/
StringFeatures.cpp
1901 lines (1582 loc) · 47.6 KB
/
StringFeatures.cpp
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#include <shogun/base/progress.h>
#include <shogun/base/ShogunEnv.h>
#include <shogun/features/StringFeatures.h>
#include <shogun/io/MemoryMappedFile.h>
#include <shogun/io/fs/FileSystem.h>
#include <shogun/io/fs/Path.h>
#include <shogun/io/ShogunErrc.h>
#include <shogun/mathematics/Math.h>
#include <shogun/preprocessor/Preprocessor.h>
#include <shogun/preprocessor/StringPreprocessor.h>
#include <shogun/mathematics/RandomNamespace.h>
#include <shogun/util/enumerate.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <stdio.h>
#include <stdlib.h>
#ifdef _WIN32
#include <tchar.h>
#include <strsafe.h>
#include <vector>
#else
#include <unistd.h>
#include <algorithm>
#include <utility>
#endif
namespace shogun
{
template<class ST> StringFeatures<ST>::StringFeatures() : Features(0)
{
init();
alphabet=std::make_shared<Alphabet>();
}
template<class ST> StringFeatures<ST>::StringFeatures(EAlphabet alpha) : Features(0)
{
init();
alphabet=std::make_shared<Alphabet>(alpha);
num_symbols=alphabet->get_num_symbols();
original_num_symbols=num_symbols;
}
template<class ST> StringFeatures<ST>::StringFeatures(const std::vector<SGVector<ST>>& string_list, EAlphabet alpha)
: StringFeatures(alpha)
{
set_features(string_list);
}
template<class ST> StringFeatures<ST>::StringFeatures(const std::vector<SGVector<ST>>& string_list, std::shared_ptr<Alphabet> alpha)
: StringFeatures(alpha)
{
set_features(string_list);
}
template<class ST> StringFeatures<ST>::StringFeatures(std::shared_ptr<Alphabet> alpha)
: Features(0)
{
ASSERT(alpha)
init();
alphabet=alpha;
num_symbols=alphabet->get_num_symbols();
original_num_symbols=num_symbols;
}
template<class ST> StringFeatures<ST>::StringFeatures(const std::shared_ptr<File>& loader, EAlphabet alpha)
: StringFeatures(alpha)
{
load(loader);
}
template<class ST> StringFeatures<ST>::~StringFeatures()
{
cleanup();
}
template<class ST> void StringFeatures<ST>::cleanup()
{
remove_all_subsets();
if (single_string.vector)
single_string = SGVector<ST>();
else
cleanup_feature_vectors(0, get_num_vectors()-1);
/*
if (single_string)
{
SG_FREE(single_string);
single_string=NULL;
}
else
cleanup_feature_vectors(0, get_num_vectors()-1);
*/
features.clear();
symbol_mask_table = SGVector<ST>();
/* start with a fresh alphabet, but instead of emptying the histogram
* create a new object (to leave the alphabet object alone if it is used
* by others)
*/
auto alpha=std::make_shared<Alphabet>(alphabet->get_alphabet());
alphabet=alpha;
}
template<class ST> void StringFeatures<ST>::cleanup_feature_vector(int32_t num)
{
ASSERT(num<get_num_vectors())
int32_t real_num=m_subset_stack->subset_idx_conversion(num);
features[real_num] = SGVector<ST>();
}
template<class ST> void StringFeatures<ST>::cleanup_feature_vectors(int32_t start, int32_t stop)
{
if(get_num_vectors())
{
ASSERT(stop<get_num_vectors())
ASSERT(stop >= start && start >= 0);
for (int32_t i=start; i<=stop; i++)
{
int32_t real_num=m_subset_stack->subset_idx_conversion(i);
features[real_num] = SGVector<ST>();
}
}
}
template<class ST> EFeatureClass StringFeatures<ST>::get_feature_class() const { return C_STRING; }
template<class ST> EFeatureType StringFeatures<ST>::get_feature_type() const { return F_UNKNOWN; }
template<class ST> std::shared_ptr<Alphabet> StringFeatures<ST>::get_alphabet() const
{
return alphabet;
}
template<class ST> std::shared_ptr<Features> StringFeatures<ST>::duplicate() const
{
return std::make_shared<StringFeatures>(*this);
}
template<class ST> SGVector<ST> StringFeatures<ST>::get_feature_vector(int32_t num)
{
if (num>=get_num_vectors())
{
error("Index out of bounds (number of strings {}, you "
"requested {})", get_num_vectors(), num);
}
int32_t l;
bool free_vec;
ST* vec=get_feature_vector(num, l, free_vec);
SGVector<ST> dst(l);
sg_memcpy(dst.vector, vec, l*sizeof(ST));
free_feature_vector(vec, num, free_vec);
return dst;
}
template<class ST> void StringFeatures<ST>::set_feature_vector(SGVector<ST> vector, int32_t num)
{
if (m_subset_stack->has_subsets())
error("A subset is set, cannot set feature vector");
if (num>=get_num_vectors())
{
error("Index out of bounds (number of strings {}, you "
"requested {})", get_num_vectors(), num);
}
if (vector.vlen<=0)
error("String has zero or negative length");
features[num] = vector.clone();
}
template<class ST> void StringFeatures<ST>::enable_on_the_fly_preprocessing()
{
preprocess_on_get=true;
}
template<class ST> void StringFeatures<ST>::disable_on_the_fly_preprocessing()
{
preprocess_on_get=false;
}
template<class ST> ST* StringFeatures<ST>::get_feature_vector(int32_t num, int32_t& len, bool& dofree)
{
if (num>=get_num_vectors())
error("Requested feature vector with index {} while total num is {}", num, get_num_vectors());
int32_t real_num=m_subset_stack->subset_idx_conversion(num);
if (!preprocess_on_get)
{
dofree=false;
len=features[real_num].vlen;
return features[real_num].vector;
}
else
{
SG_DEBUG("computing feature vector!")
ST* feat=compute_feature_vector(num, len);
dofree=true;
if (get_num_preprocessors())
{
ST* tmp_feat_before=feat;
for (int32_t i=0; i<get_num_preprocessors(); i++)
{
auto p=std::dynamic_pointer_cast<StringPreprocessor<ST>>(get_preprocessor(i));
feat=p->apply_to_string(tmp_feat_before, len);
SG_FREE(tmp_feat_before);
tmp_feat_before=feat;
}
}
// TODO: implement caching
return feat;
}
}
template<class ST> std::shared_ptr<StringFeatures<ST>> StringFeatures<ST>::get_transposed()
{
return std::make_shared<StringFeatures<ST>>(get_transposed_matrix(), alphabet);
}
template<class ST> std::vector<SGVector<ST>> StringFeatures<ST>::get_transposed_matrix()
{
int32_t num_feat=get_num_vectors();
int32_t num_vec=get_max_vector_length();
ASSERT(have_same_length())
SG_DEBUG("Allocating memory for transposed string features of size {}",
int64_t(num_feat)*num_vec);
std::vector<SGVector<ST>> sf;
sf.reserve(num_vec);
for (int32_t i=0; i<num_vec; i++)
{
sf.emplace_back(num_feat);
}
for (int32_t i=0; i<num_feat; i++)
{
int32_t len=0;
bool free_vec=false;
ST* vec=get_feature_vector(i, len, free_vec);
for (int32_t j=0; j<num_vec; j++)
sf[j].vector[i]=vec[j];
free_feature_vector(vec, i, free_vec);
}
return sf;
}
template<class ST> void StringFeatures<ST>::free_feature_vector(ST* feat_vec, int32_t num, bool dofree)
{
if (num>=get_num_vectors())
{
error(
"Trying to access string[{}] but num_str={}", num,
get_num_vectors());
}
int32_t real_num=m_subset_stack->subset_idx_conversion(num);
if (feature_cache)
feature_cache->unlock_entry(real_num);
if (dofree)
SG_FREE(feat_vec);
}
template<class ST> void StringFeatures<ST>::free_feature_vector(SGVector<ST> feat_vec, int32_t num)
{
if (num>=get_num_vectors())
{
error(
"Trying to access string[{}] but num_str={}", num,
get_num_vectors());
}
int32_t real_num=m_subset_stack->subset_idx_conversion(num);
if (feature_cache)
feature_cache->unlock_entry(real_num);
}
template<class ST> ST StringFeatures<ST>::get_feature(int32_t vec_num, int32_t feat_num)
{
ASSERT(vec_num<get_num_vectors())
int32_t len;
bool free_vec;
ST* vec=get_feature_vector(vec_num, len, free_vec);
ASSERT(feat_num<len)
ST result=vec[feat_num];
free_feature_vector(vec, vec_num, free_vec);
return result;
}
template<class ST> int32_t StringFeatures<ST>::get_vector_length(int32_t vec_num)
{
ASSERT(vec_num<get_num_vectors())
int32_t len;
bool free_vec;
ST* vec=get_feature_vector(vec_num, len, free_vec);
free_feature_vector(vec, vec_num, free_vec);
return len;
}
template<class ST> int32_t StringFeatures<ST>::get_max_vector_length() const
{
int32_t max_string_length=0;
index_t num_str=get_num_vectors();
for (int32_t i=0; i<num_str; i++)
{
max_string_length=Math::max(max_string_length,
features[m_subset_stack->subset_idx_conversion(i)].vlen);
}
return max_string_length;
}
template<class ST> int32_t StringFeatures<ST>::get_num_vectors() const
{
return m_subset_stack->has_subsets() ? m_subset_stack->get_size() : features.size();
}
template<class ST> floatmax_t StringFeatures<ST>::get_num_symbols() { return num_symbols; }
template<class ST> floatmax_t StringFeatures<ST>::get_max_num_symbols() { return Math::powl(2,sizeof(ST)*8); }
template<class ST> floatmax_t StringFeatures<ST>::get_original_num_symbols() { return original_num_symbols; }
template<class ST> int32_t StringFeatures<ST>::get_order() { return order; }
template<class ST> ST StringFeatures<ST>::get_masked_symbols(ST symbol, uint8_t mask)
{
ASSERT(symbol_mask_table)
return symbol_mask_table[mask] & symbol;
}
template<class ST> ST StringFeatures<ST>::shift_offset(ST offset, int32_t amount)
{
ASSERT(alphabet)
return (offset << (amount*alphabet->get_num_bits()));
}
template<class ST> ST StringFeatures<ST>::shift_symbol(ST symbol, int32_t amount)
{
ASSERT(alphabet)
return (symbol >> (amount*alphabet->get_num_bits()));
}
template<class ST> void StringFeatures<ST>::load_ascii_file(char* fname, bool remap_to_bin,
EAlphabet ascii_alphabet, EAlphabet binary_alphabet)
{
remove_all_subsets();
size_t blocksize=1024*1024;
size_t required_blocksize=0;
uint8_t* dummy=SG_MALLOC(uint8_t, blocksize);
uint8_t* overflow=NULL;
int32_t overflow_len=0;
cleanup();
auto alpha=std::make_shared<Alphabet>(ascii_alphabet);
auto alpha_bin=std::make_shared<Alphabet>(binary_alphabet);
FILE* f=fopen(fname, "ro");
int32_t num_vectors = 0;
if (f)
{
io::info("counting line numbers in file {}", fname);
size_t block_offs=0;
size_t old_block_offs=0;
fseek(f, 0, SEEK_END);
size_t fsize=ftell(f);
rewind(f);
if (blocksize>fsize)
blocksize=fsize;
SG_DEBUG("block_size={} file_size={}", blocksize, fsize)
auto pb = SG_PROGRESS(range(fsize));
size_t sz=blocksize;
while (sz == blocksize)
{
sz=fread(dummy, sizeof(uint8_t), blocksize, f);
for (size_t i=0; i<sz; i++)
{
block_offs++;
if (dummy[i]=='\n' || (i==sz-1 && sz<blocksize))
{
num_vectors++;
required_blocksize=Math::max(required_blocksize, block_offs-old_block_offs);
old_block_offs=block_offs;
}
}
pb.print_progress();
}
pb.complete();
io::info("found {} strings", num_vectors);
SG_FREE(dummy);
blocksize=required_blocksize;
dummy=SG_MALLOC(uint8_t, blocksize);
overflow=SG_MALLOC(uint8_t, blocksize);
features.clear();
features.resize(num_vectors);
auto pb2 =
PRange<int>(range(num_vectors), "LOADING: ", UTF8, []() {
return true;
});
rewind(f);
sz=blocksize;
int32_t lines=0;
while (sz == blocksize)
{
sz=fread(dummy, sizeof(uint8_t), blocksize, f);
size_t old_sz=0;
for (size_t i=0; i<sz; i++)
{
if (dummy[i]=='\n' || (i==sz-1 && sz<blocksize))
{
int32_t len=i-old_sz;
//io::print("i:%d len:{} old_sz:{}\n", i, len, old_sz)
features[lines] = SGVector<ST>(len);
if (remap_to_bin)
{
for (int32_t j=0; j<overflow_len; j++)
features[lines].vector[j]=alpha->remap_to_bin(overflow[j]);
for (int32_t j=0; j<len; j++)
features[lines].vector[j+overflow_len]=alpha->remap_to_bin(dummy[old_sz+j]);
alpha->add_string_to_histogram(&dummy[old_sz], len);
alpha_bin->add_string_to_histogram(features[lines].vector, features[lines].vlen);
}
else
{
for (int32_t j=0; j<overflow_len; j++)
features[lines].vector[j]=overflow[j];
for (int32_t j=0; j<len; j++)
features[lines].vector[j+overflow_len]=dummy[old_sz+j];
alpha->add_string_to_histogram(&dummy[old_sz], len);
alpha->add_string_to_histogram(features[lines].vector, features[lines].vlen);
}
// clear overflow
overflow_len=0;
//Math::display_vector(features[lines].string, len);
old_sz=i+1;
lines++;
pb2.print_progress();
}
}
pb2.complete();
for (size_t i=old_sz; i<sz; i++)
overflow[i-old_sz]=dummy[i];
overflow_len=sz-old_sz;
}
if (alpha->check_alphabet_size() && alpha->check_alphabet())
{
io::info("file successfully read");
io::info("max_string_length={}", get_max_vector_length());
io::info("num_strings={}", get_num_vectors());
}
fclose(f);
}
SG_FREE(dummy);
SG_FREE(overflow);
if (remap_to_bin)
{
alphabet=alpha_bin;
}
else
{
alphabet=alpha;
}
num_symbols=alphabet->get_num_symbols();
}
template<class ST> bool StringFeatures<ST>::load_fasta_file(const char* fname, bool ignore_invalid)
{
remove_all_subsets();
int32_t i=0;
uint64_t len=0;
uint64_t offs=0;
int32_t num=0;
MemoryMappedFile<char> f(fname);
while (true)
{
char* s=f.get_line(len, offs);
if (!s)
break;
if (len>0 && s[0]=='>')
num++;
}
if (num==0)
error("No fasta hunks (lines starting with '>') found");
cleanup();
alphabet=std::make_shared<Alphabet>(DNA);
num_symbols=alphabet->get_num_symbols();
std::vector<SGVector<ST>> strings;
strings.reserve(num);
offs=0;
for (i=0;i<num; i++)
{
uint64_t id_len=0;
char* id=f.get_line(id_len, offs);
char* fasta=f.get_line(len, offs);
char* s=fasta;
int32_t fasta_len=0;
int32_t spanned_lines=0;
while (true)
{
if (!s || len==0)
error("Error reading fasta entry in line {} len={}", 4*i+1, len);
if (s[0]=='>' || offs==f.get_size())
{
offs-=len+1; // seek to beginning
if (offs==f.get_size())
{
SG_DEBUG("at EOF")
fasta_len+=len;
}
len=fasta_len-spanned_lines;
strings.emplace_back(len);
ST* str=strings.back().vector;
int32_t idx=0;
SG_DEBUG("'{:{}}', len={}, spanned_lines={}", id, (int32_t) id_len, (int32_t) len, (int32_t) spanned_lines)
for (int32_t j=0; j<fasta_len; j++)
{
if (fasta[j]=='\n')
continue;
ST c=(ST) fasta[j];
if (ignore_invalid && !alphabet->is_valid((uint8_t) fasta[j]))
c=(ST) 'A';
if (uint64_t(idx)>=len)
error("idx={} j={} fasta_len={}, spanned_lines={} str='{:{}}'", idx, j, fasta_len, spanned_lines, (char*)str, idx);
str[idx++]=c;
}
break;
}
spanned_lines++;
fasta_len+=len+1; // including '\n'
s=f.get_line(len, offs);
}
}
return set_features(strings);
}
template<class ST> bool StringFeatures<ST>::load_fastq_file(const char* fname,
bool ignore_invalid, bool bitremap_in_single_string)
{
remove_all_subsets();
MemoryMappedFile<char> f(fname);
int32_t i=0;
uint64_t len=0;
uint64_t offs=0;
int32_t num=f.get_num_lines();
int32_t max_len=0;
if (num%4)
error("Number of lines must be divisible by 4 in fastq files");
num/=4;
cleanup();
alphabet=std::make_shared<Alphabet>(DNA);
std::vector<SGVector<ST>> strings;
ST* str=NULL;
if (bitremap_in_single_string)
{
strings.reserve(1);
strings.emplace_back(num);
f.get_line(len, offs);
f.get_line(len, offs);
order=len;
max_len=num;
offs=0;
original_num_symbols=alphabet->get_num_symbols();
str=SG_MALLOC(ST, len);
}
else
strings.resize(num);
for (i=0;i<num; i++)
{
if (!f.get_line(len, offs))
error("Error reading 'read' identifier in line {}", 4*i);
char* s=f.get_line(len, offs);
if (!s || len==0)
error("Error reading 'read' in line {} len={}", 4*i+1, len);
if (bitremap_in_single_string)
{
if (len!=(uint64_t) order)
error("read in line {} not of length {} (is {})", 4*i+1, order, len);
for (int32_t j=0; j<order; j++)
str[j]=(ST) alphabet->remap_to_bin((uint8_t) s[j]);
strings[0].vector[i]=embed_word(str, order);
}
else
{
strings[i] = SGVector<ST>(len);
str=strings[i].vector;
if (ignore_invalid)
{
for (uint64_t j=0; j<len; j++)
{
if (alphabet->is_valid((uint8_t) s[j]))
str[j]= (ST) s[j];
else
str[j]= (ST) 'A';
}
}
else
{
for (uint64_t j=0; j<len; j++)
str[j]= (ST) s[j];
}
max_len=Math::max(max_len, (int32_t) len);
}
if (!f.get_line(len, offs))
error("Error reading 'read' quality identifier in line {}", 4*i+2);
if (!f.get_line(len, offs))
error("Error reading 'read' quality in line {}", 4*i+3);
}
if (bitremap_in_single_string)
num=1;
features=std::move(strings);
return true;
}
template<class ST> bool StringFeatures<ST>::load_from_directory(char* dirname)
{
remove_all_subsets();
std::vector<std::string> children;
auto fs_registry = env();
require(!fs_registry->is_directory(dirname),
"Specified path ('{}') is not a directory!", dirname);
auto r = fs_registry->get_children(dirname, &children);
if (r)
throw io::to_system_error(r);
if (children.size() <= 0)
{
error("error calling scandir - no files found");
return false;
}
else
{
int32_t num=0;
int64_t max_buffer_size = -1;
//usually n==num_vec, but it might not in race conditions
//(file perms modified, file erased)
std::vector<SGVector<ST>> strings;
strings.reserve(children.size());
std::string buffer;
for (auto v: children)
{
auto fname = io::join_path(dirname, v);
if (fs_registry->is_directory(fname))
{
int64_t filesize = fs_registry->get_file_size(fname);
std::unique_ptr<io::RandomAccessFile> file;
if (!fs_registry->new_random_access_file(fname, &file))
{
SG_DEBUG("{}:{}", fname.c_str(), filesize);
std::string_view result;
buffer.clear();
if (max_buffer_size < filesize)
{
buffer.resize(filesize);
max_buffer_size = filesize;
}
if (file->read(0, filesize, &result, &(buffer[0])))
error("failed to read file");
int64_t sg_string_len = filesize/(int64_t)sizeof(ST);
strings.emplace_back(sg_string_len);
sg_memcpy(const_cast<char*>(result.data()), strings[num].vector, filesize);
++num;
}
}
else
SG_DEBUG("Skipping {} as it's a directory", fname.c_str());
}
if (num>0)
{
return set_features(strings);
}
}
return false;
}
template<class ST> bool StringFeatures<ST>::set_features(const std::vector<SGVector<ST>>& string_list)
{
return set_features(string_list.data(), string_list.size());
}
template<class ST> bool StringFeatures<ST>::set_features(const SGVector<ST>* p_features, int32_t p_num_vectors)
{
if (m_subset_stack->has_subsets())
error("Cannot call set_features() with subset.");
if (p_features)
{
auto alpha=std::make_shared<Alphabet>(alphabet->get_alphabet());
//compute histogram for char/byte
for (int32_t i=0; i<p_num_vectors; i++)
alpha->add_string_to_histogram( p_features[i].vector, p_features[i].vlen);
io::info("max_value_in_histogram:{}", alpha->get_max_value_in_histogram());
io::info("num_symbols_in_histogram:{}", alpha->get_num_symbols_in_histogram());
if (alpha->check_alphabet_size() && alpha->check_alphabet())
{
cleanup();
alphabet=alpha;
// TODO remove copying
features.clear();
features.reserve(p_num_vectors);
std::copy_n(p_features, p_num_vectors, std::back_inserter(features));
return true;
}
}
return false;
}
template<class ST> bool StringFeatures<ST>::append_features(std::shared_ptr<StringFeatures<ST>> sf)
{
ASSERT(sf)
if (m_subset_stack->has_subsets())
error("Cannot call set_features() with subset.");
std::vector<SGVector<ST>> new_features;
new_features.reserve(sf->get_num_vectors());
index_t sf_num_str=sf->get_num_vectors();
for (int32_t i=0; i<sf_num_str; i++)
{
int32_t real_i = sf->m_subset_stack->subset_idx_conversion(i);
new_features[i] = sf->features[real_i].clone();
}
return append_features(new_features);
}
template<class ST> bool StringFeatures<ST>::append_features(const std::vector<SGVector<ST>>& p_features)
{
if (m_subset_stack->has_subsets())
error("Cannot call set_features() with subset.");
if (features.empty())
return set_features(p_features);
auto alpha=std::make_shared<Alphabet>(alphabet->get_alphabet());
//compute histogram for char/byte
for (int32_t i=0; i<p_features.size(); i++)
alpha->add_string_to_histogram( p_features[i].vector, p_features[i].vlen);
io::info("max_value_in_histogram:{}", alpha->get_max_value_in_histogram());
io::info("num_symbols_in_histogram:{}", alpha->get_num_symbols_in_histogram());
if (alpha->check_alphabet_size() && alpha->check_alphabet())
{
for (int32_t i=0; i<p_features.size(); i++)
alphabet->add_string_to_histogram(p_features[i].vector, p_features[i].vlen);
int32_t old_num_vectors=get_num_vectors();
int32_t num_vectors=old_num_vectors+p_features.size();
std::vector<SGVector<ST>> new_features;
new_features.reserve(num_vectors);
for (int32_t i=0; i<get_num_vectors(); i++)
{
if (i<old_num_vectors)
new_features.push_back(features[i]);
else
new_features.push_back(p_features[i-old_num_vectors]);
}
this->features=std::move(new_features);
return true;
}
return false;
}
template<class ST> const std::vector<SGVector<ST>>& StringFeatures<ST>::get_string_list() const
{
if (m_subset_stack->has_subsets())
error("get features() is not possible on subset");
return features;
}
template<class ST> std::vector<SGVector<ST>>& StringFeatures<ST>::get_string_list()
{
return const_cast<std::vector<SGVector<ST>>&>(
std::as_const(*this).get_string_list());
}
template<class ST> std::vector<SGVector<ST>> StringFeatures<ST>::copy_features()
{
ASSERT(get_num_vectors()>0)
std::vector<SGVector<ST>> new_feat;
new_feat.reserve(get_num_vectors());
for (int32_t i=0; i<get_num_vectors(); i++)
{
SGVector<ST> vec =get_feature_vector(i);
new_feat.push_back(vec.clone());
free_feature_vector(vec, i);
}
return new_feat;
}
template<class ST> void StringFeatures<ST>::get_features(std::vector<SGVector<ST>>* dst)
{
*dst=copy_features();
}
template<class ST> bool StringFeatures<ST>::load_compressed(char* src, bool decompress)
{
remove_all_subsets();
FILE* file=NULL;
int32_t num_vectors = 0;
int32_t max_string_length = 0;
if (!(file=fopen(src, "r")))
return false;
cleanup();
// header shogun v0
char id[4];
if (fread(&id[0], sizeof(char), 1, file)!=1)
error("failed to read header");
ASSERT(id[0]=='S')
if (fread(&id[1], sizeof(char), 1, file)!=1)
error("failed to read header");
ASSERT(id[1]=='G')
if (fread(&id[2], sizeof(char), 1, file)!=1)
error("failed to read header");
ASSERT(id[2]=='V')
if (fread(&id[3], sizeof(char), 1, file)!=1)
error("failed to read header");
ASSERT(id[3]=='0')
//compression type
uint8_t c;
if (fread(&c, sizeof(uint8_t), 1, file)!=1)
error("failed to read compression type");
auto compressor= std::make_shared<Compressor>((E_COMPRESSION_TYPE) c);
//alphabet
uint8_t a;
alphabet.reset();
if (fread(&a, sizeof(uint8_t), 1, file)!=1)
error("failed to read compression alphabet");
alphabet=std::make_shared<Alphabet>((EAlphabet) a);
// number of vectors
if (fread(&num_vectors, sizeof(int32_t), 1, file)!=1)
error("failed to read compression number of vectors");
ASSERT(num_vectors>0)
// maximum string length
if (fread(&max_string_length, sizeof(int32_t), 1, file)!=1)
error("failed to read maximum string length");
ASSERT(max_string_length>0)
features.clear();
features.reserve(num_vectors);
// vectors
for (int32_t i=0; i<num_vectors; i++)
{
// vector len compressed
int32_t len_compressed;
if (fread(&len_compressed, sizeof(int32_t), 1, file)!=1)
error("failed to read vector length compressed");
// vector len uncompressed
int32_t len_uncompressed;
if (fread(&len_uncompressed, sizeof(int32_t), 1, file)!=1)
error("failed to read vector length uncompressed");
// vector raw data
if (decompress)
{
features.emplace_back(len_uncompressed);
uint8_t* compressed=SG_MALLOC(uint8_t, len_compressed);
if (fread(compressed, sizeof(uint8_t), len_compressed, file)!=(size_t) len_compressed)
error("failed to read compressed data (expected {} bytes)", len_compressed);
uint64_t uncompressed_size=len_uncompressed;
uncompressed_size*=sizeof(ST);
compressor->decompress(compressed, len_compressed,
(uint8_t*) features[i].vector, uncompressed_size);
SG_FREE(compressed);
ASSERT(uncompressed_size==((uint64_t) len_uncompressed)*sizeof(ST))
}
else
{
int32_t offs = std::ceil(2.0 * sizeof(int32_t) / sizeof(ST));
features.emplace_back(len_compressed+offs);
int32_t* feat32ptr=((int32_t*) (features[i].vector));
feat32ptr[0]=(int32_t) len_compressed;
feat32ptr[1]=(int32_t) len_uncompressed;
uint8_t* compressed=(uint8_t*) (&features[i].vector[offs]);
if (fread(compressed, 1, len_compressed, file)!=(size_t) len_compressed)
error("failed to read uncompressed data");
}
}
fclose(file);
return false;
}
template<class ST> bool StringFeatures<ST>::save_compressed(char* dest, E_COMPRESSION_TYPE compression, int level)
{
int32_t num_vectors = get_num_vectors();
int32_t max_string_length = get_max_vector_length();