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Remove CxoTime custom fast parser, use astropy built-in #34

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merged 3 commits into from
Apr 5, 2023
Merged

Remove CxoTime custom fast parser, use astropy built-in #34

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9147cb1
Use astropy fast time parsing not cxotime fast parsing
taldcroft Jan 2, 2023
b1ef813
Remove unused imports
taldcroft Jan 2, 2023
6190952
Clean up import cruft from old astropy
taldcroft Jan 2, 2023
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184 changes: 24 additions & 160 deletions cxotime/cxotime.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,23 +3,14 @@
import sys
import warnings
from copy import copy
from ctypes import c_int
from pathlib import Path
from typing import Union

import erfa
import numpy as np
import numpy.ctypeslib as npct
import numpy.typing as npt
from astropy.time import Time, TimeCxcSec, TimeDecimalYear, TimeYearDayTime
from astropy.time.utils import day_frac
from astropy.utils import iers

# in astropy versions < 4.2, erfa was an astropy private package:
try:
import erfa
except ModuleNotFoundError:
from astropy import _erfa as erfa

# TODO: use npt.NDArray with numpy 1.21
CxoTimeLike = Union["CxoTime", str, float, int, np.ndarray, npt.ArrayLike, None]

Expand All @@ -33,41 +24,6 @@
# allow auto downloads.
iers.conf.auto_download = False

# Input types in the parse_times.c code
array_1d_char = npct.ndpointer(dtype=np.uint8, ndim=1, flags="C_CONTIGUOUS")
array_1d_double = npct.ndpointer(dtype=np.double, ndim=1, flags="C_CONTIGUOUS")
array_1d_int = npct.ndpointer(dtype=np.intc, ndim=1, flags="C_CONTIGUOUS")

# load the library, using numpy mechanisms
libpt = npct.load_library("parse_times", Path(__file__).parent)

# Set up the return types and argument types for parse_ymdhms_times()
# int parse_ymdhms_times(char *times, int n_times, int max_str_len,
# char *delims, int *starts, int *stops, int *break_allowed,
# int *years, int *months, int *days, int *hours,
# int *minutes, double *seconds)
libpt.parse_ymdhms_times.restype = c_int
libpt.parse_ymdhms_times.argtypes = [
array_1d_char,
c_int,
c_int,
c_int,
array_1d_char,
array_1d_int,
array_1d_int,
array_1d_int,
array_1d_int,
array_1d_int,
array_1d_int,
array_1d_int,
array_1d_int,
array_1d_double,
]
libpt.check_unicode.restype = c_int

# Set up returns types and args for the unicode checker
libpt.check_unicode.argtypes = [array_1d_char, c_int]


def print_time_conversions():
"""Interface to entry_point script ``cxotime`` to print time conversions"""
Expand Down Expand Up @@ -399,84 +355,6 @@ def print_conversions(self):
print("\n".join(lines))


class FastDateParserMixin:
def set_jds_fast(self, val1):
"""Use fast C parser to parse time strings in val1 and set jd1, jd2"""
# Handle bytes or str input and flatten down to a single array of uint8.
char_size = 4 if val1.dtype.kind == "U" else 1
val1_str_len = int(val1.dtype.itemsize // char_size)
chars = val1.ravel().view(np.uint8)

if char_size == 4:
# Check that this is pure ASCII
status = libpt.check_unicode(chars, len(chars) // 4)
if status != 0:
raise ValueError("input is not pure ASCII")
# It might be possible to avoid this copy with cleverness in
# parse_times.c but leave that for another day.
chars = chars[::4]
chars = np.ascontiguousarray(chars)

# Pre-allocate output components
n_times = len(chars) // val1_str_len
year = np.zeros(n_times, dtype=np.intc)
month = np.zeros(n_times, dtype=np.intc)
day = np.zeros(n_times, dtype=np.intc)
hour = np.zeros(n_times, dtype=np.intc)
minute = np.zeros(n_times, dtype=np.intc)
second = np.zeros(n_times, dtype=np.double)

# Set up parser parameters as numpy arrays for passing to C parser
delims = np.array(self.delims, dtype=np.uint8)
starts = np.array(self.starts, dtype=np.intc)
stops = np.array(self.stops, dtype=np.intc)
break_allowed = np.array(self.break_allowed, dtype=np.intc)

# Call C parser
status = libpt.parse_ymdhms_times(
chars,
n_times,
val1_str_len,
self.has_day_of_year,
delims,
starts,
stops,
break_allowed,
year,
month,
day,
hour,
minute,
second,
)
if status == 0:
# All went well, finish the job
jd1, jd2 = erfa.dtf2d(
self.scale.upper().encode("ascii"),
year,
month,
day,
hour,
minute,
second,
)
jd1.shape = val1.shape
jd2.shape = val1.shape
self.jd1, self.jd2 = day_frac(jd1, jd2)
else:
msgs = {
1: (
"time string ends at beginning of component where break is not"
" allowed"
),
2: "time string ends in middle of component",
3: "required delimiter character not found",
4: "non-digit found where digit (0-9) required",
5: "bad day of year (1 <= doy <= 365 or 366 for leap year",
}
raise ValueError(f"fast C time string parser failed: {msgs[status]}")


class TimeSecs(TimeCxcSec):
"""
Chandra X-ray Center seconds from 1998-01-01 00:00:00 TT.
Expand All @@ -486,7 +364,7 @@ class TimeSecs(TimeCxcSec):
name = "secs"


class TimeDate(TimeYearDayTime, FastDateParserMixin):
class TimeDate(TimeYearDayTime):
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This makes sense and seems fine. I note that I'm not immediately lear on how to initialize the astropy time classes, as the docstring doesn't seem to address the items in the init signature. But that's not a cxotime issue.

Init signature:
TimeYearDayTime(
    val1,
    val2,
    scale,
    precision,
    in_subfmt,
    out_subfmt,
    from_jd=False,
)
Docstring:     
Year, day-of-year and time as "YYYY:DOY:HH:MM:SS.sss...".
The day-of-year (DOY) goes from 001 to 365 (366 in leap years).
For example, 2000:001:00:00:00.000 is midnight on January 1, 2000.

The allowed subformats are:

- 'date_hms': date + hours, mins, secs (and optional fractional secs)
- 'date_hm': date + hours, mins
- 'date': date

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These TimeFormat subclasses are defining a contained object within the Time class which is not directly set by the user. The Time class is defined in astropy/time/core.py.

"""
Year, day-of-year and time as "YYYY:DOY:HH:MM:SS.sss..." in UTC.

Expand All @@ -511,14 +389,6 @@ class TimeDate(TimeYearDayTime, FastDateParserMixin):

name = "date"

# Class attributes for fast C-parsing
delims = (0, 0, ord(":"), ord(":"), ord(":"), ord(":"), ord("."))
starts = (0, -1, 4, 8, 11, 14, 17)
stops = (3, -1, 7, 10, 13, 16, -1)
# Break before: y m d h m s f
break_allowed = (0, 0, 0, 1, 0, 1, 1)
has_day_of_year = 1

def to_value(self, parent=None, **kwargs):
if self.scale == "utc":
return super().value
Expand All @@ -531,7 +401,7 @@ def set_jds(self, val1, val2):
"""Parse the time strings contained in val1 and set jd1, jd2"""
if val2 is not None:
raise ValueError(f"cannot supply val2 for {self.name} format")
self.set_jds_fast(val1)
self.jd1, self.jd2 = self.get_jds_fast(val1, val2)


class TimeFracYear(TimeDecimalYear):
Expand All @@ -554,7 +424,7 @@ def to_value(self, parent=None, **kwargs):
value = property(to_value)


class TimeGreta(TimeDate, FastDateParserMixin):
class TimeGreta(TimeDate):
"""
Date as a string in format 'YYYYDDD.hhmmsssss', where sssss is number of
milliseconds.
Expand Down Expand Up @@ -585,12 +455,15 @@ class TimeGreta(TimeDate, FastDateParserMixin):
# stops: position where component ends (-1 => continue to end of string)

# Before: yr mon doy hour minute second frac
delims = (0, 0, 0, ord("."), 0, 0, 0)
starts = (0, -1, 4, 7, 10, 12, 14)
stops = (3, -1, 6, 9, 11, 13, -1)
# Break before: y m d h m s f
break_allowed = (0, 0, 0, 1, 0, 1, 1)
has_day_of_year = 1

fast_parser_pars = dict(
delims=(0, 0, 0, ord("."), 0, 0, 0),
starts=(0, -1, 4, 7, 10, 12, 14),
stops=(3, -1, 6, 9, 11, 13, -1),
# Break before: y m d h m s f
break_allowed=(0, 0, 0, 1, 0, 1, 1),
has_day_of_year=1,
)

def _check_val_type(self, val1, val2):
if val2 is not None:
Expand All @@ -600,18 +473,11 @@ def _check_val_type(self, val1, val2):
raise TypeError(
"Input values for {0} class must be string or number".format(self.name)
)
return val1, None

def set_jds(self, val1, val2):
"""Parse the time strings contained in val1 and set jd1, jd2"""
# If specific input subformat is required then use the Python parser.
# Also do this if Time format class does not define `use_fast_parser`
# or if the fast parser is entirely disabled.
# Allow for float input
if val1.dtype.kind in ("f", "i"):
val1 = np.array(["{:.9f}".format(x) for x in val1.flat]).reshape(val1.shape)

self.set_jds_fast(val1)
return val1, None

def to_value(self, parent=None, **kwargs):
if self.scale == "utc":
Expand All @@ -625,7 +491,7 @@ def to_value(self, parent=None, **kwargs):
value = property(to_value)


class TimeMaude(TimeDate, FastDateParserMixin):
class TimeMaude(TimeDate):
"""
Date as a 64-bit integer in format YYYYDDDhhmmsss, where sss is number of
milliseconds.
Expand Down Expand Up @@ -655,13 +521,15 @@ class TimeMaude(TimeDate, FastDateParserMixin):
# stops: position where component ends (-1 => continue to end of string)

# Before: yr mon doy hour minute second frac
use_fast_parser = True
delims = (0, 0, 0, 0, 0, 0, 0)
starts = (0, -1, 4, 7, 9, 11, 13)
stops = (3, -1, 6, 8, 10, 12, -1)
# Break before: y m d h m s f
break_allowed = (0, 0, 0, 1, 0, 1, 1)
has_day_of_year = 1
fast_parser_pars = dict(
use_fast_parser=True,
delims=(0, 0, 0, 0, 0, 0, 0),
starts=(0, -1, 4, 7, 9, 11, 13),
stops=(3, -1, 6, 8, 10, 12, -1),
# Break before: y m d h m s f,
break_allowed=(0, 0, 0, 1, 0, 1, 1),
has_day_of_year=1,
)

def _check_val_type(self, val1, val2):
if val2 is not None:
Expand All @@ -677,10 +545,6 @@ def _check_val_type(self, val1, val2):

return val1, None

def set_jds(self, val1, val2):
"""Parse the time strings contained in val1 and set jd1, jd2"""
self.set_jds_fast(val1)

def to_value(self, parent=None, **kwargs):
if self.scale == "utc":
out = super().value
Expand Down
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