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import logging |
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import math |
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from datetime import datetime, date, timedelta |
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from typing import Optional, SupportsFloat, Tuple, Union |
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import regex |
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from pint import Quantity, UnitRegistry |
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from pint.errors import PintTypeError |
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from pocketutils.core._internal import nicesize |
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from pocketutils.core.exceptions import OutOfRangeError, StringPatternError |
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from pocketutils.tools.base_tools import BaseTools |
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from pocketutils.tools.string_tools import StringTools |
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logger = logging.getLogger("pocketutils") |
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_UNIT_REG = UnitRegistry() |
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class UnitTools(BaseTools): |
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@classmethod |
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def approx_time_wrt( |
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cls, |
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now: Union[date, datetime], |
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then: Union[date, datetime], |
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*, |
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skip_today: bool = False, |
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sig: int = 3, |
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) -> str: |
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""" |
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Describes ``then`` with higher resolution for smaller differences to ``now``. |
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Examples: |
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- ``approx_time_wrt(date(2021, 1, 12), date(1996, 10, 1)) # "1996"`` |
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- ``approx_time_wrt(date(2021, 1, 12), date(2021, 10, 1)) # "2021-01-12"`` |
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- ``approx_time_wrt(date(2021, 10, 1), datetime(2021, 10, 1, 11, 55)) # "2021-01-12 11:55"`` |
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- ``approx_time_wrt(date(2021, 10, 1), datetime(2021, 10, 1, 11, 0, 0, 30, 222222)) # "2021-01-12 00:00:30"`` |
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- ``approx_time_wrt(date(2021, 10, 1), datetime(2021, 10, 1, 11, 0, 0, 2, 222222)) # "2021-01-12 00:00:02.222"`` |
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- ``approx_time_wrt(date(2021, 10, 1), datetime(2021, 10, 1, 11, 0, 0, 2, 22)) # "2021-01-12 00:00:02.000022"`` |
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""" |
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delta = now - then if now > then else then - now |
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tot_days = (delta.days) + (delta.seconds / 86400) + (delta.microseconds / 86400 / 10 ** 6) |
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tot_secs = tot_days * 86400 |
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_today = "" if skip_today and then.date() == now.date() else "%Y-%m-%d " |
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if tot_days > sig * 365.24219: |
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return str(then.year) |
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elif tot_days > sig * 30.437: |
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return then.strftime("%Y-%m") |
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elif tot_days > sig: |
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return then.strftime("%Y-%m-%d") |
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elif tot_secs > sig * 60: |
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return then.strftime(_today + "%H:%M") |
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elif tot_secs > sig: |
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return then.strftime(_today + "%H:%M:%S") |
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elif tot_secs > sig / 1000: |
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return then.strftime(_today + "%H:%M:%S") + "." + str(round(then.microsecond / 1000)) |
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else: |
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return then.strftime(_today + "%H:%M:%S.%f") |
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@classmethod |
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def delta_time_to_str(cls, delta_sec: Union[float, timedelta], *, space: str = "") -> str: |
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""" |
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Returns a pretty string from a difference in time in seconds. |
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Rounds hours and minutes to 2 decimal places, and seconds to 1. |
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Ex: delta_time_to_str(313) == 5.22min |
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delta_sec: The time in seconds |
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space: Space char between digits and units; |
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good choices are empty, ASCII space, Chars.narrownbsp, Chars.thinspace, |
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and Chars.nbsp. |
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Returns: |
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A string with units 'hr', 'min', or 's' |
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""" |
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if isinstance(delta_sec, timedelta): |
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delta_sec = delta_sec.total_seconds() |
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if abs(delta_sec) > 60 * 60 * 3: |
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return ( |
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StringTools.strip_empty_decimal(str(round(delta_sec / 60 / 60, 2))) + space + "hr" |
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) |
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elif abs(delta_sec) > 180: |
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return StringTools.strip_empty_decimal(str(round(delta_sec / 60, 2))) + space + "min" |
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else: |
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return StringTools.strip_empty_decimal(str(round(delta_sec, 1))) + space + "s" |
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@classmethod |
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def ms_to_minsec(cls, ms: int, space: str = "") -> str: |
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""" |
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Converts a number of milliseconds to one of the following formats: |
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- 10ms if < 1 sec |
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- 10:15 if < 1 hour |
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- 10:15:33 if < 1 day |
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- 5d:10:15:33 if > 1 day |
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Prepends a minus sign (−) if negative. |
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Args: |
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ms: The milliseconds |
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space: Space char between digits and 'ms' (if used); |
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good choices are empty, ASCII space, Chars.narrownbsp, |
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Chars.thinspace, and Chars.nbsp. |
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Returns: |
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A string of one of the formats above |
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""" |
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ms = abs(int(ms)) |
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seconds = int((ms / 1000) % 60) |
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minutes = int((ms / (1000 * 60)) % 60) |
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hours = int((ms / (1000 * 60 * 60)) % 24) |
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days = int(ms / (1000 * 60 * 60 * 24)) |
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z_hr = str(hours).zfill(2) |
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z_min = str(minutes).zfill(2) |
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z_sec = str(seconds).zfill(2) |
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sgn = "−" if ms < 0 else "" |
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if ms < 1000: |
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return f"{sgn}{ms}{space}ms" |
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elif days > 1: |
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return f"{days}d:{z_hr}:{z_min}:{z_sec}" |
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elif hours > 1: |
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return f"{sgn}{z_hr}:{z_min}:{z_sec}" |
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else: |
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return f"{sgn}{z_min}:{z_sec}" |
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@classmethod |
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def friendly_size(cls, n_bytes: int, *, space: str = " ") -> str: |
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""" |
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Returns a text representation of a number of bytes. |
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Uses base 2 with IEC 1998, rounded to 0 decimal places, and without a space. |
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""" |
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return nicesize(n_bytes, space=space) |
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@classmethod |
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def round_to_sigfigs(cls, num: SupportsFloat, sig_figs: int) -> float: |
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""" |
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Round to specified number of sigfigs. |
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Args: |
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num: A Python or Numpy float or something that supports __float__ |
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sig_figs: The number of significant figures, non-negative |
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Returns: |
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A Python integer |
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""" |
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if sig_figs < 0: |
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raise OutOfRangeError(f"sig_figs {sig_figs} is negative", minimum=0) |
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num = float(num) |
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if num != 0: |
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digits = -int(math.floor(math.log10(abs(num))) - (sig_figs - 1)) |
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return round(num, digits) |
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else: |
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return 0 # can't take the log of 0 |
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@classmethod |
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def format_micromolar( |
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cls, |
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micromolar: float, |
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n_sigfigs: Optional[int] = 5, |
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*, |
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adjust_units: bool = True, |
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use_sigfigs: bool = True, |
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space: str = "", |
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) -> str: |
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""" |
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Returns a concentration with units, with the units scaled as needed. |
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Can handle millimolar, micromolar, nanomolar, and picomolar. |
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Args: |
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micromolar: Value |
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n_sigfigs: For rounding; no rounding if None |
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adjust_units: If False, will always use micromolar |
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use_sigfigs: If True, rounds to a number of significant figures; otherwise round to decimal places |
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space: Space char between digits and units; |
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good choices are empty, ASCII space, Chars.narrownbsp, Chars.thinspace, and Chars.nbsp. |
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Returns: |
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The concentration with a suffix of µM, mM, nM, or mM |
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""" |
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d = micromolar |
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m = abs(d) |
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unit = "µM" |
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if adjust_units: |
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if m < 1e-6: |
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d *= 1e9 |
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unit = "fM" |
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elif m < 1e-3: |
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d *= 1e6 |
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unit = "pM" |
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elif m < 1: |
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d *= 1e3 |
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unit = "nM" |
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elif m >= 1e6: |
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d /= 1e6 |
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unit = "M" |
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elif m >= 1e3: |
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d /= 1e3 |
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unit = "mM" |
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if n_sigfigs is None: |
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pass |
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elif use_sigfigs: |
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d = cls.round_to_sigfigs(d, n_sigfigs) |
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else: |
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d = round(d, n_sigfigs) |
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if round(d) == d and str(d).endswith(".0"): |
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return str(d)[:-2] + space + unit |
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else: |
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return str(d) + space + unit |
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@classmethod |
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def split_species_micromolar(cls, text: str) -> Tuple[str, Optional[float]]: |
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""" |
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Splits a name into a chemical/concentration pair, falling back with the full name. |
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Ex: "abc 3.5uM" → (abc, 3.5) |
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Ex: "abc 3.5 µM" → (abc, 3.5) |
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Ex: "abc (3.5mM)" → (abc, 3500.0) |
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Ex: "abc 3.5mM" → (abc, None) |
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Ex: "3.5mM" → (3.5mM, None) # an edge case: don't pass in only units |
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Uses a moderately strict pattern for the drug and dose: |
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- The dose must terminate the string, except for end parenthesis or whitespace. |
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- The drug and dose must be separated by at least one non-alphanumeric, non-dot, non-hyphen character. |
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- Units must follow the digits, separated by at most whitespace, and are case-sensitive. |
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""" |
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# note the lazy ops in the first group and in the non-(alphanumeric/dot/dash) separator between the drug and dose |
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pat = regex.compile( |
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r"^\s*(.*?)(?:[^A-Za-z0-9.\-]+?[\s(\[{]*(\d+(?:.\d*)?)\s*([mµunpf]M)\s*[)\]}]*)?\s*$", |
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flags=regex.V1, |
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) |
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match = pat.fullmatch(text) |
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if match is None: |
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raise StringPatternError(f"Text {text} couldn't be parsed", value=text, pattern=pat) |
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if match.group(2) is None: |
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return text.strip(), None |
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else: |
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drug = match.group(1).strip("([{)]}") |
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dose = UnitTools.concentration_to_micromolar(float(match.group(2)), match.group(3)) |
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return drug, dose |
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@classmethod |
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def extract_micromolar(cls, text: str) -> Optional[float]: |
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""" |
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Returns what looks like a concentration with units. Accepts one of: mM, µM, uM, nM, pM. |
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Searches pretty flexibly. |
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If no matches are found, returns None. |
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If multiple matches are found, warns and returns None. |
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""" |
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# we need to make sure mM ex isn't part of a larger name |
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pat1 = regex.compile(r"(\d+(?:.\d*)?)\s*([mµunpf]M)\s*[)\]}]*", flags=regex.V1) |
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def find(pat): |
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return { |
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UnitTools.concentration_to_micromolar(float(match.group(1)), match.group(2)) |
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for match in pat.finditer(text) |
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if match is not None |
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} |
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matches = find(pat1) |
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if len(matches) == 1: |
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return next(iter(matches)) |
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elif len(matches) > 1: |
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logger.warning(f"Found {len(matches)} potential doses: {matches} . Returning None.") |
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return None |
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@classmethod |
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def concentration_to_micromolar(cls, digits: Union[str, float], units: str) -> float: |
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261
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""" |
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262
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Ex: concentration_to_micromolar(53, 'nM') # returns 0.053 |
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263
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""" |
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return float(digits) * { |
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"M": 1e6, |
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"mM": 1e3, |
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"µM": 1, |
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268
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"uM": 1, |
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269
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"nM": 1e-3, |
|
270
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"pM": 1e-6, |
|
271
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"fM": 1e-9, |
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}[units] |
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274
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@classmethod |
|
275
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def canonicalize_quantity(cls, s: str, dimensionality: str) -> Quantity: |
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|
276
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""" |
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277
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Returns a quantity in reduced units from a magnitude with units. |
|
278
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|
279
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Args: |
|
280
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|
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s: The string to parse; e.g. ``"1 m/s^2"``. |
|
281
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|
|
Unit names and symbols permitted, and spaces may be omitted. |
|
282
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dimensionality: The resulting Quantity is check against this; |
|
283
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|
|
e.g. ``"[length]/[meter]^2"`` |
|
284
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|
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|
|
285
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|
Returns: |
|
286
|
|
|
a pint ``Quantity`` |
|
287
|
|
|
|
|
288
|
|
|
Raise: |
|
289
|
|
|
PintTypeError: If the dimensionality is inconsistent |
|
290
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|
|
""" |
|
291
|
|
|
q = _UNIT_REG.Quantity(s).to_reduced_units() |
|
|
|
|
|
|
292
|
|
|
if not q.is_compatible_with(dimensionality): |
|
293
|
|
|
raise PintTypeError(f"{s} not of dimensionality {dimensionality}") |
|
294
|
|
|
return q |
|
295
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|
296
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|
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|
297
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|
|
__all__ = ["UnitTools"] |
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dmyersturnbull /
pocketutils
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