now relying on sensospot_tools for functionality

pyproject.toml

@@ -29,6 +29,7 @@ classifiers = [
 dependencies = [
     "pandas",
     "scikit-learn",
+    "sensospot_tools >= 0.2",
 ]
 
 [project.urls]

src/conda_helpers/__init__.py

@@ -3,9 +3,10 @@
 Helpers for working with data frames in a conda environment
 """
 
-__version__ = "0.0.1"
+__version__ = "0.0.2"
 
 
-from .iter_uniques import iter_uniques, select  # noqa: F401
+from sensospot_tools import select, split  # noqa: F401
+
 from .linear_regression import linear_regression  # noqa: F401
 from .mbp import add_exposure_info, normalize  # noqa: F401

src/conda_helpers/iter_uniques.py

@@ -1,60 +0,0 @@
-from __future__ import annotations
-
-from typing import Any
-
-import pandas as pd
-
-
-def _iter_uniques(
-    data: pd.DataFrame, *on: tuple[Any], _prev_values: None | tuple[Any] = None
-) -> tuple[Any, ..., pd.DataFrame]:
-    """Splits a data frame on uniques values in a column
-
-    Returns a generator of tuples with at least two elements.
-    The _last_ element is the resulting partial data frame,
-    the element(s) before are the values used to split up the original data.
-
-    Example:
-
-    for well, pos, partial_data in split_uniques(full_data, "Well", "Pos"):
-        # `well` is one of the unique values in full_data["Well"]
-        # `pos` is one of the unique values in full_data["Pos"]
-        # parital_data is a data frame, containing values for this well and pos
-
-    """
-    if _prev_values is None:
-        _prev_values = ()
-    current_column, *rest = on
-    for current_value in data[current_column].unique():
-        selection = data[current_column] == current_value
-        selected = data.loc[selection].copy()
-        values = (*_prev_values, current_value)
-        if rest:
-            yield from _iter_uniques(selected, *rest, _prev_values=values)
-        else:
-            yield *values, selected
-
-
-def iter_uniques(
-    data: pd.DataFrame, *on: tuple[Any]
-) -> tuple[Any, ..., pd.DataFrame]:
-    """Splits a data frame on uniques values in a column
-
-    Returns a generator of tuples with at least two elements.
-    The _last_ element is the resulting partial data frame,
-    the element(s) before are the values used to split up the original data.
-
-    Example:
-
-    for well, pos, partial_data in split_uniques(full_data, "Well", "Pos"):
-        # `well` is one of the unique values in full_data["Well"]
-        # `pos` is one of the unique values in full_data["Pos"]
-        # parital_data is a data frame, containing values for this well and pos
-
-    """
-    yield from _iter_uniques(data, *on)
-
-
-def select(data: pd.DataFrame, column: str, value: Any) -> pd.DataFrame:
-    selection = data[column] == value
-    return data.loc[selection].copy()

src/conda_helpers/mbp.py

@@ -1,17 +1,41 @@
 import pandas as pd
-
+from sensospot_tools import (
-from .iter_uniques import select
+    normalize as normalize_xdr_data,
+)
+from sensospot_tools import (
+    select_hdr_data,
+    split,
+)
+
+EXPOSURE_ID = "Exposure.Id"
+EXPOSURE_CHANNEL = "Exposure.Channel"
+EXPOSURE_TIME = "Exposure.Time"
+EXPOSURE_TIME_NORMALIZED = "Exposure.Time.Normalized"
 
 EXPOSURE_COLUMNS = [
-    "Exposure.Id",
+    EXPOSURE_ID,
-    "Exposure.Channel",
+    EXPOSURE_CHANNEL,
-    "Exposure.Time",
+    EXPOSURE_TIME,
-    "Exposure.Time.Normalized",
+    EXPOSURE_TIME_NORMALIZED,
 ]
 
 SATURATION_LIMIT = 2
+SPOT_SATURATION = "Spot.Saturation"
+
+TEST_OVERFLOW = "Test.Spot.Overflow"
+
+SPOT_ID_COLUMNS = ["Analysis.Name", "Well.Name", "Pos.Id"]
 
-TEST_OVERFLOW_COLUMN = "Test.Spot.Overflow"
+TIME_DEPENDENT_COLUMNS = [
+    "Bkg.Mean",
+    "Bkg.Median",
+    "Bkg.StdDev",
+    "Bkg.Sum",
+    "Spot.Mean",
+    "Spot.Median",
+    "Spot.StdDev",
+    "Spot.Sum",
+]
 
 
 def add_exposure_info(data: pd.DataFrame, analysis="hyb") -> pd.DataFrame:
@@ -22,79 +46,36 @@ def add_exposure_info(data: pd.DataFrame, analysis="hyb") -> pd.DataFrame:
         (3, "Cy5", 15, 25),
     ]
     exposure_df = pd.DataFrame(exposure_values, columns=EXPOSURE_COLUMNS)
-    return data.merge(exposure_df, on="Exposure.Id")
+    return data.merge(exposure_df, on=EXPOSURE_ID)
-
-
-def test_overflow(
-    data: pd.DataFrame, result_column: str = TEST_OVERFLOW_COLUMN
-):
-    data[result_column] = data["Spot.Saturation"] > SATURATION_LIMIT
-    return data
-
-
-def select_xdr_data(data: pd.DataFrame) -> pd.DataFrame:
-    xdr_columns = [*EXPOSURE_COLUMNS, TEST_OVERFLOW_COLUMN]
-    missing = [c for c in xdr_columns if c not in data.columns]
-    if missing:
-        message = f"Columns {missing} are missing in the data frame"
-        raise KeyError(message)
-
-    cy3_data = select(data, "Exposure.Channel", "Cy3")
-    cy5_data = select(data, "Exposure.Channel", "Cy5")
-
-    id_columns = ["Analysis.Name", "Well.Name", "Pos.Id"]
 
-    cy5_long = select(cy5_data, "Exposure.Time", 150).set_index(id_columns)
-    cy5_short = select(cy5_data, "Exposure.Time", 15).set_index(id_columns)
-
-    in_overflow = cy5_long[TEST_OVERFLOW_COLUMN]
-    cy5_long_selected = cy5_long.loc[~in_overflow].reset_index()
-    cy5_short_selected = cy5_short.loc[in_overflow].reset_index()
-
-    return pd.concat(
-        [cy3_data, cy5_long_selected, cy5_short_selected]
-    ).reset_index()
-
-
-def normalize_xdr_data(
-    data: pd.DataFrame, template="{}.Normalized"
-) -> pd.DataFrame:
-    cy5_data = select(data, "Exposure.Channel", "Cy5")
-    cy5_long_data = select(cy5_data, "Exposure.Time", 150)
-    if True in list(cy5_long_data[TEST_OVERFLOW_COLUMN].unique()):
-        message = (
-            "Some spots for long Cy5 exposure time are still in overflow. "
-            "Did you forget to select the appropriate data (select_xdr_data) ?"
-        )
-        raise ValueError(message)
-
-    time_dependend_columns = [
-        "Bkg.Mean",
-        "Bkg.Median",
-        "Bkg.StdDev",
-        "Bkg.Sum",
-        "Spot.Mean",
-        "Spot.Median",
-        "Spot.StdDev",
-        "Spot.Sum",
-    ]
-    available_columns = [
-        c for c in time_dependend_columns if c in data.columns
-    ]
-
-    for column in available_columns:
-        adjusted_column = template.format(column)
-        data[adjusted_column] = (
-            data[column]
-            * data["Exposure.Time.Normalized"]
-            / data["Exposure.Time"]
-        )
 
+def test_overflow(data: pd.DataFrame, result_column: str = TEST_OVERFLOW):
+    data[result_column] = data[SPOT_SATURATION] > SATURATION_LIMIT
     return data
 
 
 def normalize(raw_data: pd.DataFrame, analysis="hyb"):
     with_exposure_info = add_exposure_info(raw_data, analysis=analysis)
     overflow_tested = test_overflow(with_exposure_info)
-    xdr_data = select_xdr_data(overflow_tested)
+    normalized_data = (
-    return normalize_xdr_data(xdr_data)
+        _normalize_channel(data)
+        for _, data in split(overflow_tested, EXPOSURE_CHANNEL)
+    )
+    return pd.concat(normalized_data).reset_index()
+
+
+def _normalize_channel(data: pd.DataFrame) -> pd.DataFrame:
+    normalized_time = data[EXPOSURE_TIME_NORMALIZED].unique()[0]
+    hdr_data = select_hdr_data(
+        data, SPOT_ID_COLUMNS, EXPOSURE_TIME, TEST_OVERFLOW
+    )
+    available_columns = [
+        c for c in hdr_data.columns if c in TIME_DEPENDENT_COLUMNS
+    ]
+    return normalize_xdr_data(
+        hdr_data,
+        normalized_time,
+        EXPOSURE_TIME,
+        available_columns,
+        "{}.Normalized",
+    )

tests/test_conda_helpers.py

@@ -25,8 +25,8 @@ mistakes.
 def test_api():
     from conda_helpers import (
         add_exposure_info,  # noqa: F401
-        iter_uniques,  # noqa: F401
         linear_regression,  # noqa: F401
         normalize,  # noqa: F401
         select,  # noqa: F401
+        split,  # noqa: F401
     )

tests/test_iter_uniques.py

@@ -1,48 +0,0 @@
-import pandas as pd
-import pytest
-
-
-@pytest.fixture()
-def example_data():
-    return pd.DataFrame({"A": [1, 2, 2], "B": [3, 4, 3], "C": ["x", "y", "z"]})
-
-
-def test_split_uniques_one_column(example_data):
-    from conda_helpers import iter_uniques
-
-    result = list(iter_uniques(example_data, "A"))
-
-    assert len(result) == 2
-    assert isinstance(result[0], tuple)
-
-    a_value, data = result[0]
-    assert a_value == 1
-    assert list(data["C"]) == ["x"]
-
-    a_value, data = result[1]
-    assert a_value == 2
-    assert list(data["C"]) == ["y", "z"]
-
-
-def test_split_uniques_multiple_columns(example_data):
-    from conda_helpers import iter_uniques
-
-    result = list(iter_uniques(example_data, "B", "A"))
-
-    assert len(result) == 3
-    assert isinstance(result[0], tuple)
-
-    b_value, a_value, data = result[0]
-    assert b_value == 3
-    assert a_value == 1
-    assert list(data["C"]) == ["x"]
-
-    b_value, a_value, data = result[1]
-    assert b_value == 3
-    assert a_value == 2
-    assert list(data["C"]) == ["z"]
-
-    b_value, a_value, data = result[2]
-    assert b_value == 4
-    assert a_value == 2
-    assert list(data["C"]) == ["y"]

tests/test_mbp.py

@@ -51,11 +51,11 @@ def test_add_exposure_info(example_data, analysis, expected_cy3):
 
 
 def test_test_overflow(example_data):
-    from conda_helpers.mbp import TEST_OVERFLOW_COLUMN, test_overflow
+    from conda_helpers.mbp import TEST_OVERFLOW, test_overflow
 
     result = test_overflow(example_data)
 
-    assert list(result[TEST_OVERFLOW_COLUMN]) == [
+    assert list(result[TEST_OVERFLOW]) == [
         True,
         False,
         False,
@@ -68,23 +68,6 @@ def test_test_overflow(example_data):
     ]
 
 
-def test_select_xdr_data(example_data):
-    from conda_helpers.mbp import (
-        add_exposure_info,
-        select_xdr_data,
-        test_overflow,
-    )
-
-    tmp = add_exposure_info(example_data)
-    tmp = test_overflow(tmp)
-    result = select_xdr_data(tmp)
-
-    assert list(result["Exposure.Channel"]) == ["Cy3"] * 3 + ["Cy5"] * 3
-    assert list(result["Exposure.Time"]) == [200] * 3 + [150, 150, 15]
-    assert list(result["Analysis.Name"]) == list("AABABA")
-    assert list(result["Well.Name"]) == list("abaaab")
-
-
 def test_normalize(example_data):
     from conda_helpers.mbp import normalize