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from itertools import islice
import pytest
import numpy as np
from extra_data import (
H5File, KeyData, by_index, by_id,
AliasError, SourceNameError, PropertyNameError
)
def test_with_aliases(mock_sa3_control_data, mock_sa3_control_aliases):
run_without_aliases = H5File(mock_sa3_control_data)
run = run_without_aliases.with_aliases(mock_sa3_control_aliases)
def assert_equal_keydata(kd1, kd2):
assert isinstance(kd1, KeyData)
assert isinstance(kd2, KeyData)
assert kd1.source == kd2.source
assert kd1.key == kd2.key
assert kd1.train_ids == kd2.train_ids
# Test whether source alias yields identical SourceData.
assert run.alias['sa3-xgm'] is run['SA3_XTD10_XGM/XGM/DOOCS']
# Test alternative capitalisation and _ instead of -
assert run.alias['SA3_XGM'] is run['SA3_XTD10_XGM/XGM/DOOCS']
# Test __contains__()
assert "sa3-xgm" in run.alias
assert not "sa42-xgm" in run.alias
with pytest.raises(TypeError):
42 in run.alias
# Test whether source alias plus literal key yields equal KeyData.
assert_equal_keydata(
run.alias['sa3-xgm', 'pulseEnergy.wavelengthUsed'],
run['SA3_XTD10_XGM/XGM/DOOCS', 'pulseEnergy.wavelengthUsed'])
# Test whether key alias yields equal KeyData.
assert_equal_keydata(
run.alias['hv'],
run['SA3_XTD10_XGM/XGM/DOOCS', 'pulseEnergy.wavelengthUsed'])
# Test undefined aliases.
with pytest.raises(AliasError):
run.alias['foo']
run.alias['foo', 'bar']
# Test using a literal key with a key alias.
with pytest.raises(ValueError):
run.alias['hv', 'pressure']
# Test using an existing source alias for a non-existing source.
with pytest.raises(SourceNameError):
run.alias['bogus-source']
# Test using an existing key alias for a non-existing key.
with pytest.raises(PropertyNameError):
run.alias['bogus-key']
# Test re-applying the same aliases.
run2 = run.with_aliases(mock_sa3_control_aliases)
assert run._aliases == run2._aliases
# Test adding additional aliases.
run3 = run.with_aliases({'foo': 'bar'})
assert set(run._aliases.keys()) < set(run3._aliases.keys())
assert 'foo' in run3._aliases
# Test adding conflicting aliases
with pytest.raises(ValueError):
run.with_aliases({'sa3-xgm': 'x'})
# Test dropping aliases again.
run4 = run.drop_aliases()
assert not run4._aliases
# Smoke tests for __str__() and __repr__()
assert "Loaded aliases" in repr(run.alias)
assert "No aliases" in repr(run_without_aliases.alias)
str(run.alias)
def test_alias_clash(mock_sa3_control_data, mock_sa3_control_aliases):
run_without_aliases = H5File(mock_sa3_control_data)
# The aliases include 'mcp-adc' - test with an equivalent name
with pytest.raises(ValueError, match='conflicting alias'):
mock_sa3_control_aliases.update({'MCP_ADC': 'SA3_XTD10_MCP/ADC/2'})
run_without_aliases.with_aliases(mock_sa3_control_aliases)
def test_json_alias_file(mock_sa3_control_data, mock_sa3_control_aliases, tmp_path):
aliases_path = tmp_path / 'aliases.json'
aliases_path.write_text('''
{
"sa3-xgm": "SA3_XTD10_XGM/XGM/DOOCS",
"SA3_XTD10_XGM/XGM/DOOCS": {
"hv": "pulseEnergy.wavelengthUsed",
"beam-x": "beamPosition.ixPos",
"beam-y": "beamPosition.iyPos"
},
"imgfel-frames": ["SA3_XTD10_IMGFEL/CAM/BEAMVIEW:daqOutput", "data.image.pixels"],
"imgfel-frames2": ["SA3_XTD10_IMGFEL/CAM/BEAMVIEW2:daqOutput", "data.image.pixels"],
"imgfel-screen-pos": ["SA3_XTD10_IMGFEL/MOTOR/SCREEN", "actualPosition"],
"imgfel-filter-pos": ["SA3_XTD10_IMGFEL/MOTOR/FILTER", "actualPosition"],
"mcp-adc": "SA3_XTD10_MCP/ADC/1",
"mcp-mpod": "SA3_XTD10_MCP/MCPS/MPOD",
"mcp-voltage": ["SA3_XTD10_MCP/MCPS/MPOD", "channels.U3.voltage"],
"mcp-trace": ["SA3_XTD10_MCP/ADC/1:channel_5.output", "data.rawData"],
"bogus-source": "SA4_XTD20_XGM/XGM/DOOCS",
"bogus-key": ["SA3_XTD10_XGM/XGM/DOOCS", "foo"]
}
''')
run = H5File(mock_sa3_control_data).with_aliases(aliases_path)
assert run._aliases == mock_sa3_control_aliases
def test_yaml_alias_file(mock_sa3_control_data, mock_sa3_control_aliases, tmp_path):
aliases_path = tmp_path / 'aliases.yaml'
aliases_path.write_text('''
sa3-xgm: SA3_XTD10_XGM/XGM/DOOCS
SA3_XTD10_XGM/XGM/DOOCS:
hv: pulseEnergy.wavelengthUsed
beam-x: beamPosition.ixPos
beam-y: beamPosition.iyPos
imgfel-frames: [SA3_XTD10_IMGFEL/CAM/BEAMVIEW:daqOutput, data.image.pixels]
imgfel-frames2: [SA3_XTD10_IMGFEL/CAM/BEAMVIEW2:daqOutput, data.image.pixels]
imgfel-screen-pos: [SA3_XTD10_IMGFEL/MOTOR/SCREEN, actualPosition]
imgfel-filter-pos: [SA3_XTD10_IMGFEL/MOTOR/FILTER, actualPosition]
# Will be normalised to mcp-adc
MCP_ADC: SA3_XTD10_MCP/ADC/1
mcp-mpod: SA3_XTD10_MCP/MCPS/MPOD
mcp-voltage: [SA3_XTD10_MCP/MCPS/MPOD, channels.U3.voltage]
mcp-trace: [SA3_XTD10_MCP/ADC/1:channel_5.output, data.rawData]
bogus-source: SA4_XTD20_XGM/XGM/DOOCS
bogus-key: [SA3_XTD10_XGM/XGM/DOOCS, foo]
''')
run = H5File(mock_sa3_control_data).with_aliases(aliases_path)
assert run._aliases == mock_sa3_control_aliases
def test_toml_alias_file(mock_sa3_control_data, mock_sa3_control_aliases, tmp_path):
aliases_path = tmp_path / 'aliases.toml'
aliases_path.write_text('''
sa3-xgm = "SA3_XTD10_XGM/XGM/DOOCS"
imgfel-frames = ["SA3_XTD10_IMGFEL/CAM/BEAMVIEW:daqOutput", "data.image.pixels"]
imgfel-frames2 = ["SA3_XTD10_IMGFEL/CAM/BEAMVIEW2:daqOutput", "data.image.pixels"]
imgfel-screen-pos = ["SA3_XTD10_IMGFEL/MOTOR/SCREEN", "actualPosition"]
imgfel-filter-pos = ["SA3_XTD10_IMGFEL/MOTOR/FILTER", "actualPosition"]
mcp-adc = "SA3_XTD10_MCP/ADC/1"
mcp-mpod = "SA3_XTD10_MCP/MCPS/MPOD"
mcp-voltage = ["SA3_XTD10_MCP/MCPS/MPOD", "channels.U3.voltage"]
mcp-trace = ["SA3_XTD10_MCP/ADC/1:channel_5.output", "data.rawData"]
bogus-source = "SA4_XTD20_XGM/XGM/DOOCS"
bogus-key = ["SA3_XTD10_XGM/XGM/DOOCS", "foo"]
["SA3_XTD10_XGM/XGM/DOOCS"]
hv = "pulseEnergy.wavelengthUsed"
beam-x = "beamPosition.ixPos"
beam-y = "beamPosition.iyPos"
''')
run = H5File(mock_sa3_control_data).with_aliases(aliases_path)
assert run._aliases == mock_sa3_control_aliases
def test_only_aliases(mock_sa3_control_data, mock_sa3_control_aliases):
run = H5File(mock_sa3_control_data).with_aliases(mock_sa3_control_aliases)
subrun = H5File(mock_sa3_control_data).only_aliases(mock_sa3_control_aliases)
# Assume that aliases work when the _aliases property is equal.
assert run._aliases == subrun._aliases
# Test whether only the sources used in aliases are present.
assert subrun.all_sources == {
'SA3_XTD10_XGM/XGM/DOOCS',
'SA3_XTD10_IMGFEL/CAM/BEAMVIEW:daqOutput',
'SA3_XTD10_IMGFEL/CAM/BEAMVIEW2:daqOutput',
'SA3_XTD10_IMGFEL/MOTOR/SCREEN',
'SA3_XTD10_IMGFEL/MOTOR/FILTER',
'SA3_XTD10_MCP/ADC/1',
'SA3_XTD10_MCP/MCPS/MPOD',
'SA3_XTD10_MCP/ADC/1:channel_5.output',
}
# Test whether all keys are present for an aliased source.
assert subrun['SA3_XTD10_XGM/XGM/DOOCS'].keys() == run['SA3_XTD10_XGM/XGM/DOOCS'].keys()
# Test whether all keys are present for an aliased source, even if
# there are key aliases for it as well.
assert subrun['SA3_XTD10_MCP/MCPS/MPOD'].keys() == run['SA3_XTD10_MCP/MCPS/MPOD'].keys()
# Test whether only aliased keys are present for unaliased sources.
assert subrun['SA3_XTD10_IMGFEL/MOTOR/SCREEN'].keys() == {'actualPosition.value'}
# Test strict selection.
with pytest.raises(ValueError):
H5File(mock_sa3_control_data).only_aliases(
mock_sa3_control_aliases, strict=True)
# Remove bogus aliases and test strict selection again.
strict_aliases = mock_sa3_control_aliases.copy()
del strict_aliases['bogus-source']
del strict_aliases['bogus-key']
H5File(mock_sa3_control_data).only_aliases(strict_aliases, strict=True)
# Prepare a run with less trains for a single source
# (SA3_XTD10_IMGFEL/CAM/BEAMVIEW2:daqOutput) by removing all sources
# without any trains.
run = H5File(mock_sa3_control_data) \
.deselect([('SA3_XTD10_MCP/ADC/1:*', '*'),
('SA3_XTD10_IMGFEL/CAM/BEAMVIEW:*', '*')])
del strict_aliases['mcp-trace']
del strict_aliases['imgfel-frames']
# Without strict alias selection and a bogus alias.
subrun = run.only_aliases(mock_sa3_control_aliases,
require_all=True, strict=False)
np.testing.assert_array_equal(subrun.train_ids, run.train_ids[1::2])
# With strict alias selection.
subrun = run.only_aliases(strict_aliases, require_all=True, strict=True)
np.testing.assert_array_equal(subrun.train_ids, run.train_ids[1::2])
def test_preserve_aliases(mock_sa3_control_data, mock_sa3_control_aliases):
run = H5File(mock_sa3_control_data).with_aliases(mock_sa3_control_aliases)
# Test whether selection operations preserve aliases.
assert run.select_trains(by_index[:5])._aliases == run._aliases
assert run.select_trains(by_id[run.train_ids[:5]])._aliases == run._aliases
assert run.select('*')._aliases == run._aliases
assert run.deselect('*XGM*')._aliases == run._aliases
assert all([subrun._aliases == run._aliases
for subrun in run.split_trains(parts=5)])
def test_aliases_union(mock_sa3_control_data, mock_sa3_control_aliases):
run = H5File(mock_sa3_control_data).with_aliases(mock_sa3_control_aliases)
# Split the aliases into two halves and test the union.
run1 = run.with_aliases(dict(islice(mock_sa3_control_aliases.items(), 0, None, 2)))
run2 = run.with_aliases(dict(islice(mock_sa3_control_aliases.items(), 1, None, 2)))
assert run1.union(run2)._aliases == mock_sa3_control_aliases
# Split the run into two.
even_run = run.select_trains(by_id[run.train_ids[0::2]])
odd_run = run.select_trains(by_id[run.train_ids[1::2]])
# Test overlapping aliases with no conflict.
even_run.union(odd_run)
# Test conflicting aliases.
conflicting_aliases = mock_sa3_control_aliases.copy()
conflicting_aliases['hv'] = ('SA3_XTD10_XGM/XGM/DOOCS', 'pressure.pressure1')
with pytest.raises(ValueError):
even_run.union(odd_run.with_aliases(conflicting_aliases))
def test_alias_select(mock_sa3_control_data, mock_sa3_control_aliases):
run = H5File(mock_sa3_control_data).with_aliases(mock_sa3_control_aliases)
# Only source alias.
subrun = run.alias.select('sa3-xgm')
assert subrun.all_sources == {'SA3_XTD10_XGM/XGM/DOOCS'}
assert subrun.alias['sa3-xgm'].keys() == run.alias['sa3-xgm'].keys()
# Source alias and key glob.
subrun = run.alias.select('sa3-xgm', 'pressure.pressure*.value')
assert subrun.all_sources == {'SA3_XTD10_XGM/XGM/DOOCS'}
assert subrun.alias['sa3-xgm'].keys() == {
'pressure.pressure1.value', 'pressure.pressureFiltered.value'}
# Iterable of aliases and/or with key globs.
subrun = run.alias.select([('sa3-xgm', 'pressure.pressure*.value'),
'beam-x', 'mcp-voltage'])
assert subrun.all_sources == {'SA3_XTD10_XGM/XGM/DOOCS', 'SA3_XTD10_MCP/MCPS/MPOD'}
assert subrun.alias['sa3-xgm'].keys() == {
'pressure.pressure1.value', 'pressure.pressureFiltered.value',
'beamPosition.ixPos.value'}
assert subrun.alias['mcp-mpod'].keys() == {'channels.U3.voltage.value'}
# Dictionary
subrun = run.alias.select({'sa3-xgm': None, 'mcp-mpod': {'channels.U1.voltage'}})
assert subrun.all_sources == {'SA3_XTD10_XGM/XGM/DOOCS', 'SA3_XTD10_MCP/MCPS/MPOD'}
assert subrun.alias['sa3-xgm'].keys() == run.alias['sa3-xgm'].keys()
assert subrun.alias['mcp-mpod'].keys() == {'channels.U1.voltage.value'}
def test_alias_deselect(mock_sa3_control_data, mock_sa3_control_aliases):
run = H5File(mock_sa3_control_data).with_aliases(mock_sa3_control_aliases)
# De-select via alias.
subrun = run.alias.deselect([
('sa3-xgm', 'pressure.*'), ('sa3-xgm', 'current.*'),
('sa3-xgm', 'gasDosing.*'), ('sa3-xgm', 'gasSupply.*'),
('sa3-xgm', 'pressure.*'), ('sa3-xgm', 'pulseEnergy.*'),
('sa3-xgm', 'signalAdaption.*')
])
assert subrun.all_sources == run.all_sources
assert subrun.alias['sa3-xgm'].keys() == {
'beamPosition.ixPos.value', 'beamPosition.ixPos.timestamp',
'beamPosition.iyPos.value', 'beamPosition.iyPos.timestamp',
'pollingInterval.value', 'pollingInterval.timestamp'}
|
