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Implement support for Complex number datatypes
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replace usages of word "complex" to distinguish from complex datatypes
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@jhendersonHDF
jhendersonHDF committed May 3, 2024
1 parent 667b607 commit a700653
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Showing 10 changed files with 76 additions and 72 deletions.
8 changes: 4 additions & 4 deletions c++/test/tattr.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -632,7 +632,7 @@ test_attr_compound_write(FileAccPropList &fapl)
hsize_t dims2[] = {ATTR4_DIM1, ATTR4_DIM2};
DataSpace sid2(ATTR4_RANK, dims2);

// Create complex attribute for the dataset
// Create compound attribute for the dataset
Attribute attr = dataset.createAttribute(ATTR4_NAME, comp_type, sid2);

// Try to create the same attribute again (should fail)
Expand All @@ -643,7 +643,7 @@ test_attr_compound_write(FileAccPropList &fapl)
{
} // do nothing, exception expected

// Write complex attribute data
// Write compound attribute data
attr.write(comp_type, attr_data4);

PASSED();
Expand Down Expand Up @@ -2001,8 +2001,8 @@ test_attr()
test_attr_rename(curr_fapl); // Test renaming attribute
test_attr_basic_read(curr_fapl); // Test basic H5A reading code

test_attr_compound_write(curr_fapl); // Test complex datatype H5A writing code
test_attr_compound_read(curr_fapl); // Test complex datatype H5A reading code
test_attr_compound_write(curr_fapl); // Test compound datatype H5A writing code
test_attr_compound_read(curr_fapl); // Test compound datatype H5A reading code

test_attr_scalar_write(curr_fapl); // Test scalar dataspace H5A writing code
test_attr_scalar_read(curr_fapl); // Test scalar dataspace H5A reading code
Expand Down
42 changes: 22 additions & 20 deletions java/src/jni/h5aImp.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1243,12 +1243,13 @@ Java_hdf_hdf5lib_H5_H5Aread_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id,
jobjectArray buf)
{
H5T_class_t type_class;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isComplex = 0;
htri_t isComplex2 = 0;
hid_t nested_tid = H5I_INVALID_HID;
herr_t status = FAIL;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isCompound = 0;
htri_t isVlen = 0;
hid_t nested_tid = H5I_INVALID_HID;
bool isComposite = false;
herr_t status = FAIL;

UNUSED(clss);

Expand All @@ -1272,13 +1273,13 @@ Java_hdf_hdf5lib_H5_H5Aread_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id,
if ((nested_tid = H5Tget_member_type((hid_t)mem_type_id, i)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

if ((isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND)) < 0)
if ((isCompound = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

if ((isComplex2 = H5Tdetect_class((hid_t)nested_tid, H5T_VLEN)) < 0)
if ((isVlen = H5Tdetect_class((hid_t)nested_tid, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

isComplex = isComplex || isComplex2;
isComposite = isCompound || isVlen;

if (H5Tclose(nested_tid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
Expand All @@ -1289,7 +1290,7 @@ Java_hdf_hdf5lib_H5_H5Aread_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id,
isVlenStr = 1; /* Strings created by H5Tvlen_create(H5T_C_S1) */
}

if (!isStr || isComplex || isVlenStr) {
if (!isStr || isComposite || isVlenStr) {
if ((status = H5AreadVL_asstr(env, (hid_t)attr_id, (hid_t)mem_type_id, buf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
Expand Down Expand Up @@ -1447,12 +1448,13 @@ Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id,
jobjectArray buf)
{
H5T_class_t type_class;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isComplex = 0;
htri_t isComplex2 = 0;
hid_t nested_tid = H5I_INVALID_HID;
herr_t status = FAIL;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isCompound = 0;
htri_t isVlen = 0;
hid_t nested_tid = H5I_INVALID_HID;
bool isComposite = false;
herr_t status = FAIL;

UNUSED(clss);

Expand All @@ -1476,13 +1478,13 @@ Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id,
if ((nested_tid = H5Tget_member_type((hid_t)mem_type_id, i)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

if ((isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND)) < 0)
if ((isCompound = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

if ((isComplex2 = H5Tdetect_class((hid_t)nested_tid, H5T_VLEN)) < 0)
if ((isVlen = H5Tdetect_class((hid_t)nested_tid, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

isComplex = isComplex || isComplex2;
isComposite = isCompound || isVlen;

if (H5Tclose(nested_tid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
Expand All @@ -1493,7 +1495,7 @@ Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings(JNIEnv *env, jclass clss, jlong attr_id,
isVlenStr = 1; /* Strings created by H5Tvlen_create(H5T_C_S1) */
}

if (!isStr || isComplex || isVlenStr) {
if (!isStr || isComposite || isVlenStr) {
if ((status = H5AwriteVL_asstr(env, (hid_t)attr_id, (hid_t)mem_type_id, buf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
Expand Down
42 changes: 22 additions & 20 deletions java/src/jni/h5dImp.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1259,12 +1259,13 @@ Java_hdf_hdf5lib_H5_H5Dread_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_i
jobjectArray buf)
{
H5T_class_t type_class;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isComplex = 0;
htri_t isComplex2 = 0;
hid_t nested_tid = H5I_INVALID_HID;
herr_t status = FAIL;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isCompound = 0;
htri_t isVlen = 0;
hid_t nested_tid = H5I_INVALID_HID;
bool isComposite = false;
herr_t status = FAIL;

UNUSED(clss);

Expand All @@ -1288,13 +1289,13 @@ Java_hdf_hdf5lib_H5_H5Dread_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_i
if ((nested_tid = H5Tget_member_type((hid_t)mem_type_id, i)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

if ((isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND)) < 0)
if ((isCompound = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

if ((isComplex2 = H5Tdetect_class((hid_t)nested_tid, H5T_VLEN)) < 0)
if ((isVlen = H5Tdetect_class((hid_t)nested_tid, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

isComplex = isComplex || isComplex2;
isComposite = isCompound || isVlen;

if (H5Tclose(nested_tid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
Expand All @@ -1305,7 +1306,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_i
isVlenStr = 1; /* Strings created by H5Tvlen_create(H5T_C_S1) */
}

if (!isStr || isComplex || isVlenStr) {
if (!isStr || isComposite || isVlenStr) {
if ((status = H5DreadVL_asstr(env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, buf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
Expand Down Expand Up @@ -1484,12 +1485,13 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_
jobjectArray buf)
{
H5T_class_t type_class;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isComplex = 0;
htri_t isComplex2 = 0;
hid_t nested_tid = H5I_INVALID_HID;
herr_t status = FAIL;
htri_t isStr = 0;
htri_t isVlenStr = 0;
htri_t isCompound = 0;
htri_t isVlen = 0;
hid_t nested_tid = H5I_INVALID_HID;
bool isComposite = false;
herr_t status = FAIL;

UNUSED(clss);

Expand All @@ -1513,13 +1515,13 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_
if ((nested_tid = H5Tget_member_type((hid_t)mem_type_id, i)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

if ((isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND)) < 0)
if ((isCompound = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

if ((isComplex2 = H5Tdetect_class((hid_t)nested_tid, H5T_VLEN)) < 0)
if ((isVlen = H5Tdetect_class((hid_t)nested_tid, H5T_VLEN)) < 0)
H5_LIBRARY_ERROR(ENVONLY);

isComplex = isComplex || isComplex2;
isComposite = isCompound || isVlen;

if (H5Tclose(nested_tid) < 0)
H5_LIBRARY_ERROR(ENVONLY);
Expand All @@ -1530,7 +1532,7 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings(JNIEnv *env, jclass clss, jlong dataset_
isVlenStr = 1; /* Strings created by H5Tvlen_create(H5T_C_S1) */
}

if (!isStr || isComplex || isVlenStr) {
if (!isStr || isComposite || isVlenStr) {
if ((status = H5DwriteVL_asstr(env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
(hid_t)file_space_id, (hid_t)xfer_plist_id, buf)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
Expand Down
4 changes: 2 additions & 2 deletions src/H5Spublic.h
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Original file line number Diff line number Diff line change
Expand Up @@ -251,10 +251,10 @@ H5_DLL hid_t H5Scopy(hid_t space_id);
* Further dataspace types may be added later.
*
* A scalar dataspace, #H5S_SCALAR, has a single element, though that
* element may be of a complex datatype, such as a compound or array
* element may be of a composite datatype, such as a compound or array
* datatype. By convention, the rank of a scalar dataspace is always \p 0
* (zero); think of it geometrically as a single, dimensionless point,
* though that point can be complex.
* though that point can be composite.
*
* A simple dataspace, #H5S_SIMPLE, consists of a regular array of elements.
*
Expand Down
10 changes: 5 additions & 5 deletions src/H5T.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2342,7 +2342,7 @@ H5T_detect_class(const H5T_t *dt, H5T_class_t cls, bool from_api)
HGOTO_DONE(true);

/* Recurse if it's VL, compound, enum or array */
if (H5T_IS_COMPLEX(dt->shared->u.compnd.memb[i].type->shared->type))
if (H5T_IS_COMPOSITE(dt->shared->u.compnd.memb[i].type->shared->type))
if ((nested_ret = H5T_detect_class(dt->shared->u.compnd.memb[i].type, cls, from_api)) !=
false)
HGOTO_DONE(nested_ret);
Expand Down Expand Up @@ -6242,7 +6242,7 @@ H5T_set_loc(H5T_t *dt, H5VL_object_t *file, H5T_loc_t loc)
/* Recurse if it's VL, compound, enum or array */
/* (If the force_conv flag is _not_ set, the type cannot change in size, so don't recurse) */
if (dt->shared->parent->shared->force_conv &&
H5T_IS_COMPLEX(dt->shared->parent->shared->type)) {
H5T_IS_COMPOSITE(dt->shared->parent->shared->type)) {
/* Keep the old base element size for later */
old_size = dt->shared->parent->shared->size;

Expand Down Expand Up @@ -6283,7 +6283,7 @@ H5T_set_loc(H5T_t *dt, H5VL_object_t *file, H5T_loc_t loc)
/* Recurse if it's VL, compound, enum or array */
/* (If the force_conv flag is _not_ set, the type cannot change in size, so don't recurse)
*/
if (memb_type->shared->force_conv && H5T_IS_COMPLEX(memb_type->shared->type)) {
if (memb_type->shared->force_conv && H5T_IS_COMPOSITE(memb_type->shared->type)) {
/* Keep the old field size for later */
old_size = memb_type->shared->size;

Expand Down Expand Up @@ -6325,7 +6325,7 @@ H5T_set_loc(H5T_t *dt, H5VL_object_t *file, H5T_loc_t loc)
* them as part of the same blob)*/
/* (If the force_conv flag is _not_ set, the type cannot change in size, so don't recurse) */
if (dt->shared->parent->shared->force_conv &&
H5T_IS_COMPLEX(dt->shared->parent->shared->type) &&
H5T_IS_COMPOSITE(dt->shared->parent->shared->type) &&
(dt->shared->parent->shared->type != H5T_REFERENCE)) {
if ((changed = H5T_set_loc(dt->shared->parent, file, loc)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "Unable to set VL location");
Expand Down Expand Up @@ -6571,7 +6571,7 @@ H5T__upgrade_version(H5T_t *dt, unsigned new_version)
assert(dt);

/* Iterate over entire datatype, upgrading the version of components, if it's useful */
if (H5T__visit(dt, (H5T_VISIT_SIMPLE | H5T_VISIT_COMPLEX_LAST), H5T__upgrade_version_cb, &new_version) <
if (H5T__visit(dt, (H5T_VISIT_SIMPLE | H5T_VISIT_COMPOSITE_LAST), H5T__upgrade_version_cb, &new_version) <
0)
HGOTO_ERROR(H5E_DATATYPE, H5E_BADITER, FAIL, "iteration to upgrade datatype encoding version failed");

Expand Down
2 changes: 1 addition & 1 deletion src/H5Tconv_vlen.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ H5FL_BLK_DEFINE_STATIC(vlen_seq);
* Function: H5T__conv_vlen_nested_free
*
* Purpose: Recursively locates and frees any nested VLEN components of
* complex data types (including COMPOUND).
* composite data types (including COMPOUND).
*
* Return: Non-negative on success/Negative on failure.
*
Expand Down
16 changes: 8 additions & 8 deletions src/H5Tpkg.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,8 @@
/* Other public headers needed by this file */
#include "H5Spublic.h" /* Dataspace functions */

/* Macro to ease detecting "complex" datatypes (i.e. those with base types or fields) */
#define H5T_IS_COMPLEX(t) \
/* Macro to ease detecting composite datatypes (i.e. those with base types or fields) */
#define H5T_IS_COMPOSITE(t) \
((t) == H5T_COMPOUND || (t) == H5T_ENUM || (t) == H5T_VLEN || (t) == H5T_ARRAY || (t) == H5T_REFERENCE)

/* Macro to ease detecting fixed "string" datatypes */
Expand All @@ -55,7 +55,7 @@
#define H5T_IS_STRING(dt) (H5T_IS_FIXED_STRING(dt) || H5T_IS_VL_STRING(dt))

/* Macro to ease detecting atomic datatypes */
#define H5T_IS_ATOMIC(dt) (!(H5T_IS_COMPLEX((dt)->type) || (dt)->type == H5T_OPAQUE))
#define H5T_IS_ATOMIC(dt) (!(H5T_IS_COMPOSITE((dt)->type) || (dt)->type == H5T_OPAQUE))

/* Macro to ease retrieving class of shared datatype */
/* (Externally, a VL string is a string; internally, a VL string is a VL. Lie
Expand Down Expand Up @@ -100,13 +100,13 @@
#define H5O_DTYPE_VERSION_LATEST H5O_DTYPE_VERSION_4

/* Flags for visiting datatype */
#define H5T_VISIT_COMPLEX_FIRST 0x01 /* Visit complex datatype before visiting member/parent datatypes */
#define H5T_VISIT_COMPLEX_LAST 0x02 /* Visit complex datatype after visiting member/parent datatypes */
/* (setting both flags will mean visiting complex type twice) */
#define H5T_VISIT_COMPOSITE_FIRST 0x01 /* Visit composite datatype before visiting member/parent datatypes */
#define H5T_VISIT_COMPOSITE_LAST 0x02 /* Visit composite datatype after visiting member/parent datatypes */
/* (setting both flags will mean visiting composite type twice) */
#define H5T_VISIT_SIMPLE 0x04 /* Visit simple datatypes (at all) */
/* (setting H5T_VISIT_SIMPLE and _not_ setting either H5T_VISIT_COMPLEX_FIRST or H5T_VISIT_COMPLEX_LAST will
/* (setting H5T_VISIT_SIMPLE and _not_ setting either H5T_VISIT_COMPOSITE_FIRST or H5T_VISIT_COMPOSITE_LAST will
* mean visiting _only_ "simple" "leafs" in the "tree" */
/* (_not_ setting H5T_VISIT_SIMPLE and setting either H5T_VISIT_COMPLEX_FIRST or H5T_VISIT_COMPLEX_LAST will
/* (_not_ setting H5T_VISIT_SIMPLE and setting either H5T_VISIT_COMPOSITE_FIRST or H5T_VISIT_COMPOSITE_LAST will
* mean visiting all nodes _except_ "simple" "leafs" in the "tree" */

/* Define an internal macro for converting long long to long double. Mac OS 10.4 gives some
Expand Down
10 changes: 5 additions & 5 deletions src/H5Tvisit.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@
herr_t
H5T__visit(H5T_t *dt, unsigned visit_flags, H5T_operator_t op, void *op_value)
{
bool is_complex; /* Flag indicating current datatype is "complex" */
bool is_composite; /* Flag indicating current datatype is composite */
herr_t ret_value = SUCCEED; /* Return value */

FUNC_ENTER_PACKAGE
Expand All @@ -89,11 +89,11 @@ H5T__visit(H5T_t *dt, unsigned visit_flags, H5T_operator_t op, void *op_value)
assert(dt);
assert(op);

/* Check for complex datatype */
is_complex = H5T_IS_COMPLEX(dt->shared->type);
/* Check for composite datatype */
is_composite = H5T_IS_COMPOSITE(dt->shared->type);

/* If the callback is to be made on the datatype first, do that */
if (is_complex && (visit_flags & H5T_VISIT_COMPLEX_FIRST))
if (is_composite && (visit_flags & H5T_VISIT_COMPOSITE_FIRST))
if (op(dt, op_value) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_BADITER, FAIL, "operator callback failed");

Expand Down Expand Up @@ -139,7 +139,7 @@ H5T__visit(H5T_t *dt, unsigned visit_flags, H5T_operator_t op, void *op_value)
} /* end switch */

/* If the callback is to be made on the datatype last, do that */
if (is_complex && (visit_flags & H5T_VISIT_COMPLEX_LAST))
if (is_composite && (visit_flags & H5T_VISIT_COMPOSITE_LAST))
if (op(dt, op_value) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_BADITER, FAIL, "operator callback failed");

Expand Down
6 changes: 3 additions & 3 deletions src/H5Tvlen.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -948,7 +948,7 @@ H5T__vlen_reclaim(void *elem, const H5T_t *dt, H5T_vlen_alloc_info_t *alloc_info
switch (dt->shared->type) {
case H5T_ARRAY:
/* Recurse on each element, if the array's base type is array, VL, enum or compound */
if (H5T_IS_COMPLEX(dt->shared->parent->shared->type)) {
if (H5T_IS_COMPOSITE(dt->shared->parent->shared->type)) {
void *off; /* offset of field */

/* Calculate the offset member and recurse on it */
Expand All @@ -964,7 +964,7 @@ H5T__vlen_reclaim(void *elem, const H5T_t *dt, H5T_vlen_alloc_info_t *alloc_info
/* Check each field and recurse on VL, compound, enum or array ones */
for (u = 0; u < dt->shared->u.compnd.nmembs; u++) {
/* Recurse if it's VL, compound, enum or array */
if (H5T_IS_COMPLEX(dt->shared->u.compnd.memb[u].type->shared->type)) {
if (H5T_IS_COMPOSITE(dt->shared->u.compnd.memb[u].type->shared->type)) {
void *off; /* offset of field */

/* Calculate the offset member and recurse on it */
Expand All @@ -983,7 +983,7 @@ H5T__vlen_reclaim(void *elem, const H5T_t *dt, H5T_vlen_alloc_info_t *alloc_info
/* Check if there is anything actually in this sequence */
if (vl->len != 0) {
/* Recurse if it's VL, array, enum or compound */
if (H5T_IS_COMPLEX(dt->shared->parent->shared->type)) {
if (H5T_IS_COMPOSITE(dt->shared->parent->shared->type)) {
void *off; /* offset of field */

/* Calculate the offset of each array element and recurse on it */
Expand Down
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