changed defaults for xdr since sensospot bug is fixed

README.md

@@ -52,14 +52,14 @@ from .parser import parse_file, parse_folder  # noqa: F401
  - **ExposureInfo(exposure_channel, exposure_time)**  
    A named tuple for defining an exposure map. Usage will increase readability 
    and karma points.
- - **blend(data_frame, [column="Spot.Mean", limit=0.5])**  
+ - **blend(data_frame, [column="Spot.Saturation", limit=2])**  
    If provided with a data frame with multiple exposure times for the same 
    exposure channel, the function will blend theese two times together based
    on given column and limit.
  - **normalize_values(data_frame, [normalized_time=None])**  
    Adds new columns to the data frame with intensity values recalculated to the
    normalized exposure time. If no time is given, the max exposure time is used.
- - **create_xdr(data_frame, [normalized_time=None, column="Spot.Mean", limit=0.5])**  
+ - **create_xdr(data_frame, [normalized_time=None, column="Spot.Saturation", limit=2])**  
    This combines the methods `blend()` and `normalize_values()` into one call.
    What a joy! 
 

sensospot_data/dynamic_range.py

@@ -5,7 +5,7 @@ from .columns import (
     RAW_DATA_POS_ID,
     CALC_SPOT_OVERFLOW,
     META_DATA_WELL_ROW,
-    RAW_DATA_SPOT_MEAN,
+    RAW_DATA_SPOT_SAT,
     META_DATA_WELL_COLUMN,
     SETTINGS_EXPOSURE_TIME,
     SETTINGS_EXPOSURE_CHANNEL,
@@ -33,7 +33,7 @@ def _check_if_xdr_ready(data_frame):
         raise ValueError("XDR: Exposure time contains NaNs")
 
 
-def _calc_overflow_info(data_frame, column=RAW_DATA_SPOT_MEAN, limit=0.5):
+def _calc_overflow_info(data_frame, column=RAW_DATA_SPOT_SAT, limit=2):
     """ add overflow info, based on column and limit """
     data_frame.loc[:, CALC_SPOT_OVERFLOW] = data_frame[column] > limit
     return data_frame
@@ -64,7 +64,7 @@ def _reduce_overflow(data_frame):
     return result_frame.reset_index()
 
 
-def blend(data_frame, column=RAW_DATA_SPOT_MEAN, limit=0.5):
+def blend(data_frame, column=RAW_DATA_SPOT_SAT, limit=2):
     """ creates an extended dynamic range, eliminating overflowing spots """
     _check_if_xdr_ready(data_frame)
     if CALC_SPOT_OVERFLOW not in data_frame.columns:
@@ -96,8 +96,8 @@ def normalize_values(data_frame, normalized_time=None):
 def create_xdr(
     data_frame,
     normalized_time=None,
-    column=RAW_DATA_SPOT_MEAN,
+    column=RAW_DATA_SPOT_SAT,
-    limit=0.5,
+    limit=2,
 ):
     """normalize measurement exposures
 

tests/test_dynamic_range.py

@@ -79,10 +79,10 @@ def test_check_if_xdr_ready_raises_error_on_nan(exposure_df):
 
 
 def test_check_overflow_limit_defaults():
-    from sensospot_data.columns import CALC_SPOT_OVERFLOW, RAW_DATA_SPOT_MEAN
+    from sensospot_data.columns import CALC_SPOT_OVERFLOW, RAW_DATA_SPOT_SAT
     from sensospot_data.dynamic_range import _calc_overflow_info
 
-    data_frame = pandas.DataFrame(data={RAW_DATA_SPOT_MEAN: [0.1, 0.5, 0.6]})
+    data_frame = pandas.DataFrame(data={RAW_DATA_SPOT_SAT: [1, 2, 3]})
 
     result = _calc_overflow_info(data_frame)