api changes

- normilization api for measurement changed to
   `split_channels`
 - named tuple for exposure maps exposed in package as
   `ExposureInfo`

CHANGES.md

@@ -1,3 +1,13 @@
+
+0.4.0  - api changes
+--------------------
+
+ - normilization api for measurement changed to 
+   `split_channels` 
+ - named tuple for exposure maps exposed in package as
+   `ExposureInfo` 
+
+
 0.3.0  - normalization api
 --------------------------
 

README.md

@@ -9,7 +9,14 @@ Parsing the numerical output from Sensovation Sensospot image analysis.
 
     import sensospot_data
 
-    sensovation_data.process_folder(<path to results directory>)
+    # read the raw data of a folder
+    raw_data = sensospot_data.process_folder(<path to results directory>)
+
+    # split the measurement according to channels
+    channels = sensospot_data.split_channels(raw_data [, optional_exposure_map])
+
+    # normalize one channel to a specific exposure time
+    cy5_normalized = sensospot_data.normalize_channel(channels["cy5"], normalized_time=25)
 ```
 
 

sensospot_data/__init__.py

@@ -3,7 +3,7 @@
 Parsing the numerical output from Sensovations Sensospot image analysis.
 """
 
-__version__ = "0.3.0"
+__version__ = "0.4.0"
 
 VERSION_TABLE_NAME = f"v{__version__}".replace(".", "_")
 
@@ -15,4 +15,5 @@ from .parser import (  # noqa: F401
     process_folder,
     parse_multiple_files,
 )
-from .normalisation import normalize_channel, normalize_measurement  # noqa: F401
+from .parameters import ExposureInfo  # noqa: F401
+from .normalisation import normalize_channel, split_channels  # noqa: F401

sensospot_data/normalisation.py

@@ -137,6 +137,7 @@ def normalize_exposure_time(split_data_frames):
 
 def normalize_channel(channel_frame, normalized_time):
     """ add time normalized values to a channel data frames """
+    channel_frame = channel_frame.copy()
     channel_frame[COL_NAME_NORMALIZED_EXPOSURE_TIME] = normalized_time
 
     for original_col, normalized_col in COLUMN_NORMALIZATION.items():
@@ -147,7 +148,7 @@ def normalize_channel(channel_frame, normalized_time):
     return channel_frame
 
 
-def normalize_measurement(
+def split_channels(
     data_frame,
     exposure_map=None,
     overflow_column=COL_NAME_SPOT_MEAN,

sensospot_data/parameters.py

@@ -15,7 +15,7 @@ from .columns import (
     COL_NAME_PARAMETERS_CHANNEL,
 )
 
-MeasurementParams = namedtuple("MeasurementParams", ["channel", "time"])
+ExposureInfo = namedtuple("ExposureInfo", ["channel", "time"])
 
 
 def _search_measurement_params_file(folder):
@@ -44,7 +44,7 @@ def _parse_measurement_params(params_file):
         # channel_description == "[Cy3|Cy5] Green"
         channel = channel_description.rsplit(" ", 1)[-1]
         time = int(child.attrib["ExposureTimeMs"])
-        result[exposure] = MeasurementParams(channel.lower(), time)
+        result[exposure] = ExposureInfo(channel.lower(), time)
     return result
 
 

sensospot_data/parser.py

@@ -85,7 +85,7 @@ def _cleanup_data_columns(data_frame):
 
 def parse_file(data_file):
     """ parses one data file and adds metadata to result """
-    measurement_info = _extract_measurement_info(data_file)
+    measurement_info = _extract_measurement_info(Path(data_file))
     data_frame = _parse_csv(data_file)
     data_frame[COL_NAME_WELL_ROW] = measurement_info.row
     data_frame[COL_NAME_WELL_COLUMN] = measurement_info.column
@@ -129,7 +129,7 @@ def _sanity_check(data_frame):
 
 def parse_folder(folder):
     """ parses all csv files in a folder to one large dataframe """
-    file_list = _list_csv_files(folder)
+    file_list = _list_csv_files(Path(folder))
     data_frame = parse_multiple_files(file_list)
     data_frame = add_optional_measurement_parameters(data_frame, folder)
     return _sanity_check(data_frame)
@@ -137,7 +137,7 @@ def parse_folder(folder):
 
 def process_folder(folder, use_cache=True):
     """ parses all csv files in a folder, adds some checks and more data """
-    hdf5_path = folder / CACHE_FILE_NAME
+    hdf5_path = Path(folder) / CACHE_FILE_NAME
     if use_cache:
         try:
             return pandas.read_hdf(hdf5_path, _get_cache_table_name())

tests/test_normailsation.py

@@ -217,10 +217,7 @@ def test_infer_normalization_map(normalization_data_frame):
 
 def test_normalize_channel(normalization_data_frame):
     from sensospot_data.columns import COLUMN_NORMALIZATION
-    from sensospot_data.normalisation import (
+    from sensospot_data.normalisation import reduce_overflow, normalize_channel
-        reduce_overflow,
-        normalize_channel,
-    )
 
     reduced = reduce_overflow(normalization_data_frame, "Saturation", 1)
     result = normalize_channel(reduced["Cy5"], 50)
@@ -274,7 +271,7 @@ def test_normalize_exposure_time_infered_map(normalization_data_frame):
 
 def test_normalize_measurement(example_dir):
     from sensospot_data.parser import process_folder
-    from sensospot_data.normalisation import normalize_measurement
+    from sensospot_data.normalisation import split_channels
 
     sub_dir = example_dir / EXAMPLE_DIR_WITH_PARAMS
     data_frame = process_folder(sub_dir)
@@ -285,7 +282,7 @@ def test_normalize_measurement(example_dir):
         3: ExposureSetting("Cy5", 150),
     }
 
-    result = normalize_measurement(data_frame, exposure_map)
+    result = split_channels(data_frame, exposure_map)
     cy3_df, cy5_df = result["Cy3"], result["Cy5"]
 
     assert set(result.keys()) == {"Cy3", "Cy5"}

tests/test_parameters.py

@@ -69,15 +69,12 @@ def test_get_measurement_params_file_not_found(example_dir):
 
 
 def test_add_measurement_params(exposure_df):
-    from sensospot_data.parameters import (
+    from sensospot_data.parameters import ExposureInfo, _add_measurement_params
-        MeasurementParams,
-        _add_measurement_params,
-    )
 
     params = {
-        1: MeasurementParams("red", 10),
+        1: ExposureInfo("red", 10),
-        2: MeasurementParams("green", 20),
+        2: ExposureInfo("green", 20),
-        3: MeasurementParams("blue", 50),
+        3: ExposureInfo("blue", 50),
     }
 
     result = _add_measurement_params(exposure_df, params)

tests/test_sensovation_data_parser.py

@@ -3,8 +3,10 @@
 
 def test_import_api():
     from sensospot_data import CACHE_FILE_NAME  # noqa: F401
+    from sensospot_data import ExposureInfo  # noqa: F401
     from sensospot_data import parse_file  # noqa: F401
     from sensospot_data import parse_folder  # noqa: F401
     from sensospot_data import process_folder  # noqa: F401
+    from sensospot_data import normalize_channel  # noqa: F401
+    from sensospot_data import split_channels  # noqa: F401
     from sensospot_data import parse_multiple_files  # noqa: F401
-    from sensospot_data import normalize_measurement  # noqa: F401