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Merged
merged 11 commits into from
Sep 19, 2024
Merged

Logging #490

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bda9e10
replace prints by logging
rettigl Jul 18, 2024
f824bad
fixes for new matplotlib
rettigl Jul 18, 2024
fbb0af2
use base sed logger
rettigl Aug 11, 2024
469236d
add logging to mpes loader
rettigl Aug 11, 2024
37feca1
add verbosity to loader interface
rettigl Aug 12, 2024
2fbae5d
add logging to delay calibrator
rettigl Aug 12, 2024
3292658
use logging in momentum calibrator
rettigl Aug 13, 2024
e3af246
use logging in energy calibrator, and further fixes
rettigl Aug 13, 2024
2a69836
some further fixes
rettigl Aug 13, 2024
79a181d
add function to set verbosity, and use in each class
rettigl Sep 19, 2024
8716dc0
Make verbose a private property, and add getter and setters for it, t…
rettigl Sep 19, 2024
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83 changes: 56 additions & 27 deletions sed/calibrator/delay.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,11 @@
import pandas as pd

from sed.core import dfops
from sed.core.logging import set_verbosity
from sed.core.logging import setup_logging

# Configure logging
logger = setup_logging("delay")


class DelayCalibrator:
Expand All @@ -22,22 +27,30 @@ class DelayCalibrator:

Args:
config (dict, optional): Config dictionary. Defaults to None.
verbose (bool, optional): Option to print out diagnostic information.
Defaults to True.
"""

def __init__(
self,
config: dict = None,
verbose: bool = True,
) -> None:
"""Initialization of the DelayCalibrator class passes the config.

Args:
config (dict, optional): Config dictionary. Defaults to None.
verbose (bool, optional): Option to print out diagnostic information.
Defaults to True.
"""
if config is not None:
self._config = config
else:
self._config = {}

self._verbose = verbose
set_verbosity(logger, self._verbose)

self.adc_column: str = self._config["dataframe"].get("adc_column", None)
self.delay_column: str = self._config["dataframe"]["delay_column"]
self.corrected_delay_column = self._config["dataframe"].get(
Expand All @@ -47,6 +60,25 @@ def __init__(
self.calibration: dict[str, Any] = self._config["delay"].get("calibration", {})
self.offsets: dict[str, Any] = self._config["delay"].get("offsets", {})

@property
def verbose(self) -> bool:
"""Accessor to the verbosity flag.

Returns:
bool: Verbosity flag.
"""
return self._verbose

@verbose.setter
def verbose(self, verbose: bool):
"""Setter for the verbosity.

Args:
verbose (bool): Option to turn on verbose output. Sets loglevel to INFO.
"""
self._verbose = verbose
set_verbosity(logger, self._verbose)

def append_delay_axis(
self,
df: pd.DataFrame | dask.dataframe.DataFrame,
Expand All @@ -61,7 +93,7 @@ def append_delay_axis(
p1_key: str = None,
p2_key: str = None,
t0_key: str = None,
verbose: bool = True,
suppress_output: bool = False,
) -> tuple[pd.DataFrame | dask.dataframe.DataFrame, dict]:
"""Calculate and append the delay axis to the events dataframe, by converting
values from an analog-digital-converter (ADC).
Expand Down Expand Up @@ -92,8 +124,7 @@ def append_delay_axis(
Defaults to config["delay"]["p2_key"]
t0_key (str, optional): hdf5 key for t0 value (mm).
Defaults to config["delay"]["t0_key"]
verbose (bool, optional): Option to print out diagnostic information.
Defaults to True.
suppress_output (bool, optional): Option to suppress log output. Defaults to False.

Raises:
ValueError: Raised if delay parameters are not found in the file.
Expand Down Expand Up @@ -126,11 +157,11 @@ def append_delay_axis(
calibration["delay_range_mm"] = delay_range_mm
else:
# report usage of loaded parameters
if "creation_date" in calibration and verbose:
if "creation_date" in calibration and not suppress_output:
datestring = datetime.fromtimestamp(calibration["creation_date"]).strftime(
"%m/%d/%Y, %H:%M:%S",
)
print(f"Using delay calibration parameters generated on {datestring}")
logger.info(f"Using delay calibration parameters generated on {datestring}")

if adc_column is None:
adc_column = self.adc_column
Expand Down Expand Up @@ -166,8 +197,8 @@ def append_delay_axis(
calibration["datafile"] = datafile
calibration["delay_range_mm"] = (ret[0], ret[1])
calibration["time0"] = ret[2]
if verbose:
print(f"Extract delay range from file '{datafile}'.")
if not suppress_output:
logger.info(f"Extract delay range from file '{datafile}'.")
else:
raise NotImplementedError(
"Not enough parameters for delay calibration.",
Expand All @@ -179,8 +210,8 @@ def append_delay_axis(
calibration["time0"],
),
)
if verbose:
print(f"Converted delay_range (ps) = {calibration['delay_range']}")
if not suppress_output:
logger.info(f"Converted delay_range (ps) = {calibration['delay_range']}")
calibration["creation_date"] = datetime.now().timestamp()

if "delay_range" in calibration.keys():
Expand All @@ -190,8 +221,8 @@ def append_delay_axis(
calibration["adc_range"][1] - calibration["adc_range"][0]
)
self.calibration = deepcopy(calibration)
if verbose:
print(
if not suppress_output:
logger.info(
"Append delay axis using delay_range = "
f"[{calibration['delay_range'][0]}, {calibration['delay_range'][1]}]"
" and adc_range = "
Expand All @@ -214,7 +245,7 @@ def add_offsets(
preserve_mean: bool | Sequence[bool] = False,
reductions: str | Sequence[str] = None,
delay_column: str = None,
verbose: bool = True,
suppress_output: bool = False,
) -> tuple[dask.dataframe.DataFrame, dict]:
"""Apply an offset to the delay column based on a constant or other columns.

Expand All @@ -234,8 +265,7 @@ def add_offsets(
If None, the shift is applied per-dataframe-row. Defaults to None. Currently only
"mean" is supported.
delay_column (str, optional): Name of the column containing the delay values.
verbose (bool, optional): Option to print out diagnostic information.
Defaults to True.
suppress_output (bool, optional): Option to suppress log output. Defaults to False.

Returns:
tuple[dask.dataframe.DataFrame, dict]: Dataframe with the shifted delay axis and
Expand Down Expand Up @@ -299,27 +329,25 @@ def add_offsets(
if flip_delay_axis:
offsets["flip_delay_axis"] = flip_delay_axis

elif "creation_date" in offsets and verbose:
elif "creation_date" in offsets and not suppress_output:
datestring = datetime.fromtimestamp(offsets["creation_date"]).strftime(
"%m/%d/%Y, %H:%M:%S",
)
print(f"Using delay offset parameters generated on {datestring}")
logger.info(f"Using delay offset parameters generated on {datestring}")

if len(offsets) > 0:
# unpack dictionary
columns = []
weights = []
preserve_mean = []
reductions = []
if verbose:
print("Delay offset parameters:")
log_str = "Delay offset parameters:"
for k, v in offsets.items():
if k == "creation_date":
continue
if k == "constant":
constant = v
if verbose:
print(f" Constant: {constant} ")
log_str += f"\n Constant: {constant}"
elif k == "flip_delay_axis":
fda = str(v)
if fda.lower() in ["true", "1"]:
Expand All @@ -330,8 +358,7 @@ def add_offsets(
raise ValueError(
f"Invalid value for flip_delay_axis in config: {flip_delay_axis}.",
)
if verbose:
print(f" Flip delay axis: {flip_delay_axis} ")
log_str += f"\n Flip delay axis: {flip_delay_axis}"
else:
columns.append(k)
try:
Expand All @@ -343,11 +370,13 @@ def add_offsets(
preserve_mean.append(pm)
red = v.get("reduction", None)
reductions.append(red)
if verbose:
print(
f" Column[{k}]: Weight={weight}, Preserve Mean: {pm}, ",
f"Reductions: {red}.",
)
log_str += (
f"\n Column[{k}]: Weight={weight}, Preserve Mean: {pm}, "
f"Reductions: {red}."
)

if not suppress_output:
logger.info(log_str)

if len(columns) > 0:
df = dfops.offset_by_other_columns(
Expand Down
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