Merge branch 'master' of https://github.com/Loop3D/LoopStructural

Author: lachlangrose

.github/workflows/conda.yml

@@ -2,7 +2,7 @@ name: publish_conda
 
 on:
   release:
-    types: [published]
+    types: [edited, created]
 jobs:
   conda-deploy:
     name: Uploading to Loop3d for python ${{ matrix.os }})

.github/workflows/documentation.yml

@@ -2,7 +2,7 @@ name: Build documentation and deploy
 
 on:
   release:
-    types: [published]
+    types: [edited, created]
 
 jobs:
   flake8:

.github/workflows/python-publish.yml

@@ -2,7 +2,7 @@ name: Python package build and publish
 
 on:
   release:
-    types: [published]
+    types: [edited, created]
 
 jobs:
   build_wheels_macos:

CHANGELOG.md

@@ -1,5 +1,109 @@
 # Changelog
 
+### [1.3.6](https://www.github.com/Loop3D/LoopStructural/compare/v1.3.5...v1.3.6) (2021-10-12)
+
+
+### Bug Fixes
+
+* removing invalid classifiers ([5d8de87](https://www.github.com/Loop3D/LoopStructural/commit/5d8de8782cbfb41ebf229d5e87ac53f6c06f65c3))
+
+### [1.3.5](https://www.github.com/Loop3D/LoopStructural/compare/v1.3.4...v1.3.5) (2021-10-11)
+
+
+### Bug Fixes
+
+* adding aabb ([512f0a3](https://www.github.com/Loop3D/LoopStructural/commit/512f0a3ec2dddfe0032a03a1d5f24c1a039ddc9e))
+* adding gradient option for m2l wrapper ([cdce6e8](https://www.github.com/Loop3D/LoopStructural/commit/cdce6e8887f771d274ef68ad6ad94b25f745a3d5))
+* adding option to define custom mesh builder for pli ([b21fa8c](https://www.github.com/Loop3D/LoopStructural/commit/b21fa8c309590c6dd85ea28f0c456a7acb854df2))
+* changed to boolean logic for aabb ([f5a5f9b](https://www.github.com/Loop3D/LoopStructural/commit/f5a5f9b811220f534c2b667a652d063ad530294f))
+* cleaning up ([262a89d](https://www.github.com/Loop3D/LoopStructural/commit/262a89da9be5aabb3462b5a35dfea830eda6c728))
+* incorrect indexing for FDI grad constraints ([d6b8280](https://www.github.com/Loop3D/LoopStructural/commit/d6b82808e8f2716de313a9695293902b499bc27f))
+* move cg call to interpolator ([53492a2](https://www.github.com/Loop3D/LoopStructural/commit/53492a2436c6b90cf1ebe7a10283a5d8e5e49749))
+* moved generic methods to base class ([23ec788](https://www.github.com/Loop3D/LoopStructural/commit/23ec7889500863bf6f3a43e8b8b5c9a30433a190))
+* names kwarg wasn't used for multiple slices ([daebcf0](https://www.github.com/Loop3D/LoopStructural/commit/daebcf04ca0558c2f19ac60646d2e7adca8ef08a))
+* pli grad constraint weights were divided by 3 ([cedcffb](https://www.github.com/Loop3D/LoopStructural/commit/cedcffb2577257baa3bd30dc5e38ff7c5451b37a))
+* removing old lavavu wrapper, name wasn't ([9226f40](https://www.github.com/Loop3D/LoopStructural/commit/9226f40cdebd2d65ef4d723dfbc5c736a003051c))
+* renaming mesh to support for PLI ([2d07317](https://www.github.com/Loop3D/LoopStructural/commit/2d0731740958bd8ef284aa7f7f8d73f6d45734de))
+* setup.py codec and filename error ([479ae2b](https://www.github.com/Loop3D/LoopStructural/commit/479ae2b9f9805fb2061da9ae9aa7e5dac9c2f49f))
+* unstructured mesh seems to work ([3bd5e24](https://www.github.com/Loop3D/LoopStructural/commit/3bd5e248a2be44812c0d689c60ac0fa33e1c2e31))
+* updating setup.py to include metadata for pypi ([fea4317](https://www.github.com/Loop3D/LoopStructural/commit/fea4317b11a7bdbeffadc8c69f9ffc08ada4b3ca))
+
+### [1.3.4](https://www.github.com/Loop3D/LoopStructural/compare/v1.3.3...v1.3.4) (2021-10-05)
+
+
+### Bug Fixes
+
+* adding loop specific exceptions and project file ([a7664d2](https://www.github.com/Loop3D/LoopStructural/commit/a7664d261f3c6524c3e29f2c0e082ef6b5512813))
+* adding non-linear constraint template ([03b9e73](https://www.github.com/Loop3D/LoopStructural/commit/03b9e734dd058dc774dc4c755efc0a7e247e5d92))
+* adding non-linear constraint template ([1be8a45](https://www.github.com/Loop3D/LoopStructural/commit/1be8a45473828c90dc56eb23f698e8f20970a609))
+* boolean operator in surfe wrapper ([f11816e](https://www.github.com/Loop3D/LoopStructural/commit/f11816e9d1ed92076e5d9719aead0a4e3ad206a0))
+* bugfix for gradient constraints ([5fbbb08](https://www.github.com/Loop3D/LoopStructural/commit/5fbbb08733c2fbdf2975a143d996ae18a4711959))
+* constant fold axis was referencing fold_frame ([2050b68](https://www.github.com/Loop3D/LoopStructural/commit/2050b68b6ac837cb5113fdce481a78540fc1bdf5))
+* intersection visualisation was using the ([1cf531b](https://www.github.com/Loop3D/LoopStructural/commit/1cf531b51a82228133d47d2be6485d742e180e6d))
+* method names for FDI/PLI are consistent ([aebba23](https://www.github.com/Loop3D/LoopStructural/commit/aebba23b84c894e1bee75200547514793b32b4ae))
+* structural frame weights were being overwritten by ([15e7f23](https://www.github.com/Loop3D/LoopStructural/commit/15e7f23fa4207ce4ded440a99637e0d950010558))
+
+### [1.3.3](https://www.github.com/Loop3D/LoopStructural/compare/v1.3.2...v1.3.3) (2021-09-29)
+
+
+### Bug Fixes
+
+* kernel parameter for surfe wasn't being applied ([4e99bbf](https://www.github.com/Loop3D/LoopStructural/commit/4e99bbf942467d39d82f1ee8acfe52174b45bb7b))
+
+### [1.3.2](https://www.github.com/Loop3D/LoopStructural/compare/v1.3.1...v1.3.2) (2021-09-28)
+
+
+### Bug Fixes
+
+* adding missing functions to lavavu wrapper ([8a7b92c](https://www.github.com/Loop3D/LoopStructural/commit/8a7b92ca149c4798a977181c77bbc7338c2d3457))
+* adding tangents to surfepy wrapper ([1c0917e](https://www.github.com/Loop3D/LoopStructural/commit/1c0917e4b821383281fb8b507c44bf55fa9f3103))
+
+### [1.3.1](https://www.github.com/Loop3D/LoopStructural/compare/v1.3.0...v1.3.1) (2021-09-28)
+
+
+### Bug Fixes
+
+* updating workflows to run on edited  ([5b051f4](https://www.github.com/Loop3D/LoopStructural/commit/5b051f4b58e56c08a6a0f5f9366733879be7761c))
+
+## [1.3.0](https://www.github.com/Loop3D/LoopStructural/compare/v1.2.4...v1.3.0) (2021-09-27)
+
+
+### Features
+
+* updating viewer to use base class ([7c314a0](https://www.github.com/Loop3D/LoopStructural/commit/7c314a057c7217d6e120eb2398a7955e32dfa62f))
+
+
+### Bug Fixes
+
+* adding base plotting class for easy inheritance ([1a9614d](https://www.github.com/Loop3D/LoopStructural/commit/1a9614d6f3ebf63e073f261de5346a49c326b275))
+* adding builders for fold and folded frame ([a6b61fb](https://www.github.com/Loop3D/LoopStructural/commit/a6b61fb0660f37d890377a7f30a4b00b4f13a879))
+* adding callback function to builder update ([1eca6f5](https://www.github.com/Loop3D/LoopStructural/commit/1eca6f59e18f3f4b116e6f3c7396860ee26dae47))
+* adding callback to model.update ([1fe5fad](https://www.github.com/Loop3D/LoopStructural/commit/1fe5fad5a8c4ec70ef691899e942299481ede189))
+* adding callbackfunction to isosurface ([038df51](https://www.github.com/Loop3D/LoopStructural/commit/038df51d1f9fedc4499012350b02e7debbda50ef))
+* adding check to see if a feature is valid. ([c9bd3b0](https://www.github.com/Loop3D/LoopStructural/commit/c9bd3b0e1871e4b6d8644ea26dbba4f6ad3cc80c))
+* adding exception if fold frame hasn't ([59a9d66](https://www.github.com/Loop3D/LoopStructural/commit/59a9d66ec1a86a22d86fe0556d1401dde8db5afb))
+* adding exception when modelling faults with surfe ([15806d7](https://www.github.com/Loop3D/LoopStructural/commit/15806d74a8841cb6532f95f678021c26145279be))
+* adding function to generate cmap and range for ([6354712](https://www.github.com/Loop3D/LoopStructural/commit/6354712a5907ac22c4a59d7269760b00779afa74))
+* adding lavavu subclass ([b3c042f](https://www.github.com/Loop3D/LoopStructural/commit/b3c042fb87a376d107a3b39e551731f19fc2e6d3))
+* adding loop exception for interpolator ([f43a583](https://www.github.com/Loop3D/LoopStructural/commit/f43a583f8e793c2690f45246fb6d2b9c1da08e95))
+* adding set item for fold frame to change ([7d975bd](https://www.github.com/Loop3D/LoopStructural/commit/7d975bd3a7bc0dcbf2ecb7336e193f50a05b96d9))
+* adding vtk export ([7e7d63a](https://www.github.com/Loop3D/LoopStructural/commit/7e7d63a2044713eba77e8176915d591a3b6a621d))
+* changing structural frames to have a setup ([d6fcdea](https://www.github.com/Loop3D/LoopStructural/commit/d6fcdea0efee978f5aba8845c2edd6aee5d22139))
+* checking type for vector plotter + adding name ([19c7d5e](https://www.github.com/Loop3D/LoopStructural/commit/19c7d5e7f0bfbccd78aec6fabe52c39e9ecba5b0))
+* cmap not being passed for add_isosurface ([491fb34](https://www.github.com/Loop3D/LoopStructural/commit/491fb34ceb16290f08016dac605ac43234baab83))
+* creating specific builder for folded foliations ([b40ba9a](https://www.github.com/Loop3D/LoopStructural/commit/b40ba9a90294cc79ddbddc19bc1ded6591f43d07))
+* end of day fold frame ([6c49981](https://www.github.com/Loop3D/LoopStructural/commit/6c4998126fb12356cb31e173bd3638c4854efb8b))
+* error to catch when not enough data ([bdd93ea](https://www.github.com/Loop3D/LoopStructural/commit/bdd93ea928b428cb4ca2da3313eb7603b78d3afd))
+* import vtk exception ([01005b3](https://www.github.com/Loop3D/LoopStructural/commit/01005b3fb7a0483d0b2947f84d482810db1e3617))
+* process data doesn't allow bad formatted ([b9f8364](https://www.github.com/Loop3D/LoopStructural/commit/b9f83649cfebe825acc8f5f2e8839867e6a06cb4))
+* removing function to calculate intersection, ([9080877](https://www.github.com/Loop3D/LoopStructural/commit/9080877707456a86fe36649218ef27e29a660bf1))
+* removing kwargs that have value of None ([ce05b5f](https://www.github.com/Loop3D/LoopStructural/commit/ce05b5f7e142e49dfc7bb5d67bf635bc47349d0d))
+* removing normalisation from ([3216d07](https://www.github.com/Loop3D/LoopStructural/commit/3216d07efdca58f445afdfcc06de631c10c8f654))
+* removing specific builder for folded fold frame ([9eed793](https://www.github.com/Loop3D/LoopStructural/commit/9eed793cb9be6b62422b7e1237f7e77ea841ff83))
+* sections can be painted with a feature ([905eeb1](https://www.github.com/Loop3D/LoopStructural/commit/905eeb1406d3cf0c9110de3bef8288577a37807a))
+* transitioning fold frame building into ([7d12b3b](https://www.github.com/Loop3D/LoopStructural/commit/7d12b3b92d4f7f83f61553257716e26375024b06))
+* typo in parameter ([917711a](https://www.github.com/Loop3D/LoopStructural/commit/917711a4beeee4b90a203aae0de6a52772766c88))
+
 ### [1.2.4](https://www.github.com/Loop3D/LoopStructural/compare/v1.2.3...v1.2.4) (2021-09-07)
 
 

LoopStructural/interpolators/__init__.py

@@ -8,6 +8,8 @@
 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
 

LoopStructural/interpolators/base_linear_tetra.py

@@ -0,0 +1,24 @@
+# class LinearTetrahedron:
+#     def __init__(self):
+#         pass
+    
+#     def element_gradient(self, elements):
+#         ps = self.
+#         m = np.array(
+#             [[(ps[:, 1, 0] - ps[:, 0, 0]), (ps[:, 1, 1] - ps[:, 0, 1]),
+#               (ps[:, 1, 2] - ps[:, 0, 2])],
+#              [(ps[:, 2, 0] - ps[:, 0, 0]), (ps[:, 2, 1] - ps[:, 0, 1]),
+#               (ps[:, 2, 2] - ps[:, 0, 2])],
+#              [(ps[:, 3, 0] - ps[:, 0, 0]), (ps[:, 3, 1] - ps[:, 0, 1]),
+#               (ps[:, 3, 2] - ps[:, 0, 2])]])
+#         I = np.array(
+#             [[-1., 1., 0., 0.],
+#              [-1., 0., 1., 0.],
+#              [-1., 0., 0., 1.]])
+#         m = np.swapaxes(m, 0, 2)
+#         element_gradients = np.linalg.inv(m)
+
+#         element_gradients = element_gradients.swapaxes(1, 2)
+#         element_gradients = element_gradients @ I
+
+#         return element_gradients[elements,:,:]

LoopStructural/interpolators/base_structured_3d_support.py

@@ -22,7 +22,7 @@ def __init__(self,
         # we use property decorators to update these when different parts of
         # the geometry need to change
         # inisialise the private attributes
-        self._nsteps = np.array(nsteps)
+        self._nsteps = np.array(nsteps,dtype=int)
         self._step_vector = np.array(step_vector)
         self._origin = np.array(origin)  
         self.supporttype='Base'
@@ -181,4 +181,125 @@ def check_position(self, pos):
         if len(pos.shape) != 2:
             print("Position array needs to be a list of points or a point")
             return False
-        return pos
+        return pos
+
+    def global_cell_indicies(self, indexes):
+        """
+        Convert from cell indexes to global cell index
+
+        Parameters
+        ----------
+        indexes
+
+        Returns
+        -------
+
+        """
+        indexes = np.array(indexes).swapaxes(0, 2)
+        return indexes[:, :, 0] + self.nsteps_cells[None, None, 0] \
+               * indexes[:, :, 1] + self.nsteps_cells[None, None, 0] * \
+               self.nsteps_cells[None, None, 1] * indexes[:, :, 2]
+
+    def cell_corner_indexes(self, x_cell_index, y_cell_index, z_cell_index):
+        """
+        Returns the indexes of the corners of a cell given its location xi,
+        yi, zi
+
+        Parameters
+        ----------
+        x_cell_index
+        y_cell_index
+        z_cell_index
+
+        Returns
+        -------
+
+        """
+        xcorner = np.array([0, 1, 0, 0, 1, 0, 1, 1])
+        ycorner = np.array([0, 0, 1, 0, 0, 1, 1, 1])
+        zcorner = np.array([0, 0, 0, 1, 1, 1, 0, 1])
+        xcorners = x_cell_index[:, None] + xcorner[None, :]
+        ycorners = y_cell_index[:, None] + ycorner[None, :]
+        zcorners = z_cell_index[:, None] + zcorner[None, :]
+        return xcorners, ycorners, zcorners
+
+    def position_to_cell_corners(self, pos):
+
+        inside = self.inside(pos)
+        ix, iy, iz = self.position_to_cell_index(pos)
+        cornersx, cornersy, cornersz = self.cell_corner_indexes(ix, iy, iz)
+        globalidx = self.global_indicies(
+            np.dstack([cornersx, cornersy, cornersz]).T)
+        # if global index is not inside the support set to -1
+        globalidx[~inside] = -1
+        return globalidx, inside
+    
+    def node_indexes_to_position(self, xindex, yindex, zindex):
+
+        x = self.origin[0] + self.step_vector[0] * xindex
+        y = self.origin[1] + self.step_vector[1] * yindex
+        z = self.origin[2] + self.step_vector[2] * zindex
+
+        return x, y, z
+        
+    def global_index_to_cell_index(self, global_index):
+        """
+        Convert from global indexes to xi,yi,zi
+
+        Parameters
+        ----------
+        global_index
+
+        Returns
+        -------
+
+        """
+        # determine the ijk indices for the global index.
+        # remainder when dividing by nx = i
+        # remained when dividing modulus of nx by ny is j
+
+        x_index = global_index % self.nsteps_cells[0, None]
+        y_index = global_index // self.nsteps_cells[0, None] % \
+                  self.nsteps_cells[1, None]
+        z_index = global_index // self.nsteps_cells[0, None] // \
+                  self.nsteps_cells[1, None]
+        return x_index, y_index, z_index
+
+
+    def global_index_to_node_index(self, global_index):
+        """
+        Convert from global indexes to xi,yi,zi
+
+        Parameters
+        ----------
+        global_index
+
+        Returns
+        -------
+
+        """
+        # determine the ijk indices for the global index.
+        # remainder when dividing by nx = i
+        # remained when dividing modulus of nx by ny is j
+        x_index = global_index % self.nsteps[0, None]
+        y_index = global_index // self.nsteps[0, None] % \
+                  self.nsteps[1, None]
+        z_index = global_index // self.nsteps[0, None] // \
+                  self.nsteps[1, None]
+        return x_index, y_index, z_index
+    def global_node_indicies(self, indexes):
+        """
+        Convert from node indexes to global node index
+
+        Parameters
+        ----------
+        indexes
+
+        Returns
+        -------
+
+        """
+        indexes = np.array(indexes).swapaxes(0, 2)
+        return indexes[:, :, 0] + self.nsteps[None, None, 0] \
+               * indexes[:, :, 1] + self.nsteps[None, None, 0] * \
+               self.nsteps[None, None, 1] * indexes[:, :, 2]

LoopStructural/interpolators/discrete_interpolator.py

@@ -47,6 +47,7 @@ def __init__(self, support):
         self.eq_const_col = []
         self.eq_const_d = []
         self.eq_const_c_ = 0
+        self.non_linear_constraints = []
         self.constraints = {}
         self.interpolation_weights= {}
         logger.info("Creating discrete interpolator with {} degrees of freedom".format(self.nx))
@@ -177,15 +178,18 @@ def add_constraints_to_least_squares(self, A, B, idc, name='undefined'):
         rows += self.c_
         constraint_ids = rows.copy()
 
-        if name in self.constraints:            
+        if name in self.constraints:
+            count = 0
+            if '_' in name:
+                count = int(name.split('_')[0])+1
+            name = name + '_{}'.format(count)           
 
-            self.constraints[name]['A'] =  np.vstack([self.constraints[name]['A'],A])
-            self.constraints[name]['B'] =  np.hstack([self.constraints[name]['B'], B])
-            self.constraints[name]['idc'] = np.vstack([self.constraints[name]['idc'],
-                                                idc])
+            # self.constraints[name]['A'] =  A#np.vstack([self.constraints[name]['A'],A])
+            # self.constraints[name]['B'] =  B#np.hstack([self.constraints[name]['B'], B])
+            # self.constraints[name]['idc'] = idc#np.vstack([self.constraints[name]['idc'],
+            #                                     idc])
 
-        if name not in self.constraints:
-            self.constraints[name] = {'node_indexes':constraint_ids,'A':A,'B':B.flatten(),'idc':idc}
+        self.constraints[name] = {'node_indexes':constraint_ids,'A':A,'B':B.flatten(),'idc':idc}
         rows = np.tile(rows, (A.shape[-1], 1)).T
 
         self.c_ += nr
@@ -272,8 +276,11 @@ def add_equality_constraints(self, node_idx, values):
         self.eq_const_row.extend((np.arange(0, idc[outside].shape[0])))
         self.eq_const_d.extend(values[outside].tolist())
         self.eq_const_c_ += idc[outside].shape[0]
+    
+    def add_non_linear_constraints(self, nonlinear_constraint):
+        self.non_linear_constraints.append(nonlinear_constraint)
 
-    def add_tangent_ctr_pts(self, w=1.0):
+    def add_tangent_constraints(self, w=1.0):
         """
 
         Parameters
@@ -287,7 +294,7 @@ def add_tangent_ctr_pts(self, w=1.0):
         """
         points = self.get_tangent_constraints()
         if points.shape[0] > 1:
-            self.add_gradient_orthogonal_constraint(points[:,:3],points[:,3:6],w)
+            self.add_gradient_orthogonal_constraints(points[:,:3],points[:,3:6],w)
 
     def build_matrix(self, square=True, damp=True):
         """
@@ -531,11 +538,15 @@ def _solve(self, solver='cg', **kwargs):
         # check solution is not nan
         # self.support.properties[self.propertyname] = self.c
         if np.all(self.c == np.nan):
+            self.valid = False
             logger.warning("Solver not run, no scalar field")
+            return
         # if solution is all 0, probably didn't work
         if np.all(self.c[self.region] == 0):
+            self.valid = False
             logger.warning("No solution, {} scalar field 0. Add more data.".format(self.propertyname))
-
+            return
+        self.valid = True
     def update(self):
         """
         Check if the solver is up to date, if not rerun interpolation using