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Description
openedon Mar 6, 2022
jsontoh5 data/json/comp_complex.json command fails with this error:
ValueError: setting an array element with a sequence.
The error comes when converting this dataset's value (relevant HDF5/JSON content only) to a NumPy array:
"a4afebb4-9b72-11ec-b0a3-8c8590747994": {
"alias": [
"/phony_compound_var"
],
"shape": {
"class": "H5S_SIMPLE",
"dims": [
2
]
},
"type": {
"class": "H5T_COMPOUND",
"fields": [
{
"name": "yy",
"type": {
"base": {
"class": "H5T_COMPOUND",
"fields": [
{
"name": "x",
"type": {
"class": "H5T_COMPOUND",
"fields": [
{
"name": "i",
"type": {
"base": "H5T_STD_I16LE",
"class": "H5T_INTEGER"
}
},
{
"name": "j",
"type": {
"base": "H5T_STD_I32LE",
"class": "H5T_INTEGER"
}
}
]
}
},
{
"name": "y",
"type": {
"base": {
"base": "H5T_IEEE_F64LE",
"class": "H5T_FLOAT"
},
"class": "H5T_ARRAY",
"dims": [
2
]
}
}
]
},
"class": "H5T_ARRAY",
"dims": [
2
]
}
}
]
},
"value": [
[
[
[
[
1,
200000
],
[
-100000.285657,
3.1415926
]
],
[
[
2,
400000
],
[
200000.151617,
273.15
]
]
]
],
[
[
[
[
3,
600000
],
[
-200000.285657,
6.1415926
]
],
[
[
4,
800000
],
[
400000.151617,
476.15
]
]
]
]
]
}jsontoh5 version of the value as a Python object is:
[((((1, 200000), (-100000.285657, 3.1415926)), ((2, 400000), (200000.151617, 273.15))),), ((((3, 600000), (-200000.285657, 6.1415926)), ((4, 800000), (400000.151617, 476.15))),)]
The NumPy dataset's value (from h5py) is:
[([((1, 200000), [-1.00000286e+05, 3.14159260e+00]), ((2, 400000), [ 2.00000152e+05, 2.73150000e+02])],), ([((3, 600000), [-2.00000286e+05, 6.14159260e+00]), ((4, 800000), [ 4.00000152e+05, 4.76150000e+02])],)]
They differ in how the H5T_ARRAY components of the dataset's value are converted. jsontoh5 exclusively uses tuples while NumPy prefers the list in this case. The dataset's NumPy dtype in both cases is the same:
dtype([('yy', [('x', [('i', '<i2'), ('j', '<i4')]), ('y', '<f8', (2,))], (2,))])
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