count; i++) {
const uint32_t j = indices[i];
if ((j>=start)&&(j<end)) {
out[j-start] = data[i];
}
}
}
}
void biom::get_obs_data_range(const std::string &id, unsigned int start, unsigned int end, bool normalize, double* out) const {
biom::get_obs_data_range_TT(id,start,end,normalize,out);
}
void biom::get_obs_data_range(const std::string &id, unsigned int start, unsigned int end, bool normalize, float* out) const {
biom::get_obs_data_range_TT(id,start,end,normalize,out);
}
unsigned int biom::get_sample_data_direct(const std::string &id, uint32_t *& current_indices_out, double *& current_data_out) {
uint32_t idx = sample_id_index.at(id);
uint32_t start = sample_indptr[idx];
uint32_t end = sample_indptr[idx + 1];
hsize_t count[1] = {end - start};
hsize_t offset[1] = {start};
DataType indices_dtype = sample_indices.getDataType();
DataType data_dtype = sample_data.getDataType();
DataSpace indices_dataspace = sample_indices.getSpace();
DataSpace data_dataspace = sample_data.getSpace();
DataSpace indices_memspace(1, count, NULL);
DataSpace data_memspace(1, count, NULL);
indices_dataspace.selectHyperslab(H5S_SELECT_SET, count, offset);
data_dataspace.selectHyperslab(H5S_SELECT_SET, count, offset);
current_indices_out = (uint32_t*)malloc(sizeof(uint32_t) * count[0]);
if(current_indices_out == NULL) {
fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n",
sizeof(uint32_t) * count[0], __FILE__, __LINE__);
exit(EXIT_FAILURE);
}
current_data_out = (double*)malloc(sizeof(double) * count[0]);
if(current_data_out == NULL) {
fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n",
sizeof(double) * count[0], __FILE__, __LINE__);
exit(EXIT_FAILURE);
}
sample_indices.read((void*)current_indices_out, indices_dtype, indices_memspace, indices_dataspace);
sample_data.read((void*)current_data_out, data_dtype, data_memspace, data_dataspace);
return count[0];
}
double* biom::get_sample_counts() {
double *sample_counts = (double*)calloc(sizeof(double), n_samples);
for(unsigned int i = 0; i < n_obs; i++) {
unsigned int count = obs_counts_resident[i];
uint32_t *indices = obs_indices_resident[i];
double *data = obs_data_resident[i];
for(unsigned int j = 0; j < count; j++) {
uint32_t index = indices[j];
double datum = data[j];
sample_counts[index] += datum;
}
}
return sample_counts;
}