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empty spectrum gaurds #81

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53 changes: 25 additions & 28 deletions spectrum_utils/spectrum.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,9 +53,7 @@ def __init__(
self.precursor_mz = precursor_mz
self.precursor_charge = precursor_charge
if not _skip_checks and len(mz) != len(intensity):
raise ValueError(
"The m/z and intensity arrays should have equal lengths"
)
raise ValueError("The m/z and intensity arrays should have equal lengths")
self._mz = np.asarray(mz, np.float64).reshape(-1)
# Make sure the peaks are sorted by m/z.
self._intensity = np.asarray(intensity, np.float32).reshape(-1)
Expand All @@ -72,9 +70,10 @@ def mz(self) -> np.ndarray:
def intensity(self) -> np.ndarray:
return self._intensity

def round(
self, decimals: int = 0, combine: str = "sum"
) -> "MsmsSpectrumJit":
def round(self, decimals: int = 0, combine: str = "sum") -> "MsmsSpectrumJit":
if len(self._mz) == 0 or len(self._intensity) == 0:
return self

mz_round = np.round_(self._mz, decimals, np.empty_like(self._mz))
mz_unique = np.unique(mz_round)
if len(mz_unique) == len(mz_round):
Expand All @@ -88,8 +87,7 @@ def round(
# Check whether subsequent mz values got merged.
while (
i_orig + offset < len(mz_round)
and abs(mz_unique[i_unique] - mz_round[i_orig + offset])
<= 1e-06
and abs(mz_unique[i_unique] - mz_round[i_orig + offset]) <= 1e-06
):
offset += 1
# Combine the corresponding intensities.
Expand All @@ -106,7 +104,11 @@ def round(
def set_mz_range(
self, min_mz: Optional[float] = None, max_mz: Optional[float] = None
) -> "MsmsSpectrumJit":
if min_mz is None and max_mz is None:
if (
(min_mz is None and max_mz is None)
or len(self._mz) == 0
or len(self._intensity) == 0
):
return self
else:
if min_mz is None:
Expand All @@ -130,11 +132,12 @@ def remove_precursor_peak(
fragment_tol_mode: str,
isotope: int = 0,
) -> MsmsSpectrumJit:
if len(self._mz) == 0 or len(self._intensity) == 0:
return self

# TODO: This assumes [M+H]x charged ions.
adduct_mass = 1.007825
neutral_mass = (
self.precursor_mz - adduct_mass
) * self.precursor_charge
neutral_mass = (self.precursor_mz - adduct_mass) * self.precursor_charge
c_mass_diff = 1.003355
remove_mz = [
(neutral_mass + iso * c_mass_diff) / charge + adduct_mass
Expand All @@ -160,6 +163,9 @@ def remove_precursor_peak(
def filter_intensity(
self, min_intensity: float = 0.0, max_num_peaks: Optional[int] = None
) -> "MsmsSpectrumJit":
if len(self._mz) == 0 or len(self._intensity) == 0:
return self

if max_num_peaks is None:
max_num_peaks = len(self._intensity)

Expand All @@ -173,9 +179,7 @@ def filter_intensity(
start_i += 1
# Only retain at most the `max_num_peaks` most intense peaks.
mask = np.full_like(self._intensity, False, np.bool_)
mask[
intensity_idx[max(start_i, len(intensity_idx) - max_num_peaks) :]
] = True
mask[intensity_idx[max(start_i, len(intensity_idx) - max_num_peaks) :]] = True
self._mz, self._intensity = self._mz[mask], self._intensity[mask]
return self

Expand All @@ -188,13 +192,11 @@ def scale_intensity(
max_rank: Optional[int] = None,
) -> "MsmsSpectrumJit":
if scaling == "root":
self._intensity = np.power(self._intensity, 1 / degree).astype(
self._intensity = np.power(self._intensity, 1 / degree).astype(np.float32)
elif scaling == "log":
self._intensity = (np.log1p(self._intensity) / np.log(base)).astype(
np.float32
)
elif scaling == "log":
self._intensity = (
np.log1p(self._intensity) / np.log(base)
).astype(np.float32)
elif scaling == "rank":
if max_rank is None:
max_rank = len(self._intensity)
Expand Down Expand Up @@ -528,9 +530,7 @@ def remove_precursor_peak(
'values are "Da" or "ppm".'
)
self.proforma, self._annotation = None, None
self._inner.remove_precursor_peak(
fragment_tol_mass, fragment_tol_mode, isotope
)
self._inner.remove_precursor_peak(fragment_tol_mass, fragment_tol_mode, isotope)
return self

def filter_intensity(
Expand Down Expand Up @@ -619,9 +619,7 @@ def scale_intensity(
-------
MsmsSpectrum
"""
self._inner.scale_intensity(
scaling, max_intensity, degree, base, max_rank
)
self._inner.scale_intensity(scaling, max_intensity, degree, base, max_rank)
return self

def _annotate_proteoforms(
Expand Down Expand Up @@ -700,8 +698,7 @@ def _annotate_proteoforms(
pi = fa.PeakInterpretation()
while (
fragment_i < len(fragments)
and mass_diff(peak_mz, fragments[fragment_i][1])
> fragment_tol_mass
and mass_diff(peak_mz, fragments[fragment_i][1]) > fragment_tol_mass
):
fragment_i += 1
i = 0
Expand Down