6385965165

Committed 02 Oct 2023 10:05PM UTC coverage: 99.72% (+0.03%) from 99.687%

Build # 6385965165

Build Type

push

github

Committed by

web-flow

Commit Message

Parallelize histogram and MPH calculations (#63)

* Parallelize histogram and MPH calculations

* Remove extraneous variable definitions

* Formatting

* Check if multiple channels extract properly with new histogram function

Run Details

202 of 203 branches covered (0.0%)

Branch coverage included in aggregate %.

13 of 13 new or added lines in 1 file covered. (100.0%)

154 of 154 relevant lines covered (100.0%)

5.99 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

100.0

/src/mibi_bin_tools/panel_utils.py

from typing import Union, List
import pandas as pd

from alpineer import misc_utils


def make_panel(mass: Union[float, List[float]],
               target_name: Union[str, List[str], None] = None,
               low_range: Union[float, List[float]] = 0.3,
               high_range: Union[float, List[float]] = 0.0) -> pd.DataFrame:
    """ Creates single mass panel

    Args:
        mass (float | List[float]):
            central m/z for signal
        target_name (str | List[str] | None):
            naming for target. 'Target' if None
        low_range (float | List[float]):
            units below central mass to start integration
        high_range (float | List[float]):
            units above central mass to stop integration

    Returns:
        pd.DataFrame:
            single mass panel as pandas dataframe
    """

    mass = misc_utils.make_iterable(mass)
    if target_name is not None:
        target_name = misc_utils.make_iterable(target_name)
        if len(mass) != len(target_name):
            raise ValueError(
                '`mass` and `target_name` did not contain the same number of elements.  '
                'If target names aren\'t required, then set `target_name=None`.  '
            )
    else:
        target_name = [f'targ{i}' for i in range(len(mass))]

    # check for range lists
    for r in (low_range, high_range):
        if misc_utils.make_iterable(r) == r:
            if len(r) != len(mass):
                raise ValueError(
                    '`mass` and a range argument did not contain the same number of elements.  '
                    'If only one integration range is required, `low_range` and `high_range` can '
                    'be set to float values, e.g `low_range=0.3`'
                )

    low_range = misc_utils.make_iterable(low_range)
    high_range = misc_utils.make_iterable(high_range)

    if len(low_range) != len(mass):
        low_range = low_range * len(mass)
    if len(high_range) != len(mass):
        high_range = high_range * len(mass)

    rows = []
    for m, ch, low, high in zip(mass, target_name, low_range, high_range):
        rows.append({
            'Mass': m,
            'Target': ch,
            'Start': m - low,
            'Stop': m + high,
        })

    return pd.DataFrame(rows)

1	from typing import Union, List	6✔
2	import pandas as pd	6✔
3
4	from alpineer import misc_utils	6✔
5
6
7	def make_panel(mass: Union[float, List[float]],	6✔
8	target_name: Union[str, List[str], None] = None,
9	low_range: Union[float, List[float]] = 0.3,
10	high_range: Union[float, List[float]] = 0.0) -> pd.DataFrame:
11	""" Creates single mass panel
12
13	Args:
14	mass (float \| List[float]):
15	central m/z for signal
16	target_name (str \| List[str] \| None):
17	naming for target. 'Target' if None
18	low_range (float \| List[float]):
19	units below central mass to start integration
20	high_range (float \| List[float]):
21	units above central mass to stop integration
22
23	Returns:
24	pd.DataFrame:
25	single mass panel as pandas dataframe
26	"""
27
28	mass = misc_utils.make_iterable(mass)	6✔
29	if target_name is not None:	6✔
30	target_name = misc_utils.make_iterable(target_name)	6✔
31	if len(mass) != len(target_name):	6✔
32	raise ValueError(	6✔
33	'`mass` and `target_name` did not contain the same number of elements. '
34	'If target names aren\'t required, then set `target_name=None`. '
35	)
36	else:
37	target_name = [f'targ{i}' for i in range(len(mass))]	6✔
38
39	# check for range lists
40	for r in (low_range, high_range):	6✔
41	if misc_utils.make_iterable(r) == r:	6✔
42	if len(r) != len(mass):	6✔
43	raise ValueError(	6✔
44	'`mass` and a range argument did not contain the same number of elements. '
45	'If only one integration range is required, `low_range` and `high_range` can '
46	'be set to float values, e.g `low_range=0.3`'
47	)
48
49	low_range = misc_utils.make_iterable(low_range)	6✔
50	high_range = misc_utils.make_iterable(high_range)	6✔
51
52	if len(low_range) != len(mass):	6✔
53	low_range = low_range * len(mass)	6✔
54	if len(high_range) != len(mass):	6✔
55	high_range = high_range * len(mass)	6✔
56
57	rows = []	6✔
58	for m, ch, low, high in zip(mass, target_name, low_range, high_range):	6✔
59	rows.append({	6✔
60	'Mass': m,
61	'Target': ch,
62	'Start': m - low,
63	'Stop': m + high,
64	})
65
66	return pd.DataFrame(rows)	6✔

angelolab / mibi-bin-tools / 6385965165

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous