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Merge pull request #17 from LIBRA-project/lsc-measurements
Class to read LSC csv files
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,7 @@ | ||
| import pint | ||
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| ureg = pint.UnitRegistry() | ||
| ureg.setup_matplotlib() | ||
| ureg.define("neutron = 1 * particle = n") | ||
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| from . import model |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,144 @@ | ||
| import pandas as pd | ||
| from typing import List | ||
| import pint | ||
| from libra_toolbox.tritium import ureg | ||
| from datetime import datetime, timedelta | ||
| import warnings | ||
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| class LSCFileReader: | ||
| def __init__(self, file_path, vial_labels=None): | ||
| self.file_path = file_path | ||
| self.vial_labels = vial_labels | ||
| self.data = None | ||
| self.header_content = None | ||
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| def read_file(self): | ||
| # first read the file without dataframe to find the line starting with S# | ||
| header_lines = [] | ||
| with open(self.file_path, "r") as file: | ||
| lines = file.readlines() | ||
| for i, line in enumerate(lines): | ||
| if line.startswith("S#"): | ||
| start = i | ||
| break | ||
| header_lines.append(line) | ||
| self.header_content = "".join(header_lines) | ||
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| # read the file with dataframe starting from the line with S# | ||
| self.data = pd.read_csv(self.file_path, skiprows=start) | ||
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| # check if last column is all NaN | ||
| if self.data[self.data.columns[-1]].isnull().all(): | ||
| warnings.warn( | ||
| "There seem to be an issue with the last column. Is the format of the file correct?" | ||
| ) | ||
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| def get_bq1_values(self): | ||
| return self.data["Bq:1"].tolist() | ||
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| def get_bq1_values_with_labels(self): | ||
| if self.vial_labels is None: | ||
| raise ValueError("Vial labels must be provided") | ||
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| assert len(self.vial_labels) == len( | ||
| self.get_bq1_values() | ||
| ), "Vial labels and Bq:1 values are not equal in length, remember to give None as a label for missing vials" | ||
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| values = self.get_bq1_values() | ||
| labelled_values = {label: val for label, val in zip(self.vial_labels, values)} | ||
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| return labelled_values | ||
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| def get_count_times(self): | ||
| return self.data["Count Time"].tolist() | ||
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| def get_lum(self): | ||
| return self.data["LUM"].tolist() | ||
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| class LSCSample: | ||
| def __init__(self, activity: pint.Quantity, name: str): | ||
| self.activity = activity | ||
| self.name = name | ||
| # TODO add other attributes available in LSC file | ||
| self.background_substracted = False | ||
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| def __str__(self): | ||
| return f"Sample {self.name}" | ||
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| def substract_background(self, background_sample: "LSCSample"): | ||
| if self.background_substracted: | ||
| raise ValueError("Background already substracted") | ||
| self.activity -= background_sample.activity | ||
| self.background_substracted = True | ||
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| @staticmethod | ||
| def from_file(file_reader: LSCFileReader, vial_name): | ||
| values = file_reader.get_bq1_values_with_labels() | ||
| if vial_name not in values: | ||
| raise ValueError(f"Vial {vial_name} not found in the file reader.") | ||
| activity = values[vial_name] * ureg.Bq | ||
| return LSCSample(activity, vial_name) | ||
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| class LIBRASample: | ||
| def __init__(self, samples: List[LSCSample], time: str): | ||
| self.samples = samples | ||
| self._time = time | ||
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| def get_relative_time(self, start_time: str) -> timedelta: | ||
| start_time = datetime.strptime(start_time, "%m/%d/%Y %I:%M %p") | ||
| sample_time = datetime.strptime(self._time, "%m/%d/%Y %I:%M %p") | ||
| return sample_time - start_time | ||
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| def substract_background(self, background_sample: LSCSample): | ||
| for sample in self.samples: | ||
| sample.substract_background(background_sample) | ||
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| def get_soluble_activity(self): | ||
| act = 0 | ||
| for sample in self.samples[:2]: | ||
| act += sample.activity | ||
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| return act | ||
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| def get_insoluble_activity(self): | ||
| act = 0 | ||
| for sample in self.samples[2:]: | ||
| act += sample.activity | ||
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| return act | ||
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| def get_total_activity(self): | ||
| return self.get_soluble_activity() + self.get_insoluble_activity() | ||
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| class LIBRARun: | ||
| def __init__(self, samples: List[LIBRASample], start_time: str): | ||
| self.samples = samples | ||
| self.start_time = start_time | ||
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| def get_cumulative_activity(self, form: str = "total"): | ||
| # check that background has been substracted | ||
| for sample in self.samples: | ||
| for lsc_sample in sample.samples: | ||
| if not lsc_sample.background_substracted: | ||
| raise ValueError( | ||
| "Background must be substracted before calculating cumulative activity" | ||
| ) | ||
| cumulative_activity = [] | ||
| for sample in self.samples: | ||
| if form == "total": | ||
| cumulative_activity.append(sample.get_total_activity()) | ||
| elif form == "soluble": | ||
| cumulative_activity.append(sample.get_soluble_activity()) | ||
| elif form == "insoluble": | ||
| cumulative_activity.append(sample.get_insoluble_activity()) | ||
| cumulative_activity = ureg.Quantity.from_list(cumulative_activity) | ||
| cumulative_activity = cumulative_activity.cumsum() | ||
| return cumulative_activity | ||
|
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| @property | ||
| def relative_times(self): | ||
| return [sample.get_relative_time(self.start_time) for sample in self.samples] |
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