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Test H5WasmApi
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@axelboc
axelboc committed Jan 23, 2024
1 parent aeb7879 commit 762ff9e
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1 change: 1 addition & 0 deletions .vscode/settings.json
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Expand Up @@ -7,6 +7,7 @@
"css.validate": false,

"editor.defaultFormatter": "esbenp.prettier-vscode",
"[python]": { "editor.defaultFormatter": "ms-python.black-formatter" },
"editor.formatOnSave": true,
"editor.codeActionsOnSave": {
"source.fixAll.eslint": "explicit"
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4 changes: 1 addition & 3 deletions packages/app/vite.config.js
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Expand Up @@ -38,9 +38,7 @@ export default defineProject({
restoreMocks: true,
testTimeout: 15_000,
server: {
deps: {
inline: ['react-suspense-fetch'],
},
deps: { inline: ['react-suspense-fetch'] },
},
},
});
248 changes: 248 additions & 0 deletions packages/h5wasm/create_h5_sample.py
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import os
import sys
import h5py
import numpy as np

if sys.version_info.major < 3:
raise RuntimeError("Python 2 is not supported")

BASE_PATH = os.path.dirname(os.path.realpath(sys.argv[0]))
DIST_PATH = os.path.join(BASE_PATH, "dist-h5")
os.makedirs(DIST_PATH, exist_ok=True)

h5py.get_config().track_order = True


def add_empty(group, name, dtype=None):
dataset = group.create_dataset(name + "_empty", data=h5py.Empty(dtype))
return dataset


def add_scalar(group, name, data=None, dtype=None):
dataset = group.create_dataset(name + "_scalar", (), dtype, data)
return dataset


def add_array(group, name, data=None, dtype=None, shape=None):
dataset = group.create_dataset(
name + "_{0}D".format(len(shape or data.shape)), shape, dtype, data
)
return dataset


def print_h5t_class(dataset):
# https://nasa.github.io/MISR-Toolkit/html/_h5_tpublic_8h_source.html
print("H5T_class=" + str(dataset.id.get_type().get_class()))


with h5py.File(os.path.join(DIST_PATH, "sample.h5"), "w") as h5:
# === H5T_INTEGER ===

add_scalar(h5, "int8", np.int8(np.iinfo(np.int8).min))
add_array(h5, "int8", np.array([[0, 1, 2], [3, 4, 5]], np.int8))
add_scalar(h5, "int16", np.int16(np.iinfo(np.int16).min))
add_array(h5, "int16", np.array([[0, 1, 2], [3, 4, 5]], np.int16))
add_scalar(h5, "int32", np.int32(np.iinfo(np.int32).min))
add_scalar(h5, "int32_BE", 0, np.dtype(">i"))
add_array(h5, "int32", np.array([[0, 1, 2], [3, 4, 5]], np.int32))
add_scalar(h5, "int64", np.int64(np.iinfo(np.int64).min))
add_array(h5, "int64", np.array([[0, 1, 2], [3, 4, 5]], np.int64))

add_scalar(h5, "uint8", np.uint8(np.iinfo(np.uint8).max))
add_array(h5, "uint8", np.array([[0, 1, 2], [3, 4, 5]], np.uint8))
add_scalar(h5, "uint16", np.uint16(np.iinfo(np.uint16).max))
add_array(h5, "uint16", np.array([[0, 1, 2], [3, 4, 5]], np.uint16))
add_scalar(h5, "uint32", np.uint32(np.iinfo(np.uint32).max))
add_array(h5, "uint32", np.array([[0, 1, 2], [3, 4, 5]], np.uint32))
add_scalar(h5, "uint64", np.uint64(np.iinfo(np.uint64).max))
add_array(
h5,
"uint64",
np.array(
[[[0, 1], [2, 3]], [[4, 5], [6, np.uint64(np.iinfo(np.uint64).max)]]],
np.uint64,
),
)

# === H5T_FLOAT ===

add_scalar(h5, "float16", np.float16(np.finfo(np.float16).smallest_normal))
add_array(h5, "float16", np.array([[0, 1, 2], [3, 4, 5]], np.float16))
add_empty(h5, "float32", np.float32)
add_scalar(h5, "float32", np.float32(np.finfo(np.float32).smallest_normal))
add_scalar(h5, "float32_BE", 0, np.dtype(">f"))
add_array(h5, "float32", np.array([[0, 1, 2], [3, 4, 5]], np.float32))
add_scalar(h5, "float64", np.float64(np.finfo(np.float64).smallest_normal))

add_scalar(h5, "float64_nan", np.nan)
add_scalar(h5, "float64_inf", np.inf)
add_scalar(h5, "float64_ninf", np.NINF)
add_scalar(h5, "float64_zero", np.PZERO)
add_scalar(h5, "float64_nzero", np.NZERO)
add_scalar(h5, "float64_pi", np.pi)
add_array(
h5,
"float64",
np.array([[0, 1, np.inf, 3, 4], [3, 4, np.nan, 6, 7], [6, 7, np.NINF, 9, 10]]),
)

add_scalar(h5, "float128", np.float128(np.finfo(np.float128).smallest_normal))
add_array(h5, "float128", np.array([[0, 1, 2], [3, 4, 5]], np.float128))

# === H5T_TIME ===

# Not supported by h5py

# === H5T_STRING ===

add_empty(h5, "ascii_vlen", h5py.string_dtype("ascii"))
add_scalar(h5, "ascii_vlen", b"Some text")
add_scalar(
h5,
"ascii_fixed",
np.string_("Some text"),
)
add_scalar(h5, "utf8_vlen", "Some text")
add_array(h5, "utf8_vlen", np.array(["foo", "bar", "baz"], h5py.string_dtype()))
add_scalar(h5, "utf8_fixed", "Some text", h5py.string_dtype("utf-8", 9))

# === H5T_BITFIELD ===

# h5py syntax unknown

# === H5T_OPAQUE ===

add_scalar(h5, "byte_string", np.void(b"\x00\x11\x22"))
add_scalar(h5, "datetime64", np.void(np.datetime64("2019-09-22T17:38:30")))
add_scalar(h5, "datetime64_not-a-time", np.void(np.datetime64("NaT")))

# === H5T_COMPOUND (and H5T_ARRAY) ===

add_scalar(
h5,
"complex64",
np.complex64(
np.finfo(np.complex64).smallest_normal + np.finfo(np.complex64).max * 1j
),
)
add_array(
h5, "complex64", np.array([[1 + 2j, 3 + 4j], [5 + 6j, 7 + 8j]], np.complex64)
),
add_scalar(
h5,
"complex128",
np.complex128(
np.finfo(np.complex128).smallest_normal + np.finfo(np.complex128).max * 1j
),
)
add_scalar(h5, "complex128_BE", 1 + 2j, np.dtype(">c16"))
add_array(
h5, "complex128", np.array([[1 + 2j, 3 + 4j], [5 + 6j, 7 + 8j]], np.complex128)
),
add_scalar(
h5,
"complex256",
np.complex256(
np.finfo(np.complex256).smallest_normal + np.finfo(np.complex256).max * 1j
),
)
add_array(
h5, "complex256", np.array([[1 + 2j, 3 + 4j], [5 + 6j, 7 + 8j]], np.complex256)
),

add_scalar(
h5,
"compound",
(1, 2.0, "foo"),
[("bigint", np.int64), ("double", np.float64), ("utf-8", h5py.string_dtype())],
)
for_ref = add_array(
h5,
"compound",
np.array(
[(1, np.nan, "foo"), (2, np.inf, "bar"), (3, np.NZERO, "baz")],
[
("bigint", np.int64),
("double", np.float64),
("utf-8", h5py.string_dtype()),
],
),
)
add_scalar(
h5,
"compound_nested",
((True, 1 + 2j),),
[("nested", [("bool", np.bool_), ("cplx", np.complex64)])],
)

comp = add_array(
h5,
"compound_array_vlen",
np.array(
[
(
np.array([0, 1], np.float32),
np.array([0], np.uint64),
),
(
np.array([2, 3], np.float32),
np.array([0, 1], np.uint64),
),
(
np.array([4, 5], np.float32),
np.array([0, 1, 2], np.uint64),
),
],
[("arr", np.float32, (2,)), ("vlen", h5py.vlen_dtype(np.uint64))],
),
)

# === H5T_REFERENCE ===

add_scalar(h5, "reference", for_ref.ref, h5py.special_dtype(ref=h5py.Reference))
add_scalar(
h5,
"reference_region",
for_ref.regionref[0:1],
h5py.special_dtype(ref=h5py.Reference),
)

# === H5T_ENUM ===

add_empty(h5, "bool", h5py.enum_dtype({"FALSE": 0, "TRUE": 1}))
add_scalar(h5, "bool_false", False)
add_scalar(h5, "bool_true", True)
add_array(
h5, "bool", np.array([[True, False, True, True], [False, False, True, False]])
)

add_scalar(
h5,
"enum_uint8",
1,
h5py.enum_dtype({"A": 0, "B": 1}),
)
add_scalar(
h5,
"enum_int32",
256,
h5py.enum_dtype({"A": 256, "B": 257}, np.int32),
)

# === H5T_VLEN ===

# https://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
scalar_vlen = add_scalar(h5, "vlen_int8", dtype=h5py.vlen_dtype(np.int8))
scalar_vlen[()] = [0, 1]

# https://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
scalar_vlen = add_array(
h5, "vlen_int64", shape=(3,), dtype=h5py.vlen_dtype(np.int64)
)
scalar_vlen[0] = [0]
scalar_vlen[1] = [0, 1]
scalar_vlen[2] = [0, 1, 2]

# === H5T_ARRAY ===

# cf. section `H5T_COMPOUND` above
1 change: 1 addition & 0 deletions packages/h5wasm/package.json
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Expand Up @@ -60,6 +60,7 @@
"eslint": "8.56.0",
"eslint-config-galex": "4.5.2",
"react": "18.2.0",
"react-dom": "18.2.0",
"rollup": "4.9.0",
"rollup-plugin-dts": "6.1.0",
"typescript": "5.0.4",
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