reworked column names and constants

sensospot_data/columns.py

@@ -1,88 +1,97 @@
 """ Column name definitions """
 
 # original, unmodified column names
-COL_NAME_POS_X = "Pos.X"
-COL_NAME_POS_Y = "Pos.Y"
-COL_NAME_BKG_MEAN = "Bkg.Mean"
-COL_NAME_SPOT_MEAN = "Spot.Mean"
-COL_NAME_BKG_MEDIAN = "Bkg.Median"
-COL_NAME_SPOT_MEDIAN = "Spot.Median"
-COL_NAME_BKG_STDDEV = "Bkg.StdDev"
-COL_NAME_SPOT_STDDEV = "Spot.StdDev"
-COL_NAME_BKG_SUM = "Bkg.Sum"
-COL_NAME_SPOT_SUM = "Spot.Sum"
-COL_NAME_BKG_AREA = "Bkg.Area"
-COL_NAME_SPOT_AREA = "Spot.Area"
-COL_NAME_SPOT_SAT = "Spot.Sat. (%)"
-COL_NAME_POS_NOM_X = "Pos.Nom.X"
-COL_NAME_POS_NOM_Y = "Pos.Nom.Y"
+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
-COL_NAME_POS_ID = "Pos.Id"
-COL_NAME_SPOT_FOUND = "Spot.Found"
-COL_NAME_SPOT_DIAMETER = "Spot.Diameter"
+RAW_DATA_POS_ID = "Pos.Id"
+RAW_DATA_SPOT_FOUND = "Spot.Found"
+RAW_DATA_SPOT_DIAMETER = "Spot.Diameter"
+RAW_DATA_SPOT_SAT = "Spot.Sat[%]"
 
-# additional column
-COL_NAME_SPOT_OVERFLOW = "Spot.Overflow"
 
-# well information
-COL_NAME_WELL_ROW = "Well.Row"
-COL_NAME_WELL_COLUMN = "Well.Column"
+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,
+}
 
-# parsed measurement parameter information
-COL_NAME_PARAMETERS_CHANNEL = "Parameters.Channel"
-COL_NAME_PARAMETERS_TIME = "Parameters.Time"
+# meta data extracted from filename
+META_DATA_WELL_ROW = "Well.Row"
+META_DATA_WELL_COLUMN = "Well.Column"
+META_DATA_EXPOSURE_ID = "Exposure.Id"
 
-# applied exposure info
-COL_NAME_EXPOSURE_ID = "Exposure.Id"
-COL_NAME_EXPOSURE_CHANNEL = "Exposure.Channel"
-COL_NAME_EXPOSURE_TIME = "Exposure.Time"
+# parsed measurement parameter information (optional, from parameters folder)
+META_DATA_PARAMETERS_CHANNEL = "Parameters.Channel"
+META_DATA_PARAMETERS_TIME = "Parameters.Time"
 
 RAW_DATA_COLUMN_SET = {
-    COL_NAME_POS_X,
-    COL_NAME_POS_Y,
-    COL_NAME_BKG_MEAN,
-    COL_NAME_SPOT_MEAN,
-    COL_NAME_BKG_MEDIAN,
-    COL_NAME_SPOT_MEDIAN,
-    COL_NAME_BKG_STDDEV,
-    COL_NAME_SPOT_STDDEV,
-    COL_NAME_BKG_SUM,
-    COL_NAME_SPOT_SUM,
-    COL_NAME_BKG_AREA,
-    COL_NAME_SPOT_AREA,
-    COL_NAME_SPOT_SAT,
-    COL_NAME_POS_NOM_X,
-    COL_NAME_POS_NOM_Y,
-    COL_NAME_POS_ID,
-    COL_NAME_SPOT_FOUND,
-    COL_NAME_SPOT_DIAMETER,
-    COL_NAME_WELL_ROW,
-    COL_NAME_WELL_COLUMN,
-    COL_NAME_PARAMETERS_CHANNEL,
-    COL_NAME_PARAMETERS_TIME,
-    COL_NAME_EXPOSURE_ID,
+    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_WELL_ROW,
+    META_DATA_WELL_COLUMN,
+    META_DATA_EXPOSURE_ID,
+    META_DATA_PARAMETERS_CHANNEL,
+    META_DATA_PARAMETERS_TIME,
 }
 
+# settings for nominal exposure info
+SETTINGS_EXPOSURE_CHANNEL = "Exposure.Channel"
+SETTINGS_EXPOSURE_TIME = "Exposure.Time"
+
+# calculated value for dynamic range normalization
+CALC_SPOT_OVERFLOW = "Calc.Spot.Overflow"
 
 # normalized columns
-COL_NAME_NORMALIZED_EXPOSURE_TIME = f"Normalized.{COL_NAME_EXPOSURE_TIME}"
-COL_NAME_NORMALIZED_BKG_MEAN = f"Normalized.{COL_NAME_BKG_MEAN}"
-COL_NAME_NORMALIZED_SPOT_MEAN = f"Normalized.{COL_NAME_SPOT_MEAN}"
-COL_NAME_NORMALIZED_BKG_MEDIAN = f"Normalized.{COL_NAME_BKG_MEDIAN}"
-COL_NAME_NORMALIZED_SPOT_MEDIAN = f"Normalized.{COL_NAME_SPOT_MEDIAN}"
-COL_NAME_NORMALIZED_BKG_STDDEV = f"Normalized.{COL_NAME_BKG_STDDEV}"
-COL_NAME_NORMALIZED_SPOT_STDDEV = f"Normalized.{COL_NAME_SPOT_STDDEV}"
-COL_NAME_NORMALIZED_BKG_SUM = f"Normalized.{COL_NAME_BKG_SUM}"
-COL_NAME_NORMALIZED_SPOT_SUM = f"Normalized.{COL_NAME_SPOT_SUM}"
+n_prefix = "Calc.Normalized."
+CALC_NORMALIZED_EXPOSURE_TIME = f"{n_prefix}{SETTINGS_EXPOSURE_TIME}"
+CALC_NORMALIZED_BKG_MEAN = f"{n_prefix}{RAW_DATA_BKG_MEAN}"
+CALC_NORMALIZED_SPOT_MEAN = f"{n_prefix}{RAW_DATA_SPOT_MEAN}"
+CALC_NORMALIZED_BKG_MEDIAN = f"{n_prefix}{RAW_DATA_BKG_MEDIAN}"
+CALC_NORMALIZED_SPOT_MEDIAN = f"{n_prefix}{RAW_DATA_SPOT_MEDIAN}"
+CALC_NORMALIZED_BKG_STDDEV = f"{n_prefix}{RAW_DATA_BKG_STDDEV}"
+CALC_NORMALIZED_SPOT_STDDEV = f"{n_prefix}{RAW_DATA_SPOT_STDDEV}"
+CALC_NORMALIZED_BKG_SUM = f"{n_prefix}{RAW_DATA_BKG_SUM}"
+CALC_NORMALIZED_SPOT_SUM = f"{n_prefix}{RAW_DATA_SPOT_SUM}"
 
-COLUMN_NORMALIZATION = {
-    COL_NAME_BKG_MEAN: COL_NAME_NORMALIZED_BKG_MEAN,
-    COL_NAME_SPOT_MEAN: COL_NAME_NORMALIZED_SPOT_MEAN,
-    COL_NAME_BKG_MEDIAN: COL_NAME_NORMALIZED_BKG_MEDIAN,
-    COL_NAME_SPOT_MEDIAN: COL_NAME_NORMALIZED_SPOT_MEDIAN,
-    COL_NAME_BKG_STDDEV: COL_NAME_NORMALIZED_BKG_STDDEV,
-    COL_NAME_SPOT_STDDEV: COL_NAME_NORMALIZED_SPOT_STDDEV,
-    COL_NAME_BKG_SUM: COL_NAME_NORMALIZED_BKG_SUM,
-    COL_NAME_SPOT_SUM: COL_NAME_NORMALIZED_SPOT_SUM,
+# what columns to convert for normalization
+COLUMN_NORMALIZATION_MAP = {
+    RAW_DATA_BKG_MEAN: CALC_NORMALIZED_BKG_MEAN,
+    RAW_DATA_SPOT_MEAN: CALC_NORMALIZED_SPOT_MEAN,
+    RAW_DATA_BKG_MEDIAN: CALC_NORMALIZED_BKG_MEDIAN,
+    RAW_DATA_SPOT_MEDIAN: CALC_NORMALIZED_SPOT_MEDIAN,
+    RAW_DATA_BKG_STDDEV: CALC_NORMALIZED_BKG_STDDEV,
+    RAW_DATA_SPOT_STDDEV: CALC_NORMALIZED_SPOT_STDDEV,
+    RAW_DATA_BKG_SUM: CALC_NORMALIZED_BKG_SUM,
+    RAW_DATA_SPOT_SUM: CALC_NORMALIZED_SPOT_SUM,
 }