######################################################################## # # License: BSD # Created: June 20, 2005 # Author: Francesc Alted - faltet@pytables.com # # $Id: definitions.pyd 1018 2005-06-20 09:43:34Z faltet $ # ######################################################################## """Here are some definitions for sharing between extensions.""" import sys cdef extern from *: ctypedef long uintptr_t # Standard C functions. cdef extern from "time.h": ctypedef int time_t from numpy cimport dtype from libc.stdio cimport FILE #----------------------------------------------------------------------------- cdef extern from "numpy/arrayobject.h": object PyArray_Scalar(void *data, dtype descr, object itemsize) #----------------------------------------------------------------------------- # Structs and types from HDF5 cdef extern from "hdf5.h" nogil: ctypedef long long hid_t # In H5Ipublic.h ctypedef int hbool_t ctypedef int herr_t ctypedef int htri_t ctypedef unsigned int uint32_t ctypedef unsigned long long hsize_t ctypedef signed long long hssize_t ctypedef long long int64_t ctypedef unsigned long long haddr_t ctypedef haddr_t hobj_ref_t ctypedef struct hvl_t: size_t len # Length of VL data (in base type units) void *p # Pointer to VL data int H5F_ACC_TRUNC, H5F_ACC_RDONLY, H5F_ACC_RDWR, H5F_ACC_EXCL int H5F_ACC_DEBUG, H5F_ACC_CREAT int H5P_DEFAULT, H5P_DATASET_XFER, H5S_ALL int H5P_FILE_CREATE, H5P_FILE_ACCESS int H5FD_LOG_LOC_WRITE, H5FD_LOG_ALL int H5I_INVALID_HID int H5E_DEFAULT int H5T_STD_REF_OBJ int H5R_OBJ_REF_BUF_SIZE unsigned HADDR_UNDEF # Library types cdef enum H5I_type_t: H5I_UNINIT = -2 # uninitialized type H5I_BADID = -1 # invalid Type H5I_FILE = 1 # File objects H5I_GROUP = 0 # Group objects H5I_DATATYPE = 1 # Datatype objects H5I_DATASPACE = 2 # Dataspace objects H5I_DATASET = 3 # Dataset objects H5I_ATTR = 4 # Attribute objects H5I_REFERENCE = 5 # Reference objects H5I_VFL = 6 # virtual file layer H5I_GENPROP_CLS = 7 # generic property list classes H5I_GENPROP_LST = 8 # generic property lists H5I_ERROR_CLASS = 9 # error classes H5I_ERROR_MSG = 10 # error messages H5I_ERROR_STACK = 11 # error stacks H5I_NTYPES # Sentinel value - must be last # Reference types cdef enum H5R_type_t: H5R_BADTYPE = -1 # Invalid Reference Type H5R_OBJECT = 0 # Object reference H5R_DATASET_REGION = 1 # Dataset Region Reference H5R_MAXTYPE # Sentinel value - must be last # The difference between a single file and a set of mounted files cdef enum H5F_scope_t: H5F_SCOPE_LOCAL = 0 # specified file handle only H5F_SCOPE_GLOBAL = 1 # entire virtual file H5F_SCOPE_DOWN = 2 # for internal use only cdef enum H5FD_mem_t: H5FD_MEM_NOLIST = -1, # Data should not appear in the free list. # Must be negative. H5FD_MEM_DEFAULT = 0, # Value not yet set. Can also be the # datatype set in a larger allocation # that will be suballocated by the library. # Must be zero. H5FD_MEM_SUPER = 1, # Superblock data H5FD_MEM_BTREE = 2, # B-tree data H5FD_MEM_DRAW = 3, # Raw data (content of datasets, etc.) H5FD_MEM_GHEAP = 4, # Global heap data H5FD_MEM_LHEAP = 5, # Local heap data H5FD_MEM_OHDR = 6, # Object header data H5FD_MEM_NTYPES # Sentinel value - must be last cdef enum H5O_type_t: H5O_TYPE_UNKNOWN = -1 # Unknown object type H5O_TYPE_GROUP # Object is a group H5O_TYPE_DATASET # Object is a dataset H5O_TYPE_NAMED_DATATYPE # Object is a named data type cdef enum H5L_type_t: H5L_TYPE_ERROR = -1 # Invalid link type id H5L_TYPE_HARD = 0 # Hard link id H5L_TYPE_SOFT = 1 # Soft link id H5L_TYPE_EXTERNAL = 64, # External link id # Values for fill value status cdef enum H5D_fill_value_t: H5D_FILL_VALUE_ERROR = -1 H5D_FILL_VALUE_UNDEFINED = 0 H5D_FILL_VALUE_DEFAULT = 1 H5D_FILL_VALUE_USER_DEFINED = 2 # HDF5 layouts cdef enum H5D_layout_t: H5D_LAYOUT_ERROR = -1 H5D_COMPACT = 0 # raw data is very small H5D_CONTIGUOUS = 1 # the default H5D_CHUNKED = 2 # slow and fancy H5D_NLAYOUTS = 3 # this one must be last! # Byte orders cdef enum H5T_order_t: H5T_ORDER_ERROR = -1 # error H5T_ORDER_LE = 0 # little endian H5T_ORDER_BE = 1 # bit endian H5T_ORDER_VAX = 2 # VAX mixed endian H5T_ORDER_NONE = 3 # no particular order (strings, bits,..) # HDF5 signed enums cdef enum H5T_sign_t: H5T_SGN_ERROR = -1 # error H5T_SGN_NONE = 0 # this is an unsigned type H5T_SGN_2 = 1 # two's complement H5T_NSGN = 2 # this must be last! # HDF5 type classes cdef enum H5T_class_t: H5T_NO_CLASS = -1 # error H5T_INTEGER = 0 # integer types H5T_FLOAT = 1 # floating-point types H5T_TIME = 2 # date and time types H5T_STRING = 3 # character string types H5T_BITFIELD = 4 # bit field types H5T_OPAQUE = 5 # opaque types H5T_COMPOUND = 6 # compound types H5T_REFERENCE = 7 # reference types H5T_ENUM = 8 # enumeration types H5T_VLEN = 9 # variable-length types H5T_ARRAY = 10 # array types H5T_NCLASSES # this must be last # Native types hid_t H5T_C_S1 hid_t H5T_NATIVE_B8 hid_t H5T_NATIVE_CHAR hid_t H5T_NATIVE_SCHAR hid_t H5T_NATIVE_UCHAR hid_t H5T_NATIVE_SHORT hid_t H5T_NATIVE_USHORT hid_t H5T_NATIVE_INT hid_t H5T_NATIVE_UINT hid_t H5T_NATIVE_LONG hid_t H5T_NATIVE_ULONG hid_t H5T_NATIVE_LLONG hid_t H5T_NATIVE_ULLONG hid_t H5T_NATIVE_FLOAT hid_t H5T_NATIVE_DOUBLE hid_t H5T_NATIVE_LDOUBLE # "Standard" types hid_t H5T_STD_I8LE hid_t H5T_STD_I16LE hid_t H5T_STD_I32LE hid_t H5T_STD_I64LE hid_t H5T_STD_U8LE hid_t H5T_STD_U16LE hid_t H5T_STD_U32LE hid_t H5T_STD_U64LE hid_t H5T_STD_B8LE hid_t H5T_STD_B16LE hid_t H5T_STD_B32LE hid_t H5T_STD_B64LE hid_t H5T_IEEE_F32LE hid_t H5T_IEEE_F64LE hid_t H5T_STD_I8BE hid_t H5T_STD_I16BE hid_t H5T_STD_I32BE hid_t H5T_STD_I64BE hid_t H5T_STD_U8BE hid_t H5T_STD_U16BE hid_t H5T_STD_U32BE hid_t H5T_STD_U64BE hid_t H5T_STD_B8BE hid_t H5T_STD_B16BE hid_t H5T_STD_B32BE hid_t H5T_STD_B64BE hid_t H5T_IEEE_F32BE hid_t H5T_IEEE_F64BE # Types which are particular to UNIX (for Time types) hid_t H5T_UNIX_D32LE hid_t H5T_UNIX_D64LE hid_t H5T_UNIX_D32BE hid_t H5T_UNIX_D64BE # The order to retrieve atomic native datatype cdef enum H5T_direction_t: H5T_DIR_DEFAULT = 0 # default direction is inscendent H5T_DIR_ASCEND = 1 # in inscendent order H5T_DIR_DESCEND = 2 # in descendent order # Codes for defining selections cdef enum H5S_seloper_t: H5S_SELECT_NOOP = -1 H5S_SELECT_SET = 0 H5S_SELECT_OR H5S_SELECT_AND H5S_SELECT_XOR H5S_SELECT_NOTB H5S_SELECT_NOTA H5S_SELECT_APPEND H5S_SELECT_PREPEND H5S_SELECT_INVALID # Must be the last one # Character set to use for text strings cdef enum H5T_cset_t: H5T_CSET_ERROR = -1 # error H5T_CSET_ASCII = 0 # US ASCII H5T_CSET_UTF8 = 1 # UTF-8 Unicode encoding H5T_CSET_RESERVED_2 = 2 H5T_CSET_RESERVED_3 = 3 H5T_CSET_RESERVED_4 = 4 H5T_CSET_RESERVED_5 = 5 H5T_CSET_RESERVED_6 = 6 H5T_CSET_RESERVED_7 = 7 H5T_CSET_RESERVED_8 = 8 H5T_CSET_RESERVED_9 = 9 H5T_CSET_RESERVED_10 = 10 H5T_CSET_RESERVED_11 = 11 H5T_CSET_RESERVED_12 = 12 H5T_CSET_RESERVED_13 = 13 H5T_CSET_RESERVED_14 = 14 H5T_CSET_RESERVED_15 = 15 # Error stack traversal direction cdef enum H5E_direction_t: H5E_WALK_UPWARD = 0 # begin deep, end at API function H5E_WALK_DOWNWARD = 1 # begin at API function, end deep cdef enum H5E_type_t: H5E_MAJOR H5E_MINOR ctypedef struct H5E_error_t: hid_t cls_id # class ID hid_t maj_num # major error ID hid_t min_num # minor error number unsigned line # line in file where error occurs const char *func_name # function in which error occurred const char *file_name # file in which error occurred const char *desc # optional supplied description ctypedef herr_t (*H5E_walk_t)(unsigned n, H5E_error_t *err, void *data) ctypedef herr_t (*H5E_auto_t)(hid_t estack, void *data) # object info ctypedef struct H5O_info_t: unsigned long fileno # Number of file where object is located haddr_t addr # Object address in file H5O_type_t type # Basic object type unsigned rc # Reference count of object time_t atime # Access time time_t mtime # Modification time time_t ctime # Change time time_t btime # Birth time hsize_t num_attrs # number of attributes attached to object #H5O_hdr_info_t hdr # Object header information #struct { # H5_ih_info_t obj # H5_ih_info_t attr #} meta_size #------------------------------------------------------------------ # HDF5 API # Version functions herr_t H5get_libversion(unsigned *majnum, unsigned *minnum, unsigned *relnum ) herr_t H5check_version(unsigned majnum, unsigned minnum, unsigned relnum ) # misc herr_t H5free_memory(void *buf) # Operations with files hid_t H5Fcreate(char *filename, unsigned int flags, hid_t create_plist, hid_t access_plist) hid_t H5Fopen(char *name, unsigned flags, hid_t access_id) herr_t H5Fclose (hid_t file_id) htri_t H5Fis_hdf5(char *name) herr_t H5Fflush(hid_t object_id, H5F_scope_t scope) herr_t H5Fget_vfd_handle(hid_t file_id, hid_t fapl_id, void **file_handle) ssize_t H5Fget_file_image(hid_t file_id, void *buf_ptr, size_t buf_len) herr_t H5Fget_filesize(hid_t file_id, hsize_t *size) hid_t H5Fget_create_plist(hid_t file_id) # Operations with groups hid_t H5Gcreate(hid_t loc_id, char *name, hid_t lcpl_id, hid_t gcpl_id, hid_t gapl_id) hid_t H5Gopen(hid_t loc_id, char *name, hid_t gapl_id) herr_t H5Gclose(hid_t group_id) # Operations with links herr_t H5Ldelete(hid_t file_id, char *name, hid_t lapl_id) herr_t H5Lmove(hid_t src_loc_id, char *src_name, hid_t dst_loc_id, char *dst_name, hid_t lcpl, hid_t lap) # For dealing with datasets hid_t H5Dopen(hid_t file_id, char *name, hid_t dapl_id) herr_t H5Dclose(hid_t dset_id) herr_t H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, void *buf) herr_t H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, void *buf) hid_t H5Dget_type(hid_t dset_id) hid_t H5Dget_space(hid_t dset_id) herr_t H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf) hid_t H5Dget_create_plist(hid_t dataset_id) hsize_t H5Dget_storage_size(hid_t dataset_id) herr_t H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id, hsize_t *size) herr_t H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *offset, unsigned *filter_mask, haddr_t *addr, hsize_t *size) herr_t H5Dread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters, void *buf) herr_t H5Dwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, size_t data_size, const void *buf) # Functions for dealing with dataspaces hid_t H5Screate_simple(int rank, hsize_t dims[], hsize_t maxdims[]) int H5Sget_simple_extent_ndims(hid_t space_id) int H5Sget_simple_extent_dims(hid_t space_id, hsize_t dims[], hsize_t maxdims[]) herr_t H5Sselect_all(hid_t spaceid) herr_t H5Sselect_hyperslab(hid_t space_id, H5S_seloper_t op, hsize_t start[], hsize_t _stride[], hsize_t count[], hsize_t _block[]) herr_t H5Sselect_elements(hid_t space_id, H5S_seloper_t op, size_t num_elements, hsize_t *coord) herr_t H5Sclose(hid_t space_id) # Functions for dealing with datatypes H5T_class_t H5Tget_class(hid_t type_id) hid_t H5Tget_super(hid_t type) H5T_sign_t H5Tget_sign(hid_t type_id) H5T_order_t H5Tget_order(hid_t type_id) size_t H5Tget_size(hid_t type_id) herr_t H5Tset_size(hid_t type_id, size_t size) size_t H5Tget_precision(hid_t dtype_id) herr_t H5Tset_precision(hid_t type_id, size_t prec) hid_t H5Tcreate(H5T_class_t type, size_t size) hid_t H5Tvlen_create(hid_t base_type_id) hid_t H5Tcopy(hid_t type_id) herr_t H5Tclose(hid_t type_id) htri_t H5Tequal(hid_t dtype_id1, hid_t dtype_id2) # Operations defined on string data types htri_t H5Tis_variable_str(hid_t dtype_id) # Operations for compound data types int H5Tget_nmembers(hid_t type_id) char *H5Tget_member_name(hid_t type_id, unsigned membno) hid_t H5Tget_member_type(hid_t type_id, unsigned membno) hid_t H5Tget_native_type(hid_t type_id, H5T_direction_t direction) herr_t H5Tget_member_value(hid_t type_id, int membno, void *value) size_t H5Tget_member_offset(hid_t type_id, unsigned memb_no) int H5Tget_offset(hid_t type_id) herr_t H5Tinsert(hid_t parent_id, char *name, size_t offset, hid_t member_id) herr_t H5Tpack(hid_t type_id) # Operations for enumerated data types hid_t H5Tenum_create(hid_t base_id) herr_t H5Tenum_insert(hid_t type, char *name, void *value) # Operations for array data types hid_t H5Tarray_create(hid_t base_id, int ndims, hsize_t dims[]) int H5Tget_array_ndims(hid_t type_id) int H5Tget_array_dims(hid_t type_id, hsize_t dims[]) # Operations with attributes herr_t H5Adelete(hid_t loc_id, char *name) int H5Aget_num_attrs(hid_t loc_id) size_t H5Aget_name(hid_t attr_id, size_t buf_size, char *buf) hid_t H5Aopen_idx(hid_t loc_id, unsigned int idx) herr_t H5Aread(hid_t attr_id, hid_t mem_type_id, void *buf) herr_t H5Aclose(hid_t attr_id) # Operations with properties hid_t H5Pcreate(hid_t plist_id) herr_t H5Pclose(hid_t plist_id) herr_t H5Pset_cache(hid_t plist_id, int mdc_nelmts, int rdcc_nelmts, size_t rdcc_nbytes, double rdcc_w0) herr_t H5Pset_sieve_buf_size(hid_t fapl_id, hsize_t size) H5D_layout_t H5Pget_layout(hid_t plist) int H5Pget_chunk(hid_t plist, int max_ndims, hsize_t *dims) hid_t H5Pget_driver(hid_t plist_id) herr_t H5Pset_fapl_sec2(hid_t fapl_id) #herr_t H5Pget_fapl_direct(hid_t fapl_id, size_t *alignment, # size_t *block_size, size_t *cbuf_size) #herr_t H5Pset_fapl_direct(hid_t fapl_id, size_t alignment, # size_t block_size, size_t cbuf_size) herr_t H5Pset_fapl_log(hid_t fapl_id, const char *logfile, unsigned long long flags, size_t buf_size) #herr_t H5Pset_fapl_windows(hid_t fapl_id) herr_t H5Pset_fapl_stdio(hid_t fapl_id) #herr_t H5Pget_fapl_core(hid_t fapl_id, size_t *increment, # hbool_t *backing_store) herr_t H5Pset_fapl_core(hid_t fapl_id, size_t increment, hbool_t backing_store) #herr_t H5Pget_fapl_family(hid_t fapl_id, hsize_t *memb_size, # hid_t *memb_fapl_id) herr_t H5Pset_fapl_family(hid_t fapl_id, hsize_t memb_size, hid_t memb_fapl_id) #herr_t H5Pget_fapl_multi(hid_t fapl_id, H5FD_mem_t *memb_map, # hid_t *memb_fapl, const char **memb_name, # haddr_t *memb_addr, hbool_t *relax) herr_t H5Pset_fapl_multi(hid_t fapl_id, H5FD_mem_t *memb_map, hid_t *memb_fapl, char **memb_name, haddr_t *memb_addr, hbool_t relax) herr_t H5Pset_fapl_split(hid_t fapl_id, char *meta_ext, hid_t meta_plist_id, char *raw_ext, hid_t raw_plist_id) #herr_t H5Pget_fapl_mpio(hid_t fapl_id, MPI_Comm *comm, MPI_Info *info) #herr_t H5Pset_fapl_mpio(hid_t fapl_id, MPI_Comm comm, MPI_Info info) #herr_t H5Pget_fapl_mpiposix(hid_t fapl_id, MPI_Comm *comm, # hbool_t *use_gpfs_hints) #herr_t H5Pset_fapl_mpiposix(hid_t fapl_id, MPI_Comm comm, # hbool_t use_gpfs_hints) herr_t H5Pset_file_image(hid_t fapl_id, void *buf_ptr, size_t buf_len) herr_t H5Pget_userblock(hid_t plist, hsize_t *size) herr_t H5Pset_userblock(hid_t plist, hsize_t size) herr_t H5Pget_obj_track_times(hid_t ocpl_id, hbool_t *track_times) # Error Handling Interface #herr_t H5Eget_auto(hid_t estack_id, H5E_auto_t *func, void** data) herr_t H5Eset_auto(hid_t estack_id, H5E_auto_t func, void *data) herr_t H5Eprint(hid_t estack_id, FILE *stream) herr_t H5Ewalk(hid_t estack_id, H5E_direction_t dir, H5E_walk_t func, void *data) #hid_t H5Eget_current_stack(void) #herr_t H5Eclose_stack(hid_t estack_id) #ssize_t H5Eget_num(hid_t estack_id) ssize_t H5Eget_msg(hid_t mesg_id, H5E_type_t* mesg_type, char* mesg, size_t size) #herr_t H5Eclose_msg(hid_t mesg_id) #ssize_t H5Eget_class_name(hid_t class_id, char* name, size_t size) # Onject interface herr_t H5Oget_info(hid_t object_id, H5O_info_t *object_info) # Operations with filters and compression interface ctypedef int H5Z_filter_t #herr_t H5Zregister(const void *cls) herr_t H5Zunregister(H5Z_filter_t id) #htri_t H5Zfilter_avail(H5Z_filter_t id) #herr_t H5Zget_filter_info(H5Z_filter_t, unsigned int*) # Operations on the references H5I_type_t H5Iget_type(hid_t id) herr_t H5Rcreate(void *reference, hid_t loc_id, const char *name, H5R_type_t type, hid_t space_id) hid_t H5Rdereference(hid_t dset, hid_t oapl_id, H5R_type_t rtype, const void *reference) herr_t H5Oclose( hid_t object_id ) # Specific HDF5 functions for PyTables cdef extern from "H5ATTR.h" nogil: herr_t H5ATTRget_attribute(hid_t loc_id, char *attr_name, hid_t type_id, void *data) hsize_t H5ATTRget_attribute_string(hid_t loc_id, char *attr_name, char **attr_value, int *cset) hsize_t H5ATTRget_attribute_vlen_string_array(hid_t loc_id, char *attr_name, char ***attr_value, int *cset) herr_t H5ATTRset_attribute(hid_t obj_id, char *attr_name, hid_t type_id, size_t rank, hsize_t *dims, char *attr_data) herr_t H5ATTRset_attribute_string(hid_t loc_id, char *attr_name, char *attr_data, hsize_t attr_size, int cset) herr_t H5ATTRfind_attribute(hid_t loc_id, char *attr_name) herr_t H5ATTRget_type_ndims(hid_t loc_id, char *attr_name, hid_t *type_id, H5T_class_t *class_id, size_t *type_size, int *rank) herr_t H5ATTRget_dims(hid_t loc_id, char *attr_name, hsize_t *dims) # Functions for operations with ARRAY cdef extern from "H5ARRAY.h" nogil: herr_t H5ARRAYget_ndims(hid_t dataset_id, int *rank) herr_t H5ARRAYget_info(hid_t dataset_id, hid_t type_id, hsize_t *dims, hsize_t *maxdims, H5T_class_t *super_class_id, char *byteorder) # Some utilities cdef extern from "utils.h" nogil: herr_t set_cache_size(hid_t file_id, size_t cache_size) int get_objinfo(hid_t loc_id, char *name) int get_linkinfo(hid_t loc_id, char *name) hsize_t get_len_of_range(hsize_t lo, hsize_t hi, hsize_t step) hid_t create_ieee_float16(char *byteorder) hid_t create_ieee_complex64(char *byteorder) hid_t create_ieee_complex128(char *byteorder) hid_t create_ieee_complex192(char *byteorder) hid_t create_ieee_complex256(char *byteorder) herr_t set_order(hid_t type_id, char *byteorder) herr_t get_order(hid_t type_id, char *byteorder) int is_complex(hid_t type_id) herr_t truncate_dset(hid_t dataset_id, int maindim, hsize_t size) # compatibility herr_t pt_H5Pset_fapl_direct(hid_t fapl_id, size_t alignment, size_t block_size, size_t cbuf_size) herr_t pt_H5Pset_fapl_windows(hid_t fapl_id) int H5_HAVE_DIRECT_DRIVER, H5_HAVE_WINDOWS_DRIVER, H5_HAVE_IMAGE_FILE cdef extern from "utils.h": object Giterate(hid_t parent_id, hid_t loc_id, char *name) object Aiterate(hid_t loc_id) object H5UIget_info(hid_t loc_id, char *name, char *byteorder) # Type conversion routines cdef extern from "typeconv.h" nogil: void conv_float64_timeval32(void *base, unsigned long byteoffset, unsigned long bytestride, long long nrecords, unsigned long nelements, int sense) # Blosc2 registration cdef extern from "blosc2_filter.h" nogil: int register_blosc2(char **version, char **date) int FILTER_BLOSC2 # Blosc registration cdef extern from "blosc_filter.h" nogil: int register_blosc(char **version, char **date) int FILTER_BLOSC