class FeatureBase(object):
nodes: 'LCMSFeatureTreeList'
def __init__(self, nodes):
self.nodes = LCMSFeatureTreeList(nodes)
def find_time(self, time_point):
return self.nodes.find_time(time_point)
def __init__(self, nodes):
self.nodes = LCMSFeatureTreeList(nodes)
def clone(self, deep=False):
return LCMSFeatureTreeList(node.clone(deep=deep) for node in self)
def truncate_after(self, time):
_, i = self.nodes.find_time(time)
if self.nodes[i].time < time:
i += 1
self.nodes = LCMSFeatureTreeList(self.nodes[:i])
self._invalidate()
class LCMSFeature(FeatureBase):
created_at = "new"
def __init__(self, nodes=None, adducts=None, used_as_adduct=None, feature_id=None):
if nodes is None:
nodes = []
if adducts is None:
adducts = []
if used_as_adduct is None:
used_as_adduct = []
if feature_id is None:
feature_id = uid()
FeatureBase.__init__(self, nodes)
self._total_intensity = None
self._mz = None
self._last_mz = 0.0
self._times = None
self._peaks = None
self._start_time = None
self._end_time = None
self.adducts = adducts
self.used_as_adduct = used_as_adduct
self.feature_id = feature_id
self._peak_averager = RunningWeightedAverage()
if len(self) > 0:
self._feed_peak_averager()
def _feed_peak_averager(self):
for node in self:
self._peak_averager.update(node.members)
def invalidate(self, reaverage=False):
self._invalidate(reaverage)
def _invalidate(self, reaverage=False):
self._total_intensity = None
self._last_mz = self._mz if self._mz is not None else 0.
self._mz = None
self._times = None
self._peaks = None
self._start_time = None
self._end_time = None
if reaverage:
self._peak_averager = RunningWeightedAverage()
if len(self) > 0:
self._feed_peak_averager()
@property
def total_signal(self):
if self._total_intensity is None:
total = 0.
for node in self.nodes:
total += node.total_intensity()
self._total_intensity = total
return self._total_intensity
@property
def intensity(self):
return self.total_signal
@property
def neutral_mass(self):
return self.mz
@property
def mz(self):
if self._mz is None:
best_mz = self._peak_averager.current_mean
self._last_mz = self._mz = best_mz
return self._mz
@property
def times(self):
if self._times is None:
self._times = np.array(
[node.time for node in self.nodes])
return self._times
@property
def peaks(self):
if self._peaks is None:
self._peaks = tuple(node.peaks for node in self.nodes)
return self._peaks
@property
def start_time(self):
if self._start_time is None:
self._start_time = self.nodes[0].time
return self._start_time
@property
def end_time(self):
if self._end_time is None:
self._end_time = self.nodes[-1].time
return self._end_time
def overlaps_in_time(self, interval):
cond = ((self.start_time <= interval.start_time and self.end_time >= interval.end_time) or (
self.start_time >= interval.start_time and self.end_time <= interval.end_time) or (
self.start_time >= interval.start_time and self.end_time >= interval.end_time and
self.start_time <= interval.end_time) or (
self.start_time <= interval.start_time and self.end_time >= interval.start_time) or (
self.start_time <= interval.end_time and self.end_time >= interval.end_time))
return cond
def spans_in_time(self, time):
return self.start_time <= time <= self.end_time
def as_arrays(self):
rts = np.array(
[node.time for node in self.nodes], dtype=np.float64)
signal = np.array([node.total_intensity()
for node in self.nodes], dtype=np.float64)
return rts, signal
def __len__(self):
return len(self.nodes)
def __repr__(self):
return "%s(%0.4f, %0.2f, %0.2f)" % (
self.__class__.__name__, self.mz, self.start_time, self.end_time)
def _copy_chunk(self, nodes, *args, **kwargs):
x = self.__class__(LCMSFeatureTreeList(nodes))
x.used_as_adduct = list(self.used_as_adduct)
return x
def split_at(self, time):
_, i = self.nodes.find_time(time)
if self.nodes[i].time < time:
i += 1
return LCMSFeature(self.nodes[:i]), LCMSFeature(self.nodes[i:])
def split_sparse(self, delta_rt=1.):
chunks = []
current_chunk = []
last_rt = self.nodes[0].time
for node in self.nodes:
if (node.time - last_rt) > delta_rt:
x = self._copy_chunk(current_chunk)
chunks.append(x)
current_chunk = []
last_rt = node.time
current_chunk.append(node)
x = self._copy_chunk(current_chunk)
chunks.append(x)
for chunk in chunks:
chunk.created_at = self.created_at
for member in chunks:
for other in chunks:
if member == other:
continue
assert not member.overlaps_in_time(other)
return chunks
def truncate_before(self, time):
_, i = self.nodes.find_time(time)
if self.nodes[i].time < time:
i += 1
self.nodes = LCMSFeatureTreeList(self.nodes[i:])
self._invalidate()
def truncate_after(self, time):
_, i = self.nodes.find_time(time)
if self.nodes[i].time < time:
i += 1
self.nodes = LCMSFeatureTreeList(self.nodes[:i])
self._invalidate()
def clone(self, deep=False, cls=None):
if cls is None:
cls = self.__class__
c = cls(self.nodes.clone(deep=deep), list(
self.adducts), list(self.used_as_adduct))
c.feature_id = self.feature_id
c.created_at = self.created_at
return c
def insert_node(self, node):
self._peak_averager.update(node.members)
self.nodes.insert_node(node)
self._invalidate()
def insert(self, peak, time):
self._peak_averager.add(peak)
self.nodes.insert(time, [peak])
self._invalidate()
def merge(self, other):
new = self.clone()
for node in other.nodes:
node = node.clone()
new.insert_node(node)
new.created_at = "merge"
return new
@property
def apex_time(self):
rt, intensity = self.as_arrays()
return rt[np.argmax(intensity)]
def __iter__(self):
return iter(self.nodes)
def __eq__(self, other):
if other is None:
return False
if len(self) != len(other):
return False
else:
if abs(self.start_time - other.start_time) > 1e-4:
return False
elif abs(self.end_time - other.end_time) > 1e-4:
return False
else:
for a, b in zip(self, other):
if a != b:
return False
return True
def __ne__(self, other):
return not (self == other)
def __hash__(self):
return hash((self.mz, self.start_time, self.end_time))
def __getitem__(self, i):
return self.nodes[i]
def _copy_chunk(self, nodes, *args, **kwargs):
x = self.__class__(LCMSFeatureTreeList(nodes))
x.used_as_adduct = list(self.used_as_adduct)
return x
def truncate_before(self, time: float):
_, i = self.nodes.find_time(time)
if self.nodes[i].time < time:
i += 1
self.nodes = LCMSFeatureTreeList(self.nodes[i:])
self._invalidate()
def __init__(self, nodes):
self.nodes = LCMSFeatureTreeList(nodes)
class FeatureBase(object):
def __init__(self, nodes):
self.nodes = LCMSFeatureTreeList(nodes)
def find_time(self, time_point):
return self.nodes.find_time(time_point)
def truncate_after(self, time):
_, i = self.nodes.find_time(time)
if self.nodes[i].time < time:
i += 1
self.nodes = LCMSFeatureTreeList(self.nodes[:i])
self._invalidate()
class LCMSFeature(FeatureBase):
created_at = "new"
def __init__(self, nodes=None, adducts=None, used_as_adduct=None, feature_id=None):
if nodes is None:
nodes = []
if adducts is None:
adducts = []
if used_as_adduct is None:
used_as_adduct = []
if feature_id is None:
feature_id = uid()
FeatureBase.__init__(self, nodes)
self._total_intensity = None
self._mz = None
self._last_mz = 0.0
self._times = None
self._peaks = None
self._start_time = None
self._end_time = None
self.adducts = adducts
self.used_as_adduct = used_as_adduct
self.feature_id = feature_id
self._peak_averager = RunningWeightedAverage()
if len(self) > 0:
self._feed_peak_averager()
def _feed_peak_averager(self):
for node in self:
self._peak_averager.update(node.members)
def invalidate(self, reaverage=False):
self._invalidate(reaverage)
def _invalidate(self, reaverage=False):
self._total_intensity = None
self._last_mz = self._mz if self._mz is not None else 0.
self._mz = None
self._times = None
self._peaks = None
self._start_time = None
self._end_time = None
if reaverage:
self._peak_averager = RunningWeightedAverage()
if len(self) > 0:
self._feed_peak_averager()
@property
def total_signal(self):
if self._total_intensity is None:
total = 0.
for node in self.nodes:
total += node.total_intensity()
self._total_intensity = total
return self._total_intensity
@property
def intensity(self):
return self.total_signal
@property
def neutral_mass(self):
return self.mz
@property
def mz(self):
if self._mz is None:
best_mz = self._peak_averager.current_mean
self._last_mz = self._mz = best_mz
return self._mz
@property
def times(self):
if self._times is None:
self._times = np.array(
[node.time for node in self.nodes])
return self._times
@property
def peaks(self):
if self._peaks is None:
self._peaks = tuple(node.peaks for node in self.nodes)
return self._peaks
@property
def start_time(self):
if self._start_time is None:
self._start_time = self.nodes[0].time
return self._start_time
@property
def end_time(self):
if self._end_time is None:
self._end_time = self.nodes[-1].time
return self._end_time
def overlaps_in_time(self, interval):
cond = ((self.start_time <= interval.start_time and self.end_time >= interval.end_time) or (
self.start_time >= interval.start_time and self.end_time <= interval.end_time) or (
self.start_time >= interval.start_time and self.end_time >= interval.end_time and
self.start_time <= interval.end_time) or (
self.start_time <= interval.start_time and self.end_time >= interval.start_time) or (
self.start_time <= interval.end_time and self.end_time >= interval.end_time))
return cond
def as_arrays(self):
rts = np.array(
[node.time for node in self.nodes], dtype=np.float64)
signal = np.array([node.total_intensity()
for node in self.nodes], dtype=np.float64)
return rts, signal
def __len__(self):
return len(self.nodes)
def __repr__(self):
return "%s(%0.4f, %0.2f, %0.2f)" % (
self.__class__.__name__, self.mz, self.start_time, self.end_time)
def _copy_chunk(self, nodes, *args, **kwargs):
x = self.__class__(LCMSFeatureTreeList(nodes))
x.used_as_adduct = list(self.used_as_adduct)
return x
def split_at(self, time):
_, i = self.nodes.find_time(time)
if self.nodes[i].time < time:
i += 1
return LCMSFeature(self.nodes[:i]), LCMSFeature(self.nodes[i:])
def split_sparse(self, delta_rt=1.):
chunks = []
current_chunk = []
last_rt = self.nodes[0].time
for node in self.nodes:
if (node.time - last_rt) > delta_rt:
x = self._copy_chunk(current_chunk)
chunks.append(x)
current_chunk = []
last_rt = node.time
current_chunk.append(node)
x = self._copy_chunk(current_chunk)
chunks.append(x)
for chunk in chunks:
chunk.created_at = self.created_at
for member in chunks:
for other in chunks:
if member == other:
continue
assert not member.overlaps_in_time(other)
return chunks
def truncate_before(self, time):
_, i = self.nodes.find_time(time)
if self.nodes[i].time < time:
i += 1
self.nodes = LCMSFeatureTreeList(self.nodes[i:])
self._invalidate()
def truncate_after(self, time):
_, i = self.nodes.find_time(time)
if self.nodes[i].time < time:
i += 1
self.nodes = LCMSFeatureTreeList(self.nodes[:i])
self._invalidate()
def clone(self, deep=False, cls=None):
if cls is None:
cls = self.__class__
c = cls(self.nodes.clone(deep=deep), list(
self.adducts), list(self.used_as_adduct))
c.feature_id = self.feature_id
c.created_at = self.created_at
return c
def insert_node(self, node):
self._peak_averager.update(node.members)
self.nodes.insert_node(node)
self._invalidate()
def insert(self, peak, time):
self._peak_averager.add(peak)
self.nodes.insert(time, [peak])
self._invalidate()
def merge(self, other):
new = self.clone()
for node in other.nodes:
node = node.clone()
new.insert_node(node)
new.created_at = "merge"
return new
@property
def apex_time(self):
rt, intensity = self.as_arrays()
return rt[np.argmax(intensity)]
def __iter__(self):
return iter(self.nodes)
def __eq__(self, other):
if other is None:
return False
if len(self) != len(other):
return False
else:
if abs(self.start_time - other.start_time) > 1e-4:
return False
elif abs(self.end_time - other.end_time) > 1e-4:
return False
else:
for a, b in zip(self, other):
if a != b:
return False
return True
def __ne__(self, other):
return not (self == other)
def __hash__(self):
return hash((self.mz, self.start_time, self.end_time))
def __getitem__(self, i):
return self.nodes[i]