/*-------------------------------------------------------------------------
* test_compress
*
* Ensures that a FL packet table can be compressed.
* This test creates a file named TEST_COMPRESS_FILE
*
*-------------------------------------------------------------------------
*/
static int
test_compress(void)
{
hid_t fid1 = -1;
herr_t err;
hid_t table = -1;
hid_t part_t = -1;
hid_t dset_id = -1;
hid_t plist_id = -1;
size_t c;
size_t num_elems = 1;
unsigned filter_vals[1];
particle_t readPart[1];
hsize_t count;
TESTING("packet table compression");
/* Create a file. */
if((fid1 = H5Fcreate(TEST_COMPRESS_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Create a datatype for the particle struct */
part_t = make_particle_type();
HDassert(part_t != -1);
/* Create a new table with compression level 8 */
table = H5PTcreate_fl(fid1, "Compressed Test Dataset", part_t, (hsize_t)80, 8);
if( H5PTis_valid(table) < 0) TEST_ERROR;
/* We can now use this table exactly the same way we use a normal uncompressed
* packet table, and it should pass the same tests. */
/* Add many particles */
for(c = 0; c < BIG_TABLE_SIZE ; c+=8)
{
/* Append eight particles at once*/
err = H5PTappend(table, (size_t)8, &(testPart[0]));
if( err < 0) TEST_ERROR;
}
/* Count the number of packets in the table */
err = H5PTget_num_packets(table, &count);
if( err < 0) TEST_ERROR;
if( count != BIG_TABLE_SIZE ) TEST_ERROR;
/* Read particles to ensure that all of them were written correctly */
HDmemset(readPart, 0, sizeof(readPart));
for(c = 0; c < BIG_TABLE_SIZE; c++)
{
err = H5PTget_next(table, 1, readPart);
if(err < 0) TEST_ERROR;
/* Ensure that particles were read correctly */
if( cmp_par(c % 8, 0, testPart, readPart) != 0) TEST_ERROR;
}
/* Close the table */
err = H5PTclose(table);
if( err < 0) TEST_ERROR;
/* Open the packet table as a regular dataset and make sure that the
* compression filter is set.
*/
dset_id = H5Dopen2(fid1, "Compressed Test Dataset", H5P_DEFAULT);
if( dset_id < 0) TEST_ERROR;
plist_id = H5Dget_create_plist(dset_id);
if( plist_id < 0) TEST_ERROR;
err = H5Pget_filter_by_id2(plist_id, H5Z_FILTER_DEFLATE, NULL, &num_elems,
filter_vals, 0, NULL, NULL);
if( err < 0) TEST_ERROR;
/* The compression level should be 8, the value we passed in */
if(filter_vals[0] != 8) TEST_ERROR;
/* Clean up */
err = H5Pclose(plist_id);
if( err < 0) TEST_ERROR;
err = H5Dclose(dset_id);
if( err < 0) TEST_ERROR;
/* Create a new table without compression. */
table = H5PTcreate_fl(fid1, "Uncompressed Dataset", part_t, (hsize_t)80, -1);
if(table < 0) TEST_ERROR;
/* Close the packet table */
err = H5PTclose(table);
if( err < 0) TEST_ERROR;
/* Open the packet table as a regular dataset and make sure that the
* compression filter is not set.
*/
dset_id = H5Dopen2(fid1, "Uncompressed Dataset", H5P_DEFAULT);
if( dset_id < 0) TEST_ERROR;
plist_id = H5Dget_create_plist(dset_id);
if( plist_id < 0) TEST_ERROR;
H5E_BEGIN_TRY {
err = H5Pget_filter_by_id2(plist_id, H5Z_FILTER_DEFLATE, NULL, &num_elems,
filter_vals, 0, NULL, NULL);
if( err >= 0) TEST_ERROR;
} H5E_END_TRY
/* Clean up */
err = H5Pclose(plist_id);
if( err < 0) TEST_ERROR;
err = H5Dclose(dset_id);
if( err < 0) TEST_ERROR;
/* Close the datatype and the file */
err = H5Tclose(part_t);
if( err < 0) TEST_ERROR;
err = H5Fclose(fid1);
if( err < 0) TEST_ERROR;
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(plist_id);
H5Dclose(dset_id);
H5Tclose(part_t);
H5PTclose(table);
H5Fclose(fid1);
} H5E_END_TRY
H5_FAILED();
return -1;
}
/*-------------------------------------------------------------------------
* test_rw_non-native_dt
*
* test reading and writing packet table using datatypes that are not
* native.
*
*-------------------------------------------------------------------------
*/
static int test_rw_nonnative_dt(hid_t fid)
{
hid_t ptable; /* Packet table identifier */
herr_t err; /* Function return status */
hsize_t count; /* Number of records in the table */
int x; /* Loop variable */
/* Buffers to hold data */
int writeBuffer[5];
int readBuffer[5];
TESTING("reading/writing non-native packet table");
/* Initialize buffers */
for(x=0; x<5; x++) {
writeBuffer[x]=x;
readBuffer[x] = -1;
}
/* Create a fixed-length packet table within the file */
/* This table's "packets" will be simple integers and it will use no compression */
if(H5Tget_order(H5T_NATIVE_INT) == H5T_ORDER_LE) {
ptable = H5PTcreate_fl(fid, "Packet Test Dataset, Non-native", H5T_STD_I32BE, (hsize_t)100, -1);
} else {
ptable = H5PTcreate_fl(fid, "Packet Test Dataset, Non-native", H5T_STD_I32LE, (hsize_t)100, -1);
}
if(ptable == H5I_INVALID_HID)
goto out;
/* Write one packet to the packet table */
if( (err = H5PTappend(ptable, (hsize_t)1, &(writeBuffer[0]))) < 0 )
goto out;
/* Write several packets to the packet table */
if( (err = H5PTappend(ptable, (hsize_t)4, &(writeBuffer[1]))) < 0)
goto out;
if( (err = H5PTclose(ptable)) < 0)
goto out;
/* Open the Packet table */
if( (ptable = H5PTopen(fid, "Packet Test Dataset, Non-native")) < 0)
goto out;
/* Get the number of packets in the packet table. This should be five. */
if( (err = H5PTget_num_packets(ptable, &count)) < 0)
goto out;
if( (int)count != 5 )
goto out;
/* Initialize packet table's "current record" */
if( (err = H5PTcreate_index(ptable)) < 0)
goto out;
/* Iterate through packets, read each one back */
for(x=0; x<5; x++) {
if( (err = H5PTget_next(ptable, (hsize_t)1, &(readBuffer[x]))) < 0)
goto out;
if( x != readBuffer[x])
goto out;
}
/* Close the packet table */
if( (err = H5PTclose(ptable)) < 0)
goto out;
PASSED();
return 0;
out:
H5_FAILED();
if( H5PTis_valid(ptable) < 0)
H5PTclose(ptable);
return -1;
}
/*-------------------------------------------------------------------------
* test_big_table
*
* Ensures that a FL packet table will not break when many (BIG_TABLE_SIZE)
* packets are used.
*
*-------------------------------------------------------------------------
*/
static int test_big_table(hid_t fid)
{
herr_t err;
hid_t table;
hid_t part_t;
size_t c;
particle_t readPart;
hsize_t count;
TESTING("large packet table");
/* Create a datatype for the particle struct */
part_t = make_particle_type();
HDassert(part_t != -1);
/* Create a new table */
table = H5PTcreate_fl(fid, "Packet Test Dataset2", part_t, (hsize_t)33, -1);
H5Tclose(part_t);
if( H5PTis_valid(table) < 0)
goto out;
/* Add many particles */
for(c = 0; c < BIG_TABLE_SIZE ; c+=8)
{
/* Append eight particles at once*/
err = H5PTappend(table, (size_t)8, &(testPart[0]));
if( err < 0)
goto out;
}
/* Count the number of packets in the table */
err = H5PTget_num_packets(table, &count);
if( err < 0)
goto out;
if( count != BIG_TABLE_SIZE )
goto out;
/* Read particles to ensure that all of them were written correctly */
/* Also, ensure that H5PTcreate_fl set the current packet to */
/* the first packet in the table */
for(c = 0; c < BIG_TABLE_SIZE; c++)
{
err = H5PTget_next(table, 1, &readPart);
if(err < 0)
goto out;
/* Ensure that particles were read correctly */
if( cmp_par(c % 8, 0, testPart, &readPart) != 0)
goto out;
}
/* Close the table */
err = H5PTclose(table);
if( err < 0)
goto out;
PASSED();
return 0;
out:
H5_FAILED();
if( H5PTis_valid(table) < 0)
H5PTclose(table);
return -1;
}
/*-------------------------------------------------------------------------
* test_varlen
*
* Tests creation, opening, closing, writing, reading, etc. on a
* variable-length packet table.
*
*-------------------------------------------------------------------------
*/
static int test_varlen(hid_t fid)
{
herr_t err;
hid_t table=H5I_BADID;
hsize_t count;
/* Buffers to hold data */
hvl_t writeBuffer[NRECORDS];
hvl_t readBuffer[NRECORDS];
/* This example has three different sizes of "record": longs, shorts, and particles */
long longBuffer[NRECORDS];
short shortBuffer[NRECORDS];
int x;
TESTING("variable-length packet tables");
/* Initialize buffers */
for(x=0; x<NRECORDS; x++)
{
longBuffer[x] = -x;
shortBuffer[x] = x;
}
/* Fill the write buffer with a mix of variable types */
for(x=0; x<8; x+=4)
{
writeBuffer[x].len = sizeof(long);
writeBuffer[x].p = &(longBuffer[x]);
writeBuffer[x+1].len = sizeof(short);
writeBuffer[x+1].p = &(shortBuffer[x+1]);
writeBuffer[x+2].len = sizeof(long);
writeBuffer[x+2].p = &(longBuffer[x+2]);
writeBuffer[x+3].len = sizeof(particle_t);
writeBuffer[x+3].p = &(testPart[x+3]);
}
/* Create the table */
table = H5PTcreate_vl(fid, VL_TABLE_NAME, (hsize_t)1001);
if( H5PTis_valid(table) < 0)
goto out;
if( H5PTis_varlen(table) != 1)
goto out;
/* Count the number of packets in the table */
err = H5PTget_num_packets(table, &count);
if( err < 0)
goto out;
if( count != 0 )
goto out;
/* Close the table */
err = H5PTclose(table);
if( err < 0)
goto out;
/* Re-open the table */
table = H5PTopen(fid, VL_TABLE_NAME);
if( H5PTis_valid(table) < 0)
goto out;
if( H5PTis_varlen(table) != 1)
goto out;
/* Count the number of packets in the table */
err = H5PTget_num_packets(table, &count);
if( err < 0)
goto out;
if( count != 0 )
goto out;
/* Add several variable-length packets */
err = H5PTappend(table, (size_t)8, writeBuffer );
if(err < 0)
goto out;
/* Read them back */
err = H5PTread_packets(table, (hsize_t)0, 4, &(readBuffer[0]));
if( err < 0)
goto out;
err = H5PTread_packets(table, (hsize_t)4, 1, &(readBuffer[4]));
if( err < 0)
goto out;
err = H5PTread_packets(table, (hsize_t)5, (NRECORDS - 5 ), &(readBuffer[5]));
if( err < 0)
goto out;
/* Ensure that packets were read correctly */
for(x=0; x<NRECORDS; x++)
{
if( readBuffer[x].len != writeBuffer[x%4].len)
goto out;
switch(x%4)
{
case 0:
case 2:
if( *((long*)(readBuffer[x].p)) != *((long*)(writeBuffer[x].p)))
goto out;
break;
case 1:
if( *((short*)(readBuffer[x].p)) != *((short*)(writeBuffer[x].p)))
goto out;
break;
case 3:
if( cmp_par(0, 0, readBuffer[x].p, writeBuffer[x].p) < 0)
goto out;
break;
default:
goto out;
}
}
/* Free memory used by read buffer */
if(H5PTfree_vlen_readbuff(table, NRECORDS, readBuffer) <0)
goto out;
/* Read packets back using get_next */
for(x=0; x < NRECORDS; x++)
{
err = H5PTget_next(table, 1, &readBuffer[x]);
if(err < 0)
goto out;
}
/* Ensure that packets were read correctly */
for(x=0; x<NRECORDS; x++)
{
if( readBuffer[x].len != writeBuffer[x%4].len)
goto out;
switch(x%4)
{
case 0:
case 2:
if( *((long*)(readBuffer[x].p)) != *((long*)(writeBuffer[x].p)))
goto out;
break;
case 1:
if( *((short*)(readBuffer[x].p)) != *((short*)(writeBuffer[x].p)))
goto out;
break;
case 3:
if( cmp_par(0, 0, readBuffer[x].p, writeBuffer[x].p) < 0)
goto out;
break;
default:
goto out;
}
}
/* Free memory used by read buffer */
if(H5PTfree_vlen_readbuff(table, NRECORDS, readBuffer) <0)
goto out;
/* Close the table */
err = H5PTclose(table);
if( err < 0)
goto out;
PASSED();
return 0;
out:
H5_FAILED();
H5E_BEGIN_TRY
H5PTclose(table);
H5E_END_TRY
return -1;
}
int main(void)
{
hid_t fid; /* File identifier */
hid_t ptable; /* Packet table identifier */
herr_t err; /* Function return status */
hsize_t count; /* Number of records in the table */
int x; /* Loop variable */
/* Buffers to hold data */
int writeBuffer[5];
int readBuffer[5];
/* Initialize buffers */
for(x=0; x<5; x++)
{
writeBuffer[x]=x;
readBuffer[x] = -1;
}
/* Create a file using default properties */
fid=H5Fcreate("packet_table_FLexample.h5",H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT);
/* Create a fixed-length packet table within the file */
/* This table's "packets" will be simple integers and it will use compression
* level 5. */
ptable = H5PTcreate_fl(fid, "Packet Test Dataset", H5T_NATIVE_INT, (hsize_t)100, 5);
if(ptable == H5I_INVALID_HID)
goto out;
/* Write one packet to the packet table */
err = H5PTappend(ptable, (hsize_t)1, &(writeBuffer[0]) );
if(err < 0)
goto out;
/* Write several packets to the packet table */
err = H5PTappend(ptable, (hsize_t)4, &(writeBuffer[1]) );
if(err < 0)
goto out;
/* Get the number of packets in the packet table. This should be five. */
err = H5PTget_num_packets(ptable, &count);
if(err < 0)
goto out;
printf("Number of packets in packet table after five appends: %d\n", (int)count);
/* Initialize packet table's "current record" */
err = H5PTcreate_index(ptable);
if(err < 0)
goto out;
/* Iterate through packets, read each one back */
for(x=0; x<5; x++)
{
err = H5PTget_next(ptable, (hsize_t)1, &(readBuffer[x]) );
if(err < 0)
goto out;
printf("Packet %d's value is %d\n", x, readBuffer[x]);
}
/* Close the packet table */
err = H5PTclose(ptable);
if(err < 0)
goto out;
/* Close the file */
H5Fclose(fid);
return 0;
out: /* An error has occurred. Clean up and exit. */
H5PTclose(ptable);
H5Fclose(fid);
return -1;
}
/*-------------------------------------------------------------------------
* test_get_next
*
* Tests the packets written by test_append can be read by
* H5PTget_next().
*
*-------------------------------------------------------------------------
*/
static int test_get_next(hid_t fid)
{
herr_t err;
hid_t table;
particle_t readBuf[NRECORDS];
particle_t readBuf2[NRECORDS];
size_t c;
TESTING("H5PTget_next");
/* Open the table */
table = H5PTopen(fid, PT_NAME);
if( H5PTis_valid(table) < 0)
goto out;
/* Read several particles consecutively */
for(c=0; c < NRECORDS; c++)
{
err = H5PTget_next(table, 1, &readBuf[c]);
if(err < 0)
goto out;
}
/* Ensure that particles were read correctly */
for(c=0; c<NRECORDS; c++)
{
if( cmp_par(c, c, testPart, readBuf) != 0)
goto out;
}
H5PTcreate_index(table);
/* Read particles two by two */
for(c=0; c < NRECORDS / 2; c++)
{
err = H5PTget_next(table, 2, &readBuf2[c * 2]);
if(err < 0)
goto out;
}
/* Ensure that particles were read correctly */
for(c=0; c<NRECORDS; c++)
{
if( cmp_par(c, c, testPart, readBuf2) != 0)
goto out;
}
/* Close the table */
err = H5PTclose(table);
if( err < 0)
goto out;
PASSED();
return 0;
out:
H5_FAILED();
if( H5PTis_valid(table) < 0)
H5PTclose(table);
return -1;
}
int main(int argc,char *argv[]) {
struct options opts = {
0,
1,
0,
0,
-1,
1,
0,
-1,
1,
NULL,
};
getopts(argc,argv,&opts);
H5Eset_auto2(H5E_DEFAULT,NULL,NULL);
hid_t fid = H5Fopen(opts.filename,H5F_ACC_RDONLY,H5P_DEFAULT);
if(fid < 0) {
fprintf(stderr,"Failed to open %s.\n",opts.filename);
return fid;
}
if(opts.info) {
// count the number of trials in the file
hid_t trial;
int num_trials = 0;
std::stringstream trial_name;
for(;;) {
trial_name.str("");
trial_name << "/Trial" << num_trials+1;
if((trial = H5Gopen(fid,trial_name.str().c_str(),H5P_DEFAULT)) < 0)
break;
else {
print_trial_info(trial,++num_trials);
H5Gclose(trial);
}
}
H5Fclose(fid);
return 0;
}
std::stringstream data_name;
data_name << "/Trial" << opts.trial << "/Synchronous Data/Channel Data";
hid_t table = H5Dopen(fid,data_name.str().c_str(),H5P_DEFAULT);
if(table < 0) {
fprintf(stderr,"Requested trial #%d does not exist.\n",opts.trial);
return table;
}
hsize_t ncols = H5Tget_size(H5Dget_type(table))/sizeof(double);
H5Dclose(table);
table = H5PTopen(fid,data_name.str().c_str());
hsize_t nrows;
H5PTget_num_packets(table,&nrows);
// validate column and row ranges
if(opts.cols_end == -1 || opts.cols_end >= ncols)
opts.cols_end = ncols-1;
if(opts.rows_end == -1 || opts.rows_end >= nrows)
opts.rows_end = nrows-1;
opts.cols_end -= (opts.cols_end-opts.cols_start)%opts.cols_step;
opts.rows_end -= (opts.rows_end-opts.rows_start)%opts.rows_step;
if((opts.cols_start-opts.cols_end)*opts.cols_step > 0)
opts.cols_step *= -1;
if((opts.rows_start-opts.rows_end)*opts.rows_step > 0)
opts.rows_step *= -1;
int row_idx = opts.rows_start;
do {
H5PTset_index(table,row_idx);
double data[ncols];
H5PTget_next(table,1,data);
int col_idx = opts.cols_start;
do {
if(opts.binary) {
write(1,data+col_idx,sizeof(double));
} else {
printf("%e ",data[col_idx]);
}
if(col_idx == opts.cols_end)
break;
col_idx += opts.cols_step;
} while(1);
if(!opts.binary)
printf("\n");
if(row_idx == opts.rows_end)
break;
row_idx += opts.rows_step;
} while(1);
H5PTclose(table);
H5Fclose(fid);
return 0;
}
/* GetNextPackets (multiple packets)
* Gets the next numPackets packets in the packet table. Takes a
* pointer to an array of hvl_t structs where pointers to the packets
* should be stored.
* Returns 0 on success, negative on failure. Index
* is not advanced on failure.
*/
int VL_PacketTable::GetNextPackets(size_t numPackets, hvl_t * data)
{
return H5PTget_next(table_id, numPackets, data);
}
/* GetNextPacket (single packet)
* Gets the next packet in the packet table. Takes a pointer to
* an hvl_t struct where the packet should be stored.
* Returns 0 on success, negative on failure. Index
* is not advanced to the next packet on failure.
*/
int VL_PacketTable::GetNextPacket(hvl_t * data)
{
return H5PTget_next(table_id, 1, data);
}
/* GetNextPackets (multiple packets)
* Gets the next numPackets packets in the packet table. Takes a
* pointer to memory where these packets should be stored.
* Returns 0 on success, negative on failure. Index
* is not advanced on failure.
*/
int FL_PacketTable::GetNextPackets(size_t numPackets, void * data)
{
return H5PTget_next(table_id, numPackets, data);
}
/* GetNextPacket (single packet)
* Gets the next packet in the packet table. Takes a pointer to
* memory where the packet should be stored.
* Returns 0 on success, negative on failure. Index
* is not advanced to the next packet on failure.
*/
int FL_PacketTable::GetNextPacket(void * data)
{
return H5PTget_next(table_id, 1, data);
}
