Minor updates + tests for JensenPlot

pyrolite/plot/templates/__init__.py

@@ -8,6 +8,7 @@
 
 from ...util.log import Handle
 from .feldspar import FeldsparTernary
+from .jensen import JensenPlot
 from .pearce import pearceThNbYb, pearceTiNbYb
 from .QAP import QAP
 from .TAS import TAS
@@ -18,6 +19,7 @@
 __all__ = [
     "pearceThNbYb",
     "pearceTiNbYb",
+    "JensenPlot",
     "TAS",
     "USDASoilTexture",
     "QAP",

pyrolite/plot/templates/JensenPlot.py → pyrolite/plot/templates/jensen.py

@@ -1,19 +1,18 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from ...util.classification import USDASoilTexture as USDAclassifier
+from ...util.classification import JensenPlot as _JensenPlot
 from ...util.log import Handle
-from ...util.meta import (sphinx_doi_link, subkwargs, update_docstring_references)
+from ...util.meta import sphinx_doi_link, subkwargs, update_docstring_references
 from ...util.plot.axes import init_axes
 
 logger = Handle(__name__)
 
 
 @update_docstring_references
-def Jensen_Plot(ax=None, add_labels=False, color="k", **kwargs):
+def JensenPlot(ax=None, add_labels=False, color="k", **kwargs):
     """
-    Jensen Plot for classification of sub-alkaline volcanic rocks 
-    [#ref_1]_.
+    Jensen Plot for classification of sub-alkaline volcanic rocks [#ref_1]_.
 
     Parameters
     ----------
@@ -30,20 +29,20 @@ def Jensen_Plot(ax=None, add_labels=False, color="k", **kwargs):
 
     References
     ----------
-    .. [#ref_1] Jensen, L. S. (1976) A new cation plot for classifying sub-alkaline volcanic rocks. 
+    .. [#ref_1] Jensen, L. S. (1976). A new cation plot for classifying
+                sub-alkaline volcanic rocks.
                 Ontario Division of Mines. Miscellaneous Paper No. 66.
-    
+
     Notes
     -----
-    Diagram used for the classification classification of subalkalic volcanic rocks. 
-    The diagram is constructed for molar cation percentages of Al, Fe+Ti and Mg, on account of these elements' stability upon metamorphism. 
-    This particular version uses updated labels relative to Jensen (1976), in which the fields have been extended to the full range of the ternary plot. 
+    Diagram used for the classification classification of subalkalic volcanic rocks.
+    The diagram is constructed for molar cation percentages of Al, Fe+Ti and Mg,
+    on account of these elements' stability upon metamorphism.
+    This particular version uses updated labels relative to Jensen (1976),
+    in which the fields have been extended to the full range of the ternary plot.
     """
     ax = init_axes(ax=ax, projection="ternary", **kwargs)
 
-    clf = JensenPlot()
+    clf = _JensenPlot()
     clf.add_to_axes(ax=ax, color=color, add_labels=add_labels, **kwargs)
     return ax
-
-
-

pyrolite/util/classification.py

@@ -351,7 +351,7 @@ class TAS(PolygonClassifier):
 
     References
     -----------
-    .. [#ref_1] Le Bas, M.J., Le Maitre, R.W., Woolley, A.R., 1992.
+    .. [#ref_1] Le Bas, M.J., Le Maitre, R.W., Woolley, A.R. (1992).
                 The construction of the Total Alkali-Silica chemical
                 classification of volcanic rocks.
                 Mineralogy and Petrology 46, 1–22.
@@ -495,11 +495,11 @@ class QAP(PolygonClassifier):
 
     References
     -----------
-    .. [#ref_1] Streckeisen, A. Classification and nomenclature of plutonic rocks
-                recommendations of the IUGS subcommission on the systematics of
-                Igneous Rocks. Geol Rundsch 63, 773–786 (1974).
+    .. [#ref_1] Streckeisen, A. (1974). Classification and nomenclature of plutonic
+                rocks: recommendations of the IUGS subcommission on the systematics
+                of Igneous Rocks. Geol Rundsch 63, 773–786.
                 doi: {Streckeisen1974}
-    .. [#ref_2] Le Maitre,R.W. 2002. Igneous Rocks: A Classification and Glossary
+    .. [#ref_2] Le Maitre,R.W. (2002). Igneous Rocks: A Classification and Glossary
                 of Terms : Recommendations of International Union of Geological
                 Sciences Subcommission on the Systematics of Igneous Rocks.
                 Cambridge University Press, 236pp
@@ -576,10 +576,11 @@ def predict(self, df: pd.DataFrame):
         out.loc[perkalkaline_where] = "Peralkaline"
         return out
 
+
+@update_docstring_references
 class JensenPlot(PolygonClassifier):
     """
-    Jensen Plot for classification of subalkaline volcanic rocks 
-    [#ref_1]_.
+    Jensen Plot for classification of subalkaline volcanic rocks  [#ref_1]_.
 
     Parameters
     -----------
@@ -593,14 +594,21 @@ class JensenPlot(PolygonClassifier):
 
     References
     -----------
-    .. [#ref_1] Jensen, L. S. (1976) A new cation plot for classifying sub-alkaline volcanic rocks. 
+    .. [#ref_1] Jensen, L. S. (1976). A new cation plot for classifying
+                sub-alkaline volcanic rocks.
                 Ontario Division of Mines. Miscellaneous Paper No. 66.
+
+    Notes
+    -----
+    Diagram used for the classification classification of subalkalic volcanic rocks.
+    The diagram is constructed for molar cation percentages of Al, Fe+Ti and Mg,
+    on account of these elements' stability upon metamorphism.
+    This particular version uses updated labels relative to Jensen (1976),
+    in which the fields have been extended to the full range of the ternary plot.
     """
 
     def __init__(self, **kwargs):
-        src = (
-            pyrolite_datafolder(subfolder="models") / "JensenPlot" / "config.json"
-        )
+        src = pyrolite_datafolder(subfolder="models") / "JensenPlot" / "config.json"
 
         with open(src, "r") as f:
             config = json.load(f)
@@ -609,8 +617,6 @@ def __init__(self, **kwargs):
         super().__init__(**poly_config)
 
 
-
-
 class SpinelTrivalentTernary(PolygonClassifier):
     """
     Spinel Trivalent Ternary classification  - designed for data in atoms per formula unit

test/plot/templates/plot_templates.py

@@ -2,7 +2,7 @@
 
 import matplotlib.pyplot as plt
 
-from pyrolite.plot.templates import (QAP, TAS, FeldsparTernary,
+from pyrolite.plot.templates import (QAP, TAS, FeldsparTernary, JensenPlot,
                                      USDASoilTexture, pearceThNbYb,
                                      pearceTiNbYb)
 
@@ -58,7 +58,7 @@ def tearDown(self):
 
 class TestTernaryDiagrams(unittest.TestCase):
     def test_ternary_default(self):
-        for diagram in [QAP, FeldsparTernary, USDASoilTexture]:
+        for diagram in [QAP, FeldsparTernary, USDASoilTexture, JensenPlot]:
             fig, axes = plt.subplots(1)
             for a in [None, axes]:
                 with self.subTest(diagram=diagram, a=a):

test/util/util_classification.py

@@ -5,7 +5,7 @@
 
 from pyrolite.comp.codata import renormalise
 from pyrolite.util.classification import *
-from pyrolite.util.synthetic import normal_frame
+from pyrolite.util.synthetic import normal_frame, random_cov_matrix
 
 
 class TestTAS(unittest.TestCase):
@@ -127,6 +127,34 @@ def test_classifer_predict(self):
         self.assertFalse(pd.isnull(classes).all())
 
 
+class TestJensenPlot(unittest.TestCase):
+    def setUp(self):
+        self.df = normal_frame(
+            columns=["Ti + Fe(tot) mol%", "Al mol%", "Mg mol%"],
+            mean=[0.07, 0.15, 0.12],
+            cov=random_cov_matrix(2, sigmas=[0.5, 0.7]),
+            size=100,
+        )
+
+    def test_classifer_build(self):
+        cm = JensenPlot()
+
+    def test_classifer_add_to_axes(self):
+        cm = JensenPlot()
+        fig, ax = plt.subplots(1)
+        for a in [None, ax]:
+            with self.subTest(a=a):
+                cm.add_to_axes(
+                    ax=a, alpha=0.4, color="k", linewidth=0.5, add_labels=True
+                )
+
+    def test_classifer_predict(self):
+        df = self.df
+        cm = JensenPlot()
+        classes = cm.predict(df)
+        self.assertFalse(pd.isnull(classes).all())
+
+
 class TestPeralkalinity(unittest.TestCase):
     """Test the peralkalinity classifier."""