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Misc fixes 2 #391

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Misc fixes 2 #391

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4af8dc8
fix typo in config
mschwoer Nov 27, 2024
832ae92
substitute alphatims.utils.njit -> nb.njit
mschwoer Nov 27, 2024
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2 changes: 1 addition & 1 deletion alphadia/constants/default.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ library_prediction:

# define custom alphabase modifications not part of unimod or alphabase
# also used for decoy channels
custom_modififcations:
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It’s breaking in theory :D alphabase can’t use the custom mods with multiprocessing yet. So it’s not being used (yet)

custom_modifications:
# Dimethyl @K channel decoy
Dimethyl:d12@K:
composition: H(-2)2H(8)13C(2)
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6 changes: 3 additions & 3 deletions alphadia/planning.py
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Expand Up @@ -170,11 +170,11 @@ def init_alphabase(self):
"""Init alphabase by registering custom modifications."""

# register custom modifications
if "custom_modififcations" in self.config:
n_modifications = len(self.config["custom_modififcations"])
if "custom_modifications" in self.config:
n_modifications = len(self.config["custom_modifications"])
logging.info(f"Registering {n_modifications} custom modifications")

modification.add_new_modifications(self.config["custom_modififcations"])
modification.add_new_modifications(self.config["custom_modifications"])

def load_library(self):
"""
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15 changes: 4 additions & 11 deletions alphadia/quadrupole.py
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@@ -1,10 +1,3 @@
# native imports

# alphadia imports
# alpha family imports
import alphatims.utils

# third party imports
import numba as nb
import numpy as np
from numba.experimental import jitclass
Expand All @@ -13,7 +6,7 @@
from alphadia import utils


@alphatims.utils.njit
@nb.njit
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Did you check the alphatims function? I wonder why I did this in the first place ( I already see some weird numbs thing happening :D )

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this is the @alphatims.utils.njit decorator

def njit(_func=None, *args, **kwargs):
    import numba
    return numba.njit(_func, *args, **kwargs)

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So much value

def logistic(x: np.array, mu: float, sigma: float):
"""Numba implementation of the logistic function

Expand Down Expand Up @@ -41,13 +34,13 @@ def logistic(x: np.array, mu: float, sigma: float):
return y


@alphatims.utils.njit
@nb.njit
def logistic_rectangle(mu1, mu2, sigma1, sigma2, x):
y = logistic(x, mu1, sigma1) - logistic(x, mu2, sigma2)
return y


@alphatims.utils.njit
@nb.njit
def linear(x, m, b):
return m * x + b

Expand Down Expand Up @@ -267,7 +260,7 @@ def get_calibrated_cycle(self, treshold=0.01):
return new_cycle


@alphatims.utils.njit
@nb.njit
def quadrupole_transfer_function_single(
quadrupole_calibration_jit, observation_indices, scan_indices, isotope_mz
):
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29 changes: 11 additions & 18 deletions alphadia/utils.py
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Original file line number Diff line number Diff line change
@@ -1,18 +1,11 @@
# native imports
import logging
import math
import platform
import re
from ctypes import Structure, c_double

# alphadia imports
# alpha family imports
import alphatims.bruker
import alphatims.utils
import numba as nb
import numpy as np

# third party imports
import pandas as pd
import torch
from matplotlib import patches
Expand Down Expand Up @@ -203,7 +196,7 @@ def plt_limits(mobility_limits, dia_cycle_limits):
return rect


@alphatims.utils.njit()
@nb.njit()
def find_peaks_1d(a, top_n=3):
"""accepts a dense representation and returns the top three peaks"""

Expand Down Expand Up @@ -234,7 +227,7 @@ def find_peaks_1d(a, top_n=3):
return scan, dia_cycle, intensity


@alphatims.utils.njit()
@nb.njit()
def find_peaks_2d(a, top_n=3):
"""accepts a dense representation and returns the top three peaks"""
scan = []
Expand Down Expand Up @@ -268,31 +261,31 @@ def find_peaks_2d(a, top_n=3):
return scan, dia_cycle, intensity


@alphatims.utils.njit()
@nb.njit()
def amean1(array):
out = np.zeros(array.shape[0])
for i in range(len(out)):
out[i] = np.mean(array[i])
return out


@alphatims.utils.njit()
@nb.njit()
def amean0(array):
out = np.zeros(array.shape[1])
for i in range(len(out)):
out[i] = np.mean(array[:, i])
return out


@alphatims.utils.njit()
@nb.njit()
def astd0(array):
out = np.zeros(array.shape[1])
for i in range(len(out)):
out[i] = np.std(array[:, i])
return out


@alphatims.utils.njit()
@nb.njit()
def astd1(array):
out = np.zeros(array.shape[0])
for i in range(len(out)):
Expand Down Expand Up @@ -323,7 +316,7 @@ def get_isotope_column_names(colnames):
return [f"i_{i}" for i in get_isotope_columns(colnames)]


@alphatims.utils.njit()
@nb.njit()
def mass_range(mz_list, ppm_tolerance):
out_mz = np.zeros((len(mz_list), 2), dtype=mz_list.dtype)
out_mz[:, 0] = mz_list - ppm_tolerance * mz_list / (10**6)
Expand All @@ -348,12 +341,12 @@ class Point(Structure):
_fields_ = [("x", c_double), ("y", c_double)]


@alphatims.utils.njit()
@nb.njit()
def tile(a, n):
return np.repeat(a, n).reshape(-1, n).T.flatten()


@alphatims.utils.njit
@nb.njit
def make_slice_1d(start_stop):
"""Numba helper function to create a 1D slice object from a start and stop value.

Expand All @@ -373,7 +366,7 @@ def make_slice_1d(start_stop):
return np.array([[start_stop[0], start_stop[1], 1]], dtype=start_stop.dtype)


@alphatims.utils.njit
@nb.njit
def make_slice_2d(start_stop):
"""Numba helper function to create a 2D slice object from multiple start and stop value.

Expand All @@ -397,7 +390,7 @@ def make_slice_2d(start_stop):
return out


@alphatims.utils.njit
@nb.njit
def fourier_filter(dense_stack, kernel):
"""Numba helper function to apply a gaussian filter to a dense stack.
The filter is applied as convolution wrapping around the edges, calculated in fourier space.
Expand Down
2 changes: 1 addition & 1 deletion tests/unit_tests/test_planning.py
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Expand Up @@ -79,7 +79,7 @@ def test_custom_modifications():
temp_directory = tempfile.gettempdir()

config = {
"custom_modififcations": {
"custom_modifications": {
"ThisModDoesNotExists@K": {
"composition": "H(10)",
},
Expand Down
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