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test nan fill value; improve meta tests
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‎zarr/tests/test_meta.py

Lines changed: 140 additions & 59 deletions
Original file line numberDiff line numberDiff line change
@@ -1,74 +1,152 @@
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# -*- coding: utf-8 -*-
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from __future__ import absolute_import, print_function, division
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import json
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import math
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56

6-
from nose.tools import eq_ as eq, assert_is_none, assert_raises
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from nose.tools import eq_ as eq, assert_is_none, assert_raises, assert_is
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import numpy as np
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910

1011
from zarr.compat import PY2
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from zarr.meta import decode_array_metadata, encode_dtype, decode_dtype, \
12-
ZARR_FORMAT, decode_group_metadata
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ZARR_FORMAT, decode_group_metadata, encode_array_metadata
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from zarr.errors import MetadataError
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1516

16-
def test_decode_array():
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# typical
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b = '''{
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"zarr_format": %s,
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"shape": [100],
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"chunks": [10],
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"dtype": "<f8",
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"compression": "zlib",
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"compression_opts": 1,
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"fill_value": null,
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"order": "C"
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}''' % ZARR_FORMAT
17+
def test_encode_decode_array_1():
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19+
meta = dict(
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shape=(100,),
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chunks=(10,),
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dtype=np.dtype('f8'),
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compression='zlib',
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compression_opts=1,
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fill_value=None,
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order='C'
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)
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29+
meta_bytes = '''{
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"chunks": [
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10
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],
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"compression": "zlib",
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"compression_opts": 1,
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"dtype": "<f8",
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"fill_value": null,
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"order": "C",
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"shape": [
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100
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],
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"zarr_format": %s
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}''' % ZARR_FORMAT
2943
if not PY2:
30-
b = b.encode('ascii')
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meta = decode_array_metadata(b)
32-
eq(ZARR_FORMAT, meta['zarr_format'])
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eq((100,), meta['shape'])
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eq((10,), meta['chunks'])
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eq(np.dtype('<f8'), meta['dtype'])
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eq('zlib', meta['compression'])
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eq(1, meta['compression_opts'])
38-
assert_is_none(meta['fill_value'])
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eq('C', meta['order'])
40-
41-
# variations
42-
b = '''{
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"zarr_format": %s,
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"shape": [100, 100],
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"chunks": [10, 10],
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"dtype": [["a", "i4"], ["b", "S10"]],
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"compression": "blosc",
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"compression_opts": {
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"cname": "lz4",
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"clevel": 3,
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"shuffle": 2
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},
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"fill_value": 42,
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"order": "F"
55-
}''' % ZARR_FORMAT
44+
meta_bytes = meta_bytes.encode('ascii')
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# test encoding
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meta_enc = encode_array_metadata(meta)
48+
eq(meta_bytes, meta_enc)
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50+
# test decoding
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meta_dec = decode_array_metadata(meta_bytes)
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eq(ZARR_FORMAT, meta_dec['zarr_format'])
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eq(meta['shape'], meta_dec['shape'])
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eq(meta['chunks'], meta_dec['chunks'])
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eq(meta['dtype'], meta_dec['dtype'])
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eq(meta['compression'], meta_dec['compression'])
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eq(meta['compression_opts'], meta_dec['compression_opts'])
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eq(meta['order'], meta_dec['order'])
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assert_is_none(meta_dec['fill_value'])
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def test_encode_decode_array_2():
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64+
# some variations
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meta = dict(
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shape=(100, 100),
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chunks=(10, 10),
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dtype=np.dtype([('a', 'i4'), ('b', 'S10')]),
69+
compression='blosc',
70+
compression_opts=dict(cname='lz4', clevel=3, shuffle=2),
71+
fill_value=42,
72+
order='F'
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)
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meta_bytes = '''{
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"chunks": [
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10,
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10
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],
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"compression": "blosc",
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"compression_opts": {
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"clevel": 3,
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"cname": "lz4",
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"shuffle": 2
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},
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"dtype": [
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[
88+
"a",
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"<i4"
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],
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[
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"b",
93+
"|S10"
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]
95+
],
96+
"fill_value": 42,
97+
"order": "F",
98+
"shape": [
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100,
100+
100
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],
102+
"zarr_format": %s
103+
}''' % ZARR_FORMAT
56104
if not PY2:
57-
b = b.encode('ascii')
58-
meta = decode_array_metadata(b)
59-
eq(ZARR_FORMAT, meta['zarr_format'])
60-
eq((100, 100), meta['shape'])
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eq((10, 10), meta['chunks'])
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# check structured dtype
63-
eq(np.dtype([('a', 'i4'), ('b', 'S10')]), meta['dtype'])
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# check structured compression_opts
65-
eq(dict(cname='lz4', clevel=3, shuffle=2), meta['compression_opts'])
66-
# check fill value
67-
eq(42, meta['fill_value'])
68-
eq('F', meta['order'])
105+
meta_bytes = meta_bytes.encode('ascii')
106+
107+
# test encoding
108+
meta_enc = encode_array_metadata(meta)
109+
eq(meta_bytes, meta_enc)
110+
111+
# test decoding
112+
meta_dec = decode_array_metadata(meta_bytes)
113+
eq(ZARR_FORMAT, meta_dec['zarr_format'])
114+
eq(meta['shape'], meta_dec['shape'])
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eq(meta['chunks'], meta_dec['chunks'])
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eq(meta['dtype'], meta_dec['dtype'])
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eq(meta['compression'], meta_dec['compression'])
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eq(meta['compression_opts'], meta_dec['compression_opts'])
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eq(meta['order'], meta_dec['order'])
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eq(meta['fill_value'], meta_dec['fill_value'])
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def test_encode_decode_array_nan_fill_value():
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125+
for fill in math.nan, np.nan:
126+
127+
meta = dict(
128+
shape=(100,),
129+
chunks=(10,),
130+
dtype=np.dtype('f8'),
131+
compression='zlib',
132+
compression_opts=1,
133+
fill_value=fill,
134+
order='C'
135+
)
136+
137+
# test fill value round trip
138+
meta_enc = encode_array_metadata(meta)
139+
meta_dec = decode_array_metadata(meta_enc)
140+
actual = meta_dec['fill_value']
141+
print(repr(actual))
142+
print(type(actual))
143+
assert np.isnan(actual)
144+
145+
146+
def test_decode_array_unsupported_format():
69147

70148
# unsupported format
71-
b = '''{
149+
meta_bytes = '''{
72150
"zarr_format": %s,
73151
"shape": [100],
74152
"chunks": [10],
@@ -79,18 +157,21 @@ def test_decode_array():
79157
"order": "C"
80158
}''' % (ZARR_FORMAT - 1)
81159
if not PY2:
82-
b = b.encode('ascii')
160+
meta_bytes = meta_bytes.encode('ascii')
83161
with assert_raises(MetadataError):
84-
decode_array_metadata(b)
162+
decode_array_metadata(meta_bytes)
163+
164+
165+
def test_decode_array_missing_fields():
85166

86167
# missing fields
87-
b = '''{
168+
meta_bytes = '''{
88169
"zarr_format": %s
89170
}''' % ZARR_FORMAT
90171
if not PY2:
91-
b = b.encode('ascii')
172+
meta_bytes = meta_bytes.encode('ascii')
92173
with assert_raises(MetadataError):
93-
decode_array_metadata(b)
174+
decode_array_metadata(meta_bytes)
94175

95176

96177
def test_encode_decode_dtype():

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