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fix: Molecular Devices SoftMax Pro - handle reduced data blocks with empty rows correctly #1110

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Merged
nathan-stender merged 1 commit into from
Oct 28, 2025
Merged

fix: Molecular Devices SoftMax Pro - handle reduced data blocks with empty rows correctly #1110

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92 changes: 43 additions & 49 deletions src/allotropy/parsers/moldev_softmax_pro/softmax_pro_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -467,37 +467,48 @@ def update_kinetic_data_elements(
self.data_elements[position].kinetic_measures.append(value)


@dataclass(frozen=True)
class RawData:
wavelength_data: list[PlateWavelengthData]
def get_plate_dataframe(
reader: CsvReader, header: PlateHeader, columns: pd.Series[str] | None = None
) -> pd.DataFrame:
if columns is None:
columns = assert_not_none(
reader.pop_as_series(sep="\t"),
msg="unable to find data columns for plate block raw data.",
)
dimensions = assert_not_none(
NUM_WELLS_TO_PLATE_DIMENSIONS.get(header.num_wells),
msg="unable to determine plate dimensions",
)
rows = dimensions[1]

@staticmethod
def get_measurement_section(
reader: CsvReader, columns: pd.Series[str], rows: int
) -> pd.DataFrame:
lines = []
# read number of rows in plate section
for i in range(rows):
if not (line := reader.pop()):
msg = f"Expected {rows} rows in measurement table, got {i}."
raise AllotropeConversionError(msg)
lines.append(line)
reader.drop_empty()
lines = []
# read number of rows in plate section
for i in range(rows):
if not (line := reader.pop()):
msg = f"Expected {rows} rows in measurement table, got {i}."
raise AllotropeConversionError(msg)
lines.append(line)
reader.drop_empty()

# convert rows to df
data = assert_not_none(
reader.lines_as_df(lines=lines, sep="\t"),
msg="unable to find data from plate block.",
)
# convert rows to df
data = assert_not_none(
reader.lines_as_df(lines=lines, sep="\t"),
msg="unable to find data from plate block.",
)

# Truncate columns Series to match the actual number of data columns
if len(columns) >= data.shape[1]:
columns = columns.iloc[: data.shape[1]]
elif len(columns) < data.shape[1]:
data = data.loc[:, : len(columns) - 1]
# Truncate columns Series to match the actual number of data columns
if len(columns) >= data.shape[1]:
columns = columns.iloc[: data.shape[1]]
elif len(columns) < data.shape[1]:
data = data.loc[:, : len(columns) - 1]

set_columns(data, columns)
return data
set_columns(data, columns)
return data


@dataclass(frozen=True)
class RawData:
wavelength_data: list[PlateWavelengthData]


@dataclass(frozen=True)
Expand All @@ -508,13 +519,7 @@ def create(reader: CsvReader, header: PlateHeader) -> PlateRawData:
reader.pop_as_series(sep="\t"),
msg="unable to find data columns for plate block raw data.",
)
# use plate dimensions to determine how many rows of plate block to read
dimensions = assert_not_none(
NUM_WELLS_TO_PLATE_DIMENSIONS.get(header.num_wells),
msg="unable to determine plate dimensions",
)
rows = dimensions[1]
data = RawData.get_measurement_section(reader, columns, rows)
data = get_plate_dataframe(reader, header, columns=columns)

# get temperature and elapsed time (kinetic) from the first column of the first row with value
first_row_idx = int(pd.to_numeric(data.first_valid_index()))
Expand All @@ -534,7 +539,7 @@ def create(reader: CsvReader, header: PlateHeader) -> PlateRawData:

if elapsed_time is not None and header.kinetic_points > 1:
for _ in range(header.kinetic_points - 1):
data = RawData.get_measurement_section(reader, columns, rows)
data = get_plate_dataframe(reader, header, columns=columns)

elapsed_time = time_to_seconds(str(data.iloc[0, 0]))
plate_raw_data._update_kinetic_data(
Expand Down Expand Up @@ -584,15 +589,9 @@ def create(reader: CsvReader, header: PlateHeader) -> SpectrumPlateRawData:
reader.pop_as_series(sep="\t"),
msg="unable to find data columns for plate block raw data.",
)
dimensions = assert_not_none(
NUM_WELLS_TO_PLATE_DIMENSIONS.get(header.num_wells),
msg="unable to determine plate dimensions",
)
rows = dimensions[1]
wavelength_data: list[PlateWavelengthData] = []

for wavelength in header.wavelengths:
data = RawData.get_measurement_section(reader, columns, rows)
data = get_plate_dataframe(reader, header, columns=columns)
first_row_idx = int(pd.to_numeric(data.first_valid_index()))
temperature = try_non_nan_float_or_none(str(data.iloc[first_row_idx, 1]))
wavelength_data.append(
Expand All @@ -615,15 +614,10 @@ class PlateReducedData:

@staticmethod
def create(reader: CsvReader, header: PlateHeader) -> PlateReducedData:

raw_data = assert_not_none(
reader.pop_csv_block_as_df(sep="\t", header=0),
msg="Unable to find reduced data for plate block.",
)

raw_data: pd.DataFrame = get_plate_dataframe(reader, header)
# Reduced data has 2 empty columns where
start = 2
df_data = raw_data.iloc[:, start : (start + header.num_columns)]

reduced_data_elements = []
for row, *data in df_data.itertuples():
for col, str_value in zip(df_data.columns, data, strict=True):
Expand Down
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