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Merge pull request #275 from European-XFEL/fix/timepix-sources
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Fix too restrictive auto detection in Timepix component
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@philsmt
philsmt authored Dec 19, 2024
2 parents 2905b9f + 065413d commit 6e256f0
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Showing 2 changed files with 110 additions and 24 deletions.
95 changes: 71 additions & 24 deletions src/extra/components/timepix.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -33,10 +33,11 @@ class Timepix3:
Args:
data (extra_data.DataCollection): Data to access Timepix3 data from.
detector (str, optional): Name of the detector, only
needed if the data includes more than one. This should
be the first part of the source name, i.e. up to the first
slash.
detector (str or tuple, optional): Name of the detector, which
may be the domain (first part of the source name up to the
first slash) or a tuple with the explicit raw and centroided
source name. If omitted, an attempt is made to detect them
automatically.
pulses (extra.components.pulses.PulsePattern, optional): Pulse
component to pull pulse information. If omitted, an
[XrayPulses][extra.components.XrayPulses] object is
Expand All @@ -45,7 +46,7 @@ class Timepix3:

# Only support single-chip detectors for now.
_instrument_re = re.compile(
r'^(\w{3}_\w+_TIMEPIX)\/(DET|CAL)\/\w+:daqOutput.chip0$')
r'^(\w{3}_\w+_TIMEPIX)\/(CAM|DET|CAL)\/\w+:daqOutput.chip0$')

def __init__(self, data, detector=None, pulses=None, **kwargs):
# Always run detection to potentially find the raw and
Expand All @@ -59,7 +60,7 @@ def __init__(self, data, detector=None, pulses=None, **kwargs):
self._centroids_instrument_src = None

for source in sources:
if '/DET/' in source:
if '/DET/' in source or '/CAM/' in source:
self._raw_instrument_src = data[source]

if (s := source[:source.rfind(':')]) in data.control_sources:
Expand All @@ -79,7 +80,7 @@ def __init__(self, data, detector=None, pulses=None, **kwargs):
selection = {self._raw_instrument_src.source: {
'data.x', 'data.y', 'data.toa', 'data.tot'}}

if self._centroids_instrument_src is not None:
if self._has_centroid_labels():
selection[self._centroids_instrument_src.source] = {
'data.labels'}

Expand Down Expand Up @@ -107,6 +108,11 @@ def __repr__(self):
return "<{} {}: {}>".format(type(self).__name__, self._detector_name,
', '.join(data_labels))

def _has_centroid_labels(self):
"""Whether centroid labels are available."""
return (self._centroids_instrument_src is not None and
'data.labels' in self._centroids_instrument_src)

@staticmethod
def _prepare_pasha(parallel):
"""Prepare pasha context."""
Expand All @@ -124,26 +130,66 @@ def _prepare_pasha(parallel):
return pasha.ProcessContext(parallel)

@classmethod
def _find_detector(cls, data, domain=''):
def _find_detector(cls, data, prefix_or_source):
"""Try to find detector source."""

detectors = defaultdict(list)
if isinstance(prefix_or_source, tuple) and len(prefix_or_source) == 2:
# Explicit tuple of source names.

for source in data.instrument_sources:
m = cls._instrument_re.match(source)
if m is not None and (not domain or m[1] == domain):
detectors[m[1]].append(source)
def _find_sources(data, source):
sd = data[source]
domain = source.partition('/')[0]

if len(detectors) > 1:
raise ValueError('multiple detectors found, please pass one '
'explicitly:\n' + ', '.join(sorted(detectors)))
elif detectors:
return next(iter(detectors.items()))
fast_source = f'{source}:daqOutput.chip0'
if sd.is_control and fast_source in data.all_sources:
return domain, fast_source
elif sd.is_instrument:
return domain, source

if domain:
raise ValueError(f'no sources found for detector {domain}')
else:
raise ValueError('no detector found, please pass one explicitly')
raw_source, centroided_source = prefix_or_source

if not raw_source and not centroided_source:
raise ValueError('tuple of source names may not be all empty')

found_sources = []

if raw_source:
domain, source = _find_sources(data, raw_source)
found_sources.append(source)

if centroided_source:
domain, source = _find_sources(data, centroided_source)
found_sources.append(source)

return domain, found_sources

elif isinstance(prefix_or_source, str):
# Detector domain.

detectors = defaultdict(list)

for source in data.instrument_sources:
m = cls._instrument_re.match(source)
if m is not None and m[1].startswith(prefix_or_source):
detectors[m[1]].append(source)

if len(detectors) > 1:
raise ValueError('multiple detector domains found, please '
'pass one explicitly via the `detector` '
'argument:\n' + ', '.join(sorted(detectors)))
elif detectors:
return next(iter(detectors.items()))

if prefix_or_source:
raise ValueError(f'no detector sources found for '
f'{prefix_or_source}, please pass explicit '
f'source name(s)')
else:
raise ValueError('no detector detected, please narrow the '
'search with the `detector` argument')

raise TypeError(
'detector may be a string, tuple of two strings or empty')

@staticmethod
def _sort_timepix_data(train_id, pids, toa_offset, rep_rate, timewalk_lut,
Expand Down Expand Up @@ -421,7 +467,8 @@ def pixel_events(self, pulse_dim='pulseId', toa_offset=0.0,
extended_columns (bool, optional): Whether to include the
original time-of-arrival, readout position and centroid
labels for each pixel event, False by default. Labels
require centroiding data to be present.
require centroiding data processed after Feburary 2024
to be present.
parallel (int or None, optional): Nunmber of parallel
processes to use, by default 10 or a quarter of all cores
whichever is lower. Any non-positive value or 1 disable
Expand Down Expand Up @@ -471,7 +518,7 @@ def pixel_events(self, pulse_dim='pulseId', toa_offset=0.0,
hits_pidx = psh.alloc(shape=num_hits, dtype=np.int32)
hits_pos = psh.alloc(shape=num_hits, dtype=np.int32)

if extended_columns and self._centroids_instrument_src is not None:
if extended_columns and self._has_centroid_labels():
hits_label = psh.alloc(shape=num_hits, dtype=np.int32)
else:
hits_label = None
Expand Down
39 changes: 39 additions & 0 deletions tests/test_components_timepix.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,45 @@ def test_timepix3_init(mock_sqs_timepix_run):
with pytest.raises(ValueError):
tpx.centroids_instrument_src

# With explicit source names.
tpx = Timepix3(mock_sqs_timepix_run,
('SQS_EXP_TIMEPIX/DET/TIMEPIX3:daqOutput.chip0',
'SQS_EXP_TIMEPIX/CAL/TIMEPIX3:daqOutput.chip0'))
assert_equal_sourcedata(
tpx.raw_control_src,
mock_sqs_timepix_run['SQS_EXP_TIMEPIX/DET/TIMEPIX3'])
assert_equal_sourcedata(
tpx.raw_instrument_src,
mock_sqs_timepix_run['SQS_EXP_TIMEPIX/DET/TIMEPIX3:daqOutput.chip0'])
assert_equal_sourcedata(
tpx.centroids_control_src,
mock_sqs_timepix_run['SQS_EXP_TIMEPIX/CAL/TIMEPIX3'])
assert_equal_sourcedata(
tpx.centroids_instrument_src,
mock_sqs_timepix_run['SQS_EXP_TIMEPIX/CAL/TIMEPIX3:daqOutput.chip0'])

# With explicit but only one source name.
tpx = Timepix3(mock_sqs_timepix_run,
('SQS_EXP_TIMEPIX/DET/TIMEPIX3:daqOutput.chip0', ''))
assert_equal_sourcedata(
tpx.raw_control_src,
mock_sqs_timepix_run['SQS_EXP_TIMEPIX/DET/TIMEPIX3'])
assert_equal_sourcedata(
tpx.raw_instrument_src,
mock_sqs_timepix_run['SQS_EXP_TIMEPIX/DET/TIMEPIX3:daqOutput.chip0'])

with pytest.raises(ValueError):
tpx.centroids_control_src

with pytest.raises(ValueError):
tpx.centroids_instrument_src

# Explicit control source rather than instrument source
tpx = Timepix3(mock_sqs_timepix_run,
('', 'SQS_EXP_TIMEPIX/CAL/TIMEPIX3'))
assert_equal_sourcedata(
tpx.centroids_instrument_src,
mock_sqs_timepix_run['SQS_EXP_TIMEPIX/CAL/TIMEPIX3:daqOutput.chip0'])

@pytest.mark.parametrize('method', ['pixel_events', 'centroid_events'])
def test_timepix3_data(mock_sqs_timepix_run, method):
Expand Down

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