Merge pull request #18 from LIBRA-project/plotting-lsc

Plotting for new LSC classes

.github/workflows/ci.yml

@@ -1,14 +1,13 @@
 name: CI
 on: [pull_request, push]
 
-
 jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v4
-  
+
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
@@ -17,12 +16,16 @@ jobs:
       - name: Install dependencies
         run: |
           pip install .[tests]
-  
+
       - name: Run tests
         run: |
           python -m pytest test/ --cov libra_toolbox --cov-report xml --cov-report term
-      
+
+      - name: Run notebook examples
+        run: |
+          jupyter nbconvert --to python --execute docs/examples/*.ipynb
+
       # - name: Upload coverage to Codecov
       #   uses: codecov/codecov-action@v4
       #   with:
-      #     token: ${{ secrets.CODECOV_TOKEN }}
+      #     token: ${{ secrets.CODECOV_TOKEN }}

libra_toolbox/tritium/lsc_measurements.py

@@ -58,6 +58,8 @@ def get_lum(self):
 
 
 class LSCSample:
+    activity: pint.Quantity
+
     def __init__(self, activity: pint.Quantity, name: str):
         self.activity = activity
         self.name = name
@@ -83,6 +85,8 @@ def from_file(file_reader: LSCFileReader, vial_name):
 
 
 class LIBRASample:
+    samples: List[LSCSample]
+
     def __init__(self, samples: List[LSCSample], time: str):
         self.samples = samples
         self._time = time
@@ -115,6 +119,8 @@ def get_total_activity(self):
 
 
 class LIBRARun:
+    samples: List[LIBRASample]
+
     def __init__(self, samples: List[LIBRASample], start_time: str):
         self.samples = samples
         self.start_time = start_time
@@ -142,3 +148,8 @@ def get_cumulative_activity(self, form: str = "total"):
     @property
     def relative_times(self):
         return [sample.get_relative_time(self.start_time) for sample in self.samples]
+
+    @property
+    def relative_times_as_pint(self):
+        times = [t.total_seconds() * ureg.s for t in self.relative_times]
+        return ureg.Quantity.from_list(times).to(ureg.day)

libra_toolbox/tritium/plotting.py

@@ -3,13 +3,130 @@
 
 from libra_toolbox.tritium import ureg
 from libra_toolbox.tritium.model import Model, quantity_to_activity
+from libra_toolbox.tritium.lsc_measurements import LIBRASample, LIBRARun
 
+import pint
+from typing import List
 
 COLLECTION_VOLUME = 10 * ureg.ml
 LSC_SAMPLE_VOLUME = 10 * ureg.ml
 
 
-def plot_bars(measurements, index=None, bar_width=0.35, stacked=True):
+def plot_bars(
+    measurements: List[LIBRASample] | LIBRARun | dict,
+    index=None,
+    bar_width=0.35,
+    stacked=True,
+):
+    if isinstance(measurements, dict):
+        return plot_bars_old(measurements, index, bar_width, stacked)
+
+    if isinstance(measurements, LIBRARun):
+        measurements = measurements.samples
+
+    vial_1_vals = ureg.Quantity.from_list(
+        [sample.samples[0].activity for sample in measurements]
+    )
+    vial_2_vals = ureg.Quantity.from_list(
+        [sample.samples[1].activity for sample in measurements]
+    )
+    vial_3_vals = ureg.Quantity.from_list(
+        [sample.samples[2].activity for sample in measurements]
+    )
+    vial_4_vals = ureg.Quantity.from_list(
+        [sample.samples[3].activity for sample in measurements]
+    )
+
+    if index is None:
+        if stacked:
+            index = np.arange(len(measurements))
+        else:
+            group_spacing = 1  # Adjust this value to control spacing between groups
+            index = (
+                np.arange(len(measurements)) * (group_spacing / 2 + 1) * bar_width * 4
+            )
+
+    if stacked:
+        vial_3_bar = plt.bar(
+            index,
+            vial_3_vals,
+            bar_width,
+            label="Vial 3",
+            color="#FB8500",
+        )
+        vial_4_bar = plt.bar(
+            index,
+            vial_4_vals,
+            bar_width,
+            label="Vial 4",
+            color="#FFB703",
+            bottom=vial_3_vals,
+        )
+        vial_1_bar = plt.bar(
+            index,
+            vial_1_vals,
+            bar_width,
+            label="Vial 1",
+            color="#219EBC",
+            bottom=vial_3_vals + vial_4_vals,
+        )
+        vial_2_bar = plt.bar(
+            index,
+            vial_2_vals,
+            bar_width,
+            label="Vial 2",
+            color="#8ECAE6",
+            bottom=vial_3_vals + vial_4_vals + vial_1_vals,
+        )
+    else:
+        if isinstance(index, pint.Quantity) and not isinstance(
+            bar_width, pint.Quantity
+        ):
+            raise TypeError(
+                f"index and bar_width must be of the same type, got {index=}, {bar_width=}"
+            )
+
+        vial_1_bar = plt.bar(
+            index - 1.5 * bar_width,
+            vial_1_vals,
+            bar_width,
+            linewidth=2,
+            edgecolor="white",
+            label="Vial 1",
+            color="#219EBC",
+        )
+        vial_2_bar = plt.bar(
+            index - 0.5 * bar_width,
+            vial_2_vals,
+            bar_width,
+            linewidth=2,
+            edgecolor="white",
+            label="Vial 2",
+            color="#8ECAE6",
+        )
+        vial_3_bar = plt.bar(
+            index + 0.5 * bar_width,
+            vial_3_vals,
+            bar_width,
+            linewidth=2,
+            edgecolor="white",
+            label="Vial 3",
+            color="#FB8500",
+        )
+        vial_4_bar = plt.bar(
+            index + 1.5 * bar_width,
+            vial_4_vals,
+            bar_width,
+            linewidth=2,
+            edgecolor="white",
+            label="Vial 4",
+            color="#FFB703",
+        )
+
+    return index
+
+
+def plot_bars_old(measurements, index=None, bar_width=0.35, stacked=True):
     vial_1_vals = (
         np.array([sample[1].magnitude for sample in measurements.values()]) * ureg.Bq
     )

pyproject.toml

@@ -18,7 +18,7 @@ dynamic = ["version"]
 dependencies = ["numpy", "pint", "scipy", "matplotlib", "sympy", "pandas"]
 
 [project.optional-dependencies]
-tests = ["pytest>=5.4.3", "pytest-cov"]
+tests = ["pytest>=5.4.3", "pytest-cov", "nbconvert", "ipykernel"]
 
 [tool.setuptools_scm]
 write_to = "libra_toolbox/_version.py"

test/tritium/test_plotting.py

@@ -0,0 +1,94 @@
+import pytest
+import numpy as np
+from libra_toolbox.tritium.plotting import plot_bars
+from libra_toolbox.tritium.lsc_measurements import LIBRASample, LIBRARun, LSCSample
+from libra_toolbox.tritium import ureg
+
+import matplotlib.pyplot as plt
+
+
+@pytest.fixture
+def sample_measurements():
+    samples = [
+        LIBRASample(
+            samples=[
+                LSCSample(activity=1 * ureg.Bq, name="Sample 1A"),
+                LSCSample(activity=1.1 * ureg.Bq, name="Sample 1B"),
+                LSCSample(activity=1.2 * ureg.Bq, name="Sample 1C"),
+                LSCSample(activity=1.3 * ureg.Bq, name="Sample 1D"),
+            ],
+            time="11/8/2024 4:20 PM",
+        ),
+        LIBRASample(
+            samples=[
+                LSCSample(activity=2 * ureg.Bq, name="Sample 2A"),
+                LSCSample(activity=2.1 * ureg.Bq, name="Sample 2B"),
+                LSCSample(activity=2.2 * ureg.Bq, name="Sample 2C"),
+                LSCSample(activity=2.3 * ureg.Bq, name="Sample 2D"),
+            ],
+            time="11/8/2024 4:21 PM",
+        ),
+        LIBRASample(
+            samples=[
+                LSCSample(activity=3 * ureg.Bq, name="Sample 3A"),
+                LSCSample(activity=3.1 * ureg.Bq, name="Sample 3B"),
+                LSCSample(activity=3.2 * ureg.Bq, name="Sample 3C"),
+                LSCSample(activity=3.3 * ureg.Bq, name="Sample 3D"),
+            ],
+            time="11/8/2024 4:22 PM",
+        ),
+        LIBRASample(
+            samples=[
+                LSCSample(activity=4 * ureg.Bq, name="Sample 4A"),
+                LSCSample(activity=4.1 * ureg.Bq, name="Sample 4B"),
+                LSCSample(activity=4.2 * ureg.Bq, name="Sample 4C"),
+                LSCSample(activity=4.3 * ureg.Bq, name="Sample 4D"),
+            ],
+            time="11/8/2024 4:23 PM",
+        ),
+    ]
+    return samples
+
+
+@pytest.fixture
+def sample_run(sample_measurements):
+    return LIBRARun(samples=sample_measurements, start_time="11/7/2024 4:20 PM")
+
+
+def test_plot_bars_with_samples(sample_measurements):
+    plt.figure()
+    index = plot_bars(sample_measurements)
+    assert len(index) == len(sample_measurements)
+    plt.close()
+
+
+def test_plot_bars_with_run(sample_run):
+    plt.figure()
+    index = plot_bars(sample_run)
+    assert len(index) == len(sample_run.samples)
+    plt.close()
+
+
+def test_plot_bars_with_dict():
+    measurements = {
+        "sample1": [0, 1 * ureg.Bq, 2 * ureg.Bq, 3 * ureg.Bq, 4 * ureg.Bq],
+        "sample2": [0, 2 * ureg.Bq, 3 * ureg.Bq, 4 * ureg.Bq, 5 * ureg.Bq],
+    }
+    plt.figure()
+    index = plot_bars(measurements)
+    assert len(index) == len(measurements)
+    plt.close()
+
+
+def test_plot_bars_stacked(sample_measurements):
+    plt.figure()
+    index = plot_bars(sample_measurements, stacked=True)
+    assert len(index) == len(sample_measurements)
+    plt.close()
+
+
+def test_plot_bars_not_stacked(sample_measurements):
+    plt.figure()
+    index = plot_bars(sample_measurements, stacked=False)
+    assert len(index) == len(sample_measurements)
+    plt.close()