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from pathlib import Path
import numpy as np
import pytest
from dateutil import parser, tz
import rsciio.utils.date_time_tools as dtt
from rsciio.utils.distributed import get_chunk_slice
from rsciio.utils.tools import ET, DTBox, XmlToDict, dict2sarray, sanitize_msxml_float
dt = [("x", np.uint8), ("y", np.uint16), ("text", (bytes, 6))]
@pytest.fixture
def XML_TEST_NODE():
MY_PATH = Path(__file__).parent
TEST_XML_PATH = MY_PATH / ".." / "data" / "ToastedBreakFastSDD.xml"
with open(TEST_XML_PATH, "r") as fn:
weird_but_valid_xml_str = fn.read()
yield ET.fromstring(weird_but_valid_xml_str)
# fmt: off
def test_msxml_sanitization():
bad_msxml = b"""
<main>
<simpleFloat>0,2</simpleFloat>
<scientificSmall>1,9E-5</scientificSmall>
<scientificBig>0,2E10</scientificBig>
<actuallyList>0,2,3</actuallyList>
</main>
"""
sanitized_xml_bytes = sanitize_msxml_float(bad_msxml)
et = ET.fromstring(sanitized_xml_bytes)
assert et[0].text == "0.2"
assert et[1].text == "1.9E-5"
assert et[2].text == "0.2E10"
assert et[3].text == "0,2,3" # is not float
def test_default_x2d(XML_TEST_NODE):
"""test of default XmlToDict translation with attributes prefixed with @,
interchild_text_parsing set to 'first',
no flattening tags set, and dub_text_str set to '#value'
"""
x2d = XmlToDict()
pynode = x2d.dictionarize(XML_TEST_NODE)
assert (
pynode["TestXML"]["Main"]["ClassInstance"]["Sample"]["Components"][
"ComponentChildren"
]["Instance"][0]["name"]
== 'Eggs'
)
t = "With one of these components"
assert pynode["TestXML"]["Main"]["ClassInstance"]["Sample"]["#value"] == t
def test_skip_interchild_text_flatten(XML_TEST_NODE):
"""test of XmlToDict translation with interchild_text_parsing set to 'skip',
three string containing list set to flattening tags. Other kwrds - default.
"""
x2d = XmlToDict(
interchild_text_parsing='skip',
tags_to_flatten=["ClassInstance", "ComponentChildren", "Instance", "TestXML"],
)
pynode = x2d.dictionarize(XML_TEST_NODE)
assert pynode["Main"]["Sample"]["Components"]["name"][0] == "Eggs"
assert pynode["Main"]["Sample"].get("#value") is None
def test_concat_interchild_text_val_flatten(XML_TEST_NODE):
"""test of XmlToDict translator with interchild_text_parsing set to
'cat' (concatenation), four flattening tags set, and dub_text_str set
to '#text'
"""
x2d = XmlToDict(
dub_text_str="#text",
interchild_text_parsing='cat',
tags_to_flatten=["ClassInstance", "ComponentChildren", "Instance", "Main"],
)
pynode = x2d.dictionarize(XML_TEST_NODE.find("Main"))
assert pynode["Instrument"]["Type"].get("#value") is None
assert pynode["Instrument"]["Type"]["#text"] == "Toaster"
assert pynode["Sample"].get("#value") is None
assert pynode["Sample"].get("#text") is None
t = "With one of these componentsSDD risks to be Toasted."
assert pynode["Sample"]["#interchild_text"] == t
def test_list_interchild_text_val_flatten(XML_TEST_NODE):
"""test of XmlToDict translator interchild_text_parsing set to 'list'
"""
x2d = XmlToDict(
dub_text_str="#value",
interchild_text_parsing='list',
tags_to_flatten=["ClassInstance", "ComponentChildren", "Instance"]
)
pynode = x2d.dictionarize(XML_TEST_NODE.find("Main//Sample"))
assert pynode["Sample"]["#interchild_text"] == [
"With one of these components",
"",
"SDD risks to be Toasted.",
]
def x2d_subclass_for_custom_bool(XML_TEST_NODE):
"""test subclass of XmlToDict with updated eval function"""
class CustomXmlToDict(XmlToDict):
@staticmethod
def eval(string):
if string == "not today":
return False
if string == "affirmative":
return True
return XmlToDict.eval(string)
x2d = CustomXmlToDict(
dub_text_str="#value",
tags_to_flatten=["ClassInstance", "ComponentChildren", "Instance"],
)
node = XML_TEST_NODE.find("Main//Instrument")
pynode = x2d.dictionarize(node)
assert pynode["IsToasted"] is False
assert pynode["IsToasting"] is True
def test_wrong_type_x2d_initiation():
with pytest.raises(ValueError):
XmlToDict(dub_attr_pre_str=1)
with pytest.raises(ValueError):
XmlToDict(tags_to_flatten=0)
with pytest.raises(ValueError):
XmlToDict(interchild_text_parsing="simple")
with pytest.raises(ValueError):
XmlToDict(dub_text_str=2)
def _get_example(date, time, time_zone=None):
md = DTBox({"General": {"date": date, "time": time}}, box_dots=True)
if time_zone:
md.set_item("General.time_zone", time_zone)
dt = parser.parse("%sT%s" % (date, time))
dt = dt.replace(tzinfo=tz.gettz(time_zone))
iso = dt.isoformat()
else:
iso = "%sT%s" % (date, time)
dt = parser.parse(iso)
return md, dt, iso
md1, dt1, iso1 = _get_example("2014-12-27", "00:00:00", "UTC")
serial1 = 42000.00
md2, dt2, iso2 = _get_example("2124-03-25", "10:04:48", "EST")
serial2 = 81900.62833333334
md3, dt3, iso3 = _get_example("2016-07-12", "22:57:32")
serial3 = 42563.95662037037
def test_d2s_fail():
d = dict(x=5, y=10, text="abcdef")
with pytest.raises(ValueError):
dict2sarray(d)
def test_d2s_dtype():
d = dict(x=5, y=10, text="abcdef")
ref = np.zeros((1,), dtype=dt)
ref["x"] = 5
ref["y"] = 10
ref["text"] = "abcdef"
assert ref == dict2sarray(d, dtype=dt)
def test_d2s_extra_dict_ok():
d = dict(x=5, y=10, text="abcdef", other=55)
ref = np.zeros((1,), dtype=dt)
ref["x"] = 5
ref["y"] = 10
ref["text"] = "abcdef"
assert ref == dict2sarray(d, dtype=dt)
def test_d2s_sarray():
d = dict(x=5, y=10, text="abcdef")
base = np.zeros((1,), dtype=dt)
base["x"] = 65
base["text"] = "gg"
ref = np.zeros((1,), dtype=dt)
ref["x"] = 5
ref["y"] = 10
ref["text"] = "abcdef"
assert ref == dict2sarray(d, sarray=base)
def test_d2s_partial_sarray():
d = dict(text="abcdef")
base = np.zeros((1,), dtype=dt)
base["x"] = 65
base["text"] = "gg"
ref = np.zeros((1,), dtype=dt)
ref["x"] = 65
ref["y"] = 0
ref["text"] = "abcdef"
assert ref == dict2sarray(d, sarray=base)
def test_d2s_type_cast_ok():
d = dict(x="34", text=55)
ref = np.zeros((1,), dtype=dt)
ref["x"] = 34
ref["y"] = 0
ref["text"] = "55"
assert ref == dict2sarray(d, dtype=dt)
def test_d2s_type_cast_invalid():
d = dict(x="Test")
with pytest.raises(ValueError):
dict2sarray(d, dtype=dt)
def test_d2s_string_cut():
d = dict(text="Testerstring")
sa = dict2sarray(d, dtype=dt)
assert sa["text"][0] == b"Tester"
def test_d2s_array1():
dt2 = dt + [("z", (np.uint8, 4)), ("u", (np.uint16, 4))]
d = dict(z=2, u=[1, 2, 3, 4])
sa = dict2sarray(d, dtype=dt2)
np.testing.assert_array_equal(sa["z"][0], [2, 2, 2, 2])
np.testing.assert_array_equal(sa["u"][0], [1, 2, 3, 4])
def test_d2s_array2():
d = dict(x=2, y=[1, 2, 3, 4])
sa = np.zeros((4,), dtype=dt)
sa = dict2sarray(d, sarray=sa)
np.testing.assert_array_equal(sa["x"], [2, 2, 2, 2])
np.testing.assert_array_equal(sa["y"], [1, 2, 3, 4])
def test_d2s_arrayX():
dt2 = dt + [("z", (np.uint8, 4)), ("u", (np.uint16, 4))]
d = dict(z=2, u=[1, 2, 3, 4])
sa = np.zeros((4,), dtype=dt2)
sa = dict2sarray(d, sarray=sa)
np.testing.assert_array_equal(
sa["z"],
[
[2, 2, 2, 2],
]
* 4,
)
np.testing.assert_array_equal(
sa["u"],
[
[1, 2, 3, 4],
]
* 4,
)
def test_serial_date_to_ISO_format():
iso_1 = dtt.serial_date_to_ISO_format(serial1)
dt1_local = dt1.astimezone(tz.tzlocal())
assert iso_1[0] == dt1_local.date().isoformat()
assert iso_1[1] == dt1_local.time().isoformat()
assert iso_1[2] == dt1_local.tzname()
iso_2 = dtt.serial_date_to_ISO_format(serial2)
dt2_local = dt2.astimezone(tz.tzlocal())
assert iso_2[0] == dt2_local.date().isoformat()
# The below line will/can fail due to accuracy loss when converting to serial date:
# We therefore truncate milli/micro seconds
assert iso_2[1][:8] == dt2_local.time().isoformat()
assert iso_2[2] == dt2_local.tzname()
iso_3 = dtt.serial_date_to_ISO_format(serial3)
dt3_aware = dt3.replace(tzinfo=tz.tzutc())
dt3_local = dt3_aware.astimezone(tz.tzlocal())
assert iso_3[0] == dt3_local.date().isoformat()
assert iso_3[1] == dt3_local.time().isoformat()
assert iso_3[2] == dt3_local.tzname()
def test_ISO_format_to_serial_date():
res1 = dtt.ISO_format_to_serial_date(
dt1.date().isoformat(), dt1.time().isoformat(), timezone=dt1.tzname()
)
np.testing.assert_allclose(res1, serial1, atol=1e-5)
dt = dt2.astimezone(tz.tzlocal())
res2 = dtt.ISO_format_to_serial_date(
dt.date().isoformat(), dt.time().isoformat(), timezone=dt.tzname()
)
np.testing.assert_allclose(res2, serial2, atol=1e-5)
res3 = dtt.ISO_format_to_serial_date(
dt3.date().isoformat(), dt3.time().isoformat(), timezone=dt3.tzname()
)
np.testing.assert_allclose(res3, serial3, atol=1e-5)
def test_datetime_to_serial_date():
np.testing.assert_allclose(dtt.datetime_to_serial_date(dt1), serial1, atol=1e-5)
np.testing.assert_allclose(dtt.datetime_to_serial_date(dt2), serial2, atol=1e-5)
np.testing.assert_allclose(dtt.datetime_to_serial_date(dt3), serial3, atol=1e-5)
def _get_example(date, time, time_zone=None):
md = {"General": {"date": date, "time": time}}
if time_zone:
md["General"]["time_zone"] = time_zone
dt = parser.parse(f"{date}T{time}")
dt = dt.replace(tzinfo=tz.gettz(time_zone))
iso = dt.isoformat()
else:
iso = f"{date}T{time}"
dt = parser.parse(iso)
return md, dt, iso
md1, dt1, iso1 = _get_example("2014-12-27", "00:00:00", "UTC")
serial1 = 42000.00
md2, dt2, iso2 = _get_example("2124-03-25", "10:04:48", "EST")
serial2 = 81900.62833333334
md3, dt3, iso3 = _get_example("2016-07-12", "22:57:32")
serial3 = 42563.95662037037
def test_get_date_time_from_metadata():
assert dtt.get_date_time_from_metadata(md1) == "2014-12-27T00:00:00+00:00"
assert (
dtt.get_date_time_from_metadata(md1, formatting="ISO")
== "2014-12-27T00:00:00+00:00"
)
assert dtt.get_date_time_from_metadata(
md1, formatting="datetime64"
) == np.datetime64("2014-12-27T00:00:00.000000")
assert dtt.get_date_time_from_metadata(md1, formatting="datetime") == dt1
assert dtt.get_date_time_from_metadata(md2) == "2124-03-25T10:04:48-05:00"
assert dtt.get_date_time_from_metadata(md2, formatting="datetime") == dt2
assert dtt.get_date_time_from_metadata(
md2, formatting="datetime64"
) == np.datetime64("2124-03-25T10:04:48")
assert dtt.get_date_time_from_metadata(md3) == "2016-07-12T22:57:32"
assert dtt.get_date_time_from_metadata(md3, formatting="datetime") == dt3
assert dtt.get_date_time_from_metadata(
md3, formatting="datetime64"
) == np.datetime64("2016-07-12T22:57:32.000000")
assert dtt.get_date_time_from_metadata({"General": {}}) is None
assert (
dtt.get_date_time_from_metadata({"General": {"date": "2016-07-12"}})
== "2016-07-12"
)
assert dtt.get_date_time_from_metadata({"General": {"time": "12:00"}}) == "12:00:00"
assert (
dtt.get_date_time_from_metadata(
{"General": {"time": "12:00", "time_zone": "CET"}}
)
== "12:00:00"
)
@pytest.mark.parametrize(
"shape",
((10, 20, 30, 512, 512), (20, 30, 512, 512), (10, 512, 512), (512, 512))
)
def test_get_chunk_slice(shape):
chunk_arr, chunk = get_chunk_slice(shape=shape, chunks=-1) # 1 chunk
assert chunk_arr.shape == (1,)*len(shape)+(len(shape), 2)
assert chunk == tuple([(i,)for i in shape])
chunks = (1,)*(len(shape)-2) +(-1,-1)
# Eveything is 1 chunk
chunk_arr, chunk = get_chunk_slice(shape=shape, chunks=chunks)
assert chunk_arr.shape == shape[:-2]+(1, 1) + (len(shape), 2)
assert chunk == (
tuple([(1,)*i for i in shape[:-2]])+tuple([(i,) for i in shape[-2:]])
)
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