The hdfqlr package provides a high-level API for reading and writing HDF files. However, the package also provides access to the lower-level API provided by the HDFql R wrapper.
library(hdfqlr)
hql_load('path/to/hdfql-x.x.x')To access the low-level API, simply attach the hql$wrapper environment to your workspace.
attach(hql$wrapper)## The following objects are masked from hql$wrapper (pos = 4):
##
## HDFQL_ARRAY, HDFQL_ASCII, HDFQL_ATTRIBUTE, HDFQL_BIG_ENDIAN,
## HDFQL_BIGINT, HDFQL_BITFIELD, HDFQL_CHAR, HDFQL_CHUNKED,
## HDFQL_COMPACT, HDFQL_COMPOUND, HDFQL_CONTIGUOUS, hdfql_cursor,
## hdfql_cursor_, hdfql_cursor_absolute, hdfql_cursor_clear,
## hdfql_cursor_clone, hdfql_cursor_first, hdfql_cursor_get_bigint,
## hdfql_cursor_get_char, hdfql_cursor_get_count,
## hdfql_cursor_get_data_type, hdfql_cursor_get_double,
## hdfql_cursor_get_float, hdfql_cursor_get_int,
## hdfql_cursor_get_position, hdfql_cursor_get_size,
## hdfql_cursor_get_smallint, hdfql_cursor_get_tinyint,
## hdfql_cursor_get_unsigned_bigint, hdfql_cursor_get_unsigned_int,
## hdfql_cursor_get_unsigned_smallint,
## hdfql_cursor_get_unsigned_tinyint, hdfql_cursor_initialize,
## hdfql_cursor_last, hdfql_cursor_next, hdfql_cursor_previous,
## hdfql_cursor_relative, hdfql_cursor_use, hdfql_cursor_use_default,
## HDFQL_DATASET, HDFQL_DIRECTORY, HDFQL_DISABLED, HDFQL_DOUBLE,
## HDFQL_EARLIEST, HDFQL_EARLY, HDFQL_ENABLED, HDFQL_ENUMERATION,
## HDFQL_ERROR_AFTER_LAST, HDFQL_ERROR_ALREADY_EXISTS,
## HDFQL_ERROR_BEFORE_FIRST, HDFQL_ERROR_DANGLING_LINK,
## HDFQL_ERROR_EMPTY, HDFQL_ERROR_FULL, hdfql_error_get_line,
## hdfql_error_get_message, hdfql_error_get_position,
## HDFQL_ERROR_INVALID_FILE, HDFQL_ERROR_INVALID_REGULAR_EXPRESSION,
## HDFQL_ERROR_NO_ACCESS, HDFQL_ERROR_NO_ADDRESS,
## HDFQL_ERROR_NOT_ENOUGH_MEMORY, HDFQL_ERROR_NOT_ENOUGH_SPACE,
## HDFQL_ERROR_NOT_FOUND, HDFQL_ERROR_NOT_OPEN,
## HDFQL_ERROR_NOT_REGISTERED, HDFQL_ERROR_NOT_SUPPORTED,
## HDFQL_ERROR_OUTSIDE_LIMIT, HDFQL_ERROR_PARSE,
## HDFQL_ERROR_UNEXPECTED_DATA_TYPE,
## HDFQL_ERROR_UNEXPECTED_STORAGE_TYPE, HDFQL_ERROR_UNEXPECTED_TYPE,
## HDFQL_ERROR_UNKNOWN, hdfql_execute, hdfql_execute_get_status,
## HDFQL_EXTERNAL_LINK, HDFQL_FILE, HDFQL_FILL_DEFAULT,
## HDFQL_FILL_UNDEFINED, HDFQL_FILL_USER_DEFINED, HDFQL_FLOAT,
## hdfql_get_canonical_path, HDFQL_GLOBAL, HDFQL_GROUP,
## HDFQL_INCREMENTAL, HDFQL_INDEXED, HDFQL_INT, HDFQL_LATE,
## HDFQL_LATEST, HDFQL_LITTLE_ENDIAN, HDFQL_LOCAL, hdfql_mpi_get_rank,
## hdfql_mpi_get_size, HDFQL_NO, HDFQL_OPAQUE, HDFQL_REFERENCE,
## hdfql_shared_library, HDFQL_SMALLINT, HDFQL_SOFT_LINK,
## hdfql_subcursor_absolute, hdfql_subcursor_first,
## hdfql_subcursor_get_bigint, hdfql_subcursor_get_char,
## hdfql_subcursor_get_count, hdfql_subcursor_get_double,
## hdfql_subcursor_get_float, hdfql_subcursor_get_int,
## hdfql_subcursor_get_position, hdfql_subcursor_get_size,
## hdfql_subcursor_get_smallint, hdfql_subcursor_get_tinyint,
## hdfql_subcursor_get_unsigned_bigint,
## hdfql_subcursor_get_unsigned_int,
## hdfql_subcursor_get_unsigned_smallint,
## hdfql_subcursor_get_unsigned_tinyint, hdfql_subcursor_last,
## hdfql_subcursor_next, hdfql_subcursor_previous,
## hdfql_subcursor_relative, HDFQL_SUCCESS, HDFQL_TINYINT,
## HDFQL_TRACKED, HDFQL_UNDEFINED, HDFQL_UNLIMITED,
## HDFQL_UNSIGNED_BIGINT, HDFQL_UNSIGNED_INT, HDFQL_UNSIGNED_SMALLINT,
## HDFQL_UNSIGNED_TINYINT, HDFQL_UNSIGNED_VARBIGINT,
## HDFQL_UNSIGNED_VARINT, HDFQL_UNSIGNED_VARSMALLINT,
## HDFQL_UNSIGNED_VARTINYINT, HDFQL_UTF8, HDFQL_VARBIGINT,
## HDFQL_VARCHAR, HDFQL_VARDOUBLE, HDFQL_VARFLOAT,
## hdfql_variable_get_count, hdfql_variable_get_data_type,
## hdfql_variable_get_dimension, hdfql_variable_get_dimension_count,
## hdfql_variable_get_number, hdfql_variable_get_size,
## hdfql_variable_register, hdfql_variable_transient_register,
## hdfql_variable_unregister, hdfql_variable_unregister_all,
## HDFQL_VARINT, HDFQL_VARSMALLINT, HDFQL_VARTINYINT, HDFQL_VERSION,
## HDFQL_VERSION_18, HDFQL_YESThe HDFql wrapper functions can now be accessed directly. The example code from hdfql-2.1.0/example/HDFqlExample.R is included below:
example.h5 = shQuote(tempfile(fileext = ".h5"))
print(paste("HDFql version:", HDFQL_VERSION))## [1] "HDFql version: 2.1.0"# create an HDF5 file named "example.h5" and use (i.e. open) it
hdfql_execute(paste("CREATE FILE", example.h5))## [1] 0hdfql_execute(paste("USE FILE", example.h5))## [1] 0# show (i.e. get) HDF5 file currently in use and populate HDFql default cursor with it
hdfql_execute("SHOW USE FILE")## [1] 0# display HDF5 file currently in use
hdfql_cursor_first()## [1] 0print(paste("File in use:", hdfql_cursor_get_char()))## [1] "File in use: C:\\Users\\michael\\AppData\\Local\\Temp\\Rtmpyos7yO\\file2d6c30ba408e.h5"# create an attribute named "example_attribute" of data type float with an initial value of 12.4
hdfql_execute("CREATE ATTRIBUTE example_attribute AS FLOAT VALUES(12.4)")## [1] 0# select (i.e. read) data from attribute "example_attribute" and populate HDFql default cursor with it
hdfql_execute("SELECT FROM example_attribute")## [1] 0# display value of attribute "example_attribute"
hdfql_cursor_first()## [1] 0print(paste("Attribute value:", hdfql_cursor_get_float()))## [1] "Attribute value: 12.3999996185303"# create a dataset named "example_dataset" of data type int of two dimensions (size 3x2)
hdfql_execute("CREATE DATASET example_dataset AS INT(3, 2)")## [1] 0# create variable "values" and populate it with certain values
values <- array(dim = c(3, 2))
for (x in 1:2) {
for (y in 1:3) {
values[y, x] <- as.integer(x * 3 + y - 3)
}
}
# register variable "values" for subsequent use (by HDFql)
hdfql_variable_register(values)## [1] 0# insert (i.e. write) values from variable "values" into dataset "example_dataset"
hdfql_execute(paste("INSERT INTO example_dataset VALUES FROM MEMORY", hdfql_variable_get_number(values)))## [1] 0# unregister variable "values" as it is no longer used/needed (by HDFql)
hdfql_variable_unregister(values)## [1] 0# populate variable "values" with zeros (i.e. reset variable)
for (x in 1:2) {
for (y in 1:3) {
values[y, x] <- as.integer(0)
}
}
# register variable "values" for subsequent use (by HDFql)
hdfql_variable_register(values)## [1] 0# select (i.e. read) data from dataset "example_dataset" and populate variable "values" with it
hdfql_execute(paste("SELECT FROM example_dataset INTO MEMORY", hdfql_variable_get_number(values)))## [1] 0# unregister variable "values" as it is no longer used/needed (by HDFql)
hdfql_variable_unregister(values)## [1] 0# display content of variable "values"
print("Dataset value (through variable):")## [1] "Dataset value (through variable):"for (x in 1:2) {
for (y in 1:3) {
print(values[y, x])
}
}## [1] 1
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## [1] 6# another way to select (i.e. read) data from dataset "example_dataset" using HDFql default cursor
hdfql_execute("SELECT FROM example_dataset")## [1] 0# display content of HDFql default cursor
print("Dataset value (through cursor):")## [1] "Dataset value (through cursor):"while (hdfql_cursor_next() == HDFQL_SUCCESS) {
print(hdfql_cursor_get_int())
}## [1] 1
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## [1] 6# create cursor "my_cursor" and use it
my_cursor <- hdfql_cursor()
hdfql_cursor_use(my_cursor)## [1] 0# show (i.e. get) size (in bytes) of dataset "example_dataset" and populate cursor "my_cursor" with it
hdfql_execute("SHOW SIZE example_dataset")## [1] 0# display content of cursor "my_cursor"
hdfql_cursor_first()## [1] 0print(paste("Dataset size (in bytes):", hdfql_cursor_get_bigint()))## [1] "Dataset size (in bytes): 24"# close the file
hdfql_execute(paste("CLOSE FILE", example.h5))## [1] 0