apsg 1.3.5__tar.gz → 1.3.7__tar.gz

{apsg-1.3.5/src/apsg.egg-info → apsg-1.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsg
-Version: 1.3.5
+Version: 1.3.7
 Summary: APSG - The package for structural geologists
 Author-email: Ondrej Lexa <lexa.ondrej@gmail.com>
 Maintainer-email: Ondrej Lexa <lexa.ondrej@gmail.com>
@@ -59,14 +59,8 @@ Requires-Dist: ipykernel; extra == "docs"
 Requires-Dist: nbsphinx; extra == "docs"
 Requires-Dist: autodocsumm; extra == "docs"
 Provides-Extra: dev
-Requires-Dist: pytest; extra == "dev"
+Requires-Dist: apsg[docs,extra,tests]; extra == "dev"
 Requires-Dist: black; extra == "dev"
-Requires-Dist: sphinx; extra == "dev"
-Requires-Dist: sphinx_rtd_theme; extra == "dev"
-Requires-Dist: readthedocs-sphinx-search; extra == "dev"
-Requires-Dist: ipykernel; extra == "dev"
-Requires-Dist: nbsphinx; extra == "dev"
-Requires-Dist: autodocsumm; extra == "dev"
 Dynamic: license-file
 
 <img src="https://ondrolexa.github.io/apsg/apsg_banner.svg" alt="APSG logo" width="300px"/>

{apsg-1.3.5 → apsg-1.3.7}/pyproject.toml

@@ -28,16 +28,7 @@ docs = [
     "nbsphinx",
     "autodocsumm",
 ]
-dev = [
-    "pytest",
-    "black",
-    "sphinx",
-    "sphinx_rtd_theme",
-    "readthedocs-sphinx-search",
-    "ipykernel",
-    "nbsphinx",
-    "autodocsumm",
-]
+dev = ["apsg[extra,tests,docs]", "black"]
 
 [project.urls]
 Homepage = "https://github.com/ondrolexa/apsg"

{apsg-1.3.5 → apsg-1.3.7}/src/apsg/__init__.py

@@ -158,6 +158,6 @@ __all__ = (
     "quicknet",
 )
 
-__version__ = "1.3.5"
+__version__ = "1.3.7"
 __author__ = "Ondrej Lexa"
 __email__ = "lexa.ondrej@gmail.com"

{apsg-1.3.5 → apsg-1.3.7}/src/apsg/config.py

@@ -138,7 +138,6 @@ apsg_conf = dict(
     ),
     roseplot_default_kwargs=dict(
         bins=36,
-        axial=True,
         density=True,
         arrowness=0.95,
         rwidth=1,

{apsg-1.3.5 → apsg-1.3.7}/src/apsg/database/_sdbread.py

@@ -10,7 +10,7 @@ from apsg.feature._geodata import Lineation, Foliation
 from apsg.feature._container import LineationSet, FoliationSet
 
 
-class SDB(object):
+class SDB:
     """
     sqlite3 based read-only interface to PySDB database
 

{apsg-1.3.5 → apsg-1.3.7}/src/apsg/feature/_container.py

@@ -142,6 +142,14 @@ class Vector2Set(FeatureSet):
         """Return array of direction angles"""
         return np.asarray([e.direction for e in self]).T
 
+    def to_vec2(self):
+        """Return ``Vector2Set`` object with all data converted to ``Vector2``."""
+        return Vector2Set([Vector2(e) for e in self], name=self.name)
+
+    def to_dir2(self):
+        """Return ``Direction2Set`` object with all data converted to ``Direction``."""
+        return Direction2Set([Direction(e) for e in self], name=self.name)
+
     def proj(self, vec):
         """Return projections of all features in ``Vector2Set`` onto vector."""
         return type(self)([e.project() for e in self], name=self.name)
@@ -1376,6 +1384,9 @@ class EllipseSet(FeatureSet):
 
     __feature_class__ = Ellipse
 
+    def __repr__(self):
+        return f"E2({len(self)}) {self.name}"
+
     @property
     def S1(self) -> np.ndarray:
         """
@@ -1425,6 +1436,15 @@ class EllipseSet(FeatureSet):
         """
         return np.array([e.e12 for e in self])
 
+    def transform(self, F):
+        """Return transformation of all features ``EllipseSet`` by matrix 'F'.
+
+        Args:
+            F: Transformation matrix. Array-like value e.g. ``DeformationGradient3``
+
+        """
+        return type(self)([e.transform(F) for e in self], name=self.name)
+
 
 class OrientationTensor2Set(EllipseSet):
     """
@@ -1433,6 +1453,9 @@ class OrientationTensor2Set(EllipseSet):
 
     __feature_class__ = OrientationTensor2
 
+    def __repr__(self):
+        return f"M2({len(self)}) {self.name}"
+
 
 class EllipsoidSet(FeatureSet):
     """
@@ -1441,6 +1464,9 @@ class EllipsoidSet(FeatureSet):
 
     __feature_class__ = Ellipsoid
 
+    def __repr__(self):
+        return f"E({len(self)}) {self.name}"
+
     @property
     def strength(self) -> np.ndarray:
         """
@@ -1667,6 +1693,15 @@ class EllipsoidSet(FeatureSet):
         """
         return np.array([e.MAD for e in self])
 
+    def transform(self, F):
+        """Return transformation of all features ``EllipsoidSet`` by matrix 'F'.
+
+        Args:
+        F: Transformation matrix. Array-like value e.g. ``DeformationGradient3``
+
+        """
+        return type(self)([e.transform(F) for e in self], name=self.name)
+
 
 class OrientationTensor3Set(EllipsoidSet):
     """
@@ -1675,6 +1710,9 @@ class OrientationTensor3Set(EllipsoidSet):
 
     __feature_class__ = OrientationTensor3
 
+    def __repr__(self):
+        return f"M({len(self)}) {self.name}"
+
 
 class ClusterSet(object):
     """
@@ -1752,7 +1790,7 @@ class ClusterSet(object):
         """
 
         self.method = kwargs.get("method", self.method)
-        if issubclass(self.__feature_class__, (Axial2, Axial3)):
+        if issubclass(self.data.__feature_class__, (Axial2, Axial3)):
             self.Z = linkage(self.pdist, method=self.method, metric=angle_metric_axial)
         else:
             self.Z = linkage(self.pdist, method=self.method, metric=angle_metric)

{apsg-1.3.5 → apsg-1.3.7}/src/apsg/plotting/_roseplot.py

@@ -1,12 +1,13 @@
 import pickle
 
-import numpy as np
 import matplotlib.pyplot as plt
-from scipy.stats import vonmises, circmean
+import numpy as np
+from scipy.stats import circmean, vonmises
 
 from apsg.config import apsg_conf
-from apsg.plotting._plot_artists import RosePlotArtistFactory
 from apsg.feature import feature_from_json
+from apsg.math._vector import Axial2, Axial3
+from apsg.plotting._plot_artists import RosePlotArtistFactory
 
 __all__ = ["RosePlot"]
 
@@ -20,7 +21,6 @@ class RosePlot(object):
         title_kws (dict): dictionary of keyword arguments passed to matplotlib suptitle
             method.
         bins (int): Number of bins. Default 36
-        axial (bool): Directional data are axial. Defaut True
         density (bool): Use density instead of counts. Default False
         pdf (bool): Plot Von Mises density function instead histogram. Default False
         pdf_res (int): Resolution of pdf. Default 901
@@ -245,7 +245,7 @@ class RosePlot(object):
         width = 2 * np.pi / self._kwargs["bins"]
         legend = kwargs.pop("legend")
         for arg in args:
-            if self._kwargs["axial"]:
+            if issubclass(arg.__feature_class__, (Axial2, Axial3)):
                 ang = np.concatenate((arg.direction % 360, (arg.direction + 180) % 360))
                 weights = np.concatenate((abs(arg), abs(arg)))
             else:
@@ -279,7 +279,7 @@ class RosePlot(object):
             ang = arg.direction % 360
             # weights = abs(arg)
             radii = np.zeros_like(theta)
-            if self._kwargs["axial"]:
+            if issubclass(arg.__feature_class__, (Axial2, Axial3)):
                 for a in ang:
                     radii += (
                         vonmises.pdf(theta, self._kwargs["kappa"], loc=np.radians(a))
@@ -308,32 +308,21 @@ class RosePlot(object):
             bottom = bottom + radii
 
     def _muci(self, *args, **kwargs):
-        ang = np.radians(np.concatenate([arg.direction for arg in args]))
         conflevel = kwargs.pop("confidence_level")
         n_resamples = kwargs.pop("n_resamples")
-        # calculate mean and CI
-        if self._kwargs["axial"]:
-            mu = circmean(2 * ang) / 2
-            ang_shift = ang + np.pi / 2 - mu
-            bsmu = [
-                circmean(np.random.choice(2 * ang_shift, size=len(ang_shift)))
-                for i in range(n_resamples)
-            ]
-            low = np.percentile(bsmu, 100 - conflevel) / 2 + mu - np.pi / 2
-            high = np.percentile(bsmu, conflevel) / 2 + mu - np.pi / 2
-        else:
-            mu = circmean(ang)
-            ang_shift = ang + np.pi - mu
-            bsmu = [
-                circmean(np.random.choice(ang_shift, size=len(ang_shift)))
-                for i in range(n_resamples)
-            ]
-            low = np.percentile(bsmu, (100 - conflevel) / 2) + mu - np.pi
-            high = np.percentile(bsmu, 100 - (100 - conflevel) / 2) + mu - np.pi
-        radii = []
         for arg in args:
+            radii = []
             p = 0
-            if self._kwargs["axial"]:
+            ang = np.radians(arg.direction)
+            if issubclass(arg.__feature_class__, (Axial2, Axial3)):
+                mu = circmean(2 * ang) / 2
+                ang_shift = ang + np.pi / 2 - mu
+                bsmu = [
+                    circmean(np.random.choice(2 * ang_shift, size=len(ang_shift)))
+                    for i in range(n_resamples)
+                ]
+                low = np.percentile(bsmu, 100 - conflevel) / 2 + mu - np.pi / 2
+                high = np.percentile(bsmu, conflevel) / 2 + mu - np.pi / 2
                 for a in arg.direction:
                     p += vonmises.pdf(mu, self._kwargs["kappa"], loc=np.radians(a)) / 2
                     p += (
@@ -341,16 +330,28 @@ class RosePlot(object):
                         / 2
                     )
             else:
+                mu = circmean(ang)
+                ang_shift = ang + np.pi - mu
+                bsmu = [
+                    circmean(np.random.choice(ang_shift, size=len(ang_shift)))
+                    for i in range(n_resamples)
+                ]
+                low = np.percentile(bsmu, (100 - conflevel) / 2) + mu - np.pi
+                high = np.percentile(bsmu, 100 - (100 - conflevel) / 2) + mu - np.pi
                 for a in arg.direction:
                     p += vonmises.pdf(mu, self._kwargs["kappa"], loc=np.radians(a))
             radii.append(p / len(arg))
-        if self._kwargs["scaled"]:
-            radii = np.sqrt(radii)
-        mur = 1.1 * sum(radii)
-        ci_angles = np.linspace(low, high, int(5 * np.degrees(high - low)))
-        self.ax.plot([mu, mu + np.pi], [mur, mur], **kwargs)
-        self.ax.plot(ci_angles, mur * np.ones_like(ci_angles), **kwargs)
-        self.ax.plot(ci_angles + np.pi, mur * np.ones_like(ci_angles), **kwargs)
+            if self._kwargs["scaled"]:
+                radii = np.sqrt(radii)
+            mur = 1.1 * sum(radii)
+            ci_angles = np.linspace(low, high, int(5 * np.degrees(high - low)))
+            if issubclass(arg.__feature_class__, (Axial2, Axial3)):
+                self.ax.plot([mu, mu + np.pi], [mur, mur], **kwargs)
+                self.ax.plot(ci_angles, mur * np.ones_like(ci_angles), **kwargs)
+                self.ax.plot(ci_angles + np.pi, mur * np.ones_like(ci_angles), **kwargs)
+            else:
+                self.ax.plot([0, mu], [0, mur], **kwargs)
+                self.ax.plot(ci_angles, mur * np.ones_like(ci_angles), **kwargs)
 
 
 def roseartist_from_json(obj_json):

{apsg-1.3.5 → apsg-1.3.7/src/apsg.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsg
-Version: 1.3.5
+Version: 1.3.7
 Summary: APSG - The package for structural geologists
 Author-email: Ondrej Lexa <lexa.ondrej@gmail.com>
 Maintainer-email: Ondrej Lexa <lexa.ondrej@gmail.com>
@@ -59,14 +59,8 @@ Requires-Dist: ipykernel; extra == "docs"
 Requires-Dist: nbsphinx; extra == "docs"
 Requires-Dist: autodocsumm; extra == "docs"
 Provides-Extra: dev
-Requires-Dist: pytest; extra == "dev"
+Requires-Dist: apsg[docs,extra,tests]; extra == "dev"
 Requires-Dist: black; extra == "dev"
-Requires-Dist: sphinx; extra == "dev"
-Requires-Dist: sphinx_rtd_theme; extra == "dev"
-Requires-Dist: readthedocs-sphinx-search; extra == "dev"
-Requires-Dist: ipykernel; extra == "dev"
-Requires-Dist: nbsphinx; extra == "dev"
-Requires-Dist: autodocsumm; extra == "dev"
 Dynamic: license-file
 
 <img src="https://ondrolexa.github.io/apsg/apsg_banner.svg" alt="APSG logo" width="300px"/>

{apsg-1.3.5 → apsg-1.3.7}/src/apsg.egg-info/requires.txt

@@ -5,14 +5,8 @@ sqlalchemy
 pandas
 
 [dev]
-pytest
+apsg[docs,extra,tests]
 black
-sphinx
-sphinx_rtd_theme
-readthedocs-sphinx-search
-ipykernel
-nbsphinx
-autodocsumm
 
 [docs]
 sphinx