apsg 1.3.6__tar.gz → 1.3.8__tar.gz

{apsg-1.3.6/src/apsg.egg-info → apsg-1.3.8}/PKG-INFO

@@ -1,32 +1,10 @@
 Metadata-Version: 2.4
 Name: apsg
-Version: 1.3.6
+Version: 1.3.8
 Summary: APSG - The package for structural geologists
 Author-email: Ondrej Lexa <lexa.ondrej@gmail.com>
 Maintainer-email: Ondrej Lexa <lexa.ondrej@gmail.com>
-License: MIT License
-        
-        APSG - The package for structural geologists.
-        Copyright (c) 2015-2024, Ondrej Lexa
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-        
+License-Expression: MIT
 Project-URL: Homepage, https://github.com/ondrolexa/apsg
 Project-URL: Documentation, https://apsg.readthedocs.io
 Project-URL: Repository, https://github.com/ondrolexa/apsg.git
@@ -35,7 +13,6 @@ Project-URL: Changelog, https://github.com/ondrolexa/apsg/blob/master/CHANGELOG.
 Keywords: structural geology,stereonet,orientation data
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.10
@@ -85,7 +62,7 @@ APSG is the package for structural geologists. It defines several new python cla
 
 ## :hammer_and_wrench: Requirements
 
-You need Python 3.9 or later to run APSG. The package requires [NumPy](https://numpy.org/) and [SciPy](https://www.scipy.org/),
+You need Python 3.10 or later to run APSG. The package requires [NumPy](https://numpy.org/) and [SciPy](https://www.scipy.org/),
 [Matplotlib](https://matplotlib.org/), [SciPy](https://scipy.org/), [SQLAlchemy](https://www.sqlalchemy.org/)
 and [pandas](https://pandas.pydata.org/).
 

{apsg-1.3.6 → apsg-1.3.8}/README.md

@@ -20,7 +20,7 @@ APSG is the package for structural geologists. It defines several new python cla
 
 ## :hammer_and_wrench: Requirements
 
-You need Python 3.9 or later to run APSG. The package requires [NumPy](https://numpy.org/) and [SciPy](https://www.scipy.org/),
+You need Python 3.10 or later to run APSG. The package requires [NumPy](https://numpy.org/) and [SciPy](https://www.scipy.org/),
 [Matplotlib](https://matplotlib.org/), [SciPy](https://scipy.org/), [SQLAlchemy](https://www.sqlalchemy.org/)
 and [pandas](https://pandas.pydata.org/).
 

{apsg-1.3.6 → apsg-1.3.8}/pyproject.toml

@@ -4,14 +4,14 @@ dynamic = ["version"]
 description = "APSG - The package for structural geologists"
 readme = "README.md"
 requires-python = ">=3.10"
-license = { file = "LICENSE" }
+license = "MIT"
+license-files = ["LICENSE"]
 keywords = ["structural geology", "stereonet", "orientation data"]
 authors = [{ name = "Ondrej Lexa", email = "lexa.ondrej@gmail.com" }]
 maintainers = [{ name = "Ondrej Lexa", email = "lexa.ondrej@gmail.com" }]
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
 ]

{apsg-1.3.6 → apsg-1.3.8}/src/apsg/__init__.py

@@ -158,6 +158,6 @@ __all__ = (
     "quicknet",
 )
 
-__version__ = "1.3.6"
+__version__ = "1.3.8"
 __author__ = "Ondrej Lexa"
 __email__ = "lexa.ondrej@gmail.com"

{apsg-1.3.6 → apsg-1.3.8}/src/apsg/database/__init__.py

@@ -6,6 +6,7 @@ from apsg.database._alchemy import (
     Site,
     Structdata,
     Structype,
+    Attached,
     Tag,
     Unit,
 )
@@ -17,6 +18,7 @@ __all__ = (
     "Site",
     "Structdata",
     "Structype",
+    "Attached",
     "Tag",
     "Unit",
     "SDB",

{apsg-1.3.6 → apsg-1.3.8}/src/apsg/database/_alchemy.py

@@ -7,12 +7,13 @@ SQLAlchemy API to access PySDB database
 import os
 from datetime import datetime
 import contextlib
+import warnings
 
-from apsg.feature._geodata import Lineation, Foliation, Pair
-from apsg.feature._container import LineationSet, FoliationSet
+from apsg.feature._geodata import Lineation, Foliation, Pair, Fault
+from apsg.feature._container import LineationSet, FoliationSet, PairSet, FaultSet
 
 from sqlalchemy import create_engine, event
-from sqlalchemy.orm import sessionmaker
+from sqlalchemy.orm import sessionmaker, aliased
 from sqlalchemy import (
     Column,
     Float,
@@ -607,34 +608,175 @@ class SDBSession:
         else:
             return tags
 
-    def getset(self, structype, **kwargs):
+    def getset(self, structype, site={}, unit={}, tag={}):
         """Method to retrieve data from SDB database to ``FeatureSet``.
 
         Args:
-          structype (str, Structype):  structure or list of structures to retrieve
-
-        Keyword arguments are passed to sqlalchemy filter_by method
+          structype (str | Structype):  structure to retrieve
+          site (dict): keyword args passed to filter site
+          unit (dict): keyword args passed to filter unit
+          tag (dict): keyword args passed to filter tag
 
         """
         if isinstance(structype, str):
-            structypes = (
-                self.session.query(Structype).filter_by(structure=structype).all()
+            dbstruct = (
+                self.session.query(Structype).filter_by(structure=structype).first()
             )
-            assert len(structypes) == 1, f"There is no structure {structype} in db."
-            structype = structypes[0]
-        data = (
-            self.session.query(Structdata)
-            .filter_by(structype=structype, **kwargs)
-            .all()
-        )
-        if structype.planar == 1:
-            res = FoliationSet(
-                [Foliation(v.azimuth, v.inclination) for v in data],
-                name=structype.structure,
+            assert dbstruct is not None, f"There is no structure {structype} in db."
+            structype = dbstruct
+        if isinstance(structype, Structype):
+            data = (
+                self.session.query(Structdata)
+                .filter_by(structype=structype)
+                .join(Structdata.site)
+                .filter_by(**site)
+                .join(Site.unit)
+                .filter_by(**unit)
+                .join(Structdata.tags)
+                .filter_by(**tag)
+                .all()
             )
+            if structype.planar == 1:
+                res = FoliationSet(
+                    [Foliation(v.azimuth, v.inclination) for v in data],
+                    name=structype.structure,
+                )
+            else:
+                res = LineationSet(
+                    [Lineation(v.azimuth, v.inclination) for v in data],
+                    name=structype.structure,
+                )
+            return res
         else:
-            res = LineationSet(
-                [Lineation(v.azimuth, v.inclination) for v in data],
-                name=structype.structure,
+            raise ValueError("structype argument must be string or Structype")
+
+    def getpairs(self, ptype, ltype, site={}, unit={}, ptag={}, ltag={}):
+        """Method to retrieve data from SDB database to ``PairSet``.
+
+        Args:
+          ptype (str | Structype):  planar structure to retrieve
+          ltype (str | Structype):  linear structure to retrieve
+
+        Keyword Args:
+          site (dict): keyword args passed to filter site
+          unit (dict): keyword args passed to filter unit
+          ptag (dict): keyword args passed to filter planar tag
+          ltag (dict): keyword args passed to filter linear tag
+
+        """
+        if isinstance(ptype, str):
+            dbstruct = self.session.query(Structype).filter_by(structure=ptype).first()
+            assert dbstruct is not None, f"There is no structure {ptype} in db."
+            ptype = dbstruct
+        if isinstance(ltype, str):
+            dbstruct = self.session.query(Structype).filter_by(structure=ltype).first()
+            assert dbstruct is not None, f"There is no structure {ltype} in db."
+            ltype = dbstruct
+        if isinstance(ptype, Structype) and isinstance(ltype, Structype):
+            AttachPlanar = aliased(Structdata)
+            AttachLinear = aliased(Structdata)
+            TagPlanar = aliased(Tag)
+            TagLinear = aliased(Tag)
+            data = (
+                self.session.query(Attached)
+                .join(AttachPlanar, Attached.planar)
+                .filter_by(structype=ptype)
+                .join(AttachLinear, Attached.linear)
+                .filter_by(structype=ltype)
+                .join(Structdata.site)
+                .filter_by(**site)
+                .join(Site.unit)
+                .filter_by(**unit)
+                .outerjoin(TagPlanar, AttachPlanar.tags)
+                .filter_by(**ptag)
+                .outerjoin(TagLinear, AttachLinear.tags)
+                .filter_by(**ltag)
+                .all()
             )
-        return res
+            pairs = []
+            warnings.filterwarnings("error")
+            for v in data:
+                try:
+                    pair = Pair(
+                        v.planar.azimuth,
+                        v.planar.inclination,
+                        v.linear.azimuth,
+                        v.linear.inclination,
+                    )
+                    pairs.append(pair)
+                except UserWarning:
+                    print(
+                        f"Too big misfit for pair {v.planar}-{v.linear} on {v.planar.site}"
+                    )
+            warnings.resetwarnings()
+            res = PairSet(pairs, name=f"{ptype.structure}-{ltype.structure}")
+            return res
+        else:
+            raise ValueError("structype argument must be string or Structype")
+
+    def getfaults(self, ptype, ltype, sense, site={}, unit={}, ptag={}, ltag={}):
+        """Method to retrieve data from SDB database to ``FaultSet``.
+
+        Args:
+          ptype (str | Structype):  planar structure to retrieve
+          ltype (str | Structype):  linear structure to retrieve
+          sense (float or str): sense of movement +/-1 hanging-wall down/up. When str,
+              must be one of 's', 'd', 'n', 'r'.
+
+        Keyword Args:
+          site (dict): keyword args passed to filter site
+          unit (dict): keyword args passed to filter unit
+          ptag (dict): keyword args passed to filter planar tag
+          ltag (dict): keyword args passed to filter linear tag
+
+        """
+        if isinstance(ptype, str):
+            dbstruct = self.session.query(Structype).filter_by(structure=ptype).first()
+            assert dbstruct is not None, f"There is no structure {ptype} in db."
+            ptype = dbstruct
+        if isinstance(ltype, str):
+            dbstruct = self.session.query(Structype).filter_by(structure=ltype).first()
+            assert dbstruct is not None, f"There is no structure {ltype} in db."
+            ltype = dbstruct
+        if isinstance(ptype, Structype) and isinstance(ltype, Structype):
+            AttachPlanar = aliased(Structdata)
+            AttachLinear = aliased(Structdata)
+            TagPlanar = aliased(Tag)
+            TagLinear = aliased(Tag)
+            data = (
+                self.session.query(Attached)
+                .join(AttachPlanar, Attached.planar)
+                .filter_by(structype=ptype)
+                .join(AttachLinear, Attached.linear)
+                .filter_by(structype=ltype)
+                .join(Structdata.site)
+                .filter_by(**site)
+                .join(Site.unit)
+                .filter_by(**unit)
+                .outerjoin(TagPlanar, AttachPlanar.tags)
+                .filter_by(**ptag)
+                .outerjoin(TagLinear, AttachLinear.tags)
+                .filter_by(**ltag)
+                .all()
+            )
+            faults = []
+            warnings.filterwarnings("error")
+            for v in data:
+                try:
+                    fault = Fault(
+                        v.planar.azimuth,
+                        v.planar.inclination,
+                        v.linear.azimuth,
+                        v.linear.inclination,
+                        sense,
+                    )
+                    faults.append(fault)
+                except UserWarning:
+                    print(
+                        f"Too big misfit for pair {v.planar}-{v.linear} on {v.planar.site}"
+                    )
+            warnings.resetwarnings()
+            res = FaultSet(faults, name=f"{ptype.structure}-{ltype.structure}")
+            return res
+        else:
+            raise ValueError("structype argument must be string or Structype")

{apsg-1.3.6 → apsg-1.3.8}/src/apsg/feature/_container.py

@@ -1384,6 +1384,9 @@ class EllipseSet(FeatureSet):
 
     __feature_class__ = Ellipse
 
+    def __repr__(self):
+        return f"E2({len(self)}) {self.name}"
+
     @property
     def S1(self) -> np.ndarray:
         """
@@ -1433,6 +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):
     """
@@ -1441,6 +1453,9 @@ class OrientationTensor2Set(EllipseSet):
 
     __feature_class__ = OrientationTensor2
 
+    def __repr__(self):
+        return f"M2({len(self)}) {self.name}"
+
 
 class EllipsoidSet(FeatureSet):
     """
@@ -1449,6 +1464,9 @@ class EllipsoidSet(FeatureSet):
 
     __feature_class__ = Ellipsoid
 
+    def __repr__(self):
+        return f"E({len(self)}) {self.name}"
+
     @property
     def strength(self) -> np.ndarray:
         """
@@ -1675,6 +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):
     """
@@ -1683,6 +1710,9 @@ class OrientationTensor3Set(EllipsoidSet):
 
     __feature_class__ = OrientationTensor3
 
+    def __repr__(self):
+        return f"M({len(self)}) {self.name}"
+
 
 class ClusterSet(object):
     """

{apsg-1.3.6 → apsg-1.3.8}/src/apsg/feature/_geodata.py

@@ -412,8 +412,8 @@ class Fault(Pair):
         finc (float): dip of planar feature in degrees
         lazi (float): plunge direction of linear feature in degrees
         linc (float): plunge of linear feature in degrees
-        sense (float or str): sense of movement +/11 hanging-wall down/up. When str,
-            ,ust be one of 's', 'd', 'n', 'r'.
+        sense (float or str): sense of movement +/-1 hanging-wall down/up. When str,
+            must be one of 's', 'd', 'n', 'r'.
 
 
     Attributes:

{apsg-1.3.6 → apsg-1.3.8/src/apsg.egg-info}/PKG-INFO

@@ -1,32 +1,10 @@
 Metadata-Version: 2.4
 Name: apsg
-Version: 1.3.6
+Version: 1.3.8
 Summary: APSG - The package for structural geologists
 Author-email: Ondrej Lexa <lexa.ondrej@gmail.com>
 Maintainer-email: Ondrej Lexa <lexa.ondrej@gmail.com>
-License: MIT License
-        
-        APSG - The package for structural geologists.
-        Copyright (c) 2015-2024, Ondrej Lexa
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-        
+License-Expression: MIT
 Project-URL: Homepage, https://github.com/ondrolexa/apsg
 Project-URL: Documentation, https://apsg.readthedocs.io
 Project-URL: Repository, https://github.com/ondrolexa/apsg.git
@@ -35,7 +13,6 @@ Project-URL: Changelog, https://github.com/ondrolexa/apsg/blob/master/CHANGELOG.
 Keywords: structural geology,stereonet,orientation data
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.10
@@ -85,7 +62,7 @@ APSG is the package for structural geologists. It defines several new python cla
 
 ## :hammer_and_wrench: Requirements
 
-You need Python 3.9 or later to run APSG. The package requires [NumPy](https://numpy.org/) and [SciPy](https://www.scipy.org/),
+You need Python 3.10 or later to run APSG. The package requires [NumPy](https://numpy.org/) and [SciPy](https://www.scipy.org/),
 [Matplotlib](https://matplotlib.org/), [SciPy](https://scipy.org/), [SQLAlchemy](https://www.sqlalchemy.org/)
 and [pandas](https://pandas.pydata.org/).