Merge pull request #11 from cremerlab/10-small-issue-in-correct_basel…

…ine-method Bug fix for: #10 small issue in correct baseline method
cremerlab · Jan 23, 2024 · 14bb8d9 · 14bb8d9
2 parents 8ce5223 + 24a56b3
commit 14bb8d9
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diff --git a/docs/source/getting_started/algorithm.ipynb b/docs/source/getting_started/algorithm.ipynb
diff --git a/docs/source/methodology/baseline.ipynb b/docs/source/methodology/baseline.ipynb
diff --git a/docs/source/methodology/fitting.ipynb b/docs/source/methodology/fitting.ipynb
diff --git a/docs/source/methodology/peak_detection.ipynb b/docs/source/methodology/peak_detection.ipynb
diff --git a/docs/source/methodology/problem.ipynb b/docs/source/methodology/problem.ipynb
diff --git a/docs/source/methodology/scoring.ipynb b/docs/source/methodology/scoring.ipynb
diff --git a/docs/source/quickstart.ipynb b/docs/source/quickstart.ipynb
diff --git a/hplc/quant.py b/hplc/quant.py
@@ -881,8 +881,8 @@ def correct_baseline(self,
         for i in iter:
             tform_new = tform.copy()
             for j in range(i, len(tform) - i):
-                tform_new[j] = min(tform_new[j], 0.5 *
-                                   (tform_new[j+i] + tform_new[j-i]))
+                tform_new[j] = min(tform[j], 0.5 *
+                                   (tform[j+i] + tform[j-i]))
             tform = tform_new
 
         # Perform the inverse of the LLS transformation and subtract

diff --git a/setup.py b/setup.py
@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 import pathlib
 
-__version__ = "0.2.2"
+__version__ = "0.2.3"
 
 # The directory containing this file
 HERE = pathlib.Path(__file__).parent

diff --git a/tests/generate_test_data.py b/tests/generate_test_data.py
@@ -194,8 +194,12 @@
 # ##############################################################################
 # TEST DATA FOR  MANY PEAKS IN A WINDOW
 # ##############################################################################
-x = np.arange(0, 70, dt)
-locs = np.linspace(10, 55, 10)
+x = np.arange(0, 100, dt)
+_locs = np.linspace(20, 55, 10)
+locs = [10]
+for _l in _locs:
+    locs.append(_l)
+locs.append(70)
 sig = np.zeros_like(x)
 for i in range(len(locs)):
     sig += 100 * scipy.stats.norm(locs[i], 1).pdf(x)

diff --git a/tests/test_chromatogram.py b/tests/test_chromatogram.py
@@ -1,6 +1,4 @@
 # %%
-
-import importlib
 import hplc.quant
 import pandas as pd
 import numpy as np
@@ -107,25 +105,26 @@ def test_bg_estimation():
     tol = 1.5E-2
     data = pd.read_csv('./tests/test_data/test_SNIP_chrom.csv')
     chrom = hplc.quant.Chromatogram(data, cols={'time': 'x', 'signal': 'y'})
-    _df = chrom.correct_baseline(window=0.5, return_df=True)
+    _df = chrom.correct_baseline(window=0.75, return_df=True)
+    # return (chrom, _df, data)
     with pytest.warns():
-        __df = chrom.correct_baseline(window=0.5, return_df=False)
+        __df = chrom.correct_baseline(window=0.75, return_df=False)
 
     # Ensure that dataframe returning is working.
     assert _df is not None
     assert __df is None
 
-    window = int(0.5 / np.mean(np.diff(data['x'].values)))
+    window = int(0.75 / np.mean(np.diff(data['x'].values)))
     assert np.isclose(chrom.df['estimated_background'].values[window:-window],
                       data['bg'].values[window:-window], rtol=tol).all()
 
     with pytest.warns():
-        chrom.correct_baseline(window=0.5)
+        chrom.correct_baseline(window=0.75)
 
     data['y'] -= 100
     chrom = hplc.quant.Chromatogram(data, cols={'time': 'x', 'signal': 'y'})
     with pytest.warns():
-        chrom.correct_baseline(window=0.5)
+        chrom.correct_baseline(window=0.75)
 
 
 def test_shouldered_peaks():