void
io_utils::file2matrix(const std::string &file, Eigen::MatrixXd &mat, int cols )
{
std::ifstream in;
open_in_file( in, file );
if(!in){
std::cout << "[io_utils] Cannot open file: " << file << std::endl;
throw std::runtime_error("Runtime error...\n");
}
std::vector<double> data;
double val;
while ( in >> val ){
data.push_back( val );
}
// copy the vector to an eigen matrix
int rows = data.size() / cols;
mat.resize( rows, cols );
std::copy( data.data(), data.data()+data.size(), mat.data() );
for(int r = 0; r < rows; ++r)
for(int c = 0; c < cols; ++c)
{
mat(r,c) = data[cols*r + c];
}
in.close();
}
int decompress_file(void)
{
FILE *in = NULL, *out = NULL;
unsigned char *inbuf = NULL, *outbuf = NULL;
size_t inbuf_size, outbuf_size;
struct inflate_state state;
struct isal_gzip_header gz_hdr;
const int terminal = 0, implicit = 1, stripped = 2;
int ret = 0, success = 0, outfile_type = terminal;
char *infile_name = global_options.infile_name, *outfile_name =
global_options.outfile_name;
char *suffix = global_options.suffix;
size_t infile_name_len = global_options.infile_name_len;
size_t outfile_name_len = global_options.outfile_name_len;
size_t suffix_len = global_options.suffix_len;
int suffix_index = 0;
uint32_t file_time;
if (infile_name_len == stdin_file_name_len &&
memcmp(infile_name, stdin_file_name, infile_name_len) == 0) {
infile_name = NULL;
infile_name_len = 0;
}
if (outfile_name == NULL && !global_options.use_stdout) {
if (infile_name != NULL) {
outfile_type = stripped;
while (suffix_index <
sizeof(default_suffixes) / sizeof(*default_suffixes)) {
if (suffix == NULL) {
suffix = default_suffixes[suffix_index];
suffix_len = default_suffixes_lens[suffix_index];
suffix_index++;
}
outfile_name_len = infile_name_len - suffix_len;
if (infile_name_len >= suffix_len
&& memcmp(infile_name + outfile_name_len, suffix,
suffix_len) == 0)
break;
suffix = NULL;
suffix_len = 0;
}
if (suffix == NULL && global_options.test == NO_TEST) {
log_print(ERROR, "igzip: %s: unknown suffix -- ignored\n",
infile_name);
return 1;
}
}
if (global_options.name == YES_NAME) {
outfile_name_len = 0;
outfile_type = implicit;
}
if (outfile_type != terminal)
outfile_name = malloc_safe(outfile_name_len >=
MAX_FILEPATH_BUF ? outfile_name_len +
1 : MAX_FILEPATH_BUF);
}
open_in_file(&in, infile_name);
if (in == NULL)
goto decompress_file_cleanup;
file_time = get_posix_filetime(in);
inbuf_size = BLOCK_SIZE;
outbuf_size = BLOCK_SIZE;
inbuf = malloc_safe(inbuf_size);
outbuf = malloc_safe(outbuf_size);
isal_gzip_header_init(&gz_hdr);
if (outfile_type == implicit) {
gz_hdr.name = outfile_name;
gz_hdr.name_buf_len = MAX_FILEPATH_BUF;
}
isal_inflate_init(&state);
state.crc_flag = ISAL_GZIP_NO_HDR_VER;
state.next_in = inbuf;
state.avail_in = fread_safe(state.next_in, 1, inbuf_size, in, infile_name);
ret = isal_read_gzip_header(&state, &gz_hdr);
if (ret != ISAL_DECOMP_OK) {
log_print(ERROR, "igzip: Error invalid gzip header found for file %s\n",
infile_name);
goto decompress_file_cleanup;
}
if (outfile_type == implicit)
file_time = gz_hdr.time;
if (outfile_type == stripped || (outfile_type == implicit && outfile_name[0] == 0)) {
outfile_name_len = infile_name_len - suffix_len;
memcpy(outfile_name, infile_name, outfile_name_len);
outfile_name[outfile_name_len] = 0;
}
if (infile_name_len != 0 && infile_name_len == outfile_name_len
&& strncmp(infile_name, outfile_name, infile_name_len) == 0) {
log_print(ERROR, "igzip: Error input and output file names must differ\n");
goto decompress_file_cleanup;
}
if (global_options.test == NO_TEST) {
open_out_file(&out, outfile_name);
if (out == NULL)
goto decompress_file_cleanup;
}
do {
if (state.avail_in == 0) {
state.next_in = inbuf;
state.avail_in =
fread_safe(state.next_in, 1, inbuf_size, in, infile_name);
}
state.next_out = outbuf;
state.avail_out = outbuf_size;
ret = isal_inflate(&state);
if (ret != ISAL_DECOMP_OK) {
log_print(ERROR,
"igzip: Error encountered while decompressing file %s\n",
infile_name);
goto decompress_file_cleanup;
}
if (out != NULL)
fwrite_safe(outbuf, 1, state.next_out - outbuf, out, outfile_name);
} while (!feof(in) || state.avail_out == 0);
if (state.block_state != ISAL_BLOCK_FINISH)
log_print(ERROR, "igzip: Error %s does not contain a complete gzip file\n",
infile_name);
else
success = 1;
decompress_file_cleanup:
if (out != NULL && out != stdout) {
fclose(out);
if (success)
set_filetime(outfile_name, file_time);
}
if (in != NULL && in != stdin) {
fclose(in);
if (success && global_options.remove)
remove(infile_name);
}
if (global_options.outfile_name == NULL && outfile_name != NULL)
free(outfile_name);
if (inbuf != NULL)
free(inbuf);
if (outbuf != NULL)
free(outbuf);
return (success == 0);
}
int compress_file(void)
{
FILE *in = NULL, *out = NULL;
unsigned char *inbuf = NULL, *outbuf = NULL, *level_buf = NULL;
size_t inbuf_size, outbuf_size;
int level_size = 0;
struct isal_zstream stream;
struct isal_gzip_header gz_hdr;
int ret, success = 0;
char *infile_name = global_options.infile_name, *outfile_name =
global_options.outfile_name;
char *suffix = global_options.suffix;
size_t infile_name_len = global_options.infile_name_len;
size_t outfile_name_len = global_options.outfile_name_len;
size_t suffix_len = global_options.suffix_len;
int level = global_options.level;
if (suffix == NULL) {
suffix = default_suffixes[0];
suffix_len = default_suffixes_lens[0];
}
if (infile_name_len == stdin_file_name_len &&
memcmp(infile_name, stdin_file_name, infile_name_len) == 0) {
infile_name = NULL;
infile_name_len = 0;
}
if (outfile_name == NULL && infile_name != NULL && !global_options.use_stdout) {
outfile_name_len = infile_name_len + suffix_len;
outfile_name = malloc_safe(outfile_name_len + 1);
strcpy(outfile_name, infile_name);
strcat(outfile_name, suffix);
}
open_in_file(&in, infile_name);
if (in == NULL)
goto compress_file_cleanup;
if (infile_name_len != 0 && infile_name_len == outfile_name_len
&& strncmp(infile_name, outfile_name, infile_name_len) == 0) {
log_print(ERROR, "igzip: Error input and output file names must differ\n");
goto compress_file_cleanup;
}
open_out_file(&out, outfile_name);
if (out == NULL)
goto compress_file_cleanup;
inbuf_size = BLOCK_SIZE;
outbuf_size = BLOCK_SIZE;
inbuf = malloc_safe(inbuf_size);
outbuf = malloc_safe(outbuf_size);
level_size = level_size_buf[level];
level_buf = malloc_safe(level_size);
isal_gzip_header_init(&gz_hdr);
if (global_options.name == NAME_DEFAULT || global_options.name == YES_NAME) {
gz_hdr.time = get_posix_filetime(in);
gz_hdr.name = infile_name;
}
gz_hdr.os = UNIX;
gz_hdr.name_buf_len = infile_name_len + 1;
isal_deflate_init(&stream);
stream.avail_in = 0;
stream.flush = NO_FLUSH;
stream.level = level;
stream.level_buf = level_buf;
stream.level_buf_size = level_size;
stream.gzip_flag = IGZIP_GZIP_NO_HDR;
stream.next_out = outbuf;
stream.avail_out = outbuf_size;
isal_write_gzip_header(&stream, &gz_hdr);
do {
if (stream.avail_in == 0) {
stream.next_in = inbuf;
stream.avail_in =
fread_safe(stream.next_in, 1, inbuf_size, in, infile_name);
stream.end_of_stream = feof(in);
}
if (stream.next_out == NULL) {
stream.next_out = outbuf;
stream.avail_out = outbuf_size;
}
ret = isal_deflate(&stream);
if (ret != ISAL_DECOMP_OK) {
log_print(ERROR,
"igzip: Error encountered while compressing file %s\n",
infile_name);
goto compress_file_cleanup;
}
fwrite_safe(outbuf, 1, stream.next_out - outbuf, out, outfile_name);
stream.next_out = NULL;
} while (!feof(in) || stream.avail_out == 0);
success = 1;
compress_file_cleanup:
if (out != NULL && out != stdout)
fclose(out);
if (in != NULL && in != stdin) {
fclose(in);
if (success && global_options.remove)
remove(infile_name);
}
if (global_options.outfile_name == NULL && outfile_name != NULL)
free(outfile_name);
if (inbuf != NULL)
free(inbuf);
if (outbuf != NULL)
free(outbuf);
if (level_buf != NULL)
free(level_buf);
return (success == 0);
}
