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Merge pull request #1566 from NetCDF-World-Domination-Council/ejh_unlim_dims

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Fix problems with read past end of dataset but within dimension length for vars with multiple unlimited dimensions
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Ward Fisher 2019-12-23 15:08:56 -07:00 committed by GitHub
commit 8f2be58d95
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2 changed files with 176 additions and 14 deletions
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35
libhdf5/hdf5var.c
View File

@ -1922,7 +1922,8 @@ NC4_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
#endif
/* Check dimension bounds. Remember that unlimited dimensions can
* put data beyond their current length. */
* get data beyond the length of the dataset, but within the
* lengths of the unlimited dimension(s). */
for (d2 = 0; d2 < var->ndims; d2++)
{
hsize_t endindex = start[d2] + stride[d2] * (count[d2] - 1); /* last index read */
@ -1947,20 +1948,26 @@ NC4_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
if (count[d2] && endindex >= ulen)
BAIL_QUIET(NC_EEDGE);
/* Things get a little tricky here. If we're getting
a GET request beyond the end of this var's
current length in an unlimited dimension, we'll
later need to return the fill value for the
variable. */
if (start[d2] >= (hssize_t)fdims[d2])
fill_value_size[d2] = count[d2];
else if (endindex >= fdims[d2])
fill_value_size[d2] = count[d2] - ((fdims[d2] - start[d2])/stride[d2]);
/* Things get a little tricky here. If we're getting a GET
request beyond the end of this var's current length in
an unlimited dimension, we'll later need to return the
fill value for the variable. */
if (!no_read)
{
if (start[d2] >= (hssize_t)fdims[d2])
fill_value_size[d2] = count[d2];
else if (endindex >= fdims[d2])
fill_value_size[d2] = count[d2] - ((fdims[d2] - start[d2])/stride[d2]);
else
fill_value_size[d2] = 0;
count[d2] -= fill_value_size[d2];
if (count[d2] == 0)
no_read++;
if (fill_value_size[d2])
provide_fill++;
}
else
fill_value_size[d2] = 0;
count[d2] -= fill_value_size[d2];
if (fill_value_size[d2])
provide_fill++;
fill_value_size[d2] = count[d2];
}
else /* Dim is not unlimited. */
{

155
nc_test4/tst_dims3.c
View File

@ -12,6 +12,14 @@
#include <nc_tests.h>
#include "err_macros.h"
#define NDIM2 2
#define VAR_NAME "var"
#define DIM_NAME1 "y"
#define DIM_NAME2 "x"
#define NY 3
#define NX 3
#define DIM_LEN 2
int
main(int argc, char **argv)
{
@ -235,5 +243,152 @@ main(int argc, char **argv)
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("*** testing very simple case writing data with 2 unlim dims...");
{
/* This test code based on test code from Jeff Whitaker. See
* https://github.com/Unidata/netcdf4-python/issues/1413. This
* is a simplified version. */
int varid1, varid, ncid;
int dimids[NDIM2];
size_t start[1] = {0};
size_t count[1] = {NY};
int ydata[NY];
int y, i;
size_t len_in;
/* Fill Y data array. */
for (i = 0; i < NY; ++i)
ydata[i] = i;
/* Create a file. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
/* Define two unlimited dims. */
if (nc_def_dim(ncid, DIM_NAME1, NC_UNLIMITED, &dimids[0])) ERR;
if (nc_def_dim(ncid, DIM_NAME2, NC_UNLIMITED, &dimids[1])) ERR;
/* Define coord var for first dim Y. */
if (nc_def_var(ncid, DIM_NAME1, NC_INT, 1, &dimids[0], &varid1)) ERR;
/* Define a data var with dims Y,X. */
if (nc_def_var(ncid, VAR_NAME, NC_INT, NDIM2, dimids, &varid)) ERR;
/* Write data to coordinate var to extend Y. */
if (nc_put_vara_int(ncid, varid1, start, count, ydata)) ERR;
if (nc_close(ncid)) ERR;
/* Reopen the file and check. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq_dimlen(ncid, 0, &len_in)) ERR;
if (len_in != NY) ERR;
if (nc_inq_dimlen(ncid, 1, &len_in)) ERR;
if (len_in != 0) ERR;
/* Read and check each value of the coordinate var. */
for (y = 0; y < NY; y++)
{
size_t index = y;
int data_in;
if (nc_get_var1_int(ncid, varid1, &index, &data_in)) ERR;
if (data_in != y) ERR;
}
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("*** testing simple case writing data with 2 unlim dims...");
{
/* This test code based on test code from Jeff Whitaker. See
* https://github.com/Unidata/netcdf4-python/issues/1413. This
* is a simplified version. */
int varid1, varid, ncid;
int dimids[NDIM2];
size_t start[1] = {0};
size_t count[1] = {NY};
size_t start2[NDIM2] = {0, 2};
size_t count2[NDIM2] = {1, 1};
int ydata[NY];
int data = TEST_VAL_42;
int x, y, i;
/* Fill Y data array. */
for (i = 0; i < NY; ++i)
ydata[i] = i;
/* Create a file. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
/* Define two unlimited dims. */
if (nc_def_dim(ncid, DIM_NAME1, NC_UNLIMITED, &dimids[0])) ERR;
if (nc_def_dim(ncid, DIM_NAME2, NC_UNLIMITED, &dimids[1])) ERR;
/* Define coord var for first dim Y. */
if (nc_def_var(ncid, DIM_NAME1, NC_INT, 1, &dimids[0], &varid1)) ERR;
/* Define a data var with dims Y,X. */
if (nc_def_var(ncid, VAR_NAME, NC_INT, NDIM2, dimids, &varid)) ERR;
/* Write data to coordinate var to extend Y. */
if (nc_put_vara_int(ncid, varid1, start, count, ydata)) ERR;
if (nc_sync(ncid)) ERR;
/* write a single data point to the 2d variable */
if (nc_put_vara_int(ncid, varid, start2, count2, &data)) ERR;
if (nc_close(ncid)) ERR;
/* Reopen the file and check. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
/* Read and check each value with nc_get_var1_int(). */
for (x = 0; x < NX; x++)
{
for (y = 0; y < NY; y++)
{
size_t index[NDIM2] = {y, x};
int data_in;
if (nc_get_var1_int(ncid, varid, index, &data_in)) ERR;
if (y == start2[0] && x == start2[1])
{
if (data_in != data) ERR;
}
else
{
if (data_in != NC_FILL_INT) ERR;
}
}
}
/* Read and check each row with nc_get_vara_int(). */
for (y = 0; y < NY; y++)
{
size_t start_row[NDIM2] = {y, 0};
size_t count_row[NDIM2] = {1, NX};
int data_in[NX];
if (nc_get_vara_int(ncid, varid, start_row, count_row,
data_in)) ERR;
if (y == start2[0])
{
/* This row has data. */
for (x = 0; x < NX; x++)
if (data_in[x] != (x == start2[1] ? TEST_VAL_42 : NC_FILL_INT)) ERR;
}
else
{
/* This row is all fill. */
for (x = 0; x < NX; x++)
{
printf("y %d x %d data %d\n", y, x, data_in[x]);
if (data_in[x] != NC_FILL_INT) ERR;
}
}
}
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}