pyrolite 0.0.14__zip

ProgramData/Anaconda3_64/Lib/site-packages/pyrolite/__init__.py

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+import sys
+import logging
+from ._version import get_versions
+
+__version__ = get_versions()["version"]
+del get_versions
+
+# http://docs.python-guide.org/en/latest/writing/logging/
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+logging.captureWarnings(True)

ProgramData/Anaconda3_64/Lib/site-packages/pyrolite/_version.py

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+
+# This file was generated by 'versioneer.py' (0.18) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+{
+ "date": "2019-01-10T15:35:23+0800",
+ "dirty": false,
+ "error": null,
+ "full-revisionid": "92999f23ac48a00a8ddb00ad9469cf92c67dba75",
+ "version": "0.0.14"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)

ProgramData/Anaconda3_64/Lib/site-packages/pyrolite/alteration.py

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+import numpy as np
+import pandas as pd
+import logging
+
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+logger = logging.getLogger(__name__)
+
+
+def CIA(df: pd.DataFrame):
+    """
+    Chemical Index of Alteration
+    type:   molecular
+    ref:    Nesbitt and Young (1982)
+    """
+    return 100 * df.Al2O3 / (df.Al2O3 + df.CaO + df.Na2O + df.K2O)
+
+
+def CIW(df: pd.DataFrame):
+    """
+    Chemical Index of Weathering
+    type:   molecular
+    ref:    Harnois (1988)
+    """
+    return 100.0 * df.Al2O3 / (df.Al2O3 + df.CaO + df.Na2O)
+
+
+def PIA(df: pd.DataFrame):
+    """
+    Plagioclase Index of Alteration
+    type:   molecular
+    ref:    Fedo et al. (1995)
+    """
+    return 100.0 * (df.Al2O3 - df.K2O) / (df.Al2O3 + df.CaO + df.Na2O - df.K2O)
+
+
+def SAR(df: pd.DataFrame):
+    """
+    Silica-Alumina Ratio
+    type:   molecular
+    ref:
+    """
+    return df.SiO2 / df.Al2O3
+
+
+def SiTiIndex(df: pd.DataFrame):
+    """
+    Silica-Titania Index
+    Jayaverdena and Izawa (1994)
+    type:   molecular
+    ref:
+    """
+    # may need to recalculate titania from titanium ppm
+    si_ti = df.SiO2 / df.TiO2
+    si_al = df.SiO2 / df.Al2O3
+    al_ti = df.Al2O3 / df.TiO2
+    return si_ti / (si_ti + si_al + al_ti)
+
+
+def WIP(df: pd.DataFrame):
+    """
+    Weathering Index of Parker
+    Parker (1970)
+    type:   molecular
+    ref:
+    """
+    return 2 * df.Na2O / 0.35 + df.MgO / 0.9 + 2 * df.K2O / 0.25 + df.CaO / 0.7

ProgramData/Anaconda3_64/Lib/site-packages/pyrolite/classification.py

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+import os
+import sys
+from pathlib import Path
+import pickle
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+from matplotlib.patches import Polygon
+from matplotlib.collections import PatchCollection
+import logging
+import joblib
+
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+logger = logging.getLogger(__name__)
+
+
+class ClassifierModel(object):
+    def __init__(self, rebuild=False, deterministic=False):
+        self.clsf_modelname = str(type(self).__name__)
+        if __name__ == "__main__":
+            modeldir = Path(os.getcwd()) / "models"
+        else:
+            modeldir = Path(__file__).resolve().parent / "data" / "models"
+        self.diskname = modeldir / str(self.clsf_modelname)
+        self.deterministic = deterministic
+        self.clsf = None
+        # Try load classifer
+        if rebuild:
+            self.rebuild_clsf()
+        try:
+            self.clsf = self.load_clsf(self.diskname.with_suffix(".clsf.gz"))
+            # logger.info(f'Loaded {self.diskname}')
+        except:
+            self.rebuild_clsf()
+
+    def rebuild_clsf(self):
+        self.clsf = self.build_clsf()
+        self.dump_clsf(self.diskname.with_suffix(".clsf.gz"))
+        # logger.info(f'Built {self.clsf_modelname}')
+
+    def load_clsf(self, file):
+        assert file.exists() and file.is_file()
+        # logger.info(f'Loading {self.diskname}')
+        return joblib.load(file)
+
+    def build_clsf(self):
+        # logger.info(f'Building {self.clsf_modelname}')
+        clsf = None
+        return clsf
+
+    def dump_clsf(self, filename):
+        joblib.dump(self.clsf, filename, compress=("gzip", 3))
+        # logger.info(f'Dumped {filename}')
+        assert filename.exists() and filename.is_file()
+
+    def classify(self, df: pd.DataFrame):
+        return self.clsf.predict(df)
+
+    def __str__(self):
+        pass
+
+    def __repr__(self):
+        pass
+
+
+class SimpleDeterministicClassifer(object):
+    def __init__(self, parent: ClassifierModel):
+        self.parent = parent
+        self.fields = None
+        self.load_fields()
+
+    def load_fields(self):
+        if self.parent:
+            self.clsf_modelname = str(self.parent.clsf_modelname)
+            self.modeldir = self.parent.diskname.resolve()
+            af = self.modeldir / str(self.clsf_modelname + ".modelfields")
+            if af.exists() and af.is_file():
+                # logger.info(f'''Loading {self.clsf_modelname} classifer fields from "allfile".''')
+                loadup = joblib.load(af)
+                self.fclasses = [k for (k, v) in loadup.items()]
+                self.fields = {c: loadup[c] for ix, c in enumerate(self.fclasses)}
+            else:
+                # logger.info(f'Loading {self.clsf_modelname} classifer fields from files.')
+                fieldfiles = self.modeldir.glob(self.clsf_modelname + ".*.modelfield")
+                loadup = [joblib.load(f) for f in fieldfiles]
+                self.fclasses = [f.suffix.replace(".", "") for f in loadup]
+                self.fields = {c: loadup[ix] for ix, c in enumerate(self.fclasses)}
+            # logger.info(f'''Loaded {self.clsf_modelname} classifer fields.''')
+        else:
+            pass
+
+    def add_to_axes(self, ax=None, **kwargs):
+        polys = [(c, self.fields[c]) for c in self.fclasses if self.fields[c]["poly"]]
+        if ax is None:
+            fig, ax = plt.subplots(1)
+        pgns = []
+        for c, f in polys:
+            label = f["names"]
+            pg = Polygon(f["poly"], closed=True, **kwargs)
+            pgns.append(pg)
+            x, y = pg.get_xy().T
+            ax.annotate(c, xy=(np.nanmean(x), np.nanmean(y)))
+            ax.add_patch(pg)
+        # ax.add_collection(PatchCollection(pgns), autolim=True)
+
+    def predict(self, df: pd.DataFrame, cols: list = ["x", "y"]):
+        points = df.loc[:, cols].values
+        polys = [
+            Polygon(self.fields[c]["poly"], closed=True) for c in self.fclasses
+        ]  # if self.fields[c]['poly']
+        indexes = np.array([p.contains_points(points) for p in polys]).T
+        notfound = np.logical_not(indexes.sum(axis=-1))
+        out = pd.Series(index=df.index)
+        outlist = list(map(lambda ix: self.fclasses[ix], np.argmax(indexes, axis=-1)))
+        out.loc[:] = outlist
+        out.loc[(notfound)] = "none"
+        return out
+
+
+class PeralkalinityClassifier(object):
+    def __init__(self, parent: ClassifierModel):
+        self.parent = parent
+        self.fields = None
+
+    def predict(self, df: pd.DataFrame):
+        TotalAlkali = df.Na2O + df.K2O
+        perkalkaline_where = (df.Al2O3 < (TotalAlkali + df.CaO)) & (
+            TotalAlkali > df.Al2O3
+        )
+        metaluminous_where = (df.Al2O3 > (TotalAlkali + df.CaO)) & (
+            TotalAlkali < df.Al2O3
+        )
+        peraluminous_where = (df.Al2O3 < (TotalAlkali + df.CaO)) & (
+            TotalAlkali < df.Al2O3
+        )
+        out = pd.Series(index=df.index)
+        out.loc[peraluminous_where] = "Peraluminous"
+        out.loc[metaluminous_where] = "Metaluminous"
+        out.loc[perkalkaline_where] = "Peralkaline"
+        return out
+
+
+class Geochemistry(object):
+    class peralkalinity(ClassifierModel):
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, deterministic=True, **kwargs)
+
+        def build_clsf(self):
+            return PeralkalinityClassifier(self)
+
+    class TAS(ClassifierModel):
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, deterministic=True, **kwargs)
+
+        def build_clsf(self):
+            return SimpleDeterministicClassifer(self)
+
+        def add_to_axes(self, ax=None, **kwargs):
+            if ax is None:
+                fig, ax = plt.subplots(1)
+            self.clsf.add_to_axes(ax=ax, **kwargs)
+            ax.set_xlim((35, 85))
+            ax.set_ylim((0, 20))
+            ax.set_ylabel("$Na_2O + K_2O$")
+            ax.set_xlabel("$SiO_2$")
+
+        def classify(self, df: pd.DataFrame):
+            return self.clsf.predict(df, cols=["SiO2", "TotalAlkali"])
+
+
+class Petrology(object):
+    class aphanitic(ClassifierModel):
+        """
+        QAPF Diagram
+        """
+
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, deterministic=True, **kwargs)
+
+        def build_clsf(self):
+            # Build
+            clsf = "thing"
+            return clsf
+
+    class phaneritic(ClassifierModel):
+        """
+        QAPF Diagram
+        """
+
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, deterministic=True, **kwargs)
+
+        def build_clsf(self):
+            # Build
+            clsf = "thing"
+            return clsf
+
+    class gabbroic(ClassifierModel):
+        """
+        Pyroxene-Olivine-Plagioclase
+        """
+
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, deterministic=True, **kwargs)
+
+        def build_clsf(self):
+            # Build
+            clsf = "thing"
+            return clsf
+
+    class ultramafic(ClassifierModel):
+        """
+        Olivine-Orthopyroxene-Clinopyroxene
+        """
+
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, deterministic=True, **kwargs)
+
+        def build_clsf(self):
+            # Build
+            clsf = "thing"
+            return clsf

ProgramData/Anaconda3_64/Lib/site-packages/pyrolite/comp/__init__.py

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+# from .aggregate import *
+# from .impute import *
+# from .codata import *
+# from .renorm import *
+
+import logging
+
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+logger = logging.getLogger(__name__)