/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * For details of the HDF libraries, see the HDF Documentation at: * http://hdfgroup.org/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif /* __cplusplus */ #include #include #include #include #include "hdf5.h" #include "h5util.h" #define SKIP_UNUSED_DUMP_ROUTINES /* size of hyperslab buffer when a dataset is bigger than H5TOOLS_MALLOCSIZE */ hsize_t H5TOOLS_BUFSIZE = (32 * 1024 * 1024); /* 32 MB */ int H5TOOLS_TEXT_BLOCK = 16; /* Number of elements on a line in a text export file */ /* * Pointer to the JNI's Virtual Machine; used for callback functions. */ JavaVM *jvm; jobject copy_callback; jobject close_callback; jobject create_callback; jobject compare_callback; jobject get_callback; jobject set_callback; jobject delete_callback; H5E_auto2_t efunc; void *edata; /********************/ /* Local Prototypes */ /********************/ #ifndef SKIP_UNUSED_DUMP_ROUTINES static int h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj); static int h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj); #endif static int h5str_is_zero(const void *_mem, size_t size); static hid_t h5str_get_native_type(hid_t type); static hid_t h5str_get_little_endian_type(hid_t type); static hid_t h5str_get_big_endian_type(hid_t type); static htri_t h5str_detect_vlen(hid_t tid); static htri_t h5str_detect_vlen_str(hid_t tid); static int h5tools_dump_simple_data(JNIEnv *env, FILE *stream, hid_t container, hid_t type, void *_mem, hsize_t nelmts); static int h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t block_nelmts); static int render_bin_output_region_data_blocks(FILE *stream, hid_t region_id, hid_t container, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata); static int render_bin_output_region_blocks(FILE *stream, hid_t region_space, hid_t region_id, hid_t container); static int render_bin_output_region_data_points(FILE *stream, hid_t region_space, hid_t region_id, hid_t container, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata); static int render_bin_output_region_points(FILE *stream, hid_t region_space, hid_t region_id, hid_t container); /* Strings for output */ #define H5_TOOLS_GROUP "GROUP" #define H5_TOOLS_DATASET "DATASET" #define H5_TOOLS_DATATYPE "DATATYPE" #define H5_TOOLS_ATTRIBUTE "ATTRIBUTE" /** frees memory held by array of strings */ void h5str_array_free (char **strs, size_t len) { size_t i; if (!strs || len <= 0) return; for (i = 0; i < len; i++) { if (strs[i]) HDfree(strs[i]); } /* for (i=0; i 0) { str->s = (char *)HDmalloc(len); str->max = len; str->s[0] = '\0'; } /* end if */ } /* end h5str_new */ /** free string memory */ void h5str_free (h5str_t *str) { if (str && str->max > 0) { HDfree(str->s); HDmemset(str, 0, sizeof(h5str_t)); } /* end if */ } /* end h5str_free */ /** reset the max size of the string */ /* * TODO: no error return. malloc can fail. */ void h5str_resize (h5str_t *str, size_t new_len) { char *new_str; if (!str || new_len <= 0 || str->max == new_len) return; if (NULL == (new_str = (char *) HDmalloc(new_len))) return; if (new_len > str->max) /* increase memory */ HDstrcpy(new_str, str->s); else HDstrncpy(new_str, str->s, new_len - 1); HDfree(str->s); str->s = new_str; str->max = new_len; } /* end h5str_resize */ /* appends a copy of the string pointed to by cstr to the h5str. Return Value: the char string point to str->s */ char* h5str_append (h5str_t *str, const char* cstr) { size_t len; if (!str) return NULL; else if (!cstr) return str->s; len = HDstrlen(str->s) + HDstrlen(cstr); while (len >= str->max) /* not enough to hold the new string, double the space */ { h5str_resize(str, str->max * 2); } return HDstrcat(str->s, cstr); } /* end h5str_append */ /* * Converts the given data point string into a real data point. * * Returns: * SUCCESS: Length of string token processed * FAILURE: 0 */ size_t h5str_convert (JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_buf, size_t out_buf_offset) { unsigned char *ucptr = NULL; static char fmt_llong[8], fmt_ullong[8]; H5T_class_t tclass = H5T_NO_CLASS; const char delimiter[] = " ," H5_COMPOUND_BEGIN_INDICATOR H5_COMPOUND_END_INDICATOR \ H5_ARRAY_BEGIN_INDICATOR H5_ARRAY_END_INDICATOR \ H5_VLEN_BEGIN_INDICATOR H5_VLEN_END_INDICATOR; size_t typeSize = 0; hid_t mtid = H5I_INVALID_HID; char *this_str = NULL; char *token; char *cptr = NULL; int n; size_t retVal = 0; if (!in_str) H5_NULL_ARGUMENT_ERROR(ENVONLY, "h5str_convert: in_str is NULL"); if (!out_buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "h5str_convert: out_buf is NULL"); this_str = *in_str; cptr = &(((char *) out_buf)[out_buf_offset]); ucptr = &(((unsigned char *) out_buf)[out_buf_offset]); if (H5T_NO_CLASS == (tclass = H5Tget_class(tid))) H5_LIBRARY_ERROR(ENVONLY); if (!(typeSize = H5Tget_size(tid))) H5_LIBRARY_ERROR(ENVONLY); /* Build default formats for long long types */ if (!fmt_llong[0]) { if (HDsprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsprintf failure"); if (HDsprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsprintf failure"); } /* end if */ switch (tclass) { case H5T_FLOAT: { token = HDstrtok(this_str, delimiter); switch (typeSize) { case sizeof(float): { float tmp_float = 0.0f; sscanf(token, "%f", &tmp_float); HDmemcpy(cptr, &tmp_float, sizeof(float)); break; } case sizeof(double): { double tmp_double = 0.0; sscanf(token, "%lf", &tmp_double); HDmemcpy(cptr, &tmp_double, sizeof(double)); break; } #if H5_SIZEOF_LONG_DOUBLE != 0 && H5_SIZEOF_LONG_DOUBLE != H5_SIZEOF_DOUBLE case sizeof(long double): { long double tmp_ldouble = 0.0; sscanf(token, "%Lf", &tmp_ldouble); HDmemcpy(cptr, &tmp_ldouble, sizeof(long double)); break; } #endif default: H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_convert: floating-point datatype size didn't match any of expected sizes"); break; } retVal = typeSize; break; } case H5T_STRING: { size_t len = HDstrlen(this_str); if (len > 0) { HDstrncpy(cptr, this_str, typeSize); cptr[typeSize - 1] = '\0'; retVal = typeSize; } else { cptr = NULL; } break; } case H5T_INTEGER: { H5T_sign_t nsign = H5T_SGN_ERROR; if (H5T_SGN_ERROR == (nsign = H5Tget_sign(tid))) H5_LIBRARY_ERROR(ENVONLY); token = HDstrtok(this_str, delimiter); switch (typeSize) { case sizeof(char): { unsigned char tmp_uchar = 0; signed char tmp_char = 0; if (H5T_SGN_NONE == nsign) { sscanf(token, "%hhu", &tmp_uchar); HDmemcpy(cptr, &tmp_uchar, sizeof(unsigned char)); } else { sscanf(token, "%hhd", &tmp_char); HDmemcpy(cptr, &tmp_char, sizeof(char)); } break; } case sizeof(short): { unsigned short tmp_ushort = 0; short tmp_short = 0; if (H5T_SGN_NONE == nsign) { sscanf(token, "%hu", &tmp_ushort); HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short)); } else { sscanf(token, "%hd", &tmp_short); HDmemcpy(&tmp_short, cptr, sizeof(short)); } break; } case sizeof(int): { unsigned int tmp_uint = 0; int tmp_int = 0; if (H5T_SGN_NONE == nsign) { sscanf(token, "%u", &tmp_uint); HDmemcpy(cptr, &tmp_uint, sizeof(unsigned int)); } else { sscanf(token, "%d", &tmp_int); HDmemcpy(cptr, &tmp_int, sizeof(int)); } break; } #if H5_SIZEOF_LONG != H5_SIZEOF_INT case sizeof(long): { unsigned long tmp_ulong = 0; long tmp_long = 0; if (H5T_SGN_NONE == nsign) { sscanf(token, "%lu", &tmp_ulong); HDmemcpy(cptr, &tmp_ulong, sizeof(unsigned long)); } else { sscanf(token, "%ld", &tmp_long); HDmemcpy(cptr, &tmp_long, sizeof(long)); } break; } #endif #if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG case sizeof(long long): { unsigned long long tmp_ullong = 0; long long tmp_llong = 0; if (H5T_SGN_NONE == nsign) { sscanf(token, fmt_ullong, &tmp_ullong); HDmemcpy(cptr, &tmp_ullong, sizeof(unsigned long long)); } else { sscanf(token, fmt_llong, &tmp_llong); HDmemcpy(cptr, &tmp_llong, sizeof(long long)); } break; } #endif default: H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_convert: integer datatype size didn't match any of expected sizes"); break; } retVal = typeSize; break; } case H5T_COMPOUND: { unsigned i; size_t member_offset; if ((n = H5Tget_nmembers(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); /* Skip whitespace and compound indicators */ while (*this_str == ' ') this_str++; if (*this_str == '{') this_str++; while (*this_str == ' ') this_str++; for (i = 0; i < (unsigned) n; i++) { member_offset = H5Tget_member_offset(tid, i); if ((mtid = H5Tget_member_type(tid, i)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!h5str_convert(ENVONLY, &this_str, container, mtid, out_buf, member_offset)) { CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); goto done; } /* Skip whitespace and commas */ while (*this_str == ' ') this_str++; if (*this_str == ',') this_str++; while (*this_str == ' ') this_str++; if (H5Tclose(mtid) < 0) H5_LIBRARY_ERROR(ENVONLY); mtid = H5I_INVALID_HID; } /* Skip whitespace and compound indicators */ while (*this_str == ' ') this_str++; if (*this_str == '}') this_str++; while (*this_str == ' ') this_str++; retVal = typeSize * (size_t) n; break; } /* TODO handle reference writing */ case H5T_REFERENCE: cptr = NULL; break; case H5T_ENUM: { void *value; token = HDstrtok(this_str, delimiter); switch (typeSize) { case sizeof(char): { unsigned char tmp_uchar = 0; value = &tmp_uchar; break; } case sizeof(short): { unsigned short tmp_ushort = 0; value = &tmp_ushort; break; } #if H5_SIZEOF_LONG != H5_SIZEOF_INT case sizeof(long): { unsigned long tmp_ulong = 0; value = &tmp_ulong; break; } #endif #if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG case sizeof(long long): { unsigned long long tmp_ullong = 0; value = &tmp_ullong; break; } #endif default: { unsigned int tmp_uint = 0; value = &tmp_uint; break; } } if (H5Tenum_valueof(tid, token, value) < 0) H5_LIBRARY_ERROR(ENVONLY); HDmemcpy(ucptr, value, typeSize); retVal = typeSize; break; } case H5T_ARRAY: { hsize_t i, dims[H5S_MAX_RANK], total_elmts; size_t baseTypeSize; int rank = 0; /* Skip whitespace and array indicators */ while (*this_str == ' ') this_str++; if (*this_str == '[') this_str++; while (*this_str == ' ') this_str++; if ((mtid = H5Tget_super(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!(baseTypeSize = H5Tget_size(mtid))) H5_LIBRARY_ERROR(ENVONLY); if ((rank = H5Tget_array_ndims(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (H5Tget_array_dims2(tid, dims) < 0) H5_LIBRARY_ERROR(ENVONLY); for (i = 0, total_elmts = 1; i < (hsize_t) rank; i++) total_elmts *= dims[i]; if (NULL == (cptr = (char *) HDcalloc((size_t)total_elmts, baseTypeSize))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_convert: failed to allocate array buffer"); for (i = 0; i < total_elmts; i++) { if (!(h5str_convert(ENVONLY, &this_str, container, mtid, out_buf, i * baseTypeSize))) { CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); goto done; } /* Skip whitespace and commas */ while (*this_str == ' ') this_str++; if (*this_str == ',') this_str++; while (*this_str == ' ') this_str++; } if (H5Tclose(mtid) < 0) H5_LIBRARY_ERROR(ENVONLY); mtid = H5I_INVALID_HID; /* Skip whitespace and array indicators */ while (*this_str == ' ') this_str++; if (*this_str == ']') this_str++; while (*this_str == ' ') this_str++; retVal = typeSize * total_elmts; break; } case H5T_VLEN: { size_t i, baseTypeSize; hvl_t *vl_buf = (hvl_t *) out_buf; char cur_char; if ((mtid = H5Tget_super(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!(baseTypeSize = H5Tget_size(mtid))) H5_LIBRARY_ERROR(ENVONLY); if (NULL == (vl_buf->p = HDmalloc(baseTypeSize))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_convert: failed to allocate vlen buffer"); vl_buf->len = 1; /* Skip whitespace and vlen indicators */ while (*this_str == ' ') this_str++; if (*this_str == '(') this_str++; while (*this_str == ' ') this_str++; cur_char = *this_str; for (i = 0; cur_char != ')' && cur_char != '\0'; i++) { if (i >= vl_buf->len) { char *tmp_realloc; if (NULL == (tmp_realloc = (char *) HDrealloc(vl_buf->p, vl_buf->len * 2 * baseTypeSize))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_convert: failed to reallocate vlen buffer"); vl_buf->len *= 2; vl_buf->p = tmp_realloc; } if (!(h5str_convert(ENVONLY, &this_str, container, mtid, vl_buf->p, i * baseTypeSize))) { CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); vl_buf->len = i; goto done; } /* Skip whitespace and commas */ while (*this_str == ' ') this_str++; if (*this_str == ',') this_str++; while (*this_str == ' ') this_str++; } vl_buf->len = i; if (H5Tclose(mtid) < 0) H5_LIBRARY_ERROR(ENVONLY); mtid = H5I_INVALID_HID; /* Skip whitespace and vlen indicators */ while (*this_str == ' ') this_str++; if (*this_str == ')') this_str++; while (*this_str == ' ') this_str++; retVal = typeSize; break; } case H5T_NCLASSES: case H5T_NO_CLASS: { H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_convert: invalid datatype class"); break; } case H5T_TIME: case H5T_BITFIELD: case H5T_OPAQUE: default: { /* All other types get copied raw */ HDmemcpy(ucptr, this_str, typeSize); retVal = typeSize; break; } } /* end switch */ done: if (mtid >= 0) H5Tclose(mtid); return retVal; } /* end h5str_convert */ /*------------------------------------------------------------------------- * Function: h5str_sprint_reference * * Purpose: Object reference -- show the name of the referenced object. * * Return: Nothing *------------------------------------------------------------------------- */ void h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_p) { ssize_t buf_size; char *ref_name = NULL; const H5R_ref_t *ref_vp = (H5R_ref_t *)ref_p; UNUSED(container); if (!h5str_append(out_str, " \"")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); buf_size = H5Rget_file_name(ref_vp, NULL, 0); if (buf_size) { ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1); if (H5Rget_file_name(ref_vp, ref_name, buf_size + 1) >= 0) { ref_name[buf_size] = '\0'; if (!h5str_append(out_str, ref_name)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } HDfree(ref_name); ref_name = NULL; } buf_size = H5Rget_obj_name(ref_vp, H5P_DEFAULT, NULL, 0); if (buf_size) { ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1); if (H5Rget_obj_name(ref_vp, H5P_DEFAULT, ref_name, buf_size + 1) >= 0) { ref_name[buf_size] = '\0'; if (!h5str_append(out_str, ref_name)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } HDfree(ref_name); ref_name = NULL; } if (H5Rget_type(ref_vp) == H5R_ATTR) { buf_size = H5Rget_attr_name(ref_vp, NULL, 0); if (buf_size) { ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1); if (H5Rget_attr_name(ref_vp, ref_name, buf_size + 1) >= 0) { ref_name[buf_size] = '\0'; if (!h5str_append(out_str, ref_name)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } HDfree(ref_name); ref_name = NULL; } } if (!h5str_append(out_str, "\"")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); done: if (ref_name) HDfree(ref_name); } /* * Prints the value of a data point into a string. * * Returns: * SUCCESS: Total number of characters printed * FAILURE: 0 */ size_t h5str_sprintf (JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *in_buf, size_t in_buf_len, int expand_data) { unsigned char *ucptr = (unsigned char *) in_buf; static char fmt_llong[8], fmt_ullong[8]; H5T_class_t tclass = H5T_NO_CLASS; size_t typeSize = 0; H5T_sign_t nsign = H5T_SGN_ERROR; hid_t mtid = H5I_INVALID_HID; hid_t obj = H5I_INVALID_HID; char *cptr = (char *) in_buf; char *this_str = NULL; int n; size_t retVal = 0; if (!out_str) H5_NULL_ARGUMENT_ERROR(ENVONLY, "h5str_sprintf: out_str is NULL"); if (!in_buf) H5_NULL_ARGUMENT_ERROR(ENVONLY, "h5str_sprintf: in_buf is NULL"); if (H5T_NO_CLASS == (tclass = H5Tget_class(tid))) H5_LIBRARY_ERROR(ENVONLY); if (!(typeSize = H5Tget_size(tid))) H5_LIBRARY_ERROR(ENVONLY); if (!(nsign = H5Tget_sign(tid))) H5_LIBRARY_ERROR(ENVONLY); /* Build default formats for long long types */ if (!fmt_llong[0]) { if (HDsnprintf(fmt_llong, sizeof(fmt_llong), "%%%sd", H5_PRINTF_LL_WIDTH) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); if (HDsnprintf(fmt_ullong, sizeof(fmt_ullong), "%%%su", H5_PRINTF_LL_WIDTH) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } /* end if */ switch (tclass) { case H5T_FLOAT: { switch (typeSize) { case sizeof(float): { float tmp_float = 0.0f; HDmemcpy(&tmp_float, cptr, sizeof(float)); if (NULL == (this_str = (char *) HDmalloc(25))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%g", tmp_float) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); break; } case sizeof(double): { double tmp_double = 0.0; HDmemcpy(&tmp_double, cptr, sizeof(double)); if (NULL == (this_str = (char *) HDmalloc(25))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%g", tmp_double) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); break; } #if H5_SIZEOF_LONG_DOUBLE != 0 && H5_SIZEOF_LONG_DOUBLE != H5_SIZEOF_DOUBLE case sizeof(long double): { long double tmp_ldouble = 0.0; HDmemcpy(&tmp_ldouble, cptr, sizeof(long double)); if (NULL == (this_str = (char *) HDmalloc(27))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%Lf", tmp_ldouble) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); break; } #endif default: H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_sprintf: floating-point datatype size didn't match any of expected sizes"); break; } break; } case H5T_STRING: { htri_t is_variable; char *tmp_str; if ((is_variable = H5Tis_variable_str(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (is_variable) { /* cp_vp is the pointer into the struct where a `char*' is stored. So we have * to dereference the pointer to get the `char*' to pass to HDstrlen(). */ tmp_str = *(char **)in_buf; if (NULL != tmp_str) typeSize = HDstrlen(tmp_str); } else { tmp_str = cptr; } /* Check for NULL pointer for string */ if (!tmp_str) { if (NULL == (this_str = (char *) HDmalloc(5))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); HDstrncpy(this_str, "NULL", 5); } else { if (typeSize > 0) { if (NULL == (this_str = (char *) HDmalloc(typeSize + 1))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); HDstrncpy(this_str, tmp_str, typeSize); this_str[typeSize] = '\0'; } } break; } case H5T_INTEGER: { if (H5T_SGN_ERROR == (nsign = H5Tget_sign(tid))) H5_LIBRARY_ERROR(ENVONLY); switch (typeSize) { case sizeof(char): { unsigned char tmp_uchar = 0; char tmp_char = 0; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_uchar, cptr, sizeof(unsigned char)); if (NULL == (this_str = (char *) HDmalloc(7))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%hhu", tmp_uchar) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } else { HDmemcpy(&tmp_char, cptr, sizeof(char)); if (NULL == (this_str = (char *) HDmalloc(7))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%hhd", tmp_char) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } break; } case sizeof(short): { unsigned short tmp_ushort = 0; short tmp_short = 0; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short)); if (NULL == (this_str = (char *) HDmalloc(9))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%hu", tmp_ushort) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } else { HDmemcpy(&tmp_short, cptr, sizeof(short)); if (NULL == (this_str = (char *) HDmalloc(9))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%hd", tmp_short) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } break; } case sizeof(int): { unsigned int tmp_uint = 0; int tmp_int = 0; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_uint, cptr, sizeof(unsigned int)); if (NULL == (this_str = (char *) HDmalloc(14))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%u", tmp_uint) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } else { HDmemcpy(&tmp_int, cptr, sizeof(int)); if (NULL == (this_str = (char *) HDmalloc(14))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%d", tmp_int) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } break; } #if H5_SIZEOF_LONG != H5_SIZEOF_INT case sizeof(long): { unsigned long tmp_ulong = 0; long tmp_long = 0; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_ulong, cptr, sizeof(unsigned long)); if (NULL == (this_str = (char *) HDmalloc(23))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%lu", tmp_ulong) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } else { HDmemcpy(&tmp_long, cptr, sizeof(long)); if (NULL == (this_str = (char *) HDmalloc(23))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%ld", tmp_long) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } break; } #endif #if H5_SIZEOF_LONG_LONG != H5_SIZEOF_LONG case sizeof(long long): { unsigned long long tmp_ullong = 0; long long tmp_llong = 0; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_ullong, cptr, sizeof(unsigned long long)); if (NULL == (this_str = (char *) HDmalloc(25))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, fmt_ullong, tmp_ullong) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } else { HDmemcpy(&tmp_llong, cptr, sizeof(long long)); if (NULL == (this_str = (char *) HDmalloc(25))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, fmt_llong, tmp_llong) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } break; } #endif default: H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_sprintf: integer datatype size didn't match any of expected sizes"); break; } break; } case H5T_COMPOUND: { unsigned i; size_t offset; if ((n = H5Tget_nmembers(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!h5str_append(out_str, H5_COMPOUND_BEGIN_INDICATOR)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); for (i = 0; i < (unsigned) n; i++) { offset = H5Tget_member_offset(tid, i); if ((mtid = H5Tget_member_type(tid, i)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &cptr[offset], in_buf_len, expand_data)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if ((i + 1) < (unsigned) n) if (!h5str_append(out_str, ", ")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (H5Tclose(mtid) < 0) H5_LIBRARY_ERROR(ENVONLY); mtid = H5I_INVALID_HID; } if (!h5str_append(out_str, H5_COMPOUND_END_INDICATOR)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; } case H5T_ENUM: { char enum_name[1024]; if (H5Tenum_nameof(tid, cptr, enum_name, sizeof enum_name) >= 0) { if (!h5str_append(out_str, enum_name)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } else { size_t i; if (NULL == (this_str = (char *) HDmalloc(4 * (typeSize + 1)))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (1 == typeSize) { if (HDsprintf(this_str, "%#02x", ucptr[0]) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } else { for (i = 0; i < typeSize; i++) if (HDsprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } } break; } case H5T_REFERENCE: { if (h5str_is_zero(cptr, typeSize)) { if (!h5str_append(out_str, "NULL")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; } if (H5Tequal(tid, H5T_STD_REF)) { H5O_type_t obj_type = -1; /* Object type */ H5R_type_t ref_type; /* Reference type */ const H5R_ref_t *ref_vp = (H5R_ref_t *)cptr; ref_type = H5Rget_type(ref_vp); H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type); switch (ref_type) { case H5R_OBJECT1: { /* Object references -- show the type and OID of the referenced object. */ H5O_info2_t oi; if((obj = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= 0) { H5Oget_info3(obj, &oi, H5O_INFO_BASIC); if(H5Oclose(obj) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } else CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (NULL == (this_str = (char *) HDmalloc(14))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%u-", (unsigned) oi.type) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); if (!h5str_append(out_str, this_str)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); HDfree(this_str); this_str = NULL; switch (obj_type) { case H5O_TYPE_GROUP: if (!h5str_append(out_str, H5_TOOLS_GROUP)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; case H5O_TYPE_DATASET: if (!h5str_append(out_str, H5_TOOLS_DATASET)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; case H5O_TYPE_NAMED_DATATYPE: if (!h5str_append(out_str, H5_TOOLS_DATATYPE)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; case H5O_TYPE_MAP: case H5O_TYPE_UNKNOWN: case H5O_TYPE_NTYPES: default: break; } /* end switch */ H5Oclose(obj); h5str_sprint_reference(ENVONLY, out_str, container, ref_vp); /* Print OID */ { char *token_str; H5Otoken_to_str(tid, &oi.token, &token_str); if (NULL == (this_str = (char *) HDmalloc(64 + strlen(token_str) + 1))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (HDsprintf(this_str, "%lu:%s", oi.fileno, token_str) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); H5free_memory(token_str); } } break; case H5R_DATASET_REGION1: if (!h5str_append(out_str, H5_TOOLS_DATASET)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr); break; case H5R_OBJECT2: switch (obj_type) { case H5O_TYPE_GROUP: if (!h5str_append(out_str, H5_TOOLS_GROUP)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; case H5O_TYPE_DATASET: if (!h5str_append(out_str, H5_TOOLS_DATASET)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; case H5O_TYPE_NAMED_DATATYPE: if (!h5str_append(out_str, H5_TOOLS_DATATYPE)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; case H5O_TYPE_MAP: case H5O_TYPE_UNKNOWN: case H5O_TYPE_NTYPES: default: break; } /* end switch */ h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr); break; case H5R_DATASET_REGION2: if (!h5str_append(out_str, H5_TOOLS_DATASET)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr); break; case H5R_ATTR: if (!h5str_append(out_str, H5_TOOLS_ATTRIBUTE)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); h5str_sprint_reference(ENVONLY, out_str, container, (void*)cptr); break; case H5R_BADTYPE: case H5R_MAXTYPE: default: break; } /* end switch */ } else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) { /* (H5R_DSET_REG_REF_BUF_SIZE == typeSize) */ H5_LIBRARY_ERROR(ENVONLY); } else if (H5Tequal(tid, H5T_STD_REF_OBJ)) { /* (H5R_OBJ_REF_BUF_SIZE == typeSize) */ H5_LIBRARY_ERROR(ENVONLY); } break; } case H5T_ARRAY: { hsize_t dims[H5S_MAX_RANK], i, total_elmts; size_t baseSize; int rank = 0; if (!h5str_append(out_str, H5_ARRAY_BEGIN_INDICATOR)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if ((mtid = H5Tget_super(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!(baseSize = H5Tget_size(mtid))) H5_LIBRARY_ERROR(ENVONLY); if ((rank = H5Tget_array_ndims(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (H5Tget_array_dims2(tid, dims) < 0) H5_LIBRARY_ERROR(ENVONLY); for (i = 0, total_elmts = 1; i < (hsize_t) rank; i++) total_elmts *= dims[i]; for (i = 0; i < total_elmts; i++) { if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &(cptr[i * baseSize]), in_buf_len, expand_data)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if ((i + 1) < total_elmts) if (!h5str_append(out_str, ", ")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } if (!h5str_append(out_str, H5_ARRAY_END_INDICATOR)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (H5Tclose(mtid) < 0) H5_LIBRARY_ERROR(ENVONLY); mtid = H5I_INVALID_HID; break; } case H5T_VLEN: { unsigned int i; size_t baseSize; hvl_t *vl_buf = (hvl_t *) in_buf; if ((mtid = H5Tget_super(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!(baseSize = H5Tget_size(mtid))) H5_LIBRARY_ERROR(ENVONLY); if (!h5str_append(out_str, H5_VLEN_BEGIN_INDICATOR)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); for (i = 0; i < (unsigned) vl_buf->len; i++) { if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &(((char *) vl_buf->p)[i * baseSize]), vl_buf->len, expand_data)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if ((i + 1) < (unsigned) vl_buf->len) if (!h5str_append(out_str, ", ")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } if (!h5str_append(out_str, H5_VLEN_END_INDICATOR)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (H5Tclose(mtid) < 0) H5_LIBRARY_ERROR(ENVONLY); mtid = H5I_INVALID_HID; break; } case H5T_NO_CLASS: case H5T_NCLASSES: { H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_sprintf: invalid datatype class"); break; } case H5T_TIME: case H5T_BITFIELD: case H5T_OPAQUE: default: { size_t i; /* All other types get printed as hexadecimal */ if (NULL == (this_str = (char *) HDmalloc(4 * (typeSize + 1)))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (1 == typeSize) { if (HDsprintf(this_str, "%#02x", ucptr[0]) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } else { for (i = 0; i < typeSize; i++) if (HDsprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); } break; } } if (this_str) { if (!h5str_append(out_str, this_str)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); HDfree(this_str); this_str = NULL; } /* end if */ retVal = HDstrlen(out_str->s); done: if (mtid >= 0) H5Tclose(mtid); return retVal; } /* end h5str_sprintf */ /*------------------------------------------------------------------------- * Purpose: Print the data values from a dataset referenced by region blocks. * * Description: * This is a special case subfunction to print the data in a region reference of type blocks. * * Return: * The function returns FAIL if there was an error, otherwise SUCEED *------------------------------------------------------------------------- */ static int h5str_print_region_data_blocks (JNIEnv *env, hid_t region_id, h5str_t *str, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata) { unsigned indx; hsize_t *dims1 = NULL; hsize_t *start = NULL; hsize_t *count = NULL; hsize_t blkndx; hsize_t total_size[H5S_MAX_RANK]; hsize_t numelem; hsize_t numindex; size_t jndx; size_t type_size; hid_t mem_space = H5I_INVALID_HID; hid_t sid1 = H5I_INVALID_HID; void *region_buf = NULL; int ret_value = FAIL; if (ndims < 0) H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_print_region_data_blocks: ndims < 0"); if (nblocks < 0) H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_print_region_data_blocks: nblocks < 0"); /* Get the dataspace of the dataset */ if ((sid1 = H5Dget_space(region_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); /* Allocate space for the dimension array */ if (NULL == (dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_print_region_data_blocks: failed to allocate dimension array buffer"); /* Find the dimensions of each data space from the block coordinates */ for (jndx = 0, numelem = 1; jndx < (size_t) ndims; jndx++) { dims1[jndx] = ptdata[jndx + (size_t)ndims] - ptdata[jndx] + 1; numelem = dims1[jndx] * numelem; } /* end for */ /* Create dataspace for reading buffer */ if ((mem_space = H5Screate_simple(ndims, dims1, NULL)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!(type_size = H5Tget_size(type_id))) H5_LIBRARY_ERROR(ENVONLY); if (NULL == (region_buf = HDmalloc(type_size * (size_t)numelem))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_print_region_data_blocks: failed to allocate region buffer"); /* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */ /* 1 2 n 1 2 n */ if (NULL == (start = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_print_region_data_blocks: failed to allocate hyperslab start buffer"); if (NULL == (count = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_print_region_data_blocks: failed to allocate hyperslab count buffer"); for (blkndx = 0; blkndx < (hsize_t) nblocks; blkndx++) { for (indx = 0; indx < (unsigned) ndims; indx++) { start[indx] = ptdata[indx + blkndx * (hsize_t)ndims * 2]; count[indx] = dims1[indx]; } /* end for */ if (H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) < 0) H5_LIBRARY_ERROR(ENVONLY); if (H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) < 0) H5_LIBRARY_ERROR(ENVONLY); if (H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0) H5_LIBRARY_ERROR(ENVONLY); for (numindex = 0; numindex < numelem; numindex++) { if (!h5str_sprintf(ENVONLY, str, region_id, type_id, ((char *)region_buf + numindex * type_size), 0, 1)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (numindex + 1 < numelem) if (!h5str_append(str, ", ")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } /* end for (jndx = 0; jndx < numelem; jndx++, region_elmtno++, ctx.cur_elmt++) */ } /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */ ret_value = SUCCEED; done: if (count) HDfree(count); if (start) HDfree(start); if (region_buf) HDfree(region_buf); if (mem_space >= 0) H5Sclose(mem_space); if (dims1) HDfree(dims1); if (sid1 >= 0) H5Sclose(sid1); return ret_value; } /* end h5str_print_region_data_blocks */ int h5str_dump_region_blocks_data (JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id) { hssize_t nblocks; hsize_t alloc_size; hsize_t *ptdata = NULL; hid_t dtype = H5I_INVALID_HID; hid_t type_id = H5I_INVALID_HID; int ndims = -1; int ret_value = FAIL; /* * This function fails if the region does not have blocks. */ H5E_BEGIN_TRY { nblocks = H5Sget_select_hyper_nblocks(region); } H5E_END_TRY; if (nblocks < 0) H5_LIBRARY_ERROR(ENVONLY); if ((ndims = H5Sget_simple_extent_ndims(region)) < 0) H5_LIBRARY_ERROR(ENVONLY); /* Print block information */ alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]); if (alloc_size == (hsize_t)((size_t) alloc_size)) { if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t) alloc_size))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_region_blocks_data: failed to allocate region block buffer"); if (H5Sget_select_hyper_blocklist(region, (hsize_t) 0, (hsize_t) nblocks, ptdata) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((dtype = H5Dget_type(region_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (h5str_print_region_data_blocks(ENVONLY, region_id, str, ndims, type_id, nblocks, ptdata) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */ ret_value = SUCCEED; done: if (type_id >= 0) H5Tclose(type_id); if (dtype >= 0) H5Tclose(dtype); if (ptdata) HDfree(ptdata); return ret_value; } /* end h5str_dump_region_blocks_data */ #ifndef SKIP_UNUSED_DUMP_ROUTINES static int h5str_dump_region_blocks (JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id) { hssize_t nblocks; hsize_t alloc_size; hsize_t *ptdata = NULL; char tmp_str[256]; int ndims = -1; int ret_value = FAIL; UNUSED(region_id); /* * This function fails if the region does not have blocks. */ H5E_BEGIN_TRY { nblocks = H5Sget_select_hyper_nblocks(region); } H5E_END_TRY; if (nblocks < 0) H5_LIBRARY_ERROR(ENVONLY); if ((ndims = H5Sget_simple_extent_ndims(region)) < 0) H5_LIBRARY_ERROR(ENVONLY); /* Print block information */ alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]); if (alloc_size == (hsize_t)((size_t) alloc_size)) { int i; if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t) alloc_size))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_region_blocks: failed to allocate region block buffer"); if (H5Sget_select_hyper_blocklist(region, (hsize_t) 0, (hsize_t) nblocks, ptdata) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!h5str_append(str, " {")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); for (i = 0; i < nblocks; i++) { int j; if (!h5str_append(str, " ")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); /* Start coordinates and opposite corner */ for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long) ptdata[i * 2 * ndims + j]) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure"); if (!h5str_append(str, tmp_str)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; if (HDsprintf(tmp_str, "%s%lu", j ? "," : ")-(", (unsigned long) ptdata[i * 2 * ndims + j + ndims]) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure"); if (!h5str_append(str, tmp_str)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } if (!h5str_append(str, ") ")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); tmp_str[0] = '\0'; } if (!h5str_append(str, " }")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */ ret_value = SUCCEED; done: if (ptdata) HDfree(ptdata); return ret_value; } /* end h5str_dump_region_blocks */ #endif /*------------------------------------------------------------------------- * Purpose: Print the data values from a dataset referenced by region points. * * Description: * This is a special case subfunction to print the data in a region reference of type points. * * Return: * The function returns FAIL on error, otherwise SUCCEED *------------------------------------------------------------------------- */ static int h5str_print_region_data_points (JNIEnv *env, hid_t region_space, hid_t region_id, h5str_t *str, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata) { hsize_t *dims1 = NULL; hsize_t total_size[H5S_MAX_RANK]; size_t jndx; size_t type_size; hid_t mem_space = H5I_INVALID_HID; void *region_buf = NULL; int ret_value = FAIL; UNUSED(ptdata); if (npoints < 0) H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_print_region_data_points: npoints < 0"); /* Allocate space for the dimension array */ if (NULL == (dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_print_region_data_points: failed to allocate dimension array buffer"); dims1[0] = (hsize_t)npoints; /* Create dataspace for reading buffer */ if ((mem_space = H5Screate_simple(1, dims1, NULL)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!(type_size = H5Tget_size(type_id))) H5_LIBRARY_ERROR(ENVONLY); if (NULL == (region_buf = HDmalloc(type_size * (size_t)npoints))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_print_region_data_points: failed to allocate region buffer"); if (H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0) H5_LIBRARY_ERROR(ENVONLY); for (jndx = 0; jndx < (size_t) npoints; jndx++) { if (H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!h5str_sprintf(ENVONLY, str, region_id, type_id, ((char *)region_buf + jndx * type_size), 0, 1)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (jndx + 1 < (size_t) npoints) if (!h5str_append(str, ", ")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } /* end for (jndx = 0; jndx < npoints; jndx++, elmtno++) */ ret_value = SUCCEED; done: if (region_buf) HDfree(region_buf); if (mem_space >= 0) H5Sclose(mem_space); if (dims1) HDfree(dims1); return ret_value; } /* end h5str_print_region_data_points */ int h5str_dump_region_points_data (JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id) { hssize_t npoints; hsize_t alloc_size; hsize_t *ptdata = NULL; hid_t dtype = H5I_INVALID_HID; hid_t type_id = H5I_INVALID_HID; int ndims = -1; int ret_value = FAIL; /* * This function fails if the region does not have points. */ H5E_BEGIN_TRY { npoints = H5Sget_select_elem_npoints(region); } H5E_END_TRY; if (npoints < 0) H5_LIBRARY_ERROR(ENVONLY); if ((ndims = H5Sget_simple_extent_ndims(region)) < 0) H5_LIBRARY_ERROR(ENVONLY); /* Print point information */ if (npoints > 0) { alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]); if (alloc_size == (hsize_t)((size_t) alloc_size)) { if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t) alloc_size))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_region_points_data: failed to allocate region point data buffer"); if (H5Sget_select_elem_pointlist(region, (hsize_t) 0, (hsize_t) npoints, ptdata) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((dtype = H5Dget_type(region_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (h5str_print_region_data_points(ENVONLY, region, region_id, str, ndims, type_id, npoints, ptdata) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } } ret_value = SUCCEED; done: if (type_id >= 0) H5Tclose(type_id); if (dtype >= 0) H5Tclose(dtype); if (ptdata) HDfree(ptdata); return ret_value; } /* end h5str_dump_region_points_data */ #ifndef SKIP_UNUSED_DUMP_ROUTINES static int h5str_dump_region_points (JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id) { hssize_t npoints; hsize_t alloc_size; hsize_t *ptdata = NULL; char tmp_str[256]; int ndims = -1; int ret_value = FAIL; UNUSED(region_id); /* * This function fails if the region does not have points. */ H5E_BEGIN_TRY { npoints = H5Sget_select_elem_npoints(region); } H5E_END_TRY; if (npoints < 0) H5_LIBRARY_ERROR(ENVONLY); if ((ndims = H5Sget_simple_extent_ndims(region)) < 0) H5_LIBRARY_ERROR(ENVONLY); /* Print point information */ if (npoints > 0) { int i; alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]); if (alloc_size == (hsize_t)((size_t) alloc_size)) { if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t) alloc_size))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_region_points: failed to allocate region point buffer"); if (H5Sget_select_elem_pointlist(region, (hsize_t) 0, (hsize_t) npoints, ptdata) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!h5str_append(str, " {")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); for (i = 0; i < npoints; i++) { int j; if (!h5str_append(str, " ")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long) (ptdata[i * ndims + j])) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: HDsprintf failure"); if (!h5str_append(str, tmp_str)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } /* end for (j = 0; j < ndims; j++) */ if (!h5str_append(str, ") ")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } /* end for (i = 0; i < npoints; i++) */ if (!h5str_append(str, " }")) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } /* end if (alloc_size == (hsize_t)((size_t) alloc_size)) */ } /* end if (npoints > 0) */ ret_value = SUCCEED; done: if (ptdata) HDfree(ptdata); return ret_value; } /* end h5str_dump_region_points */ #endif static int h5str_is_zero (const void *_mem, size_t size) { const unsigned char *mem = (const unsigned char *) _mem; while (size-- > 0) if (mem[size]) return 0; return 1; } /* end h5str_is_zero */ /*------------------------------------------------------------------------- * Function: h5str_detect_vlen * * Purpose: Recursive check for any variable length data in given type. * * Return: * 1 : type contains any variable length data * 0 : type doesn't contain any variable length data * Negative value: error occurred *------------------------------------------------------------------------- */ static htri_t h5str_detect_vlen (hid_t tid) { htri_t ret = FAIL; /* Recursively detect any vlen data values in type (compound, array ...) */ ret = H5Tdetect_class(tid, H5T_VLEN); if ((ret == 1) || (ret < 0)) goto done; /* Recursively detect any vlen string in type (compound, array ...) */ ret = h5str_detect_vlen_str(tid); if ((ret == 1) || (ret < 0)) goto done; done: return ret; } /* end h5str_detect_vlen */ /*------------------------------------------------------------------------- * Function: h5str_detect_vlen_str * * Purpose: Recursive check for variable length string of a datatype. * * Return: * TRUE : type conatains any variable length string * FALSE : type doesn't contain any variable length string * Negative value: error occur * *------------------------------------------------------------------------- */ static htri_t h5str_detect_vlen_str (hid_t tid) { H5T_class_t tclass = H5T_NO_CLASS; htri_t ret = 0; ret = H5Tis_variable_str(tid); if((ret == 1) || (ret < 0)) goto done; tclass = H5Tget_class(tid); if(tclass == H5T_ARRAY || tclass == H5T_VLEN) { hid_t btid = H5Tget_super(tid); if(btid < 0) { ret = (htri_t)btid; goto done; } /* end if */ ret = h5str_detect_vlen_str(btid); if((ret == 1) || (ret < 0)) { H5Tclose(btid); goto done; } /* end if */ } /* end if */ else if(tclass == H5T_COMPOUND) { unsigned i = 0; int n = H5Tget_nmembers(tid); if (n < 0) goto done; for(i = 0; i < (unsigned) n; i++) { hid_t mtid = H5Tget_member_type(tid, i); ret = h5str_detect_vlen_str(mtid); if((ret == 1) || (ret < 0)) { H5Tclose(mtid); goto done; } H5Tclose(mtid); } /* end for */ } /* end else */ done: return ret; } /* end h5str_detect_vlen_str */ /*------------------------------------------------------------------------- * Function: h5str_get_native_type * * Purpose: Wrapper around H5Tget_native_type() to work around * Problems with bitfields. * * Return: Success: datatype ID * Failure: FAIL *------------------------------------------------------------------------- */ static hid_t h5str_get_native_type (hid_t type) { H5T_class_t type_class; hid_t p_type = H5I_INVALID_HID; if ((type_class = H5Tget_class(type)) < 0) goto done; if (type_class == H5T_BITFIELD) p_type = H5Tcopy(type); else p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT); done: return(p_type); } /* end h5str_get_native_type */ /*------------------------------------------------------------------------- * Function: h5str_get_little_endian_type * * Purpose: Get a little endian type from a file type * * Return: Success: datatype ID * Failure: FAIL *------------------------------------------------------------------------- */ static hid_t h5str_get_little_endian_type (hid_t tid) { H5T_class_t type_class; H5T_sign_t sign; size_t size; hid_t p_type = H5I_INVALID_HID; if ((type_class = H5Tget_class(tid)) < 0) goto done; if (!(size = H5Tget_size(tid))) goto done; if ((sign = H5Tget_sign(tid)) < 0) goto done; switch ( type_class ) { case H5T_INTEGER: { if ( size == 1 && sign == H5T_SGN_2 ) p_type = H5Tcopy(H5T_STD_I8LE); else if ( size == 2 && sign == H5T_SGN_2 ) p_type = H5Tcopy(H5T_STD_I16LE); else if ( size == 4 && sign == H5T_SGN_2 ) p_type = H5Tcopy(H5T_STD_I32LE); else if ( size == 8 && sign == H5T_SGN_2 ) p_type = H5Tcopy(H5T_STD_I64LE); else if ( size == 1 && sign == H5T_SGN_NONE ) p_type = H5Tcopy(H5T_STD_U8LE); else if ( size == 2 && sign == H5T_SGN_NONE ) p_type = H5Tcopy(H5T_STD_U16LE); else if ( size == 4 && sign == H5T_SGN_NONE ) p_type = H5Tcopy(H5T_STD_U32LE); else if ( size == 8 && sign == H5T_SGN_NONE ) p_type = H5Tcopy(H5T_STD_U64LE); break; } case H5T_FLOAT: { if ( size == 4 ) p_type = H5Tcopy(H5T_IEEE_F32LE); else if ( size == 8 ) p_type = H5Tcopy(H5T_IEEE_F64LE); break; } case H5T_BITFIELD: { if ( size == 1 ) p_type = H5Tcopy(H5T_STD_B8LE); else if ( size == 2 ) p_type = H5Tcopy(H5T_STD_B16LE); else if ( size == 4 ) p_type = H5Tcopy(H5T_STD_B32LE); else if ( size == 8 ) p_type = H5Tcopy(H5T_STD_B64LE); break; } case H5T_NO_CLASS: case H5T_NCLASSES: { goto done; break; } case H5T_TIME: case H5T_OPAQUE: case H5T_STRING: case H5T_COMPOUND: case H5T_REFERENCE: case H5T_ENUM: case H5T_VLEN: case H5T_ARRAY: break; default: break; } done: return(p_type); } /* end h5str_get_little_endian_type */ /*------------------------------------------------------------------------- * Function: h5str_get_big_endian_type * * Purpose: Get a big endian type from a file type * * Return: Success: datatype ID * Failure: FAIL *------------------------------------------------------------------------- */ static hid_t h5str_get_big_endian_type (hid_t tid) { H5T_class_t type_class; H5T_sign_t sign; size_t size; hid_t p_type = H5I_INVALID_HID; if ((type_class = H5Tget_class(tid)) < 0) goto done; if (!(size = H5Tget_size(tid))) goto done; if ((sign = H5Tget_sign(tid)) < 0) goto done; switch ( type_class ) { case H5T_INTEGER: { if ( size == 1 && sign == H5T_SGN_2 ) p_type = H5Tcopy(H5T_STD_I8BE); else if ( size == 2 && sign == H5T_SGN_2 ) p_type = H5Tcopy(H5T_STD_I16BE); else if ( size == 4 && sign == H5T_SGN_2 ) p_type = H5Tcopy(H5T_STD_I32BE); else if ( size == 8 && sign == H5T_SGN_2 ) p_type = H5Tcopy(H5T_STD_I64BE); else if ( size == 1 && sign == H5T_SGN_NONE ) p_type = H5Tcopy(H5T_STD_U8BE); else if ( size == 2 && sign == H5T_SGN_NONE ) p_type = H5Tcopy(H5T_STD_U16BE); else if ( size == 4 && sign == H5T_SGN_NONE ) p_type = H5Tcopy(H5T_STD_U32BE); else if ( size == 8 && sign == H5T_SGN_NONE ) p_type = H5Tcopy(H5T_STD_U64BE); break; } case H5T_FLOAT: { if ( size == 4 ) p_type = H5Tcopy(H5T_IEEE_F32BE); else if ( size == 8 ) p_type = H5Tcopy(H5T_IEEE_F64BE); break; } case H5T_BITFIELD: { if ( size == 1 ) p_type = H5Tcopy(H5T_STD_B8BE); else if ( size == 2 ) p_type = H5Tcopy(H5T_STD_B16BE); else if ( size == 4 ) p_type = H5Tcopy(H5T_STD_B32BE); else if ( size == 8 ) p_type = H5Tcopy(H5T_STD_B64BE); break; } case H5T_NO_CLASS: case H5T_NCLASSES: { goto done; break; } case H5T_TIME: case H5T_OPAQUE: case H5T_STRING: case H5T_COMPOUND: case H5T_REFERENCE: case H5T_ENUM: case H5T_VLEN: case H5T_ARRAY: break; default: break; } done: return(p_type); } /* end h5str_get_big_endian_type */ /*------------------------------------------------------------------------- * Function: render_bin_output * * Purpose: Write one element of memory buffer to a binary file stream * * Return: Success: SUCCEED * Failure: FAIL *------------------------------------------------------------------------- */ static int h5str_render_bin_output (FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t block_nelmts) { unsigned char *mem = (unsigned char*)_mem; H5T_class_t type_class; hsize_t block_index; size_t size; /* datum size */ int ret_value = 0; if (!(size = H5Tget_size(tid))) { ret_value = FAIL; goto done; } if ((type_class = H5Tget_class(tid)) < 0) { ret_value = FAIL; goto done; } switch (type_class) { case H5T_INTEGER: case H5T_FLOAT: case H5T_ENUM: { block_index = block_nelmts * size; while (block_index > 0) { size_t bytes_in = 0; /* # of bytes to write */ size_t bytes_wrote = 0; /* # of bytes written */ if (block_index > sizeof(size_t)) bytes_in = sizeof(size_t); else bytes_in = (size_t)block_index; bytes_wrote = fwrite(mem, 1, bytes_in, stream); if (bytes_wrote != bytes_in || (0 == bytes_wrote && ferror(stream))) { ret_value = FAIL; break; } block_index -= (hsize_t)bytes_wrote; mem = mem + bytes_wrote; } break; } case H5T_STRING: { unsigned char tempuchar; unsigned int i; H5T_str_t pad; char *s; if ((pad = H5Tget_strpad(tid)) < 0) { ret_value = FAIL; goto done; } for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char *)_mem) + block_index * size; if (H5Tis_variable_str(tid)) { s = *(char**) mem; if (s != NULL) size = HDstrlen(s); } else { s = (char *) mem; } for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) { HDmemcpy(&tempuchar, &s[i], sizeof(unsigned char)); if (1 != fwrite(&tempuchar, sizeof(unsigned char), 1, stream)) { ret_value = FAIL; break; } } /* i */ if (ret_value < 0) break; } /* for (block_index = 0; block_index < block_nelmts; block_index++) */ break; } case H5T_COMPOUND: { unsigned j; size_t offset; hid_t memb = H5I_INVALID_HID; int nmembs; if ((nmembs = H5Tget_nmembers(tid)) < 0) { ret_value = FAIL; goto done; } for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; for (j = 0; j < (unsigned) nmembs; j++) { offset = H5Tget_member_offset(tid, j); memb = H5Tget_member_type(tid, j); if (h5str_render_bin_output(stream, container, memb, mem + offset, 1) < 0) { H5Tclose(memb); ret_value = FAIL; break; } H5Tclose(memb); } if (ret_value < 0) break; } break; } case H5T_ARRAY: { hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts; hid_t memb; int k, ndims; /* Get the array's base datatype for each element */ if ((memb = H5Tget_super(tid)) < 0) { ret_value = FAIL; goto done; } if ((ndims = H5Tget_array_ndims(tid)) < 0) { ret_value = FAIL; goto done; } if (H5Tget_array_dims2(tid, dims) < 0) { ret_value = FAIL; goto done; } /* Calculate the number of array elements */ for (k = 0, nelmts = 1; k < ndims; k++) { temp_nelmts = nelmts; temp_nelmts *= dims[k]; nelmts = (size_t) temp_nelmts; } for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; /* dump the array element */ if (h5str_render_bin_output(stream, container, memb, mem, nelmts) < 0) { ret_value = FAIL; break; } } H5Tclose(memb); break; } case H5T_VLEN: { hsize_t nelmts; hid_t memb; /* Get the VL sequences's base datatype for each element */ if ((memb = H5Tget_super(tid)) < 0) { ret_value = FAIL; goto done; } for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; /* Get the number of sequence elements */ nelmts = ((hvl_t *) mem)->len; /* dump the array element */ if (h5str_render_bin_output(stream, container, memb, ((char *) (((hvl_t *) mem)->p)), nelmts) < 0) { ret_value = FAIL; break; } } H5Tclose(memb); break; } case H5T_REFERENCE: { if (H5Tequal(tid, H5T_STD_REF)) { hid_t region_id = H5I_INVALID_HID; hid_t region_space = H5I_INVALID_HID; H5S_sel_type region_type; /* Region data */ for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; if((region_id = H5Ropen_object((const H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) < 0) continue; else { if((region_space = H5Ropen_region((const H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) >= 0) { if (!h5str_is_zero(mem, H5Tget_size(H5T_STD_REF))) { region_type = H5Sget_select_type(region_space); if (region_type == H5S_SEL_POINTS) ret_value = render_bin_output_region_points(stream, region_space, region_id, container); else ret_value = render_bin_output_region_blocks(stream, region_space, region_id, container); } H5Sclose(region_space); } /* end if (region_space >= 0) */ H5Dclose(region_id); } if ((region_type = H5Sget_select_type(region_space)) < 0) { H5Sclose(region_space); H5Dclose(region_id); continue; } if (ret_value < 0) break; } } else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) { ; } else if (H5Tequal(tid, H5T_STD_REF_OBJ)) { ; } break; } case H5T_NO_CLASS: case H5T_NCLASSES: { ret_value = FAIL; goto done; break; } case H5T_TIME: case H5T_BITFIELD: case H5T_OPAQUE: default: for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; if (size != fwrite(mem, sizeof(char), size, stream)) { ret_value = FAIL; break; } } break; } done: return ret_value; } /* end h5str_render_bin_output */ /*------------------------------------------------------------------------- * Purpose: Print the data values from a dataset referenced by region blocks. * * Description: * This is a special case subfunction to print the data in a region reference of type blocks. * * Return: * The function returns FAIL if there was an error, otherwise SUCEED * *------------------------------------------------------------------------- */ static int render_bin_output_region_data_blocks (FILE *stream, hid_t region_id, hid_t container, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata) { hsize_t *dims1 = NULL; hsize_t *start = NULL; hsize_t *count = NULL; hsize_t numelem; hsize_t total_size[H5S_MAX_RANK]; size_t type_size; hid_t sid1 = H5I_INVALID_HID; hid_t mem_space = H5I_INVALID_HID; void *region_buf = NULL; int blkndx; int jndx; int ret_value = SUCCEED; /* Get the dataspace of the dataset */ if ((sid1 = H5Dget_space(region_id)) < 0) { ret_value = FAIL; goto done; } /* Allocate space for the dimension array */ if (NULL == (dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) { ret_value = FAIL; goto done; } /* Find the dimensions of each data space from the block coordinates */ for (jndx = 0, numelem = 1; jndx < ndims; jndx++) { dims1[jndx] = ptdata[jndx + ndims] - ptdata[jndx] + 1; numelem = dims1[jndx] * numelem; } /* Create dataspace for reading buffer */ if ((mem_space = H5Screate_simple(ndims, dims1, NULL)) < 0) { ret_value = FAIL; goto done; } if (!(type_size = H5Tget_size(type_id))) { ret_value = FAIL; goto done; } if (NULL == (region_buf = HDmalloc(type_size * (size_t)numelem))) { ret_value = FAIL; goto done; } /* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */ /* 1 2 n 1 2 n */ if (NULL == (start = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) { ret_value = FAIL; goto done; } if (NULL == (count = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) { ret_value = FAIL; goto done; } for (blkndx = 0; blkndx < nblocks; blkndx++) { for (jndx = 0; jndx < ndims; jndx++) { start[jndx] = ptdata[jndx + blkndx * ndims * 2]; count[jndx] = dims1[jndx]; } if (H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) < 0) { ret_value = FAIL; goto done; } if (H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) < 0) { ret_value = FAIL; goto done; } if (H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0) { ret_value = FAIL; goto done; } if (h5str_render_bin_output(stream, container, type_id, (char *)region_buf, numelem) < 0) { ret_value = FAIL; goto done; } /* Render the region data element end */ } /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */ done: if (count) HDfree(count); if (start) HDfree(start); if (region_buf) HDfree(region_buf); if (mem_space >= 0) H5Sclose(mem_space); if (dims1) HDfree(dims1); if (sid1 >= 0) H5Sclose(sid1); return ret_value; } /* end render_bin_output_region_data_blocks */ /*------------------------------------------------------------------------- * Purpose: Print some values from a dataset referenced by region blocks. * * Description: * This is a special case subfunction to dump a region reference using blocks. * * Return: * The function returns False if ERROR, otherwise True * *------------------------------------------------------------------------- */ static int render_bin_output_region_blocks (FILE *stream, hid_t region_space, hid_t region_id, hid_t container) { hssize_t nblocks; hsize_t alloc_size; hsize_t *ptdata = NULL; hid_t dtype = H5I_INVALID_HID; hid_t type_id = H5I_INVALID_HID; int ndims; int ret_value = SUCCEED; if ((nblocks = H5Sget_select_hyper_nblocks(region_space)) < 0) { ret_value = FAIL; goto done; } if (nblocks > 0) { /* Print block information */ if ((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) { ret_value = FAIL; goto done; } alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]); if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t)alloc_size))) { ret_value = FAIL; goto done; } if (H5Sget_select_hyper_blocklist(region_space, (hsize_t)0, (hsize_t)nblocks, ptdata) < 0) { ret_value = FAIL; goto done; } if ((dtype = H5Dget_type(region_id)) < 0) { ret_value = FAIL; goto done; } if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) { ret_value = FAIL; goto done; } if (render_bin_output_region_data_blocks(stream, region_id, container, ndims, type_id, nblocks, ptdata) < 0) { ret_value = FAIL; goto done; } } done: if (type_id >= 0) H5Tclose(type_id); if (dtype >= 0) H5Tclose(dtype); if (ptdata) HDfree(ptdata); return ret_value; } /* end render_bin_output_region_blocks */ /*------------------------------------------------------------------------- * Purpose: Print the data values from a dataset referenced by region points. * * Description: * This is a special case subfunction to print the data in a region reference of type points. * * Return: * The function returns FAIL on error, otherwise SUCCEED * *------------------------------------------------------------------------- */ static int render_bin_output_region_data_points (FILE *stream, hid_t region_space, hid_t region_id, hid_t container, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata) { hsize_t *dims1 = NULL; size_t type_size; hid_t mem_space = H5I_INVALID_HID; void *region_buf = NULL; int ret_value = SUCCEED; UNUSED(ptdata); if (!(type_size = H5Tget_size(type_id))) { ret_value = FAIL; goto done; } if (NULL == (region_buf = HDmalloc(type_size * (size_t)npoints))) { ret_value = FAIL; goto done; } /* Allocate space for the dimension array */ if (NULL == (dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims))) { ret_value = FAIL; goto done; } dims1[0] = (hsize_t)npoints; if ((mem_space = H5Screate_simple(1, dims1, NULL)) < 0) { ret_value = FAIL; goto done; } if (H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0) { ret_value = FAIL; goto done; } if (H5Sget_simple_extent_dims(region_space, dims1, NULL) < 0) { ret_value = FAIL; goto done; } if (h5str_render_bin_output(stream, container, type_id, (char *)region_buf, (hsize_t)npoints) < 0) { ret_value = FAIL; goto done; } done: if (dims1) HDfree(dims1); if (mem_space >= 0) H5Sclose(mem_space); if (region_buf) HDfree(region_buf); return ret_value; } /* end render_bin_output_region_data_points */ /*------------------------------------------------------------------------- * Purpose: Print some values from a dataset referenced by region points. * * Description: * This is a special case subfunction to dump a region reference using points. * * Return: * The function returns False if the last dimension has been reached, otherwise True * *------------------------------------------------------------------------- */ static int render_bin_output_region_points (FILE *stream, hid_t region_space, hid_t region_id, hid_t container) { hssize_t npoints; hsize_t alloc_size; hsize_t *ptdata = NULL; hid_t dtype = H5I_INVALID_HID; hid_t type_id = H5I_INVALID_HID; int ndims; int ret_value = SUCCEED; if ((npoints = H5Sget_select_elem_npoints(region_space)) < 0) { ret_value = FAIL; goto done; } if (npoints > 0) { /* Allocate space for the dimension array */ if ((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) { ret_value = FAIL; goto done; } alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]); if (NULL == (ptdata = (hsize_t *) HDmalloc((size_t)alloc_size))) { ret_value = FAIL; goto done; } if (H5Sget_select_elem_pointlist(region_space, (hsize_t)0, (hsize_t)npoints, ptdata) < 0) { ret_value = FAIL; goto done; } if ((dtype = H5Dget_type(region_id)) < 0) { ret_value = FAIL; goto done; } if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) { ret_value = FAIL; goto done; } if (render_bin_output_region_data_points(stream, region_space, region_id, container, ndims, type_id, npoints, ptdata) < 0) { ret_value = FAIL; goto done; } } done: if (type_id >= 0) H5Tclose(type_id); if (dtype >= 0) H5Tclose(dtype); if (ptdata) HDfree(ptdata); return ret_value; } /* end render_bin_output_region_points */ int h5str_dump_simple_dset (JNIEnv *env, FILE *stream, hid_t dset, int binary_order) { hsize_t elmtno; /* counter */ hsize_t zero[8]; /* vector of zeros */ hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/ size_t i; /* counter */ hid_t f_space = H5I_INVALID_HID; /* file data space */ int ndims; int carry; /* counter carry value */ /* Print info */ hsize_t p_nelmts; /* total selected elmts */ size_t p_type_nbytes; /* size of memory type */ /* Stripmine info */ unsigned char *sm_buf = NULL; /* buffer for raw data */ hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */ hsize_t sm_nbytes; /* bytes per stripmine */ hsize_t sm_nelmts; /* elements per stripmine */ hid_t sm_space = H5I_INVALID_HID; /* stripmine data space */ /* Hyperslab info */ hsize_t hs_offset[H5S_MAX_RANK]; /* starting offset */ hsize_t hs_size[H5S_MAX_RANK]; /* size this pass */ hsize_t hs_nelmts; /* elements in request */ /* VL data special information */ unsigned int vl_data = 0; /* contains VL datatypes */ hid_t p_type = H5I_INVALID_HID; hid_t f_type = H5I_INVALID_HID; int ret_value = FAIL; if (dset < 0) H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_dump_simple_dset: dset ID < 0"); if ((f_type = H5Dget_type(dset)) < 0) H5_LIBRARY_ERROR(ENVONLY); switch (binary_order) { case 1: { if ((p_type = h5str_get_native_type(f_type)) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; } case 2: { if ((p_type = h5str_get_little_endian_type(f_type)) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; } case 3: { if ((p_type = h5str_get_big_endian_type(f_type)) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); break; } default: { if ((p_type = H5Tcopy(f_type)) < 0) H5_LIBRARY_ERROR(ENVONLY); break; } } if ((f_space = H5Dget_space(dset)) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) { if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0) H5_LIBRARY_ERROR(ENVONLY); /* Calculate the number of elements we're going to print */ p_nelmts = 1; if (ndims > 0) { for (i = 0; i < (size_t) ndims; i++) p_nelmts *= total_size[i]; } /* end if */ if (p_nelmts > 0) { /* Check if we have VL data in the dataset's datatype */ if (h5str_detect_vlen(p_type) != 0) vl_data = 1; /* * Determine the strip mine size and allocate a buffer. The strip mine is * a hyperslab whose size is manageable. */ if (!(sm_nbytes = p_type_nbytes = H5Tget_size(p_type))) H5_LIBRARY_ERROR(ENVONLY); if (ndims > 0) { for (i = (size_t)ndims; i > 0; --i) { hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes; if ( size == 0 ) /* datum size > H5TOOLS_BUFSIZE */ size = 1; sm_size[i - 1] = (((total_size[i - 1]) < (size)) ? (total_size[i - 1]) : (size)); sm_nbytes *= sm_size[i - 1]; } } if (sm_nbytes > 0) { if (NULL == (sm_buf = (unsigned char *) HDmalloc((size_t)sm_nbytes))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_dset: failed to allocate sm_buf"); sm_nelmts = sm_nbytes / p_type_nbytes; if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0) H5_LIBRARY_ERROR(ENVONLY); /* The stripmine loop */ HDmemset(hs_offset, 0, sizeof hs_offset); HDmemset(zero, 0, sizeof zero); for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) { /* Calculate the hyperslab size */ if (ndims > 0) { for (i = 0, hs_nelmts = 1; i < (size_t) ndims; i++) { hs_size[i] = (((total_size[i] - hs_offset[i]) < (sm_size[i])) ? (total_size[i] - hs_offset[i]) : (sm_size[i])); hs_nelmts *= hs_size[i]; } if (H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0) H5_LIBRARY_ERROR(ENVONLY); if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0) H5_LIBRARY_ERROR(ENVONLY); } else { if (H5Sselect_all(f_space) < 0) H5_LIBRARY_ERROR(ENVONLY); if (H5Sselect_all(sm_space) < 0) H5_LIBRARY_ERROR(ENVONLY); hs_nelmts = 1; } /* Read the data */ if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) H5_LIBRARY_ERROR(ENVONLY); if (binary_order == 99) { if (h5tools_dump_simple_data(ENVONLY, stream, dset, p_type, sm_buf, hs_nelmts) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } else { if (h5str_render_bin_output(stream, dset, p_type, sm_buf, hs_nelmts) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } /* Reclaim any VL memory, if necessary */ if (vl_data) { if (H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0) H5_LIBRARY_ERROR(ENVONLY); } /* Calculate the next hyperslab offset */ for (i = (size_t)ndims, carry = 1; i > 0 && carry; --i) { hs_offset[i - 1] += hs_size[i - 1]; if (hs_offset[i - 1] == total_size[i - 1]) hs_offset[i - 1] = 0; else carry = 0; } } } } } ret_value = SUCCEED; done: if (sm_space >= 0) H5Sclose(sm_space); if (sm_buf) HDfree(sm_buf); if (f_space >= 0) H5Sclose(f_space); if (p_type >= 0) H5Tclose(p_type); if (f_type >= 0) H5Tclose(f_type); return ret_value; } /* end h5str_dump_simple_dset */ htri_t H5Tdetect_variable_str(hid_t tid) { htri_t ret_val = 0; if (H5Tget_class(tid) == H5T_COMPOUND) { unsigned i; unsigned nm = (unsigned)H5Tget_nmembers(tid); for(i = 0; i < nm; i++) { htri_t status = 0; hid_t mtid = 0; if((mtid = H5Tget_member_type(tid, i)) < 0) return FAIL; /* exit immediately on error */ if((status = H5Tdetect_variable_str(mtid)) < 0) return status; /* exit immediately on error */ ret_val |= status; H5Tclose (mtid); } /* end for */ } /* end if */ else ret_val = H5Tis_variable_str(tid); return ret_val; } /* end H5Tdetect_variable_str */ static int h5tools_dump_simple_data (JNIEnv *env, FILE *stream, hid_t container, hid_t type, void *_mem, hsize_t nelmts) { unsigned char *mem = (unsigned char *)_mem; h5str_t buffer; /* string into which to render */ hsize_t i; /* element counter */ size_t size; /* datum size */ int line_count; int ret_value = 0; if (!(size = H5Tget_size(type))) H5_LIBRARY_ERROR(ENVONLY); for (i = 0, line_count = 0; i < nelmts; i++, line_count++) { size_t bytes_in = 0; /* # of bytes to write */ void *memref = mem + i * size; /* Render the data element*/ h5str_new(&buffer, 32 * size); if (!buffer.s) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5tools_dump_simple_data: failed to allocate buffer"); if (!(bytes_in = h5str_sprintf(ENVONLY, &buffer, container, type, memref, 0, 1))) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (i > 0) { if (HDfprintf(stream, ", ") < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure"); if (line_count >= H5TOOLS_TEXT_BLOCK) { line_count = 0; if (HDfprintf(stream, "\n") < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure"); } } if (HDfprintf(stream, "%s", buffer.s) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure"); h5str_free(&buffer); } /* end for (i = 0; i < nelmts... */ if (HDfprintf(stream, "\n") < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure"); done: if (buffer.s) h5str_free(&buffer); return ret_value; } /* end h5tools_dump_simple_data */ /* * Utility Java APIs * Functions designed to workaround issues with the Java-C interface */ /* * Class: hdf_hdf5lib_H5 * Method: H5AreadComplex * Signature: (JJ[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5AreadComplex (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf) { h5str_t h5str; jstring jstr; size_t size; size_t i; hid_t p_type = H5I_INVALID_HID; jsize n; char *readBuf = NULL; herr_t status = FAIL; UNUSED(clss); HDmemset(&h5str, 0, sizeof(h5str_t)); if ((p_type = H5Tget_native_type(mem_type_id, H5T_DIR_DEFAULT)) < 0) H5_LIBRARY_ERROR(ENVONLY); size = (((H5Tget_size(mem_type_id))>(H5Tget_size(p_type))) ? (H5Tget_size(mem_type_id)) : (H5Tget_size(p_type))); if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) <= 0) { CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadComplex: read buffer length <= 0"); } if (NULL == (readBuf = (char *) HDmalloc((size_t)n * size))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AreadComplex: failed to allocate read buffer"); if ((status = H5Aread(attr_id, mem_type_id, readBuf)) < 0) H5_LIBRARY_ERROR(ENVONLY); h5str_new(&h5str, 4 * size); if (!h5str.s) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AreadComplex: failed to allocate string buffer"); for (i = 0; i < (size_t) n; i++) { h5str.s[0] = '\0'; if (!h5str_sprintf(ENVONLY, &h5str, attr_id, mem_type_id, readBuf + (i * size), 0, 0)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s))) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); ENVPTR->SetObjectArrayElement(ENVONLY, buf, (jsize) i, jstr); CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); ENVPTR->DeleteLocalRef(ENVONLY, jstr); } /* end for */ done: if (h5str.s) h5str_free(&h5str); if (readBuf) HDfree(readBuf); if (p_type >= 0) H5Tclose(p_type); return status; } /* * Copies the content of one attribute to another attribute * Class: hdf_hdf5lib_H5 * Method: H5Acopy * Signature: (JJ)I */ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Acopy (JNIEnv *env, jclass clss, jlong src_id, jlong dst_id) { hssize_t npoints; hsize_t total_size = 0; size_t type_size; jbyte *buf = NULL; hid_t tid = H5I_INVALID_HID; hid_t sid = H5I_INVALID_HID; herr_t retVal = FAIL; UNUSED(clss); if ((sid = H5Aget_space((hid_t)src_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((tid = H5Aget_type((hid_t)src_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((npoints = H5Sget_simple_extent_npoints(sid)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!(type_size = H5Tget_size(tid))) H5_LIBRARY_ERROR(ENVONLY); total_size = (hsize_t)npoints * (hsize_t)type_size; if (NULL == (buf = (jbyte *) HDmalloc((size_t)total_size * sizeof(jbyte)))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Acopy: failed to allocate buffer"); if ((retVal = H5Aread((hid_t)src_id, tid, buf)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (H5Tclose(tid) < 0) H5_LIBRARY_ERROR(ENVONLY); tid = H5I_INVALID_HID; if ((tid = H5Aget_type((hid_t)dst_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((retVal = H5Awrite((hid_t)dst_id, tid, buf)) < 0) H5_LIBRARY_ERROR(ENVONLY); done: if (buf) HDfree(buf); if (tid >= 0) H5Tclose(tid); if (sid >= 0) H5Sclose(sid); return (jint)retVal; } /* end Java_hdf_hdf5lib_H5_H5Acopy */ /* * Copies the content of one dataset to another dataset * Class: hdf_hdf5lib_H5 * Method: H5Dcopy * Signature: (JJ)I */ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Dcopy (JNIEnv *env, jclass clss, jlong src_id, jlong dst_id) { hssize_t npoints; hsize_t total_size = 0, total_allocated_size; size_t type_size; jbyte *buf = NULL; hid_t tid = H5I_INVALID_HID; hid_t sid = H5I_INVALID_HID; herr_t retVal = FAIL; UNUSED(clss); if (!(total_allocated_size = H5Dget_storage_size((hid_t)src_id))) return 0; /* nothing to write */ if ((sid = H5Dget_space((hid_t)src_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((tid = H5Dget_type((hid_t)src_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((npoints = H5Sget_simple_extent_npoints(sid)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (!(type_size = H5Tget_size(tid))) H5_LIBRARY_ERROR(ENVONLY); total_size = (hsize_t)npoints * (hsize_t)type_size; if (NULL == (buf = (jbyte *) HDmalloc((size_t)total_size * sizeof(jbyte)))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dcopy: failed to allocate buffer"); if ((retVal = H5Dread((hid_t)src_id, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf)) < 0) H5_LIBRARY_ERROR(ENVONLY); if (H5Tclose(tid) < 0) H5_LIBRARY_ERROR(ENVONLY); tid = H5I_INVALID_HID; if ((tid = H5Dget_type((hid_t)dst_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); if ((retVal = H5Dwrite((hid_t)dst_id, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf)) < 0) H5_LIBRARY_ERROR(ENVONLY); done: if (buf) HDfree(buf); if (tid >= 0) H5Tclose(tid); if (sid >= 0) H5Sclose(sid); return (jint)retVal; } /* end Java_hdf_hdf5lib_H5_H5Dcopy */ /* * ///////////////////////////////////////////////////////////////////////////////// * // * // * // Add these methods so that we don't need to call H5Gget_objtype_by_idx * // in a loop to get information for all the objects in a group, which takes * // a lot of time to finish if the number of objects is more than 10,000 * // * ///////////////////////////////////////////////////////////////////////////////// */ #ifdef __cplusplus herr_t obj_info_all(hid_t g_id, const char *name, const H5L_info2_t *linfo, void *op_data); herr_t obj_info_max(hid_t g_id, const char *name, const H5L_info2_t *linfo, void *op_data); int H5Gget_obj_info_max(hid_t, char **, int *, int *, H5O_token_t *, long); int H5Gget_obj_info_full( hid_t loc_id, char **objname, int *otype, int *ltype, unsigned long *fno, H5O_token_t *obj_token, int indexType, int indexOrder); #else static herr_t obj_info_all(hid_t g_id, const char *name, const H5L_info2_t *linfo, void *op_data); static herr_t obj_info_max(hid_t g_id, const char *name, const H5L_info2_t *linfo, void *op_data); static int H5Gget_obj_info_max(hid_t, char **, int *, int *, H5O_token_t *, long); static int H5Gget_obj_info_full( hid_t loc_id, char **objname, int *otype, int *ltype, unsigned long *fno, H5O_token_t *obj_token, int indexType, int indexOrder); #endif typedef struct info_all { char **objname; int *otype; int *ltype; H5O_token_t *obj_token; unsigned long *fno; unsigned long idxnum; int count; } info_all_t; /* * Class: hdf_hdf5lib_H5 * Method: H5Gget_obj_info_full * Signature: (JLjava/lang/String;[Ljava/lang/String;[I[I[J[JIII)I */ /* * NOTE: This is a dangerous call! The caller can supply any value they'd like * for 'n' and if it exceeds the number of links in the group, we will most likely * end up overwriting memory heap-tracking info. */ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1full (JNIEnv *env, jclass clss, jlong loc_id, jstring group_name, jobjectArray objName, jintArray oType, jintArray lType, jlongArray fNo, jobjectArray oToken, jint n, jint indx_type, jint indx_order) { unsigned long *fnos = NULL; H5O_token_t *tokens = NULL; const char *gName = NULL; char **oName = NULL; jboolean isCopy; jstring str; jobject token; jint *otarr = NULL; jint *ltarr = NULL; jlong *fnoP = NULL; hid_t gid = (hid_t)loc_id; int i; int indexType = indx_type; int indexOrder = indx_order; herr_t ret_val = FAIL; UNUSED(clss); if (NULL == oType) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_full: oType is NULL"); if (NULL == lType) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_full: lType is NULL"); if (NULL == oToken) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_full: oToken is NULL"); if (NULL == fNo) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_full: fNo is NULL"); PIN_INT_ARRAY(ENVONLY, oType, otarr, &isCopy, "H5Gget_obj_info_full: oType not pinned"); PIN_INT_ARRAY(ENVONLY, lType, ltarr, &isCopy, "H5Gget_obj_info_full: lType not pinned"); PIN_LONG_ARRAY(ENVONLY, fNo, fnoP, &isCopy, "H5Gget_obj_info_full: fNo not pinned"); if (NULL == (oName = (char **) HDcalloc((size_t)n, sizeof(*oName)))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Gget_obj_info_full: failed to allocate buffer for object name"); if (NULL == (tokens = (H5O_token_t *) HDcalloc((size_t)n, sizeof(H5O_token_t)))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Gget_obj_info_full: failed to allocate buffer for object tokens"); if (NULL == (fnos = (unsigned long *) HDcalloc((size_t)n, sizeof(unsigned long)))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Gget_obj_info_full: failed to allocate buffer for file number info"); if (group_name) { PIN_JAVA_STRING(ENVONLY, group_name, gName, &isCopy, "H5Gget_obj_info_full: group_name not pinned"); if ((gid = H5Gopen2((hid_t)loc_id, gName, H5P_DEFAULT)) < 0) H5_LIBRARY_ERROR(ENVONLY); } if ((ret_val = H5Gget_obj_info_full(gid, oName, (int *)otarr, (int *)ltarr, fnos, tokens, indexType, indexOrder)) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_obj_info_full: retrieval of object info failed"); for (i = 0; i < n; i++) { fnoP[i] = (jlong)fnos[i]; if (oName[i]) { if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, oName[i]))) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); ENVPTR->SetObjectArrayElement(ENVONLY, objName, i, (jobject)str); CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); ENVPTR->DeleteLocalRef(ENVONLY, str); } /* end if */ /* Create an H5O_token_t object */ if (NULL == (token = create_H5O_token_t(ENVONLY, &tokens[i], TRUE))) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); ENVPTR->SetObjectArrayElement(ENVONLY, oToken, i, token); CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); ENVPTR->DeleteLocalRef(ENVONLY, token); } done: if (gName) { H5Gclose(gid); UNPIN_JAVA_STRING(ENVONLY, group_name, gName); } if (fnos) HDfree(fnos); if (tokens) HDfree(tokens); if (oName) h5str_array_free(oName, (size_t)n); if (fnoP) UNPIN_LONG_ARRAY(ENVONLY, fNo, fnoP, (ret_val < 0) ? JNI_ABORT : 0); if (ltarr) UNPIN_INT_ARRAY(ENVONLY, lType, ltarr, (ret_val < 0) ? JNI_ABORT : 0); if (otarr) UNPIN_INT_ARRAY(ENVONLY, oType, otarr, (ret_val < 0) ? JNI_ABORT : 0); return ret_val; } /* end Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1full */ /* * Class: hdf_hdf5lib_H5 * Method: H5Gget_obj_info_max * Signature: (J[Ljava/lang/String;[I[I[JJI)I */ /* * NOTE: This is a dangerous call! The caller can supply any value they'd like * for 'n' and if it exceeds the number of links reachable from the group, we * will most likely end up overwriting memory heap-tracking info. */ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1max (JNIEnv *env, jclass clss, jlong loc_id, jobjectArray objName, jintArray oType, jintArray lType, jobjectArray oToken, jlong maxnum, jint n) { H5O_token_t *tokens = NULL; jboolean isCopy; jstring str; jobject token; char **oName = NULL; jint *otarr = NULL; jint *ltarr = NULL; int i; herr_t ret_val = FAIL; UNUSED(clss); if (NULL == oType) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_max: oType is NULL"); if (NULL == lType) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_max: lType is NULL"); if (NULL == oToken) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Gget_obj_info_max: oToken is NULL"); PIN_INT_ARRAY(ENVONLY, oType, otarr, &isCopy, "H5Gget_obj_info_max: oType not pinned"); PIN_INT_ARRAY(ENVONLY, lType, ltarr, &isCopy, "H5Gget_obj_info_max: lType not pinned"); if (NULL == (oName = (char **) HDcalloc((size_t)n, sizeof(*oName)))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Gget_obj_info_max: failed to allocate buffer for object name"); if (NULL == (tokens = (H5O_token_t *) HDcalloc((size_t)n, sizeof(H5O_token_t)))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Gget_obj_info_max: failed to allocate buffer for object tokens"); if ((ret_val = H5Gget_obj_info_max((hid_t)loc_id, oName, (int *)otarr, (int *)ltarr, tokens, maxnum)) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "H5Gget_obj_info_max: retrieval of object info failed"); for (i = 0; i < n; i++) { if (oName[i]) { if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, oName[i]))) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); ENVPTR->SetObjectArrayElement(ENVONLY, objName, i, (jobject)str); CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); ENVPTR->DeleteLocalRef(ENVONLY, str); } /* Create an H5O_token_t object */ if (NULL == (token = create_H5O_token_t(ENVONLY, &tokens[i], TRUE))) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); ENVPTR->SetObjectArrayElement(ENVONLY, oToken, i, token); CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); ENVPTR->DeleteLocalRef(ENVONLY, token); } /* end for */ done: if (tokens) HDfree(tokens); if (oName) h5str_array_free(oName, (size_t)n); if (ltarr) UNPIN_INT_ARRAY(ENVONLY, lType, ltarr, (ret_val < 0) ? JNI_ABORT : 0); if (otarr) UNPIN_INT_ARRAY(ENVONLY, oType, otarr, (ret_val < 0) ? JNI_ABORT : 0); return ret_val; } /* end Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1max */ int H5Gget_obj_info_full (hid_t loc_id, char **objname, int *otype, int *ltype, unsigned long *fno, H5O_token_t *obj_token, int indexType, int indexOrder) { info_all_t info; info.objname = objname; info.otype = otype; info.ltype = ltype; info.idxnum = 0; info.fno = fno; info.obj_token = obj_token; info.count = 0; if (H5Literate2(loc_id, (H5_index_t)indexType, (H5_iter_order_t)indexOrder, NULL, obj_info_all, (void *)&info) < 0) { /* * Reset info stats; most importantly, reset the count. */ info.objname = objname; info.otype = otype; info.ltype = ltype; info.idxnum = 0; info.fno = fno; info.obj_token = obj_token; info.count = 0; /* Iteration failed, try normal alphabetical order */ if (H5Literate2(loc_id, H5_INDEX_NAME, H5_ITER_INC, NULL, obj_info_all, (void *)&info) < 0) return -1; } return info.count; } /* end H5Gget_obj_info_full */ int H5Gget_obj_info_max (hid_t loc_id, char **objname, int *otype, int *ltype, H5O_token_t *obj_token, long maxnum) { info_all_t info; info.objname = objname; info.otype = otype; info.ltype = ltype; info.idxnum = (unsigned long)maxnum; info.obj_token = obj_token; info.count = 0; if (H5Lvisit2(loc_id, H5_INDEX_NAME, H5_ITER_NATIVE, obj_info_max, (void *)&info) < 0) return -1; return info.count; } /* end H5Gget_obj_info_max */ herr_t obj_info_all (hid_t loc_id, const char *name, const H5L_info2_t *info, void *op_data) { info_all_t *datainfo = (info_all_t *)op_data; H5O_info2_t object_info; htri_t object_exists; size_t str_len; datainfo->otype[datainfo->count] = -1; datainfo->ltype[datainfo->count] = -1; datainfo->obj_token[datainfo->count] = H5O_TOKEN_UNDEF; str_len = HDstrlen(name); if (NULL == (datainfo->objname[datainfo->count] = (char *) HDmalloc(str_len + 1))) goto done; HDstrncpy(datainfo->objname[datainfo->count], name, str_len); (datainfo->objname[datainfo->count])[str_len] = '\0'; if ((object_exists = H5Oexists_by_name(loc_id, name, H5P_DEFAULT)) < 0) goto done; if (object_exists) { if (H5Oget_info_by_name3(loc_id, name, &object_info, H5O_INFO_ALL, H5P_DEFAULT) < 0) goto done; datainfo->otype[datainfo->count] = object_info.type; datainfo->ltype[datainfo->count] = info->type; datainfo->fno[datainfo->count] = object_info.fileno; HDmemcpy(&datainfo->obj_token[datainfo->count], &object_info.token, sizeof(object_info.token)); } done: datainfo->count++; return SUCCEED; } /* end obj_info_all */ herr_t obj_info_max (hid_t loc_id, const char *name, const H5L_info2_t *info, void *op_data) { info_all_t *datainfo = (info_all_t *)op_data; H5O_info2_t object_info; size_t str_len; datainfo->otype[datainfo->count] = -1; datainfo->ltype[datainfo->count] = -1; datainfo->objname[datainfo->count] = NULL; datainfo->obj_token[datainfo->count] = H5O_TOKEN_UNDEF; /* This will be freed by h5str_array_free(oName, n) */ str_len = HDstrlen(name); if (NULL == (datainfo->objname[datainfo->count] = (char *) HDmalloc(str_len + 1))) goto done; HDstrncpy(datainfo->objname[datainfo->count], name, str_len); (datainfo->objname[datainfo->count])[str_len] = '\0'; if (H5Oget_info3(loc_id, &object_info, H5O_INFO_ALL) < 0) goto done; datainfo->otype[datainfo->count] = object_info.type; datainfo->ltype[datainfo->count] = info->type; HDmemcpy(&datainfo->obj_token[datainfo->count], &object_info.token, sizeof(object_info.token)); done: datainfo->count++; if (datainfo->count >= (int)datainfo->idxnum) return 1; else return SUCCEED; } /* end obj_info_max */ /* * Class: hdf_hdf5lib_H5 * Method: H5export_dataset * Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;I)V */ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5export_1dataset (JNIEnv *env, jclass clss, jstring file_export_name, jstring file_name, jstring object_path, jint binary_order) { const char *file_export = NULL; const char *object_name = NULL; const char *fileName = NULL; jboolean isCopy; herr_t ret_val = FAIL; hid_t file_id = H5I_INVALID_HID; hid_t dataset_id = H5I_INVALID_HID; FILE *stream = NULL; UNUSED(clss); if (NULL == file_export_name) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_export_name is NULL"); if (NULL == file_name) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_name is NULL"); if (NULL == object_path) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: object_path is NULL"); PIN_JAVA_STRING(ENVONLY, file_name, fileName, NULL, "H5export_dataset: file name not pinned"); if ((file_id = H5Fopen(fileName, (unsigned)H5F_ACC_RDWR, (hid_t)H5P_DEFAULT)) < 0) H5_LIBRARY_ERROR(ENVONLY); PIN_JAVA_STRING(ENVONLY, object_path, object_name, &isCopy, "H5export_dataset: object_path not pinned"); if ((dataset_id = H5Dopen2(file_id, object_name, H5P_DEFAULT)) < 0) H5_LIBRARY_ERROR(ENVONLY); PIN_JAVA_STRING(ENVONLY, file_export_name, file_export, NULL, "H5export_dataset: file_export name not pinned"); if (NULL == (stream = HDfopen(file_export, "w+"))) H5_JNI_FATAL_ERROR(ENVONLY, "HDfopen failed"); if ((ret_val = h5str_dump_simple_dset(ENVONLY, stream, dataset_id, binary_order)) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_simple_dset failed"); if (stream) { HDfclose(stream); stream = NULL; } done: if (stream) HDfclose(stream); if (file_export) UNPIN_JAVA_STRING(ENVONLY, file_export_name, file_export); if (object_name) UNPIN_JAVA_STRING(ENVONLY, object_path, object_name); if (fileName) UNPIN_JAVA_STRING(ENVONLY, file_name, fileName); if (dataset_id >= 0) H5Dclose(dataset_id); if (file_id >= 0) H5Fclose(file_id); } /* end Java_hdf_hdf5lib_H5_H5export_1dataset */ #ifdef __cplusplus } #endif