sensospot_parser/sensospot_data/columns.py

""" Column name definitions """

# original, unmodified column names
RAW_DATA_POS_X = "Pos.X"
RAW_DATA_POS_Y = "Pos.Y"
RAW_DATA_BKG_MEAN = "Bkg.Mean"
RAW_DATA_SPOT_MEAN = "Spot.Mean"
RAW_DATA_BKG_MEDIAN = "Bkg.Median"
RAW_DATA_SPOT_MEDIAN = "Spot.Median"
RAW_DATA_BKG_STDDEV = "Bkg.StdDev"
RAW_DATA_SPOT_STDDEV = "Spot.StdDev"
RAW_DATA_BKG_SUM = "Bkg.Sum"
RAW_DATA_SPOT_SUM = "Spot.Sum"
RAW_DATA_BKG_AREA = "Bkg.Area"
RAW_DATA_SPOT_AREA = "Spot.Area"
RAW_DATA_POS_NOM_X = "Pos.Nom.X"
RAW_DATA_POS_NOM_Y = "Pos.Nom.Y"

# replacement column names
RAW_DATA_POS_ID = "Pos.Id"
RAW_DATA_SPOT_FOUND = "Spot.Found"
RAW_DATA_SPOT_DIAMETER = "Spot.Diameter"
RAW_DATA_SPOT_SAT = "Spot.Saturation"


RAW_DATA_COLUMNS_RENAME_MAP = {
    " ID ": RAW_DATA_POS_ID,
    "Found": RAW_DATA_SPOT_FOUND,
    "Dia.": RAW_DATA_SPOT_DIAMETER,
    "Spot.Sat. (%)": RAW_DATA_SPOT_SAT,
}

# meta data extracted from filename and path
META_DATA_ANALYSIS_NAME = "Analysis.Name"
META_DATA_WELL_NAME = "Well.Name"
META_DATA_WELL_ROW = "Well.Row"
META_DATA_WELL_COLUMN = "Well.Column"
META_DATA_EXPOSURE_ID = "Exposure.Id"

# parsed measurement parameter information (optional, from parameters folder)
META_DATA_PARAMETERS_CHANNEL = "Parameters.Channel"
META_DATA_PARAMETERS_TIME = "Parameters.Time"

PARSED_DATA_COLUMN_SET = {
    RAW_DATA_POS_X,
    RAW_DATA_POS_Y,
    RAW_DATA_BKG_MEAN,
    RAW_DATA_SPOT_MEAN,
    RAW_DATA_BKG_MEDIAN,
    RAW_DATA_SPOT_MEDIAN,
    RAW_DATA_BKG_STDDEV,
    RAW_DATA_SPOT_STDDEV,
    RAW_DATA_BKG_SUM,
    RAW_DATA_SPOT_SUM,
    RAW_DATA_BKG_AREA,
    RAW_DATA_SPOT_AREA,
    RAW_DATA_SPOT_SAT,
    RAW_DATA_POS_NOM_X,
    RAW_DATA_POS_NOM_Y,
    RAW_DATA_POS_ID,
    RAW_DATA_SPOT_FOUND,
    RAW_DATA_SPOT_DIAMETER,
    META_DATA_ANALYSIS_NAME,
    META_DATA_WELL_NAME,
    META_DATA_WELL_ROW,
    META_DATA_WELL_COLUMN,
    META_DATA_EXPOSURE_ID,
    META_DATA_PARAMETERS_CHANNEL,
    META_DATA_PARAMETERS_TIME,
}

# list of columns to ensure a pandas numeric type
RAW_DATA_NUMERIC_COLUMNS = {
    RAW_DATA_POS_ID,
    RAW_DATA_POS_X,
    RAW_DATA_POS_Y,
    RAW_DATA_POS_NOM_X,
    RAW_DATA_POS_NOM_Y,
    RAW_DATA_BKG_MEAN,
    RAW_DATA_BKG_MEDIAN,
    RAW_DATA_BKG_STDDEV,
    RAW_DATA_BKG_SUM,
    RAW_DATA_SPOT_MEAN,
    RAW_DATA_SPOT_MEDIAN,
    RAW_DATA_SPOT_STDDEV,
    RAW_DATA_SPOT_SUM,
    RAW_DATA_SPOT_DIAMETER,
    META_DATA_EXPOSURE_ID,
    META_DATA_WELL_COLUMN,
}


# set of columns directly dependent on exposure time

EXPOSURE_DEPENDENT_COLUMNS = {
    RAW_DATA_BKG_MEAN,
    RAW_DATA_BKG_MEDIAN,
    RAW_DATA_BKG_STDDEV,
    RAW_DATA_BKG_SUM,
    RAW_DATA_SPOT_MEAN,
    RAW_DATA_SPOT_MEDIAN,
    RAW_DATA_SPOT_STDDEV,
    RAW_DATA_SPOT_SUM,
}

# common indexes

INDEX_COLUMNS_WELL = (
    META_DATA_ANALYSIS_NAME,
    META_DATA_WELL_NAME,
    META_DATA_WELL_ROW,
)

INDEX_COLUMNS_POS = (
    META_DATA_ANALYSIS_NAME,
    META_DATA_WELL_NAME,
    META_DATA_WELL_ROW,
    RAW_DATA_POS_ID,
)