fix: merge origin/intrusion to local intrusion

.github/workflows/windows_CI.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Installing dependencies
         shell: bash -l {0}
         run: |
-          conda install -c conda-forge cython numpy scipy scikit-image scikit-learn pyamg flake8 pytest networkx
+          conda install -c conda-forge cython numpy scipy scikit-image scikit-learn pyamg flake8 pytest networkx osqp
       - name: Checking formatting of code
         shell: bash -l {0}
         run: |

.vs/VSWorkspaceState.json

@@ -0,0 +1,13 @@
+{
+  "ExpandedNodes": [
+    "",
+    "\\LoopStructural",
+    "\\LoopStructural\\modelling",
+    "\\LoopStructural\\modelling\\core",
+    "\\LoopStructural\\modelling\\fault",
+    "\\LoopStructural\\modelling\\intrusions",
+    "\\LoopStructural\\modelling\\intrusions\\old"
+  ],
+  "SelectedNode": "\\LoopStructural\\modelling\\intrusions\\old\\intrusion_frame.py",
+  "PreviewInSolutionExplorer": false
+}

CHANGELOG.md

@@ -1,5 +1,59 @@
 # Changelog
 
+### [1.4.3](https://www.github.com/Loop3D/LoopStructural/compare/v1.4.2...v1.4.3) (2022-02-21)
+
+
+### Bug Fixes
+
+* :ambulance: added scale parameter for calculate_topo matrix. ([839e0e0](https://www.github.com/Loop3D/LoopStructural/commit/839e0e07fd8333c70ca71c0d8cf356ccd2e9e604))
+* :bug: adding experimental flag for loopstructural ([f810479](https://www.github.com/Loop3D/LoopStructural/commit/f810479f6d057d21f9229ae645d39257b051d906))
+* :bug: changes support barycentre to property ([d2e1f0b](https://www.github.com/Loop3D/LoopStructural/commit/d2e1f0b54d71eb2cdae3a92e9fcbce9a7e189d26))
+* :bug: fixing bugs for flake8 ([9dce30c](https://www.github.com/Loop3D/LoopStructural/commit/9dce30c012ba6543a7936275a4452c25d30412fc))
+* :bug: small changes to pass tests. ([14c7580](https://www.github.com/Loop3D/LoopStructural/commit/14c758044d36962b6b63d7af7dd6783638539023))
+* :zap: changing aabb to sparse matrix ([2cbdab7](https://www.github.com/Loop3D/LoopStructural/commit/2cbdab7feb1cafe4491766f056b3fe58e32ac706))
+* adding isnan to inequality check ([d780300](https://www.github.com/Loop3D/LoopStructural/commit/d7803005971e8e72663ebe2538251407079cb30b))
+* adding node inequality constraints ([de33914](https://www.github.com/Loop3D/LoopStructural/commit/de3391403a7012895f7bf1bf170862ca2cfa6ed7))
+* adding option to use mkl ([22883ba](https://www.github.com/Loop3D/LoopStructural/commit/22883ba59c13476ff77f91265268d10e56cd8a84))
+* adding p2 interpolator for 3d :) ([5d0acfb](https://www.github.com/Loop3D/LoopStructural/commit/5d0acfb99458f2cacfbbfe099164e32ebe2a6d3b))
+* bug with equality constraints ([b192cff](https://www.github.com/Loop3D/LoopStructural/commit/b192cff05987b6ad9350ade53208943afca18823))
+* changing base unstructred support to work ([50ca16b](https://www.github.com/Loop3D/LoopStructural/commit/50ca16b70ddafd29ead061e153fe2b0652ca0e2b))
+* correct ordering of shape functions ([6f2f113](https://www.github.com/Loop3D/LoopStructural/commit/6f2f113abb42a14c4b5278a635066f1696bf062d))
+* minor fix to variogram saving wavelength guess as attribute ([2dbc29e](https://www.github.com/Loop3D/LoopStructural/commit/2dbc29e0696fe25bc3f55afb6cee1bea7bb9d9f1))
+* modifying for 3d/generic case. ([c6a8ea3](https://www.github.com/Loop3D/LoopStructural/commit/c6a8ea3dcfdb7098d9e77df83f87e0f50036b670))
+* norm constraints p2 ([93d3165](https://www.github.com/Loop3D/LoopStructural/commit/93d31654a9403f285a5ce3e4cfc3c6b4f91becf5))
+* region funct type incorrect causing ([a5d27f1](https://www.github.com/Loop3D/LoopStructural/commit/a5d27f1569e0337971cc4997c673333ff1842d83))
+* storing constraints as numpy array ([6c75379](https://www.github.com/Loop3D/LoopStructural/commit/6c753799019e19bb69d8621d5020787d5c42339f))
+
+
+### Documentation
+
+* :memo: adding warning that analysis module is experimental ([0574e57](https://www.github.com/Loop3D/LoopStructural/commit/0574e57bc639fe809b3e9b02531ce0e10742ea36))
+* :memo: updating documentation for evaluate model ([1dcc716](https://www.github.com/Loop3D/LoopStructural/commit/1dcc716c6ae5cb0c77a54bf794ee14e077a874ce))
+
+### [1.4.2](https://www.github.com/Loop3D/LoopStructural/compare/v1.4.1...v1.4.2) (2022-02-07)
+
+
+### Bug Fixes
+
+* actually fixing divide by zero ([ef4d7d0](https://www.github.com/Loop3D/LoopStructural/commit/ef4d7d036a24730a5c296f8e7779d76e405b98ce))
+* added function for plotting structural frames ([69dbc6d](https://www.github.com/Loop3D/LoopStructural/commit/69dbc6d12999952d6266d003e8e7bda37551670c))
+* adding mpl syntax for 3d view points ([cc7788f](https://www.github.com/Loop3D/LoopStructural/commit/cc7788f62f82b4bdc4bba242c394212ed94e6d5d))
+* bug where data is not float ([e6f7e1f](https://www.github.com/Loop3D/LoopStructural/commit/e6f7e1fb6c09d4702bc49218d5b7b4e73385de7a))
+* bug with calculating average fault ori ([a2099cd](https://www.github.com/Loop3D/LoopStructural/commit/a2099cd0477a18a6448d5e556795b0e40a1f05a6))
+* commenting out osqp ([c2fd2da](https://www.github.com/Loop3D/LoopStructural/commit/c2fd2da4c5f6b84424cbd0fa0f3e940b7cadeb4f))
+* crashing when all constraints of a type outside of box ([7907f58](https://www.github.com/Loop3D/LoopStructural/commit/7907f5814a4e2a0672c3fb73616325e533549809))
+* extra checks ([ba6f391](https://www.github.com/Loop3D/LoopStructural/commit/ba6f39134e02daf996e59fd321d2698ce1dee040))
+* fault interpolation taking a long time ([78fa916](https://www.github.com/Loop3D/LoopStructural/commit/78fa9163bc0b5fd84ef93302541dbf2da474749b))
+* faults interpolation mesh was not being adjusted ([33722f6](https://www.github.com/Loop3D/LoopStructural/commit/33722f6c103701a7c7bf5dadb88c3bd422752622))
+* faults not rescaling when incorrect norm vectors used ([9706f25](https://www.github.com/Loop3D/LoopStructural/commit/9706f255c612af4ea702c89f870826eed380167b))
+* faults not visible in model ([32cbb2a](https://www.github.com/Loop3D/LoopStructural/commit/32cbb2a849c7f0c87da4adc2485013973eb2380b))
+* faults with no value data not interpolating ([bf55ec6](https://www.github.com/Loop3D/LoopStructural/commit/bf55ec684cd4635f7396a4245a79b2e9adf81697))
+* interpolator type is now an enum ([8197552](https://www.github.com/Loop3D/LoopStructural/commit/81975524f9ee487d8de489501b5fd2455150d20f))
+* norm constraint out of model cause crash ([20692e2](https://www.github.com/Loop3D/LoopStructural/commit/20692e21dd7b97911e1b38f66ba405dfc152cb5f))
+* number of constraints warning message ([9abcc04](https://www.github.com/Loop3D/LoopStructural/commit/9abcc042947b06f80db121aa48f9a9c1f0648b81))
+* removed divide by 0 error ([9f17489](https://www.github.com/Loop3D/LoopStructural/commit/9f17489cf8f233651778e817f7fd9c3258bc7d9f))
+* updating logging ([f77f915](https://www.github.com/Loop3D/LoopStructural/commit/f77f9156dfae6a58ea4a31b4b577dd2f207d2b8a))
+
 ### [1.4.1](https://www.github.com/Loop3D/LoopStructural/compare/v1.4.0...v1.4.1) (2021-12-06)
 
 

LoopStructural/__init__.py

@@ -1,6 +1,4 @@
 """
-
-
 LoopStructural API
 =======================
 
@@ -12,6 +10,7 @@
 from pathlib import Path
 from .version import __version__
 
+experimental = False
 ch = logging.StreamHandler()
 formatter = logging.Formatter(
     "%(levelname)s: %(asctime)s: %(filename)s:%(lineno)d -- %(message)s"

LoopStructural/analysis/__init__.py

@@ -4,6 +4,14 @@
 
 Various tools for analysing loopstructural models, including calculating fault intersections and fault toplogies
 """
-from ._fault_displacement import displacement_missfit
-from ._fault_intersection import calculate_fault_intersections
-from ._topology import calculate_fault_topology_matrix
+from LoopStructural.utils import getLogger
+import LoopStructural
+
+logger = getLogger(__name__)
+if LoopStructural.experimental:
+    logger.warning(
+        "LoopStructural.analysis is experimental and may not perform as expected"
+    )
+    from ._fault_displacement import displacement_missfit
+    from ._fault_intersection import calculate_fault_intersections
+    from ._topology import calculate_fault_topology_matrix

LoopStructural/analysis/_topology.py

@@ -4,7 +4,7 @@
 logger = getLogger(__name__)
 
 
-def calculate_fault_topology_matrix(model, xyz=None, threshold=0.001):
+def calculate_fault_topology_matrix(model, xyz=None, threshold=0.001, scale=True):
     """Calculate fault ellipsoid and hw/fw
 
     Parameters
@@ -13,12 +13,18 @@ def calculate_fault_topology_matrix(model, xyz=None, threshold=0.001):
         the model containing the faults
     xyz : np.array
         xyz locations in model coordinates
-
+    threshold : float
+        threshold for determining if point is inside fault volume
+    scale : bool
+        flag whether to rescale xyz to model coordinates
     Returns
     -------
     topology_matrix : np.array
         matrix containing nan (outside), 0 (footwall), 1 (hangingwall)
     """
+    if xyz is not None and scale == True:
+        logger.warning("Scaling XYZ to model coordinate system")
+        xyz = model.scale(xyz, inplace=False)
     if xyz is None:
         xyz = model.regular_grid(rescale=False, shuffle=False)
     topology_matrix = np.zeros((xyz.shape[0], len(model.faults)))

LoopStructural/datasets/__init__.py

@@ -16,4 +16,4 @@
 from ._base import value_headers
 from ._base import load_unconformity
 from ._base import load_duplex
-from ._base import load_tabular_intrusion
+from ._base import load_tabular_intrusion

LoopStructural/datasets/_base.py

@@ -143,6 +143,7 @@ def strike_dip_headers():
 def normal_vector_headers():
     return ["X", "Y", "Z", "nx", "ny", "nz"]
 
+
 def load_tabular_intrusion():
     """Model dataset sampled for a model of a tabular intrusion
 
@@ -154,5 +155,5 @@ def load_tabular_intrusion():
     """
     module_path = dirname(__file__)
     data = pd.read_csv(join(module_path, Path("data/tabular_intrusion.csv")))
-    bb = np.array([[0, 0, 0], [5,5,5]])
-    return data, bb
+    bb = np.array([[0, 0, 0], [5, 5, 5]])
+    return data, bb

LoopStructural/interpolators/__init__.py

@@ -2,17 +2,60 @@
 Interpolators and interpolation supports
 
 """
-from LoopStructural.interpolators.discrete_fold_interpolator import (
-    DiscreteFoldInterpolator,
+from enum import IntEnum
+
+from LoopStructural.utils import getLogger
+import LoopStructural
+
+logger = getLogger(__name__)
+
+
+class InterpolatorType(IntEnum):
+    """
+    Enum for the different interpolator types
+
+    1-9 should cover interpolators with supports
+    9+ are data supported
+    """
+
+    BASE = 0
+    BASE_DISCRETE = 1
+    FINITE_DIFFERENCE = 2
+    DISCRETE_FOLD = 3
+    PIECEWISE_LINEAR = 4
+    PIECEWISE_QUADRATIC = 5
+    BASE_DATA_SUPPORTED = 10
+    SURFE = 11
+
+
+from LoopStructural.interpolators._geological_interpolator import GeologicalInterpolator
+from LoopStructural.interpolators._discrete_interpolator import DiscreteInterpolator
+from LoopStructural.interpolators.supports import (
+    TetMesh,
+    StructuredGrid,
+    UnStructuredTetMesh,
+    P1Unstructured2d,
+    P2Unstructured2d,
+    StructuredGrid2D,
+    P2UnstructuredTetMesh,
 )
-from LoopStructural.interpolators.finite_difference_interpolator import (
+
+
+from LoopStructural.interpolators._finite_difference_interpolator import (
     FiniteDifferenceInterpolator,
 )
 from LoopStructural.interpolators.piecewiselinear_interpolator import (
     PiecewiseLinearInterpolator,
 )
-from LoopStructural.interpolators.structured_tetra import TetMesh
-from LoopStructural.interpolators.unstructured_tetra import UnStructuredTetMesh
-from LoopStructural.interpolators.structured_grid import StructuredGrid
-from LoopStructural.interpolators.geological_interpolator import GeologicalInterpolator
-from LoopStructural.interpolators.discrete_interpolator import DiscreteInterpolator
+from LoopStructural.interpolators._discrete_fold_interpolator import (
+    DiscreteFoldInterpolator,
+)
+
+try:
+    from LoopStructural.interpolators._surfe_wrapper import SurfeRBFInterpolator
+except ImportError:
+    logger.warning('Can\'t import surfepy - to install "pip install surfe"')
+
+logger.warning("Using experimental interpolators: P1Interpolator and P2Interpolator")
+from ._p1interpolator import P1Interpolator
+from ._p2interpolator import P2Interpolator

LoopStructural/interpolators/discrete_fold_interpolator.py → LoopStructural/interpolators/_discrete_fold_interpolator.py

@@ -4,16 +4,15 @@
 import logging
 
 import numpy as np
-from LoopStructural.interpolators.cython.dsi_helper import fold_cg
 
-from LoopStructural.interpolators.piecewiselinear_interpolator import (
-    PiecewiseLinearInterpolator,
-)
+from LoopStructural.interpolators import PiecewiseLinearInterpolator, InterpolatorType
 
 from LoopStructural.utils import getLogger
 
 logger = getLogger(__name__)
 
+from .cython.dsi_helper import fold_cg
+
 
 class DiscreteFoldInterpolator(PiecewiseLinearInterpolator):
     """ """
@@ -31,7 +30,7 @@ def __init__(self, support, fold):
         """
 
         PiecewiseLinearInterpolator.__init__(self, support)
-        self.type = ["foldinterpolator"]
+        self.type = InterpolatorType.DISCRETE_FOLD
         self.fold = fold
 
     @classmethod
@@ -128,7 +127,7 @@ def add_fold_constraints(
         ]
         # calculate the fold geometry for the elements barycentre
         deformed_orientation, fold_axis, dgz = self.fold.get_deformed_orientation(
-            self.support.barycentre()
+            self.support.barycentre
         )
         element_idx = np.arange(self.support.n_elements)
         np.random.shuffle(element_idx)
@@ -251,5 +250,5 @@ def add_fold_constraints(
             B = np.zeros(A.shape[0])
             idc = np.array(idc[:ncons, :])
             self.add_constraints_to_least_squares(
-                A, B, fold_regularisation[1], idc, name="fold regularisation 3"
+                A, B, fold_regularisation[2], idc, name="fold regularisation 3"
             )