/
t_relay_io_hdf5.cpp
1372 lines (988 loc) · 37.8 KB
/
t_relay_io_hdf5.cpp
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//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
// Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
//
// Produced at the Lawrence Livermore National Laboratory
//
// LLNL-CODE-666778
//
// All rights reserved.
//
// This file is part of Conduit.
//
// For details, see: http://software.llnl.gov/conduit/.
//
// Please also read conduit/LICENSE
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright notice,
// this list of conditions and the disclaimer below.
//
// * Redistributions in binary form must reproduce the above copyright notice,
// this list of conditions and the disclaimer (as noted below) in the
// documentation and/or other materials provided with the distribution.
//
// * Neither the name of the LLNS/LLNL nor the names of its contributors may
// be used to endorse or promote products derived from this software without
// specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY,
// LLC, THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY
// DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
// OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
// HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
// STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
// IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
//
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
//-----------------------------------------------------------------------------
///
/// file: t_relay_io_hdf5.cpp
///
//-----------------------------------------------------------------------------
#include "conduit_relay.hpp"
#include "conduit_relay_io_hdf5.hpp"
#include "hdf5.h"
#include <iostream>
#include "gtest/gtest.h"
using namespace conduit;
using namespace conduit::relay;
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_by_file_name)
{
uint32 a_val = 20;
uint32 b_val = 8;
uint32 c_val = 13;
uint32 d_val = 121;
Node n;
n["a"] = a_val;
n["b"] = b_val;
n["c"] = c_val;
EXPECT_EQ(n["a"].as_uint32(), a_val);
EXPECT_EQ(n["b"].as_uint32(), b_val);
EXPECT_EQ(n["c"].as_uint32(), c_val);
// write our node as a group @ "myobj"
io::hdf5_write(n,"tout_hdf5_wr.hdf5:myobj");
// directly read our object
Node n_load;
io::hdf5_read("tout_hdf5_wr.hdf5:myobj",n_load);
n_load.print_detailed();
EXPECT_EQ(n_load["a"].as_uint32(), a_val);
EXPECT_EQ(n_load["b"].as_uint32(), b_val);
EXPECT_EQ(n_load["c"].as_uint32(), c_val);
Node n_load_2;
// read from root of hdf5 file
io::hdf5_read("tout_hdf5_wr.hdf5",n_load_2);
EXPECT_EQ(n_load_2["myobj/a"].as_uint32(), a_val);
EXPECT_EQ(n_load_2["myobj/b"].as_uint32(), b_val);
EXPECT_EQ(n_load_2["myobj/c"].as_uint32(), c_val);
Node n_load_generic;
// read from root of hdf5 file
io::load("tout_hdf5_wr.hdf5",n_load_generic);
EXPECT_EQ(n_load_generic["myobj/a"].as_uint32(), a_val);
EXPECT_EQ(n_load_generic["myobj/b"].as_uint32(), b_val);
EXPECT_EQ(n_load_generic["myobj/c"].as_uint32(), c_val);
// save load from generic io interface
io::save(n_load_generic["myobj"],"tout_hdf5_wr_generic.hdf5:myobj");
n_load_generic["myobj/d"] = d_val;
io::load_merged("tout_hdf5_wr_generic.hdf5",n_load_generic);
EXPECT_EQ(n_load_generic["myobj/a"].as_uint32(), a_val);
EXPECT_EQ(n_load_generic["myobj/b"].as_uint32(), b_val);
EXPECT_EQ(n_load_generic["myobj/c"].as_uint32(), c_val);
EXPECT_EQ(n_load_generic["myobj/d"].as_uint32(), d_val);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_special_paths)
{
uint32 a_val = 20;
uint32 b_val = 8;
Node n;
n["a"] = a_val;
n["b"] = b_val;
EXPECT_EQ(n["a"].as_uint32(), a_val);
EXPECT_EQ(n["b"].as_uint32(), b_val);
// write our node as a group @ "/myobj"
io::hdf5_write(n,"tout_hdf5_wr_special_paths_1.hdf5:/myobj");
// write our node as a group @ "/"
// make sure "/" works
io::hdf5_write(n,"tout_hdf5_wr_special_paths_2.hdf5:/");
// make sure empty after ":" this works
io::hdf5_write(n,"tout_hdf5_wr_special_paths_3.hdf5:");
Node n_load;
io::hdf5_read("tout_hdf5_wr_special_paths_2.hdf5:/",n_load);
EXPECT_EQ(n_load["a"].as_uint32(), a_val);
EXPECT_EQ(n_load["b"].as_uint32(), b_val);
n_load.reset();
io::hdf5_read("tout_hdf5_wr_special_paths_2.hdf5:/",n_load);
EXPECT_EQ(n_load["a"].as_uint32(), a_val);
EXPECT_EQ(n_load["b"].as_uint32(), b_val);
n_load.reset();
io::hdf5_read("tout_hdf5_wr_special_paths_2.hdf5:",n_load);
EXPECT_EQ(n_load["a"].as_uint32(), a_val);
EXPECT_EQ(n_load["b"].as_uint32(), b_val);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_string)
{
uint32 a_val = 20;
std::string s_val = "{string value!}";
Node n;
n["a"] = a_val;
n["s"] = s_val;
EXPECT_EQ(n["a"].as_uint32(), a_val);
EXPECT_EQ(n["s"].as_string(), s_val);
// write our node as a group @ "myobj"
io::hdf5_write(n,"tout_hdf5_wr_string.hdf5:myobj");
Node n_out;
io::hdf5_read("tout_hdf5_wr_string.hdf5:myobj",n_out);
EXPECT_EQ(n_out["a"].as_uint32(), a_val);
EXPECT_EQ(n_out["s"].as_string(), s_val);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_array)
{
Node n_in(DataType::float64(10));
float64_array val_in = n_in.value();
for(index_t i=0;i<10;i++)
{
val_in[i] = 3.1415 * i;
}
// write our node as a group @ "myobj"
io::hdf5_write(n_in,"tout_hdf5_wr_array.hdf5:myobj");
Node n_out;
io::hdf5_read("tout_hdf5_wr_array.hdf5:myobj",n_out);
float64_array val_out = n_out.value();
for(index_t i=0;i<10;i++)
{
EXPECT_EQ(val_in[i],val_out[i]);
}
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, write_and_read_conduit_leaf_to_hdf5_dataset_handle)
{
std::string ofname = "tout_hdf5_wr_conduit_leaf_to_hdf5_dataset_handle.hdf5";
hid_t h5_file_id = H5Fcreate(ofname.c_str(),
H5F_ACC_TRUNC,
H5P_DEFAULT,
H5P_DEFAULT);
// create a dataset for a 16-bit signed integer array with 2 elements
hid_t h5_dtype = H5T_NATIVE_SHORT;
hsize_t num_eles = 2;
hid_t h5_dspace_id = H5Screate_simple(1,
&num_eles,
NULL);
// create new dataset
hid_t h5_dset_id = H5Dcreate(h5_file_id,
"mydata",
h5_dtype,
h5_dspace_id,
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);
Node n;
n.set(DataType::c_short(2));
short_array vals = n.value();
vals[0] = -16;
vals[1] = -16;
// this should succeed
io::hdf5_write(n,h5_dset_id);
// this should also succeed
vals[1] = 16;
io::hdf5_write(n,h5_dset_id);
n.set(DataType::uint16(10));
// this should fail
EXPECT_THROW(io::hdf5_write(n,h5_dset_id),Error);
Node n_read;
io::hdf5_read(h5_dset_id,n_read);
// check values of data
short_array read_vals = n_read.value();
EXPECT_EQ(-16,read_vals[0]);
EXPECT_EQ(16,read_vals[1]);
H5Sclose(h5_dspace_id);
H5Dclose(h5_dset_id);
H5Fclose(h5_file_id);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, write_conduit_object_to_hdf5_group_handle)
{
std::string ofname = "tout_hdf5_wr_conduit_object_to_hdf5_group_handle.hdf5";
hid_t h5_file_id = H5Fcreate(ofname.c_str(),
H5F_ACC_TRUNC,
H5P_DEFAULT,
H5P_DEFAULT);
hid_t h5_group_id = H5Gcreate(h5_file_id,
"mygroup",
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);
Node n;
n["a/b"].set(DataType::int16(2));
int16_array vals = n["a/b"].value();
vals[0] =-16;
vals[1] =-16;
// this should succeed
io::hdf5_write(n,h5_group_id);
n["a/c"] = "mystring";
// this should also succeed
vals[1] = 16;
io::hdf5_write(n,h5_group_id);
n["a/b"].set(DataType::uint16(10));
// this should fail
EXPECT_THROW(io::hdf5_write(n,h5_group_id),Error);
Node n_read;
io::hdf5_read(h5_group_id,n_read);
// check values of data
int16_array read_vals = n_read["a/b"].value();
EXPECT_EQ(-16,read_vals[0]);
EXPECT_EQ(16,read_vals[1]);
EXPECT_EQ("mystring",n_read["a/c"].as_string());
H5Gclose(h5_group_id);
H5Fclose(h5_file_id);
}
//-----------------------------------------------------------------------------
// This variant tests when a caller code has already opened a HDF5 file
// and has a handle ready.
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_by_file_handle)
{
uint32 a_val = 20;
uint32 b_val = 8;
uint32 c_val = 13;
Node n;
n["a"] = a_val;
n["b"] = b_val;
n["c"] = c_val;
EXPECT_EQ(n["a"].as_uint32(), a_val);
EXPECT_EQ(n["b"].as_uint32(), b_val);
EXPECT_EQ(n["c"].as_uint32(), c_val);
std::string test_file_name = "tout_hdf5_write_read_by_file_handle.hdf5";
// Set up hdf5 file and group that caller code would already have.
hid_t h5_file_id = H5Fcreate(test_file_name.c_str(),
H5F_ACC_TRUNC,
H5P_DEFAULT,
H5P_DEFAULT);
// Prepare group that caller code wants conduit to save it's tree to that
// group. (could also specify group name for conduit to create via
// hdf5_path argument to write call.
hid_t h5_group_id = H5Gcreate(h5_file_id,
"sample_group_name",
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);
io::hdf5_write(n,h5_group_id);
hid_t status = H5Gclose(h5_group_id);
// Another variant of this - caller code has a pre-existing group they
// want to write into, but they want to use the 'group name' arg to do it
// Relay should be able to write into existing group.
h5_group_id = H5Gcreate(h5_file_id,
"sample_group_name2",
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);
io::hdf5_write(n,h5_file_id, "sample_group_name2");
status = H5Gclose(h5_group_id);
status = H5Fclose(h5_file_id);
h5_file_id = H5Fopen(test_file_name.c_str(),
H5F_ACC_RDONLY,
H5P_DEFAULT);
// Caller code switches to group it wants to read in. (could also
// specify group name for conduit to read out via hdf5_path arg to read
// call)
h5_group_id = H5Gopen(h5_file_id, "sample_group_name", 0);
Node n_load;
io::hdf5_read(h5_group_id, n_load);
status = H5Gclose(h5_group_id);
status = H5Fclose(h5_file_id);
EXPECT_EQ(n_load["a"].as_uint32(), a_val);
EXPECT_EQ(n_load["b"].as_uint32(), b_val);
EXPECT_EQ(n_load["c"].as_uint32(), c_val);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_to_existing_dset)
{
Node n_in(DataType::uint32(2));
uint32_array val_in = n_in.value();
val_in[0] = 1;
val_in[1] = 2;
// Set up hdf5 file and group that caller code would already have.
hid_t h5_file_id = H5Fcreate("tout_hdf5_wr_existing_dset.hdf5",
H5F_ACC_TRUNC,
H5P_DEFAULT,
H5P_DEFAULT);
io::hdf5_write(n_in,h5_file_id,"myarray");
val_in[0] = 3;
val_in[1] = 4;
io::hdf5_write(n_in,h5_file_id,"myarray");
// trying to write an incompatible dataset will throw an error
Node n_incompat;
n_incompat = 64;
EXPECT_THROW(io::hdf5_write(n_incompat,h5_file_id,"myarray"),
conduit::Error);
H5Fclose(h5_file_id);
// check that the second set of values are the ones we get back
Node n_read;
io::hdf5_read("tout_hdf5_wr_existing_dset.hdf5:myarray",n_read);
uint32_array val = n_read.value();
EXPECT_EQ(val[0],3);
EXPECT_EQ(val[1],4);
Node n_w2;
n_w2["myarray"].set_external(n_read);
n_w2["a/b/c"].set_uint64(123);
// this should be compatible
io::hdf5_write(n_w2,"tout_hdf5_wr_existing_dset.hdf5");
n_read.reset();
io::hdf5_read("tout_hdf5_wr_existing_dset.hdf5",n_read);
uint32_array myarray_val = n_read["myarray"].value();
uint64 a_b_c_val = n_read["a/b/c"].value();
EXPECT_EQ(myarray_val[0],3);
EXPECT_EQ(myarray_val[1],4);
EXPECT_EQ(a_b_c_val,123);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_leaf_arrays)
{
Node n;
n["v_int8"].set(DataType::int8(5));
n["v_int16"].set(DataType::int16(5));
n["v_int32"].set(DataType::int32(5));
n["v_int64"].set(DataType::int64(5));
n["v_uint8"].set(DataType::uint8(5));
n["v_uint16"].set(DataType::uint16(5));
n["v_uint32"].set(DataType::uint32(5));
n["v_uint64"].set(DataType::uint64(5));
n["v_float32"].set(DataType::float32(5));
n["v_float64"].set(DataType::float64(5));
n["v_string"].set("my_string");
int8 *v_int8_ptr = n["v_int8"].value();
int16 *v_int16_ptr = n["v_int16"].value();
int32 *v_int32_ptr = n["v_int32"].value();
int64 *v_int64_ptr = n["v_int64"].value();
uint8 *v_uint8_ptr = n["v_uint8"].value();
uint16 *v_uint16_ptr = n["v_uint16"].value();
uint32 *v_uint32_ptr = n["v_uint32"].value();
uint64 *v_uint64_ptr = n["v_uint64"].value();
float32 *v_float32_ptr = n["v_float32"].value();
float64 *v_float64_ptr = n["v_float64"].value();
for(index_t i=0; i < 5; i++)
{
v_int8_ptr[i] = -8;
v_int16_ptr[i] = -16;
v_int32_ptr[i] = -32;
v_int64_ptr[i] = -64;
v_uint8_ptr[i] = 8;
v_uint16_ptr[i] = 16;
v_uint32_ptr[i] = 32;
v_uint64_ptr[i] = 64;
v_float32_ptr[i] = 32.0;
v_float64_ptr[i] = 64.0;
}
n.print_detailed();
io::hdf5_write(n,"tout_hdf5_wr_leaf_arrays.hdf5");
Node n_load;
io::hdf5_read("tout_hdf5_wr_leaf_arrays.hdf5",n_load);
n_load.print_detailed();
int8_array v_int8_out = n_load["v_int8"].value();
int16_array v_int16_out = n_load["v_int16"].value();
int32_array v_int32_out = n_load["v_int32"].value();
int64_array v_int64_out = n_load["v_int64"].value();
EXPECT_EQ(v_int8_out.number_of_elements(),5);
EXPECT_EQ(v_int16_out.number_of_elements(),5);
EXPECT_EQ(v_int32_out.number_of_elements(),5);
EXPECT_EQ(v_int64_out.number_of_elements(),5);
uint8_array v_uint8_out = n_load["v_uint8"].value();
uint16_array v_uint16_out = n_load["v_uint16"].value();
uint32_array v_uint32_out = n_load["v_uint32"].value();
uint64_array v_uint64_out = n_load["v_uint64"].value();
EXPECT_EQ(v_uint8_out.number_of_elements(),5);
EXPECT_EQ(v_uint16_out.number_of_elements(),5);
EXPECT_EQ(v_uint32_out.number_of_elements(),5);
EXPECT_EQ(v_uint64_out.number_of_elements(),5);
float32_array v_float32_out = n_load["v_float32"].value();
float64_array v_float64_out = n_load["v_float64"].value();
EXPECT_EQ(v_float32_out.number_of_elements(),5);
EXPECT_EQ(v_float64_out.number_of_elements(),5);
std::string v_string_out = n_load["v_string"].as_string();
EXPECT_EQ(v_string_out,"my_string");
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_empty)
{
Node n;
n["path/to/empty"];
n.print_detailed();
io::hdf5_write(n,"tout_hdf5_wr_empty.hdf5");
Node n_load;
io::hdf5_read("tout_hdf5_wr_empty.hdf5",n_load);
n_load.print_detailed();
EXPECT_EQ(n["path/to/empty"].dtype().id(),
n_load["path/to/empty"].dtype().id());
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, hdf5_write_zero_sized_leaf)
{
// this tests
Node n;
n["a"].set(DataType::float64(0));
n.print_detailed();
io::hdf5_write(n,"tout_hdf5_w_0.hdf5");
EXPECT_EQ(n["a"].dtype().number_of_elements(),0);
EXPECT_EQ(n["a"].dtype().id(),DataType::FLOAT64_ID);
Node n_load;
io::hdf5_read("tout_hdf5_w_0.hdf5",n_load);
n_load.print_detailed();
EXPECT_EQ(n_load["a"].dtype().number_of_elements(),0);
EXPECT_EQ(n_load["a"].dtype().id(),DataType::FLOAT64_ID);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_write_read_childless_object)
{
Node n;
n["path/to/empty"].set(DataType::object());
n.print_detailed();
io::hdf5_write(n,"tout_hdf5_wr_cl_obj.hdf5");
Node n_load;
io::hdf5_read("tout_hdf5_wr_cl_obj.hdf5",n_load);
n_load.print_detailed();
EXPECT_EQ(n["path/to/empty"].dtype().id(),
n_load["path/to/empty"].dtype().id());
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_test_write_incompat)
{
Node n;
n["a/b/leaf"] = DataType::uint32(2);
n["a/b/grp/leaf"].set_uint32(10);
uint32_array vals = n["a/b/leaf"].value();
vals[0] = 1;
vals[1] = 2;
io::hdf5_write(n,"tout_hdf5_test_write_incompat.hdf5");
n.print();
Node n2;
n2["a/b/leaf/v"] = DataType::float64(2);
n2["a/b/grp/leaf/v"].set_float64(10.0);
n2.print();
hid_t h5_file_id = H5Fopen("tout_hdf5_test_write_incompat.hdf5",
H5F_ACC_RDWR,
H5P_DEFAULT);
try
{
io::hdf5_write(n2,h5_file_id);
}
catch(Error &e)
{
CONDUIT_INFO(e.message());
}
H5Fclose(h5_file_id);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, auto_endian)
{
Node n;
n["a"].set_int64(12345689);
n["b"].set_int64(-12345689);
if(Endianness::machine_is_big_endian())
{
n.endian_swap_to_little();
}
else
{
n.endian_swap_to_big();
}
io::hdf5_write(n,"tout_hdf5_wr_opp_endian.hdf5");
Node n_load;
io::hdf5_read("tout_hdf5_wr_opp_endian.hdf5",n_load);
EXPECT_EQ(n_load["a"].as_int64(),12345689);
EXPECT_EQ(n_load["b"].as_int64(),-12345689);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, hdf5_path_exists)
{
std::string test_file_name = "tout_hdf5_wr_hdf5_path_exists.hdf5";
Node n;
n["a/b/c/d"] = 10;
n["a/b/c/f"] = 20;
io::hdf5_write(n,test_file_name);
hid_t h5_file_id = H5Fopen(test_file_name.c_str(),
H5F_ACC_RDONLY,
H5P_DEFAULT);
hid_t h5_grp_a = H5Gopen(h5_file_id, "a", 0);
EXPECT_TRUE(io::hdf5_has_path(h5_file_id,"a"));
EXPECT_TRUE(io::hdf5_has_path(h5_file_id,"a/b"));
EXPECT_TRUE(io::hdf5_has_path(h5_file_id,"a/b/c"));
EXPECT_TRUE(io::hdf5_has_path(h5_file_id,"a/b/c/d"));
EXPECT_TRUE(io::hdf5_has_path(h5_file_id,"a/b/c/f"));
EXPECT_TRUE(io::hdf5_has_path(h5_grp_a,"b"));
EXPECT_TRUE(io::hdf5_has_path(h5_grp_a,"b/c"));
EXPECT_TRUE(io::hdf5_has_path(h5_grp_a,"b/c/d"));
EXPECT_TRUE(io::hdf5_has_path(h5_grp_a,"b/c/f"));
EXPECT_FALSE(io::hdf5_has_path(h5_file_id,"BAD"));
EXPECT_FALSE(io::hdf5_has_path(h5_file_id,"a/BAD"));
EXPECT_FALSE(io::hdf5_has_path(h5_file_id,"a/b/BAD"));
EXPECT_FALSE(io::hdf5_has_path(h5_file_id,"a/b/c/BAD"));
EXPECT_FALSE(io::hdf5_has_path(h5_file_id,"a/b/c/d/e/f/g"));
EXPECT_FALSE(io::hdf5_has_path(h5_grp_a,"BAD"));
EXPECT_FALSE(io::hdf5_has_path(h5_grp_a,"b/BAD"));
EXPECT_FALSE(io::hdf5_has_path(h5_grp_a,"b/c/BAD"));
EXPECT_FALSE(io::hdf5_has_path(h5_grp_a,"b/c/d/e/f/g"));
H5Gclose(h5_grp_a);
H5Fclose(h5_file_id);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, hdf5_create_append_methods)
{
std::string test_file_name = "tout_hdf5_open_append.hdf5";
if(utils::is_file(test_file_name))
{
utils::remove_file(test_file_name);
}
Node n;
n["a/b/c/d"] = 10;
io::hdf5_write(n,test_file_name,true);
n.reset();
n["a/b/c/e"] = 20;
io::hdf5_write(n,test_file_name,true);
Node n_load;
io::hdf5_read(test_file_name,n_load);
EXPECT_TRUE(n_load.has_path("a"));
EXPECT_TRUE(n_load.has_path("a/b"));
EXPECT_TRUE(n_load.has_path("a/b/c"));
EXPECT_TRUE(n_load.has_path("a/b/c/d"));
EXPECT_TRUE(n_load.has_path("a/b/c/e"));
EXPECT_EQ(n_load["a/b/c/d"].to_int32(),10);
EXPECT_EQ(n_load["a/b/c/e"].to_int32(),20);
io::hdf5_write(n,test_file_name,false);
n_load.reset();
io::hdf5_read(test_file_name,n_load);
EXPECT_FALSE(n_load.has_path("a/b/c/d"));
EXPECT_EQ(n_load["a/b/c/e"].to_int32(),20);
n.reset();
n["a/b/c/d"] = 10;
io::hdf5_save(n,test_file_name);
n_load.reset();
io::hdf5_read(test_file_name,n_load);
EXPECT_FALSE(n_load.has_path("a/b/c/e"));
EXPECT_EQ(n_load["a/b/c/d"].to_int32(),10);
n.reset();
n["a/b/c/e"] = 20;
io::hdf5_write(n,test_file_name,true);
n.reset();
n["a/b/c/e"] = 20;
io::hdf5_append(n,test_file_name);
n_load.reset();
io::hdf5_read(test_file_name,n_load);
EXPECT_TRUE(n_load.has_path("a/b/c/d"));
EXPECT_TRUE(n_load.has_path("a/b/c/e"));
EXPECT_EQ(n_load["a/b/c/d"].to_int32(),10);
EXPECT_EQ(n_load["a/b/c/e"].to_int32(),20);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, hdf5_create_open_methods)
{
std::string test_file_name = "tout_hdf5_open_and_create.hdf5";
Node n;
n["a/b/c/d"] = 10;
hid_t h5_file_id = io::hdf5_create_file(test_file_name);
io::hdf5_write(n,h5_file_id);
io::hdf5_close_file(h5_file_id);
h5_file_id = io::hdf5_open_file_for_read(test_file_name);
EXPECT_TRUE(io::hdf5_has_path(h5_file_id,"a"));
EXPECT_TRUE(io::hdf5_has_path(h5_file_id,"a/b"));
EXPECT_TRUE(io::hdf5_has_path(h5_file_id,"a/b/c"));
EXPECT_TRUE(io::hdf5_has_path(h5_file_id,"a/b/c/d"));
Node n_read;
io::hdf5_read(h5_file_id,"a/b/c/d",n_read);
EXPECT_EQ(10,n_read.to_int());
io::hdf5_close_file(h5_file_id);
h5_file_id = io::hdf5_open_file_for_read_write(test_file_name);
Node n2;
n2 = 12;
io::hdf5_write(n2,h5_file_id,"a/b/c/e");
EXPECT_TRUE(io::hdf5_has_path(h5_file_id,"a/b/c/e"));
io::hdf5_read(h5_file_id,"a/b/c/e",n_read);
EXPECT_EQ(12,n_read.to_int());
io::hdf5_close_file(h5_file_id);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_save_generic_options)
{
// 5k zeros, should compress well, but under default
// threshold size
Node n;
n["value"] = DataType::float64(5000);
Node opts;
opts["hdf5/chunking/threshold"] = 2000;
opts["hdf5/chunking/chunk_size"] = 2000;
std::string tout_std = "tout_hdf5_save_generic_default_options.hdf5";
std::string tout_cmp = "tout_hdf5_save_generic_test_options.hdf5";
if(utils::is_file(tout_std))
{
utils::remove_file(tout_std);
}
if(utils::is_file(tout_cmp))
{
utils::remove_file(tout_cmp);
}
io::save(n,tout_std, "hdf5");
io::save(n,tout_cmp, "hdf5", opts);
EXPECT_TRUE(utils::is_file(tout_std));
EXPECT_TRUE(utils::is_file(tout_cmp));
int64 tout_std_fs = utils::file_size(tout_std);
int64 tout_cmp_fs = utils::file_size(tout_cmp);
CONDUIT_INFO("fs test: std = "
<< tout_std_fs
<< ", cmp ="
<< tout_cmp_fs);
EXPECT_TRUE(tout_cmp_fs < tout_std_fs);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, conduit_hdf5_group_list_children)
{
Node n;
n["path/sub1/a"];
n["path/sub1/b"];
n["path/sub1/c"];
n["path/sub2/d"];
n["path/sub2/e"];
n["path/sub2/f"];
std::string tout = "tout_hdf5_grp_chld_names.hdf5";
if(utils::is_file(tout))
{
utils::remove_file(tout);
}
io::save(n,tout, "hdf5");
EXPECT_TRUE(utils::is_file(tout));
hid_t h5_file_id = io::hdf5_open_file_for_read(tout);
std::vector<std::string> cnames;
io::hdf5_group_list_child_names(h5_file_id,"/",cnames);
EXPECT_EQ(cnames.size(),1);
EXPECT_EQ(cnames[0],"path");
io::hdf5_group_list_child_names(h5_file_id,"path",cnames);
EXPECT_EQ(cnames.size(),2);
EXPECT_EQ(cnames[0],"sub1");
EXPECT_EQ(cnames[1],"sub2");
io::hdf5_group_list_child_names(h5_file_id,"path/sub1",cnames);
EXPECT_EQ(cnames.size(),3);
EXPECT_EQ(cnames[0],"a");
EXPECT_EQ(cnames[1],"b");
EXPECT_EQ(cnames[2],"c");
io::hdf5_group_list_child_names(h5_file_id,"path/sub2",cnames);
EXPECT_EQ(cnames.size(),3);
EXPECT_EQ(cnames[0],"d");
EXPECT_EQ(cnames[1],"e");
EXPECT_EQ(cnames[2],"f");
// check leaf, which has no children
// this doesn't throw an error, but it creates an empty list
io::hdf5_group_list_child_names(h5_file_id,"path/sub1/a",cnames);
EXPECT_EQ(cnames.size(),0);
// totally bogus paths will trigger an error
EXPECT_THROW(io::hdf5_group_list_child_names(h5_file_id,"this/isnt/right",cnames),Error);
// empty string won't work in this case
EXPECT_THROW(io::hdf5_group_list_child_names(h5_file_id,"",cnames),Error);
}
//-----------------------------------------------------------------------------
TEST(conduit_relay_io_hdf5, check_if_file_is_hdf5_file)
{
Node n;
n["path/mydata"] = 20;
std::string tout = "tout_hdf5_check_hdf5_file.hdf5";
if(utils::is_file(tout))
{
utils::remove_file(tout);
}
io::save(n,tout, "hdf5");
// this should be recoged as hdf5
EXPECT_TRUE(io::is_hdf5_file(tout));
// check behavior with files that have open handles
hid_t h5_file_id = io::hdf5_open_file_for_read_write(tout);
EXPECT_TRUE(io::is_hdf5_file(tout));