bumped version

sensospot_data/__init__.py

@@ -3,17 +3,14 @@
 Parsing the numerical output from Sensovations Sensospot image analysis.
 """
 
-__version__ = "0.5.2"
+__version__ = "0.5.3"
 
 
 from pathlib import Path
 
 import click
 
-from .utils import (  # noqa: F401
+from .utils import split, apply_exposure_map  # noqa: F401
-    split,
-    apply_exposure_map,
-)
 from .parser import parse_file, parse_folder  # noqa: F401
 from .parameters import ExposureInfo  # noqa: F401
 from .dynamic_range import blend, create_xdr, normalize_values  # noqa: F401

sensospot_data/columns.py

@@ -31,6 +31,7 @@ RAW_DATA_COLUMNS_RENAME_MAP = {
 }
 
 # meta data extracted from filename
+META_DATA_WELL_NAME = "Well.Name"
 META_DATA_WELL_ROW = "Well.Row"
 META_DATA_WELL_COLUMN = "Well.Column"
 META_DATA_EXPOSURE_ID = "Exposure.Id"
@@ -58,6 +59,7 @@ RAW_DATA_COLUMN_SET = {
     RAW_DATA_POS_ID,
     RAW_DATA_SPOT_FOUND,
     RAW_DATA_SPOT_DIAMETER,
+    META_DATA_WELL_NAME,
     META_DATA_WELL_ROW,
     META_DATA_WELL_COLUMN,
     META_DATA_EXPOSURE_ID,

sensospot_data/dynamic_range.py

@@ -3,9 +3,9 @@ from pandas.api.types import is_numeric_dtype
 from .utils import split
 from .columns import (
     RAW_DATA_POS_ID,
+    RAW_DATA_SPOT_SAT,
     CALC_SPOT_OVERFLOW,
     META_DATA_WELL_ROW,
-    RAW_DATA_SPOT_SAT,
     META_DATA_WELL_COLUMN,
     SETTINGS_EXPOSURE_TIME,
     SETTINGS_EXPOSURE_CHANNEL,
@@ -58,7 +58,9 @@ def _reduce_overflow(data_frame):
         diff = rf_index - nf_index | nf_index - rf_index
         if diff:
             num = len(diff)
-            raise ValueError(f"XDR: Scan Data is incomplete, differs on {num} probes")
+            raise ValueError(
+                f"XDR: Scan Data is incomplete, differs on {num} probes"
+            )
         result_frame.loc[mask] = next_frame.loc[mask]
 
     return result_frame.reset_index()

sensospot_data/parser.py

@@ -12,11 +12,12 @@ import pandas
 from .columns import (
     RAW_DATA_POS_ID,
     META_DATA_WELL_ROW,
+    META_DATA_WELL_NAME,
     RAW_DATA_COLUMN_SET,
     META_DATA_EXPOSURE_ID,
     META_DATA_WELL_COLUMN,
-    RAW_DATA_COLUMNS_RENAME_MAP,
     RAW_DATA_NORMALIZATION_MAP,
+    RAW_DATA_COLUMNS_RENAME_MAP,
 )
 from .parameters import add_optional_measurement_parameters
 
@@ -76,6 +77,10 @@ def parse_file(data_file):
     """
     measurement_info = _extract_measurement_info(Path(data_file))
     data_frame = _parse_csv(data_file)
+    # normalized well name
+    data_frame[
+        META_DATA_WELL_NAME
+    ] = f"{measurement_info.row}{measurement_info.column:02d}"
     data_frame[META_DATA_WELL_ROW] = measurement_info.row
     data_frame[META_DATA_WELL_COLUMN] = measurement_info.column
     data_frame[META_DATA_EXPOSURE_ID] = measurement_info.exposure
@@ -129,7 +134,7 @@ def _sanity_check(data_frame):
         )
     # set the right data type for measurement columns
     for raw_column in RAW_DATA_NORMALIZATION_MAP:
-        data_frame[raw_column] = pandas.to_numeric(data_frame[raw_column])   
+        data_frame[raw_column] = pandas.to_numeric(data_frame[raw_column])
     return data_frame
 
 

tests/test_dynamic_range.py

@@ -79,7 +79,7 @@ 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_SAT
+    from sensospot_data.columns import RAW_DATA_SPOT_SAT, CALC_SPOT_OVERFLOW
     from sensospot_data.dynamic_range import _calc_overflow_info
 
     data_frame = pandas.DataFrame(data={RAW_DATA_SPOT_SAT: [1, 2, 3]})

tests/test_parser.py

@@ -168,12 +168,14 @@ def test_parse_file(example_file):
         "Pos.Nom.X",
         "Pos.Nom.Y",
         "Spot.Diameter",
+        "Well.Name",
         "Well.Row",
         "Well.Column",
         "Exposure.Id",
     }
 
     assert set(result.columns) == columns
+    assert result["Well.Name"][0] == "A01"
     assert result["Well.Row"][0] == "A"
     assert result["Well.Column"][0] == 1
     assert result["Exposure.Id"][0] == 1

tests/test_utils.py

@@ -177,4 +177,3 @@ def test_apply_exposure_map_from_parameters_raises_error(
         apply_exposure_map(data_frame_without_params, None)
 
     assert str(excinfo.value).startswith("Exposure Map: measurement")
-