Merge pull request #20 from cremerlab/18-param-bounds-large-time-dime…

…nsion 18 param bounds large time dimension
cremerlab · Aug 14, 2024 · ce44dac · ce44dac
2 parents dd5cf37 + bf28235
commit ce44dac
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diff --git a/docs/source/methodology/baseline.ipynb b/docs/source/methodology/baseline.ipynb
@@ -303,13 +303,13 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Performing baseline correction: 100%|██████████| 187/187 [00:00<00:00, 406.72it/s]\n"
+      "Performing baseline correction: 100%|██████████| 187/187 [00:00<00:00, 477.28it/s]\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x171398b80>"
+       "<matplotlib.legend.Legend at 0x16ac59ba0>"
       ]
      },
      "execution_count": 5,

diff --git a/docs/source/methodology/fitting.ipynb b/docs/source/methodology/fitting.ipynb
@@ -73,7 +73,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x303a12a70>"
+       "<matplotlib.legend.Legend at 0x16b72b940>"
       ]
      },
      "execution_count": 1,
@@ -154,13 +154,13 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Performing baseline correction: 100%|██████████| 299/299 [00:00<00:00, 3910.85it/s]\n"
+      "Performing baseline correction: 100%|██████████| 299/299 [00:00<00:00, 2725.64it/s]\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x30408a500>"
+       "<matplotlib.legend.Legend at 0x16b8d2380>"
       ]
      },
      "execution_count": 2,
@@ -260,7 +260,7 @@
     "By default, `hplc-py` applies broad, permissive bounds on these parameters given \n",
     "information of the chromatogram. The default bounds given to each parameter are \n",
     "\n",
-    "* $A \\in [0.1 \\times A_0, 10 \\times A_0]$ where $A_0$ is the initial guess for the amplitude.\n",
+    "* $A \\in [0.01 \\times A_0, 100 \\times A_0]$ where $A_0$ is the initial guess for the amplitude.\n",
     "* $\\tau \\in [t_{min}, t_{max}]$ where $t_{min}$ and $t_{max}$ correspond to the minimum and maximum times in the peak window.\n",
     "* $\\sigma_{bounds} \\in [dt, \\frac{t_{max} - t_{min}}{2}]$ where $dt$ corresponds to the time sampling interval of the chromatogram.\n",
     "* $\\alpha \\in (-\\inf, +\\inf)$.\n",
@@ -330,7 +330,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x303c21630>"
+       "<matplotlib.legend.Legend at 0x1739eab90>"
       ]
      },
      "execution_count": 6,

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/tutorials/calibration_curve.ipynb b/docs/source/tutorials/calibration_curve.ipynb
diff --git a/docs/source/tutorials/quickstart.ipynb b/docs/source/tutorials/quickstart.ipynb
diff --git a/hplc/__init__.py b/hplc/__init__.py
@@ -2,4 +2,4 @@
 from . import io
 __author__ = """Griffin Chure and Jonas Cremer"""
 __email__ = """[email protected]"""
-__version__ = "0.2.6"
+__version__ = "0.2.7"
diff --git a/hplc/quant.py b/hplc/quant.py
diff --git a/setup.py b/setup.py
@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 import pathlib
 
-__version__ = "0.2.6"
+__version__ = "0.2.7"
 
 # The directory containing this file
 HERE = pathlib.Path(__file__).parent

diff --git a/tests/test_chromatogram.py b/tests/test_chromatogram.py
@@ -127,6 +127,14 @@ def test_bg_estimation():
     with pytest.warns():
         chrom.correct_baseline(window=0.75)
 
+    # Test that the correct exception is thrown if the window is too small.
+    try:
+        with pytest.warns():
+            chrom.correct_baseline(window=np.diff(_df['x'].values)[0])
+            assert False
+    except ValueError:
+        assert True
+
 
 def test_shouldered_peaks():
     """
@@ -479,6 +487,7 @@ def test_generic_param_bounding():
     """
     df = pd.read_csv('./tests/test_data/test_integration_window_chrom.csv')
     chrom = hplc.quant.Chromatogram(df)
+
     # Adjust the parameters
     adjustments = {'amplitude': [0.9, 1.1],
                    'location': [-1, 1],
@@ -496,3 +505,13 @@ def test_generic_param_bounding():
              'skew': [-10, 10]}
     for k, v in adj_pars.items():
         assert np.array(truth[k] == v).all()
+
+    # Make sure that incorrect bounds throw a value error.
+    adjustments = {'scale': [10, 11]}
+    try:
+        _ = chrom.fit_peaks(param_bounds=adjustments,
+                            correct_baseline=False,
+                            verbose=False)
+        assert False
+    except ValueError:
+        assert True