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Add BL1 process parameters to metadata and setpoints to environment #80

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Merged
michaelosthege merged 1 commit into from
May 7, 2025
Merged

Add BL1 process parameters to metadata and setpoints to environment #80

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9 changes: 8 additions & 1 deletion bletl/parsing/bl1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -199,10 +199,14 @@ def parse(
references = extract_references(data)
comments = extract_comments(data, references)
measurements = extract_measurements(data)
environment = extract_environment(data, process_parameters, comments)
# Also put process parameters into the metadata
for k, v in process_parameters.items():
metadata[f"process_parameter_{k}"] = v

data = BLData(
model=BioLectorModel.BL1,
environment=extract_environment(data, process_parameters, comments),
environment=environment,
filtersets=filtersets,
references=references,
measurements=measurements,
Expand Down Expand Up @@ -454,6 +458,9 @@ def extract_environment(dfraw, process_parameters: dict, comments: pandas.DataFr
df = utils.__to_typed_cols__(dfraw, ocol_ncol_type)
df["shaker_setpoint"] = process_parameters["shaking"]
df["temp_setpoint"] = process_parameters["temperature"]
df["humidity_setpoint"] = process_parameters["humidity"]
df["O2_setpoint"] = process_parameters["O2"]
df["CO2_setpoint"] = process_parameters["CO2"]
# process the comments column to extract setpoint changes
for t_comment, cmts in zip(comments["time"], comments["user_comment"]):
# multiple comments may be ,-separated in one line
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11 changes: 7 additions & 4 deletions bletl/parsing/blpro.py
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Expand Up @@ -73,7 +73,7 @@ def parse(

bld = BLData(
model=BioLectorModel.BLPro,
environment=extract_environment(data),
environment=extract_environment(data, metadata),
filtersets=extract_filtersets(metadata),
references=extract_references(data),
measurements=extract_measurements(data),
Expand Down Expand Up @@ -353,7 +353,7 @@ def extract_measurements(dfraw):
return standardize(df)


def extract_environment(dfraw):
def extract_environment(dfraw, metadata):
ocol_ncol_type = [
("Cycle", "cycle", int),
("Time", "time", float),
Expand All @@ -368,8 +368,11 @@ def extract_environment(dfraw):
("Shaker", "shaker_actual", float),
]
df = utils.__to_typed_cols__(dfraw[dfraw["Type"] == "R"], ocol_ncol_type)
# TODO: write initial setpoints (temp & shaker) into df
# TODO: parse setpoint changes (temp & shaker) from comments
# Write initial setpoints (temp & shaker) into df
df["humidity_setpoint"] = float(metadata["process"]["humidity"])
df["O2_setpoint"] = float(metadata["process"]["o2"])
df["CO2_setpoint"] = float(metadata["process"]["co2"])
# TODO: parse setpoint changes (temp & shaker) from profiles in the metadata
# TODO: clean up -9999.0 values in co2 column
return standardize(df)

Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "bletl"
version = "1.5.4"
version = "1.6.0"
description = "Package for parsing and transforming BioLector raw data."
readme = "README.md"
requires-python = ">=3.8"
Expand Down
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