1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344
|
import numpy as np
import pytest
from extra_data import RunDirectory, by_id, by_index
from extra_data.exceptions import PropertyNameError, SourceNameError, NoDataError
def test_get_sourcedata(mock_spb_raw_run):
run = RunDirectory(mock_spb_raw_run)
am0 = run['SPB_DET_AGIPD1M-1/DET/0CH0:xtdf']
assert len(am0.files) == 1
assert am0.section == 'INSTRUMENT'
assert am0.is_instrument
assert not am0.is_control
assert am0.index_groups == {'header', 'detector', 'image', 'trailer'}
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
assert len(xgm.files) == 2
assert xgm.section == 'CONTROL'
assert xgm.is_control
assert not xgm.is_instrument
assert xgm.index_groups == {''}
def test_keys(mock_spb_raw_run):
run = RunDirectory(mock_spb_raw_run)
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
# Control keys can omit .value suffix, but .keys() will not list that.
assert 'beamPosition.ixPos.value' in xgm
assert 'beamPosition.ixPos' in xgm
assert 'beamPosition.ixPos.value' in xgm.keys()
assert 'beamPosition.ixPos.timestamp' in xgm.keys()
assert 'beamPosition.ixPos' not in xgm.keys()
assert xgm['beamPosition.ixPos.value'].dtype == np.dtype('f4')
assert xgm['beamPosition.ixPos'].dtype == np.dtype('f4')
# .keys(inc_timestamp=False) will give us only the name before '.value'
assert 'beamPosition.ixPos.value' not in xgm.keys(inc_timestamps=False)
assert 'beamPosition.ixPos.timestamp' not in xgm.keys(inc_timestamps=False)
assert 'beamPosition.ixPos' in xgm.keys(inc_timestamps=False)
# Recreate the run and xgm objects so we can test one_key() when the
# FileAccess caches are empty.
run = RunDirectory(mock_spb_raw_run)
xgm = run["SPB_XTD9_XGM/DOOCS/MAIN"]
# Make sure that one_key() does indeed return a valid key for
# control/instrument sources.
assert xgm.one_key() in xgm.keys()
xgm_output = run['SPB_XTD9_XGM/DOOCS/MAIN:output']
assert xgm_output.one_key() in xgm_output.keys()
# Test one_key() with index group.
am0 = run['SPB_DET_AGIPD1M-1/DET/0CH0:xtdf']
assert am0.one_key('image').startswith('image.')
with pytest.raises(ValueError):
# Asking for a de-selected index group.
assert am0.select_keys('header.*').one_key('image')
with pytest.raises(ValueError):
# Not an index group of this source.
assert am0.one_key('data')
def test_select_keys(mock_spb_raw_run):
run = RunDirectory(mock_spb_raw_run)
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
# Select exact key
xpos_key = 'beamPosition.ixPos.value'
assert xgm.select_keys('beamPosition.ixPos.value').keys() == {xpos_key}
assert xgm.select_keys('beamPosition.ixPos').keys() == {xpos_key}
assert xgm.select_keys({'beamPosition.ixPos.value'}).keys() == {xpos_key}
assert xgm.select_keys({'beamPosition.ixPos'}).keys() == {xpos_key}
# Select all keys
all_keys = xgm.keys()
assert xgm.select_keys(set()).keys() == all_keys
assert xgm.select_keys(None).keys() == all_keys
assert xgm.select_keys('*').keys() == all_keys
# Select keys with glob pattern
beampos_keys = {
'beamPosition.ixPos.value', 'beamPosition.ixPos.timestamp',
'beamPosition.iyPos.value', 'beamPosition.iyPos.timestamp'
}
assert xgm.select_keys('beamPosition.*').keys() == beampos_keys
assert xgm.select_keys('beamPosition.*').select_keys('*').keys() == beampos_keys
# select keys on INSTRUMENT data
am0 = run['SPB_DET_AGIPD1M-1/DET/0CH0:xtdf']
key = 'image.data'
assert am0.select_keys(key).keys() == {key}
assert am0.select_keys('*').keys() == am0.keys()
with pytest.raises(PropertyNameError):
am0.select_keys('data.image')
def test_select_trains(mock_spb_raw_run):
run = RunDirectory(mock_spb_raw_run)
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
assert len(xgm.train_ids) == 64
sel = xgm.select_trains(by_id[10020:10040])
assert sel.train_ids == list(range(10020, 10040))
sel = xgm.select_trains(by_index[:10])
assert sel.train_ids == list(range(10000, 10010))
sel = xgm.select_trains(by_index[999995:999999])
assert sel.train_ids == []
assert sel.keys() == xgm.keys()
sel = xgm[by_id[10020:10040]]
assert sel.train_ids == list(range(10020, 10040))
sel = xgm[by_index[:10]]
assert sel.train_ids == list(range(10000, 10010))
sel = xgm[10]
assert sel.train_ids == [10010]
sel = xgm[999:1000]
assert sel.train_ids == []
assert sel.keys() == xgm.keys()
def test_split_trains(mock_spb_raw_run):
run = RunDirectory(mock_spb_raw_run)
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
assert len(xgm.train_ids) == 64
chunks = list(xgm.split_trains(3))
assert len(chunks) == 3
assert {len(c.train_ids) for c in chunks} == {21, 22}
# The middle chunk spans across 2 files
assert [len(c.files) for c in chunks] == [1, 2, 1]
chunks = list(xgm.split_trains(3, trains_per_part=20))
assert len(chunks) == 4
assert {len(c.train_ids) for c in chunks} == {16}
def test_union(mock_spb_raw_run):
run = RunDirectory(mock_spb_raw_run)
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
am0 = run['SPB_DET_AGIPD1M-1/DET/0CH0:xtdf']
sel = xgm.select_trains(np.s_[:10]).union(xgm.select_trains(np.s_[-10:]))
assert sel.train_ids == list(range(10000, 10010)) + list(range(10054, 10064))
with pytest.raises(ValueError):
xgm.union(am0)
sel = xgm.select_trains(np.s_[:10]) | xgm.select_trains(np.s_[-10:])
assert sel.train_ids == list(range(10000, 10010)) + list(range(10054, 10064))
sel = xgm.select_trains(np.s_[:10])
sel |= xgm.select_trains(np.s_[-10:])
assert sel.train_ids == list(range(10000, 10010)) + list(range(10054, 10064))
def test_run_value(mock_spb_raw_run):
run = RunDirectory(mock_spb_raw_run)
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
am0 = run['SPB_DET_AGIPD1M-1/DET/0CH0:xtdf']
value = xgm.run_value('pulseEnergy.conversion.value')
assert isinstance(value, np.float64)
run_dict = xgm.run_values()
assert 'pulseEnergy.conversion.value' in run_dict
assert 'pulseEnergy.conversion.timestamp' in run_dict
values_dict = xgm.run_values(inc_timestamps=False)
assert 'pulseEnergy.conversion' in values_dict
assert 'pulseEnergy.conversion.timestamp' not in values_dict
with pytest.raises(ValueError):
# no run values for instrument sources
am0.run_values()
def test_device_class(mock_spb_raw_run):
run = RunDirectory(mock_spb_raw_run)
xgm_ctrl = run['SPB_XTD9_XGM/DOOCS/MAIN']
assert xgm_ctrl.device_class == 'DoocsXGM'
xgm_inst = run['SPB_XTD9_XGM/DOOCS/MAIN:output']
assert xgm_inst.device_class is None
def test_euxfel_path_infos(mock_spb_raw_run):
run = RunDirectory(mock_spb_raw_run)
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
assert xgm.storage_class is None # Not an EuXFEL path.
assert xgm.data_category == 'RAW'
assert xgm.aggregator == 'DA01'
# Changed to preserve the behaviour of above, as using a voview
# file with 0-len datasets anyway causes a return of None. It
# therefore attempts to use the regular .files property instead,
# either suceeding or failing as badly as it would with a voview.
run = RunDirectory(mock_spb_raw_run).select_trains(np.s_[:0])
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
assert xgm.storage_class is None
assert xgm.aggregator == 'DA01'
@pytest.mark.parametrize('source', [
'SPB_XTD9_XGM/DOOCS/MAIN', # Control data.
'SPB_IRU_CAM/CAM/SIDEMIC:daqOutput', # Pipeline data.
'SPB_DET_AGIPD1M-1/DET/0CH0:xtdf' # XTDF data.
])
def test_data_counts_modes(mock_reduced_spb_proc_run, source):
run = RunDirectory(mock_reduced_spb_proc_run)
sd = run[source]
import pandas as pd
for index_group in [None, *sd.index_groups]:
count1 = sd.data_counts(index_group=index_group)
assert isinstance(count1, pd.Series)
assert count1.index.tolist() == sd.train_ids
count2 = sd.data_counts(labelled=False, index_group=index_group)
assert isinstance(count2, np.ndarray)
assert len(count2) == len(sd.train_ids)
np.testing.assert_equal(count1, count2)
def test_data_counts_values(mock_reduced_spb_proc_run):
run = RunDirectory(mock_reduced_spb_proc_run)
# control data
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
assert (xgm.data_counts().values == 1).all()
with pytest.raises(ValueError):
xgm.data_counts(index_group='data')
# instrument data
camera = run['SPB_IRU_CAM/CAM/SIDEMIC:daqOutput']
assert (camera.data_counts().values == 1).all()
with pytest.raises(ValueError):
camera.data_counts(index_group='not-data')
am0 = run['SPB_DET_AGIPD1M-1/DET/0CH0:xtdf']
num_images = am0['image.data'].shape[0]
assert am0.data_counts().values.sum() >= num_images
assert am0.data_counts(index_group='image').values.sum() == num_images
with pytest.raises(ValueError):
am0.data_counts(index_group='preamble')
def test_drop_empty_trains(mock_reduced_spb_proc_run):
run = RunDirectory(mock_reduced_spb_proc_run)
am0 = run['SPB_DET_AGIPD1M-1/DET/0CH0:xtdf']
# Compare all index groups with `require_any`.
np.testing.assert_equal(
am0.drop_empty_trains().train_ids,
run.select(am0.source, '*', require_any=True).train_ids)
# Compare one specific index group with `require_all`.
np.testing.assert_equal(
am0.drop_empty_trains(index_group='image').train_ids,
run.select(am0.source, 'image.*', require_all=True).train_ids)
with pytest.raises(ValueError):
am0.drop_empty_trains(index_group='preamble')
def test_train_id_coordinates(mock_reduced_spb_proc_run):
run = RunDirectory(mock_reduced_spb_proc_run)
# control data.
xgm = run['SPB_XTD9_XGM/DOOCS/MAIN']
np.testing.assert_equal(
xgm.train_id_coordinates(),
xgm.train_id_coordinates(''))
np.testing.assert_equal(
xgm.train_id_coordinates(),
xgm['pulseEnergy.conversion'].train_id_coordinates())
with pytest.raises(ValueError):
xgm.train_id_coordinates('data')
# instrument data.
camera = run['SPB_IRU_CAM/CAM/SIDEMIC:daqOutput']
np.testing.assert_equal(
camera.train_id_coordinates(),
camera.train_id_coordinates('data'))
np.testing.assert_equal(
camera.train_id_coordinates(),
camera['data.image.pixels'].train_id_coordinates())
with pytest.raises(ValueError):
camera.train_id_coordinates('image')
# xtdf data.
am0 = run['SPB_DET_AGIPD1M-1/DET/0CH0:xtdf']
np.testing.assert_equal(
am0.train_id_coordinates('header'),
am0['header.pulseCount'].train_id_coordinates())
np.testing.assert_equal(
am0.train_id_coordinates('image'),
am0['image.data'].train_id_coordinates())
# Should fail due to multiple index groups with differing counts.
with pytest.raises(ValueError):
am0.train_id_coordinates()
def test_legacy_sourcedata(mock_modern_spb_proc_run):
run = RunDirectory(mock_modern_spb_proc_run)
det_mod0 = 'SPB_DET_AGIPD1M-1/DET/0CH0:xtdf'
corr_mod0 = 'SPB_DET_AGIPD1M-1/CORR/0CH0:output'
# True (canonical) source works as normal
sd = run[corr_mod0]
assert sd.canonical_name == corr_mod0
assert not sd.is_legacy
# Obtaining SourceData object via legacy name emits a warning.
with pytest.warns(DeprecationWarning):
sd = run[det_mod0]
assert sd.source == det_mod0
assert sd.canonical_name == corr_mod0
assert sd.is_legacy
|