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import numpy as np
import pytest
# numpy.exceptions exists from 1.25 onwards, but for Python 3.8 we still support
# numpy 1.24. We can clean this up once we require Python >= 3.9.
try:
from numpy.exceptions import AxisError
except ImportError:
from numpy import AxisError
from extra_data import RunDirectory, stack_data, stack_detector_data
from extra_data.stacking import StackView
def test_stack_data(mock_fxe_raw_run):
test_run = RunDirectory(mock_fxe_raw_run)
tid, data = test_run.train_from_id(10000, devices=[('FXE_DET_LPD1M-1/DET/*', 'image.data')])
comb = stack_data(data, 'image.data')
assert comb.shape == (128, 1, 16, 256, 256)
def test_stack_detector_data(mock_fxe_raw_run):
test_run = RunDirectory(mock_fxe_raw_run)
tid, data = test_run.train_from_id(10000, devices=[('*1M*/DET/*', 'image.data')])
comb = stack_detector_data(data, 'image.data')
assert comb.shape == (128, 1, 16, 256, 256)
def test_stack_detector_data_missing(mock_fxe_raw_run):
test_run = RunDirectory(mock_fxe_raw_run)
tid, data = test_run.train_from_id(10000, devices=[('*/DET/*', 'image.data')])
# Three variants of missing data:
# 1. Source missing
del data['FXE_DET_LPD1M-1/DET/3CH0:xtdf']
# 2. Key missing
del data['FXE_DET_LPD1M-1/DET/7CH0:xtdf']['image.data']
# 3. Empty array
missing = ['FXE_DET_LPD1M-1/DET/{}CH0:xtdf'.format(m) for m in (1, 5, 9, 15)]
for module in missing:
data[module]['image.data'] = np.zeros((0, 1, 256, 256), dtype=np.uint16)
comb = stack_detector_data(data, 'image.data', fillvalue=22)
assert comb.shape == (128, 1, 16, 256, 256)
assert not (comb[:, :, 0] == 22).any() # Control
assert (comb[:, :, 3] == 22).all() # Source missing
assert (comb[:, :, 7] == 22).all() # Key missing
assert (comb[:, :, 5] == 22).all() # Empty array
# default fillvalue for int is 0
comb = stack_detector_data(data, 'image.data')
assert (comb[:, :, 3] == 0).all()
with pytest.raises(ValueError):
comb = stack_detector_data(data, 'image.data', fillvalue=np.nan)
def test_stack_detector_data_stackview(mock_fxe_raw_run):
test_run = RunDirectory(mock_fxe_raw_run)
tid, data = test_run.train_from_id(10000, devices=[('*/DET/*', 'image.data')])
# Three variants of missing data:
# 1. Source missing
del data['FXE_DET_LPD1M-1/DET/3CH0:xtdf']
# 2. Key missing
del data['FXE_DET_LPD1M-1/DET/7CH0:xtdf']['image.data']
# 3. Empty array
missing = ['FXE_DET_LPD1M-1/DET/{}CH0:xtdf'.format(m) for m in (1, 5, 9, 15)]
for module in missing:
data[module]['image.data'] = np.zeros((0, 1, 256, 256), dtype=np.uint16)
comb = stack_detector_data(data, 'image.data', fillvalue=22, real_array=False)
assert comb.shape == (128, 1, 16, 256, 256)
assert not (comb[:, :, 0] == 22).any() # Control
assert (comb[:, :, 3] == 22).all() # Source missing
assert (comb[:, :, 7] == 22).all() # Key missing
assert (comb[:, :, 5] == 22).all() # Empty array
# Slice across all modules
pulse = comb[0, 0]
assert pulse.shape == (16, 256, 256)
assert not (pulse[0] == 22).any()
assert (pulse[3] == 22).all()
assert (pulse[7] == 22).all()
assert (pulse[5] == 22).all()
pulse_arr = pulse.asarray()
assert pulse_arr.shape == (16, 256, 256)
assert pulse_arr.max() == 22
assert pulse_arr.min() == 0
def test_stack_detector_data_wrong_pulses(mock_fxe_raw_run):
test_run = RunDirectory(mock_fxe_raw_run)
tid, data = test_run.train_from_id(10000, devices=[('*/DET/*', 'image.data')])
misshaped = ['FXE_DET_LPD1M-1/DET/{}CH0:xtdf'.format(m) for m in (12, 13)]
for module in misshaped:
data[module]['image.data'] = np.zeros((64, 1, 256, 256), dtype=np.uint16)
with pytest.raises(ValueError) as excinfo:
comb = stack_detector_data(data, 'image.data')
assert '(64, 1, 256, 256)' in str(excinfo.value)
def test_stack_detector_data_wrong_shape(mock_fxe_raw_run):
test_run = RunDirectory(mock_fxe_raw_run)
tid, data = test_run.train_from_id(10000, devices=[('*/DET/*', 'image.data')])
misshaped = ['FXE_DET_LPD1M-1/DET/{}CH0:xtdf'.format(m) for m in (0, 15)]
for module in misshaped:
data[module]['image.data'] = np.zeros((128, 1, 512, 128), dtype=np.uint16)
with pytest.raises(ValueError) as excinfo:
comb = stack_detector_data(data, 'image.data')
assert '(128, 1, 512, 128)' in str(excinfo.value)
def test_stack_detector_data_type_error(mock_fxe_raw_run):
test_run = RunDirectory(mock_fxe_raw_run)
tid, data = test_run.train_from_id(10000, devices=[('*/DET/*', 'image.data')])
module = 'FXE_DET_LPD1M-1/DET/3CH0:xtdf'
data[module]['image.data'] = data[module]['image.data'].astype(np.float32)
with pytest.raises(ValueError) as excinfo:
comb = stack_detector_data(data, 'image.data')
assert "dtype('float32')" in str(excinfo.value)
def test_stack_detector_data_extra_mods(mock_fxe_raw_run):
test_run = RunDirectory(mock_fxe_raw_run)
tid, data = test_run.train_from_id(10000, devices=[('*/DET/*', 'image.data')])
data.setdefault(
'FXE_DET_LPD1M-1/DET/16CH0:xtdf',
{'image.data': np.zeros((128, 1, 256, 256), dtype=np.uint16)},
)
with pytest.raises(IndexError) as excinfo:
comb = stack_detector_data(data, 'image.data')
assert "16" in str(excinfo.value)
def test_stack_detector_data_jungfrau(mock_jungfrau_run):
run = RunDirectory(mock_jungfrau_run)
_, data = run.select('*JF4M/DET/*', 'data.adc').train_from_index(0)
comb = stack_detector_data(
data, 'data.adc', modules=8, pattern=r'/DET/JNGFR(\d+)', starts_at=1
)
assert comb.shape == (16, 8, 512, 1024)
def test_stack_detector_data_jungfrau_keep_dims(mock_jungfrau_run):
run = RunDirectory(mock_jungfrau_run)
_, data = run.select('*JF4M/DET/*', 'data.adc').train_from_index(0, keep_dims=True)
comb = stack_detector_data(
data, 'data.adc', modules=8, pattern=r'/DET/JNGFR(\d+)', starts_at=1
)
assert comb.shape == (1, 16, 8, 512, 1024)
def test_stackview_squeeze():
# Squeeze not dropping stacking dim
data = {0: np.zeros((1, 4)), 1: np.zeros((1, 4))}
sv = StackView(data, 2, (1, 4), data[0], 0, stack_axis=0)
assert sv.shape == (2, 1, 4)
assert sv.squeeze().shape == (2, 4)
# Squeeze dropping stacking dim
data = {0: np.zeros((1, 4))}
sv = StackView(data, 1, (1, 4), data[0].dtype, 0, stack_axis=0)
assert sv.shape == (1, 1, 4)
assert sv.squeeze().shape == (4,)
assert sv.squeeze(axis=0).shape == (1, 4)
assert sv.squeeze(axis=-2).shape == (1, 4)
with pytest.raises(AxisError):
sv.squeeze(axis=4)
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