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Fix writing of character data to v5 MAT file
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As reported by #251
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@tbeu
tbeu committed Sep 4, 2024
1 parent e8fa037 commit 8407b4e
Showing 1 changed file with 63 additions and 18 deletions.
81 changes: 63 additions & 18 deletions src/mat5.c
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Original file line number Diff line number Diff line change
Expand Up @@ -262,7 +262,7 @@ GetTypeBufSize(matvar_t *matvar, size_t *size)
break;
}
case MAT_C_CHAR:
if ( MAT_T_UINT8 == matvar->data_type || MAT_T_INT8 == matvar->data_type )
if ( MAT_T_INT8 == matvar->data_type )
err = Mul(&data_bytes, nelems, Mat_SizeOf(MAT_T_UINT16));
else
err = Mul(&data_bytes, nelems, Mat_SizeOf(matvar->data_type));
Expand Down Expand Up @@ -876,6 +876,56 @@ WriteCompressedCharData(mat_t *mat, z_streamp z, void *data, size_t N, enum mati
} while ( z->avail_out == 0 );
}
break;
case MAT_T_INT8: {
mat_uint8_t *ptr;
mat_uint16_t c;
int i;

/* Matlab can't read MAT_C_CHAR as uint8, needs uint16 */
data_size = 2;
data_tag[0] = MAT_T_UINT16;
data_tag[1] = N * data_size;
z->next_in = ZLIB_BYTE_PTR(data_tag);
z->avail_in = 8;
do {
z->next_out = buf;
z->avail_out = buf_size;
deflate(z, Z_NO_FLUSH);
byteswritten += fwrite(buf, 1, buf_size - z->avail_out, (FILE *)mat->fp);
} while ( z->avail_out == 0 );

/* exit early if this is an empty data */
if ( NULL == data || N < 1 )
break;

z->next_in = (Bytef *)data;
z->avail_in = data_size * N;
ptr = (mat_uint8_t *)data;
for ( i = 0; i < N; i++ ) {
c = (mat_uint16_t) * (char *)ptr;
z->next_in = ZLIB_BYTE_PTR(&c);
z->avail_in = 2;
do {
z->next_out = buf;
z->avail_out = buf_size;
deflate(z, Z_NO_FLUSH);
byteswritten += fwrite(buf, 1, buf_size - z->avail_out, (FILE *)mat->fp);
} while ( z->avail_out == 0 );
ptr++;
}
/* Add/Compress padding to pad to 8-byte boundary */
if ( N * data_size % 8 ) {
z->next_in = pad;
z->avail_in = 8 - (N * data_size % 8);
do {
z->next_out = buf;
z->avail_out = buf_size;
deflate(z, Z_NO_FLUSH);
byteswritten += fwrite(buf, 1, buf_size - z->avail_out, (FILE *)mat->fp);
} while ( z->avail_out == 0 );
}
break;
}
case MAT_T_UNKNOWN:
/* Sometimes empty char data will have MAT_T_UNKNOWN, so just write a data tag */
data_tag[0] = MAT_T_UINT16;
Expand Down Expand Up @@ -1018,7 +1068,7 @@ ReadNextCell(mat_t *mat, matvar_t *matvar)
mat_uint32_t nBytes;
mat_uint32_t array_flags;

memset(&uncomp_buf, 0, sizeof(uncomp_buf));
memset(uncomp_buf, 0, sizeof(uncomp_buf));
for ( i = 0; i < nelems; i++ ) {
cells[i] = Mat_VarCalloc();
if ( NULL == cells[i] ) {
Expand Down Expand Up @@ -1394,7 +1444,7 @@ ReadNextStructField(mat_t *mat, matvar_t *matvar)
mat_uint32_t uncomp_buf[16];
mat_uint32_t array_flags, len, fieldname_size;

memset(&uncomp_buf, 0, sizeof(uncomp_buf));
memset(uncomp_buf, 0, sizeof(uncomp_buf));
/* Field name length */
err = Inflate(mat, matvar->internal->z, uncomp_buf, 8, &bytesread);
if ( err ) {
Expand Down Expand Up @@ -2265,7 +2315,7 @@ WriteCompressedTypeArrayFlags(mat_t *mat, matvar_t *matvar, z_streamp z)
return byteswritten;
}

memset(&uncomp_buf, 0, sizeof(uncomp_buf));
memset(uncomp_buf, 0, sizeof(uncomp_buf));
/* Array Flags */
array_flags = matvar->class_type & CLASS_TYPE_MASK;
if ( matvar->isComplex )
Expand Down Expand Up @@ -2346,7 +2396,7 @@ WriteCompressedType(mat_t *mat, matvar_t *matvar, z_streamp z)
return byteswritten;
}

memset(&uncomp_buf, 0, sizeof(uncomp_buf));
memset(uncomp_buf, 0, sizeof(uncomp_buf));
err = Mat_MulDims(matvar, &nelems);
if ( err ) {
Mat_Critical("Integer multiplication overflow");
Expand Down Expand Up @@ -2525,7 +2575,7 @@ WriteCompressedCellArrayField(mat_t *mat, matvar_t *matvar, z_streamp z)
if ( NULL == matvar || NULL == mat || NULL == z )
return 0;

memset(&uncomp_buf, 0, sizeof(uncomp_buf));
memset(uncomp_buf, 0, sizeof(uncomp_buf));
uncomp_buf[0] = MAT_T_MATRIX;
if ( MAT_C_EMPTY != matvar->class_type ) {
int err = GetCellArrayFieldBufSize(matvar, &field_buf_size);
Expand Down Expand Up @@ -2659,7 +2709,7 @@ WriteCompressedStructField(mat_t *mat, matvar_t *matvar, z_streamp z)
return byteswritten;
}

memset(&uncomp_buf, 0, sizeof(uncomp_buf));
memset(uncomp_buf, 0, sizeof(uncomp_buf));
uncomp_buf[0] = MAT_T_MATRIX;
if ( MAT_C_EMPTY != matvar->class_type ) {
int err = GetStructFieldBufSize(matvar, &field_buf_size);
Expand Down Expand Up @@ -2788,7 +2838,7 @@ Mat_WriteCompressedEmptyVariable5(mat_t *mat, const char *name, int rank, const
/* Array Flags */
array_flags = MAT_C_DOUBLE;

memset(&uncomp_buf, 0, sizeof(uncomp_buf));
memset(uncomp_buf, 0, sizeof(uncomp_buf));
uncomp_buf[0] = MAT_T_MATRIX;
err = GetEmptyMatrixMaxBufSize(name, rank, &empty_matrix_max_buf_size);
if ( err || empty_matrix_max_buf_size > UINT32_MAX )
Expand Down Expand Up @@ -5015,7 +5065,7 @@ Mat_VarWrite5(mat_t *mat, matvar_t *matvar, int compress)
if ( matvar->class_type == MAT_C_SPARSE )
nzmax = ((mat_sparse_t *)matvar->data)->nzmax;

memset(&uncomp_buf, 0, sizeof(uncomp_buf));
memset(uncomp_buf, 0, sizeof(uncomp_buf));
uncomp_buf[0] = MAT_T_MATRIX;
err = GetMatrixMaxBufSize(matvar, &matrix_max_buf_size);
if ( err ) {
Expand Down Expand Up @@ -5119,20 +5169,15 @@ Mat_VarWrite5(mat_t *mat, matvar_t *matvar, int compress)
err = deflate(z, Z_FINISH);
fwrite(comp_buf, 1, buf_size * sizeof(*comp_buf) - z->avail_out, (FILE *)mat->fp);
} while ( err != Z_STREAM_END && z->avail_out == 0 );
#if 0
if ( byteswritten % 8 )
for ( i = 0; i < 8-(byteswritten % 8); i++ )
fwrite(&pad1,1,1,(FILE*)mat->fp);
#endif
(void)deflateEnd(z);
free(z);
#endif
}
end = ftello((FILE *)mat->fp);
if ( start != -1L && end != -1L ) {
nBytes = (int)(end - start);
(void)fseeko((FILE *)mat->fp, (mat_off_t) - (nBytes + 4), SEEK_CUR);
fwrite(&nBytes, 4, 1, (FILE *)mat->fp);
const mat_uint32_t _nBytes = (mat_uint32_t)(end - start);
(void)fseeko((FILE *)mat->fp, start - 4, SEEK_SET);
fwrite(&_nBytes, 4, 1, (FILE *)mat->fp);
(void)fseeko((FILE *)mat->fp, end, SEEK_SET);
} else {
Mat_Critical("Couldn't determine file position");
Expand Down Expand Up @@ -5187,7 +5232,7 @@ Mat_VarReadNextInfo5(mat_t *mat)
mat_uint32_t uncomp_buf[16];
size_t bytesread = 0;

memset(&uncomp_buf, 0, sizeof(uncomp_buf));
memset(uncomp_buf, 0, sizeof(uncomp_buf));
matvar = Mat_VarCalloc();
if ( NULL == matvar ) {
Mat_Critical("Couldn't allocate memory");
Expand Down

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